diff --git a/cl-base.owl b/cl-base.owl index d6e4617c6..1dd8717e0 100644 --- a/cl-base.owl +++ b/cl-base.owl @@ -22,7 +22,7 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - + An ontology of cell types. Cell Ontology @@ -38,7 +38,7 @@ See PMID:15693950, PMID:12799354, PMID:20123131, PMID:21208450; Contact Alexander Diehl, addiehl@buffalo.edu, university at buffalo. - 2024-08-16 + 2024-09-26 @@ -214,6 +214,12 @@ + + + + + + @@ -461,15 +467,15 @@ - + - + - + - + @@ -545,6 +551,12 @@ + + + + + + @@ -670,7 +682,7 @@ - + @@ -1199,6 +1211,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -1260,6 +1273,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -1392,6 +1406,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -1475,7 +1490,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - @@ -1484,7 +1498,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + @@ -1646,6 +1660,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -1790,6 +1805,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -1816,7 +1832,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + @@ -1848,6 +1864,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -1910,6 +1927,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -2330,6 +2348,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -2616,6 +2635,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -3610,7 +3630,8 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + + @@ -3642,14 +3663,38 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + + + + + - A neurectoderm derived cell that lines the neural lumen. + + + + + + + + + + + + + A neuroepithelial glial cell, derived from a radial glial cell originating from the neuroectoderm, lines the ventricles of the brain and the central canal of the spinal cord. This cell is characterized by the presence of cilia on its apical surface, which can be motile or non-motile. BTO:0001724 FMA:70550 ZFA:0009033 - ependymocyte + ependymocyte ependymal cell @@ -3657,10 +3702,14 @@ Covers cells actively being cultured or stored in a quiescent state for future u - A neurectoderm derived cell that lines the neural lumen. + A neuroepithelial glial cell, derived from a radial glial cell originating from the neuroectoderm, lines the ventricles of the brain and the central canal of the spinal cord. This cell is characterized by the presence of cilia on its apical surface, which can be motile or non-motile. GOC:tfm JB:jb + PMID:34335193 + PMID:37008045 PMID:9550134 + doi:/10.3389/fncel.2021.703951 + https://www.britannica.com/science/ependymal-cell @@ -3668,13 +3717,19 @@ Covers cells actively being cultured or stored in a quiescent state for future u ZFA:0009033 + + + + ependymocyte + doi:10.53347/rID-51713 + - + @@ -3838,12 +3893,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - - - - - - An endothelial cell that lines the vasculature. ZFA:0009036 @@ -3935,12 +3984,36 @@ Covers cells actively being cultured or stored in a quiescent state for future u + + + + + + + + + + + + + + + + + + Any epithelial cell that is part of some squamous epithelium. CALOHA:TS-1249 ZFA:0009039 squamous epithelial cell + + + + Any epithelial cell that is part of some squamous epithelium. + FBC:Autogenerated + @@ -3956,21 +4029,29 @@ Covers cells actively being cultured or stored in a quiescent state for future u - A flattened epithelial cell of mesenchymal origin that lines the serous cavity. + + + + + + + A flat, squamous-like epithelial cell of mesodermal origin. It forms the mesothelium, which lines the body's serous cavities including the pleural, peritoneal, and pericardial spaces. This cell plays a crucial role in synthesizing and secreting lubricants, such as glycosaminoglycans and surfactants, which minimize friction between adjacent tissues during movement. FMA:66773 ZFA:0009040 mesotheliocyte + Mesothelial cells, which morphologically resemble squamous epithelial cells, express both epithelial markers (cytokeratins) and mesenchymal markers (vimentin), reflecting their mesodermal origin. They feature surface microvilli and apical-basal polarity. Under certain conditions, they can undergo mesothelial-to-mesenchymal transition. These cells also produce extracellular matrix proteins, maintain serosal homeostasis, and facilitate fluid transport. mesothelial cell - A flattened epithelial cell of mesenchymal origin that lines the serous cavity. + A flat, squamous-like epithelial cell of mesodermal origin. It forms the mesothelium, which lines the body's serous cavities including the pleural, peritoneal, and pericardial spaces. This cell plays a crucial role in synthesizing and secreting lubricants, such as glycosaminoglycans and surfactants, which minimize friction between adjacent tissues during movement. GOC:tfm ISBN:0721662544 + PMID:26106328 @@ -3978,6 +4059,12 @@ Covers cells actively being cultured or stored in a quiescent state for future u ZFA:0009040 + + + + Mesothelial cells, which morphologically resemble squamous epithelial cells, express both epithelial markers (cytokeratins) and mesenchymal markers (vimentin), reflecting their mesodermal origin. They feature surface microvilli and apical-basal polarity. Under certain conditions, they can undergo mesothelial-to-mesenchymal transition. These cells also produce extracellular matrix proteins, maintain serosal homeostasis, and facilitate fluid transport. + PMID:26106328 + @@ -4008,10 +4095,19 @@ Covers cells actively being cultured or stored in a quiescent state for future u + An epithelial cell, organized into multiple layers, with only the basal layer being in contact with the basement membrane. ZFA:0009042 stratified epithelial cell + + + + An epithelial cell, organized into multiple layers, with only the basal layer being in contact with the basement membrane. + Wikipedia:Epithelium + doi:/10.1016/B978-0-12-410424-2.00003-2 + https://www.biologyonline.com/dictionary/stratified-epithelium + @@ -4035,7 +4131,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + @@ -4367,6 +4463,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -4405,8 +4502,14 @@ Covers cells actively being cultured or stored in a quiescent state for future u A tissue-resident macrophage of the reticuloendothelial system found on the luminal surface of the hepatic sinusoids involved in erythrocyte clearance. Markers include F4/80+, CD11b-low, CD68-positive, sialoadhesin-positive, CD163/SRCR-positive. Irregular, with long processes including lamellipodia extending into the sinusoid lumen, have flattened nucleus with cytoplasm containing characteristic invaginations of the plasma membrane (vermiform bodies); lie within the sinusoid lumen attached to the endothelial surface; derived from the bone marrow, form a major part of the body's mononuclear phagocyte system. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Kupffer cells are tissue-resident macrophages located in the liver. They are an integral part of the mononuclear phagocyte system and are responsible for the phagocytosis of dead or dying cells, microbes, and other foreign substances. Kupffer cells account for approximately 80-90% of tissue-resident macrophages in the body. They are found within the lumen of liver sinusoids and interface with microbial populations and products. +The primary role of Kupffer cells is to maintain homeostasis in the liver. They continuously filter and cleanse the blood that flows through the liver, removing pathogens, endotoxins, particulate matter, aged and dysfunctional red blood cells, and miscellaneous waste products. These cells also play an important role in maintaining iron homeostasis. During the process of phagocytosis, Kupffer cells recycle iron from degraded red blood cells, which is then utilized in the formation of new erythrocytes. +Kupffer cells also play key roles in various immune responses and inflammatory processes. They secrete various types of cytokines and chemokines, which contribute to the activation and mobilization of other immune cells. They can also produce reactive oxygen species and nitric oxide, which have microbicidal actions. Although their activity is essential for host defense, excessive or prolonged activation of Kupffer cells may contribute to hepatic injury, inflammation, and fibrosis. BTO:0000685 FMA:14656 + https://cellxgene.cziscience.com/cellguide/CL_0000091 hepatic macrophage littoral cell of hepatic sinusoid liver macrophage @@ -4436,6 +4539,20 @@ Covers cells actively being cultured or stored in a quiescent state for future u PMID:15771589 PMID:17105582 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Kupffer cells are tissue-resident macrophages located in the liver. They are an integral part of the mononuclear phagocyte system and are responsible for the phagocytosis of dead or dying cells, microbes, and other foreign substances. Kupffer cells account for approximately 80-90% of tissue-resident macrophages in the body. They are found within the lumen of liver sinusoids and interface with microbial populations and products. +The primary role of Kupffer cells is to maintain homeostasis in the liver. They continuously filter and cleanse the blood that flows through the liver, removing pathogens, endotoxins, particulate matter, aged and dysfunctional red blood cells, and miscellaneous waste products. These cells also play an important role in maintaining iron homeostasis. During the process of phagocytosis, Kupffer cells recycle iron from degraded red blood cells, which is then utilized in the formation of new erythrocytes. +Kupffer cells also play key roles in various immune responses and inflammatory processes. They secrete various types of cytokines and chemokines, which contribute to the activation and mobilization of other immune cells. They can also produce reactive oxygen species and nitric oxide, which have microbicidal actions. Although their activity is essential for host defense, excessive or prolonged activation of Kupffer cells may contribute to hepatic injury, inflammation, and fibrosis. + DOI:10.1002/cphy.c120026 + DOI:10.1007/978-1-4939-1311-4_10 + DOI:10.1016/j.immuni.2022.08.002 + DOI:10.1038/nri.2017.11 + DOI:10.1111/j.1478-3231.2006.01342.x + @@ -4488,6 +4605,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -4645,6 +4763,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -5046,6 +5165,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -5701,8 +5821,14 @@ Covers cells actively being cultured or stored in a quiescent state for future u A vertebrate phagocyte with a single nucleus. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Mononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. +In addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses. +Mononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer. BTO:0001433 ZFA:0009064 + https://cellxgene.cziscience.com/cellguide/CL_0000113 mononuclear phagocyte @@ -5721,6 +5847,18 @@ Covers cells actively being cultured or stored in a quiescent state for future u GOC:tfm ISBN:0781735149 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Mononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. +In addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses. +Mononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer. + DOI:10.1016/j.coi.2005.11.008 + DOI:10.1038/nri3087 + DOI:10.3389/fimmu.2019.01893 + @@ -5748,6 +5886,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -5959,10 +6098,17 @@ Covers cells actively being cultured or stored in a quiescent state for future u An inhibitory neuron and the sole output neuron of the cerebellar cortex, the Purkinje cell's soma is located between the granular and molecular layers of the cerebellum. It is one of the largest neural cells in the mammalian brain, ranging from 50 to 80 micrometres in diameter. Purkinje cells have planar, fan-shaped dendrites that branch extensively with little overlap. This cell type receives synaptic input from parallel fibres, which modulate high-frequency spike activity known as "simple spikes," and climbing fibres, which modulate infrequent calcium spike activity known as "complex spikes". Purkinje cells are involved in motor coordination, particularly in correcting movements in progress. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Purkinje cells, named after the Czech anatomist Jan Evangelista Purkyně who discovered them, are unique inhibitory neurons in the cerebellar cortex. They are a critical part of the vertebrate nervous system as they provide the only signal output from the cortex to the cerebellar nuclei. They are one of the few types of neurons that are large enough to be seen with the naked eye. The most distinct hallmark of Purkinje cells is their elaborate dendritic arbor, which forms a broad and intricately branching structure resembling a tree. These numerous branches each receive excitatory synaptic inputs from more than 100,000 parallel fibers; in addition, a single climbing fiber makes hundreds of synapses to the soma and proximal dendrites. A single long axon forms an inhibitory projection to the cerebellar nuclei. +Purkinje cells play key roles in the coordination of fine, voluntary motor movements and balance. As the sole output of all motor coordination in the cerebellar cortex, they serve as a central relay in the cerebro-cerebellar loop. Each Purkinje cell receives two types of synaptic input: one from parallel fibers (which are axons of granule cells), and the other from climbing fibers (originating from the inferior olivary nucleus). The Purkinje cells process and integrate these diverse kinds of input signals to generate output that controls timing and coordination of movements. +Purkinje neurons show considerable synaptic plasticity. Throughout life, these cells continue to undergo long-term potentiation and depression at parallel fiber synapses, which cause long-lasting increase or decrease, respectively, of synaptic transmission and have been proposed as mechanisms for motor learning. +Purkinje cells are also known to be implicated in a variety of diseases. Their progressive loss is a prime feature in certain types of ataxia, a collective term used to describe conditions characterized by loss of muscular control and coordination. Furthermore, a significant reduction in the density of Purkinje cells has been reported in conditions such as autism and Huntington’s disease. BTO:0001011 CALOHA:TS-0845 FMA:67969 ZFA:0009071 + https://cellxgene.cziscience.com/cellguide/CL_0000121 Purkinje neuron cerebellar Purkinje cell PC @@ -5982,6 +6128,21 @@ Covers cells actively being cultured or stored in a quiescent state for future u PMID:33288911 PMID:38168772 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Purkinje cells, named after the Czech anatomist Jan Evangelista Purkyně who discovered them, are unique inhibitory neurons in the cerebellar cortex. They are a critical part of the vertebrate nervous system as they provide the only signal output from the cortex to the cerebellar nuclei. They are one of the few types of neurons that are large enough to be seen with the naked eye. The most distinct hallmark of Purkinje cells is their elaborate dendritic arbor, which forms a broad and intricately branching structure resembling a tree. These numerous branches each receive excitatory synaptic inputs from more than 100,000 parallel fibers; in addition, a single climbing fiber makes hundreds of synapses to the soma and proximal dendrites. A single long axon forms an inhibitory projection to the cerebellar nuclei. +Purkinje cells play key roles in the coordination of fine, voluntary motor movements and balance. As the sole output of all motor coordination in the cerebellar cortex, they serve as a central relay in the cerebro-cerebellar loop. Each Purkinje cell receives two types of synaptic input: one from parallel fibers (which are axons of granule cells), and the other from climbing fibers (originating from the inferior olivary nucleus). The Purkinje cells process and integrate these diverse kinds of input signals to generate output that controls timing and coordination of movements. +Purkinje neurons show considerable synaptic plasticity. Throughout life, these cells continue to undergo long-term potentiation and depression at parallel fiber synapses, which cause long-lasting increase or decrease, respectively, of synaptic transmission and have been proposed as mechanisms for motor learning. +Purkinje cells are also known to be implicated in a variety of diseases. Their progressive loss is a prime feature in certain types of ataxia, a collective term used to describe conditions characterized by loss of muscular control and coordination. Furthermore, a significant reduction in the density of Purkinje cells has been reported in conditions such as autism and Huntington’s disease. + DOI:10.1007/s12311-018-0985-7 + DOI:10.1038/nrn3886 + DOI:10.7554/eLife.63668 + https://www.ncbi.nlm.nih.gov/books/NBK545154/ + https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/purkinje-cell + @@ -6074,10 +6235,9 @@ Covers cells actively being cultured or stored in a quiescent state for future u - - + @@ -6110,11 +6270,19 @@ Covers cells actively being cultured or stored in a quiescent state for future u A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Glial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons. +These different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning. +Oligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. +Microglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response. +Despite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis. BTO:0002606 CALOHA:TS-0415 FBbt:00005144 FMA:54536 ZFA:0009073 + https://cellxgene.cziscience.com/cellguide/CL_0000125 neuroglial cell neuroglia @@ -6129,6 +6297,22 @@ Covers cells actively being cultured or stored in a quiescent state for future u A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons. MESH:D009457 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Glial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons. +These different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning. +Oligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. +Microglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response. +Despite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis. + DOI:10.1002/glia.24343 + DOI:10.1038/nn1988 + DOI:10.1101/cshperspect.a020602 + DOI:10.1126/science.aat0473 + DOI:10.3389/fncel.2017.00024 + @@ -6315,6 +6499,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -6361,7 +6546,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - A central nervous system macrophage found in the parenchyma of the central nervous system. Marker include CD11b-positive, F4/80-positive, and CD68-positive. + A transcriptomically distinct central nervous system macrophage found in the parenchyma of the central nervous system. Marker include CD11b-positive, F4/80-positive, and CD68-positive. brain macrophage BTO:0000078 @@ -6381,7 +6566,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - A central nervous system macrophage found in the parenchyma of the central nervous system. Marker include CD11b-positive, F4/80-positive, and CD68-positive. + A transcriptomically distinct central nervous system macrophage found in the parenchyma of the central nervous system. Marker include CD11b-positive, F4/80-positive, and CD68-positive. GOC:add GOC:dsd GOC:tfm @@ -6434,10 +6619,9 @@ Covers cells actively being cultured or stored in a quiescent state for future u - - + @@ -7087,6 +7271,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -7216,6 +7401,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -7443,10 +7629,16 @@ Covers cells actively being cultured or stored in a quiescent state for future u A specialized, columnar, mucus secreting epithelial cell shaped like a flask or goblet. A narrow basal end contains the nucleus while the apical end is swollen by the accumulation of mucus laden secretory granules. Short microvilli project from the apical plasma membrane. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Goblet cells are specialized, simple columnar, secretory epithelial cells that are mostly found in the respiratory and intestinal tracts. The term "goblet" refers to their shape, which resembles a flask or goblet, specially at their apical end which is swollen due to the accumulation of secretory granules. +The primary function of goblet cells is to to protect and lubricate the underlying tissues by secreting large quantities of mucin, a complex glycoprotein, which forms mucus when hydrated. In the respiratory tract, the mucus secreted by these cells traps dust, bacteria, viruses, and other potentially harmful particles in the inhaled air, preventing them from reaching the delicate tissues of the lungs. In the intestines, the goblet cells secrete mucus that acts as a protective barrier shielding the intestinal epithelium from dietary antigens, pathogens and prevents the intestinal epithelium from being eroded by the actions of the digestive enzymes and the abrasive action of passing food material. +Goblet cells are capable of rapidly altering their secretory output in response to stimuli. For example, irritants like smoke or dust can trigger an increased rate of mucus production, as the body attempts to flush out the harmful particles. Conversely, in conditions such as chronic bronchitis and cystic fibrosis, overactive goblet cells can create a thick accumulation of mucus that obstructs the airways and fosters bacterial growth. Lastly, goblet cells are not static, rather, they undergo a dynamic process known as goblet cell metaplasia-differentiation, wherein non-goblet cells in response to chronic injury or inflammation, can differentiate into goblet cells leading to an accumulation of these cells in the tissue, known as goblet cell hyperplasia. BTO:0001540 FMA:13148 ZFA:0009094 http://en.wikipedia.org/wiki/Goblet_cell + https://cellxgene.cziscience.com/cellguide/CL_0000160 chalice cell goblet cell @@ -7459,6 +7651,20 @@ Covers cells actively being cultured or stored in a quiescent state for future u MESH:D020397 http://en.wikipedia.org/wiki/Goblet_cell + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Goblet cells are specialized, simple columnar, secretory epithelial cells that are mostly found in the respiratory and intestinal tracts. The term "goblet" refers to their shape, which resembles a flask or goblet, specially at their apical end which is swollen due to the accumulation of secretory granules. +The primary function of goblet cells is to to protect and lubricate the underlying tissues by secreting large quantities of mucin, a complex glycoprotein, which forms mucus when hydrated. In the respiratory tract, the mucus secreted by these cells traps dust, bacteria, viruses, and other potentially harmful particles in the inhaled air, preventing them from reaching the delicate tissues of the lungs. In the intestines, the goblet cells secrete mucus that acts as a protective barrier shielding the intestinal epithelium from dietary antigens, pathogens and prevents the intestinal epithelium from being eroded by the actions of the digestive enzymes and the abrasive action of passing food material. +Goblet cells are capable of rapidly altering their secretory output in response to stimuli. For example, irritants like smoke or dust can trigger an increased rate of mucus production, as the body attempts to flush out the harmful particles. Conversely, in conditions such as chronic bronchitis and cystic fibrosis, overactive goblet cells can create a thick accumulation of mucus that obstructs the airways and fosters bacterial growth. Lastly, goblet cells are not static, rather, they undergo a dynamic process known as goblet cell metaplasia-differentiation, wherein non-goblet cells in response to chronic injury or inflammation, can differentiate into goblet cells leading to an accumulation of these cells in the tissue, known as goblet cell hyperplasia. + DOI:10.1016/S1357-2725(02)00083-3 + DOI:10.1038/s41575-022-00675-x + DOI:10.1165/ajrcmb.25.5.f218 + DOI:10.1242/bio.20121701 + https://www.ncbi.nlm.nih.gov/books/NBK553208/ + @@ -7538,6 +7744,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -7591,10 +7798,16 @@ Covers cells actively being cultured or stored in a quiescent state for future u An endocrine cell that is located in the epithelium of the gastrointestinal tract or in the pancreas. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Enteroendocrine cells are a specialized subset of cells located within the epithelial lining of both the small and large intestines, as well as the stomach and pancreas. Constituting less than 1% of the total population of intestinal cells, they are differentiated from a common intestinal cell progenitor, thus sharing lineage with absorptive and goblet cells of the intestines. +The distinct characteristic feature of an enteroendocrine cell is its inherent capacity to synthesize and secrete a plethora of gut hormones such as serotonin, somatostatin, neurotensin, cholecystokinin, secretin, gastric inhibitory peptide, motilin, and glucagon-like peptide-1. Integrated within this complex network of signaling agents, these substances control various aspects of the digestive system. Each enteroendocrine cell has its unique combination of hormones to release, determined by its position along the intestinal tract. Intriguingly, these hormones not only modulate local gut function, including motility, absorption and secretion, but also potentiate distant actions on other systems such as endocrine, nervous and immune and play a role in the feeling of satiety. +The release of these hormones from enteroendocrine cells is a highly regulated and dynamic process. The cells are equipped with sensory receptors localized on its luminal side that respond to various stimuli, including changes in nutrient composition, chemical or mechanical changes in the gut lumen, or even signals arising from commensal microbiota. This sensory input stimulates a signaling cascade within the cell, culminating in the release of specific hormones into the interstitial fluid. These hormones then make their way into the bloodstream, acting on their respective target receptors to mediate their duties. The multifunctional characteristics of enteroendocrine cells make them crucial for maintaining gut homeostasis and the overall physiological well being of the body. BTO:0003865 FMA:62930 MESH:D019858 ZFA:0009097 + https://cellxgene.cziscience.com/cellguide/CL_0000164 enteroendocrine cell @@ -7605,6 +7818,20 @@ Covers cells actively being cultured or stored in a quiescent state for future u GOC:tfm SANBI:mhl + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Enteroendocrine cells are a specialized subset of cells located within the epithelial lining of both the small and large intestines, as well as the stomach and pancreas. Constituting less than 1% of the total population of intestinal cells, they are differentiated from a common intestinal cell progenitor, thus sharing lineage with absorptive and goblet cells of the intestines. +The distinct characteristic feature of an enteroendocrine cell is its inherent capacity to synthesize and secrete a plethora of gut hormones such as serotonin, somatostatin, neurotensin, cholecystokinin, secretin, gastric inhibitory peptide, motilin, and glucagon-like peptide-1. Integrated within this complex network of signaling agents, these substances control various aspects of the digestive system. Each enteroendocrine cell has its unique combination of hormones to release, determined by its position along the intestinal tract. Intriguingly, these hormones not only modulate local gut function, including motility, absorption and secretion, but also potentiate distant actions on other systems such as endocrine, nervous and immune and play a role in the feeling of satiety. +The release of these hormones from enteroendocrine cells is a highly regulated and dynamic process. The cells are equipped with sensory receptors localized on its luminal side that respond to various stimuli, including changes in nutrient composition, chemical or mechanical changes in the gut lumen, or even signals arising from commensal microbiota. This sensory input stimulates a signaling cascade within the cell, culminating in the release of specific hormones into the interstitial fluid. These hormones then make their way into the bloodstream, acting on their respective target receptors to mediate their duties. The multifunctional characteristics of enteroendocrine cells make them crucial for maintaining gut homeostasis and the overall physiological well being of the body. + DOI:10.1038/s41574-019-0168-8 + DOI:10.1111/j.1463-1326.2011.01438.x + DOI:10.1196/annals.1294.001 + DOI:10.1210/endrev/bnaa018 + DOI:10.7554/elife.78512 + @@ -7682,9 +7909,15 @@ The modern definition of neurosecretion has evolved to include the release of an A cell that stores epinephrine secretory vesicles. During times of stress, the nervous system signals the vesicles to secrete their hormonal content. Their name derives from their ability to stain a brownish color with chromic salts. Characteristically, they are located in the adrenal medulla and paraganglia of the sympathetic nervous system. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Chromaffin cells, also known as pheochromocytes, are neuroendocrine cells that are typically located in the adrenal medulla, the innermost part of the adrenal gland, which is situated on top of each kidney. Chromaffin cells are also found in small clusters, known as paraganglia, in various locations throughout the body, including the sympathetic nervous system. They derive their name from their ability to stain a brownish-black color upon exposure to chromic salts, a feature made possible due to their high content of granules rich in catecholamines and catecholamine-related neurotransmitters. +The primary function of chromaffin cells is the synthesis and release of catecholamines, specifically epinephrine (adrenaline) and norepinephrine (noradrenaline). These neurotransmitters are vital stress hormones that, when released by the adrenal chromaffing cells into the bloodstream, prepare the body for the 'fight or flight' response. This response can enhance the body's performance in a dangerous situation by increasing heart rate, elevating blood sugar, and increasing blood flow to the muscles. The chromaffin cells in paraganglia are responsible for the local release of catecholamines and play a role in regulating blood pressure and other autonomic functions. +In addition to their role in stress response, chromaffin cells also contribute to the body's immune response. They secrete several peptides including antimicrobial peptides, and the discovery of LPS and cytokine receptors on chromaffin cells suggests that the adrenal medulla may participate in some aspects of the immune response. BTO:0000259 FMA:69263 ZFA:0009099 + https://cellxgene.cziscience.com/cellguide/CL_0000166 phaeochromocyte chromaffin cell @@ -7695,6 +7928,20 @@ The modern definition of neurosecretion has evolved to include the release of an A cell that stores epinephrine secretory vesicles. During times of stress, the nervous system signals the vesicles to secrete their hormonal content. Their name derives from their ability to stain a brownish color with chromic salts. Characteristically, they are located in the adrenal medulla and paraganglia of the sympathetic nervous system. MESH:D019439 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Chromaffin cells, also known as pheochromocytes, are neuroendocrine cells that are typically located in the adrenal medulla, the innermost part of the adrenal gland, which is situated on top of each kidney. Chromaffin cells are also found in small clusters, known as paraganglia, in various locations throughout the body, including the sympathetic nervous system. They derive their name from their ability to stain a brownish-black color upon exposure to chromic salts, a feature made possible due to their high content of granules rich in catecholamines and catecholamine-related neurotransmitters. +The primary function of chromaffin cells is the synthesis and release of catecholamines, specifically epinephrine (adrenaline) and norepinephrine (noradrenaline). These neurotransmitters are vital stress hormones that, when released by the adrenal chromaffing cells into the bloodstream, prepare the body for the 'fight or flight' response. This response can enhance the body's performance in a dangerous situation by increasing heart rate, elevating blood sugar, and increasing blood flow to the muscles. The chromaffin cells in paraganglia are responsible for the local release of catecholamines and play a role in regulating blood pressure and other autonomic functions. +In addition to their role in stress response, chromaffin cells also contribute to the body's immune response. They secrete several peptides including antimicrobial peptides, and the discovery of LPS and cytokine receptors on chromaffin cells suggests that the adrenal medulla may participate in some aspects of the immune response. + DOI:10.1002/cphy.c190003 + DOI:10.1016/j.biocel.2016.02.003 + DOI:10.3389/fendo.2018.00711 + DOI:10.3389/fimmu.2022.977175 + DOI:10.3389/fimmu.2022.977175/full + @@ -7760,6 +8007,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -8282,6 +8530,11 @@ The modern definition of neurosecretion has evolved to include the release of an A Leydig cell is a testosterone-secreting cell in the interstitial area, between the seminiferous tubules, in the testis. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Leydig cells are a testosterone-secreting cell in the interstitial area in the testes of males. They are named after Franz Leydig, a German anatomist who discovered these cells in 1850. Uniquely situated within the soft connective tissue surrounding the seminiferous tubules, Leydig cells form an integral part of the male reproductive system. They are usually polygonal cells characterized by well developed smooth endoplasmic reticulum, high lipid content and a large round nucleus. They are found across mammalian species, including humans. +The primary function of Leydig cells is the production of androgens, the male sex hormones, the most notable of which is testosterone. Leydig cells synthesize testosterone from cholesterol through a series of enzymatic reactions. The production and release of testosterone are mainly regulated by the luteinizing hormone (LH) released by the anterior pituitary gland. In response to LH, Leydig cells convert cholesterol into testosterone, which then plays a crucial role in the development and maintenance of primary and secondary male sexual characteristics. These include the formation and maturation of male reproductive organs, onset of spermatogenesis, and the presentation of male secondary sexual traits such as the deepening of the voice, growth of facial hair, development of muscles, and a broadening of shoulders. +Apart from testosterone production, Leydig cells also secrete insulin-like factor 3 (INSL3) that is essential for testicular descent during embryonic development in males. Dysregulation or loss of Leydig cells can lead to numerous conditions like testosterone deficiency, infertility, and certain forms of testicular cancer. Although not typical, Leydig cells can regenerate if they are damaged, ensuring the continuous production of testosterone and maintaining male reproductive health. They provide an excellent model to study cell differentiation and hormone regulation, thereby enhancing our understanding of reproductive biology and associated disorders. interstitial cell BTO:0000755 CALOHA:TS-1150 @@ -8289,6 +8542,7 @@ The modern definition of neurosecretion has evolved to include the release of an FMA:72297 MESH:D007985 ZFA:0009108 + https://cellxgene.cziscience.com/cellguide/CL_0000178 interstitial cell of Leydig Note that the Amphibian Anatomy Ontology (AA) has a class 'leydig cells' but this is unrelated @@ -8301,6 +8555,20 @@ The modern definition of neurosecretion has evolved to include the release of an GOC:tfm PMID:12050120 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Leydig cells are a testosterone-secreting cell in the interstitial area in the testes of males. They are named after Franz Leydig, a German anatomist who discovered these cells in 1850. Uniquely situated within the soft connective tissue surrounding the seminiferous tubules, Leydig cells form an integral part of the male reproductive system. They are usually polygonal cells characterized by well developed smooth endoplasmic reticulum, high lipid content and a large round nucleus. They are found across mammalian species, including humans. +The primary function of Leydig cells is the production of androgens, the male sex hormones, the most notable of which is testosterone. Leydig cells synthesize testosterone from cholesterol through a series of enzymatic reactions. The production and release of testosterone are mainly regulated by the luteinizing hormone (LH) released by the anterior pituitary gland. In response to LH, Leydig cells convert cholesterol into testosterone, which then plays a crucial role in the development and maintenance of primary and secondary male sexual characteristics. These include the formation and maturation of male reproductive organs, onset of spermatogenesis, and the presentation of male secondary sexual traits such as the deepening of the voice, growth of facial hair, development of muscles, and a broadening of shoulders. +Apart from testosterone production, Leydig cells also secrete insulin-like factor 3 (INSL3) that is essential for testicular descent during embryonic development in males. Dysregulation or loss of Leydig cells can lead to numerous conditions like testosterone deficiency, infertility, and certain forms of testicular cancer. Although not typical, Leydig cells can regenerate if they are damaged, ensuring the continuous production of testosterone and maintaining male reproductive health. They provide an excellent model to study cell differentiation and hormone regulation, thereby enhancing our understanding of reproductive biology and associated disorders. + DOI:10.1016/j.coemr.2019.03.001 + DOI:10.1093/biolre/ioy059 + DOI:10.1210/clinem/dgaa603 + DOI:10.3389/fendo.2014.00006 + https://www.ncbi.nlm.nih.gov/books/NBK556007/#:~:text=Leydig%20cells%20are%20the%20primary,secondary%20sexual%20characteristics%20and%20behaviors. + @@ -8325,6 +8593,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -8440,10 +8709,17 @@ The modern definition of neurosecretion has evolved to include the release of an The main structural component of the liver. They are specialized epithelial cells that are organized into interconnected plates called lobules. Majority of cell population of liver, polygonal in shape, arranged in plates or trabeculae between sinusoids; may have single nucleus or binucleated. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Hepatocytes are the major cell type constituting 70-80% of the liver's cytoplasmic mass, playing crucial roles in maintaining the body's metabolic homeostasis. Dimensions of mature hepatocytes typically range from 20 to 30 μm in humans, but size may vary depending on their location within the liver lobule. Hepatocytes are characterized by high biosynthetic, enzymatic, and endocytic activity. They contain abundant mitochondria, smooth and rough endoplasmic reticulum, peroxisomes, lysosomes, and a large nucleus that is often binucleate. +The liver consists of three zones - the periportal Zone 1, midzone 2, and pericentral Zone 3 - which have differential nutrient and oxygen status, and damage susceptibility; hepatocytes in the different zones show signifcant functional heterogeneity ('hepatocyte functional zonation'). Hepatocytes are involved in a multitude of critical functions including the metabolism of lipids, carbohydrates, and proteins, the synthesis of serum proteins (e.g., albumin, transferrin, and lipoproteins), the detoxification and excretion of endogenous and exogenous substances, the storage of vitamins and minerals, and the production and secretion of bile. +Heterocytes demonstrate a remarkable regenerative capacity, which enables the liver to recover from injury and loss of tissue mass. Notably, hepatocytes perform biotransformation with both phase I and phase II enzymes, which modify drugs, xenobiotics, and various substances for elimination from the body. Phase I enzymes, such as cytochrome P450, catalyze both oxidative and reductive reactions of many xenobiotics; many of the products of phase I enzymes are substrates for the phase II enzymes, which catalyze conjugation reactions. +Alterations in hepatocyte function have significant implications for overall human health and disease. Certain conditions, such as hepatitis, cirrhosis, and liver cancer, can profoundly affect hepatocyte structure and function, thereby disrupting the liver's ability to perform its vital roles within the body. As the primary site for drug metabolism, changes in hepatocyte function can also impact the effectiveness and toxicity of pharmaceuticals. The regenerative ability of hepatocytes makes them valuable cells for liver regenerative medicine and bioartificial liver support systems, and their study has provided significant insights into liver biology and disease. BTO:0000575 CALOHA:TS-0454 FMA:14515 ZFA:0009111 + https://cellxgene.cziscience.com/cellguide/CL_0000182 Hepatocytes are reportedly MHC Class I-positive and MHC Class II-positive. @@ -8459,6 +8735,20 @@ The modern definition of neurosecretion has evolved to include the release of an PMID:19717280 http://en.wikipedia.org/wiki/Hepatocyte + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Hepatocytes are the major cell type constituting 70-80% of the liver's cytoplasmic mass, playing crucial roles in maintaining the body's metabolic homeostasis. Dimensions of mature hepatocytes typically range from 20 to 30 μm in humans, but size may vary depending on their location within the liver lobule. Hepatocytes are characterized by high biosynthetic, enzymatic, and endocytic activity. They contain abundant mitochondria, smooth and rough endoplasmic reticulum, peroxisomes, lysosomes, and a large nucleus that is often binucleate. +The liver consists of three zones - the periportal Zone 1, midzone 2, and pericentral Zone 3 - which have differential nutrient and oxygen status, and damage susceptibility; hepatocytes in the different zones show signifcant functional heterogeneity ('hepatocyte functional zonation'). Hepatocytes are involved in a multitude of critical functions including the metabolism of lipids, carbohydrates, and proteins, the synthesis of serum proteins (e.g., albumin, transferrin, and lipoproteins), the detoxification and excretion of endogenous and exogenous substances, the storage of vitamins and minerals, and the production and secretion of bile. +Heterocytes demonstrate a remarkable regenerative capacity, which enables the liver to recover from injury and loss of tissue mass. Notably, hepatocytes perform biotransformation with both phase I and phase II enzymes, which modify drugs, xenobiotics, and various substances for elimination from the body. Phase I enzymes, such as cytochrome P450, catalyze both oxidative and reductive reactions of many xenobiotics; many of the products of phase I enzymes are substrates for the phase II enzymes, which catalyze conjugation reactions. +Alterations in hepatocyte function have significant implications for overall human health and disease. Certain conditions, such as hepatitis, cirrhosis, and liver cancer, can profoundly affect hepatocyte structure and function, thereby disrupting the liver's ability to perform its vital roles within the body. As the primary site for drug metabolism, changes in hepatocyte function can also impact the effectiveness and toxicity of pharmaceuticals. The regenerative ability of hepatocytes makes them valuable cells for liver regenerative medicine and bioartificial liver support systems, and their study has provided significant insights into liver biology and disease. + DOI:10.1016/j.biocel.2011.11.011 + DOI:10.1055/s-2007-1007096 + DOI:10.1083/jcb.201903090 + DOI:10.1111/j.1439-0396.2007.00752.x + @@ -8564,6 +8854,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -8620,7 +8911,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + @@ -8882,7 +9173,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + @@ -9307,19 +9598,20 @@ The modern definition of neurosecretion has evolved to include the release of an - + - + + - + - A cell specialized to detect and transduce light. + A cell specialized in detecting light stimuli that are involved in visual perception. BTO:0001060 CALOHA:TS-0868 FBbt:00004211 @@ -9329,16 +9621,10 @@ The modern definition of neurosecretion has evolved to include the release of an photoreceptor cell https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg - - - - - true - - A cell specialized to detect and transduce light. + A cell specialized in detecting light stimuli that are involved in visual perception. MESH:D010786 @@ -9640,6 +9926,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -9671,6 +9958,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -9704,6 +9992,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -9803,6 +10092,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -9870,6 +10160,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -9878,11 +10169,8 @@ The modern definition of neurosecretion has evolved to include the release of an A cell with more than one nucleus. - AEO:0000203 - WBbt:0008074 - syncitium - syncytial cell - syncytium + multinucleated cells + polynuclear cells multinucleate cell @@ -9890,6 +10178,19 @@ The modern definition of neurosecretion has evolved to include the release of an A cell with more than one nucleus. FB:ma + Wikipedia:Multinucleate + + + + + multinucleated cells + Wikipedia:Multinucleate + + + + + polynuclear cells + Wikipedia:Multinucleate @@ -10328,13 +10629,39 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + + + + + + + + + + + + A stratified epithelial cell that is part of squamous epithelium, characterized by multiple layers of cells. The basal layer is directly attached to the basement membrane and the apical layer consists of flattened squamous cells. This provides a protective barrier, commonly found in areas subject to abrasion, such as the skin, oral cavity, and esophagus. ZFA:0009144 stratified squamous epithelial cell + + + + A stratified epithelial cell that is part of squamous epithelium, characterized by multiple layers of cells. The basal layer is directly attached to the basement membrane and the apical layer consists of flattened squamous cells. This provides a protective barrier, commonly found in areas subject to abrasion, such as the skin, oral cavity, and esophagus. + PMID:30422572 + Wikipedia:Epithelium + Wikipedia:Stratified_squamous_epithelium + @@ -10347,13 +10674,38 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + + + + + + + + + + + + A stratified epithelial cell that is part of cuboidal epithelium, characterized by multiple layers of cuboidal cells forming the apical layer. This provides a protective lining for ducts in large glands, such as sweat glands. ZFA:0009145 stratified cuboidal epithelial cell + + + + A stratified epithelial cell that is part of cuboidal epithelium, characterized by multiple layers of cuboidal cells forming the apical layer. This provides a protective lining for ducts in large glands, such as sweat glands. + PMID:30422572 + Wikipedia:Stratified_cuboidal_epithelium + @@ -10654,7 +11006,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + @@ -10663,12 +11015,12 @@ The modern definition of neurosecretion has evolved to include the release of an - + - Any cell that only exists in Eukaryota. + Any cell that in taxon some Eukaryota. MESH:D005057 eukaryotic cell @@ -10676,7 +11028,7 @@ The modern definition of neurosecretion has evolved to include the release of an - Any cell that only exists in Eukaryota. + Any cell that in taxon some Eukaryota. FBC:Autogenerated @@ -10699,7 +11051,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + @@ -10708,17 +11060,17 @@ The modern definition of neurosecretion has evolved to include the release of an - + - Any cell that only exists in Eumycetozoa. + Any cell that in taxon some Eumycetozoa. Eumycetozoan cell - Any cell that only exists in Eumycetozoa. + Any cell that in taxon some Eumycetozoa. FBC:Autogenerated @@ -11136,6 +11488,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -11902,8 +12255,19 @@ The modern definition of neurosecretion has evolved to include the release of an + + + + + + + + + + + + - @@ -11911,10 +12275,15 @@ The modern definition of neurosecretion has evolved to include the release of an An epithelial cell that lines the peripheral gas exchange region of the lungs of air-breathing vertebrates. + + 2024-09-02T08:27:21Z BTO:0000395 CALOHA:TS-2168 FMA:62499 + MESH:D056809 alveolar epithelial cell + alveolus of lung epithelial cell + epithelial cell of alveolus of lung pneumocyte pneumonocyte @@ -12246,10 +12615,9 @@ The modern definition of neurosecretion has evolved to include the release of an - - + @@ -12342,7 +12710,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + @@ -12524,6 +12892,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -12572,6 +12941,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -12619,7 +12989,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + @@ -12708,7 +13078,7 @@ The modern definition of neurosecretion has evolved to include the release of an GOC:tfm MESH:D014327 PMID:37630754 - doi:10.1007/978-3-030-84725-8 + doi:10.1007/978-3-030-84725-8 @@ -12944,6 +13314,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -13092,7 +13463,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + @@ -13103,7 +13474,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + @@ -13249,11 +13620,10 @@ The modern definition of neurosecretion has evolved to include the release of an - - + @@ -13395,6 +13765,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -13509,7 +13880,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + @@ -13942,6 +14313,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -14248,7 +14620,9 @@ The modern definition of neurosecretion has evolved to include the release of an - + + An epithelial cell that forms a syncytium, which is a multinucleated cell resulting from the fusion of multiple cells. + Wikipedia:Syncytium syncytial epithelial cell @@ -14382,7 +14756,6 @@ The modern definition of neurosecretion has evolved to include the release of an - @@ -14391,7 +14764,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + @@ -14420,6 +14793,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -14451,6 +14825,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -14563,6 +14938,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -14738,21 +15114,20 @@ The modern definition of neurosecretion has evolved to include the release of an - - + A stem cell that gives rise to the follicle cells that surround the oocyte in female arthropods. somatic stem cell FBbt:00004903 follicle stem cell (sensu Arthropoda) - - + + - + https://github.com/obophenotype/cell-ontology/issues/1943 @@ -15055,6 +15430,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -15476,11 +15852,10 @@ The modern definition of neurosecretion has evolved to include the release of an - - + @@ -15506,12 +15881,11 @@ The modern definition of neurosecretion has evolved to include the release of an - - + @@ -15576,11 +15950,10 @@ The modern definition of neurosecretion has evolved to include the release of an - - + @@ -15675,10 +16048,9 @@ The modern definition of neurosecretion has evolved to include the release of an - - + @@ -15707,6 +16079,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -15877,10 +16250,9 @@ The modern definition of neurosecretion has evolved to include the release of an - - + @@ -15893,14 +16265,14 @@ The modern definition of neurosecretion has evolved to include the release of an FBbt:00004904 follicle cell of egg chamber - - + + - + @@ -16177,7 +16549,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + @@ -16553,15 +16925,21 @@ The modern definition of neurosecretion has evolved to include the release of an - + A supporting cell for the developing female gamete in the ovary of mammals. They develop from the coelomic epithelial cells of the gonadal ridge. Granulosa cells form a single layer around the mammalian oocyte in the primordial ovarian follicle and advance to form a multilayered cumulus oophorus surrounding the ovum in the Graafian follicle. The major functions of granulosa cells include the production of steroids and LH receptors. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Granulosa cells are a type of somatic cell most commonly known for their crucial role within the ovarian follicles of female mammalian species. Named for their grainy appearance, they are situated in the follicular epithelium, lining the inner part of the follicle and directly surrounding the oocyte. These cells stand as an integral part of the ovarian structure and function. +One of the primary roles of granulosa cells is to aid in the production and secretion of sex hormones, particularly estrogen. They achieve this by working in tandem with theca cells, which stay attached to the external layer of the follicle. Theca cells produce androstenedione (a type of androgen) which granulosa cells then convert into estradiol, a form of estrogen, with the help of the enzyme aromatase. Moreover, granulosa cells participate in luteinization, transforming into luteal granulosa cells as a response to the luteinizing hormone during ovulation. This allows the formation of the corpus luteum, responsible for the secretion of progesterone necessary to maintain pregnancy. +Granulosa cells also play a significant role in follicular development and oocyte maturation, involving close communication with the contained oocyte. They support the oocyte through the provision of nutrients and growth factors, control its meiotic cycle and ensure it is appropriately oriented and instructed for impending ovulation. Furthermore, granulosa cells contribute to the formation of the zona pellucida and the follicular fluid, providing an optimal environment for the oocyte's growth and maturation. These cells, thus, perform multiple vital roles, underscoring their importance in fertility and reproductive health. BTO:0000542 CALOHA:TS-0729 FMA:18718 ZFA:0009227 + https://cellxgene.cziscience.com/cellguide/CL_0000501 granulosa cell of ovary granulosa cell @@ -16572,6 +16950,20 @@ The modern definition of neurosecretion has evolved to include the release of an A supporting cell for the developing female gamete in the ovary of mammals. They develop from the coelomic epithelial cells of the gonadal ridge. Granulosa cells form a single layer around the mammalian oocyte in the primordial ovarian follicle and advance to form a multilayered cumulus oophorus surrounding the ovum in the Graafian follicle. The major functions of granulosa cells include the production of steroids and LH receptors. MESH:D006107 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Granulosa cells are a type of somatic cell most commonly known for their crucial role within the ovarian follicles of female mammalian species. Named for their grainy appearance, they are situated in the follicular epithelium, lining the inner part of the follicle and directly surrounding the oocyte. These cells stand as an integral part of the ovarian structure and function. +One of the primary roles of granulosa cells is to aid in the production and secretion of sex hormones, particularly estrogen. They achieve this by working in tandem with theca cells, which stay attached to the external layer of the follicle. Theca cells produce androstenedione (a type of androgen) which granulosa cells then convert into estradiol, a form of estrogen, with the help of the enzyme aromatase. Moreover, granulosa cells participate in luteinization, transforming into luteal granulosa cells as a response to the luteinizing hormone during ovulation. This allows the formation of the corpus luteum, responsible for the secretion of progesterone necessary to maintain pregnancy. +Granulosa cells also play a significant role in follicular development and oocyte maturation, involving close communication with the contained oocyte. They support the oocyte through the provision of nutrients and growth factors, control its meiotic cycle and ensure it is appropriately oriented and instructed for impending ovulation. Furthermore, granulosa cells contribute to the formation of the zona pellucida and the follicular fluid, providing an optimal environment for the oocyte's growth and maturation. These cells, thus, perform multiple vital roles, underscoring their importance in fertility and reproductive health. + DOI:10.1016/j.ejogrb.2004.01.010 + DOI:10.1093/humrep/del408 + DOI:10.1093/humupd/6.3.279 + DOI:10.1210/jcem-28-3-355 + DOI:10.3389/fendo.2019.00832/full + @@ -16587,8 +16979,14 @@ The modern definition of neurosecretion has evolved to include the release of an A cell found throughout the gastrointestinal tract and in the pancreas. They secrete somatostatin in both an endocrine and paracrine manner. Somatostatin inhibits gastrin, cholecystokinin, insulin, glucagon, pancreatic enzymes, and gastric hydrochloric acid. A variety of substances which inhibit gastric acid secretion (vasoactive intestinal peptide, calcitonin gene-related peptide, cholecystokinin, beta-adrenergic agonists, and gastric inhibitory peptide) are thought to act by releasing somatostatin. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Type D enteroendocrine cells, also known as D or delta cells, are specialized hormone-releasing cells found in the pancreas and also scattered throughout the lining of the gastrointestinal tract in mammals, notably within the stomach and the upper part of the small intestine known as the duodenum. The primary role of D cells is to produce and secrete somatostatin, a potent paracrine inhibitor. +In the gastrointestinal tract, somatostatin slows down digestion. It reduces gastric acid secretion and slows down the rate of gastric emptying, thereby prolonging and controling the digestive p. Functionally, these effects are aimed at sustaining nutrient absorption to optimize energy extraction from consumed food. +In the pancreas, D cells maintain a vital role in endocrine regulation. D cells in the pancreatic islands secrete somatostatin to inhibit the release of both insulin and glucagon from type A cells and B cells, glucoregulatory hormones that control blood sugar levels. Hence, D cells contribute considerably to the homeostasis of the body's metabolic processes. It is also noteworthy that dysfunctional D cells or irregular somatostatin signaling has been associated with certain pathologies such as neuroendocrine tumors and gastric ulcers. FMA:62935 ZFA:0009228 + https://cellxgene.cziscience.com/cellguide/CL_0000502 D cell type D enteroendocrine cell @@ -16599,6 +16997,19 @@ The modern definition of neurosecretion has evolved to include the release of an A cell found throughout the gastrointestinal tract and in the pancreas. They secrete somatostatin in both an endocrine and paracrine manner. Somatostatin inhibits gastrin, cholecystokinin, insulin, glucagon, pancreatic enzymes, and gastric hydrochloric acid. A variety of substances which inhibit gastric acid secretion (vasoactive intestinal peptide, calcitonin gene-related peptide, cholecystokinin, beta-adrenergic agonists, and gastric inhibitory peptide) are thought to act by releasing somatostatin. MESH:D019864 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Type D enteroendocrine cells, also known as D or delta cells, are specialized hormone-releasing cells found in the pancreas and also scattered throughout the lining of the gastrointestinal tract in mammals, notably within the stomach and the upper part of the small intestine known as the duodenum. The primary role of D cells is to produce and secrete somatostatin, a potent paracrine inhibitor. +In the gastrointestinal tract, somatostatin slows down digestion. It reduces gastric acid secretion and slows down the rate of gastric emptying, thereby prolonging and controling the digestive p. Functionally, these effects are aimed at sustaining nutrient absorption to optimize energy extraction from consumed food. +In the pancreas, D cells maintain a vital role in endocrine regulation. D cells in the pancreatic islands secrete somatostatin to inhibit the release of both insulin and glucagon from type A cells and B cells, glucoregulatory hormones that control blood sugar levels. Hence, D cells contribute considerably to the homeostasis of the body's metabolic processes. It is also noteworthy that dysfunctional D cells or irregular somatostatin signaling has been associated with certain pathologies such as neuroendocrine tumors and gastric ulcers. + DOI:10.1016/j.pharmthera.2015.05.007 + DOI:10.1038/s41574-018-0020-6 + DOI:10.1093/annonc/mdh216 + https://www.sciencedirect.com/topics/neuroscience/somatostatin-cell + @@ -16794,8 +17205,14 @@ The modern definition of neurosecretion has evolved to include the release of an An epithelial cell found in the basal part of the intestinal glands (crypts of Lieberkuhn) including the appendix. Paneth cells synthesize and secrete lysozyme and cryptdins. Numerous in the deeper parts of the intestinal crypts, particularly in the duodenum, rich in zinc, contain large acidophilic granules, with irregular apical microvilli and prominent membrane-bound vacuoles containing matrix. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Paneth cells are specialized epithelial cells that are primarily located at the bottom of the crypts of Lieberkühn in the small intestine, where they play a pivotal role in maintaining gut homeostasis. They have also been found in smaller numbers in the colonic crypts and other parts of the gastrointestinal tract. Paneth cells are characterized by large acidophilic granules, which take up most of the cytoplasmic volume, causing the nucleus to be pushed toward the base of the cell. +Paneth cells function as a part of the innate immune system. The large granules inside the cells are filled with antimicrobial peptides, such as defensins and lysozymes. Upon bacterial intrusion or cellular signaling indicating a potential infection, Paneth cells release the granules containing the antimicrobial substances into the crypt lumen, effectively serving as the first line of defense against bacterial invasion within the gastrointestinal tract. In essence, Paneth cells serve as guardians, protecting the intestinal stem cells from harmful pathogens that may disturb the gut ecosystem. +In addition to their primary role in immunity, Paneth cells are also crucial for supporting the stem cell niche in the intestinal crypts. They are located adjacent to Lgr5+ stem cells and secrete various growth factors such as EGF, TGF-alpha, Wnt3, and Notch ligand Dll4. These factors regulate the self-renewal and differentiation of these stem cells, which continuously replenish the intestinal epithelium. Consequently, any abnormality or dysfunction in Paneth cells could lead to a disturbance in gut homeostasis, possibly resulting in various illnesses such as inflammatory bowel disease. BTO:0000993 FMA:62897 + https://cellxgene.cziscience.com/cellguide/CL_0000510 paneth cell @@ -16815,6 +17232,20 @@ The modern definition of neurosecretion has evolved to include the release of an PMID:29184701 PMID:32308658 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Paneth cells are specialized epithelial cells that are primarily located at the bottom of the crypts of Lieberkühn in the small intestine, where they play a pivotal role in maintaining gut homeostasis. They have also been found in smaller numbers in the colonic crypts and other parts of the gastrointestinal tract. Paneth cells are characterized by large acidophilic granules, which take up most of the cytoplasmic volume, causing the nucleus to be pushed toward the base of the cell. +Paneth cells function as a part of the innate immune system. The large granules inside the cells are filled with antimicrobial peptides, such as defensins and lysozymes. Upon bacterial intrusion or cellular signaling indicating a potential infection, Paneth cells release the granules containing the antimicrobial substances into the crypt lumen, effectively serving as the first line of defense against bacterial invasion within the gastrointestinal tract. In essence, Paneth cells serve as guardians, protecting the intestinal stem cells from harmful pathogens that may disturb the gut ecosystem. +In addition to their primary role in immunity, Paneth cells are also crucial for supporting the stem cell niche in the intestinal crypts. They are located adjacent to Lgr5+ stem cells and secrete various growth factors such as EGF, TGF-alpha, Wnt3, and Notch ligand Dll4. These factors regulate the self-renewal and differentiation of these stem cells, which continuously replenish the intestinal epithelium. Consequently, any abnormality or dysfunction in Paneth cells could lead to a disturbance in gut homeostasis, possibly resulting in various illnesses such as inflammatory bowel disease. + DOI:10.1007/s00018-002-8412-z + DOI:10.1038/nature09637 + DOI:10.1038/nrmicro2546 + DOI:10.1146/annurev-physiol-030212-183744 + DOI:10.3389/fimmu.2020.00587 + @@ -17035,6 +17466,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -17063,7 +17495,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + @@ -17115,7 +17547,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + @@ -17124,17 +17556,17 @@ The modern definition of neurosecretion has evolved to include the release of an - + - Any cell that only exists in Fungi. + Any cell that in taxon some Fungi. fungal cell - Any cell that only exists in Fungi. + Any cell that in taxon some Fungi. FBC:Autogenerated @@ -17207,8 +17639,8 @@ The modern definition of neurosecretion has evolved to include the release of an - + @@ -17346,21 +17778,20 @@ The modern definition of neurosecretion has evolved to include the release of an - - + A neuron that develops during the early segmentation stages in teleosts, before the neural tube is formed. ZFA:0009242 primary neuron (sensu Teleostei) - - + + - + https://github.com/obophenotype/cell-ontology/pull/1950 @@ -17473,21 +17904,20 @@ The modern definition of neurosecretion has evolved to include the release of an - - + A neuron of teleosts that develops later than a primary neuron, typically during the larval stages. ZFA:0009246 secondary neuron (sensu Teleostei) - - + + - + https://github.com/obophenotype/cell-ontology/pull/1950 @@ -18045,6 +18475,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -18210,6 +18641,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -18306,6 +18738,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -18834,6 +19267,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -19020,6 +19454,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -19161,6 +19596,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -19652,6 +20088,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -19807,6 +20244,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -19899,6 +20337,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -19981,6 +20420,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -20165,9 +20605,15 @@ The modern definition of neurosecretion has evolved to include the release of an A subtype of enteroendocrine cells found in the gastrointestinal mucosa, particularly in the glands of pyloric antrum; duodenum; and ileum. These cell type secretes serotonin and some neurotransmitters including enkephalins and substance P. Their secretory granules stain readily with silver (argentaffin stain). + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Type EC enteroendocrine cells, also known as enterochromaffin cells, are a vital hormone-secreting cell type found in the gastrointestinal tract. These cells are named after their location in the intestines (“entero”) and because they are stainable by chromium salts (“chromaffin”). +The primary function of type EC enteroendocrine cells is to act as chemosensors and lies in their capacity to produce and secrete serotonin, also known as 5-hydroxytryptamine (5-HT). Serotonin is a neurotransmitter that plays a significant role in modulating motility, secretion, vasodilation, perception of pain, and appetite in the gastrointestinal system. However, its function is not limited to the gastrointestinal tract; once secreted, serotonin is distributed via the bloodstream and contributes to regulating mood, appetite, and sleep in the brain. +Via specific chemosensory receptors type EC enteroendocrine cells are able to respond to various environmental, metabolic, and homeostatic stimuli and transduce information from the gut to the nervous system: Food intake, particularly the ingestion of fats and carbohydrates, prompts these cells to produce and release serotonin; the mechanical stimulus of food in the lumen can also trigger release. The distribution, function, and responsiveness of type EC cells reveal them as a crucial link between the intestinal environment, the nervous system, and the regulation of numerous bodily functions. FMA:62934 FMA:83132 MESH:D004759 + https://cellxgene.cziscience.com/cellguide/CL_0000577 Kulchitsky cell argentaffin cell enterochromaffin cell @@ -20181,6 +20627,19 @@ The modern definition of neurosecretion has evolved to include the release of an A subtype of enteroendocrine cells found in the gastrointestinal mucosa, particularly in the glands of pyloric antrum; duodenum; and ileum. These cell type secretes serotonin and some neurotransmitters including enkephalins and substance P. Their secretory granules stain readily with silver (argentaffin stain). PMID:9505449 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Type EC enteroendocrine cells, also known as enterochromaffin cells, are a vital hormone-secreting cell type found in the gastrointestinal tract. These cells are named after their location in the intestines (“entero”) and because they are stainable by chromium salts (“chromaffin”). +The primary function of type EC enteroendocrine cells is to act as chemosensors and lies in their capacity to produce and secrete serotonin, also known as 5-hydroxytryptamine (5-HT). Serotonin is a neurotransmitter that plays a significant role in modulating motility, secretion, vasodilation, perception of pain, and appetite in the gastrointestinal system. However, its function is not limited to the gastrointestinal tract; once secreted, serotonin is distributed via the bloodstream and contributes to regulating mood, appetite, and sleep in the brain. +Via specific chemosensory receptors type EC enteroendocrine cells are able to respond to various environmental, metabolic, and homeostatic stimuli and transduce information from the gut to the nervous system: Food intake, particularly the ingestion of fats and carbohydrates, prompts these cells to produce and release serotonin; the mechanical stimulus of food in the lumen can also trigger release. The distribution, function, and responsiveness of type EC cells reveal them as a crucial link between the intestinal environment, the nervous system, and the regulation of numerous bodily functions. + DOI:10.1016/0166-4328(96)00075-7 + DOI:10.1016/j.cell.2017.05.034 + DOI:10.1038/s41574-019-0168-8 + DOI:10.1073/pnas.1804938115 + @@ -20464,6 +20923,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -20827,6 +21287,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -20883,9 +21344,15 @@ The modern definition of neurosecretion has evolved to include the release of an A tissue-resident macrophage found in the alveoli of the lungs. Ingests small inhaled particles resulting in degradation and presentation of the antigen to immunocompetent cells. Markers include F4/80-positive, CD11b-/low, CD11c-positive, CD68-positive, sialoadhesin-positive, dectin-1-positive, MR-positive, CX3CR1-negative. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Alveolar macrophages are unique tissue-resident macrophages found in the lungs, specifically in the air sacs or alveoli where gas exchange occurs. They are characterized by specific surface markers including: F4/80-positive, CD11b-/low, CD11c-positive, CD68-positive, sialoadhesin-positive, dectin-1-positive, MR-positive, CX3CR1-negative. These specialized immune cells form a crucial part of the body's defense mechanism, playing important roles in pulmonary health and homeostasis. They are the first line of defense in the pulmonary immune response, acting as scavengers that patrol the alveoli and engulf foreign particles like bacteria, dust, and other debris that enter the lungs through inhalation. +The primary function of these alveolar macrophages is phagocytosis, whereby they consume and digest foreign substances, dead cells, and other particulates. In the lung, alveolar macrophages are also responsible for clearing surfactant. Additionally, alveolar macrophages also play an integral role in initiating the immune response, as they secrete several pro-inflammatory cytokines and chemokines that recruit other immune cells to the site of infection or inflammation. +Beyond their role in host defense, alveolar macrophages contribute to tissue remodeling and wound repair in the lungs, aiding in maintaining lung integrity. They also regulate local inflammation and control the immune response to prevent excessive inflammation that may be harmful. However, an imbalance in the function of alveolar macrophages can contribute to various lung diseases. Abnormal alveolar macrophage activation has been implicated in chronic inflammatory diseases such as emphysema, asthma, and fibrosis. BTO:0000802 CALOHA:TS-0030 FMA:83023 + https://cellxgene.cziscience.com/cellguide/CL_0000583 dust cell MF.Lu @@ -20909,6 +21376,19 @@ The modern definition of neurosecretion has evolved to include the release of an GO_REF:0000031 MESH:D016676 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Alveolar macrophages are unique tissue-resident macrophages found in the lungs, specifically in the air sacs or alveoli where gas exchange occurs. They are characterized by specific surface markers including: F4/80-positive, CD11b-/low, CD11c-positive, CD68-positive, sialoadhesin-positive, dectin-1-positive, MR-positive, CX3CR1-negative. These specialized immune cells form a crucial part of the body's defense mechanism, playing important roles in pulmonary health and homeostasis. They are the first line of defense in the pulmonary immune response, acting as scavengers that patrol the alveoli and engulf foreign particles like bacteria, dust, and other debris that enter the lungs through inhalation. +The primary function of these alveolar macrophages is phagocytosis, whereby they consume and digest foreign substances, dead cells, and other particulates. In the lung, alveolar macrophages are also responsible for clearing surfactant. Additionally, alveolar macrophages also play an integral role in initiating the immune response, as they secrete several pro-inflammatory cytokines and chemokines that recruit other immune cells to the site of infection or inflammation. +Beyond their role in host defense, alveolar macrophages contribute to tissue remodeling and wound repair in the lungs, aiding in maintaining lung integrity. They also regulate local inflammation and control the immune response to prevent excessive inflammation that may be harmful. However, an imbalance in the function of alveolar macrophages can contribute to various lung diseases. Abnormal alveolar macrophage activation has been implicated in chronic inflammatory diseases such as emphysema, asthma, and fibrosis. + DOI:10.1007/s00424-017-1965-3 + DOI:10.1016/j.cellimm.2018.01.005 + DOI:10.1038/nri3600 + DOI:10.14348/molcells.2021.0058 + @@ -21707,6 +22187,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -22075,6 +22556,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -22494,9 +22976,16 @@ The modern definition of neurosecretion has evolved to include the release of an A secretory cell that is grouped together with other cells of the same type to form grape shaped clusters known as acini (singular acinus). + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Acinar cells are specialized exocrine gland cells that secrete specific enzymes and fluids to aid in digestion. Found primarily in the pancreas and salivary glands, the term acinar is derived from the Latin word 'acinus' which means 'grape'; this is because acinar cells are arranged in a grape-like cluster around small ducts, formulating an acinus structure. +In the salivary glands, acinar cells secrete digestive enzymes as well as other substances such as mucus and water. These secretions service the initial stages of the digestive process, preparing the consumed food for onward digestion in the stomach and intestines by lubricating and partially breaking it down. +In the pancreas, acinar cells are responsible for synthesizing and secreting a significant amount of digestive enzymes, such as trypsin, chymotrypsin, and amylase. These enzymes are stored in zymogen granules inside the acinar cells until they are dispatched into the small intestine. Once within the small intestine, they break down proteins, carbohydrates, and fats into substances that can be absorbed. This is vital to the effective and efficient digestion and absorption of nutrients from the food we consume. +Acinar cells have high protein synthesis rates and are susceptible to accumulation of misfolded proteins; the subsequential induction of ER stress is thought to be involved in the development of pancreatitis, a serious inflammatory disease of the exocrine pancreas. FMA:83625 MESH:D061354 ZFA:0009277 + https://cellxgene.cziscience.com/cellguide/CL_0000622 acinic cell acinous cell @@ -22509,6 +22998,21 @@ The modern definition of neurosecretion has evolved to include the release of an GOC:tfm http://www.copewithcytokines.de + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Acinar cells are specialized exocrine gland cells that secrete specific enzymes and fluids to aid in digestion. Found primarily in the pancreas and salivary glands, the term acinar is derived from the Latin word 'acinus' which means 'grape'; this is because acinar cells are arranged in a grape-like cluster around small ducts, formulating an acinus structure. +In the salivary glands, acinar cells secrete digestive enzymes as well as other substances such as mucus and water. These secretions service the initial stages of the digestive process, preparing the consumed food for onward digestion in the stomach and intestines by lubricating and partially breaking it down. +In the pancreas, acinar cells are responsible for synthesizing and secreting a significant amount of digestive enzymes, such as trypsin, chymotrypsin, and amylase. These enzymes are stored in zymogen granules inside the acinar cells until they are dispatched into the small intestine. Once within the small intestine, they break down proteins, carbohydrates, and fats into substances that can be absorbed. This is vital to the effective and efficient digestion and absorption of nutrients from the food we consume. +Acinar cells have high protein synthesis rates and are susceptible to accumulation of misfolded proteins; the subsequential induction of ER stress is thought to be involved in the development of pancreatitis, a serious inflammatory disease of the exocrine pancreas. + DOI:10.1007/BF00710764 + DOI:10.1038/nrgastro.2013.36 + DOI:10.1097/MOG.0b013e32832ebfac + DOI:10.1111/prd.12116 + DOI:10.1152/physrev.00011.2011 + @@ -22937,6 +23441,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -23406,8 +23911,8 @@ The modern definition of neurosecretion has evolved to include the release of an - + @@ -23426,7 +23931,7 @@ The modern definition of neurosecretion has evolved to include the release of an - A phagocytic cell formed by the fusion of macrophages, occurs in chronic inflammatory responses to persistent microorganism such as M.tuberculosis, component of granulomas. Sometimes used to refer to megakaryocytes. + A phagocytic syncytial cell formed by the fusion of macrophages, occurs in chronic inflammatory responses to persistent microorganism such as M.tuberculosis, component of granulomas. Sometimes used to refer to megakaryocytes. BTO:0003107 FMA:83035 MESH:D015726 @@ -23435,6 +23940,7 @@ The modern definition of neurosecretion has evolved to include the release of an macrophage polykaryon multinucleate giant cell syncytial giant cell + MGC Role or process: Chronic infection, granulomatous inflammation. Consider also megakaryocyte (CL:0000556) as sometimes multinucleated giant cell is used to refer to this. multinucleated giant cell @@ -23448,11 +23954,13 @@ The modern definition of neurosecretion has evolved to include the release of an - A phagocytic cell formed by the fusion of macrophages, occurs in chronic inflammatory responses to persistent microorganism such as M.tuberculosis, component of granulomas. Sometimes used to refer to megakaryocytes. + A phagocytic syncytial cell formed by the fusion of macrophages, occurs in chronic inflammatory responses to persistent microorganism such as M.tuberculosis, component of granulomas. Sometimes used to refer to megakaryocytes. GOC:add GOC:tfm ISBN:0702022918 ISBN:0702024783 + PMID:33348900 + Wikipedia:Giant_cell @@ -23489,6 +23997,13 @@ The modern definition of neurosecretion has evolved to include the release of an ISBN:0702022918 ISBN:0702024783 + + + + MGC + PMID:33348900 + + @@ -23698,10 +24213,17 @@ The modern definition of neurosecretion has evolved to include the release of an A specialized kidney epithelial cell, contained within a glomerulus, that contains "feet" that interdigitate with the "feet" of other podocytes. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Podocytes are highly specialized, terminally differentiated glomerular visceral epithelial cells that wrap around the capillaries in the kidneys. They play an essential role in kidney function, particularly in the filtration selectivity of the glomerulus. Each podocyte is characterized by a unique architecture with a large cell body, ‘major processes’ extending outwardly from the cell body and ‘foot processes’, also known as pedicels, which surround. the glomerular capillary loops +Podocytes represent the last barrier of the glomerular filtration membrane in the kidney. This barrier prevents the leakage of plasma proteins from the blood into the urine, hence maintaining protein homeostasis in the body. The foot processes of the podocytes interdigitate with those from neighboring cells. The cell-cell junctions between the foot processes, the slit-diaphragms, are thought to create a molecular sensor of renal filtration that prevents the passage of macromolecules while allowing water and small solutes to pass. +Podocytes also contribute to the glomerular basement membrane by secreting collagen and maintain glomerular endothelial cell fenestration by secreting VEGFA. They have been shown to play a role in inducing cytoskeletal regulation, cell adhesion, and inflammatory response, consistent with their essential function in the kidney. +The importance of podocytes is further emphasized by the effects of their damage or loss. Abnormalities in podocytes often result in severe kidney diseases (podocytopathies), including focal segmental glomerulosclerosis (FSGS) and minimal change disease (MCD). Injury to the podocytes can result in "effacement" or flattening of foot processes, leading to increased permeability of the filtration barrier and proteinuria (an excess of serum protein in urine) which is a common symptom of kidney diseases. epithelial cell of visceral layer of glomerular capsule BTO:0002295 FMA:70967 ZFA:0009285 + https://cellxgene.cziscience.com/cellguide/CL_0000653 glomerular podocyte glomerular visceral epithelial cell kidney podocyte @@ -23718,6 +24240,21 @@ The modern definition of neurosecretion has evolved to include the release of an GOC:tfm https://doi.org/10.1101/2021.10.10.463829 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Podocytes are highly specialized, terminally differentiated glomerular visceral epithelial cells that wrap around the capillaries in the kidneys. They play an essential role in kidney function, particularly in the filtration selectivity of the glomerulus. Each podocyte is characterized by a unique architecture with a large cell body, ‘major processes’ extending outwardly from the cell body and ‘foot processes’, also known as pedicels, which surround. the glomerular capillary loops +Podocytes represent the last barrier of the glomerular filtration membrane in the kidney. This barrier prevents the leakage of plasma proteins from the blood into the urine, hence maintaining protein homeostasis in the body. The foot processes of the podocytes interdigitate with those from neighboring cells. The cell-cell junctions between the foot processes, the slit-diaphragms, are thought to create a molecular sensor of renal filtration that prevents the passage of macromolecules while allowing water and small solutes to pass. +Podocytes also contribute to the glomerular basement membrane by secreting collagen and maintain glomerular endothelial cell fenestration by secreting VEGFA. They have been shown to play a role in inducing cytoskeletal regulation, cell adhesion, and inflammatory response, consistent with their essential function in the kidney. +The importance of podocytes is further emphasized by the effects of their damage or loss. Abnormalities in podocytes often result in severe kidney diseases (podocytopathies), including focal segmental glomerulosclerosis (FSGS) and minimal change disease (MCD). Injury to the podocytes can result in "effacement" or flattening of foot processes, leading to increased permeability of the filtration barrier and proteinuria (an excess of serum protein in urine) which is a common symptom of kidney diseases. + DOI:10.1038/s41467-022-33748-1 + DOI:10.1038/s41572-020-0196-7 + DOI:10.1146/annurev-physiol-020911-153238 + DOI:10.1159/000481633 + DOI:10.3389/fcell.2021.771931 + @@ -23858,6 +24395,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -23905,6 +24443,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -24064,7 +24603,15 @@ The modern definition of neurosecretion has evolved to include the release of an An endothelial cell that has small pores, or fenestrations, which allow for the efficient exchange of substances between the blood and surrounding tissues. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Fenestrated cells are specialized epithelial cells that are characterized by a distinctive structural feature, fenestrations or tiny pores, which allow an exchange of substances such as fluids, nutrients, and waste between blood vessels and the surrounding tissue environments. These cells are present in various types of epithelial tissues in the human body, including the intestinal tract, endocrine glands, and certain parts of the renal system. +There are multiple types of endothelial cell fenestrations. The most common type is found in systemic capillaries of the endocrine tissue (e.g., pancreatic islets), gastrointestinal mucosa, and renal peritubular capillaries. Here, the fenestrated cells have fenestrations in their peripheral cytoplasm with a unique thin and permeable diaphragm that provides a high degree of selectivity, blocking the passage of larger molecules while allowing the free movement of smaller ones. In contrast, other types of fenestrations, such as the discontinuous epithelium of the liver sinusoidal endothelial cells, do not have diaphragms. +Characteristically, fenestrated cells play a vital role in the filtering process of body systems. They are a key part of the glomeruli in the kidneys where blood is filtered under high pressure. The fenestrations present in the endothelial cells lining the capillaries of the glomerulus allow the free passage of water and small solute molecules towards the Bowman's capsule, leaving behind larger proteins and cells in the blood, thereby aiding in the filtration and waste removal process. +In the endocrine system, fenestrated cells in glandular capillaries allow the prompt release of hormones into the bloodstream. These cells have tightly clustered fenestrations which increase the surface area available for passive diffusion, improving the efficiency of hormone secretion. In villi of the small intestine, these cells increase absorption efficiency, permitting the exchange of water, electrolytes, and nutrients. +Overall, fenestrated cells contribute immensely to important physiological processes of filtration, absorption, and secretion, primarily connecting our body's circulation system with the surrounding tissues and organs. ZFA:0009286 + https://cellxgene.cziscience.com/cellguide/CL_0000666 window cell fenestrated endothelial cell @@ -24075,6 +24622,22 @@ The modern definition of neurosecretion has evolved to include the release of an An endothelial cell that has small pores, or fenestrations, which allow for the efficient exchange of substances between the blood and surrounding tissues. DOI:10.1007/978-3-211-99390-3_133 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Fenestrated cells are specialized epithelial cells that are characterized by a distinctive structural feature, fenestrations or tiny pores, which allow an exchange of substances such as fluids, nutrients, and waste between blood vessels and the surrounding tissue environments. These cells are present in various types of epithelial tissues in the human body, including the intestinal tract, endocrine glands, and certain parts of the renal system. +There are multiple types of endothelial cell fenestrations. The most common type is found in systemic capillaries of the endocrine tissue (e.g., pancreatic islets), gastrointestinal mucosa, and renal peritubular capillaries. Here, the fenestrated cells have fenestrations in their peripheral cytoplasm with a unique thin and permeable diaphragm that provides a high degree of selectivity, blocking the passage of larger molecules while allowing the free movement of smaller ones. In contrast, other types of fenestrations, such as the discontinuous epithelium of the liver sinusoidal endothelial cells, do not have diaphragms. +Characteristically, fenestrated cells play a vital role in the filtering process of body systems. They are a key part of the glomeruli in the kidneys where blood is filtered under high pressure. The fenestrations present in the endothelial cells lining the capillaries of the glomerulus allow the free passage of water and small solute molecules towards the Bowman's capsule, leaving behind larger proteins and cells in the blood, thereby aiding in the filtration and waste removal process. +In the endocrine system, fenestrated cells in glandular capillaries allow the prompt release of hormones into the bloodstream. These cells have tightly clustered fenestrations which increase the surface area available for passive diffusion, improving the efficiency of hormone secretion. In villi of the small intestine, these cells increase absorption efficiency, permitting the exchange of water, electrolytes, and nutrients. +Overall, fenestrated cells contribute immensely to important physiological processes of filtration, absorption, and secretion, primarily connecting our body's circulation system with the surrounding tissues and organs. + DOI:10.1002/ar.1092200109 + DOI:10.1016/0306-4522(86)90162-4 + DOI:10.1016/j.devcel.2012.11.003 + DOI:10.1038/s41467-022-31571-2 + DOI:10.1152/ajprenal.90601.2008 + @@ -24372,7 +24935,7 @@ The modern definition of neurosecretion has evolved to include the release of an - + @@ -24470,6 +25033,7 @@ The modern definition of neurosecretion has evolved to include the release of an + @@ -24549,10 +25113,16 @@ radial glial cells acting as neural progenitors throughout life. An absorptive cell of the gut epithelium that endocytoses microorganisms and intact macromolecules from the gut lumen and transports them to the subepithelial space where they are presented to antigen-presenting cells and lymphocytes. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +M cells, or microfold cells, of the gut are specialized epithelial cells found in the lining of the gut, specifically in the follicle-associated epithelium of mucosa-associated lymphoid tissue, where they function as sentries against toxins and pathogens. M cells are characterized by apical microfolds (hence their alternate name) which express unique adhesion molecules that enable them to sample the luminal macromolecules. +Other morphological features that distinguish M cells from other intestinal mucosal cells include sparse microvilli and a reduced thickness of the glycocalyx, which permits adhesion while not hindering the transport of molecules. They also have unique intraepithelial invaginations on the basolateral side which are filled with macrophages and other immune cells that can process the engulfed macromolecules quickly. +These morphological characteristics enable M cells to serve a dual role in immune responses. They initiate the immune response by transporting antigens (such as toxic or pathogenic substances) across the epithelial layer to lymphocytes and antigen-presenting cells in the underlying lymphoid tissue. This specialized transport process is called 'transcytosis.' They also have specialized molecules like glycoprotein-2 for bacterial uptake. Simultaneously, M cells help maintain immune tolerance to food antigens and commensal bacteria, preventing unnecessary reactions to non-pathogenic substances and hypersensitivity conditions. While these functions are crucial for well-being, M cell dysfunction can lead to serious conditions like Crohn's disease and other inflammatory bowel diseases. M cell BTO:0003600 FMA:62929 ZFA:0009293 + https://cellxgene.cziscience.com/cellguide/CL_0000682 M-cell microfold cell @@ -24567,6 +25137,20 @@ radial glial cells acting as neural progenitors throughout life. GOC:jb GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +M cells, or microfold cells, of the gut are specialized epithelial cells found in the lining of the gut, specifically in the follicle-associated epithelium of mucosa-associated lymphoid tissue, where they function as sentries against toxins and pathogens. M cells are characterized by apical microfolds (hence their alternate name) which express unique adhesion molecules that enable them to sample the luminal macromolecules. +Other morphological features that distinguish M cells from other intestinal mucosal cells include sparse microvilli and a reduced thickness of the glycocalyx, which permits adhesion while not hindering the transport of molecules. They also have unique intraepithelial invaginations on the basolateral side which are filled with macrophages and other immune cells that can process the engulfed macromolecules quickly. +These morphological characteristics enable M cells to serve a dual role in immune responses. They initiate the immune response by transporting antigens (such as toxic or pathogenic substances) across the epithelial layer to lymphocytes and antigen-presenting cells in the underlying lymphoid tissue. This specialized transport process is called 'transcytosis.' They also have specialized molecules like glycoprotein-2 for bacterial uptake. Simultaneously, M cells help maintain immune tolerance to food antigens and commensal bacteria, preventing unnecessary reactions to non-pathogenic substances and hypersensitivity conditions. While these functions are crucial for well-being, M cell dysfunction can lead to serious conditions like Crohn's disease and other inflammatory bowel diseases. + DOI:10.1038/nature08529 + DOI:10.1093/jb/mvv121 + DOI:10.1136/gut.47.5.735 + https://www.ncbi.nlm.nih.gov/books/NBK534232/ + https://www.sciencedirect.com/topics/medicine-and-dentistry/microfold-cell + @@ -25013,8 +25597,14 @@ radial glial cells acting as neural progenitors throughout life. A cell that stores and secretes pancreatic polypeptide hormone. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +PP cells, also known as pancreatic polypeptide cells (and previously called F cells or gamma cells), are enteroendocrine cells predominantly found in the islets of Langerhans in the head of the pancreas. They are one of the four main endocrine cell types present in the pancreatic islets, along with type A, B and D cells. PP cells are notable for their production of pancreatic polypeptide, an anorexigenic hormone that modulates food intake and energy homeostasis. +By secreting pancreatic polypeptide, PP cells play a significant role in the management of both digestive and appetite regulation. Upon ingestion of food, there is a significant increase in the secretion of pancreatic polypeptide, which then reduces biliary secretion and helps slow down the movement of food through the digestive tract. This allows more time for digestion to take place and nutrients to be absorbed, promoting the efficient use of dietary intake. The pancreatic polypeptide further reduces appetite by interacting with the hypothalamus, the area of the brain responsible for control of hunger. +Given their important role in digestion, malfunction or damage to PP cells can lead to a disturbance in the digestive process and contribute to some disease conditions. For example, an overproduction of pancreatic polypeptide can result in conditions such as pancreatic tumors and diabetes. Conversely, an under secretion might contribute to obesity due to impaired dietary control. Furthermore, PP cells may also play a role in the body's energy balance, suggesting their implication in conditions related to energy metabolism. FMA:62938 FMA:83409 + https://cellxgene.cziscience.com/cellguide/CL_0000696 type F enteroendocrine cell PP cell @@ -25027,6 +25617,20 @@ radial glial cells acting as neural progenitors throughout life. JB:jb PMID:15153415 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +PP cells, also known as pancreatic polypeptide cells (and previously called F cells or gamma cells), are enteroendocrine cells predominantly found in the islets of Langerhans in the head of the pancreas. They are one of the four main endocrine cell types present in the pancreatic islets, along with type A, B and D cells. PP cells are notable for their production of pancreatic polypeptide, an anorexigenic hormone that modulates food intake and energy homeostasis. +By secreting pancreatic polypeptide, PP cells play a significant role in the management of both digestive and appetite regulation. Upon ingestion of food, there is a significant increase in the secretion of pancreatic polypeptide, which then reduces biliary secretion and helps slow down the movement of food through the digestive tract. This allows more time for digestion to take place and nutrients to be absorbed, promoting the efficient use of dietary intake. The pancreatic polypeptide further reduces appetite by interacting with the hypothalamus, the area of the brain responsible for control of hunger. +Given their important role in digestion, malfunction or damage to PP cells can lead to a disturbance in the digestive process and contribute to some disease conditions. For example, an overproduction of pancreatic polypeptide can result in conditions such as pancreatic tumors and diabetes. Conversely, an under secretion might contribute to obesity due to impaired dietary control. Furthermore, PP cells may also play a role in the body's energy balance, suggesting their implication in conditions related to energy metabolism. + DOI:10.1016/j.febslet.2014.07.005 + DOI:10.1016/j.mce.2015.06.028 + DOI:10.1038/s41580-020-00317-7 + DOI:10.1210/jc.2003-030630 + DOI:10.1369/00221554155835 + @@ -25253,21 +25857,27 @@ radial glial cells acting as neural progenitors throughout life. - + + - - + - Specialized ependymal cell that produces the cerebrospinal fluid from the blood and secretes it into the lumen of the brain and spinal chord. + + + + + + + A specialized ependymal cell that is part of the choroid plexus epithelium, responsible for producing cerebrospinal fluid (CSF) by selectively filtering and modifying blood plasma components before secreting it into the brain and spinal cord. This cell is characterized by a brush border on its apical surface, which enhances the secretion of CSF. 2023-08-04T08:48:30Z choroid plexus cell @@ -25276,15 +25886,17 @@ radial glial cells acting as neural progenitors throughout life. epithelial cell of choroid plexus + A choroid plexus epithelial cell possesses non-motile 9+0 cilia. While these cilia can exhibit transient motility during development, they generally do not contribute significantly to the directional flow of cerebrospinal fluid (CSF). Instead, they are primarily involved in sensory functions. choroid plexus epithelial cell - Specialized ependymal cell that produces the cerebrospinal fluid from the blood and secretes it into the lumen of the brain and spinal chord. + A specialized ependymal cell that is part of the choroid plexus epithelium, responsible for producing cerebrospinal fluid (CSF) by selectively filtering and modifying blood plasma components before secreting it into the brain and spinal cord. This cell is characterized by a brush border on its apical surface, which enhances the secretion of CSF. GOC:add GOC:tfm JB:jb + PMID:15561411 PMID:9550134 @@ -25299,6 +25911,12 @@ radial glial cells acting as neural progenitors throughout life. ZFA:0009304 + + + + A choroid plexus epithelial cell possesses non-motile 9+0 cilia. While these cilia can exhibit transient motility during development, they generally do not contribute significantly to the directional flow of cerebrospinal fluid (CSF). Instead, they are primarily involved in sensory functions. + PMID:25729351 + @@ -25441,11 +26059,12 @@ radial glial cells acting as neural progenitors throughout life. - + + - + Cumulus cell is a specialized granulosa cell that surrounds and nourishes the oocyte. This cell-type surrounds the fully-grown oocyte to form a cumulus-oocyte complex (abbr. COC). The terms cumulus oophorus cells, cumulus granulosa cells, cumulus oophorous granulosa cells, granulosa-cumulus cells are used to make a distinction between this cell and the other functionally different subpopulation of granulosa cells at the wall of the Graafian follicle. @@ -25639,7 +26258,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -25830,8 +26449,14 @@ radial glial cells acting as neural progenitors throughout life. A cell of a layer of transitional epithelium in the wall of the proximal urethra, bladder, ureter or renal pelvis, external to the lamina propria. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Urothelial cells are a unique type of epithelial cell found lining the urinary tract system. They form the urothelium, a specialized, multi-layered epithelium that lines major portions of the urinary tract, including the renal pelvis, ureters, bladder, and the proximal part of the urethra. The distinct characteristic of urothelial cells is their ability to stretch and contract depending on the volume of liquid they contain - a feature that facilitates the essential role they play in maintaining the functionality and integrity of the urinary system. +The primary function of urothelial cells is to provide an impermeable barrier to urine, preventing the toxic components present in the urine from seeping back into the body's bloodstream. The urothelium consists of a superficial umbrella cell layer, 1–2 layers of intermediate cells, and a basal cell layer. The umbrella layer is composed of large, mostly binucleated cells that are covered in an asymmetrical unit membrane, the uroplakin plaques. These plaques function to seal the apical membrane of the bladder from the toxic and highly variable contents of urine. The lipid bilayer structure of uroplakin plaques has an exceptionally high concentration of uroplakins that contribute to the barrier function of the urothelium. +Beyond their mechanical function, urothelial cells also play a role in sensing and signaling changes in the urinary system. They express a number of sensor molecules or respond to thermal, mechanical and chemical stimuli and can release chemical mediators. This allows them to act as sensory transducers because they detect changes in the filling state of the bladder and transmit this information to the nervous system. Moreover, these versatile cells contribute to the defense mechanism against urinary tract pathogens. They respond to bacterial infections by releasing chemical messengers, cytokines and chemokines, to attract immune cells, and also can engulf pathogens via endocytosis. FMA:84127 ZFA:0009308 + https://cellxgene.cziscience.com/cellguide/CL_0000731 urinary tract transitional epithelial cell urothelial cell @@ -25844,6 +26469,20 @@ radial glial cells acting as neural progenitors throughout life. MA:ma doi:10.1038/s41385-022-00565-0 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Urothelial cells are a unique type of epithelial cell found lining the urinary tract system. They form the urothelium, a specialized, multi-layered epithelium that lines major portions of the urinary tract, including the renal pelvis, ureters, bladder, and the proximal part of the urethra. The distinct characteristic of urothelial cells is their ability to stretch and contract depending on the volume of liquid they contain - a feature that facilitates the essential role they play in maintaining the functionality and integrity of the urinary system. +The primary function of urothelial cells is to provide an impermeable barrier to urine, preventing the toxic components present in the urine from seeping back into the body's bloodstream. The urothelium consists of a superficial umbrella cell layer, 1–2 layers of intermediate cells, and a basal cell layer. The umbrella layer is composed of large, mostly binucleated cells that are covered in an asymmetrical unit membrane, the uroplakin plaques. These plaques function to seal the apical membrane of the bladder from the toxic and highly variable contents of urine. The lipid bilayer structure of uroplakin plaques has an exceptionally high concentration of uroplakins that contribute to the barrier function of the urothelium. +Beyond their mechanical function, urothelial cells also play a role in sensing and signaling changes in the urinary system. They express a number of sensor molecules or respond to thermal, mechanical and chemical stimuli and can release chemical mediators. This allows them to act as sensory transducers because they detect changes in the filling state of the bladder and transmit this information to the nervous system. Moreover, these versatile cells contribute to the defense mechanism against urinary tract pathogens. They respond to bacterial infections by releasing chemical messengers, cytokines and chemokines, to attract immune cells, and also can engulf pathogens via endocytosis. + DOI:10.1002/nau.22195 + DOI:10.1038/ki.2009.73 + DOI:10.1038/ncpuro0672 + DOI:10.1038/s41579-020-0324-0 + DOI:10.1152/physrev.00041.2019 + @@ -26004,7 +26643,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -26367,6 +27006,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -26537,8 +27177,6 @@ radial glial cells acting as neural progenitors throughout life. - - @@ -26558,13 +27196,8 @@ radial glial cells acting as neural progenitors throughout life. - - - - - - A bipolar neuron found in the retina that is synapsed by rod photoreceptor cells but not by cone photoreceptor cells. These neurons depolarize in response to light. + FMA:67750 ZFA:0009321 @@ -26579,6 +27212,12 @@ radial glial cells acting as neural progenitors throughout life. GOC:tfm PMID:14689473 + + + + + PMID:38627529 + @@ -26654,7 +27293,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -26685,7 +27324,7 @@ radial glial cells acting as neural progenitors throughout life. FMB cone bipolar cell type 2 cone bipolar cell (sensu Mus) - + @@ -26705,7 +27344,7 @@ radial glial cells acting as neural progenitors throughout life. - + PMID:27565351 @@ -26979,6 +27618,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -28213,13 +28853,14 @@ radial glial cells acting as neural progenitors throughout life. + - A specialized multinuclear osteoclast associated with the absorption and removal of bone. + A specialized multinuclear osteoclast, forming a syncytium through the fusion of mononuclear precursor cells, associated with the absorption and removal of bone. multinucleated osteoclast Morphology: multinucleated, highly vesicular. multinuclear osteoclast @@ -28233,9 +28874,11 @@ radial glial cells acting as neural progenitors throughout life. - A specialized multinuclear osteoclast associated with the absorption and removal of bone. + A specialized multinuclear osteoclast, forming a syncytium through the fusion of mononuclear precursor cells, associated with the absorption and removal of bone. GOC:add PMID:12713016 + PMID:29379067 + PMID:38903088 PMID:9415452 @@ -28600,6 +29243,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -28897,6 +29541,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -29411,6 +30056,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -29777,6 +30423,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -29874,6 +30521,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -29948,6 +30596,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -30030,6 +30679,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -31187,6 +31837,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -31309,6 +31960,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -31710,6 +32362,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -32175,6 +32828,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -32327,7 +32981,9 @@ radial glial cells acting as neural progenitors throughout life. + + @@ -33227,6 +33883,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -33256,6 +33913,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -33552,6 +34210,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -33590,6 +34249,12 @@ radial glial cells acting as neural progenitors throughout life. A monocyte that responds rapidly to microbial stimuli by secreting cytokines and antimicrobial factors and which is characterized by high expression of CCR2 in both rodents and humans, negative for the lineage markers CD3, CD19, and CD20, and of larger size than non-classical monocytes. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Classical monocytes are a subtype of monocytes that are characterized by high CD14 but no CD16 expression. Emerging from the bone marrow and entering the bloodstream, these cells play central roles in immune responses and regulation of inflammation. CD14-positive CD16-negative monocytes form the majority of circulating monocytes in the body, typically contributing to around 80-90% of the total monocyte pool. +The primary function of the classical monocytes is to serve in the frontline of host defense against infections. They are primed to migrate to sites of infection, and they express pattern recognition receptors that help them identify and phagocytose pathogens, leading to their destruction. Classical monocytes also contribute to inflammation by producing several pro-inflammatory cytokines including interleukins and tumor necrosis factors. +In response to specific signals from tissues under pathological conditions, such as infection or injury, classical monocytes can leave the bloodstream and migrate towards the affected sites. Following their arrival, these cells differentiate into diverse cell types including macrophages and dendritic cells to combat specific pathogens or injury. Dysregulated monocyte activity can lead to the development of many human diseases including inflammation, infection, tissue injury, and various autoimmune diseases. + https://cellxgene.cziscience.com/cellguide/CL_0000860 inflammatory monocyte @@ -33613,6 +34278,20 @@ radial glial cells acting as neural progenitors throughout life. PMID:20628149 PMID:20870168 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Classical monocytes are a subtype of monocytes that are characterized by high CD14 but no CD16 expression. Emerging from the bone marrow and entering the bloodstream, these cells play central roles in immune responses and regulation of inflammation. CD14-positive CD16-negative monocytes form the majority of circulating monocytes in the body, typically contributing to around 80-90% of the total monocyte pool. +The primary function of the classical monocytes is to serve in the frontline of host defense against infections. They are primed to migrate to sites of infection, and they express pattern recognition receptors that help them identify and phagocytose pathogens, leading to their destruction. Classical monocytes also contribute to inflammation by producing several pro-inflammatory cytokines including interleukins and tumor necrosis factors. +In response to specific signals from tissues under pathological conditions, such as infection or injury, classical monocytes can leave the bloodstream and migrate towards the affected sites. Following their arrival, these cells differentiate into diverse cell types including macrophages and dendritic cells to combat specific pathogens or injury. Dysregulated monocyte activity can lead to the development of many human diseases including inflammation, infection, tissue injury, and various autoimmune diseases. + DOI:10.1038/nri.2017.28 + DOI:10.1111/sji.12883 + DOI:10.1182/blood-2009-07-235028 + DOI:10.3389/fimmu.2015.00423/full + DOI:10.3389/fimmu.2019.02035 + @@ -33643,6 +34322,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -33815,6 +34495,12 @@ radial glial cells acting as neural progenitors throughout life. An elicited macrophage that is recruited into the tissues in response to injury and infection as part of an inflammatory response, expresses high levels of pro-inflammatory cytokines, ROS and NO, and shows potent microbicidal activity. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Inflammatory macrophages, also sometimes referred to as M1 or classically activated macrophages, play an important role in the inflammatory response. The M1/M2 classification is based upon macrophage polarization rather than macrophage location and refers to macrophage activation towards either a more inflammatory or more resolving phenotype, respectively, although the functional diversity of macrophages is more nuanced than such a dichotomy suggests. +Inflammatory macrophages are derived from monocytes recruited to a site of infection or injury. M1 macrophages are classically activated, typically by IFN-γ or lipopolysaccharide (LPS). Upon sensing signs of inflammation, they quickly respond by increasing their pro-inflammatory activity. They achieve this by producing a range of signaling molecules, such as nitric oxide, reactive oxygen species, and numerous cytokines such as tumor necrosis factor-alpha (TNF-alpha) and interleukin-1, -6 and -12. The release of these potent molecules helps to recruit other immune cells to the site, killing off pathogenic organisms and facilitation inflammation. At the same time, M1 macrophages can also present antigens to T cells, thereby helping to induce an adaptive immune response. Over time, these macrophages may transition in phenotype and function to help resolve the inflammation and promote tissue repair. +Despite the beneficial role of inflammatory macrophages in dealing with pathogens, chronic activation of these cells can lead to harmful effects. Over time, continuous production of pro-inflammatory molecules can cause damage to tissues and organs. This is seen in certain chronic inflammatory diseases, such as atherosclerosis, diabetes, obesity, asthma, and various autoimmune disorders. In such situations, the normally protective function of inflammatory macrophages is not properly controlled, which can contribute to disease pathology. + https://cellxgene.cziscience.com/cellguide/CL_0000863 classically activated macrophage M1 macrophage @@ -33835,6 +34521,19 @@ radial glial cells acting as neural progenitors throughout life. GO_REF:0000031 PMID:19132917 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Inflammatory macrophages, also sometimes referred to as M1 or classically activated macrophages, play an important role in the inflammatory response. The M1/M2 classification is based upon macrophage polarization rather than macrophage location and refers to macrophage activation towards either a more inflammatory or more resolving phenotype, respectively, although the functional diversity of macrophages is more nuanced than such a dichotomy suggests. +Inflammatory macrophages are derived from monocytes recruited to a site of infection or injury. M1 macrophages are classically activated, typically by IFN-γ or lipopolysaccharide (LPS). Upon sensing signs of inflammation, they quickly respond by increasing their pro-inflammatory activity. They achieve this by producing a range of signaling molecules, such as nitric oxide, reactive oxygen species, and numerous cytokines such as tumor necrosis factor-alpha (TNF-alpha) and interleukin-1, -6 and -12. The release of these potent molecules helps to recruit other immune cells to the site, killing off pathogenic organisms and facilitation inflammation. At the same time, M1 macrophages can also present antigens to T cells, thereby helping to induce an adaptive immune response. Over time, these macrophages may transition in phenotype and function to help resolve the inflammation and promote tissue repair. +Despite the beneficial role of inflammatory macrophages in dealing with pathogens, chronic activation of these cells can lead to harmful effects. Over time, continuous production of pro-inflammatory molecules can cause damage to tissues and organs. This is seen in certain chronic inflammatory diseases, such as atherosclerosis, diabetes, obesity, asthma, and various autoimmune disorders. In such situations, the normally protective function of inflammatory macrophages is not properly controlled, which can contribute to disease pathology. + DOI:10.1038/s41392-023-01452-1 + DOI:10.1186/s12935-021-02089-2 + DOI:10.3389/fimmu.2015.00263 + DOI:10.3389/fimmu.2020.583084 + @@ -34029,6 +34728,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -34245,6 +34945,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -34335,6 +35036,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -34437,6 +35139,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -34553,6 +35256,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -34653,6 +35357,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -34968,6 +35673,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -35408,6 +36114,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -35489,6 +36196,13 @@ radial glial cells acting as neural progenitors throughout life. An elicited macrophage characterized by low production of pro-inflammatory and Th1 polarizing cytokines and high expression of arginase-1, and associated with tissue remodelling. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Alternatively activated macrophages, also referred to as M2 macrophages, are immune cells originating from monocytes. The M1/M2 classification is based upon macrophage polarization rather than macrophage location and refers to macrophage activation towards either a more inflammatory or more resolving phenotype, respectively, although the functional diversity of macrophages is more nuanced than such a dichotomy suggests. +M2 macrophages cells are differentiated from their precursors generally in response to Th2 cytokines, such as interleukin-4 (IL-4), interleukin-10 (IL-10), and interleukin-13 (IL-13). Tissue-resident macrophages are also sometimes said to have an “M2-like” phenotype. M2 macrophages play key roles in immunoregulation and disease resolution. +Functionally, alternatively activated macrophages are essential in wound healing and tissue repair and remodeling, largely due to their potent anti-inflammatory actions and their ability to promote angiogenesis. They achieve these functions by the production of specific growth factors and signaling proteins including Arg1, Ym1/2, Fizz1, and TGF-β. Additionally, they provide defense against specific categories of pathogens, particularly parasites, through specific communication with Th2 cells. +However, dysfunction of M2 macrophages can be harmful. Alternatively activated macrophages have been associated with several pathological conditions such as asthma, fibrosis, and tumor progression. This is due to their capacity to inhibit inflammatory responses, promote unneeded wound healing processes, and support tumour growth and spreading. Furthermore, complex roles have been observed in metabolic disorders, cardiovascular diseases, and neurodegenerative diseases, showing the diverse functional spectrum of these cells. + https://cellxgene.cziscience.com/cellguide/CL_0000890 M2 macrophage Role or process: tissue remodeling. @@ -35509,6 +36223,20 @@ radial glial cells acting as neural progenitors throughout life. GO_REF:0000031 PMID:20510870 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Alternatively activated macrophages, also referred to as M2 macrophages, are immune cells originating from monocytes. The M1/M2 classification is based upon macrophage polarization rather than macrophage location and refers to macrophage activation towards either a more inflammatory or more resolving phenotype, respectively, although the functional diversity of macrophages is more nuanced than such a dichotomy suggests. +M2 macrophages cells are differentiated from their precursors generally in response to Th2 cytokines, such as interleukin-4 (IL-4), interleukin-10 (IL-10), and interleukin-13 (IL-13). Tissue-resident macrophages are also sometimes said to have an “M2-like” phenotype. M2 macrophages play key roles in immunoregulation and disease resolution. +Functionally, alternatively activated macrophages are essential in wound healing and tissue repair and remodeling, largely due to their potent anti-inflammatory actions and their ability to promote angiogenesis. They achieve these functions by the production of specific growth factors and signaling proteins including Arg1, Ym1/2, Fizz1, and TGF-β. Additionally, they provide defense against specific categories of pathogens, particularly parasites, through specific communication with Th2 cells. +However, dysfunction of M2 macrophages can be harmful. Alternatively activated macrophages have been associated with several pathological conditions such as asthma, fibrosis, and tumor progression. This is due to their capacity to inhibit inflammatory responses, promote unneeded wound healing processes, and support tumour growth and spreading. Furthermore, complex roles have been observed in metabolic disorders, cardiovascular diseases, and neurodegenerative diseases, showing the diverse functional spectrum of these cells. + DOI:10.1038/s41392-023-01452-1 + DOI:10.1186/s12935-021-02089-2 + DOI:10.3389/fimmu.2015.00263 + DOI:10.3389/fimmu.2020.583084 + @@ -35541,6 +36269,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -35649,6 +36378,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -38669,6 +39399,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -38743,6 +39474,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -38839,6 +39571,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -43364,6 +44097,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -44013,6 +44747,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -44092,6 +44827,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -44274,6 +45010,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -44398,6 +45135,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -44593,6 +45331,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -44662,6 +45401,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -44782,6 +45522,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -45080,7 +45821,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -45469,7 +46210,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -45485,7 +46226,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -45909,6 +46650,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -46183,6 +46925,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -46803,6 +47546,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -47068,6 +47812,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -47122,6 +47867,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -47240,6 +47986,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -47382,6 +48129,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -47586,6 +48334,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -47800,6 +48549,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -47843,10 +48593,6 @@ radial glial cells acting as neural progenitors throughout life. - - - - @@ -47931,7 +48677,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -47970,7 +48716,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -48038,7 +48784,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -48077,7 +48823,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -48598,6 +49344,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -48684,6 +49431,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -49012,6 +49760,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -49161,6 +49910,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -49615,6 +50365,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -49693,6 +50444,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -49849,6 +50601,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -49899,6 +50652,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -49957,6 +50711,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -50043,6 +50798,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -50137,6 +50893,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -50207,6 +50964,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -50273,6 +51031,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -50356,6 +51115,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -50588,6 +51348,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -50633,6 +51394,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -53269,11 +54031,18 @@ radial glial cells acting as neural progenitors throughout life. A secretory cell found in pancreatic acini that secretes digestive enzymes and mucins. This cell is a typical zymogenic cell, have a basal nucleus and basophilic cytoplasm consisting of regular arrays of granular endoplasmic reticulum with mitochondria and dense secretory granules. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Pancreatic acinar cells are the functional units of the exocrine pancreas. These cells are structurally arranged in small clusters - or acini - with a small central lumen, and their primary function is to produce and secrete enzymes that facilitate digestion of proteins, carbohydrates, and fats within the small intestine. +Some of the most important digestive enzymes synthesized by the pancreatic acinar cells include amylase, which digests carbohydrates, lipase, which breaks down fats, and several proteases such as trypsin and chymotrypsin which are vital for the digestion of proteins. Importantly, these enzymes are produced as proenzymes or zymogens to avoid autolysis, or the breakdown of the pancreas itself. +The release of these enzymes by the pancreatic acinar cells is strictly regulated by hormones and neurochemicals. Cholecystokinin (CCK) released from the enteroendocrine cells in the duodenum cause the release of these enzymes. Moreover, acinar cells also respond to another hormone, secretin, by releasing bicarbonate-rich fluid which helps to neutralize the gastric acid in the duodenum. +Dysregulation in the function of pancreatic acinar cells can lead to severe health issues, including pancreatitis, which is characterized by inflammatory damage to the organ due to the premature activation of digestive enzymes. 2010-06-24T03:16:29Z BTO:0000028 CALOHA:TS-0737 FMA:63032 ZFA:0005739 + https://cellxgene.cziscience.com/cellguide/CL_0002064 acinar cell of pancreas @@ -53294,6 +54063,20 @@ radial glial cells acting as neural progenitors throughout life. PMID:20395539 http://www.copewithcytokines.de/cope.cgi?key=pancreatic%20acinar%20cells + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Pancreatic acinar cells are the functional units of the exocrine pancreas. These cells are structurally arranged in small clusters - or acini - with a small central lumen, and their primary function is to produce and secrete enzymes that facilitate digestion of proteins, carbohydrates, and fats within the small intestine. +Some of the most important digestive enzymes synthesized by the pancreatic acinar cells include amylase, which digests carbohydrates, lipase, which breaks down fats, and several proteases such as trypsin and chymotrypsin which are vital for the digestion of proteins. Importantly, these enzymes are produced as proenzymes or zymogens to avoid autolysis, or the breakdown of the pancreas itself. +The release of these enzymes by the pancreatic acinar cells is strictly regulated by hormones and neurochemicals. Cholecystokinin (CCK) released from the enteroendocrine cells in the duodenum cause the release of these enzymes. Moreover, acinar cells also respond to another hormone, secretin, by releasing bicarbonate-rich fluid which helps to neutralize the gastric acid in the duodenum. +Dysregulation in the function of pancreatic acinar cells can lead to severe health issues, including pancreatitis, which is characterized by inflammatory damage to the organ due to the premature activation of digestive enzymes. + DOI:10.1016/0165-6147(89)90192-2 + DOI:10.1038/nrgastro.2013.36 + DOI:10.1097/01.mog.0000239863.96833.c0 + https://www.ncbi.nlm.nih.gov/books/NBK54134/ + @@ -53362,8 +54145,15 @@ radial glial cells acting as neural progenitors throughout life. An enteroendocrine cell that produces glucagon. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Type A enteroendocrine cells, also known as alpha cells or A cells, are a species of endocrine cells primarily located in the pancreatic islets of Langerhans; they have also been identified within the lining of the stomach. Functionally, these cells are pivotal in glucose metabolism and homeostasis, accounting for about 20% of the total population of cells in the pancreatic islets. +The primary role of type A enteroendocrine cells involves the synthesis, storage, and secretion of the peptide hormone glucagon, which is critical in energy regulation throughout the body. In response to a decrease in blood glucose levels, the pancreatic A cells are stimulated to secrete glucagon into the bloodstream. Glucagon acts on its target cells, mainly in the liver, to stimulate glycogenolysis and gluconeogenesis processes, thereby increasing blood glucose levels back to normal. In this way, pancreatic A cells play an integral role in maintaining glucose homeostasis and preventing hypoglycemia. +Pancreatic A cells also participate in the local regulation of islet activities as glucagon acts through glucagon receptors on A, B and D type cells within the islets. Recent studies have also shown that Pancreatic A cells play a role in the generation and regeneration of B type cells. Following beta cell injuries pancreatic A cells increase in numbers and produce Glucagon-like peptide-1 (GLP-1), which increases the proliferation and cytoprotection of beta cells. In response to extreme injury of B type cells pancreatic A cells can transform (transdifferentiate) into functioning B type cells. +Until recently, glucagon has been considered a pancreas-specific hormone; however, extrapancreatic glucagon has been reported in patients who had undergone complete, and glucagon-positive cells been identified in the human stomach, indicating that Type A enteroendocrine cells are not restricted to the pancreas. 2010-09-10T10:48:54Z FMA:62939 + https://cellxgene.cziscience.com/cellguide/CL_0002067 type A enteroendocrine cell @@ -53373,6 +54163,21 @@ radial glial cells acting as neural progenitors throughout life. GOC:tfm ISBN:0412046911 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Type A enteroendocrine cells, also known as alpha cells or A cells, are a species of endocrine cells primarily located in the pancreatic islets of Langerhans; they have also been identified within the lining of the stomach. Functionally, these cells are pivotal in glucose metabolism and homeostasis, accounting for about 20% of the total population of cells in the pancreatic islets. +The primary role of type A enteroendocrine cells involves the synthesis, storage, and secretion of the peptide hormone glucagon, which is critical in energy regulation throughout the body. In response to a decrease in blood glucose levels, the pancreatic A cells are stimulated to secrete glucagon into the bloodstream. Glucagon acts on its target cells, mainly in the liver, to stimulate glycogenolysis and gluconeogenesis processes, thereby increasing blood glucose levels back to normal. In this way, pancreatic A cells play an integral role in maintaining glucose homeostasis and preventing hypoglycemia. +Pancreatic A cells also participate in the local regulation of islet activities as glucagon acts through glucagon receptors on A, B and D type cells within the islets. Recent studies have also shown that Pancreatic A cells play a role in the generation and regeneration of B type cells. Following beta cell injuries pancreatic A cells increase in numbers and produce Glucagon-like peptide-1 (GLP-1), which increases the proliferation and cytoprotection of beta cells. In response to extreme injury of B type cells pancreatic A cells can transform (transdifferentiate) into functioning B type cells. +Until recently, glucagon has been considered a pancreas-specific hormone; however, extrapancreatic glucagon has been reported in patients who had undergone complete, and glucagon-positive cells been identified in the human stomach, indicating that Type A enteroendocrine cells are not restricted to the pancreas. + DOI:10.1016/j.diabres.2018.06.013 + DOI:10.1210/en.2016-1748 + DOI:10.2337/db15-1541 + DOI:10.2337/dbi19-0002 + DOI:10.3389/fphys.2012.00349/full + @@ -53998,7 +54803,13 @@ radial glial cells acting as neural progenitors throughout life. - Specialized elongated ventricular ependymal cell that has processes that extend to the outer, or pial, surface of the CNS. Resemble spongioblasts seen in developing brain. Found in the adult brain in the third ventricle, cerebral aqueduct, spinal canal and floor of the fourth ventricle. + + + + + + + A specialized elongated ventricular ependymal cell that has processes that extend to the outer, or pial, surface of the CNS. A tanycyte is found in the adult brain, specifically in the third ventricle, cerebral aqueduct, spinal canal, and floor of the fourth ventricle. This cell type is involved in hormonal regulation, gatekeeping molecules between the bloodstream and cerebrospinal fluid, metabolic sensing, and regulating food intake. 2010-07-15T11:21:11Z BTO:0001953 @@ -54010,10 +54821,16 @@ radial glial cells acting as neural progenitors throughout life. - Specialized elongated ventricular ependymal cell that has processes that extend to the outer, or pial, surface of the CNS. Resemble spongioblasts seen in developing brain. Found in the adult brain in the third ventricle, cerebral aqueduct, spinal canal and floor of the fourth ventricle. + A specialized elongated ventricular ependymal cell that has processes that extend to the outer, or pial, surface of the CNS. A tanycyte is found in the adult brain, specifically in the third ventricle, cerebral aqueduct, spinal canal, and floor of the fourth ventricle. This cell type is involved in hormonal regulation, gatekeeping molecules between the bloodstream and cerebrospinal fluid, metabolic sensing, and regulating food intake. GOC:tfm http://neurolex.org/wiki/Category:Tanycyte + + + + stretch cell + PMID:29351662 + @@ -54221,6 +55038,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -56605,12 +57423,6 @@ radial glial cells acting as neural progenitors throughout life. - - - - - - @@ -56620,8 +57432,14 @@ radial glial cells acting as neural progenitors throughout life. A multi-ciliated epithelial cell located in the trachea and bronchi, characterized by a columnar shape and motile cilia on its apical surface. These cilia facilitate mucociliary clearance by moving mucus and trapped particles toward the pharynx. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Ciliated columnar cells of the tracheobronchial tree compose the inner lining of the tracheobronchial tree, the system of airways consisting of trachea, bronchi and bronchioles that allow passage of air into the lungs, where gas exchange occurs. A defining feature of these endo-epithelial cells are the tiny hair-like structures covering their surface, known as cilia. The nucleus is located at the base of the cell, and the area above it is rich in mitochondria and well-developed endoplasmic reticulum, both crucial for the energy-intensive process of cilia operation. +The primary function of these ciliated cells is to keep the respiratory tract clean via mucociliary clearance or the respiratory escalator. These cells create a two-layered 'coat': The lower "sol" layer is watery where the cilia can beat in coordinated waves, and the upper "gel" layer is thick and sticky, trapping inhaled particles, such as dust, bacteria, viruses, and other potentially harmful substances. This rhythmical beating of the cilia then moves the mucus and trapped particles upwards and out of the respiratory tract, which is then either coughed out or swallowed. +Damage or dysfunction of these ciliated cells, as seen in diseases such as primary ciliary dyskinesia, cystic fibrosis, or chronic bronchitis, may lead to reduced or ineffective mucociliary clearance and an increased susceptibility to respiratory infections. 2010-08-24T03:38:29Z FMA:70542 + https://cellxgene.cziscience.com/cellguide/CL_0002145 These cells possess numerous cilia on their surface, typically ranging from 200 to 300 per cell. The cilia vary in length, measuring between 6 to 7 μm in the upper airways (trachea) and becoming shorter, around 4 μm, in the smaller airways (terminal bronchioles). These cells form a two-layered 'coat' in the airway: the lower 'sol' layer is watery, allowing the cilia to beat in coordinated waves, while the upper 'gel' layer is thick and sticky, trapping inhaled particles. @@ -56634,6 +57452,19 @@ radial glial cells acting as neural progenitors throughout life. GOC:tfm PMID:28400610 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Ciliated columnar cells of the tracheobronchial tree compose the inner lining of the tracheobronchial tree, the system of airways consisting of trachea, bronchi and bronchioles that allow passage of air into the lungs, where gas exchange occurs. A defining feature of these endo-epithelial cells are the tiny hair-like structures covering their surface, known as cilia. The nucleus is located at the base of the cell, and the area above it is rich in mitochondria and well-developed endoplasmic reticulum, both crucial for the energy-intensive process of cilia operation. +The primary function of these ciliated cells is to keep the respiratory tract clean via mucociliary clearance or the respiratory escalator. These cells create a two-layered 'coat': The lower "sol" layer is watery where the cilia can beat in coordinated waves, and the upper "gel" layer is thick and sticky, trapping inhaled particles, such as dust, bacteria, viruses, and other potentially harmful substances. This rhythmical beating of the cilia then moves the mucus and trapped particles upwards and out of the respiratory tract, which is then either coughed out or swallowed. +Damage or dysfunction of these ciliated cells, as seen in diseases such as primary ciliary dyskinesia, cystic fibrosis, or chronic bronchitis, may lead to reduced or ineffective mucociliary clearance and an increased susceptibility to respiratory infections. + DOI:10.1101/cshperspect.a028241 + DOI:10.1146/annurev-physiol-021014-071931 + DOI:10.1152/ajplung.00329.2019 + DOI:10.1159/000196486 + @@ -56873,6 +57704,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -57428,6 +58260,13 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + A cell within the follicle of an ovary. @@ -57841,6 +58680,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -58399,8 +59239,14 @@ radial glial cells acting as neural progenitors throughout life. A cell type found in the gastrointestinal and respiratory tracts that is characterized by the presence of a tuft of blunt, squat microvilli (120-140 per cell). Function of this cell type is not known. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Brush cells, also referred to as tuft cells or multivesicular cells, are a specialized type of epithelial cell mainly noted for their characteristic 'brush border' composed of microvilli. These cells reside in the epithelial lining of tissue organs such as the respiratory tract, gastrointestinal tract, and the bile ducts. The name derives from their distinct appearance under the microscope, which resembles a brush due to the dense layer of microvilli protruding into the lumen. +A key function of brush cells is chemosensation: They express a variety of signaling molecules and receptors that enable them to detect specific chemical stimuli in the environment and act as sensory transducers. Many of these receptors are responsive to luminal content, which makes brush cells vital for regulating and coordinating appropriate physiological responses to changes in these substances. +Recent research has also elucidated an important role for these cells in immunity. Intestinal brush cells have been found to be the source of a cytokine called interleukin-25, which can initiate type 2 immune responses during parasitic infections. This immune function, along with the chemosensing abilities, signifies that brush cells could serve crucial roles in health and disease, although much research is still required to fully elucidate their myriad roles in physiology and pathology. Overall, brush cells are a versatile cell type, whose distinct morphology and functional capabilities allow them to perform a unique set of functions within the body. 2010-09-02T02:28:53Z FMA:67978 + https://cellxgene.cziscience.com/cellguide/CL_0002204 caveolated cell fibrillovesicular cell multivesicular cell @@ -58416,6 +59262,20 @@ radial glial cells acting as neural progenitors throughout life. ISBN:0517223651 PMID:15817800 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Brush cells, also referred to as tuft cells or multivesicular cells, are a specialized type of epithelial cell mainly noted for their characteristic 'brush border' composed of microvilli. These cells reside in the epithelial lining of tissue organs such as the respiratory tract, gastrointestinal tract, and the bile ducts. The name derives from their distinct appearance under the microscope, which resembles a brush due to the dense layer of microvilli protruding into the lumen. +A key function of brush cells is chemosensation: They express a variety of signaling molecules and receptors that enable them to detect specific chemical stimuli in the environment and act as sensory transducers. Many of these receptors are responsive to luminal content, which makes brush cells vital for regulating and coordinating appropriate physiological responses to changes in these substances. +Recent research has also elucidated an important role for these cells in immunity. Intestinal brush cells have been found to be the source of a cytokine called interleukin-25, which can initiate type 2 immune responses during parasitic infections. This immune function, along with the chemosensing abilities, signifies that brush cells could serve crucial roles in health and disease, although much research is still required to fully elucidate their myriad roles in physiology and pathology. Overall, brush cells are a versatile cell type, whose distinct morphology and functional capabilities allow them to perform a unique set of functions within the body. + DOI:10.1007/978-3-211-99390-3_83 + DOI:10.1038/nature16161 + DOI:10.1111/j.1469-7580.2005.00403.x + DOI:10.3389/fphys.2015.00087 + DOI:10.5114/ceji.2022.124416 + @@ -58997,7 +59857,13 @@ radial glial cells acting as neural progenitors throughout life. A lens fiber cell that develops from primary lens fiber; located towards the center of lens; cell organelles are normally degraded or in the process of being degraded. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Secondary lens fibers are a specialized type of elongated cells located within the structure of the eye's lens. They play an essential role in vision by enabling light transmission and focus on the retina, which allows for clear, distinct vision. These cells are characterized by their lack of nuclei and organelles, their orderly alignment, and their high protein content, particularly crystallins. +Lens fibers are differentiated from equatorial epithelial cells of the lens in a process that involves cell elongation, denucleation and tight packing, which serve to reduce light scattering occurrences in the eye. This differentiation accelerates substantially after birth in comparison to during embryogenesis and continues throughout life, contributing to the growth of the eye lens. Secondary lens fibers are specifically those cells that are newly differentiated and cover the old lens fiber core. This process also leads to the removal of light-obstructing cellular components, mainly nuclei and organelles, making these fibers transparent and ideal for their function. +The fibers carry out their primary function of light refraction via a high concentration of specialized proteins known as crystallins, which form a gradient of refractive index together with the cytoplasm. This index manipulation facilitates precise light focus onto the retina. Secondary lens fibers also contribute to the lens's shape and biomechanical properties through intercellular interactions, particularly at the sutures where the ends of the fibers meet. Any disruption to secondary lens fibers can lead to vision problems, including cataracts, which is the clouding of the lens resulting from the aggregation of crystallin proteins. 2010-09-07T10:53:39Z + https://cellxgene.cziscience.com/cellguide/CL_0002225 secondary lens fibre @@ -59010,6 +59876,20 @@ radial glial cells acting as neural progenitors throughout life. GOC:tfm ISBN:0517223651 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Secondary lens fibers are a specialized type of elongated cells located within the structure of the eye's lens. They play an essential role in vision by enabling light transmission and focus on the retina, which allows for clear, distinct vision. These cells are characterized by their lack of nuclei and organelles, their orderly alignment, and their high protein content, particularly crystallins. +Lens fibers are differentiated from equatorial epithelial cells of the lens in a process that involves cell elongation, denucleation and tight packing, which serve to reduce light scattering occurrences in the eye. This differentiation accelerates substantially after birth in comparison to during embryogenesis and continues throughout life, contributing to the growth of the eye lens. Secondary lens fibers are specifically those cells that are newly differentiated and cover the old lens fiber core. This process also leads to the removal of light-obstructing cellular components, mainly nuclei and organelles, making these fibers transparent and ideal for their function. +The fibers carry out their primary function of light refraction via a high concentration of specialized proteins known as crystallins, which form a gradient of refractive index together with the cytoplasm. This index manipulation facilitates precise light focus onto the retina. Secondary lens fibers also contribute to the lens's shape and biomechanical properties through intercellular interactions, particularly at the sutures where the ends of the fibers meet. Any disruption to secondary lens fibers can lead to vision problems, including cataracts, which is the clouding of the lens resulting from the aggregation of crystallin proteins. + DOI:10.1016/B978-1-4377-1926-0.10005-0 + DOI:10.1016/j.biocel.2007.10.034 + DOI:10.1098/rstb.2010.0324 + DOI:10.1136/bmjophth-2020-000459 + https://www.sciencedirect.com/topics/immunology-and-microbiology/lens-fiber + @@ -59448,6 +60328,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -59849,8 +60730,15 @@ radial glial cells acting as neural progenitors throughout life. A cell that is found in a zone occupying the bottom region of the crypt; provide the source of most of the cell types of the intestinal epithelium; proliferate by mitotic division; differentiates into columnar or goblet cells. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Intestinal crypt stem cells, also known as crypt base columnar cells, are a unique type of cell, characterized by the highly specific marker LGR5, found in the intestinal epithelium. Situated at the bottom of the minute pockets known as crypts of Lieberkühn, these are undifferentiated cells that have the ability to perpetually self-renew, as well as differentiate into various other cell types that constitute the epithelial lining of the intestine. +The fundamental role of intestinal crypt stem cells is to provide a constant supply of new cells to maintain the cellular turnover of the intestinal epithelium, a tissue known for rapid self-renewal. These stem cells are nurtured and protected by specialized epithelial and mesenchymal cells, and together constitute the intestinal stem cell niche. +An important function of intestinal crypt stem cells is to sustain the balance between cell division and programmed cell death, called apoptosis, to ensure the integrity of the intestinal lining. Given their active proliferation rate, these stem cells initiate the creation of diverse differentiated cell types, including enterocytes (the primary absorptive cells in the intestinal lumen), goblet cells (that produce mucus to protect the epithelial layer), enteroendocrine cells (involved in producing gastrointestinal hormones), and Paneth cells (involved in secreting antimicrobial peptides). This diversity in output regulates the physiological activities of the gut ranging from nutrient absorption, hormone secretion, bacterial balance, to immunity. +Research studies suggest that dysregulation in intestinal crypt stem cell proliferation and differentiation is associated with several intestinal disorders including intestinal cancer, and various enteropathies. 2010-09-08T09:21:22Z FMA:63379 + https://cellxgene.cziscience.com/cellguide/CL_0002250 stem cell of intestinal crypt of Lieberkuhn intestinal crypt stem cell @@ -59862,6 +60750,21 @@ radial glial cells acting as neural progenitors throughout life. GOC:tfm ISBN:0517223651 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Intestinal crypt stem cells, also known as crypt base columnar cells, are a unique type of cell, characterized by the highly specific marker LGR5, found in the intestinal epithelium. Situated at the bottom of the minute pockets known as crypts of Lieberkühn, these are undifferentiated cells that have the ability to perpetually self-renew, as well as differentiate into various other cell types that constitute the epithelial lining of the intestine. +The fundamental role of intestinal crypt stem cells is to provide a constant supply of new cells to maintain the cellular turnover of the intestinal epithelium, a tissue known for rapid self-renewal. These stem cells are nurtured and protected by specialized epithelial and mesenchymal cells, and together constitute the intestinal stem cell niche. +An important function of intestinal crypt stem cells is to sustain the balance between cell division and programmed cell death, called apoptosis, to ensure the integrity of the intestinal lining. Given their active proliferation rate, these stem cells initiate the creation of diverse differentiated cell types, including enterocytes (the primary absorptive cells in the intestinal lumen), goblet cells (that produce mucus to protect the epithelial layer), enteroendocrine cells (involved in producing gastrointestinal hormones), and Paneth cells (involved in secreting antimicrobial peptides). This diversity in output regulates the physiological activities of the gut ranging from nutrient absorption, hormone secretion, bacterial balance, to immunity. +Research studies suggest that dysregulation in intestinal crypt stem cell proliferation and differentiation is associated with several intestinal disorders including intestinal cancer, and various enteropathies. + DOI:10.1016/j.cell.2013.07.004 + DOI:10.1038/s41575-018-0081-y + DOI:10.1038/s41580-020-0278-0 + DOI:10.1101/gad.1674008 + DOI:10.1111/j.1365-2184.2009.00642.x + @@ -60657,11 +61560,17 @@ radial glial cells acting as neural progenitors throughout life. A PP cell located in the islets of the pancreas. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Pancreatic polypeptide (PP) cells (also called F or gamma cells) are unique endocrine cells located within the Islets of Langerhans in the pancreas. PP cells are one of the rarer pancreatic cell types and are more prevalent in the head and neck of the pancreas. They are critical in normal pancreatic physiological functions and are involved in the development of pancreatic endocrine disorders. +The primary function of PP cells is the production and secretion of the pancreatic polypeptide hormone (PP). This hormone plays a crucial role in several gastrointestinal functions and metabolic responses. The release of the PP hormone is stimulated after eating, especially in protein-rich meals, leading to it being present in large amounts during digestion. The fundamental role of PP is to self-regulate pancreatic secretion activities ensuring its exocrine and endocrine functions are under control. +The pancreatic polypeptide hormone from PP cells also aids in adapting to low physical activity and fasting by reducing the production of insulin and glucagon and inhibiting the hepatic glucose production. Additionally, this hormone influences gut motility by slowing down the gastric emptying and reducing small intestinal transit, thereby controlling the pace at which nutritional substances are absorbed. Because of these functions, any malfunction or irregularity in PP cells can result in various disorders such as diabetes and pancreatic diseases. 2010-09-10T03:30:31Z BTO:0000805 FMA:70588 MESH:D050418 ZFA:0005742 + https://cellxgene.cziscience.com/cellguide/CL_0002275 PP cell of pancreatic islet PP-cell of pancreatic islet pancreatic polypeptide-secreting cell @@ -60676,6 +61585,20 @@ radial glial cells acting as neural progenitors throughout life. A PP cell located in the islets of the pancreas. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Pancreatic polypeptide (PP) cells (also called F or gamma cells) are unique endocrine cells located within the Islets of Langerhans in the pancreas. PP cells are one of the rarer pancreatic cell types and are more prevalent in the head and neck of the pancreas. They are critical in normal pancreatic physiological functions and are involved in the development of pancreatic endocrine disorders. +The primary function of PP cells is the production and secretion of the pancreatic polypeptide hormone (PP). This hormone plays a crucial role in several gastrointestinal functions and metabolic responses. The release of the PP hormone is stimulated after eating, especially in protein-rich meals, leading to it being present in large amounts during digestion. The fundamental role of PP is to self-regulate pancreatic secretion activities ensuring its exocrine and endocrine functions are under control. +The pancreatic polypeptide hormone from PP cells also aids in adapting to low physical activity and fasting by reducing the production of insulin and glucagon and inhibiting the hepatic glucose production. Additionally, this hormone influences gut motility by slowing down the gastric emptying and reducing small intestinal transit, thereby controlling the pace at which nutritional substances are absorbed. Because of these functions, any malfunction or irregularity in PP cells can result in various disorders such as diabetes and pancreatic diseases. + DOI:10.1016/B978-0-12-819402-7.00001-2 + DOI:10.1016/B978-012369442-3/50154-9 + DOI:10.1016/j.mce.2015.06.028 + DOI:10.1038/s42255-019-0148-2 + DOI:10.3389/fendo.2023.1192311 + @@ -61289,6 +62212,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -61310,6 +62234,7 @@ radial glial cells acting as neural progenitors throughout life. A resident stromal cell located in the synovial membrane and responsible for the production of immune-related cytokines and chemokines. This cell type secretes glycoproteins and hyaluronic acid, has abundant granular endoplasmic reticulum, but contains fewer vacuoles and vesicles. + 2010-09-13T03:39:14Z BTO:0003652 @@ -61323,7 +62248,6 @@ radial glial cells acting as neural progenitors throughout life. A resident stromal cell located in the synovial membrane and responsible for the production of immune-related cytokines and chemokines. This cell type secretes glycoproteins and hyaluronic acid, has abundant granular endoplasmic reticulum, but contains fewer vacuoles and vesicles. - GOC:tfm ISBN:0517223651 PMID:34433485 @@ -61348,6 +62272,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -61356,7 +62281,7 @@ radial glial cells acting as neural progenitors throughout life. - + A synovial cell that is macrophage-like, characterized by surface ruffles or lamellipodia, plasma membrane invaginations and associated micropinocytotic vesicles, Golgi apparatus and little granular endoplasmic reticulum. 2010-09-13T03:39:17Z @@ -61365,14 +62290,14 @@ radial glial cells acting as neural progenitors throughout life. Type A cells are usually round and located in the upper part of the synovial intima. type A synovial cell - + - + PMID:10770586 @@ -61404,8 +62329,14 @@ radial glial cells acting as neural progenitors throughout life. A cell that is part of pigmented ciliary epithelium. This cell type uptakes sodium and chloride ions from stromal interstitium and passes the ions to non-pigmented ciliary epithelial cells via gap junctions. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Pigmented ciliary epithelial cells, which are a type of pigment cell, have a crucial function within the eye's ciliary body. The ciliary body, located behind the iris, is one of the eye’s most vital structures and consists of two types of epithelial cells: the pigmented and the non-pigmented ciliary epithelial cells. The pigmented ciliary epithelial cells form the outer layer of the ciliary body and exhibit a black or brown pigmentation due to the melanin they contain. +One key function of pigmented ciliary epithelial cells is to aid in the formation of aqueous humor, an intraocular fluid that nourishes the cornea and lens, and maintains intraocular pressure which is essential for the eye’s shape and light refraction. These cells facilitate this function in conjunction with the non-pigmented ciliary epithelial cells. Together, the pigmented and non-pigmented ciliary epithelial cells form a bilayer epithelium that allows the secretion of aqueous humor through a bi-directional fluid transport mechanism. +Pigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, a physiological frontier that controls the entry and exit of various substances from the blood to the aqueous humor and vice versa. The pigmentation in these cells, intensified by melanin, helps to absorb scattered light coming into the eye, reducing any potential damage and glare. 2010-09-13T04:09:27Z FMA:70606 + https://cellxgene.cziscience.com/cellguide/CL_0002303 PE cell @@ -61419,6 +62350,17 @@ radial glial cells acting as neural progenitors throughout life. A cell that is part of pigmented ciliary epithelium. This cell type uptakes sodium and chloride ions from stromal interstitium and passes the ions to non-pigmented ciliary epithelial cells via gap junctions. PMID:15106942 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Pigmented ciliary epithelial cells, which are a type of pigment cell, have a crucial function within the eye's ciliary body. The ciliary body, located behind the iris, is one of the eye’s most vital structures and consists of two types of epithelial cells: the pigmented and the non-pigmented ciliary epithelial cells. The pigmented ciliary epithelial cells form the outer layer of the ciliary body and exhibit a black or brown pigmentation due to the melanin they contain. +One key function of pigmented ciliary epithelial cells is to aid in the formation of aqueous humor, an intraocular fluid that nourishes the cornea and lens, and maintains intraocular pressure which is essential for the eye’s shape and light refraction. These cells facilitate this function in conjunction with the non-pigmented ciliary epithelial cells. Together, the pigmented and non-pigmented ciliary epithelial cells form a bilayer epithelium that allows the secretion of aqueous humor through a bi-directional fluid transport mechanism. +Pigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, a physiological frontier that controls the entry and exit of various substances from the blood to the aqueous humor and vice versa. The pigmentation in these cells, intensified by melanin, helps to absorb scattered light coming into the eye, reducing any potential damage and glare. + DOI:10.1016/S1569-2590(05)10005-6 + DOI:10.1111/j.1444-0938.2002.tb02384.x + @@ -61915,6 +62857,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -61951,7 +62894,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -61990,7 +62933,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -62433,7 +63376,13 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell type that lacks the columnar shape typical for other respiratory epithelial cells. This cell type is able to differentiate into other respiratory epithelial cells in response to injury. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +The basal epithelial cells of the tracheobronchial tree are critical components found in the lining of the airway passages, including the trachea and bronchi. They are keratin-5-positive, nonciliated, cuboidal cells and typically tightly attached to the basement membrane. In humans, the proportion of basal cells in the respiratory epithelium gradually decreases going down the tracheobronchial tree: they represent approximately 34% of the cells in the trachea, 27% in the large airways, and 10% in the small airways, although it is worth noting that there are differences in the compositions of the tracheobronchial epithelia between different species. +Basal epithelial cells serve as the basal layer of the tracheobronchial epithelium, providing both structural and regenerative support for the epithelial tissue that lines the upper regions of the respiratory tract. They serve as progenitor or stem cells that are capable of differentiating into multiple cell types, such as ciliated and secretory cells. This gives them a central role in homeostatic maintenance of the epithelium, and in repairing damaged epithelium after an injury or during disease. This regenerative capacity is crucial in maintaining the integrity of the tracheobronchial surface, especially given its continual exposure to inhaled irritants and microorganisms. +In addition to their primary restorative function, basal epithelial cells are also involved in the initial immune response within the tracheobronchial tree. Equipped with pattern recognition receptors, these cells can identify and respond to pathogenic organisms, triggering an immune response and producing a range of inflammatory mediators, such as cytokines and chemokines, to help combat infections. 2010-09-20T02:10:36Z + https://cellxgene.cziscience.com/cellguide/CL_0002329 basal epithelial cell of tracheobronchial tree @@ -62444,6 +63393,18 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell type that lacks the columnar shape typical for other respiratory epithelial cells. This cell type is able to differentiate into other respiratory epithelial cells in response to injury. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +The basal epithelial cells of the tracheobronchial tree are critical components found in the lining of the airway passages, including the trachea and bronchi. They are keratin-5-positive, nonciliated, cuboidal cells and typically tightly attached to the basement membrane. In humans, the proportion of basal cells in the respiratory epithelium gradually decreases going down the tracheobronchial tree: they represent approximately 34% of the cells in the trachea, 27% in the large airways, and 10% in the small airways, although it is worth noting that there are differences in the compositions of the tracheobronchial epithelia between different species. +Basal epithelial cells serve as the basal layer of the tracheobronchial epithelium, providing both structural and regenerative support for the epithelial tissue that lines the upper regions of the respiratory tract. They serve as progenitor or stem cells that are capable of differentiating into multiple cell types, such as ciliated and secretory cells. This gives them a central role in homeostatic maintenance of the epithelium, and in repairing damaged epithelium after an injury or during disease. This regenerative capacity is crucial in maintaining the integrity of the tracheobronchial surface, especially given its continual exposure to inhaled irritants and microorganisms. +In addition to their primary restorative function, basal epithelial cells are also involved in the initial immune response within the tracheobronchial tree. Equipped with pattern recognition receptors, these cells can identify and respond to pathogenic organisms, triggering an immune response and producing a range of inflammatory mediators, such as cytokines and chemokines, to help combat infections. + DOI:10.1165/rcmb.2013-0049OC + DOI:10.1186/s12931-014-0160-8 + DOI:10.2353/ajpath.2010.090870 + @@ -62485,7 +63446,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -62663,6 +63624,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -62852,6 +63814,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -62931,6 +63894,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -63027,6 +63991,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -63110,6 +64075,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -63170,6 +64136,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -63232,6 +64199,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -63294,6 +64262,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -63484,6 +64453,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -63595,6 +64565,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -63686,6 +64657,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -63815,6 +64787,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -63976,6 +64949,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -64340,7 +65314,13 @@ radial glial cells acting as neural progenitors throughout life. A simple columnar epithelial cell that secretes mucin. Rough endoplasmic reticulum, mitochondria, the nucleus, and other organelles are concentrated in the basal portion. The apical plasma membrane projects microvilli to increase surface area for secretion. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +The respiratory goblet cell is a highly specialized cell type found primarily within the respiratory tract, including the nose, trachea, and lungs. Named because their shape resembles a goblet - a drinking vessel with a wide body and narrow neck - these cells form a vital part of the respiratory system's protective mechanisms. They are found within the columnar epithelium lining these organs, which forms a barrier between the internal body and the exterior environment. +A principal function of the respiratory goblet cell is the production and secretion of mucus, a carbohydrate-rich, viscous and gel-like substance that plays a critical role in trapping dust, bacteria, viruses, and other airborne particles that are inhaled. The mucus secreted by the goblet cells covers the lining of the respiratory tract, effectively catching these particles and preventing them from reaching the lungs and causing infection. Mucus also provides hydration and lubrication to the respiratory tract surfaces, which is important in maintaining the tissue's health and functioning. +In addition to their mucus-secreting capabilities, respiratory goblet cells also play a significant role in the body's inflammatory responses. When the respiratory system is exposed to irritants or pathogens, the number and activity of goblet cells often increase, leading to a higher production of mucus. This is a protective response designed to trap and neutralize the harmful substances more effectively. However, in conditions like chronic obstructive pulmonary disease (COPD) and asthma, an overproliferation of goblet cells, also known as goblet cell hyperplasia, can lead to excessive mucus production and airway obstruction. 2010-09-23T04:42:27Z + https://cellxgene.cziscience.com/cellguide/CL_0002370 respiratory mucosa goblet cells respiratory goblet cell @@ -64352,6 +65332,20 @@ radial glial cells acting as neural progenitors throughout life. GOC:tfm ISBN:0721662544 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +The respiratory goblet cell is a highly specialized cell type found primarily within the respiratory tract, including the nose, trachea, and lungs. Named because their shape resembles a goblet - a drinking vessel with a wide body and narrow neck - these cells form a vital part of the respiratory system's protective mechanisms. They are found within the columnar epithelium lining these organs, which forms a barrier between the internal body and the exterior environment. +A principal function of the respiratory goblet cell is the production and secretion of mucus, a carbohydrate-rich, viscous and gel-like substance that plays a critical role in trapping dust, bacteria, viruses, and other airborne particles that are inhaled. The mucus secreted by the goblet cells covers the lining of the respiratory tract, effectively catching these particles and preventing them from reaching the lungs and causing infection. Mucus also provides hydration and lubrication to the respiratory tract surfaces, which is important in maintaining the tissue's health and functioning. +In addition to their mucus-secreting capabilities, respiratory goblet cells also play a significant role in the body's inflammatory responses. When the respiratory system is exposed to irritants or pathogens, the number and activity of goblet cells often increase, leading to a higher production of mucus. This is a protective response designed to trap and neutralize the harmful substances more effectively. However, in conditions like chronic obstructive pulmonary disease (COPD) and asthma, an overproliferation of goblet cells, also known as goblet cell hyperplasia, can lead to excessive mucus production and airway obstruction. + DOI:10.1016/S1357-2725(02)00083-3 + DOI:10.1111/febs.15731 + DOI:10.1165/ajrcmb.25.5.f218 + DOI:10.2147/COPD.S38938 + DOI:10.3109/01902148.2013.791733 + @@ -64409,26 +65403,26 @@ radial glial cells acting as neural progenitors throughout life. - + - A transversely striated, synctial muscle cell, formed by the fusion of myoblasts. + A transversely striated, multinucleated syncytial muscle cell, formed by the fusion of myoblasts during muscle development. 2010-09-24T01:13:01Z FBbt:00005812 - myotubule - single cell sarcomere + myofiber + myofibril myotube - A transversely striated, synctial muscle cell, formed by the fusion of myoblasts. + A transversely striated, multinucleated syncytial muscle cell, formed by the fusion of myoblasts during muscle development. GOC:dos GOC:tfm ISBN:0323052908 @@ -64440,6 +65434,18 @@ radial glial cells acting as neural progenitors throughout life. FBbt:00005812 + + + + myofiber + FBbt:00005812 + + + + + myofibril + FBbt:00005812 + @@ -64506,26 +65512,55 @@ radial glial cells acting as neural progenitors throughout life. - + + + + + + - A glioblast cell that develops from a migratory neural crest cell. The SCP is embedded among neurons (axons) with minimal extracellular spaces separating them from nerve cell membranes and has no basal lamina. In rodents SCPs are the only cells in the Schwann cell linage that expresses Cdh19. + + + + + + + A multipotent progenitor cell that develops from a migratory neural crest cell. The schwann cell precursor is embedded among axons, with minimal extracellular space separating them from nerve cell membranes. This cell lacks a basal lamina, which distinguishes it from more mature Schwann cells. In rodents, cadherin-19 (Cdh19) serves as a specific marker for this developmental stage. 2010-09-24T02:06:10Z Schwann cell precursor cell + SCP + Schwann cell precursor are capable of differentiating into Schwann cells and other cell types such as melanocytes, neurons, and mesenchymal cells. Schwann cell precursor - A glioblast cell that develops from a migratory neural crest cell. The SCP is embedded among neurons (axons) with minimal extracellular spaces separating them from nerve cell membranes and has no basal lamina. In rodents SCPs are the only cells in the Schwann cell linage that expresses Cdh19. + A multipotent progenitor cell that develops from a migratory neural crest cell. The schwann cell precursor is embedded among axons, with minimal extracellular space separating them from nerve cell membranes. This cell lacks a basal lamina, which distinguishes it from more mature Schwann cells. In rodents, cadherin-19 (Cdh19) serves as a specific marker for this developmental stage. GOC:tfm + PMID:15580626 + PMID:30971890 + PMID:35815410 + + + + + SCP + PMID:35815410 + + + + + + Schwann cell precursor are capable of differentiating into Schwann cells and other cell types such as melanocytes, neurons, and mesenchymal cells. + PMID:35815410 @@ -65343,7 +66378,7 @@ radial glial cells acting as neural progenitors throughout life. - A myeloid dendritic cell found in the blood that is CD1c-positive. + A myeloid dendritic cell that is CD1c-positive. 2010-10-04T02:39:01Z @@ -65361,7 +66396,7 @@ radial glial cells acting as neural progenitors throughout life. - A myeloid dendritic cell found in the blood that is CD1c-positive. + A myeloid dendritic cell that is CD1c-positive. GOC:dsd GOC:tfm PMID:20204387 @@ -65957,6 +66992,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -66248,6 +67284,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -67074,6 +68111,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -67655,6 +68693,7 @@ radial glial cells acting as neural progenitors throughout life. A progenitor cell of the central nervous system that can differentiate into oligodendrocytes or type-2 astrocytes. This cell originates from multiple structures within the developing brain including the medial ganglion eminence and the lateral ganglionic eminence. These cells migrate throughout the central nervous system and persist into adulthood where they play an important role in remyelination of injured neurons. + This cell type can be purified from optic nerves and other regions of the embryonic, postnatal and adult rat CNS and can be differentiated in vitro to oligodendrocytes and type-2 astrocytes. Some references use the terms 'oligodendrocyte precursor cell' and 'oligodendrocyte type-2 astrocyte (O-2A) progenitor' to refer to the same entity (e.g., PMID:10704434), while others describe an oligodendrocyte type-2 astrocyte (O-2A) progenitor cell as the precurosr to oligodendrocyte- and type-2 astrocyte- progenitor cells (e.g, ISBN:9780702028991). 2010-11-10T02:51:34Z oligodendrocyte-type 2 astrocyte (O-2A) progenitor cell oligodendrocyte/type-2 astrocyte progenitor cell @@ -67663,7 +68702,6 @@ radial glial cells acting as neural progenitors throughout life. O2A/OPC - This cell type can be purified from optic nerves and other regions of the embryonic, postnatal and adult rat CNS and can be differentiated in vitro to oligodendrocytes and type-2 astrocytes. Some references use the terms 'oligodendrocyte precursor cell' and 'oligodendrocyte type-2 astrocyte (O-2A) progenitor' to refer to the same entity (e.g., PMID:10704434), while others describe an oligodendrocyte type-2 astrocyte (O-2A) progenitor cell as the precurosr to oligodendrocyte- and type-2 astrocyte- progenitor cells (e.g, ISBN:9780702028991). oligodendrocyte precursor cell @@ -67678,6 +68716,14 @@ radial glial cells acting as neural progenitors throughout life. PMID:24133281 PMID:9826671 + + + + This cell type can be purified from optic nerves and other regions of the embryonic, postnatal and adult rat CNS and can be differentiated in vitro to oligodendrocytes and type-2 astrocytes. Some references use the terms 'oligodendrocyte precursor cell' and 'oligodendrocyte type-2 astrocyte (O-2A) progenitor' to refer to the same entity (e.g., PMID:10704434), while others describe an oligodendrocyte type-2 astrocyte (O-2A) progenitor cell as the precurosr to oligodendrocyte- and type-2 astrocyte- progenitor cells (e.g, ISBN:9780702028991). + ISBN:9780702028991 + PMID:10704434 + PMID:2182078 + @@ -67705,14 +68751,6 @@ radial glial cells acting as neural progenitors throughout life. PMID:11756508 - - - - This cell type can be purified from optic nerves and other regions of the embryonic, postnatal and adult rat CNS and can be differentiated in vitro to oligodendrocytes and type-2 astrocytes. Some references use the terms 'oligodendrocyte precursor cell' and 'oligodendrocyte type-2 astrocyte (O-2A) progenitor' to refer to the same entity (e.g., PMID:10704434), while others describe an oligodendrocyte type-2 astrocyte (O-2A) progenitor cell as the precurosr to oligodendrocyte- and type-2 astrocyte- progenitor cells (e.g, ISBN:9780702028991). - ISBN:9780702028991 - PMID:10704434 - PMID:2182078 - @@ -68845,6 +69883,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -68927,6 +69966,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -69597,7 +70637,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -70588,11 +71628,10 @@ radial glial cells acting as neural progenitors throughout life. - - + @@ -70660,6 +71699,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -70703,6 +71743,7 @@ radial glial cells acting as neural progenitors throughout life. A specialized epithelial cell that contains "feet" that interdigitate with the "feet" of other glomerular epithelial cells in the mesonephros. + 2011-02-08T01:58:30Z mesonephric glomerular visceral epithelial cell @@ -70712,7 +71753,6 @@ radial glial cells acting as neural progenitors throughout life. A specialized epithelial cell that contains "feet" that interdigitate with the "feet" of other glomerular epithelial cells in the mesonephros. - GOC:tfm @@ -71436,8 +72476,15 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell of the intrahepatic portion of the bile duct. These cells are flattened or cuboidal in shape, and have a small nuclear-to-cytoplasmic ratio relative to large/extrahepatic cholangiocytes. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Intrahepatic cholangiocytes represent a subset of the biliary epithelial cells that form a network of tubes in the liver called the biliary tree The intrahepatic cholangiocytes reside specifically in the intrahepatic bile ducts and play a crucial role in liver physiology and bile production and secretion, thereby aiding in the digestion and absorption of fats in the small intestine. These specific cholangiocytes arise from bipotent hepatoblasts, whereas extrahepatic cholangiocytes share an embryologic origin with the ventral pancreas. +Recent research suggests that there is also heterogeneity within populations of intrahepatic cholangiocytes with different transcriptional profiles, proliferative capacity, and biological function; for example, subpopulations differ in calcium-mobilizing receptors. +The primary function of intrahepatic cholangiocytes is related to bile formation and maintenance of its flow. In addition to their secretory and absorptive activities, they are involved in the regulation of bile composition, volume, and alkalinization, contributing to the neutralization of the acidic chyme (partly digested food) that enters the intestine from the stomach. Intrahepatic cholangiocytes are also recognized for their role in liver regeneration and repair, often proliferating in response to injury. +Intrahepatic cholangiocytes take part in certain pathological conditions, like primary biliary cirrhosis and cholangiocarcinoma. Changes in these cells often lead to abnormalities in bile formation and transport, causing cholestatic liver diseases. Overall, the primary and secondary functional activities of intrahepatic cholangiocytes are vital in maintaining liver function, digestive processes, and contributing to the body's response to liver injury. 2011-02-28T01:20:20Z ZFA:0009379 + https://cellxgene.cziscience.com/cellguide/CL_0002538 small bile duct cholangiocyte intrahepatic cholangiocyte @@ -71455,6 +72502,20 @@ radial glial cells acting as neural progenitors throughout life. GOC:tfm PMID:23720296 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Intrahepatic cholangiocytes represent a subset of the biliary epithelial cells that form a network of tubes in the liver called the biliary tree The intrahepatic cholangiocytes reside specifically in the intrahepatic bile ducts and play a crucial role in liver physiology and bile production and secretion, thereby aiding in the digestion and absorption of fats in the small intestine. These specific cholangiocytes arise from bipotent hepatoblasts, whereas extrahepatic cholangiocytes share an embryologic origin with the ventral pancreas. +Recent research suggests that there is also heterogeneity within populations of intrahepatic cholangiocytes with different transcriptional profiles, proliferative capacity, and biological function; for example, subpopulations differ in calcium-mobilizing receptors. +The primary function of intrahepatic cholangiocytes is related to bile formation and maintenance of its flow. In addition to their secretory and absorptive activities, they are involved in the regulation of bile composition, volume, and alkalinization, contributing to the neutralization of the acidic chyme (partly digested food) that enters the intestine from the stomach. Intrahepatic cholangiocytes are also recognized for their role in liver regeneration and repair, often proliferating in response to injury. +Intrahepatic cholangiocytes take part in certain pathological conditions, like primary biliary cirrhosis and cholangiocarcinoma. Changes in these cells often lead to abnormalities in bile formation and transport, causing cholestatic liver diseases. Overall, the primary and secondary functional activities of intrahepatic cholangiocytes are vital in maintaining liver function, digestive processes, and contributing to the body's response to liver injury. + DOI:10.1002/hep.31252 + DOI:10.1016/j.ajpath.2023.02.012 + DOI:10.1016/j.biocel.2010.06.020 + DOI:10.1016/j.gastha.2022.07.015 + @@ -71606,9 +72667,15 @@ radial glial cells acting as neural progenitors throughout life. An endothelial cell that is part of the vein. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Vein endothelial cells form a thin layer of squamous cells, the endothelium, lining the interior surface of veins throughout the body. They shape the inner cellular lining of the entire vascular system, including the heart, playing a crucial role in blood circulation. The unique characteristic compact arrangement of these cells enables veins to act as a barrier between the blood (that can contain foreign substances) and the surrounding venous tissue and maintain the integrity of the vascular system. +The primary function of vein endothelial cells is to control the exchange of substances between the bloodstream and the surrounding tissues. They facilitate selective transportation of molecules depending on their size and solubility, including gases, nutrients, hormones, and waste products. Vein endothelial cells also play a protective role by inhibiting the translocation of toxins or pathogens from blood to tissues. Additionally, these cells are involved in blood coagulation and inflammation response, primarily by producing substances that inhibit blood clot formation under normal conditions and initiating clotting when necessary. +Another significant function of vein endothelial cells is the regulation of blood flow and blood pressure. They produce and release several substances, including nitric oxide and prostacyclin, which help in controlling vasodilation and vasoconstriction, thereby regulating blood pressure. These cells are also responsible for angiogenesis, the formation of new blood vessels, which is crucial during wound healing and in the formation of granulation tissue. Consequently, any dysfunction in vein endothelial cells can lead to severe health problems like atherosclerosis, hypertension, and thrombosis. 2011-02-28T03:48:11Z FMA:62104 KUPO:0001099 + https://cellxgene.cziscience.com/cellguide/CL_0002543 endothelial cell of vein venous endothelial cell @@ -71627,6 +72694,19 @@ radial glial cells acting as neural progenitors throughout life. An endothelial cell that is part of the vein. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Vein endothelial cells form a thin layer of squamous cells, the endothelium, lining the interior surface of veins throughout the body. They shape the inner cellular lining of the entire vascular system, including the heart, playing a crucial role in blood circulation. The unique characteristic compact arrangement of these cells enables veins to act as a barrier between the blood (that can contain foreign substances) and the surrounding venous tissue and maintain the integrity of the vascular system. +The primary function of vein endothelial cells is to control the exchange of substances between the bloodstream and the surrounding tissues. They facilitate selective transportation of molecules depending on their size and solubility, including gases, nutrients, hormones, and waste products. Vein endothelial cells also play a protective role by inhibiting the translocation of toxins or pathogens from blood to tissues. Additionally, these cells are involved in blood coagulation and inflammation response, primarily by producing substances that inhibit blood clot formation under normal conditions and initiating clotting when necessary. +Another significant function of vein endothelial cells is the regulation of blood flow and blood pressure. They produce and release several substances, including nitric oxide and prostacyclin, which help in controlling vasodilation and vasoconstriction, thereby regulating blood pressure. These cells are also responsible for angiogenesis, the formation of new blood vessels, which is crucial during wound healing and in the formation of granulation tissue. Consequently, any dysfunction in vein endothelial cells can lead to severe health problems like atherosclerosis, hypertension, and thrombosis. + DOI:10.1007/s00441-008-0706-5 + DOI:10.1038/s41569-022-00770-1 + DOI:10.1038/s41598-021-01360-w + DOI:10.3390/ijms20184411 + @@ -72219,7 +73299,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -72635,7 +73715,13 @@ radial glial cells acting as neural progenitors throughout life. A mesenchymal stem cell of adipose tissue. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Mesenchymal stem cells of adipose tissue, also known commonly as adipose-derived stem cells (ADSCs), are a population of adult stem cells that can be obtained easily from adipose tissues. They have many of the same regenerative properties as other mesenchymal stem cells, but are more easily accessible than bone marrow-derived stem cells. +Adipose-derived stem cells show immense promise in the field of regenerative medicine due to their ability to differentiate into adipocytes, chondrocytes, myocytes, osteoblasts, and other cell types. ADSCs also possess immunomodulatory and homeostatic functions: they have the ability to suppress immune responses and provide a therapeutic environment for tissue repair and regeneration, as well as supporting the proliferation of adipocytes and the overall expansion of adipose tissue and contributing to the tissue's ability to react to demands of energy storage and mobilization. Dysfunction of these cells may contribute to metabolic complications observed in obesity and diabetes. +ADSCs have been used for therapeutic applications such as pathological wound healing, severe refractory acute graft-versus-host disease, and idiopathic thrombocytopenic purpura. 2011-03-01T09:57:17Z + https://cellxgene.cziscience.com/cellguide/CL_0002570 mesenchymal stem cell of adipose mesenchymal stem cell of adipose tissue @@ -72646,6 +73732,20 @@ radial glial cells acting as neural progenitors throughout life. A mesenchymal stem cell of adipose tissue. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Mesenchymal stem cells of adipose tissue, also known commonly as adipose-derived stem cells (ADSCs), are a population of adult stem cells that can be obtained easily from adipose tissues. They have many of the same regenerative properties as other mesenchymal stem cells, but are more easily accessible than bone marrow-derived stem cells. +Adipose-derived stem cells show immense promise in the field of regenerative medicine due to their ability to differentiate into adipocytes, chondrocytes, myocytes, osteoblasts, and other cell types. ADSCs also possess immunomodulatory and homeostatic functions: they have the ability to suppress immune responses and provide a therapeutic environment for tissue repair and regeneration, as well as supporting the proliferation of adipocytes and the overall expansion of adipose tissue and contributing to the tissue's ability to react to demands of energy storage and mobilization. Dysfunction of these cells may contribute to metabolic complications observed in obesity and diabetes. +ADSCs have been used for therapeutic applications such as pathological wound healing, severe refractory acute graft-versus-host disease, and idiopathic thrombocytopenic purpura. + DOI:10.1016/j.biopha.2019.108765 + DOI:10.1016/j.tibtech.2006.01.010 + DOI:10.1038/s41536-019-0083-6 + DOI:10.1096/fj.202100332R + DOI:10.1111/dgd.12049 + @@ -72740,10 +73840,16 @@ radial glial cells acting as neural progenitors throughout life. A glial cell that myelinates or ensheathes axons in the peripheral nervous system. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Schwann cells, also known as neurolemmocytes, are a type of glial cell located in the peripheral nervous system. These cells play a significant role in the healthy functioning of nerves by producing myelin, a fatty substance that forms a coating around nerve fibers. Myelin serves as an insulator and enhances the speed and efficiency of electrical nerve impulses; a single Schwann cell can myelinate a single axon. Myelination starts by the elongation and envelopment of the Schwann cell around the axon, followed by the synthesis and deposition of myelin layers. Some studies suggest that Schwann cells may regulate neuronal action potential, muscular contraction, and the sensitive response. +While Schwann cells are most commonly known for the formation of the myelin sheath, some Schwann cells do not form myelin: Remak Schwann cells, a class of nonmyelinating Schwann cells, ensheath axons with smaller diameter, such as C fiber nociceptors in sciatic nerves and form Remak bundles. +Schwann cells are found along both motor and sensory neurons and are crucial for the advancement and recovery of peripheral nerve injuries, due to their capacity to support nerve regeneration. In cases of nerve injury, Schwann cells play a vital role in recovery by initiating Wallerian degeneration, a process in which the part of the axon distal to the injury site degrades and is then cleared away. Following this, Schwann cells can guide the regrowth of the nerve, providing a conducive environment for axon regeneration. They remodel themselves into a regenerative phenotype, proliferate, and organize themselves into bands of Büngner that provide physical and chemical guidance for the regrowths of axons. This function of Schwann cells in the repair and regeneration of nervous system highlights their therapeutic potential in peripheral nerve injury treatments. 2011-03-02T01:19:27Z BTO:0001220 CALOHA:TS-0898 MESH:D012583 + https://cellxgene.cziscience.com/cellguide/CL_0002573 neurolemmocyte @@ -72757,6 +73863,20 @@ radial glial cells acting as neural progenitors throughout life. GOC:tfm PMID:16807057 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Schwann cells, also known as neurolemmocytes, are a type of glial cell located in the peripheral nervous system. These cells play a significant role in the healthy functioning of nerves by producing myelin, a fatty substance that forms a coating around nerve fibers. Myelin serves as an insulator and enhances the speed and efficiency of electrical nerve impulses; a single Schwann cell can myelinate a single axon. Myelination starts by the elongation and envelopment of the Schwann cell around the axon, followed by the synthesis and deposition of myelin layers. Some studies suggest that Schwann cells may regulate neuronal action potential, muscular contraction, and the sensitive response. +While Schwann cells are most commonly known for the formation of the myelin sheath, some Schwann cells do not form myelin: Remak Schwann cells, a class of nonmyelinating Schwann cells, ensheath axons with smaller diameter, such as C fiber nociceptors in sciatic nerves and form Remak bundles. +Schwann cells are found along both motor and sensory neurons and are crucial for the advancement and recovery of peripheral nerve injuries, due to their capacity to support nerve regeneration. In cases of nerve injury, Schwann cells play a vital role in recovery by initiating Wallerian degeneration, a process in which the part of the axon distal to the injury site degrades and is then cleared away. Following this, Schwann cells can guide the regrowth of the nerve, providing a conducive environment for axon regeneration. They remodel themselves into a regenerative phenotype, proliferate, and organize themselves into bands of Büngner that provide physical and chemical guidance for the regrowths of axons. This function of Schwann cells in the repair and regeneration of nervous system highlights their therapeutic potential in peripheral nerve injury treatments. + DOI:10.1002/glia.23892 + DOI:10.1016/B978-0-444-52902-2.00005-9 + DOI:10.1016/j.biocel.2006.05.007 + DOI:10.1186/1742-2094-8-110 + DOI:10.1186/s13064-020-00140-y + @@ -72871,6 +73991,7 @@ radial glial cells acting as neural progenitors throughout life. A glial cell that is part of the perineurium. This cell type has thin long bipolar cytoplasmic processes, pinocytotic vesicles, fragments of external lamina and/or external lamina-like material, attachment plaques, and desmosome-like junctions. Perineurial cells historically have been referred to as fibroblasts because of shape; however, unlike fibroblasts, a perineurial cell: does not have a compact nucleus and large endoplasmic reticulum; does have a double basement membrane opposed to a single basal lamina; is carefully joined to other perineurial cells by tight junctions into a single sheet as opposed to arranged in a large mass; and finally, can surround a small axon bundle at a nerve terminal whereas a fibroblast cannot. + 2011-03-02T03:03:58Z perineurial glial cell @@ -72886,7 +74007,6 @@ radial glial cells acting as neural progenitors throughout life. NCIT:C41442 PMID:25818566 http://en.wikipedia.org/wiki/Perineurium - @@ -73230,7 +74350,13 @@ radial glial cells acting as neural progenitors throughout life. A blood vessel endothelial cell that is part of the retina. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Retinal blood vessel endothelial cells constitute the innermost lining of the blood vessels found in the retina, the light-sensitive layer of tissue at the back of the eye. The primary role of these cells revolves around their location within the retinal vascular system, forming the structure of the blood-retinal barrier, a subset of the larger blood-ocular barrier system. +The endothelial cells are particularly involved in the growth of new retinal blood vessels from pre-existing ones (angiogenesis); this is critical in managing the amount of oxygen and essential nutrients delivered to the ocular tissues. They are crucial for maintaining homeostasis in the retinal environment by controlling the exchange of molecules between the blood and the retina. Furthermore, they mediate immune cell trafficking, supporting the immune privilege of the eye by preventing the unrestricted infiltration of inflammatory cells into the retina, thus maintaining ocular health and normal vision. +The malfunction or dysfunction of retinal blood vessel endothelial cells is implicated in numerous ocular pathologies, particularly diabetic retinopathy, which is one of the leading causes of blindness worldwide. In such conditions, the compromise in the integrity of the blood-retinal barrier and excess angiogenesis can lead to retinal edema and pathological neovascularization, resulting in vision loss. 2011-03-06T03:28:27Z + https://cellxgene.cziscience.com/cellguide/CL_0002585 @@ -73248,6 +74374,19 @@ radial glial cells acting as neural progenitors throughout life. A blood vessel endothelial cell that is part of the retina. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Retinal blood vessel endothelial cells constitute the innermost lining of the blood vessels found in the retina, the light-sensitive layer of tissue at the back of the eye. The primary role of these cells revolves around their location within the retinal vascular system, forming the structure of the blood-retinal barrier, a subset of the larger blood-ocular barrier system. +The endothelial cells are particularly involved in the growth of new retinal blood vessels from pre-existing ones (angiogenesis); this is critical in managing the amount of oxygen and essential nutrients delivered to the ocular tissues. They are crucial for maintaining homeostasis in the retinal environment by controlling the exchange of molecules between the blood and the retina. Furthermore, they mediate immune cell trafficking, supporting the immune privilege of the eye by preventing the unrestricted infiltration of inflammatory cells into the retina, thus maintaining ocular health and normal vision. +The malfunction or dysfunction of retinal blood vessel endothelial cells is implicated in numerous ocular pathologies, particularly diabetic retinopathy, which is one of the leading causes of blindness worldwide. In such conditions, the compromise in the integrity of the blood-retinal barrier and excess angiogenesis can lead to retinal edema and pathological neovascularization, resulting in vision loss. + DOI:0.1016/j.preteyeres.2015.08.001 + DOI:10.1016/j.preteyeres.2012.08.004 + DOI:10.1038/nature04482 + DOI:10.5301/EJO.2010.6049 + @@ -73283,9 +74422,16 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell of the retinal pigmented epithelium. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Retinal pigment epithelial (RPE) cells form a single layer of cells at the back of the eye sandwiched between the neurosensory retina and the choroid, playing a significant role in maintaining vision health. These pigment-laden cells are highly specialized and perform an array of metabolic and transport functions essential for the maintenance of the photoreceptor cells (rods and cones) in the retina. The pigmentation of RPE cells actively aids in the absorption of excess light and the prevention of light scattering, thus enhancing the eye's optical properties. +The retinal pigment epithelium forms a key part of the blood/retina barrier. The cells have long sheet-like microvilli on their apical membrane that project into the light-sensitive outer segments of the photoreceptors, forming a close structural interaction. The basolateral membrane of the RPE interacts with the underlying Bruch’s membrane, which separates the RPE cells from fenestrated endothelium of the choriocapillaris. +RPE cells support the photoreceptor by providing them with oxygen and nutrients (such as glucose, retinol and fatty acids) and removing waste products. They also recycle the visual pigment, in a process called the "visual cycle", where the RPE cells play a vital role in the regeneration of visual pigment (11-cis retinol) following the absorption of light. This is essential for the maintenance of photoreceptor excitability. +Beyond this, RPE cells take part in the phagocytosis process, where they digest the shed ends of photoreceptor outer segments, thus, preventing the build-up of waste residue that could otherwise harm retinal health. They also secrete various factors, including growth factors required to maintain the structural integrity of choriocapillaris endothelium and photoreceptors, as well as immunosuppressive factors that play an important role in establishing the immune privilege of the eye. 2011-03-06T03:37:09Z BTO:0004910 FMA:75802 + https://cellxgene.cziscience.com/cellguide/CL_0002586 @@ -73297,6 +74443,20 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell of the retinal pigmented epithelium. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Retinal pigment epithelial (RPE) cells form a single layer of cells at the back of the eye sandwiched between the neurosensory retina and the choroid, playing a significant role in maintaining vision health. These pigment-laden cells are highly specialized and perform an array of metabolic and transport functions essential for the maintenance of the photoreceptor cells (rods and cones) in the retina. The pigmentation of RPE cells actively aids in the absorption of excess light and the prevention of light scattering, thus enhancing the eye's optical properties. +The retinal pigment epithelium forms a key part of the blood/retina barrier. The cells have long sheet-like microvilli on their apical membrane that project into the light-sensitive outer segments of the photoreceptors, forming a close structural interaction. The basolateral membrane of the RPE interacts with the underlying Bruch’s membrane, which separates the RPE cells from fenestrated endothelium of the choriocapillaris. +RPE cells support the photoreceptor by providing them with oxygen and nutrients (such as glucose, retinol and fatty acids) and removing waste products. They also recycle the visual pigment, in a process called the "visual cycle", where the RPE cells play a vital role in the regeneration of visual pigment (11-cis retinol) following the absorption of light. This is essential for the maintenance of photoreceptor excitability. +Beyond this, RPE cells take part in the phagocytosis process, where they digest the shed ends of photoreceptor outer segments, thus, preventing the build-up of waste residue that could otherwise harm retinal health. They also secrete various factors, including growth factors required to maintain the structural integrity of choriocapillaris endothelium and photoreceptors, as well as immunosuppressive factors that play an important role in establishing the immune privilege of the eye. + DOI:10.1111/febs.16018 + DOI:10.1152/physrev.00021.2004 + DOI:10.3389/fphar.2021.727870/full + https://www.sciencedirect.com/topics/chemistry/retinal-pigment + @@ -73971,7 +75131,7 @@ radial glial cells acting as neural progenitors throughout life. - An astrocyte of the cerebral cortex. + A transcriptomically distinct astrocyte that is found in the cerebral cortex. 2011-03-06T06:57:36Z @@ -73982,7 +75142,7 @@ radial glial cells acting as neural progenitors throughout life. - An astrocyte of the cerebral cortex. + A transcriptomically distinct astrocyte that is found in the cerebral cortex. GOC:tfm @@ -74465,8 +75625,14 @@ radial glial cells acting as neural progenitors throughout life. An endothelial cell of the umbilical vein. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Endothelial cells of the umbilical vein form the inner lining of the veins found in the umbilical cord. They are involved in tube formation and migration which are essential for angiogenesis, the process of generating new blood vessels; this is critical during the fetal stage for the development of the circulatory system. Endothelial cells of the umbilical vein also play a role in controlling the passage of white blood cells into tissues during inflammatory responses. +Because human umbilical vein endothelial cells (HUVECs) can easily be derived from the umbilical cord, and because they express common endothelial cell markers, they have been used as an epithelial cell model for studies on cell proliferation, migration, angiogenesis, and inflammation. They have been used as models for vascular diseases like atherosclerosis, for investigating how tumor cells infiltrate blood vessels and form metastases. +Thus, while endothelial cells of the umbilical vein play a critical role in vascular biology, they also represent a powerful tool in disease studies and potential treatment strategies. 2011-03-14T11:36:51Z BTO:0004296 + https://cellxgene.cziscience.com/cellguide/CL_0002618 endothelial cell of umbilical vein @@ -74475,6 +75641,20 @@ radial glial cells acting as neural progenitors throughout life. An endothelial cell of the umbilical vein. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Endothelial cells of the umbilical vein form the inner lining of the veins found in the umbilical cord. They are involved in tube formation and migration which are essential for angiogenesis, the process of generating new blood vessels; this is critical during the fetal stage for the development of the circulatory system. Endothelial cells of the umbilical vein also play a role in controlling the passage of white blood cells into tissues during inflammatory responses. +Because human umbilical vein endothelial cells (HUVECs) can easily be derived from the umbilical cord, and because they express common endothelial cell markers, they have been used as an epithelial cell model for studies on cell proliferation, migration, angiogenesis, and inflammation. They have been used as models for vascular diseases like atherosclerosis, for investigating how tumor cells infiltrate blood vessels and form metastases. +Thus, while endothelial cells of the umbilical vein play a critical role in vascular biology, they also represent a powerful tool in disease studies and potential treatment strategies. + DOI:10.1002/cyto.a.20952 + DOI:10.1007/s12015-006-0015-x + DOI:10.1172/JCI107470 + DOI:10.3390/app10030938 + https://www.ncbi.nlm.nih.gov/books/NBK53254/ + @@ -74565,7 +75745,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -75020,7 +76200,13 @@ radial glial cells acting as neural progenitors throughout life. A basal cell in the respiratory tract. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Respiratory basal cells are highly specialized cells that serve a crucial role in the human airway epithelium, predominantly found lining the surfaces of the trachea and bronchi. These cells exhibit a distinctive columnar shape and are attached directly to the basal lamina. They are characterized by the presence of high amounts of cytoplasmic keratins, predominantly keratin 5 and 14, and transcription factor tumor protein (tp63), which set them apart from other types of lung epithelial cells such as ciliated cells and secretory cells. +Basal cells are essential for maintaining airway integrity. They make up one third of all respiratory epithelial cells and serve as stem cells as they can transform into different cell types, like goblet cells, ciliated cells, and club cells, when needed for homeostatic maintenance of the epithelial barrier or to repair and restore a healthy cellular environment after injury. +Their position at the interface between the internal environment and the external atmosphere makes these cells a first line of defense against air-borne irritants, allergens, and pathogens. Their robust, intrinsic reparative properties facilitate effective recovery from such adversities. However, damage to respiratory basal cells or abnormalities in their function are associated with several respiratory pathologies such as asthma, chronic obstructive pulmonary disease, and lung cancer. Therefore, understanding these cells' function, and their role in disease, is crucial for the development of new therapeutic strategies for respiratory disorders. 2011-06-21T03:11:10Z + https://cellxgene.cziscience.com/cellguide/CL_0002633 airway basal cell airway basal stem cell @@ -75033,6 +76219,18 @@ radial glial cells acting as neural progenitors throughout life. GOC:tfm PMID:20699479 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Respiratory basal cells are highly specialized cells that serve a crucial role in the human airway epithelium, predominantly found lining the surfaces of the trachea and bronchi. These cells exhibit a distinctive columnar shape and are attached directly to the basal lamina. They are characterized by the presence of high amounts of cytoplasmic keratins, predominantly keratin 5 and 14, and transcription factor tumor protein (tp63), which set them apart from other types of lung epithelial cells such as ciliated cells and secretory cells. +Basal cells are essential for maintaining airway integrity. They make up one third of all respiratory epithelial cells and serve as stem cells as they can transform into different cell types, like goblet cells, ciliated cells, and club cells, when needed for homeostatic maintenance of the epithelial barrier or to repair and restore a healthy cellular environment after injury. +Their position at the interface between the internal environment and the external atmosphere makes these cells a first line of defense against air-borne irritants, allergens, and pathogens. Their robust, intrinsic reparative properties facilitate effective recovery from such adversities. However, damage to respiratory basal cells or abnormalities in their function are associated with several respiratory pathologies such as asthma, chronic obstructive pulmonary disease, and lung cancer. Therefore, understanding these cells' function, and their role in disease, is crucial for the development of new therapeutic strategies for respiratory disorders. + DOI:10.1186/s12931-022-02042-5 + DOI:10.3389/falgy.2021.787128 + DOI:110.1038/s41385-020-00370-7 + @@ -75985,7 +77183,13 @@ radial glial cells acting as neural progenitors throughout life. An endothelial stalk cell is a specialized endothelial cell that follows behind the tip cell of an angiogenic sprout. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Endothelial stalk cells are specialized vascular cells vital in angiogenesis, a process through which new blood vessels are formed from pre-existing ones; specifically, endothelial stalk cells are involved in sprouting angiogenesis, where they help form the body of new blood vessels. +Vascular sprouting relies on the coordinated activity of migrating endothelial tip cells at the forefront and proliferating stalk cells that elongate the sprout. The process is tightly controlled by different growths factors: Vascular Endothelial Growth Factor acts on endothelial cells, inducing them to become endothelial tip cells that initiate sprouting. After sprouting initiation, activation of Notch signaling suppresses differentiation toward a tip cell phenotype and some of the endothelial cells differentiate into stalk cells, which follow tip cells, multiply, and elongate to provide a structural backbone to the growing vessel sprout. +In contrast to endothelial tip cells, which migrate and lead the angiogenic sprout, endothelial stalk cells behind the sprouts continue forming the tube or lumen for blood flow and facilitate maturation and stability of the new vessel. The delicate balance between the activities of stalk and tip cells during angiogenesis is crucial to build a functional vascular network. Dysfunctions in endothelial stalk cells can lead to pathological conditions such as impaired wound healing, unregulated tumor growth, and metastasis due to abnormal angiogenesis. 2011-08-16T01:49:32Z + https://cellxgene.cziscience.com/cellguide/CL_0002671 endothelial stalk cell @@ -75996,6 +77200,19 @@ radial glial cells acting as neural progenitors throughout life. GOC:tfm PMID:21521739 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Endothelial stalk cells are specialized vascular cells vital in angiogenesis, a process through which new blood vessels are formed from pre-existing ones; specifically, endothelial stalk cells are involved in sprouting angiogenesis, where they help form the body of new blood vessels. +Vascular sprouting relies on the coordinated activity of migrating endothelial tip cells at the forefront and proliferating stalk cells that elongate the sprout. The process is tightly controlled by different growths factors: Vascular Endothelial Growth Factor acts on endothelial cells, inducing them to become endothelial tip cells that initiate sprouting. After sprouting initiation, activation of Notch signaling suppresses differentiation toward a tip cell phenotype and some of the endothelial cells differentiate into stalk cells, which follow tip cells, multiply, and elongate to provide a structural backbone to the growing vessel sprout. +In contrast to endothelial tip cells, which migrate and lead the angiogenic sprout, endothelial stalk cells behind the sprouts continue forming the tube or lumen for blood flow and facilitate maturation and stability of the new vessel. The delicate balance between the activities of stalk and tip cells during angiogenesis is crucial to build a functional vascular network. Dysfunctions in endothelial stalk cells can lead to pathological conditions such as impaired wound healing, unregulated tumor growth, and metastasis due to abnormal angiogenesis. + DOI:10.1007/s12079-019-00511-z + DOI:10.1016/j.cmet.2013.08.001 + DOI:10.1101/cshperspect.a006569 + DOI:10.3389/fcell.2021.642352 + @@ -76248,6 +77465,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -77732,6 +78950,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -77792,6 +79011,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -79815,7 +81035,13 @@ radial glial cells acting as neural progenitors throughout life. Specialized epithelial cells involved in the maintenance of osmotic homeostasis. They are characterized by abundant mitochondria and ion transporters. In amniotes, they are present in the renal system. In freshwater fish, ionocytes in the skin and gills help maintain osmotic homeostasis by absorbing salt from the external environment. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Ionocytes are specialized cells predominantly found in the mammalian respiratory and renal systems as well as in the gills, skin, and intestinal tract of fish. These cells play crucial roles in maintaining ion and acid-base homeostasis. Ionocytes demonstrate remarkable plasticity and are able to adapt themselves in response to changes in environmental conditions such as pH, salinity, ion concentration, and temperature. +These cells work by selectively absorbing specific ions from the environment, thus maintaining the body's internal ionic balance. The most commonly absorbed ions include sodium (Na+), chloride (Cl-), calcium (Ca2+), and hydrogen (H+). Moreover, ionocytes contribute to acid-base regulation. In response to acidosis or alkalosis, ionocytes can either excrete or retain hydrogen (H+) and bicarbonate (HCO3-) ions to readjust the blood pH. Further, experimental evidence suggests a functional complexity of ionocytes, implying diverse roles beyond ion regulation. Recent research highlights ionocytes' involvement in ammonia excretion and the regulation of extracellular fluid volume, highlighting their contribution to the overall homeostatic process. +Malfunctioning ionocytes have been implicated in various diseases, including cystic fibrosis which is caused by mutations in the chloride channel CFTR, an ionocyte marker. ZFA:0005323 + https://cellxgene.cziscience.com/cellguide/CL_0005006 ionocyte @@ -79827,6 +81053,20 @@ radial glial cells acting as neural progenitors throughout life. PMID:17555741 PMID:19268451 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Ionocytes are specialized cells predominantly found in the mammalian respiratory and renal systems as well as in the gills, skin, and intestinal tract of fish. These cells play crucial roles in maintaining ion and acid-base homeostasis. Ionocytes demonstrate remarkable plasticity and are able to adapt themselves in response to changes in environmental conditions such as pH, salinity, ion concentration, and temperature. +These cells work by selectively absorbing specific ions from the environment, thus maintaining the body's internal ionic balance. The most commonly absorbed ions include sodium (Na+), chloride (Cl-), calcium (Ca2+), and hydrogen (H+). Moreover, ionocytes contribute to acid-base regulation. In response to acidosis or alkalosis, ionocytes can either excrete or retain hydrogen (H+) and bicarbonate (HCO3-) ions to readjust the blood pH. Further, experimental evidence suggests a functional complexity of ionocytes, implying diverse roles beyond ion regulation. Recent research highlights ionocytes' involvement in ammonia excretion and the regulation of extracellular fluid volume, highlighting their contribution to the overall homeostatic process. +Malfunctioning ionocytes have been implicated in various diseases, including cystic fibrosis which is caused by mutations in the chloride channel CFTR, an ionocyte marker. + DOI:10.1016/j.jcf.2019.09.010 + DOI:10.1038/s41586-018-0393-7 + DOI:10.1038/s41598-023-30603-1 + DOI:10.1146/annurev-pathol-042420-094031 + DOI:10.3389/fmars.2020.00709 + @@ -79916,7 +81156,13 @@ radial glial cells acting as neural progenitors throughout life. A cuboidal epithelial cell of the kidney which regulates sodium and potassium balance. The activity of sodium and potassium channels on the apical membrane of the cell is regulated by aldosterone and vasopressin. In mammals this cell type is located in the renal collecting duct system. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Renal principal cells are the major cell type in the initial collecting tubule and the cortical and outer medullary collecting ducts, as well as the connecting tubule, in the nephrons of the kidneys. +A key function of renal principal cells is the regulation of water balance in the body. These cells express aquaporin-2 (AQP2) water channels, which facilitate the reabsorption of water from the fluid within the renal tubule lumen back into the blood. The translocation of AQP2 to the cell membrane is controlled by the hormone vasopressin: In response to high vasopressin levels, AQP2 moves to the cell membrane, allowing water to pass through effectively and be reabsorbed, therefore concentrating the urine. Conversely, in low vasopressin conditions, AQP2 is removed from the membrane, reducing water reabsorption and diluting the urine. +Renal principal cells are also involved in the regulation of sodium and potassium levels in the body. They have sodium channels (ENaC) in their luminal membranes which permit the reabsorption of sodium ions from the tubule fluid back into the blood, resulting in a net reabsorption of sodium ions into the systemic circulation. This process is controlled, in part, by the hormone aldosterone. Additionally, renal principal cells contain potassium channels that facilitate the secretion of potassium ions into the urine. The activities of these channels, in coordination with other cell types in the nephron, are critical for maintaining electrolyte balance and overall body homeostasis. ZFA:0005322 + https://cellxgene.cziscience.com/cellguide/CL_0005009 renal principal cell @@ -79926,6 +81172,18 @@ radial glial cells acting as neural progenitors throughout life. A cuboidal epithelial cell of the kidney which regulates sodium and potassium balance. The activity of sodium and potassium channels on the apical membrane of the cell is regulated by aldosterone and vasopressin. In mammals this cell type is located in the renal collecting duct system. CL:CVS + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Renal principal cells are the major cell type in the initial collecting tubule and the cortical and outer medullary collecting ducts, as well as the connecting tubule, in the nephrons of the kidneys. +A key function of renal principal cells is the regulation of water balance in the body. These cells express aquaporin-2 (AQP2) water channels, which facilitate the reabsorption of water from the fluid within the renal tubule lumen back into the blood. The translocation of AQP2 to the cell membrane is controlled by the hormone vasopressin: In response to high vasopressin levels, AQP2 moves to the cell membrane, allowing water to pass through effectively and be reabsorbed, therefore concentrating the urine. Conversely, in low vasopressin conditions, AQP2 is removed from the membrane, reducing water reabsorption and diluting the urine. +Renal principal cells are also involved in the regulation of sodium and potassium levels in the body. They have sodium channels (ENaC) in their luminal membranes which permit the reabsorption of sodium ions from the tubule fluid back into the blood, resulting in a net reabsorption of sodium ions into the systemic circulation. This process is controlled, in part, by the hormone aldosterone. Additionally, renal principal cells contain potassium channels that facilitate the secretion of potassium ions into the urine. The activities of these channels, in coordination with other cell types in the nephron, are critical for maintaining electrolyte balance and overall body homeostasis. + DOI:10.1016/j.krcp.2013.07.005 + DOI:10.2215/CJN.05760513 + DOI:10.2215/CJN.08580813 + @@ -79942,8 +81200,15 @@ radial glial cells acting as neural progenitors throughout life. A cuboidal epithelial cell of the kidney that regulates acid/base balance. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Renal intercalated cells are specialized cells located in the collecting duct system of the kidneys. The primary role of intercalated cells is to reabsorb bicarbonate ions and secrete hydrogen ions, thereby maintaining the acid-base homeostasis in the blood. They comprise two main subtypes primarily distinguished by their functional and morphological attributes: alpha and beta intercalated cells. +Alpha intercalated cells are more predominant when the body is in a state of acidosis, a condition characterized by an increased acidity of the blood. These cells are specialized in secreting excessive hydrogen ions into the urine through a mechanism involving vacuolar H+-ATPase and H+/K+-ATPase pumps on their apical membranes. They simultaneously reabsorb bicarbonate ions from the tubular fluid and return them to the bloodstream via mechanisms involving carbonic anhydrase II and bicarbonate/chloride exchangers on the basolateral membrane. This dual process helps to increase blood pH towards normal levels. +When the body is in a state of alkalosis, a condition characterized by lowered levels of hydrogen ions in the blood, beta intercalated cells are more predominant. They primarily reabsorb hydrogen ions from the tubular fluid through vacuolar H+-ATPase and H+/K+-ATPase pumps on their basolateral membranes, while secreting bicarbonate ions into the urine via pendrin, a bicarbonate/chloride exchanger in the apical membrane. These mechanisms work together to decrease blood pH towards normal levels. +In summary, renal intercalated cells play a critical role in the delicate balance of the body’s pH, safeguarding the body from potential harm caused by acidemia or alkalemia. FMA:86560 ZFA:0009375 + https://cellxgene.cziscience.com/cellguide/CL_0005010 intercalated cell Intercalated cells are also called “mitochondria-rich cells”, reflecting the high levels of round mitochondria at their apical pole, or in their cytoplasm, a distribution that is quite different from that of other kidney tubule cells, which accumulated mitochondria around the basolateral membrane. These cells also have numerous irregular apical microvilli compared with the surrounding segment-specific cells. Intercalated cells lack a central cilium, at least in the cortex, which also differentiates them from the adjacent principal cells. @@ -79955,6 +81220,20 @@ radial glial cells acting as neural progenitors throughout life. A cuboidal epithelial cell of the kidney that regulates acid/base balance. CL:CVS + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Renal intercalated cells are specialized cells located in the collecting duct system of the kidneys. The primary role of intercalated cells is to reabsorb bicarbonate ions and secrete hydrogen ions, thereby maintaining the acid-base homeostasis in the blood. They comprise two main subtypes primarily distinguished by their functional and morphological attributes: alpha and beta intercalated cells. +Alpha intercalated cells are more predominant when the body is in a state of acidosis, a condition characterized by an increased acidity of the blood. These cells are specialized in secreting excessive hydrogen ions into the urine through a mechanism involving vacuolar H+-ATPase and H+/K+-ATPase pumps on their apical membranes. They simultaneously reabsorb bicarbonate ions from the tubular fluid and return them to the bloodstream via mechanisms involving carbonic anhydrase II and bicarbonate/chloride exchangers on the basolateral membrane. This dual process helps to increase blood pH towards normal levels. +When the body is in a state of alkalosis, a condition characterized by lowered levels of hydrogen ions in the blood, beta intercalated cells are more predominant. They primarily reabsorb hydrogen ions from the tubular fluid through vacuolar H+-ATPase and H+/K+-ATPase pumps on their basolateral membranes, while secreting bicarbonate ions into the urine via pendrin, a bicarbonate/chloride exchanger in the apical membrane. These mechanisms work together to decrease blood pH towards normal levels. +In summary, renal intercalated cells play a critical role in the delicate balance of the body’s pH, safeguarding the body from potential harm caused by acidemia or alkalemia. + DOI:10.1152/ajprenal.2000.279.1.F195 + DOI:10.1161/HYPERTENSIONAHA.121.16492 + DOI:10.1681/ASN.V1011 + DOI:10.2215/CJN.08880914 + @@ -79981,7 +81260,12 @@ radial glial cells acting as neural progenitors throughout life. A cuboidal epithelial cell of the kidney which secretes acid and reabsorbs base to regulate acid/base balance. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Renal alpha-intercalated cells are located within the connecting tubules and collecting ducts of the kidneys, which are components of the kidney's complex nephron system. Along with beta-intercalated cells, they play a critical role in the body’s acid-base balance. +Renal alpha-intercalated cells contain an abundance of proton pumps and enzymes like carbonic anhydrase, which aid in the transport of hydrogen ions for secretion in the urine. The bicarbonate/chloride transporters on their apical membrane meanwhile take up bicarbonate ions from the urine and supply them back into the blood. Through this mechanism, these cells contribute significantly to the neutrality of blood pH, and dysfunction of renal alpha-intercalated cells often leads to distal renal tubular acidosis, a condition resulting in acidic blood and alkaline urine. ZFA:0009376 + https://cellxgene.cziscience.com/cellguide/CL_0005011 type A intercalated cell type A-IC @@ -79994,6 +81278,18 @@ radial glial cells acting as neural progenitors throughout life. A cuboidal epithelial cell of the kidney which secretes acid and reabsorbs base to regulate acid/base balance. CL:CVS + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Renal alpha-intercalated cells are located within the connecting tubules and collecting ducts of the kidneys, which are components of the kidney's complex nephron system. Along with beta-intercalated cells, they play a critical role in the body’s acid-base balance. +Renal alpha-intercalated cells contain an abundance of proton pumps and enzymes like carbonic anhydrase, which aid in the transport of hydrogen ions for secretion in the urine. The bicarbonate/chloride transporters on their apical membrane meanwhile take up bicarbonate ions from the urine and supply them back into the blood. Through this mechanism, these cells contribute significantly to the neutrality of blood pH, and dysfunction of renal alpha-intercalated cells often leads to distal renal tubular acidosis, a condition resulting in acidic blood and alkaline urine. + DOI:10.1016/j.semnephrol.2019.04.005 + DOI:10.1152/physiol.00008.2011 + DOI:10.1172/JCI63492 + DOI:10.3390/diseases2020071 + @@ -80024,21 +81320,71 @@ radial glial cells acting as neural progenitors throughout life. + + + + + + + + + + + + + + + - A ciliated epithelial cell with many cilia. + + + + + + + + + + + + + + A columnar/cuboidal epithelial cell with multiple motile cilia on its apical surface. These cells facilitate the movement of liquids such as mucus or cerebrospinal fluid across the epithelial surface. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +The multi-ciliated epithelial cell are terminally differentiated epithelia that line brain ventricles, the respiratory tract and parts of the female and male reproductive organs in animals, playing critical roles in the maintenance of homeostasis through ciliary motion. They are characterized by the presence of hundreds of motile cilia, hair-like microtubule-based organelles that beat in a coordinated fashion to direct fluid flow over the cell surface. +Multi-ciliated epithelial cells have fundamental roles in the proper functioning of many organ systems. In the respiratory system, they line the airways and orchestrate the coordinated movement of mucus, effectively clearing the airways of inhaled particles and pathogens. These cells are also vital in the ventricular system of the brain where they facilitate cerebrospinal fluid circulation, thus contributing to the maintenance of the brain's microenvironment. In the fallopian tube, multi-ciliated epithelial cells aid in the transport of oocytes from the ovary to the uterus, a process crucial to reproduction. +The formation and function of multi-ciliated epithelial cells is a highly regulated process that involves several stages of development including cell specification, centriole multiplication, and ciliogenesis. Any disruption in these processes can result in dysfunctional or decreased numbers of cilia, which can lead to a myriad of health issues, ranging from chronic respiratory infections to infertility. multi-ciliated cell multiciliated cell ZFA:0005242 + https://cellxgene.cziscience.com/cellguide/CL_0005012 multiciliated epithelial cell MCC + While the term 'multi-ciliated epithelial cell' refers to cells with multiple motile cilia, there are exceptions where epithelial cells may have multiple non-motile cilia. Examples include olfactory sensory neurons, which have non-motile cilia for sensory detection, and choroid plexus epithelial cells, which possess multiple non-motile cilia with transient motility during development. Multiciliated cells are essential for human health, and their dysfunction can lead to various diseases known as ciliopathies, such as primary ciliary dyskinesia. This condition affects the respiratory system, brain ventricles, and reproductive system, leading to chronic respiratory infections, hydrocephalus, and infertility multi-ciliated epithelial cell - A ciliated epithelial cell with many cilia. + A columnar/cuboidal epithelial cell with multiple motile cilia on its apical surface. These cells facilitate the movement of liquids such as mucus or cerebrospinal fluid across the epithelial surface. CL:CVS + PMID:28400610 + PMID:30422572 + PMID:38032388 + + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +The multi-ciliated epithelial cell are terminally differentiated epithelia that line brain ventricles, the respiratory tract and parts of the female and male reproductive organs in animals, playing critical roles in the maintenance of homeostasis through ciliary motion. They are characterized by the presence of hundreds of motile cilia, hair-like microtubule-based organelles that beat in a coordinated fashion to direct fluid flow over the cell surface. +Multi-ciliated epithelial cells have fundamental roles in the proper functioning of many organ systems. In the respiratory system, they line the airways and orchestrate the coordinated movement of mucus, effectively clearing the airways of inhaled particles and pathogens. These cells are also vital in the ventricular system of the brain where they facilitate cerebrospinal fluid circulation, thus contributing to the maintenance of the brain's microenvironment. In the fallopian tube, multi-ciliated epithelial cells aid in the transport of oocytes from the ovary to the uterus, a process crucial to reproduction. +The formation and function of multi-ciliated epithelial cells is a highly regulated process that involves several stages of development including cell specification, centriole multiplication, and ciliogenesis. Any disruption in these processes can result in dysfunctional or decreased numbers of cilia, which can lead to a myriad of health issues, ranging from chronic respiratory infections to infertility. + DOI:10.1016/j.cub.2014.08.047 + DOI:10.1038/nrm.2017.21 + DOI:10.1101/cshperspect.a028233 @@ -80052,6 +81398,15 @@ radial glial cells acting as neural progenitors throughout life. MCC + + + + While the term 'multi-ciliated epithelial cell' refers to cells with multiple motile cilia, there are exceptions where epithelial cells may have multiple non-motile cilia. Examples include olfactory sensory neurons, which have non-motile cilia for sensory detection, and choroid plexus epithelial cells, which possess multiple non-motile cilia with transient motility during development. Multiciliated cells are essential for human health, and their dysfunction can lead to various diseases known as ciliopathies, such as primary ciliary dyskinesia. This condition affects the respiratory system, brain ventricles, and reproductive system, leading to chronic respiratory infections, hydrocephalus, and infertility + PMID:22118931 + PMID:23959957 + PMID:25729351 + PMID:26378583 + @@ -80214,7 +81569,13 @@ radial glial cells acting as neural progenitors throughout life. Ghrelin secreting cells found in the endocrine pancreas. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Pancreatic epsilon cells are a specialized type of endocrine cell found in the islets of Langerhans, a region of the pancreas responsible for hormone production. These clusters of cells constitute only about 1% of the pancreatic islet cell population, making them a relatively small yet significant component of the pancreas. Pancreatic epsilon cells have a round or ovoid shape with occasional cytoplasmic extensions and are characterized by small and spherical granules. +The principal function of pancreatic epsilon cells involves the synthesis and release of the hormone ghrelin, a peptide hormone predominantly produced in the stomach; pancreatic epsilon cells are one of the few sites outside the gastrointestinal tract known to produce this hormone. Ghrelin has multiple vital roles, playing a significant part in generating hunger sensations, promoting fat storage, and influencing various metabolic processes. It also stimulates the release of Growth Hormone (GH) from the anterior pituitary gland. +During fetal development, when they form a layer around the islet, epsilon cells are an important source of ghrelin, likely secreting the hormone into the circulation; their numbers decrease in adults. While research on pancreatic epsilon cells is still ongoing, these cells have been implicated in several disease states, most notably Type 2 diabetes and metabolic syndrome. The dysfunction or reduction in the number of pancreatic epsilon cells can lead to anomalies in ghrelin production, impacting overall metabolic homeostasis and glucose regulation. ZFA:0005598 + https://cellxgene.cziscience.com/cellguide/CL_0005019 pancreatic E cell @@ -80227,6 +81588,20 @@ radial glial cells acting as neural progenitors throughout life. Ghrelin secreting cells found in the endocrine pancreas. PMID:14970313 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Pancreatic epsilon cells are a specialized type of endocrine cell found in the islets of Langerhans, a region of the pancreas responsible for hormone production. These clusters of cells constitute only about 1% of the pancreatic islet cell population, making them a relatively small yet significant component of the pancreas. Pancreatic epsilon cells have a round or ovoid shape with occasional cytoplasmic extensions and are characterized by small and spherical granules. +The principal function of pancreatic epsilon cells involves the synthesis and release of the hormone ghrelin, a peptide hormone predominantly produced in the stomach; pancreatic epsilon cells are one of the few sites outside the gastrointestinal tract known to produce this hormone. Ghrelin has multiple vital roles, playing a significant part in generating hunger sensations, promoting fat storage, and influencing various metabolic processes. It also stimulates the release of Growth Hormone (GH) from the anterior pituitary gland. +During fetal development, when they form a layer around the islet, epsilon cells are an important source of ghrelin, likely secreting the hormone into the circulation; their numbers decrease in adults. While research on pancreatic epsilon cells is still ongoing, these cells have been implicated in several disease states, most notably Type 2 diabetes and metabolic syndrome. The dysfunction or reduction in the number of pancreatic epsilon cells can lead to anomalies in ghrelin production, impacting overall metabolic homeostasis and glucose regulation. + DOI:10.1007/s00125-008-1238-y + DOI:10.1152/physrev.00012.2004 + DOI:10.1210/en.2018-00833 + DOI:10.3389/fendo.2022.904004 + DOI:10.3390/ijms20081867 + @@ -80486,6 +81861,12 @@ radial glial cells acting as neural progenitors throughout life. Multi fate stem cell that gives rise to both hepatocytes and cholangiocytes as descendants. The term often refers to fetal precursors of hepatocytes (differently from 'hepatic stem cell', usually applied to the self-renewing pool of hepatocyte precursors in the adult liver). Hepatoblasts may also be endogenous, as some stem cells found in the liver come from the bone marrow via blood circulation. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Hepatoblasts are immature precursor cells that predominate during the early stages of liver development, specifically in the embryonic phase of life. They first arise from the endoderm, one of the three primary germ layers in the very early embryo, and then differentiate into two distinct mature liver cell types - the hepatocytes and cholangiocytes. +During liver organogenesis hepatoblasts proliferate and migrate into the septum transversum to form the liver bud. Proliferation and differentiation of these cells are regulated by several soluble factors, such as hepatocyte growth factor, which is a mitogen of both hepatoblasts and mature hepatocytes. As they start to differentiate into hepatocytes and cholangiocytes, the cells begin to express hepatic markers like albumin and alpha-fetoprotein. +Although hepatoblasts are specified embryonic liver cells that are bipotential for hepatocytes and cholangiocytes, a subset of liver cells (called oval cells) has been identified in adults that express stem cell markers, such as CD133 and cKIT, and has been suggested to have the same potential as hepatoblasts to differentiate into hepatocytes and cholangiocytes. + https://cellxgene.cziscience.com/cellguide/CL_0005026 hepatoblast https://github.com/obophenotype/cell-ontology/issues/800 @@ -80500,6 +81881,20 @@ radial glial cells acting as neural progenitors throughout life. PMID:26798363 https://orcid.org/0000-0003-1940-6740 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Hepatoblasts are immature precursor cells that predominate during the early stages of liver development, specifically in the embryonic phase of life. They first arise from the endoderm, one of the three primary germ layers in the very early embryo, and then differentiate into two distinct mature liver cell types - the hepatocytes and cholangiocytes. +During liver organogenesis hepatoblasts proliferate and migrate into the septum transversum to form the liver bud. Proliferation and differentiation of these cells are regulated by several soluble factors, such as hepatocyte growth factor, which is a mitogen of both hepatoblasts and mature hepatocytes. As they start to differentiate into hepatocytes and cholangiocytes, the cells begin to express hepatic markers like albumin and alpha-fetoprotein. +Although hepatoblasts are specified embryonic liver cells that are bipotential for hepatocytes and cholangiocytes, a subset of liver cells (called oval cells) has been identified in adults that express stem cell markers, such as CD133 and cKIT, and has been suggested to have the same potential as hepatoblasts to differentiate into hepatocytes and cholangiocytes. + DOI:10.1016/j.stem.2014.04.010 + DOI:10.1093/jb/mvr001 + DOI:10.1242/dev.031369 + DOI:10.1242/dev.114215 + DOI:10.5966/sctm.2015-0051 + @@ -80508,6 +81903,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -80572,6 +81968,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -80665,7 +82062,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -81089,6 +82486,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -81128,7 +82526,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + @@ -81160,7 +82558,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + @@ -81335,7 +82733,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + @@ -81344,17 +82742,18 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + - A somatic muscle cell that is oblquely striated. Examples include the somatic muscles of nematodes. + A somatic muscle cell that is obliquely striated and mononucleated. Examples include the somatic muscles of nematodes. obliquely striated somatic muscle cell - A somatic muscle cell that is oblquely striated. Examples include the somatic muscles of nematodes. + A somatic muscle cell that is obliquely striated and mononucleated. Examples include the somatic muscles of nematodes. PMID:8720463 + doi:10.3908/wormatlas.1.7 @@ -81634,18 +83033,18 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + A skeletal muscle satellite cell that has become mitotically active - typically following muscle damage. activated skeletal muscle satellite cell - + - + More accurately - transformation_of ? @@ -81729,6 +83128,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -82065,7 +83465,6 @@ Covers cells actively being cultured or stored in a quiescent state for future u - @@ -82089,7 +83488,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + @@ -82350,7 +83749,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u An endothelial cell of the venule that is squamous shaped. This is in contrast to the cubodial shape of high endothelial venule cells. - GOC:tfm + GOC:tfm @@ -82600,7 +83999,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + @@ -82666,7 +84065,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + @@ -82829,7 +84228,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + @@ -83048,6 +84447,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -83136,7 +84536,13 @@ Covers cells actively being cultured or stored in a quiescent state for future u An intestinal stem cell that is located in the small intestine crypt of Liberkuhn. These stem cells reside at the bottom of crypts in the small intestine and are highly proliferative. They either differentiate into transit amplifying cells or self-renew to form new stem cells. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Intestinal crypt stem cells of the small intestine are a type of adult stem cell intimately involved in the continuous replenishment of the intestinal epithelium, the innermost layer of the intestine responsible for nutrient absorption. These cells, located within the crypts of Lieberkühn, are the origin of various cell lineages that make up the functional units of the small intestine. They possess self-renewal ability, an essential feature of stem cells, which allows them to maintain a steady population in the small intestine. +One of the critical roles of intestinal crypt stem cells is to drive the continual renewal process taking place in the small intestine every 3-5 days. By proliferating intensively, these cells produce transient amplifying (TA) cells that are characterized by quick division and progressive differentiation. These cells eventually differentiate into specialized cell types, encompassing absorptive enterocytes, mucin-secreting goblet cells, hormone-secreting enteroendocrine cells, and Paneth cells, all of which have essential roles in digestion and nutrient absorption in the small intestine. +Intestinal crypt stem cells of the small intestine are also play a significant part in injury recovery. Under regular conditions, these cells primarily exist in an active state, facilitating the constant renovation of the gut lining. However, upon injury or loss of regular intestinal crypt stem cells reserve intestinal stem cells, a slow-cycling and radio-resistant population, can be stimulated to take over the duties of active crypt stem cells. Such plasticity provides a powerful regenerative mechanism that ensures the intestinal epithelium's function and structural integrity amidst diverse conditions. crypt stem cell of small intestine + https://cellxgene.cziscience.com/cellguide/CL_0009017 stem cell of small intestine crypt of Lieberkuhn @@ -83149,6 +84555,18 @@ Covers cells actively being cultured or stored in a quiescent state for future u PMID:20683682 https://orcid.org/0000-0003-4183-8865 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Intestinal crypt stem cells of the small intestine are a type of adult stem cell intimately involved in the continuous replenishment of the intestinal epithelium, the innermost layer of the intestine responsible for nutrient absorption. These cells, located within the crypts of Lieberkühn, are the origin of various cell lineages that make up the functional units of the small intestine. They possess self-renewal ability, an essential feature of stem cells, which allows them to maintain a steady population in the small intestine. +One of the critical roles of intestinal crypt stem cells is to drive the continual renewal process taking place in the small intestine every 3-5 days. By proliferating intensively, these cells produce transient amplifying (TA) cells that are characterized by quick division and progressive differentiation. These cells eventually differentiate into specialized cell types, encompassing absorptive enterocytes, mucin-secreting goblet cells, hormone-secreting enteroendocrine cells, and Paneth cells, all of which have essential roles in digestion and nutrient absorption in the small intestine. +Intestinal crypt stem cells of the small intestine are also play a significant part in injury recovery. Under regular conditions, these cells primarily exist in an active state, facilitating the constant renovation of the gut lining. However, upon injury or loss of regular intestinal crypt stem cells reserve intestinal stem cells, a slow-cycling and radio-resistant population, can be stimulated to take over the duties of active crypt stem cells. Such plasticity provides a powerful regenerative mechanism that ensures the intestinal epithelium's function and structural integrity amidst diverse conditions. + DOI:10.1016/j.celrep.2020.107952 + DOI:10.1038/s41575-018-0081-y + DOI:10.1073/pnas.1607327113 + @@ -84082,6 +85500,12 @@ Covers cells actively being cultured or stored in a quiescent state for future u An intestinal crypt stem cell that is located in the colon. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Intestinal crypt stem cells of the colon, also known as colon crypt base columnar (CBC) cells, are highly specialized cells primarily responsible for the constant self-renewal of the colonic epithelium. These cells are found in the crypts of Lieberkühn - deeply invaginated sections of the colon's mucosal layer. +The prime function of intestinal crypt stem cells of the colon is to serve as the source of constant cell regeneration in the colon. Every few days, these stem cells divide and differentiate into the various other types of intestinal cells, such as enterocytes, goblet cells, and enteroendocrine cells. +A constant renewal cycle is necessary due to the harsh environment of the colon where cells continuously encounter abrasive food matter and potential pathogens, leading to a high turnover rate. When the colon's mucosal layer suffers damage, a rapid response is triggered whereby colon crypt stem cells divide faster and are directed to injured sites to repair the epithelial layer. Dysregulation of these cells' function or proliferation can contribute to disorders such as colorectal cancer. + https://cellxgene.cziscience.com/cellguide/CL_0009043 intestinal crypt stem cell of colon @@ -84092,6 +85516,20 @@ Covers cells actively being cultured or stored in a quiescent state for future u An intestinal crypt stem cell that is located in the colon. http://orcid.org/0000-0003-3440-1876 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Intestinal crypt stem cells of the colon, also known as colon crypt base columnar (CBC) cells, are highly specialized cells primarily responsible for the constant self-renewal of the colonic epithelium. These cells are found in the crypts of Lieberkühn - deeply invaginated sections of the colon's mucosal layer. +The prime function of intestinal crypt stem cells of the colon is to serve as the source of constant cell regeneration in the colon. Every few days, these stem cells divide and differentiate into the various other types of intestinal cells, such as enterocytes, goblet cells, and enteroendocrine cells. +A constant renewal cycle is necessary due to the harsh environment of the colon where cells continuously encounter abrasive food matter and potential pathogens, leading to a high turnover rate. When the colon's mucosal layer suffers damage, a rapid response is triggered whereby colon crypt stem cells divide faster and are directed to injured sites to repair the epithelial layer. Dysregulation of these cells' function or proliferation can contribute to disorders such as colorectal cancer. + DOI:10.1016/j.cell.2013.07.004 + DOI:10.1038/s41575-018-0081-y + DOI:10.1073/pnas.1607327113 + DOI:10.1111/j.1365-2184.2009.00642.x + DOI:10.1186/s12943-019-0962-x + @@ -86009,9 +87447,17 @@ Covers cells actively being cultured or stored in a quiescent state for future u A reticular cell involved in directing B cells and T cells to specific regions within a tissue. 2022-03-21T15:20:33Z + FRC fibroblastic reticular cell https://github.com/obophenotype/cell-ontology/issues/1472 + + + + FRC + PMID:35440118 + + @@ -86597,31 +88043,16 @@ Covers cells actively being cultured or stored in a quiescent state for future u - - - - - - - - - - - - - - - - - - - An epithelial cell that is part_of a alveolus of lung. + OBSOLETE. An epithelial cell that is part_of a alveolus of lung. + + MESH:D056809 alveolus of lung epithelial cell - May be merged with pneumocyte in future - epithelial cell of alveolus of lung + This cell type is exactly the same as 'pulmonary alveolar epithelial cell'. + obsolete epithelial cell of alveolus of lung + true @@ -86799,19 +88230,19 @@ Covers cells actively being cultured or stored in a quiescent state for future u - + Any photoreceptor cell that is part of some camera-type eye. camera type eye photoreceptor cell camera-type eye photoreceptor cell - + - + https://github.com/obophenotype/cell-ontology/issues/2245 @@ -87408,6 +88839,12 @@ Covers cells actively being cultured or stored in a quiescent state for future u A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. +After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. +Disorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis. + https://cellxgene.cziscience.com/cellguide/CL_0011012 neural crest cell @@ -87418,6 +88855,19 @@ Covers cells actively being cultured or stored in a quiescent state for future u https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-9900-7880 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. +After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. +Disorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis. + DOI:10.1002/dvg.23276 + DOI:10.1242/dev.193193 + DOI:10.3389/fcell.2020.00635/full + https://doi.org/10.1016/j.ydbio.2011.12.042 + @@ -87695,6 +89145,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -87788,6 +89239,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -87865,6 +89317,7 @@ Covers cells actively being cultured or stored in a quiescent state for future u + @@ -88618,6 +90071,12 @@ plexiform layer using GABA. An ionocyte that is part of the lung epithelium. The cells from this type are major sources of the CFTR protein in human and mice. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +The pulmonary ionocyte is a relatively newly identified, specific epithelial cell type found primarily in the pulmonary or respiratory system. Discovered through novel mapping techniques in 2018, these cells are surprisingly rare, making up less than 2% of the cells in the lung's airway, yet they play an essential role in the airway surface liquid and mucus regulation, a crucial factor in lung health. +The main responsibility of the pulmonary ionocyte pertains to the regulation and mobilization of chloride ions. They express a high level of CFTR (Cystic Fibrosis Transmembrane Conductance Regulator) gene, which encodes a protein channel across the membrane of cells that produce mucus, sweat, saliva, tears, and digestive enzymes. The activity of CFTR regulates the movement of chloride ions and fluids in and out of cells, which helps maintain a balance of fluid in the organs they are expressed in. If CFTR is dysfunctional, it can cause conditions such as cystic fibrosis, characterized by thick, sticky mucus that can clog the lungs and obstruct the pancreas, leading to respiratory and digestive issues. +The discovery of this cell type offers new doors to the treatment and further understanding of diseases like cystic fibrosis. Increased understanding of pulmonary ionocytes could contribute to the development of novel therapeutic approaches to manipulate the function of CFTR in the lungs and other organs affected by dysfunctional CFTR. + https://cellxgene.cziscience.com/cellguide/CL_0017000 pulmonary ionocyte @@ -88629,6 +90088,18 @@ plexiform layer using GABA. PMID:30069044 PMID:30069046 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +The pulmonary ionocyte is a relatively newly identified, specific epithelial cell type found primarily in the pulmonary or respiratory system. Discovered through novel mapping techniques in 2018, these cells are surprisingly rare, making up less than 2% of the cells in the lung's airway, yet they play an essential role in the airway surface liquid and mucus regulation, a crucial factor in lung health. +The main responsibility of the pulmonary ionocyte pertains to the regulation and mobilization of chloride ions. They express a high level of CFTR (Cystic Fibrosis Transmembrane Conductance Regulator) gene, which encodes a protein channel across the membrane of cells that produce mucus, sweat, saliva, tears, and digestive enzymes. The activity of CFTR regulates the movement of chloride ions and fluids in and out of cells, which helps maintain a balance of fluid in the organs they are expressed in. If CFTR is dysfunctional, it can cause conditions such as cystic fibrosis, characterized by thick, sticky mucus that can clog the lungs and obstruct the pancreas, leading to respiratory and digestive issues. +The discovery of this cell type offers new doors to the treatment and further understanding of diseases like cystic fibrosis. Increased understanding of pulmonary ionocytes could contribute to the development of novel therapeutic approaches to manipulate the function of CFTR in the lungs and other organs affected by dysfunctional CFTR. + DOI:10.1038/s41586-018-0393-7 + DOI:10.1146/annurev-pathol-042420-094031 + DOI:10.1172/JCI171268 + @@ -89236,6 +90707,7 @@ plexiform layer using GABA. + @@ -90178,6 +91650,12 @@ plexiform layer using GABA. Any goblet cell that is part of some lung epithelium. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Lung goblet cells are critical components of the respiratory tract, specifically found in the bronchial segments. They are secretory epithelial cells known for their signature "goblet" or cup-like shape. Their primary function is to produce and secrete mucus that aids in trapping airborne particles and pathogens, preventing them from reaching the delicate environment of the lung. As part of the lung's epithelial lining, they act as frontline defenders, maintaining lung health and function. +The lung goblet cells are densely packed with granules containing mucin glycoproteins, the primary component of mucus. As mucus is produced and secreted, it moves towards the lumen of the lungs where the cilia, hair-like structures of the neighboring ciliated epithelial cells, help to navigate it upwards and out of the respiratory tract. This coordinated action ensures the expulsion of unwanted particles and pathogens, effectively cleaning the respiratory tract. +Dysfunction or abnormal proliferation of lung goblet cells can result in pathological conditions such as chronic obstructive pulmonary disorder (COPD) and asthma, where excessive mucus production leads to airway obstruction. Furthermore, lung goblet cells respond to a variety of stimuli, including toxins, allergens, irritants, and infections, adjusting their mucus production accordingly. + https://cellxgene.cziscience.com/cellguide/CL_1000143 lung goblet cell @@ -90187,6 +91665,20 @@ plexiform layer using GABA. Any goblet cell that is part of some lung epithelium. FBC:Autogenerated + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Lung goblet cells are critical components of the respiratory tract, specifically found in the bronchial segments. They are secretory epithelial cells known for their signature "goblet" or cup-like shape. Their primary function is to produce and secrete mucus that aids in trapping airborne particles and pathogens, preventing them from reaching the delicate environment of the lung. As part of the lung's epithelial lining, they act as frontline defenders, maintaining lung health and function. +The lung goblet cells are densely packed with granules containing mucin glycoproteins, the primary component of mucus. As mucus is produced and secreted, it moves towards the lumen of the lungs where the cilia, hair-like structures of the neighboring ciliated epithelial cells, help to navigate it upwards and out of the respiratory tract. This coordinated action ensures the expulsion of unwanted particles and pathogens, effectively cleaning the respiratory tract. +Dysfunction or abnormal proliferation of lung goblet cells can result in pathological conditions such as chronic obstructive pulmonary disorder (COPD) and asthma, where excessive mucus production leads to airway obstruction. Furthermore, lung goblet cells respond to a variety of stimuli, including toxins, allergens, irritants, and infections, adjusting their mucus production accordingly. + DOI:10.1038/s41385-018-0039-y + DOI:10.1038/s41385-020-00370-7 + DOI:10.1159/000512268 + DOI:10.1513/AnnalsATS.201802-128AW + https://www.ncbi.nlm.nih.gov/books/NBK553208/ + @@ -90242,6 +91734,7 @@ plexiform layer using GABA. + @@ -90288,6 +91781,7 @@ plexiform layer using GABA. + @@ -90425,6 +91919,11 @@ plexiform layer using GABA. A neuroendocrine cell that is part of respiratory epithelium of the lung and is involved in the sensory detection of environmental stimuli, including hypoxia, nicotine and air pressure. Ultrastructurally, this cell type is characterized by the presence of cytoplasmic dense core granules, which are considered the storage sites of amine and peptide hormones. Lung neuroendocrine cells are innervated and appear as solitary cells or as clustered masses, localized at airway bifurcation sites, called neuroepithelial bodies that can release serotonin in response to hypoxia and interact with sensory nerve terminals. Lung neuroendocrine cells also function as reserve stem cells that repair the surrounding epithelium after injury. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Lung neuroendocrine cells, also commonly known as pulmonary neuroendocrine cells (PNECs), are predominantly located in the respiratory epithelium of the bronchial and bronchiolar airways in the lungs. These cells, characterised by their small size and granular appearance, have a distinctive morphology that sets them apart from other lung cells. They are considered part of the diffuse neuroendocrine system due to their scattered distribution through the epithelium and have been classified into solitary cells and clustered forms known as neuroepithelial bodies. +The primary function of PNECs is linked to regulation and maintenance of the lung environment. They are sensory in nature and can secrete various bioactive substances such as serotonin, calcitonin, calcitonin gene-related peptides, and bombesin-like peptides which modulate airway smooth muscle tone and influence gut motility. For example, they act as oxygen sensors in response to hypoxia and are responsible for releasing neuropeptides that can induce responses. Moreover, PNECs provide an afferent function as they are equipped with long microvilli that project into the lumen of the bronchus and react to changes in the chemical composition of the luminal content. + https://cellxgene.cziscience.com/cellguide/CL_1000223 pulmonary neuroendocrine cell PNEC @@ -90439,6 +91938,17 @@ plexiform layer using GABA. doi:10.3109/01902148209069653 doi:10.7554/eLife.78216 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Lung neuroendocrine cells, also commonly known as pulmonary neuroendocrine cells (PNECs), are predominantly located in the respiratory epithelium of the bronchial and bronchiolar airways in the lungs. These cells, characterised by their small size and granular appearance, have a distinctive morphology that sets them apart from other lung cells. They are considered part of the diffuse neuroendocrine system due to their scattered distribution through the epithelium and have been classified into solitary cells and clustered forms known as neuroepithelial bodies. +The primary function of PNECs is linked to regulation and maintenance of the lung environment. They are sensory in nature and can secrete various bioactive substances such as serotonin, calcitonin, calcitonin gene-related peptides, and bombesin-like peptides which modulate airway smooth muscle tone and influence gut motility. For example, they act as oxygen sensors in response to hypoxia and are responsible for releasing neuropeptides that can induce responses. Moreover, PNECs provide an afferent function as they are equipped with long microvilli that project into the lumen of the bronchus and react to changes in the chemical composition of the luminal content. + DOI:10.1016/bs.ctdb.2018.12.002 + DOI:10.1016/j.devcel.2020.09.024 + DOI:10.1242/dmm.046920 + @@ -90560,22 +92070,18 @@ plexiform layer using GABA. - + - + + + - - - - - - - Any ciliated cell that is part of some lung. + An epithelial cell that is part of the lung epithelium. This cell is characterised by the presence of cilia on its apical surface. @@ -90584,8 +92090,8 @@ plexiform layer using GABA. - Any ciliated cell that is part of some lung. - FBC:Autogenerated + An epithelial cell that is part of the lung epithelium. This cell is characterised by the presence of cilia on its apical surface. + PMID:27864314 @@ -90605,6 +92111,7 @@ plexiform layer using GABA. + @@ -92699,7 +94206,13 @@ plexiform layer using GABA. An enterocyte that is part of the epithelium of small intestine. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Enterocytes of the epithelium of the small intestine are specialized cells that reside in the lining of the small intestine, and are primarily responsible for the essential process of nutrient absorption. These cells are columnar epithelial cells with an apical surface lined with microvilli, a feature referred to as the 'brush border', to maximize the surface area available for absorption. +Enterocytes play a critical role in both the digestion and absorption of nutrients from food. Their extensive brush border contains enzymes that further assist in nutrient breakdown and transport proteins that transfer nutrients, such as glucose, amino acids, lipids, and vitamins, across the cell membrane. +The enterocytes of the small intestine also participate in the barrier function of the gut lining. Enterocytes are connected by tight junctions, which act as a primary defense line against pathogenic invasion by maintaining intestinal barrier integrity. Additionally, their cell surface is coated in glycocalyx and mucus which forms a defensive barrier preventing the penetration of harmful bacteria into the systemic circulation. FMA:263086 + https://cellxgene.cziscience.com/cellguide/CL_1000334 enterocyte of epithelium of small intestine @@ -92715,6 +94228,19 @@ plexiform layer using GABA. An enterocyte that is part of the epithelium of small intestine. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Enterocytes of the epithelium of the small intestine are specialized cells that reside in the lining of the small intestine, and are primarily responsible for the essential process of nutrient absorption. These cells are columnar epithelial cells with an apical surface lined with microvilli, a feature referred to as the 'brush border', to maximize the surface area available for absorption. +Enterocytes play a critical role in both the digestion and absorption of nutrients from food. Their extensive brush border contains enzymes that further assist in nutrient breakdown and transport proteins that transfer nutrients, such as glucose, amino acids, lipids, and vitamins, across the cell membrane. +The enterocytes of the small intestine also participate in the barrier function of the gut lining. Enterocytes are connected by tight junctions, which act as a primary defense line against pathogenic invasion by maintaining intestinal barrier integrity. Additionally, their cell surface is coated in glycocalyx and mucus which forms a defensive barrier preventing the penetration of harmful bacteria into the systemic circulation. + DOI:10.1038/nrgastro.2013.35 + DOI:10.1038/nri3738 + DOI:10.1084/jem.20191130 + DOI:10.3389/fphys.2021.699152/full + @@ -92882,7 +94408,12 @@ plexiform layer using GABA. An enterocyte that is part of the epithelium proper of ileum. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Enterocytes of the epithelium proper of the ileum, commonly known as ileal enterocytes, are specialized epithelial cells found lining the inner surface of the ileum, the final section of the small intestine in the human body. They play a pivotal role in nutrient absorption, digestive metabolic functions, and the maintenance of the host’s immune response. +Like enterocytes in other parts of the intestine, ileal enterocytes exhibit distinct characteristics specific to their function and role. They have microvilli on their apical surfaces to increase absorption and are important in the absorption of vitamins and the reabsorption of bile salts. These cells also produce enzymes that metabolize lipids and xenobiotics. FMA:263102 + https://cellxgene.cziscience.com/cellguide/CL_1000342 enterocyte of epithelium proper of ileum @@ -92892,6 +94423,17 @@ plexiform layer using GABA. An enterocyte that is part of the epithelium proper of ileum. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Enterocytes of the epithelium proper of the ileum, commonly known as ileal enterocytes, are specialized epithelial cells found lining the inner surface of the ileum, the final section of the small intestine in the human body. They play a pivotal role in nutrient absorption, digestive metabolic functions, and the maintenance of the host’s immune response. +Like enterocytes in other parts of the intestine, ileal enterocytes exhibit distinct characteristics specific to their function and role. They have microvilli on their apical surfaces to increase absorption and are important in the absorption of vitamins and the reabsorption of bile salts. These cells also produce enzymes that metabolize lipids and xenobiotics. + DOI:10.1038/nri3738 + DOI:10.1084/jem.20191130 + DOI:10.1111/j.1365-2249.2011.04523.x + @@ -93003,11 +94545,18 @@ plexiform layer using GABA. A columnar cell of the colon that is part of the colonic epithelium. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Enterocytes of the colon are specialized epithelial cells located in the lining of the colon, the largest part of the large intestine. These cells play a critical role in absorbing water, electrolytes, and certain vitamins from the food material passed on from the small intestine. With a unique structure of finger-like protrusions referred to as microvilli, the enterocytes increase their surface area for effective absorption. The colon is the last part of the digestive system, and as such, it is responsible for compacting undigested food materials and forming fecal matter. Enterocytes of the colon facilitate this process effectively through absorption of water. +Enterocytes are known for their high regeneration potential, replenishing every 4-5 days, enabling the healthy functioning of the colon. They originate from stem cells located in the crypt of the colon and differentiate into mature enterocytes as they migrate upwards towards the luminal surface. This constant turnover aids in maintaining the intestinal barrier, preventing the entry of detrimental substances into the systemic circulation. Their tight junctions with other epithelial cells provide a robust barrier against invasive pathogens. +Enterocytes of the colon are involved in the communication with the gut microbiota. These cells harbor enzymes necessary for the metabolism of short-chain fatty acids, which are the byproducts of the fermentation process by gut bacteria. Short-chain fatty acids serve as a major energy source for colonocytes and are important for maintaining colonic health. The dysfunction of enterocytes, therefore, could lead to disorders such as inflammatory bowel disease or colorectal cancer. FMA:263114 + https://cellxgene.cziscience.com/cellguide/CL_1000347 colonocyte + enterocyte of colon vacuolar absorptive cell of epithelium of colon - enterocyte of colon + colonocyte @@ -93021,6 +94570,20 @@ plexiform layer using GABA. A columnar cell of the colon that is part of the colonic epithelium. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Enterocytes of the colon are specialized epithelial cells located in the lining of the colon, the largest part of the large intestine. These cells play a critical role in absorbing water, electrolytes, and certain vitamins from the food material passed on from the small intestine. With a unique structure of finger-like protrusions referred to as microvilli, the enterocytes increase their surface area for effective absorption. The colon is the last part of the digestive system, and as such, it is responsible for compacting undigested food materials and forming fecal matter. Enterocytes of the colon facilitate this process effectively through absorption of water. +Enterocytes are known for their high regeneration potential, replenishing every 4-5 days, enabling the healthy functioning of the colon. They originate from stem cells located in the crypt of the colon and differentiate into mature enterocytes as they migrate upwards towards the luminal surface. This constant turnover aids in maintaining the intestinal barrier, preventing the entry of detrimental substances into the systemic circulation. Their tight junctions with other epithelial cells provide a robust barrier against invasive pathogens. +Enterocytes of the colon are involved in the communication with the gut microbiota. These cells harbor enzymes necessary for the metabolism of short-chain fatty acids, which are the byproducts of the fermentation process by gut bacteria. Short-chain fatty acids serve as a major energy source for colonocytes and are important for maintaining colonic health. The dysfunction of enterocytes, therefore, could lead to disorders such as inflammatory bowel disease or colorectal cancer. + DOI:10.1007/s11894-010-0130-3 + DOI:10.1038/nrgastro.2013.35 + DOI:10.1038/nri3738 + DOI:10.1084/jem.20191130 + DOI:10.3389/fimmu.2019.00277 + @@ -94838,9 +96401,15 @@ plexiform layer using GABA. A blood vessel endothelial cell that is part of an arterial endothelium. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Endothelial cells of the artery, also referred to as arterial endothelial cells, form an integral part of the arterial system. They form a single layer, known as the endothelium, lining the interior surface of arteries, and are able to respond to the high-pressure and flow conditions present in arteries. The primary role of these cells is to provide a barrier between the vessel wall and the blood, exhibiting selective permeability to regulate the movement of liquids, gases, and blood-borne substances across the vascular wall. +Arterial endothelial cells significantly contribute to maintaining vascular homeostasis. They are at the forefront of sensations and responses to mechanical stimuli, like shear stress and blood pressure changes. An additional key function pertains to the production of nitric oxide, which helps to regulate vascular tone and blood pressure, prevents platelet aggregation, limits leukocyte adhesion to the endothelium, and inhibits smooth muscle cell proliferation. These varied but connected functions help to preclude the development of atherosclerosis, ensuring normal circulation and arterial health. +Moreover, these cells play a pivotal role in inflammation and coagulation processes. During inflammatory events, they express various adhesion molecules, aiding in leukocyte recruitment and rolling onto the vessel walls for immune response. They also produce anticoagulant and procoagulant substances, involved in blood clotting and clot dissolution, respectively. Dysregulation of the usual functions of arterial endothelial cells can result in serious pathophysiological conditions, such as atherosclerosis, hypertension, and other cardiovascular diseases. BTO:0004758 FMA:67761 KUPO:0001095 + https://cellxgene.cziscience.com/cellguide/CL_1000413 arterial endothelial cell @@ -94852,6 +96421,20 @@ plexiform layer using GABA. A blood vessel endothelial cell that is part of an arterial endothelium. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Endothelial cells of the artery, also referred to as arterial endothelial cells, form an integral part of the arterial system. They form a single layer, known as the endothelium, lining the interior surface of arteries, and are able to respond to the high-pressure and flow conditions present in arteries. The primary role of these cells is to provide a barrier between the vessel wall and the blood, exhibiting selective permeability to regulate the movement of liquids, gases, and blood-borne substances across the vascular wall. +Arterial endothelial cells significantly contribute to maintaining vascular homeostasis. They are at the forefront of sensations and responses to mechanical stimuli, like shear stress and blood pressure changes. An additional key function pertains to the production of nitric oxide, which helps to regulate vascular tone and blood pressure, prevents platelet aggregation, limits leukocyte adhesion to the endothelium, and inhibits smooth muscle cell proliferation. These varied but connected functions help to preclude the development of atherosclerosis, ensuring normal circulation and arterial health. +Moreover, these cells play a pivotal role in inflammation and coagulation processes. During inflammatory events, they express various adhesion molecules, aiding in leukocyte recruitment and rolling onto the vessel walls for immune response. They also produce anticoagulant and procoagulant substances, involved in blood clotting and clot dissolution, respectively. Dysregulation of the usual functions of arterial endothelial cells can result in serious pathophysiological conditions, such as atherosclerosis, hypertension, and other cardiovascular diseases. + DOI:10.1007/s00441-008-0706-5 + DOI:10.1007/s10456-021-09785-7 + DOI:10.1016/j.ccm.2021.08.005 + DOI:10.1016/j.jvs.2004.03.043 + DOI:10.1177/153857440303700107 + @@ -95537,7 +97120,13 @@ plexiform layer using GABA. An epithelial cell that is part of the lacrimal sac. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Epithelial cells of the lacrimal sac play a significant role in the physiology of tear drainage, acting as an integral part of the lacrimal drainage system. The lacrimal sac is part of the nasolacrimal duct system, a conduit which connects the eye to the nasal cavity, and is lined by multilayered, non-keratinizing, squamous epithelial cells. +The epithelial cells of the lacrimal sac are specialized for the purpose of maintaining a moist environment and protecting the surface of the eye. They form a barrier that traps and removes potential contaminants from the tear film during the drainage process. These cells also actively contribute to tear turnover by expediting the drainage of excess tears. Dysfunctional epithelial cells of the lacrimal sac can lead to dacryocystitis, a condition characterized by inflammation of the lacrimal sac. +Epithelial cells of the lacrimal sac also perform various other tasks which ensure the overall health of the eye. They are involved in the regulation of immune responses within the lacrimal apparatus and may have a possible role in host-microbiome interactions. Thus, epithelial cells of the lacrimal sac play a multifaceted role in tear drainage and ocular surface defence, directly translating to eye health and vision quality. FMA:70560 + https://cellxgene.cziscience.com/cellguide/CL_1000436 epithelial cell of lacrimal sac @@ -95547,6 +97136,20 @@ plexiform layer using GABA. An epithelial cell that is part of the lacrimal sac. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Epithelial cells of the lacrimal sac play a significant role in the physiology of tear drainage, acting as an integral part of the lacrimal drainage system. The lacrimal sac is part of the nasolacrimal duct system, a conduit which connects the eye to the nasal cavity, and is lined by multilayered, non-keratinizing, squamous epithelial cells. +The epithelial cells of the lacrimal sac are specialized for the purpose of maintaining a moist environment and protecting the surface of the eye. They form a barrier that traps and removes potential contaminants from the tear film during the drainage process. These cells also actively contribute to tear turnover by expediting the drainage of excess tears. Dysfunctional epithelial cells of the lacrimal sac can lead to dacryocystitis, a condition characterized by inflammation of the lacrimal sac. +Epithelial cells of the lacrimal sac also perform various other tasks which ensure the overall health of the eye. They are involved in the regulation of immune responses within the lacrimal apparatus and may have a possible role in host-microbiome interactions. Thus, epithelial cells of the lacrimal sac play a multifaceted role in tear drainage and ocular surface defence, directly translating to eye health and vision quality. + DOI:10.1007/s004290050160 + DOI:10.1111/j.1442-9071.2012.02818.x + DOI:10.1167/tvst.8.4.32 + DOI:10.2147/OPTH.S26048 + DOI:10.3389/fimmu.2022.918619 + @@ -96020,6 +97623,7 @@ plexiform layer using GABA. + @@ -96104,8 +97708,14 @@ plexiform layer using GABA. An epithelial cell that is part of the collecting duct of renal tubule. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Kidney collecting duct epithelial cells are a specialized type of cells that form an integral part of the renal system. Located in the collecting duct system of the kidneys, these cells are responsible for one of the final steps in the process of urine formation, and they are instrumental in the fine tuning of the volume and composition of urine by reabsorbing water and certain solutes back into the bloodstream. +These cells express specific channels and carriers that actively and passively transport ions and water. They also have channels on their membranes, such as sodium channels and potassium channels, involved in reabsorbing or secreting these electrolytes depending upon the body's needs. The function of renal collecting duct epithelial cells can be regulated by a variety of hormones, including vasopressin (antidiuretic hormone), which can modulate the ion channels and carriers and hence indirectly influence body fluid homeostasis. +Aside from their function in ion and water balance, kidney collecting duct epithelial cells also aid in maintaining the body's acid-base balance. They have specialized functionality to secret hydrogen ions into the tubular lumen, which contributes to acid excretion. Any dysfunction may have serious implications and lead to various renal or systemic diseases, exemplifying the importance of these cells in maintaining overall body homeostasis. FMA:70982 KUPO:0001059 + https://cellxgene.cziscience.com/cellguide/CL_1000454 epithelial cell of renal collecting tubule @@ -96130,6 +97740,19 @@ plexiform layer using GABA. An epithelial cell that is part of the collecting duct of renal tubule. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Kidney collecting duct epithelial cells are a specialized type of cells that form an integral part of the renal system. Located in the collecting duct system of the kidneys, these cells are responsible for one of the final steps in the process of urine formation, and they are instrumental in the fine tuning of the volume and composition of urine by reabsorbing water and certain solutes back into the bloodstream. +These cells express specific channels and carriers that actively and passively transport ions and water. They also have channels on their membranes, such as sodium channels and potassium channels, involved in reabsorbing or secreting these electrolytes depending upon the body's needs. The function of renal collecting duct epithelial cells can be regulated by a variety of hormones, including vasopressin (antidiuretic hormone), which can modulate the ion channels and carriers and hence indirectly influence body fluid homeostasis. +Aside from their function in ion and water balance, kidney collecting duct epithelial cells also aid in maintaining the body's acid-base balance. They have specialized functionality to secret hydrogen ions into the tubular lumen, which contributes to acid excretion. Any dysfunction may have serious implications and lead to various renal or systemic diseases, exemplifying the importance of these cells in maintaining overall body homeostasis. + DOI:10.1016/j.ajpath.2014.01.014 + DOI:10.1016/j.semnephrol.2019.04.005 + DOI:10.2215/CJN.05760513 + DOI:10.2215/CJN.08880914 + @@ -96988,8 +98611,14 @@ plexiform layer using GABA. An epithelial cell that is part of the bile duct. Cholangiocytes contribute to bile secretion via net release of bicarbonate and water. They are cuboidal epithelium in the small interlobular bile ducts, but become columnar and mucus secreting in larger bile ducts approaching the porta hepatis and the extrahepatic ducts. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Cholangiocytes, also known as biliary epithelial cells, are specialized epithelial cells that line the biliary tract, which constitutes the gall bladder and bile ducts inside the liver. Crucial to the maintenance of the liver's health and function, cholangiocytes have a key role in the modification and secretion of bile, a fluid produced by hepatocytes that is essential to digestion and the absorption of fats and vitamins. +Cholangiocytes accomplish their primary function through the expression of a variety of transport proteins located on their apical and basolateral membranes, which propel bile acids and other contents of the bile into the biliary lumen. The hepatic bile, once secreted by the hepatocytes, is further modified by cholangiocytes via secretion and absorption processes. These processes help in the regulation of bile volume and composition, which is fundamental in ensuring the efficient digestion of dietary fats and fat-soluble vitamins and the excretion of cholesterol. +In addition to their role in bile modification, cholangiocytes also perform several other integral functions. For instance, these cells express Toll-like receptors (TLRs) which allow cholangiocytes to initiate an immune response against pathogens in the biliary lumen. When functioning normally, these cells contribute to biliary integrity, hepatic architecture, and overall hepatic physiology. However, when they become pathological, they are involved in the progression of liver diseases, such as primary biliary cirrhosis and cholangiocarcinoma – the malignancy of the biliary tract. FMA:86481 ZFA:0009397 + https://cellxgene.cziscience.com/cellguide/CL_1000488 epithelial cell of bile duct cholangiocyte @@ -97008,6 +98637,20 @@ plexiform layer using GABA. PMID:16550043 PMID:18356246 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Cholangiocytes, also known as biliary epithelial cells, are specialized epithelial cells that line the biliary tract, which constitutes the gall bladder and bile ducts inside the liver. Crucial to the maintenance of the liver's health and function, cholangiocytes have a key role in the modification and secretion of bile, a fluid produced by hepatocytes that is essential to digestion and the absorption of fats and vitamins. +Cholangiocytes accomplish their primary function through the expression of a variety of transport proteins located on their apical and basolateral membranes, which propel bile acids and other contents of the bile into the biliary lumen. The hepatic bile, once secreted by the hepatocytes, is further modified by cholangiocytes via secretion and absorption processes. These processes help in the regulation of bile volume and composition, which is fundamental in ensuring the efficient digestion of dietary fats and fat-soluble vitamins and the excretion of cholesterol. +In addition to their role in bile modification, cholangiocytes also perform several other integral functions. For instance, these cells express Toll-like receptors (TLRs) which allow cholangiocytes to initiate an immune response against pathogens in the biliary lumen. When functioning normally, these cells contribute to biliary integrity, hepatic architecture, and overall hepatic physiology. However, when they become pathological, they are involved in the progression of liver diseases, such as primary biliary cirrhosis and cholangiocarcinoma – the malignancy of the biliary tract. + DOI:10.1016/j.jcmgh.2015.05.005 + DOI:10.1016/j.jhep.2012.10.011 + DOI:10.1038/s41575-019-0125-y + DOI:10.1152/ajpgi.00227.2012 + DOI:10.5009/gnl16033 + @@ -97123,7 +98766,14 @@ plexiform layer using GABA. A mesothelial cell that is part of the pleura. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Mesothelial cells of the pleura form a significant part of the pleural membrane, a thin, double-layered serous membrane that lines the thoracic cavity and encompasses the lungs. These specialized cells contribute to the pleura's key function of producing a lubricating serous fluid, which reduces friction between the lung's outer surface (visceral pleura) and the inner lining of the thoracic cavity (parietal pleura) during respiration. +The cellular structure of mesothelial cells, characterized by microvilli on their surface, aids in the secretion and absorption of the pleural fluid, effectively supporting the smooth expansion and contraction of the lungs. Dysregulation in mesothelial cells can lead to pathologies, including pleural effusion and malignant mesothelioma. +Mesothelial cells of the pleura display unique immunologic properties. They act as a first line of defense against infection because they are able to recognize pathogens and respond by secreting various cytokines and chemokines. Additionally, these cells are directly involved in the translocation of immune cells into the pleural cavity during inflammatory response, thereby playing an active role in the immune response within the pleural environment. +In the event of pleural injury, these cells are also involved in the mesothelial-mesenchymal transition, a process that allows mesothelial cells to transdifferentiate into myofibroblasts and promote tissue repair. FMA:86737 + https://cellxgene.cziscience.com/cellguide/CL_1000491 pleural mesothelial cell mesothelial cell of pleura @@ -97134,6 +98784,20 @@ plexiform layer using GABA. A mesothelial cell that is part of the pleura. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Mesothelial cells of the pleura form a significant part of the pleural membrane, a thin, double-layered serous membrane that lines the thoracic cavity and encompasses the lungs. These specialized cells contribute to the pleura's key function of producing a lubricating serous fluid, which reduces friction between the lung's outer surface (visceral pleura) and the inner lining of the thoracic cavity (parietal pleura) during respiration. +The cellular structure of mesothelial cells, characterized by microvilli on their surface, aids in the secretion and absorption of the pleural fluid, effectively supporting the smooth expansion and contraction of the lungs. Dysregulation in mesothelial cells can lead to pathologies, including pleural effusion and malignant mesothelioma. +Mesothelial cells of the pleura display unique immunologic properties. They act as a first line of defense against infection because they are able to recognize pathogens and respond by secreting various cytokines and chemokines. Additionally, these cells are directly involved in the translocation of immune cells into the pleural cavity during inflammatory response, thereby playing an active role in the immune response within the pleural environment. +In the event of pleural injury, these cells are also involved in the mesothelial-mesenchymal transition, a process that allows mesothelial cells to transdifferentiate into myofibroblasts and promote tissue repair. + DOI:10.1016/j.ccm.2021.08.005 + DOI:10.1016/j.coi.2020.04.005 + DOI:10.1152/ajplung.90587.2008 + DOI:10.3389/fphys.2014.00284 + @@ -97200,7 +98864,13 @@ plexiform layer using GABA. A mesothelial cell that is part of the visceral pleura. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Mesothelial cells of visceral pleura are specialized epithelial cells that line the inner layer of the pleura, the membrane that envelops the lungs. Positioned adjacent to the lung tissue, these cells form a protective barrier and contribute to the structure of the visceral pleura. They are characterized by their cuboidal to squamous epithelial shape and the presence of microvilli on their surface, a feature aiding in fluid and solute exchange between the pleura and the lungs. +The primary function of mesothelial cells of visceral pleura is to secrete a lubricating serous fluid to facilitate smooth, frictionless lung movement within the thoracic cavity during respiration. This helps in the prevention of trauma or damage stemming from the constant rubbing of the lung tissue against the chest wall, hence playing a pivotal role in maintaining respiratory function. Besides fluid secretion, these cells have an essential role in the transportation of fluids and particles across the pleura, as well as in inflammation, wound healing, and tissue repair processes within the pleura. +Mesothelial cells of visceral pleura are notably implicated in the development of pleural diseases such as pleural effusion and pleural mesothelioma, a rare and aggressive form of cancer primarily linked with exposure to asbestos. Alterations, such as hyperplasia or metaplasia, may occur in these mesothelial cells under pathological conditions. FMA:86739 + https://cellxgene.cziscience.com/cellguide/CL_1000493 mesothelial cell of visceral pleura @@ -97211,6 +98881,20 @@ plexiform layer using GABA. A mesothelial cell that is part of the visceral pleura. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Mesothelial cells of visceral pleura are specialized epithelial cells that line the inner layer of the pleura, the membrane that envelops the lungs. Positioned adjacent to the lung tissue, these cells form a protective barrier and contribute to the structure of the visceral pleura. They are characterized by their cuboidal to squamous epithelial shape and the presence of microvilli on their surface, a feature aiding in fluid and solute exchange between the pleura and the lungs. +The primary function of mesothelial cells of visceral pleura is to secrete a lubricating serous fluid to facilitate smooth, frictionless lung movement within the thoracic cavity during respiration. This helps in the prevention of trauma or damage stemming from the constant rubbing of the lung tissue against the chest wall, hence playing a pivotal role in maintaining respiratory function. Besides fluid secretion, these cells have an essential role in the transportation of fluids and particles across the pleura, as well as in inflammation, wound healing, and tissue repair processes within the pleura. +Mesothelial cells of visceral pleura are notably implicated in the development of pleural diseases such as pleural effusion and pleural mesothelioma, a rare and aggressive form of cancer primarily linked with exposure to asbestos. Alterations, such as hyperplasia or metaplasia, may occur in these mesothelial cells under pathological conditions. + DOI:10.1016/S1357-2725(03)00242-5 + DOI:10.1152/physrev.00026.2003 + DOI:10.1371/journal.pone.0276978 + DOI:10.3389/fphys.2014.00221 + DOI:10.3390/jdb7020007 + @@ -97312,7 +98996,7 @@ plexiform layer using GABA. - + @@ -97738,7 +99422,7 @@ plexiform layer using GABA. - + @@ -97772,7 +99456,7 @@ plexiform layer using GABA. - + @@ -99411,11 +101095,31 @@ plexiform layer using GABA. An endothelial cell that is part of the glomerular capillary of the kidney. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +The glomerular capillary endothelial cell comprises an intrinsic component of the glomerulus in the kidney. Glomeruli contain a network of capillaries where the first step of blood filtration takes place, with glomerular capillary endothelial cells acting as an integral part of this process. Unlike regular endothelial cells that line the vasculature, unique fenestrations (openings) characterize these cells, allowing for enhanced permeability and filtration efficacy. +Together with the glomerular basement membrane and podocytes, the glomerular endothelial cells form the glomerular filtration barrier, which is responsible for blood filtration and therefore critical for removal of waste products, such as urea and creatinine, and excess substances, such as glucose and ions, from the bloodstream. The glomerular capillary endothelial cells' fenestrations permit the free flow of a variety of particles, barring larger, negatively charged proteins like serum albumin, enabling the formation of an ultrafiltrate. This ultrafiltrate is the primitive form of urine, which then passes through the proximal tubule for further processing and ultimately helps maintain systemic fluid and electrolyte balance. +Moreover, the glomerular capillary endothelial cells are also believed to play a crucial role in renal pathologies. Any compromise to their structural integrity or functional performance can lead to kidney diseases, including but not limited to, diabetic nephropathy and glomerulonephritis. For instance, in diabetes, persistent hyperglycemia can injure these cells, leading to a compromised glomerular filtration barrier and proteinuria, indicating the loss of proteins in the urine. KUPO:0001037 + https://cellxgene.cziscience.com/cellguide/CL_1001005 glomerular capillary endothelial cell + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +The glomerular capillary endothelial cell comprises an intrinsic component of the glomerulus in the kidney. Glomeruli contain a network of capillaries where the first step of blood filtration takes place, with glomerular capillary endothelial cells acting as an integral part of this process. Unlike regular endothelial cells that line the vasculature, unique fenestrations (openings) characterize these cells, allowing for enhanced permeability and filtration efficacy. +Together with the glomerular basement membrane and podocytes, the glomerular endothelial cells form the glomerular filtration barrier, which is responsible for blood filtration and therefore critical for removal of waste products, such as urea and creatinine, and excess substances, such as glucose and ions, from the bloodstream. The glomerular capillary endothelial cells' fenestrations permit the free flow of a variety of particles, barring larger, negatively charged proteins like serum albumin, enabling the formation of an ultrafiltrate. This ultrafiltrate is the primitive form of urine, which then passes through the proximal tubule for further processing and ultimately helps maintain systemic fluid and electrolyte balance. +Moreover, the glomerular capillary endothelial cells are also believed to play a crucial role in renal pathologies. Any compromise to their structural integrity or functional performance can lead to kidney diseases, including but not limited to, diabetic nephropathy and glomerulonephritis. For instance, in diabetes, persistent hyperglycemia can injure these cells, leading to a compromised glomerular filtration barrier and proteinuria, indicating the loss of proteins in the urine. + DOI:10.1016/j.biocel.2010.05.015 + DOI:10.1016/j.yexcr.2012.02.032 + DOI:10.1111/j.1523-1755.2005.00260.x + DOI:10.2337/diacare.28.1.164 + DOI:10.3389/fphys.2021.689083 + @@ -99802,7 +101506,12 @@ plexiform layer using GABA. An endothelial cell that lines the interior surface of the afferent arteriole and maintains vascular tone. This cell responds to changing ion concentrations and blood pressure by releasing vasoactive substances, in order to regulate blood flow into the glomeruli, which is essential for glomerular filtration. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Kidney afferent arteriole endothelial cells are a specialized type of cell located within the kidneys, forming the inner lining of the afferent arterioles, which are responsible for delivering blood to the glomeruli - capillary networks responsible for filtration - from where the process of urine formation begins in the nephrons. +The endothelial cells in the kidney afferent arterioles have a key function in regulating the blood flow and filtration. They have autocrine and paracrine signaling capabilities, meaning they can signal to themselves and other nearby cells. They produce nitric oxide, prostacyclin, and endothelin, which are powerful vasodilators and vasoconstrictors that regulate renal blood flow. These cells also engage in the mitigation of kidney injury and inflammation by promoting repair and regeneration, demonstrating the multifaceted roles these cells play in maintaining renal health. KUPO:0001039 + https://cellxgene.cziscience.com/cellguide/CL_1001096 kidney afferent arteriole endothelial cell @@ -99816,6 +101525,16 @@ plexiform layer using GABA. PMID:24066938 PMID:25834230 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Kidney afferent arteriole endothelial cells are a specialized type of cell located within the kidneys, forming the inner lining of the afferent arterioles, which are responsible for delivering blood to the glomeruli - capillary networks responsible for filtration - from where the process of urine formation begins in the nephrons. +The endothelial cells in the kidney afferent arterioles have a key function in regulating the blood flow and filtration. They have autocrine and paracrine signaling capabilities, meaning they can signal to themselves and other nearby cells. They produce nitric oxide, prostacyclin, and endothelin, which are powerful vasodilators and vasoconstrictors that regulate renal blood flow. These cells also engage in the mitigation of kidney injury and inflammation by promoting repair and regeneration, demonstrating the multifaceted roles these cells play in maintaining renal health. + DOI:10.1046/j.0001-6772.2003.01205.x + DOI:10.1093/ndt/gfl308 + @@ -99870,7 +101589,13 @@ plexiform layer using GABA. Any endothelial cell that is part of some renal efferent arteriole. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Kidney efferent arteriole endothelial cells constitute a vital component of the kidney's microvascular system. They are unique endothelial cells found lining the walls of efferent arterioles, which transport blood away from the glomeruli in the kidney. +The primary responsibilities of the kidney efferent arteriole endothelial cells involve controling renal blood flow, regulating glomerular filtration rate (GFR), and managing perfusion pressure. They do this by contracting and relaxing, effectively narrowing and widening the arteriole's lumen thereby controling the volume and rate of blood flow to the peritubular capillaries and creating the pressure gradient necessary for filtration in the glomerulus. +Furthermore, kidney efferent arteriole endothelial cells show a high degree of plasticity in response to pathophysiological stimuli and can undergo structural and functional changes based on local needs. In conditions like hypertension and diabetes, these cells can experience hypertrophy and endothelial dysfunction, contributing to the progression of renal disease. KUPO:0001042 + https://cellxgene.cziscience.com/cellguide/CL_1001099 kidney efferent arteriole endothelial cell @@ -99881,6 +101606,19 @@ plexiform layer using GABA. Any endothelial cell that is part of some renal efferent arteriole. FBC:Autogenerated + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Kidney efferent arteriole endothelial cells constitute a vital component of the kidney's microvascular system. They are unique endothelial cells found lining the walls of efferent arterioles, which transport blood away from the glomeruli in the kidney. +The primary responsibilities of the kidney efferent arteriole endothelial cells involve controling renal blood flow, regulating glomerular filtration rate (GFR), and managing perfusion pressure. They do this by contracting and relaxing, effectively narrowing and widening the arteriole's lumen thereby controling the volume and rate of blood flow to the peritubular capillaries and creating the pressure gradient necessary for filtration in the glomerulus. +Furthermore, kidney efferent arteriole endothelial cells show a high degree of plasticity in response to pathophysiological stimuli and can undergo structural and functional changes based on local needs. In conditions like hypertension and diabetes, these cells can experience hypertrophy and endothelial dysfunction, contributing to the progression of renal disease. + DOI:10.1016/j.semcdb.2014.08.002 + DOI:10.1016/j.semnephrol.2015.01.010 + DOI:10.1038/s41581-021-00411-9 + DOI:10.1681/ASN.2019111179 + @@ -100281,7 +102019,14 @@ plexiform layer using GABA. A cell that is part of some vasa recta ascending limb. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +The vasa recta ascending limb cells are specialized epithelial cells that are part of the vasa recta in the kidney, a crucial component of the renal medulla that functions as a counter-current exchanger to maintain the concentration gradient required for water reabsorption. These particular cells are located in the ascending limb of the vasa recta, which takes blood flow from the medulla back to the cortex. +The primary function of vasa recta ascending limb cells is to preserve the renal medulla's hypertonicity, necessary for the kidney's urine concentration mechanism. Unlike the vasa recta descending limb cells, the venous-like epithelial cells of the ascending vasa recta are highly fenestrated and lack pericyte coverage, which facilitates water reuptake. +As the blood flows through the ascending limb, it loses solutes and gains water, which is driven by the high solute concentration in the surrounding interstitium. This process acts in concert with cellular action in the descending limb and contributions from the so-called Loop of Henle, which helps with water and sodium chloride retrieval from the urine. +In the context of normal physiological processes, the function of the vasa recta ascending limb cells is essential in maintaining the body's overall fluid balance, electrolyte concentration, and systemic blood pressure. Any dysfunction in these cells may lead to impaired urine concentration or dilution capability of the kidney, potentially resulting in conditions like diabetes insipidus or hyponatremia. KUPO:0001074 + https://cellxgene.cziscience.com/cellguide/CL_1001131 It is known in some mammalian species that this cell may express PV-1, a component of the fenestral diaphragm. @@ -100293,6 +102038,21 @@ plexiform layer using GABA. true + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +The vasa recta ascending limb cells are specialized epithelial cells that are part of the vasa recta in the kidney, a crucial component of the renal medulla that functions as a counter-current exchanger to maintain the concentration gradient required for water reabsorption. These particular cells are located in the ascending limb of the vasa recta, which takes blood flow from the medulla back to the cortex. +The primary function of vasa recta ascending limb cells is to preserve the renal medulla's hypertonicity, necessary for the kidney's urine concentration mechanism. Unlike the vasa recta descending limb cells, the venous-like epithelial cells of the ascending vasa recta are highly fenestrated and lack pericyte coverage, which facilitates water reuptake. +As the blood flows through the ascending limb, it loses solutes and gains water, which is driven by the high solute concentration in the surrounding interstitium. This process acts in concert with cellular action in the descending limb and contributions from the so-called Loop of Henle, which helps with water and sodium chloride retrieval from the urine. +In the context of normal physiological processes, the function of the vasa recta ascending limb cells is essential in maintaining the body's overall fluid balance, electrolyte concentration, and systemic blood pressure. Any dysfunction in these cells may lead to impaired urine concentration or dilution capability of the kidney, potentially resulting in conditions like diabetes insipidus or hyponatremia. + DOI:10.1016/B978-0-323-35515-5.00009-9 + DOI:10.1053/j.ajkd.2005.01.008 + DOI:10.1081/jdi-100101958 + DOI:10.1111/apha.12026 + DOI:10.1152/ajpregu.00657.2002 + @@ -100843,7 +102603,13 @@ plexiform layer using GABA. A cell that is part of some vasa recta descending limb. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Vasa recta descending limb cells are specialized epithelial cells found in the vasa recta, a network of blood vessels in the renal medulla. These cells line the interior surface of the descending limb of the vasa recta and play a crucial role in the filtering and regulation of substances within the blood. +In contrast to vasa recta ascending limb cells, the arterial-like epithelial cells of the descending vasa recta are non-fenestrated and covered by a pericyte layer that regulates the medullary blood flow. They help keeping the body’s fluid and electrolyte balance in check through a process known as countercurrent exchange system, in which the cells of the descending limb are permeable to water but relatively impermeable to solutes, such as sodium and urea. As the blood descends into the medulla along its descending limb, water passively diffuses out of the vasa recta, concentrating the blood in solutes. +In addition to their central role in water and solute exchange, these cells contribute to maintaining the medullary osmotic gradient, a critical function to concentrate urine. The osmotic gradient is created by the counterflow of water and solutes between the descending and ascending limbs of the vasa recta and the adjacent Loop of Henle. The selective permeability of the descending limb cells allows them to maintain this gradient, which in turn helps to conserve water, a vital role in the overall function of the renal system. Thus, vasa recta descending limb cells have a significant function in renal physiology, particularly in osmoregulation and fluid balance. KUPO:0001071 + https://cellxgene.cziscience.com/cellguide/CL_1001285 It is known in some mammalian species that this cell may express the urea transporter B. @@ -100855,6 +102621,19 @@ plexiform layer using GABA. true + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Vasa recta descending limb cells are specialized epithelial cells found in the vasa recta, a network of blood vessels in the renal medulla. These cells line the interior surface of the descending limb of the vasa recta and play a crucial role in the filtering and regulation of substances within the blood. +In contrast to vasa recta ascending limb cells, the arterial-like epithelial cells of the descending vasa recta are non-fenestrated and covered by a pericyte layer that regulates the medullary blood flow. They help keeping the body’s fluid and electrolyte balance in check through a process known as countercurrent exchange system, in which the cells of the descending limb are permeable to water but relatively impermeable to solutes, such as sodium and urea. As the blood descends into the medulla along its descending limb, water passively diffuses out of the vasa recta, concentrating the blood in solutes. +In addition to their central role in water and solute exchange, these cells contribute to maintaining the medullary osmotic gradient, a critical function to concentrate urine. The osmotic gradient is created by the counterflow of water and solutes between the descending and ascending limbs of the vasa recta and the adjacent Loop of Henle. The selective permeability of the descending limb cells allows them to maintain this gradient, which in turn helps to conserve water, a vital role in the overall function of the renal system. Thus, vasa recta descending limb cells have a significant function in renal physiology, particularly in osmoregulation and fluid balance. + DOI:10.1053/j.ajkd.2005.01.008 + DOI:10.1081/jdi-100101958 + DOI:10.1111/apha.12026#apha12026-bib-0039 + DOI:10.1152/ajpregu.00657.2002 + @@ -101164,7 +102943,13 @@ plexiform layer using GABA. Any renal principal cell that is part of some collecting duct of renal tubule. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +The kidney collecting duct principal cell is a highly specialized type of cell found in the late distal convoluted tubule and collecting duct of the kidney's nephron. Principal cells are located at the final segments of the renal tubules, where they play a pivotal role in key homeostatic processes. +One of their fundamental functions of kidney collecting duct principal cells is the regulation of water reabsorption, which is mediated by aquaporins (water channel proteins). Antidiuretic hormones, such as vasopressin, can stimulate the redistribution of these water channels from an intracellular pools to the apical plasma membrane of the principal cell; translocation of aquaporin (specifically, AQP2) is associated with an increase of osmotic water permeability. The water reabsorption affects the concentration of the final urine; these cells are therefore directly involved in the maintenance of the body's fluid balance. +Kidney collecting duct principal cells also participate in sodium and potassium ions regulation. They reabsorb sodium ions from the tubular fluid back into the bloodstream, a process facilitated by the action of aldosterone, a hormone released by the adrenal glands. Similarly, the principal cells secrete potassium ions into the tubular fluid in response to aldosterone, contributing to the regulation of potassium levels in the body. Impaired function of cells can lead to various renal diseases and disorders, highlighting the vital role of kidney collecting duct principal cells in the body's homeostatic processes. KUPO:0001128 + https://cellxgene.cziscience.com/cellguide/CL_1001431 kidney collecting duct principal cell @@ -101181,6 +102966,19 @@ plexiform layer using GABA. Any renal principal cell that is part of some collecting duct of renal tubule. FBC:Autogenerated + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +The kidney collecting duct principal cell is a highly specialized type of cell found in the late distal convoluted tubule and collecting duct of the kidney's nephron. Principal cells are located at the final segments of the renal tubules, where they play a pivotal role in key homeostatic processes. +One of their fundamental functions of kidney collecting duct principal cells is the regulation of water reabsorption, which is mediated by aquaporins (water channel proteins). Antidiuretic hormones, such as vasopressin, can stimulate the redistribution of these water channels from an intracellular pools to the apical plasma membrane of the principal cell; translocation of aquaporin (specifically, AQP2) is associated with an increase of osmotic water permeability. The water reabsorption affects the concentration of the final urine; these cells are therefore directly involved in the maintenance of the body's fluid balance. +Kidney collecting duct principal cells also participate in sodium and potassium ions regulation. They reabsorb sodium ions from the tubular fluid back into the bloodstream, a process facilitated by the action of aldosterone, a hormone released by the adrenal glands. Similarly, the principal cells secrete potassium ions into the tubular fluid in response to aldosterone, contributing to the regulation of potassium levels in the body. Impaired function of cells can lead to various renal diseases and disorders, highlighting the vital role of kidney collecting duct principal cells in the body's homeostatic processes. + DOI:10.1007/s11906-015-0538-0 + DOI:10.1016/B978-0-12-386456-7.05402-2 + DOI:10.1016/j.biocel.2022.106261 + DOI:10.1073/pnas.1710964114 + @@ -102993,6 +104791,7 @@ plexiform layer using GABA. + @@ -103043,7 +104842,13 @@ plexiform layer using GABA. Glandular cell of seminal vesicle epithelium. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Seminal vesicle glandular cells belong to a specialized group of epithelial cells that form the internal lining of the seminal vesicles, a pair of male reproductive organs. These cells are located within the complex tubuloalveolar glands that make up the seminal vesicles and are known for their unique pseudostratified columnar epithelium structure. +The primary function of these cells is the secretion of a variety of substances that ultimately constitute around 70% of the fluid volume of semen. Seminal cells produce a high-fructose fluid that serves as an energy source for the spermatozoa and promotes their motility. They also secrete other essential substances like proteins, enzymes, vitamin C, prostaglandins, and various other compounds. Collectively, these substances help in the nourishment, protection, and transportation of the spermatozoa throughout the male reproductive system and during the ejaculation process. +Secondary to the production of seminal fluid, the seminal vesicle glandular cells also play a role in the contraction of the seminal vesicles during ejaculation. The contraction of these glands, induced by sympathetic nerves, ensures the efficient propulsion of the seminal fluid mixed with spermatozoa into the ejaculatory ducts and subsequently to the urethra. Notably, any malfunction or pathological condition affecting these cells can impact male fertility, emphasizing the importance of understanding the intricate functions of seminal vesicle glandular cells in maintaining the healthy physiological function of male reproduction. CALOHA:TS-1283 + https://cellxgene.cziscience.com/cellguide/CL_1001597 seminal vesicle glandular cells seminal vesicle glandular cell @@ -103054,6 +104859,20 @@ plexiform layer using GABA. Glandular cell of seminal vesicle epithelium. NPX:PDR + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Seminal vesicle glandular cells belong to a specialized group of epithelial cells that form the internal lining of the seminal vesicles, a pair of male reproductive organs. These cells are located within the complex tubuloalveolar glands that make up the seminal vesicles and are known for their unique pseudostratified columnar epithelium structure. +The primary function of these cells is the secretion of a variety of substances that ultimately constitute around 70% of the fluid volume of semen. Seminal cells produce a high-fructose fluid that serves as an energy source for the spermatozoa and promotes their motility. They also secrete other essential substances like proteins, enzymes, vitamin C, prostaglandins, and various other compounds. Collectively, these substances help in the nourishment, protection, and transportation of the spermatozoa throughout the male reproductive system and during the ejaculation process. +Secondary to the production of seminal fluid, the seminal vesicle glandular cells also play a role in the contraction of the seminal vesicles during ejaculation. The contraction of these glands, induced by sympathetic nerves, ensures the efficient propulsion of the seminal fluid mixed with spermatozoa into the ejaculatory ducts and subsequently to the urethra. Notably, any malfunction or pathological condition affecting these cells can impact male fertility, emphasizing the importance of understanding the intricate functions of seminal vesicle glandular cells in maintaining the healthy physiological function of male reproduction. + DOI:10.1007/978-3-030-32300-4_26 + DOI:10.1007/s00265-006-0178-0 + DOI:10.1111/j.1439-0272.1992.tb02636.x + https://www.ncbi.nlm.nih.gov/books/NBK499854/ + https://www.sciencedirect.com/topics/veterinary-science-and-veterinary-medicine/seminal-vesicle + @@ -103258,7 +105077,7 @@ plexiform layer using GABA. - Endothelial cells forming the walls of the capillaries within the cerebral cortex. + A distinct endothelial cell forming the walls of the capillaries within the cerebral cortex. CALOHA:TS-2372 cerebral cortex endothelial cells endothelial cells of cerebral cortex @@ -103268,7 +105087,7 @@ plexiform layer using GABA. - Endothelial cells forming the walls of the capillaries within the cerebral cortex. + A distinct endothelial cell forming the walls of the capillaries within the cerebral cortex. NPX:PDR @@ -104272,7 +106091,7 @@ plexiform layer using GABA. - + @@ -104308,7 +106127,7 @@ plexiform layer using GABA. - + @@ -107635,7 +109454,7 @@ plexiform layer using GABA. Lamp5 cortical interneuron - A GABAergic neuron located in the cerebral cortex that expresses Lamp5 + A transcriptomically distinct GABAergic neuron located in the cerebral cortex that expresses Lamp5. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_subclass', clusters Lamp5. ILX:0770149 @@ -107645,9 +109464,10 @@ plexiform layer using GABA. - A GABAergic neuron located in the cerebral cortex that expresses Lamp5 + A transcriptomically distinct GABAergic neuron located in the cerebral cortex that expresses Lamp5. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_subclass', clusters Lamp5. PMID:30382198 PMID:37824655 + https://cellxgene.cziscience.com/e/e4ddac12-f48f-4455-8e8d-c2a48a683437.cxg/ @@ -107812,7 +109632,7 @@ plexiform layer using GABA. sncg cortical interneuron - A GABAergic neuron located in the cerebral cortex that expresses Gamma-synuclein + A transcriptomically distinct GABAergic neuron located in the cerebral cortex that expresses Gamma-synuclein. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_subclass', clusters Sncg. ILX:0770150 @@ -107822,9 +109642,10 @@ plexiform layer using GABA. - A GABAergic neuron located in the cerebral cortex that expresses Gamma-synuclein + A transcriptomically distinct GABAergic neuron located in the cerebral cortex that expresses Gamma-synuclein. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_subclass', clusters Sncg. PMID:33186530 PMID:37824655 + https://cellxgene.cziscience.com/e/e4ddac12-f48f-4455-8e8d-c2a48a683437.cxg/ @@ -107859,9 +109680,18 @@ plexiform layer using GABA. VIP cortical interneuron - A GABAergic neuron located in the cerebral cortex that expresses vasoactive intestinal polypeptide + A transcriptomically distinct cortical GABAergic neuron that expresses the vasocactive intestinal polypeptide and that has its soma located in the cerebral cortex. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_subclass', cluster Vip. + This neuronal type is distinguished by its heterogeneous morphology and electrophysiological characteristics (Pronneke et al., 2015,2020; Apicella and Marchionni, 2022). Variations in morphology and firing patterns are observed in human cortical VIP interneurons. In a study by Lee et al., 2023, four distinct subtypes of VIP neurons were identified, each exhibiting unique morphologies, soma locations, and electrophysiological properties. These subtypes are defined according to their transcriptomic markers: LBH-VIP and CCD184-VIP, both of which display a bipolar morphology with axons and dendrites extending across cortical layers; and SY16-VIP and ADAMTSL1-VIP, characterized by a dendritic arbor that spreads horizontally within the same layer as the soma (Lee et al., 2023). Disruption or malfunction of VIP cortical interneuron is implicated in neurodevelopmental disorders such as Rett Syndrome and Dravet Syndrome (Goff and Goldberg 2021). + VIP interneuron + VIP neuron + VIP-Expressing GABAergic Neuron + Vip GABAergic neuron ILX:0770151 + VIP type + VIP-IN + Vip + cortical VIP neuron VIP GABAergic cortical interneuron @@ -107869,9 +109699,67 @@ plexiform layer using GABA. - A GABAergic neuron located in the cerebral cortex that expresses vasoactive intestinal polypeptide + A transcriptomically distinct cortical GABAergic neuron that expresses the vasocactive intestinal polypeptide and that has its soma located in the cerebral cortex. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_subclass', cluster Vip. PMID:33186530 PMID:37824655 + https://cellxgene.cziscience.com/e/e4ddac12-f48f-4455-8e8d-c2a48a683437.cxg/ + + + + + This neuronal type is distinguished by its heterogeneous morphology and electrophysiological characteristics (Pronneke et al., 2015,2020; Apicella and Marchionni, 2022). Variations in morphology and firing patterns are observed in human cortical VIP interneurons. In a study by Lee et al., 2023, four distinct subtypes of VIP neurons were identified, each exhibiting unique morphologies, soma locations, and electrophysiological properties. These subtypes are defined according to their transcriptomic markers: LBH-VIP and CCD184-VIP, both of which display a bipolar morphology with axons and dendrites extending across cortical layers; and SY16-VIP and ADAMTSL1-VIP, characterized by a dendritic arbor that spreads horizontally within the same layer as the soma (Lee et al., 2023). Disruption or malfunction of VIP cortical interneuron is implicated in neurodevelopmental disorders such as Rett Syndrome and Dravet Syndrome (Goff and Goldberg 2021). + PMID:26420784 + PMID:31210267 + PMID:33794534 + PMID:35221922 + + + + + VIP interneuron + PMID:33108272 + + + + + VIP neuron + PMID:33108272 + + + + + VIP-Expressing GABAergic Neuron + PMID:35221922 + + + + + Vip GABAergic neuron + ILX:0770151 + + + + + VIP type + PMID:37824655 + + + + + VIP-IN + PMID:33794534 + + + + + Vip + ILX:0770151 + + + + + cortical VIP neuron + PMID:36384143 @@ -107882,7 +109770,7 @@ plexiform layer using GABA. - + @@ -107898,8 +109786,7 @@ plexiform layer using GABA. - - + @@ -107907,19 +109794,52 @@ plexiform layer using GABA. sst cortical interneuron - A GABAergic neuron located in the cerebral cortex that expresses somatostatin (sst) + A transcriptomically distinct GABAergic neuron located in the cerebral cortex that expresses somatostatin (sst). The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: MGE-derived interneurons', Author Categories: 'CrossArea_subclass', cluster Sst. ILX:0770152 + SOM+ inhibitory interneuron + SST+ IN + somatostatin-expressing inhibitory interneuron + In the mouse cortex, sst GABAergic cortical interneurons show heterogeneous electrophysiological signatures varying between low-threshold spiking (LTS), regular-spiking and fast-spiking (Song, Y. H., Yoon, J., & Lee, S. H. 2021). Sst GABAergic cortical interneurons have multiple functional roles in the brain. In the mouse, they involved in the generation of slow-waves during the sleep phase of non-rapid eye-movement (NREM) (Funk, C. M. et al., 2017), they maintain synaptic plasticity during motor learning (Adler, A., Zhao, R., et al., 2021), they enhance visual perception in the V1 cortical area by suppressing the activity of pyramidal excitatory neurons (Song, YH. et al., 2020). In humans, malfunctioning of sst GABAergic cortical interneurons is associated with neurodegenerative and psychiatric disorders such as Parkinson's disease, Alzheimer's disease, major depressive disorder, bipolar disorder and schizophrenia as individuals affected by these pathologies show a decrease of expression of SST in the brain (Song YH., Yoon J. et al., 2021). sst GABAergic cortical interneuron - A GABAergic neuron located in the cerebral cortex that expresses somatostatin (sst) + A transcriptomically distinct GABAergic neuron located in the cerebral cortex that expresses somatostatin (sst). The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: MGE-derived interneurons', Author Categories: 'CrossArea_subclass', cluster Sst. PMID:27477017 + PMID:33742131 PMID:37824655 + https://cellxgene.cziscience.com/e/9c63201d-bfd9-41a8-bbbc-18d947556f3d.cxg/ + + + + + SOM+ inhibitory interneuron + PMID:30001424 + + + + + SST+ IN + PMID:33742131 + + + + + somatostatin-expressing inhibitory interneuron + PMID:30001424 + + + + + In the mouse cortex, sst GABAergic cortical interneurons show heterogeneous electrophysiological signatures varying between low-threshold spiking (LTS), regular-spiking and fast-spiking (Song, Y. H., Yoon, J., & Lee, S. H. 2021). Sst GABAergic cortical interneurons have multiple functional roles in the brain. In the mouse, they involved in the generation of slow-waves during the sleep phase of non-rapid eye-movement (NREM) (Funk, C. M. et al., 2017), they maintain synaptic plasticity during motor learning (Adler, A., Zhao, R., et al., 2021), they enhance visual perception in the V1 cortical area by suppressing the activity of pyramidal excitatory neurons (Song, YH. et al., 2020). In humans, malfunctioning of sst GABAergic cortical interneurons is associated with neurodegenerative and psychiatric disorders such as Parkinson's disease, Alzheimer's disease, major depressive disorder, bipolar disorder and schizophrenia as individuals affected by these pathologies show a decrease of expression of SST in the brain (Song YH., Yoon J. et al., 2021). + PMID:28821651 + PMID:30792151 + PMID:32494634 + PMID:33742131 @@ -107930,7 +109850,7 @@ plexiform layer using GABA. - + @@ -107946,8 +109866,7 @@ plexiform layer using GABA. - - + @@ -107955,7 +109874,7 @@ plexiform layer using GABA. pvalb cortical interneuron - A GABAergic interneuron located in the cerebral cortex that expresses Parvalbumin. + A transcriptomically distinct GABAergic interneuron with a soma located in a cerebral cortex and it expresses Parvalbumin. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: MGE-derived interneurons', Author Categories: 'CrossArea_subclass', cluster Pvalb. ILX:0770154 @@ -107965,9 +109884,10 @@ plexiform layer using GABA. - A GABAergic interneuron located in the cerebral cortex that expresses Parvalbumin. + A transcriptomically distinct GABAergic interneuron with a soma located in a cerebral cortex and it expresses Parvalbumin. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: MGE-derived interneurons', Author Categories: 'CrossArea_subclass', cluster Pvalb. PMID:27477017 PMID:37824655 + https://cellxgene.cziscience.com/e/9c63201d-bfd9-41a8-bbbc-18d947556f3d.cxg/ @@ -108238,7 +110158,8 @@ plexiform layer using GABA. - + + @@ -108278,7 +110199,8 @@ plexiform layer using GABA. - + + @@ -108365,7 +110287,8 @@ plexiform layer using GABA. - + + @@ -108408,7 +110331,8 @@ plexiform layer using GABA. - + + @@ -108550,7 +110474,7 @@ plexiform layer using GABA. chandelier PV interneuron - A pvalb GABAergic cortical interneuron that is recognizable by the straight terminal axonal 'cartridges' of vertically oriented strings of synaptic boutons. Chandelier PV cells' boutons target exclusively the axon initial segment (AIS) of pyramidal cells, with a single cell innervating hundreds of pyramidal cells in a clustered manner. + A transcriptomically distinct pvalb GABAergic cortical interneuron that is recognizable by the straight terminal axonal 'cartridges' of vertically oriented strings of synaptic boutons. Chandelier PV cells' boutons target exclusively the axon initial segment (AIS) of pyramidal cells, with a single cell innervating hundreds of pyramidal cells in a clustered manner. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_subclass', clusters Chandelier. ILX:0107356 Chandelier PV @@ -108562,8 +110486,9 @@ plexiform layer using GABA. - A pvalb GABAergic cortical interneuron that is recognizable by the straight terminal axonal 'cartridges' of vertically oriented strings of synaptic boutons. Chandelier PV cells' boutons target exclusively the axon initial segment (AIS) of pyramidal cells, with a single cell innervating hundreds of pyramidal cells in a clustered manner. + A transcriptomically distinct pvalb GABAergic cortical interneuron that is recognizable by the straight terminal axonal 'cartridges' of vertically oriented strings of synaptic boutons. Chandelier PV cells' boutons target exclusively the axon initial segment (AIS) of pyramidal cells, with a single cell innervating hundreds of pyramidal cells in a clustered manner. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_subclass', clusters Chandelier. PMID:27477017 + https://cellxgene.cziscience.com/e/9c63201d-bfd9-41a8-bbbc-18d947556f3d.cxg/ @@ -108597,20 +110522,23 @@ plexiform layer using GABA. L6b glut - A glutamatergic neuron with a soma found in cortical layer 6b. They are transcriptomically related to corticothalamic-projecting neurons but have differential projections to the thalamus or anterior cingulate. + A glutamatergic neuron with a soma found in cortical layer 6b. They are transcriptomically related to corticothalamic-projecting neurons but have differential projections to the thalamus or anterior cingulate. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: Deep layer (non-IT) excitatory neuron', Author Categories: 'CrossArea_subclass', cluster L6b. + ILX:0770163 + L6b glutamatergic cortical neuron - A glutamatergic neuron with a soma found in cortical layer 6b. They are transcriptomically related to corticothalamic-projecting neurons but have differential projections to the thalamus or anterior cingulate. + A glutamatergic neuron with a soma found in cortical layer 6b. They are transcriptomically related to corticothalamic-projecting neurons but have differential projections to the thalamus or anterior cingulate. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: Deep layer (non-IT) excitatory neuron', Author Categories: 'CrossArea_subclass', cluster L6b. DOI:10.1101/2020.10.19.34312 PMID:30382198 PMID:37824655 + https://cellxgene.cziscience.com/e/d01c9dff-abd1-4825-bf30-2eb2ba74597e.cxg/ @@ -108708,7 +110636,7 @@ plexiform layer using GABA. L5 ET glut - A glutamatergic neuron, with a soma found in the deeper portion of L5, that has long-range axonal projections including deep subcortical targets outside of the telencephalon and, in some cases, the spinal cord. While the L5 ET neuron projections are not limited to ET targets, they are clearly differentiated from the neuron subclasses whose projections are constrained to intratelencephalic (IT) targets. L5 ET neurons are generally the largest excitatory cortical neurons, typically having a thick apical dendrite with a prominent dendritic tuft in layer 1 and displaying burst-firing physiological characteristics. + A transcriptomically distinct glutamatergic neuron, with a soma found in the deeper portion of L5, that has long-range axonal projections including deep subcortical targets outside of the telencephalon and, in some cases, the spinal cord. While the L5 ET neuron projections are not limited to ET targets, they are clearly differentiated from the neuron subclasses whose projections are constrained to intratelencephalic (IT) targets. L5 ET neurons are generally the largest excitatory cortical neurons, typically having a thick apical dendrite with a prominent dendritic tuft in layer 1 and displaying burst-firing physiological characteristics. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: Deep layer (non-IT) excitatory neurons ', Author Categories: 'CrossArea_subclass', clusters L5 ET. subcerebral projection (SCPN) neuron Pyramidal tract-like (PT-l) @@ -108723,9 +110651,10 @@ plexiform layer using GABA. - A glutamatergic neuron, with a soma found in the deeper portion of L5, that has long-range axonal projections including deep subcortical targets outside of the telencephalon and, in some cases, the spinal cord. While the L5 ET neuron projections are not limited to ET targets, they are clearly differentiated from the neuron subclasses whose projections are constrained to intratelencephalic (IT) targets. L5 ET neurons are generally the largest excitatory cortical neurons, typically having a thick apical dendrite with a prominent dendritic tuft in layer 1 and displaying burst-firing physiological characteristics. + A transcriptomically distinct glutamatergic neuron, with a soma found in the deeper portion of L5, that has long-range axonal projections including deep subcortical targets outside of the telencephalon and, in some cases, the spinal cord. While the L5 ET neuron projections are not limited to ET targets, they are clearly differentiated from the neuron subclasses whose projections are constrained to intratelencephalic (IT) targets. L5 ET neurons are generally the largest excitatory cortical neurons, typically having a thick apical dendrite with a prominent dendritic tuft in layer 1 and displaying burst-firing physiological characteristics. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: Deep layer (non-IT) excitatory neurons ', Author Categories: 'CrossArea_subclass', clusters L5 ET. PMID:34616075 PMID:37824655 + https://cellxgene.cziscience.com/e/d01c9dff-abd1-4825-bf30-2eb2ba74597e.cxg/ @@ -108796,7 +110725,7 @@ plexiform layer using GABA. L6 CT glut - A corticothalamic-projecting neuron with a soma found in cortical layer 6. + A transcriptomically distinct corticothalamic-projecting neuron with a soma found in cortical layer 6. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: Deep layer (non-IT) excitatory neurons', Author Categories: 'CrossArea_subclass', clusters L6 CT. L6 CT @@ -108806,9 +110735,10 @@ plexiform layer using GABA. - A corticothalamic-projecting neuron with a soma found in cortical layer 6. + A transcriptomically distinct corticothalamic-projecting neuron with a soma found in cortical layer 6. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: Deep layer (non-IT) excitatory neurons', Author Categories: 'CrossArea_subclass', clusters L6 CT. PMID:34616075 PMID:37824655 + https://cellxgene.cziscience.com/e/d01c9dff-abd1-4825-bf30-2eb2ba74597e.cxg/ @@ -108842,7 +110772,7 @@ plexiform layer using GABA. L5/6 NP glut MOp - A near-projecting glutamatergic neuron with a soma found in layer 5/6 of the primary motor cortex. + A transcriptomically distinct near-projecting glutamatergic neuron with a soma found in layer 5/6 of the primary motor cortex. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: Deep layer (non-IT) excitatory neurons', Author Categories: 'CrossArea_subclass', cluster L5/6 NP. ILX:0770161 L5/6 NP M1 @@ -108854,9 +110784,10 @@ plexiform layer using GABA. - A near-projecting glutamatergic neuron with a soma found in layer 5/6 of the primary motor cortex. + A transcriptomically distinct near-projecting glutamatergic neuron with a soma found in layer 5/6 of the primary motor cortex. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: Deep layer (non-IT) excitatory neurons', Author Categories: 'CrossArea_subclass', cluster L5/6 NP. PMID:31209381 PMID:34616075 + https://cellxgene.cziscience.com/e/d01c9dff-abd1-4825-bf30-2eb2ba74597e.cxg/ @@ -109132,7 +111063,7 @@ plexiform layer using GABA. - A type of mesothelial fibroblast that is derived from the neural crest, is localized on blood vessels, and is a key component of the pia and arachnoid membranes surrounding the brain. + A transcriptomically distinct type of mesothelial fibroblast that is derived from the neural crest, is localized on blood vessels, and is a key component of the pia and arachnoid membranes surrounding the brain. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: Non-neuronal cells', Author Categories: 'CrossArea_subclass', clusters VLMC. ILX:0770143 VLMC @@ -109143,11 +111074,12 @@ plexiform layer using GABA. - A type of mesothelial fibroblast that is derived from the neural crest, is localized on blood vessels, and is a key component of the pia and arachnoid membranes surrounding the brain. + A transcriptomically distinct type of mesothelial fibroblast that is derived from the neural crest, is localized on blood vessels, and is a key component of the pia and arachnoid membranes surrounding the brain. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: Non-neuronal cells', Author Categories: 'CrossArea_subclass', clusters VLMC. PMID:27284195 PMID:29443965 PMID:30096314 PMID:37824655 + https://cellxgene.cziscience.com/e/5346f9c6-755e-4336-94cc-38706ec00c2f.cxg/ @@ -109268,9 +111200,9 @@ plexiform layer using GABA. - - - + + + A type of mouse mesothelial fibroblast that is derived from the neural crest, is localized on blood vessels, and is a key component of the pia and arachnoid membranes surrounding the brain. VLMC (Mus musculus) @@ -109278,34 +111210,34 @@ plexiform layer using GABA. vascular leptomeningeal cell (Mmus) - + - + - + - + PMID:30096314 - + PMID:30096314 - + PMID:30096314 @@ -109572,7 +111504,6 @@ plexiform layer using GABA. An interneuron that is derived from the caudal ganglionic eminence. - CGE interneuron caudal ganglionic eminence derived GABAergic cortical interneuron CGE cortical interneuron CGE interneuron @@ -109580,7 +111511,7 @@ plexiform layer using GABA. CGE-derived cell CGE-derived interneuron - caudal ganglionic eminence derived interneuron + caudal ganglionic eminence derived cortical interneuron @@ -109590,13 +111521,6 @@ plexiform layer using GABA. PMID:37824655 PMID:37824663 - - - - CGE interneuron - PMID:37824663 - - @@ -109967,7 +111891,8 @@ in the label. See comments in issue 2357. - + + @@ -111208,7 +113133,8 @@ in the label. See comments in issue 2357. - + + @@ -111333,7 +113259,7 @@ in the label. See comments in issue 2357. sst chodl cortical interneuron - A sst GABAergic cortical interneuron that also expresses Chodl. These neurons are rare and correspond to the only known cortical interneurons with long-range projection. + A transcriptomically distinct sst GABAergic cortical interneuron that also expresses Chodl. These neurons are rare and correspond to the only known cortical interneurons with long-range projection. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: MGE-derived interneurons', Author Categories: 'CrossArea_subclass', clusters Sst Chodl. long-range GABAergic interneuron @@ -111342,11 +113268,12 @@ in the label. See comments in issue 2357. - A sst GABAergic cortical interneuron that also expresses Chodl. These neurons are rare and correspond to the only known cortical interneurons with long-range projection. + A transcriptomically distinct sst GABAergic cortical interneuron that also expresses Chodl. These neurons are rare and correspond to the only known cortical interneurons with long-range projection. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: MGE-derived interneurons', Author Categories: 'CrossArea_subclass', clusters Sst Chodl. PMID:15845086 PMID:31209381 PMID:33372656 PMID:37824655 + https://cellxgene.cziscience.com/e/9c63201d-bfd9-41a8-bbbc-18d947556f3d.cxg/ @@ -111354,13 +113281,20 @@ in the label. See comments in issue 2357. - + + + + + + + + An interneuron located in the cerebral cortex that expresses the oxytocin receptor. These interneurons also express somatostatin. @@ -112054,6 +113988,11 @@ in the label. See comments in issue 2357. A neurecto-epithelial cell that is part of the basal layer of the subcommissural organ and specializes in the secretion of proteins into the subarachnoid space. Hypendymal cells have similar characteristics to ependymal cells and express SCO-spondin. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Hypendymal cells are secretory cells located between the ependymal layer and the posterior commissure, forming the hypendmal layer of the subcommissural organ (SCO), a highly conserved gland that is part of the circumventricular system within the brain. +Hypendymal cells are bipolar cells with a thin apical pole and basal process. Most of the ultrastructural characteristics of these cells are similar to those described for the ependymal cells (which are arranged into another layer – the ependyma). However, ependymal cells release their secretion into the ventricular cerebrospinal fluid whereas hypendymal cells project processes to the local blood vessels and to the subarachnoidal space. + https://cellxgene.cziscience.com/cellguide/CL_4023181 hypendymal cell @@ -112065,6 +114004,17 @@ in the label. See comments in issue 2357. PMID:26778959 PMID:9579598 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Hypendymal cells are secretory cells located between the ependymal layer and the posterior commissure, forming the hypendmal layer of the subcommissural organ (SCO), a highly conserved gland that is part of the circumventricular system within the brain. +Hypendymal cells are bipolar cells with a thin apical pole and basal process. Most of the ultrastructural characteristics of these cells are similar to those described for the ependymal cells (which are arranged into another layer – the ependyma). However, ependymal cells release their secretion into the ventricular cerebrospinal fluid whereas hypendymal cells project processes to the local blood vessels and to the subarachnoidal space. + DOI:10.1002/(SICI)1097-0029(19980415)41:2<98::AID-JEMT2>3.0.CO;2-M + DOI:10.1111/joa.13709 + DOI:10.3389/fncel.2015.00480 + @@ -112648,6 +114598,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances A large epithelial cell found in the thymus. This cell type may internalize thymocytes through extensions of plasma membrane. The cell surface and cytoplasmic vacuoles of a thymic nurse cell express MHC Class I and MHC Class II antigens. The interaction of these antigens with a developing thymocyte determines whether the thymocyte undergoes positive or negative selection. + 2022-02-18T12:43:20Z thymic nurse cell @@ -112655,7 +114606,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances A large epithelial cell found in the thymus. This cell type may internalize thymocytes through extensions of plasma membrane. The cell surface and cytoplasmic vacuoles of a thymic nurse cell express MHC Class I and MHC Class II antigens. The interaction of these antigens with a developing thymocyte determines whether the thymocyte undergoes positive or negative selection. - https://en.wikipedia.org/wiki/Thymic_nurse_cell @@ -112718,6 +114668,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances An epithelial cell that is part of the fallopian tube epithelium that secretes mucous fluid and oviduct-specific products through the stimulation of estrogen and luteinizing hormone. The fallopian tube secretory cell has approximately the same height as the ciliated cell and is usually a more narrow columnar cell. The nucleus is ovoid and perpendicular to the long axis of the cell. The chromatin is more dense and the nucleolus smaller than that seen in the ciliated cell. + 2022-03-03T10:39:31Z oviduct secretory epithelial cell uterine tube secretory epithelial cell @@ -112729,7 +114680,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances An epithelial cell that is part of the fallopian tube epithelium that secretes mucous fluid and oviduct-specific products through the stimulation of estrogen and luteinizing hormone. The fallopian tube secretory cell has approximately the same height as the ciliated cell and is usually a more narrow columnar cell. The nucleus is ovoid and perpendicular to the long axis of the cell. The chromatin is more dense and the nucleolus smaller than that seen in the ciliated cell. - https://doi.org/10.1186/1477-7827-7-129 https://doi.org/10.3390/cells8080933 https://www.proteinatlas.org/learn/dictionary/normal/fallopian+tube @@ -112762,6 +114712,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances An epithelial ciliated cell that is part of the fallopian tube. This cell type is found mainly on the apex of the mucosal folds and contributes, together with peristaltic contractions, to the self-propulsion of spermatozoa, the transport of ovum during ovulation and the transport of the fertilized ovum to the intramural fallopian tube. A fallopian tube ciliated cell has a columnar shape and contains an oval or round nucleus, often located perpendicular or parallel to the long axis of the cell. + 2022-03-08T12:40:19Z oviduct ciliated cell uterine tube ciliated epithelial cell @@ -112772,7 +114723,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances An epithelial ciliated cell that is part of the fallopian tube. This cell type is found mainly on the apex of the mucosal folds and contributes, together with peristaltic contractions, to the self-propulsion of spermatozoa, the transport of ovum during ovulation and the transport of the fertilized ovum to the intramural fallopian tube. A fallopian tube ciliated cell has a columnar shape and contains an oval or round nucleus, often located perpendicular or parallel to the long axis of the cell. - PMID:16565155 @@ -112800,6 +114750,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances A specialized epithelial cell that contains "feet" that interdigitate with the "feet" of other glomerular epithelial cells in the pronephros. + 2022-03-11T14:38:32Z pronephric glomerular visceral epithelial cell pronephric podocyte @@ -112808,7 +114759,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances A specialized epithelial cell that contains "feet" that interdigitate with the "feet" of other glomerular epithelial cells in the pronephros. - PMID:10322630 @@ -112967,6 +114917,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + @@ -112976,6 +114927,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances Epithelial cell of the descending thin limb of the short loop (cortical) nephron limited to the outer medulla (mainly inner strip). It is known in some mammalian species that the short descending limb of the loop of Henle selectively expresses the serine protease Corin, the homeobox TF Uncx, and the urea channel Slc14a2. + 2022-05-13T11:00:29Z epithelial cell of the descending thin limb of the short loop of Henle @@ -112985,7 +114937,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances Epithelial cell of the descending thin limb of the short loop (cortical) nephron limited to the outer medulla (mainly inner strip). It is known in some mammalian species that the short descending limb of the loop of Henle selectively expresses the serine protease Corin, the homeobox TF Uncx, and the urea channel Slc14a2. - PMID:33769951 @@ -113064,6 +115015,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances A renal alpha-intercalated cell that is part of the collecting duct of the renal tubule. + 2022-05-31T11:15:10Z kidney collecting duct intercalated cell type A @@ -113073,7 +115025,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances A renal alpha-intercalated cell that is part of the collecting duct of the renal tubule. - PMID:31249312 PMID:9890303 @@ -113470,12 +115421,21 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - - + + + + + + + + + + + + - + @@ -113485,15 +115445,15 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - An absorptive epithelial cell of the human intestine expressing bestrophin-4 (BEST4) calcium-activated ion channels. + An enterocyte of the human intestine expressing bestrophin-4 (BEST4) calcium-activated ion channels. 2022-09-07T12:34:20Z - BEST4+ intestinal epithelial cell, human + BEST4+ enteroycte - An absorptive epithelial cell of the human intestine expressing bestrophin-4 (BEST4) calcium-activated ion channels. + An enterocyte of the human intestine expressing bestrophin-4 (BEST4) calcium-activated ion channels. PMID:24223998 PMID:35176508 @@ -113560,7 +115520,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances An amacrine cell that uses glycine as a neurotransmitter. - https://doi.org/10.1016/j.cell.2020.08.013 + https://doi.org/10.1016/j.cell.2020.08.013 @@ -113642,7 +115602,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - + @@ -114883,6 +116843,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + @@ -115280,21 +117241,21 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - + An epithelial cell that is part of a ureteric bud. A ureteric bud cell has the potential to induce metanephric mesenchymal cells to proliferate and convert to epithelia that form renal tubules via: (1) the secretion of multiple diffusible growth factors that rescue renal progenitors from apoptosis and stimulate them to proliferate and (2) contact-dependent mechanisms that induce mesenchymal-epithelial conversion. https://orcid.org/0000-0002-1425-877X 2023-10-13T11:22:42Z UB cell ureteric bud cell - + - + PMID:9374839 @@ -117980,6 +119941,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + @@ -118435,6 +120397,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + @@ -118445,7 +120408,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - + A supporting cell that is part of the ovary and differentiates into a granulosa cell. A pre-granulosa cell develops from an early supporting gonadal cell by repressing testis determination, which can then proliferate to form primordial follicles. @@ -118492,15 +120455,15 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - + + - - + + - A follicular cell of ovary that differentiates from a granulosa cell during the secondary follicle stage. Mural granulosa cells line the inner surface of the follicle wall, surrounding the fluid-filled antral cavity. These cells produce oestrogen during the follicular phase in response to follicle-stimulating hormone (FSH), and progesterone after ovulation in response to luteinizing hormone (LH). + A follicular cell of ovary that differentiates from a cuboidal granulosa cell during the secondary follicle stage. Mural granulosa cells line the inner surface of the follicle wall, surrounding the fluid-filled antral cavity. These cells produce oestrogen during the follicular phase in response to follicle-stimulating hormone (FSH), and progesterone after ovulation in response to luteinizing hormone (LH). 2024-06-07T12:15:13Z @@ -118512,7 +120475,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - A follicular cell of ovary that differentiates from a granulosa cell during the secondary follicle stage. Mural granulosa cells line the inner surface of the follicle wall, surrounding the fluid-filled antral cavity. These cells produce oestrogen during the follicular phase in response to follicle-stimulating hormone (FSH), and progesterone after ovulation in response to luteinizing hormone (LH). + A follicular cell of ovary that differentiates from a cuboidal granulosa cell during the secondary follicle stage. Mural granulosa cells line the inner surface of the follicle wall, surrounding the fluid-filled antral cavity. These cells produce oestrogen during the follicular phase in response to follicle-stimulating hormone (FSH), and progesterone after ovulation in response to luteinizing hormone (LH). PMID:27815559 PMID:33970370 PMID:34198768 @@ -119240,6 +121203,126 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + + + + + + + + + + + + + + + + + A granulosa cell that has a squamous morphology and form a single layer around the oocyte in primordial follicles. This cell develops directly into a cuboidal granulosa cell during the primordial-to-primary follicle transition. + + 2024-09-24T13:13:24Z + flattened granulosa cell + pre-granulosa cell + squamous GC + Often in literature squamous granulosa cell and pre-granulosa cell are used as synonyms. However, this term only makes reference to the quiescent granulosa cells that surround the primordial ovarian follicle, while a pre-granulosa cell proliferates to form the primordial follicle (and thus cells become the squamous granulosa cells). + squamous granulosa cell + + + + + A granulosa cell that has a squamous morphology and form a single layer around the oocyte in primordial follicles. This cell develops directly into a cuboidal granulosa cell during the primordial-to-primary follicle transition. + PMID:28892263 + + + + + flattened granulosa cell + PMID:22402964 + + + + + pre-granulosa cell + PMID:33914868 + + + + + squamous GC + PMID:33914868 + + + + + + Often in literature squamous granulosa cell and pre-granulosa cell are used as synonyms. However, this term only makes reference to the quiescent granulosa cells that surround the primordial ovarian follicle, while a pre-granulosa cell proliferates to form the primordial follicle (and thus cells become the squamous granulosa cells). + https://orcid.org/0000-0001-6677-8489 + + + + + + + + + + + + + + + + A granulosa cell that has a cuboidal morphology and develops from squamous granulosa cell during the transition between primordial follicle to primary follicle. Cuboidal granulosa cells proliferate to form a second layer within secondary follicles. + + 2024-09-24T13:14:57Z + columnar granulosa cell + cuboidal epithelial granulosa cell + columnar GC + cuboidal GC + cuboidal granulosa cell + + + + + A granulosa cell that has a cuboidal morphology and develops from squamous granulosa cell during the transition between primordial follicle to primary follicle. Cuboidal granulosa cells proliferate to form a second layer within secondary follicles. + PMID:28892263 + + + + + columnar granulosa cell + PMID:19001500 + + + + + cuboidal epithelial granulosa cell + PMID:31849844 + + + + + columnar GC + PMID:19001500 + + + + + + cuboidal GC + PMID:33914868 + + + + + @@ -119532,6 +121615,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + @@ -119557,6 +121641,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + @@ -119569,7 +121654,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - A GABAergic interneuron that has its soma located in the striatum and that has an enriched expression of the gene TAC3. + A GABAergic interneuron that has its soma located in the striatum and that has an enriched expression of the genes TAC3 and LHX6. 2024-03-05T14:29:32Z TAC3 interneuron @@ -119578,7 +121663,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - A GABAergic interneuron that has its soma located in the striatum and that has an enriched expression of the gene TAC3. + A GABAergic interneuron that has its soma located in the striatum and that has an enriched expression of the genes TAC3 and LHX6. PMID:32999462 PMID:34727523 @@ -119595,6 +121680,7 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + @@ -120033,11 +122119,10 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - + @@ -120240,6 +122325,507 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + + + + + + + + + + + + A tanycyte cell found in the ventromedial and dorsomedial nuclei of the hypothalamus. This type of tanycyte extends its protrusions close to parenchymal neurons without contacting blood vessels. It expresses the glial marker S-100β. + + 2024-08-19T13:06:16Z + DMH tanycyte + VMH tanycyte + In rodents, a1 tanycytes are known to express DARPP-32, GPR50, NA Vimentin, Connexin 43, GLT-1, GLUT1(+) (Goodman and Hajihosseini 2015; Prevot et al., 2018). + alpha1-tanycyte + + + + + A tanycyte cell found in the ventromedial and dorsomedial nuclei of the hypothalamus. This type of tanycyte extends its protrusions close to parenchymal neurons without contacting blood vessels. It expresses the glial marker S-100β. + PMID:16344112 + PMID:26578855 + wikipedia:Tanycyte + + + + + DMH tanycyte + PMID:29351662 + + + + + VMH tanycyte + PMID:29351662 + + + + + In rodents, a1 tanycytes are known to express DARPP-32, GPR50, NA Vimentin, Connexin 43, GLT-1, GLUT1(+) (Goodman and Hajihosseini 2015; Prevot et al., 2018). + PMID:26578855 + + + + + + + + + + + + + + + + + + + + + A type of tanycyte found in the dorsomedial arcuate nucleus of the hypothalamus. This mono-ciliated tanycyte extends its protrusion to the arcuate nucleus and expresses the glial marker S-100β. + + 2024-08-19T13:13:20Z + dmARH tanycyte + In rodents, this type of tanycyte is more developmentally advanced than alpha1 tanycytes, shows a high neurogenic competence and expresses the following markers DARPP-32, Vimentin, GPR50, Connexin-43, GLT-1, GLUT1(+) (Goodman and Hajihosseini 2015; Prevot et al., 2018) + alpha2-tanycyte + + + + + A type of tanycyte found in the dorsomedial arcuate nucleus of the hypothalamus. This mono-ciliated tanycyte extends its protrusion to the arcuate nucleus and expresses the glial marker S-100β. + PMID:16344112 + PMID:26578855 + PMID:29351662 + wikipedia:Tanycyte + + + + + dmARH tanycyte + PMID:29351662 + + + + + In rodents, this type of tanycyte is more developmentally advanced than alpha1 tanycytes, shows a high neurogenic competence and expresses the following markers DARPP-32, Vimentin, GPR50, Connexin-43, GLT-1, GLUT1(+) (Goodman and Hajihosseini 2015; Prevot et al., 2018) + PMID:26578855 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A type of tanycyte found in the lateral infundibular recess of the brain. This tanycyte has an elongated morphology with multiple microvilli extending to the third ventricle in the lateral zones of the median eminence. This type of tanycyte expresses FGF receptors 1 and 2, is in contact with GnRH neurons, and is involved in the release of gonadotropin-releasing hormone (GnRH). + + 2024-08-19T13:17:32Z + vmARH tanycyte + beta1-tanycyte + + + + + A type of tanycyte found in the lateral infundibular recess of the brain. This tanycyte has an elongated morphology with multiple microvilli extending to the third ventricle in the lateral zones of the median eminence. This type of tanycyte expresses FGF receptors 1 and 2, is in contact with GnRH neurons, and is involved in the release of gonadotropin-releasing hormone (GnRH). + PMID:16344112 + PMID:26578855 + PMID:29351662 + Wikipedia:Tanycyte + + + + + vmARH tanycyte + PMID:29351662 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A type of tanycyte found in the floor of the infundibular recess in the brain. This tanycyte has an elongated morphology with multiple microvilli extending medially and ventrally to the median eminence, contacting the pial surface and blood vessels. This type of tanycyte expresses FGF receptors 1 and 2, is in contact with GnRH neurons, and is involved in the release of gonadotropin-releasing hormone (GnRH). + + 2024-08-19T13:21:39Z + ME tanycyte + beta2-tanycyte + + + + + A type of tanycyte found in the floor of the infundibular recess in the brain. This tanycyte has an elongated morphology with multiple microvilli extending medially and ventrally to the median eminence, contacting the pial surface and blood vessels. This type of tanycyte expresses FGF receptors 1 and 2, is in contact with GnRH neurons, and is involved in the release of gonadotropin-releasing hormone (GnRH). + PMID:16344112 + PMID:26578855 + PMID:29351662 + wikipedia:Tanycyte + + + + + ME tanycyte + PMID:29351662 + + + + + + + + + + + + + + + + A progenitor cell of the central nervous system that differentiates exclusively onto neurons. This progenitor cell is found in a hippocampus subventricular zone, developing cortex and spinal cord of the central nervous system. + + 2024-09-02T11:42:12Z + NRP + In vitro cultures of embryonic mouse neural tubes show that neuronal-restricted precursors (NRPs) are derived from multipotent neuroepithelial cells to give rise to neurons. This progression suggests a linear relationship between multipotent progenitors and neuronal-restricted differentiation. (Mayer-Proschel et al., 1997). In the spinal cord of rats, neural-restricted precursor cells give rise cholinergic, GABAergic, glutametergic neurons (Cao and Howard et al., 2002). + neuronal-restricted precursor + + + + + A progenitor cell of the central nervous system that differentiates exclusively onto neurons. This progenitor cell is found in a hippocampus subventricular zone, developing cortex and spinal cord of the central nervous system. + PMID:10467245 + + + + + NRP + + PMID:12429182 + + + + + In vitro cultures of embryonic mouse neural tubes show that neuronal-restricted precursors (NRPs) are derived from multipotent neuroepithelial cells to give rise to neurons. This progression suggests a linear relationship between multipotent progenitors and neuronal-restricted differentiation. (Mayer-Proschel et al., 1997). In the spinal cord of rats, neural-restricted precursor cells give rise cholinergic, GABAergic, glutametergic neurons (Cao and Howard et al., 2002). + PMID:12429182 + PMID:9354325 + + + + + + + + + + + + + + + + + + + + + + + + + + + + A progenitor cell of the central nervous system that differentiates exclusively onto astrocytes. This progenitor cell expresses CD44 and S100 calcium-binding protein B. + + 2024-09-02T11:44:45Z + ARP + astrocyte precursor cell + In vitro, this progenitor cell can differentiate from glial-restricted precursor cells. + astrocyte-restricted precursor + + + + + A progenitor cell of the central nervous system that differentiates exclusively onto astrocytes. This progenitor cell expresses CD44 and S100 calcium-binding protein B. + PMID:15531362 + PMID:33052610 + + + + + ARP + + PMID:33052610 + + + + + astrocyte precursor cell + PMID:33052610 + + + + + In vitro, this progenitor cell can differentiate from glial-restricted precursor cells. + PMID:33052610 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A GABAergic interneuron expressing PTHLH and PVALB that has its soma in a striatum. This GABAergic interneuron type presents a spatial expression gradient of PVALB in the mouse striatum. + + 2024-09-17T10:20:15Z + PTHLH/PVALB cell + PTHLH +/PVALB+ interneuron + According to spatial transcriptomic data in the human striatum, pthlh-expressing interneurons are one of the most abundant population of interneurons in the striatum (Leonardo D. Garma, et al., 2024). + striatal pthlh-expressing interneuron + + + + + A GABAergic interneuron expressing PTHLH and PVALB that has its soma in a striatum. This GABAergic interneuron type presents a spatial expression gradient of PVALB in the mouse striatum. + PMID:30134177 + PMID:37292997 + + + + + PTHLH/PVALB cell + PMID:37292997 + + + + + PTHLH +/PVALB+ interneuron + PMID:37292997 + + + + + According to spatial transcriptomic data in the human striatum, pthlh-expressing interneurons are one of the most abundant population of interneurons in the striatum (Leonardo D. Garma, et al., 2024). + PMID:37292997 + + + + + + + + + + + + + + + A pthlh-expressing interneuron that expresses MOXD1 and has its soma in a striatum. + + 2024-09-17T10:26:57Z + striatal PTHLH MOXD1 expressing interneuron + + + + + A pthlh-expressing interneuron that expresses MOXD1 and has its soma in a striatum. + PMID:30134177 + + + + + + + + + + A midbrain dopaminergic neuron that has its soma located in a substantia nigra. This dopaminergic neuron type is highly metabolically active and it is involved in the regulation of movement, cognition, motivation and reward. Neurodegeneration of this dopaminergic neuronal type causes loss in fine motor control in Parkinson's Disease. + + 2024-09-16T13:09:29Z + SNpc dopaminergic neuron + substantia nigra dopaminergic neuron + + + + + A midbrain dopaminergic neuron that has its soma located in a substantia nigra. This dopaminergic neuron type is highly metabolically active and it is involved in the regulation of movement, cognition, motivation and reward. Neurodegeneration of this dopaminergic neuronal type causes loss in fine motor control in Parkinson's Disease. + PMID:32826893 + PMID:35308118 + + + + + SNpc dopaminergic neuron + PMID:35308118 + + + + + + + + + + + + + + + + + + + + + + + + + + + A GABAergic interneuron that has its soma in the anterior section of the substantia nigra pars reticulata. This GABAergic interneuron is characterized by the expression of Six3 and Foxp1 and it develops from Nkx6-2 expressing neuronal progenitors in the ventrolateral midbrain-diencephalon region. + + 2024-09-23T13:56:01Z + aSNpr + GABAergic interneuron of the anterior substantia nigra pars reticulata + + + + + A GABAergic interneuron that has its soma in the anterior section of the substantia nigra pars reticulata. This GABAergic interneuron is characterized by the expression of Six3 and Foxp1 and it develops from Nkx6-2 expressing neuronal progenitors in the ventrolateral midbrain-diencephalon region. + PMID:36148148 + + + + + aSNpr + PMID:36148148 + + + + + + + + + + + + + + + + A GABAergic interneuron that has its soma in the posterior section of the substantia nigra pars reticulata. This GABAergic interneuron is characterised by the expression of the transcription factors Pax5, Ctip2 and Pou6f2 and it develops from the ventrolateral r1 neuroepithelium expresing NKX61. + + 2024-09-23T14:49:11Z + pSNpr + GABAergic interneuron of the posterior substantia nigra pars reticulata + + + + + A GABAergic interneuron that has its soma in the posterior section of the substantia nigra pars reticulata. This GABAergic interneuron is characterised by the expression of the transcription factors Pax5, Ctip2 and Pou6f2 and it develops from the ventrolateral r1 neuroepithelium expresing NKX61. + PMID:36148148 + + + + + pSNpr + PMID:36148148 + + + + @@ -120501,6 +123087,945 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + An endothelial cell that lines an artery in the fetal circulatory system. + + 2024-08-16T13:52:25Z + endothelial cell of fetal artery + fetal arterial EC + fetal artery EC + fetal artery endothelial cell + + + + + An endothelial cell that lines an artery in the fetal circulatory system. + PMID:34497389 + + + + + endothelial cell of fetal artery + PMID:34497389 + + + + + fetal arterial EC + PMID:34497389 + + + + + fetal artery EC + PMID:34497389 + + + + + + + + + A pericyte that is in an early stage of development, found in newly forming or remodeling blood vessels. An immature pericyte is characterized by it's mesenchymal stem cell-like properties and high proliferative capacity, which allows it to differentiate into various types of pericytes and contribute to the structural and functional maturation of the vasculature. Immature pericytes are stellate in new vessels and elongated with less protrusions in remodeling vessels. + + 2024-08-19T11:32:32Z + imPCs + immature PCs + immature pericyte + + + + + A pericyte that is in an early stage of development, found in newly forming or remodeling blood vessels. An immature pericyte is characterized by it's mesenchymal stem cell-like properties and high proliferative capacity, which allows it to differentiate into various types of pericytes and contribute to the structural and functional maturation of the vasculature. Immature pericytes are stellate in new vessels and elongated with less protrusions in remodeling vessels. + PMID:21839917 + PMID:28564607 + PMID:32466671 + PMID:34497389 + PMID:36685855 + + + + + imPCs + PMID:28564607 + + + + + + immature PCs + PMID:28564607 + + + + + + + + + + An endothelial cell that lines the veins in the fetal circulatory system. + + 2024-09-05T15:45:32Z + fetal venous endothelial cell + fetal vein EC + fetal venous EC + fetal vein endothelial cell + + + + + An endothelial cell that lines the veins in the fetal circulatory system. + doi:10.1101/2021.04.07.438755 + + + + + fetal venous endothelial cell + doi:10.1101/2021.04.07.438755 + + + + + fetal vein EC + doi:10.1101/2021.04.07.438755 + + + + + + fetal venous EC + doi:10.1101/2021.04.07.438755 + + + + + + + + + + A specialized pericyte that actively participates in the formation of new blood vessels during angiogenesis by undergoing phenotypic changes, increasing proliferation, and interacting closely with endothelial cells. + + 2024-09-06T08:41:39Z + angiogenic pericyte + + + + + A specialized pericyte that actively participates in the formation of new blood vessels during angiogenesis by undergoing phenotypic changes, increasing proliferation, and interacting closely with endothelial cells. + PMID:24853910 + PMID:34497389 + + + + + + + + + + + + + + + + + + + + + An enterocyte that is part of the colon, in the early stages of differentiation, located in the intestinal crypt-villus axis. + + 2024-09-24T11:50:13Z + early enterocyte of colon + early colonocyte + + + + + An enterocyte that is part of the colon, in the early stages of differentiation, located in the intestinal crypt-villus axis. + PMID:28049136 + PMID:36060223 + + + + + early enterocyte of colon + doi:10.1101/2021.01.13.426602 + + + + + + + + + + + + + + + + + + + + + + + + + + An enterocyte in the early stages of development, located above the transit-amplifying cell zone in the intestinal crypt-villus axis. + + 2024-09-24T12:11:09Z + early enterocyte + + + + + An enterocyte in the early stages of development, located above the transit-amplifying cell zone in the intestinal crypt-villus axis. + PMID:20683682 + PMID:35235783 + + + + + + + + + + + + + + + + + + + + + + + + + An enterocyte of the human small intestine expressing bestrophin-4 (BEST4) calcium-activated ion channels. These enterocytes have a disinctive transcriptomic profile and are scattered through the small intestine epithelium. + + 2024-07-25T13:05:50Z + small intestine BEST4+ enterocyte + + + + + An enterocyte of the human small intestine expressing bestrophin-4 (BEST4) calcium-activated ion channels. These enterocytes have a disinctive transcriptomic profile and are scattered through the small intestine epithelium. + PMID:24223998 + PMID:34497389 + + + + + + + + + + + + + + + + + + + + + An enterocyte of the human colon expressing bestrophin-4 (BEST4) calcium-activated ion channels. These cells have a distinct transcriptomic profile compared to other enterocytes and are scattered through the colon epithelium. + + 2024-07-25T13:21:19Z + BEST4+ colonocyte + + + + + An enterocyte of the human colon expressing bestrophin-4 (BEST4) calcium-activated ion channels. These cells have a distinct transcriptomic profile compared to other enterocytes and are scattered through the colon epithelium. + PMID:24223998 + PMID:34497389 + + + + + + + + + + + + + + + + An ependymal cell that lines the lateral, third, and fourth ventricles of the brain. The cell is characterized by multiple motile cilia on its apical surface, which beats in a coordinated manner to facilitate the movement of cerebrospinal fluid (CSF), contributing to brain homeostasis. + + 2024-08-20T10:06:15Z + multiciliated ependymal cells + E1 + multiciliated ependymal cell, with an average of 16 motile cilia per cell, exhibits two types of planar cell polarity (PCP): rotational polarity, with unidirectional cilia orientation, and translational polarity, with asymmetric cilia positioning in the apical area. This location-specific PCP varies across the ventricular wall, aligning with the direction of CSF flow. These cells are interconnected by adherens and gap junctions, which support intercellular communication and maintain the structural integrity of the ependymal layer. Unlike some other cell types, these cells lack tight junctions. + multiciliated ependymal cell + + + + + An ependymal cell that lines the lateral, third, and fourth ventricles of the brain. The cell is characterized by multiple motile cilia on its apical surface, which beats in a coordinated manner to facilitate the movement of cerebrospinal fluid (CSF), contributing to brain homeostasis. + PMID:25045600 + PMID:28067220 + PMID:37008045 + + + + + multiciliated ependymal cells + PMID:25045600 + + + + + E1 + PMID:28067220 + PMID:37008045 + + + + + + multiciliated ependymal cell, with an average of 16 motile cilia per cell, exhibits two types of planar cell polarity (PCP): rotational polarity, with unidirectional cilia orientation, and translational polarity, with asymmetric cilia positioning in the apical area. This location-specific PCP varies across the ventricular wall, aligning with the direction of CSF flow. These cells are interconnected by adherens and gap junctions, which support intercellular communication and maintain the structural integrity of the ependymal layer. Unlike some other cell types, these cells lack tight junctions. + PMID:25045600 + PMID:27311928 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A multinucleate cell formed by the fusion of multiple uninuclear cells through plasma membrane fusion. This process leads to a single large cell containing multiple nuclei within a shared cytoplasm. + + 2024-08-15T10:38:46Z + syncytium + SC + syncytial cell + + + + + A multinucleate cell formed by the fusion of multiple uninuclear cells through plasma membrane fusion. This process leads to a single large cell containing multiple nuclei within a shared cytoplasm. + PMID:20851884 + Wikipedia:Syncytium + + + + + syncytium + WBbt:0008074 + + + + + SC + PMID:9067520 + + + + + + + + + + + + + + + + + + + + + + + + + + + + A capillary endothelial cell that is part of the intestinal villus. This cell is highly fenestrated, with fenestrations most numerous at the villus tips, and plays a vital role in nutrient absorption and maintaining the selective permeability of the intestinal barrier. + + 2024-09-17T10:03:25Z + villus blood capillary endothelial cells + villus tip endothelial cell + intestinal villus capillary endothelial cell + + + + + A capillary endothelial cell that is part of the intestinal villus. This cell is highly fenestrated, with fenestrations most numerous at the villus tips, and plays a vital role in nutrient absorption and maintaining the selective permeability of the intestinal barrier. + PMID:18480313 + PMID:35810168 + PMID:38051275 + + + + + villus blood capillary endothelial cells + PMID:35810168 + + + + + villus tip endothelial cell + PMID:38051275 + + + + + + + + + + + + + + + A specialized fibroblastic reticular cell that is part of gut-associated lymphoid tissue (GALT), responsible for forming a structural network that facilitates immune cell interactions. This cell is found in Peyer's patches, cryptopatches, and isolated lymphoid follicles. It plays crucial roles in maintaining intestinal immunity by controlling innate lymphoid cell homeostasis and function, organizing lymphoid structures, and contributing to intestinal microbiome balance. + + 2024-09-19T11:22:18Z + Intestinal fibroblastic reticular cells develop from both perivascular and subepithelial progenitors during Peyer's patch formation. Intestinal fibroblastic reticular cells express key markers such as CCL19, CCL21, CXCL13, TNFSF13B (also known as BAFF), and produce IL-7, which are important for their immune regulatory functions and the organization of lymphoid structures. + Ccl19-expressing fibroblastic reticular cell + solitary intestinal lymphoid tissue fibroblastic reticular cell + gut-associated secondary lymphoid organs fibroblastic reticular cell + intestinal fibroblastic reticular cell + + + + + A specialized fibroblastic reticular cell that is part of gut-associated lymphoid tissue (GALT), responsible for forming a structural network that facilitates immune cell interactions. This cell is found in Peyer's patches, cryptopatches, and isolated lymphoid follicles. It plays crucial roles in maintaining intestinal immunity by controlling innate lymphoid cell homeostasis and function, organizing lymphoid structures, and contributing to intestinal microbiome balance. + PMID:33707780 + PMID:35440118 + + + + + Intestinal fibroblastic reticular cells develop from both perivascular and subepithelial progenitors during Peyer's patch formation. Intestinal fibroblastic reticular cells express key markers such as CCL19, CCL21, CXCL13, TNFSF13B (also known as BAFF), and produce IL-7, which are important for their immune regulatory functions and the organization of lymphoid structures. + PMID:33707780 + PMID:35440118 + + + + + Ccl19-expressing fibroblastic reticular cell + PMID:35440118 + + + + + solitary intestinal lymphoid tissue fibroblastic reticular cell + PMID:35440118 + + + + + gut-associated secondary lymphoid organs fibroblastic reticular cell + PMID:35440118 + + + + + + + + + + + + + + + + + + + + + A fibroblast that is part of the subserosa of intestine. This cell interacts with immune cells and play roles in inflammation and fibrosis. In certain conditions, such as Crohn's disease, subserosal fibroblast may differentiate into myofibroblasts. + + 2024-09-19T12:58:29Z + intestinal subserosal fibroblast + + + + + A fibroblast that is part of the subserosa of intestine. This cell interacts with immune cells and play roles in inflammation and fibrosis. In certain conditions, such as Crohn's disease, subserosal fibroblast may differentiate into myofibroblasts. + PMID:23143399 + PMID:26694715 + PMID:38877292 + + + + + + + + + + + + + + + + + + + + + + An epithelial cell that is part of the crypt of Lieberkuhn, originating from intestinal stem cells and giving rise to enteroendocrine cells (EECs). In mouse and human, this cell can be characterized by the expression of Neurog3, and has the ability to proliferate and differentiate into multiple EEC subtypes. Its proliferative potential contributes to crypt growth, distinguishing it from fully differentiated EECs. + + 2024-09-20T12:13:26Z + EEC Progenitor + The EEC progenitor is also present in other organisms; for example, flies have EEC progenitors but lack intestinal crypts and do not express the same markers. Instead, they are Dl+ and Pros+. + intestinal enteroendocrine progenitor + + + + + An epithelial cell that is part of the crypt of Lieberkuhn, originating from intestinal stem cells and giving rise to enteroendocrine cells (EECs). In mouse and human, this cell can be characterized by the expression of Neurog3, and has the ability to proliferate and differentiate into multiple EEC subtypes. Its proliferative potential contributes to crypt growth, distinguishing it from fully differentiated EECs. + PMID:31756561 + PMID:32531023 + PMID:35913117 + PMID:38260422 + doi:/10.1038/s41467-021-27901-5 + + + + + EEC Progenitor + PMID:31756561 + + + + + + The EEC progenitor is also present in other organisms; for example, flies have EEC progenitors but lack intestinal crypts and do not express the same markers. Instead, they are Dl+ and Pros+. + PMID:25670791 + + + + + + + + + + + + + + + A fibroblast located adjacent to the intestinal epithelium in both the small intestine and colon, specifically around the crypts. This cell is characterized by the expression of PDGFRα and various collagen isoforms, including COL4A5 and COL4A6. It secretes signalling molecules like TGF-β, Wnt ligands, and BMPs, which are crucial for epithelial homeostasis, intestinal stem cell support, and basement membrane formation. + + 2024-09-23T09:59:27Z + S2 fibroblast + S2 mesenchymal cells + The S2 fibroblast population has been identified as a subset of intestinal fibroblasts located near the epithelial lining. This population is divided into two subtypes: S2a and S2b. S2a is involved in epithelial differentiation, while S2b, located at the top of the crypt, regulates intestinal stem cell proliferation, niche formation, and wound healing. + subepithelial intestinal fibroblast + + + + + A fibroblast located adjacent to the intestinal epithelium in both the small intestine and colon, specifically around the crypts. This cell is characterized by the expression of PDGFRα and various collagen isoforms, including COL4A5 and COL4A6. It secretes signalling molecules like TGF-β, Wnt ligands, and BMPs, which are crucial for epithelial homeostasis, intestinal stem cell support, and basement membrane formation. + PMID:30270042 + PMID:33430285 + PMID:33916891 + PMID:37080817 + + + + + S2 fibroblast + PMID:30270042 + PMID:33916891 + + + + + S2 mesenchymal cells + PMID:33916891 + + + + + The S2 fibroblast population has been identified as a subset of intestinal fibroblasts located near the epithelial lining. This population is divided into two subtypes: S2a and S2b. S2a is involved in epithelial differentiation, while S2b, located at the top of the crypt, regulates intestinal stem cell proliferation, niche formation, and wound healing. + PMID:30270042 + PMID:33916891 + PMID:37495570 + + + + + + + + + + + + + + + + + + + + + A subepithelial intestinal fibroblast that is located adjacent to the base of the crypt of Lieberkühn, near the intestinal stem cells. Characterized by low PDGFRα expression, this cell is crucial for maintaining the intestinal stem cell niche. Crypt-bottom fibroblast secretes key signaling molecules including canonical Wnt ligands (Wnt2, Wnt2b), Wnt potentiators (Rspo3), and BMP inhibitors (Grem1), which collectively regulate intestinal stem cell function and epithelial homeostasis. + + 2024-09-23T10:23:18Z + CBFs + bottom pericryptic-associated fibroblasts + crypt-bottom fibroblast + + + + + A subepithelial intestinal fibroblast that is located adjacent to the base of the crypt of Lieberkühn, near the intestinal stem cells. Characterized by low PDGFRα expression, this cell is crucial for maintaining the intestinal stem cell niche. Crypt-bottom fibroblast secretes key signaling molecules including canonical Wnt ligands (Wnt2, Wnt2b), Wnt potentiators (Rspo3), and BMP inhibitors (Grem1), which collectively regulate intestinal stem cell function and epithelial homeostasis. + PMID:33916891 + doi:/10.1371/journal.pbio.3001032 + + + + + CBFs + doi:/10.1371/journal.pbio.3001032 + + + + + + bottom pericryptic-associated fibroblasts + PMID:33916891 + + + + + + + + + + + + + + + A subepithelial intestinal fibroblast that is located adjacent to the top of the crypt of Lieberkuhn. Characterized by high experession of PDGFRα, this cell secretes a range of signaling factors, including WNTs and BMPs, that drive epithelial differentiation, creating a gradient that regulates the balance between stem cell maintenance and differentiation. + + 2024-09-23T11:14:04Z + CTFs + S2b fibroblast + top pericryptic fibroblast + S2b fibroblasts are located at the top of the crypt and express NRG1 and NPY. + crypt-top fibroblast + + + + + A subepithelial intestinal fibroblast that is located adjacent to the top of the crypt of Lieberkuhn. Characterized by high experession of PDGFRα, this cell secretes a range of signaling factors, including WNTs and BMPs, that drive epithelial differentiation, creating a gradient that regulates the balance between stem cell maintenance and differentiation. + PMID:33916891 + doi:/10.1371/journal.pbio.3001032 + + + + + CTFs + doi:/10.1371/journal.pbio.3001032 + + + + + + S2b fibroblast + PMID:37495570 + + + + + top pericryptic fibroblast + PMID:33916891 + + + + + S2b fibroblasts are located at the top of the crypt and express NRG1 and NPY. + PMID:37495570 + + + + + + + + + + + + + + + + + + + + + A stromal cell that serves as a precursor to the theca cell layers in the ovary growing follicles. This cell is present in the early stages of follicular growth, particularly in smaller follicles. Unlike mature theca cell, a pre-theca cell is initially non-steroidogenic and lacks luteinizing hormone receptors. + + 2024-09-25T11:15:57Z + early theca cell + progenitor theca cell + pre-theca cell + + + + + A stromal cell that serves as a precursor to the theca cell layers in the ovary growing follicles. This cell is present in the early stages of follicular growth, particularly in smaller follicles. Unlike mature theca cell, a pre-theca cell is initially non-steroidogenic and lacks luteinizing hormone receptors. + PMID:20628033 + PMID:31320652 + PMID:36205477 + + + + + early theca cell + PMID:36205477 + + + + + progenitor theca cell + PMID:31320652 + + + + + + + + + An enterocyte found in the follicle-associated epithelium (FAE) that covers Peyer's patches and other mucosa-associated lymphoid tissues. This cell has reduced absorptive capacity and expresses higher levels of chemokines CCL20 and CXCL16, compared to regular villus enterocytes. It contributes to antigen sampling and immune interactions, supporting the specialized function of the FAE in mucosal immunity. + + 2024-09-25T15:28:25Z + follicle-associated epithelium enterocyte + FAE enterocyte + follicular enterocyte + follicle associated enterocyte + + + + + An enterocyte found in the follicle-associated epithelium (FAE) that covers Peyer's patches and other mucosa-associated lymphoid tissues. This cell has reduced absorptive capacity and expresses higher levels of chemokines CCL20 and CXCL16, compared to regular villus enterocytes. It contributes to antigen sampling and immune interactions, supporting the specialized function of the FAE in mucosal immunity. + PMID:29339448 + PMID:34634036 + PMID:7107724 + + + + + follicle-associated epithelium enterocyte + PMID:7107724 + + + + + FAE enterocyte + PMID:7107724 + + + + + + follicular enterocyte + PMID:7107724 + + + + + + + + + + + + + + + + + + + + + + A cuboidal epithelial cell that is part of the intercalated duct of salivary gland. This cell expresses proteins commonly associated with acinar cells and displays calcium signaling characteristics similar to secretory cells, indicating an active role in the secretory process rather than ion reabsorption. + + + 2024-09-11T09:55:55Z + intercalated duct cell + salivary intercalated duct cells + Id cell + intercalated cell of salivary gland + + + + + A cuboidal epithelial cell that is part of the intercalated duct of salivary gland. This cell expresses proteins commonly associated with acinar cells and displays calcium signaling characteristics similar to secretory cells, indicating an active role in the secretory process rather than ion reabsorption. + PMID:30855909 + PMID:35799078 + PMID:36726292 + PMID:37724716 + + + + + intercalated duct cell + PMID:37724716 + + + + + salivary intercalated duct cells + PMID:37724716 + + + + + Id cell + PMID:35799078 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + An columnar/cuboidal epithelial cell that is part of the striated duct of salivary gland, characterized by basal striations formed by infoldings of the plasma membrane. This cell play a crucial role in modifying the electrolyte composition and concentration of saliva through active ion transport, particularly the absorption of sodium and secretion of potassium. + + + 2024-09-11T10:00:25Z + SD cells + striated duct cells + striated cell of salivary gland + + + + + An columnar/cuboidal epithelial cell that is part of the striated duct of salivary gland, characterized by basal striations formed by infoldings of the plasma membrane. This cell play a crucial role in modifying the electrolyte composition and concentration of saliva through active ion transport, particularly the absorption of sodium and secretion of potassium. + PMID:30855909 + PMID:34147989 + PMID:36726292 + + + + + SD cells + PMID:11590591 + + + + + striated duct cells + PMID:11590591 + + + + @@ -120606,6 +124131,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -121620,6 +125151,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -122034,12 +125571,6 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - - - - - - @@ -122340,6 +125871,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -122646,6 +126183,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -123810,12 +127353,30 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + + + + + + + + + + + + @@ -123942,6 +127503,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -123972,6 +127539,18 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + + + + + + @@ -124002,12 +127581,24 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + + + + + + @@ -124092,6 +127683,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -124860,6 +128457,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -125016,6 +128619,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -126180,6 +129789,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -126804,6 +130419,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -126852,6 +130473,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -127026,6 +130653,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -127038,6 +130671,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -127380,6 +131019,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -127566,6 +131211,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -127632,6 +131283,18 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + + + + + + @@ -127998,6 +131661,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -128094,6 +131763,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -128118,6 +131793,12 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + @@ -128214,6 +131895,18 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + + + + + + @@ -128232,12 +131925,30 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances + + + + + + + + + + + + + + + + + + @@ -128550,14 +132261,14 @@ Midget bipolar cells (imb, fmb) have larger axon terminals at greater distances - + - + - + diff --git a/cl.obo b/cl.obo index 9a060af21..557afc05e 100644 --- a/cl.obo +++ b/cl.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: releases/2024-08-16 +data-version: releases/2024-09-26 subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" subsetdef: attribute_slim "" @@ -19,6 +19,7 @@ subsetdef: eye_upper_slim "a subset of general classes related to specific cell subsetdef: functional_classification "" subsetdef: general_cell_types_upper_slim "a subset of general classes of cell types in the cell ontology." subsetdef: gocheck_do_not_annotate "" +subsetdef: gocheck_obsoletion_candidate "" subsetdef: goslim_agr "" subsetdef: goslim_candida "" subsetdef: goslim_chembl "" @@ -99,7 +100,7 @@ ontology: cl property_value: dc:description "An ontology of cell types." xsd:string property_value: dc:title "Cell Ontology" xsd:string property_value: has_ontology_root_term CL:0000000 -property_value: owl:versionInfo "2024-08-16" xsd:string +property_value: owl:versionInfo "2024-09-26" xsd:string property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 @@ -119,7 +120,7 @@ is_a: BFO:0000040 id: CHEBI:36080 is_a: BFO:0000002 is_a: PR:000018263 ! amino acid chain -is_a: PR:000064867 ! protein-containing molecular entity +is_a: PR:000050567 ! protein-containing material entity equivalent_to: PR:000000001 ! protein [Term] @@ -145,7 +146,7 @@ disjoint_from: GO:0032991 ! protein-containing complex disjoint_from: GO:0043226 ! organelle relationship: has_part GO:0005634 {gci_filler="PATO:0001407", gci_relation="bearer_of"} ! nucleus relationship: has_part GO:0005634 {gci_filler="PATO:0001908", gci_relation="bearer_of"} ! nucleus -relationship: RO:0002160 NCBITaxon:131567 ! only in taxon cellular organisms +relationship: RO:0002162 NCBITaxon:131567 ! in taxon cellular organisms [Term] id: CL:0000001 @@ -333,6 +334,7 @@ xref: WBbt:0006800 xref: ZFA:0005769 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000015 ! male germ cell +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000413 ! haploid cell intersection_of: CL:0000015 ! male germ cell intersection_of: bearer_of PATO:0001375 ! haploid @@ -360,6 +362,7 @@ xref: FMA:67338 xref: WBbt:0006798 xref: ZFA:0009006 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000408 {is_inferred="true"} ! male gamete relationship: RO:0002202 CL:0000018 ! develops from spermatid @@ -390,6 +393,7 @@ subset: cellxgene_subset xref: MA:0000388 xref: ncithesaurus:Egg xref: VHOG:0001530 +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000586 {is_inferred="true"} ! germ cell intersection_of: CL:0000586 ! germ cell intersection_of: capable_of GO:0048477 ! oogenesis @@ -420,9 +424,8 @@ xref: WBbt:0006797 xref: ZFA:0001109 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000021 {is_inferred="true"} ! female germ cell -is_a: CL:0000255 ! eukaryotic cell relationship: participates_in GO:0007143 ! female meiotic nuclear division -relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa [Term] id: CL:0000024 @@ -465,6 +468,7 @@ synonym: "nurse cell" RELATED [] xref: BTO:0000953 xref: FBbt:00004878 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: BFO:0000002 +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000412 ! polyploid cell is_a: CL:4029002 ! germline-derived nurse cell relationship: RO:0002202 CL:0000722 ! develops from cystoblast @@ -505,6 +509,7 @@ subset: cellxgene_subset xref: ZFA:0009010 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000055 ! non-terminally differentiated cell +is_a: CL:0000255 ! eukaryotic cell relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell [Term] @@ -519,7 +524,7 @@ xref: FMA:70563 xref: ZFA:0009011 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0000255 ! eukaryotic cell -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata [Term] id: CL:0000032 @@ -528,6 +533,7 @@ def: "A cell of a platelike structure, especially a thickened plate of ectoderm synonym: "neural placode cell" EXACT [] xref: ZFA:0009012 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002321 ! embryonic cell (metazoa) relationship: RO:0002202 CL:0000114 ! develops from surface ectodermal cell @@ -551,6 +557,7 @@ synonym: "animal stem cell" EXACT [] xref: CALOHA:TS-2086 xref: FMA:63368 xref: ZFA:0005957 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0011115 ! precursor cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0017145 ! stem cell division @@ -676,6 +683,7 @@ xref: FMA:83553 xref: ZFA:0009017 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0002194 {is_inferred="true"} ! monopoietic cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002194 ! monopoietic cell intersection_of: capable_of GO:0030224 ! monocyte differentiation intersection_of: has_part CL:0017503 ! basophilic cytoplasm @@ -724,6 +732,7 @@ synonym: "neutrophilic granuloblast" RELATED [] xref: ZFA:0009018 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000834 ! neutrophil progenitor cell is_a: CL:0000835 {is_inferred="true"} ! myeloblast +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000835 ! myeloblast intersection_of: capable_of GO:0030223 ! neutrophil differentiation intersection_of: has_part PR:000001944 ! transcription factor PU.1 @@ -1039,7 +1048,8 @@ subset: cellxgene_subset xref: VHOG:0001532 xref: XAO:0000031 xref: ZFA:0009032 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000000 ! cell intersection_of: has_part GO:0005929 ! cilium relationship: has_part GO:0005929 ! cilium @@ -1047,15 +1057,20 @@ relationship: has_part GO:0005929 ! cilium [Term] id: CL:0000065 name: ependymal cell -def: "A neurectoderm derived cell that lines the neural lumen." [GOC:tfm, JB:jb, PMID:9550134] +def: "A neuroepithelial glial cell, derived from a radial glial cell originating from the neuroectoderm, lines the ventricles of the brain and the central canal of the spinal cord. This cell is characterized by the presence of cilia on its apical surface, which can be motile or non-motile." [doi:/10.3389/fncel.2021.703951, GOC:tfm, https://www.britannica.com/science/ependymal-cell, JB:jb, PMID:34335193, PMID:37008045, PMID:9550134] subset: cellxgene_subset subset: human_reference_atlas -synonym: "ependymocyte" EXACT [] +synonym: "ependymocyte" NARROW [doi:10.53347/rID-51713] xref: BTO:0001724 xref: FMA:70550 xref: ZFA:0009033 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000067 ! ciliated epithelial cell +is_a: CL:0000125 ! glial cell is_a: CL:0000710 ! neurecto-epithelial cell +intersection_of: CL:0000710 ! neurecto-epithelial cell +intersection_of: part_of UBERON:0004670 ! ependyma +relationship: part_of UBERON:0004670 ! ependyma +relationship: RO:0002207 CL:0000681 ! directly develops from radial glial cell property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -1073,7 +1088,7 @@ xref: FBbt:00000124 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ xref: FMA:66768 xref: WBbt:0003672 xref: ZFA:0009034 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell disjoint_from: CL:0000738 ! leukocyte relationship: part_of UBERON:0000483 ! epithelium property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI @@ -1123,7 +1138,6 @@ is_a: CL:0002139 ! endothelial cell of vascular tree intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0001981 ! blood vessel relationship: part_of UBERON:0004638 ! blood vessel endothelium -relationship: RO:0002202 CL:0002546 ! develops from embryonic blood vessel endothelial progenitor cell property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -1159,15 +1173,20 @@ property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000076 name: squamous epithelial cell +def: "Any epithelial cell that is part of some squamous epithelium." [FBC:Autogenerated] subset: cellxgene_subset xref: CALOHA:TS-1249 xref: ZFA:0009039 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell +intersection_of: CL:0000066 ! epithelial cell +intersection_of: part_of UBERON:0006914 ! squamous epithelium +relationship: part_of UBERON:0006914 ! squamous epithelium [Term] id: CL:0000077 name: mesothelial cell -def: "A flattened epithelial cell of mesenchymal origin that lines the serous cavity." [GOC:tfm, ISBN:0721662544] +def: "A flat, squamous-like epithelial cell of mesodermal origin. It forms the mesothelium, which lines the body's serous cavities including the pleural, peritoneal, and pericardial spaces. This cell plays a crucial role in synthesizing and secreting lubricants, such as glycosaminoglycans and surfactants, which minimize friction between adjacent tissues during movement." [GOC:tfm, ISBN:0721662544, PMID:26106328] +comment: Mesothelial cells, which morphologically resemble squamous epithelial cells, express both epithelial markers (cytokeratins) and mesenchymal markers (vimentin), reflecting their mesodermal origin. They feature surface microvilli and apical-basal polarity. Under certain conditions, they can undergo mesothelial-to-mesenchymal transition. These cells also produce extracellular matrix proteins, maintain serosal homeostasis, and facilitate fluid transport. {xref="PMID:26106328"} subset: cellxgene_subset subset: human_reference_atlas synonym: "mesotheliocyte" EXACT [] @@ -1176,6 +1195,7 @@ xref: ZFA:0009040 {sssom:mapping_justification="https://w3id.org/semapv/vocab/Un is_a: CL:0000076 ! squamous epithelial cell is_a: CL:0000213 ! lining cell is_a: CL:0002078 ! meso-epithelial cell +relationship: part_of UBERON:0001136 ! mesothelium property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -1187,6 +1207,7 @@ is_a: CL:0000076 ! squamous epithelial cell [Term] id: CL:0000079 name: stratified epithelial cell +def: "An epithelial cell, organized into multiple layers, with only the basal layer being in contact with the basement membrane." [doi:/10.1016/B978-0-12-410424-2.00003-2, https://www.biologyonline.com/dictionary/stratified-epithelium, Wikipedia:Epithelium] subset: cellxgene_subset xref: ZFA:0009042 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 @@ -1198,7 +1219,7 @@ id: CL:0000080 name: circulating cell def: "A cell which moves among different tissues of the body, via blood, lymph, or other medium." [GOC:add] xref: ZFA:0009043 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0000179 ! haemolymphatic fluid relationship: part_of UBERON:0000179 ! haemolymphatic fluid @@ -1333,7 +1354,9 @@ synonym: "stellate cell of von Kupffer" EXACT [] synonym: "von Kupffer cell" EXACT [] xref: BTO:0000685 xref: FMA:14656 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000091 is_a: CL:0000864 {is_inferred="true"} ! tissue-resident macrophage +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000864 ! tissue-resident macrophage intersection_of: capable_of GO:0034102 ! erythrocyte clearance intersection_of: RO:0001025 UBERON:0001281 ! located in hepatic sinusoid @@ -1348,6 +1371,7 @@ relationship: RO:0002104 PR:000001925 ! has plasma membrane part scavenger recep relationship: RO:0002104 PR:000002064 ! has plasma membrane part macrosialin relationship: RO:0015016 PR:000001012 ! has low plasma membrane amount integrin alpha-M property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nKupffer cells are tissue-resident macrophages located in the liver. They are an integral part of the mononuclear phagocyte system and are responsible for the phagocytosis of dead or dying cells, microbes, and other foreign substances. Kupffer cells account for approximately 80-90% of tissue-resident macrophages in the body. They are found within the lumen of liver sinusoids and interface with microbial populations and products.\nThe primary role of Kupffer cells is to maintain homeostasis in the liver. They continuously filter and cleanse the blood that flows through the liver, removing pathogens, endotoxins, particulate matter, aged and dysfunctional red blood cells, and miscellaneous waste products. These cells also play an important role in maintaining iron homeostasis. During the process of phagocytosis, Kupffer cells recycle iron from degraded red blood cells, which is then utilized in the formation of new erythrocytes.\nKupffer cells also play key roles in various immune responses and inflammatory processes. They secrete various types of cytokines and chemokines, which contribute to the activation and mobilization of other immune cells. They can also produce reactive oxygen species and nitric oxide, which have microbicidal actions. Although their activity is essential for host defense, excessive or prolonged activation of Kupffer cells may contribute to hepatic injury, inflammation, and fibrosis." xsd:string {xref="DOI:10.1002/cphy.c120026", xref="DOI:10.1007/978-1-4939-1311-4_10", xref="DOI:10.1016/j.immuni.2022.08.002", xref="DOI:10.1038/nri.2017.11", xref="DOI:10.1111/j.1478-3231.2006.01342.x"} [Term] id: CL:0000092 @@ -1364,6 +1388,7 @@ xref: ZFA:0009047 {sssom:mapping_justification="https://w3id.org/semapv/vocab/Un is_a: CL:0000518 ! phagocyte (sensu Vertebrata) is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte is_a: CL:0001035 {is_inferred="true"} ! bone cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: capable_of GO:0045453 ! bone resorption intersection_of: has_part PR:000001850 ! cathepsin K @@ -1407,6 +1432,7 @@ xref: FMA:62854 xref: ZFA:0009048 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000081 ! blood cell is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: capable_of GO:0008015 ! blood circulation intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -1490,6 +1516,7 @@ xref: CALOHA:TS-0603 xref: FMA:66784 is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte is_a: CL:0002274 ! histamine secreting cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: capable_of GO:0002349 ! histamine production involved in inflammatory response intersection_of: capable_of GO:0002539 ! prostaglandin production involved in inflammatory response @@ -1681,12 +1708,14 @@ def: "A vertebrate phagocyte with a single nucleus." [GOC:add, GOC:tfm, ISBN:078 subset: cellxgene_subset subset: human_reference_atlas xref: BTO:0001433 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000113 xref: ZFA:0009064 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000518 {is_inferred="true"} ! phagocyte (sensu Vertebrata) is_a: CL:0000842 ! mononuclear cell intersection_of: CL:0000518 ! phagocyte (sensu Vertebrata) intersection_of: bearer_of PATO:0001407 ! mononucleate property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nMononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. \nIn addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses.\nMononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer." xsd:string {xref="DOI:10.1016/j.coi.2005.11.008", xref="DOI:10.1038/nri3087", xref="DOI:10.3389/fimmu.2019.01893"} [Term] id: CL:0000114 @@ -1711,6 +1740,7 @@ xref: FMA:66772 xref: ZFA:0009065 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000213 ! lining cell +is_a: CL:0000255 ! eukaryotic cell relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell property_value: RO:0002175 NCBITaxon:9606 @@ -1780,11 +1810,13 @@ synonym: "Purkinje neuron" EXACT [PMID:28821816] xref: BTO:0001011 xref: CALOHA:TS-0845 xref: FMA:67969 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000121 xref: ZFA:0009071 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000117 ! CNS neuron (sensu Vertebrata) is_a: CL:0000527 ! efferent neuron is_a: CL:1001611 ! cerebellar neuron relationship: RO:0002100 UBERON:0002129 ! has soma location cerebellar cortex +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nPurkinje cells, named after the Czech anatomist Jan Evangelista Purkyně who discovered them, are unique inhibitory neurons in the cerebellar cortex. They are a critical part of the vertebrate nervous system as they provide the only signal output from the cortex to the cerebellar nuclei. They are one of the few types of neurons that are large enough to be seen with the naked eye. The most distinct hallmark of Purkinje cells is their elaborate dendritic arbor, which forms a broad and intricately branching structure resembling a tree. These numerous branches each receive excitatory synaptic inputs from more than 100,000 parallel fibers; in addition, a single climbing fiber makes hundreds of synapses to the soma and proximal dendrites. A single long axon forms an inhibitory projection to the cerebellar nuclei.\nPurkinje cells play key roles in the coordination of fine, voluntary motor movements and balance. As the sole output of all motor coordination in the cerebellar cortex, they serve as a central relay in the cerebro-cerebellar loop. Each Purkinje cell receives two types of synaptic input: one from parallel fibers (which are axons of granule cells), and the other from climbing fibers (originating from the inferior olivary nucleus). The Purkinje cells process and integrate these diverse kinds of input signals to generate output that controls timing and coordination of movements.\nPurkinje neurons show considerable synaptic plasticity. Throughout life, these cells continue to undergo long-term potentiation and depression at parallel fiber synapses, which cause long-lasting increase or decrease, respectively, of synaptic transmission and have been proposed as mechanisms for motor learning. \nPurkinje cells are also known to be implicated in a variety of diseases. Their progressive loss is a prime feature in certain types of ataxia, a collective term used to describe conditions characterized by loss of muscular control and coordination. Furthermore, a significant reduction in the density of Purkinje cells has been reported in conditions such as autism and Huntington’s disease." xsd:string {xref="DOI:10.1007/s12311-018-0985-7", xref="DOI:10.1038/nrn3886", xref="DOI:10.7554/eLife.63668", xref="https://www.ncbi.nlm.nih.gov/books/NBK545154/", xref="https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/purkinje-cell"} [Term] id: CL:0000122 @@ -1805,8 +1837,7 @@ id: CL:0000123 name: neuron associated cell (sensu Vertebrata) subset: cellxgene_subset is_a: CL:0000095 ! neuron associated cell -is_a: CL:0000255 ! eukaryotic cell -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell [Term] @@ -1830,9 +1861,11 @@ xref: BTO:0002606 xref: CALOHA:TS-0415 xref: FBbt:00005144 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:54536 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000125 xref: ZFA:0009073 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000095 ! neuron associated cell property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nGlial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons.\nThese different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning.\nOligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. \nMicroglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response.\nDespite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis." xsd:string {xref="DOI:10.1002/glia.24343", xref="DOI:10.1038/nn1988", xref="DOI:10.1101/cshperspect.a020602", xref="DOI:10.1126/science.aat0473", xref="DOI:10.3389/fncel.2017.00024"} [Term] id: CL:0000126 @@ -1885,7 +1918,7 @@ property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000129 name: microglial cell -def: "A central nervous system macrophage found in the parenchyma of the central nervous system. Marker include CD11b-positive, F4/80-positive, and CD68-positive." [GOC:add, GOC:dsd, GOC:tfm, http://en.wikipedia.org/wiki/Microglia, ISBN:0721601464, MESH:D017628, PMID:11517395, PMID:12430718, PMID:14561199, PMID:14612429, PMID:16177057, PMID:19461673, PMID:2089275] +def: "A transcriptomically distinct central nervous system macrophage found in the parenchyma of the central nervous system. Marker include CD11b-positive, F4/80-positive, and CD68-positive." [GOC:add, GOC:dsd, GOC:tfm, http://en.wikipedia.org/wiki/Microglia, ISBN:0721601464, MESH:D017628, PMID:11517395, PMID:12430718, PMID:14561199, PMID:14612429, PMID:16177057, PMID:19461673, PMID:2089275] comment: Unlike macroglial cells, microglial cells arise from hematopoietic stem cells in the yolk sac during early embryogenesis that populate the central nervous system. They derive from embryonic mesoderm and are not from neuroectoderm where glioblast develops from. Markers: Mouse: CD11b+, F4/80+, CD68+. They represent ~12% of the cells in the CNS, but they are not uniformly distributed within the CNS. A normal adult mouse brain has approximately 3.5x10e6 microglia. Microglia are also reportedly CD3-negative, CD4-positive, CD8-negative, CD11b-positive, CD11c-high, CD14-negative, CD19-negative, CD45-low, CD56-negative, CD163-negative, CD200R-positive, CD281-positive, CD282-positive, CD283-positive, CD284-positive, CD285-positive, CD286-positive, CD287-positive, CD288-positive, CD289-positive, Gr1-negative, nestin-positive, and PU.1-positive. {xref="PMID:23616747"} subset: cellxgene_subset subset: human_reference_atlas @@ -1901,6 +1934,7 @@ xref: FMA:54539 xref: ZFA:0009077 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000125 ! glial cell is_a: CL:0000878 ! central nervous system macrophage +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000125 ! glial cell intersection_of: capable_of GO:0045087 ! innate immune response intersection_of: part_of UBERON:0001017 ! central nervous system @@ -1918,8 +1952,7 @@ property_value: RO:0002175 NCBITaxon:9606 id: CL:0000130 name: neuron associated cell (sensu Nematoda and Protostomia) is_a: CL:0000095 ! neuron associated cell -is_a: CL:0000255 ! eukaryotic cell -relationship: RO:0002160 NCBITaxon:33317 ! only in taxon Protostomia +relationship: RO:0002162 NCBITaxon:33317 ! in taxon Protostomia [Term] id: CL:0000131 @@ -2141,6 +2174,7 @@ xref: VHOG:0001679 xref: ZFA:0009091 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000147 ! pigment cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000147 ! pigment cell intersection_of: has_part GO:0042470 ! melanosome intersection_of: RO:0002202 CL:0000541 ! develops from melanoblast @@ -2185,6 +2219,7 @@ subset: general_cell_types_upper_slim xref: FMA:16014 xref: ZFA:0009092 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000151 ! secretory cell intersection_of: part_of UBERON:0002365 ! exocrine gland relationship: part_of UBERON:0002365 ! exocrine gland @@ -2266,12 +2301,14 @@ synonym: "chalice cell" EXACT [] xref: BTO:0001540 xref: FMA:13148 xref: http://en.wikipedia.org/wiki/Goblet_cell +xref: https://cellxgene.cziscience.com/cellguide/CL_0000160 xref: ZFA:0009094 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell relationship: capable_of GO:0070254 ! mucus secretion relationship: has_part GO:0005902 ! microvillus relationship: has_part GO:0098594 ! mucin granule property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/thumb/c/c4/404_Goblet_Cell_new.jpg/800px-404_Goblet_Cell_new.jpg" xsd:string {xref="http://cnx.org/content/col11496/1.6/", xref="https://commons.wikimedia.org/w/index.php?curid=30131227"} +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nGoblet cells are specialized, simple columnar, secretory epithelial cells that are mostly found in the respiratory and intestinal tracts. The term \"goblet\" refers to their shape, which resembles a flask or goblet, specially at their apical end which is swollen due to the accumulation of secretory granules. \nThe primary function of goblet cells is to to protect and lubricate the underlying tissues by secreting large quantities of mucin, a complex glycoprotein, which forms mucus when hydrated. In the respiratory tract, the mucus secreted by these cells traps dust, bacteria, viruses, and other potentially harmful particles in the inhaled air, preventing them from reaching the delicate tissues of the lungs. In the intestines, the goblet cells secrete mucus that acts as a protective barrier shielding the intestinal epithelium from dietary antigens, pathogens and prevents the intestinal epithelium from being eroded by the actions of the digestive enzymes and the abrasive action of passing food material.\nGoblet cells are capable of rapidly altering their secretory output in response to stimuli. For example, irritants like smoke or dust can trigger an increased rate of mucus production, as the body attempts to flush out the harmful particles. Conversely, in conditions such as chronic bronchitis and cystic fibrosis, overactive goblet cells can create a thick accumulation of mucus that obstructs the airways and fosters bacterial growth. Lastly, goblet cells are not static, rather, they undergo a dynamic process known as goblet cell metaplasia-differentiation, wherein non-goblet cells in response to chronic injury or inflammation, can differentiate into goblet cells leading to an accumulation of these cells in the tissue, known as goblet cell hyperplasia." xsd:string {xref="DOI:10.1016/S1357-2725(02)00083-3", xref="DOI:10.1038/s41575-022-00675-x", xref="DOI:10.1165/ajrcmb.25.5.f218", xref="DOI:10.1242/bio.20121701", xref="https://www.ncbi.nlm.nih.gov/books/NBK553208/"} [Term] id: CL:0000161 @@ -2305,6 +2342,7 @@ is_a: CL:0000151 ! secretory cell is_a: CL:0000164 {gci_relation="part_of", gci_filler="UBERON:0000945"} ! enteroendocrine cell is_a: CL:0000164 {gci_filler="UBERON:0000160", gci_relation="part_of"} ! enteroendocrine cell is_a: CL:0000164 {gci_filler="UBERON:0001264", gci_relation="part_of"} ! enteroendocrine cell +is_a: CL:0000255 ! eukaryotic cell relationship: part_of UBERON:0000949 ! endocrine system property_value: RO:0002175 NCBITaxon:9606 @@ -2315,10 +2353,12 @@ def: "An endocrine cell that is located in the epithelium of the gastrointestina subset: cellxgene_subset xref: BTO:0003865 xref: FMA:62930 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000164 xref: MESH:D019858 xref: ZFA:0009097 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000150 ! glandular epithelial cell is_a: CL:0000163 ! endocrine cell +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nEnteroendocrine cells are a specialized subset of cells located within the epithelial lining of both the small and large intestines, as well as the stomach and pancreas. Constituting less than 1% of the total population of intestinal cells, they are differentiated from a common intestinal cell progenitor, thus sharing lineage with absorptive and goblet cells of the intestines.\nThe distinct characteristic feature of an enteroendocrine cell is its inherent capacity to synthesize and secrete a plethora of gut hormones such as serotonin, somatostatin, neurotensin, cholecystokinin, secretin, gastric inhibitory peptide, motilin, and glucagon-like peptide-1. Integrated within this complex network of signaling agents, these substances control various aspects of the digestive system. Each enteroendocrine cell has its unique combination of hormones to release, determined by its position along the intestinal tract. Intriguingly, these hormones not only modulate local gut function, including motility, absorption and secretion, but also potentiate distant actions on other systems such as endocrine, nervous and immune and play a role in the feeling of satiety.\nThe release of these hormones from enteroendocrine cells is a highly regulated and dynamic process. The cells are equipped with sensory receptors localized on its luminal side that respond to various stimuli, including changes in nutrient composition, chemical or mechanical changes in the gut lumen, or even signals arising from commensal microbiota. This sensory input stimulates a signaling cascade within the cell, culminating in the release of specific hormones into the interstitial fluid. These hormones then make their way into the bloodstream, acting on their respective target receptors to mediate their duties. The multifunctional characteristics of enteroendocrine cells make them crucial for maintaining gut homeostasis and the overall physiological well being of the body." xsd:string {xref="DOI:10.1038/s41574-019-0168-8", xref="DOI:10.1111/j.1463-1326.2011.01438.x", xref="DOI:10.1196/annals.1294.001", xref="DOI:10.1210/endrev/bnaa018", xref="DOI:10.7554/elife.78512"} [Term] id: CL:0000165 @@ -2348,9 +2388,11 @@ subset: cellxgene_subset synonym: "phaeochromocyte" EXACT [] xref: BTO:0000259 xref: FMA:69263 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000166 xref: ZFA:0009099 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000029 ! neural crest derived neuron is_a: CL:0000568 ! amine precursor uptake and decarboxylation cell +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nChromaffin cells, also known as pheochromocytes, are neuroendocrine cells that are typically located in the adrenal medulla, the innermost part of the adrenal gland, which is situated on top of each kidney. Chromaffin cells are also found in small clusters, known as paraganglia, in various locations throughout the body, including the sympathetic nervous system. They derive their name from their ability to stain a brownish-black color upon exposure to chromic salts, a feature made possible due to their high content of granules rich in catecholamines and catecholamine-related neurotransmitters.\nThe primary function of chromaffin cells is the synthesis and release of catecholamines, specifically epinephrine (adrenaline) and norepinephrine (noradrenaline). These neurotransmitters are vital stress hormones that, when released by the adrenal chromaffing cells into the bloodstream, prepare the body for the 'fight or flight' response. This response can enhance the body's performance in a dangerous situation by increasing heart rate, elevating blood sugar, and increasing blood flow to the muscles. The chromaffin cells in paraganglia are responsible for the local release of catecholamines and play a role in regulating blood pressure and other autonomic functions.\nIn addition to their role in stress response, chromaffin cells also contribute to the body's immune response. They secrete several peptides including antimicrobial peptides, and the discovery of LPS and cytokine receptors on chromaffin cells suggests that the adrenal medulla may participate in some aspects of the immune response." xsd:string {xref="DOI:10.1002/cphy.c190003", xref="DOI:10.1016/j.biocel.2016.02.003", xref="DOI:10.3389/fendo.2018.00711", xref="DOI:10.3389/fimmu.2022.977175", xref="DOI:10.3389/fimmu.2022.977175/full"} [Term] id: CL:0000167 @@ -2370,6 +2412,7 @@ xref: BTO:0000783 xref: ZFA:0009101 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000154 ! protein secreting cell is_a: CL:0000167 ! peptide hormone secreting cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0030073 ! insulin secretion relationship: capable_of GO:0030073 ! insulin secretion @@ -2526,6 +2569,7 @@ xref: BTO:0000755 xref: CALOHA:TS-1150 xref: EMAPA:29655 xref: FMA:72297 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000178 xref: MESH:D007985 xref: ZFA:0009108 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 @@ -2533,6 +2577,7 @@ is_a: CL:0000177 ! testosterone secreting cell is_a: CL:4030031 ! interstitial cell relationship: part_of UBERON:0005212 ! Leydig cell region of testis relationship: RO:0002202 CL:0009091 ! develops from Leydig stem cell +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nLeydig cells are a testosterone-secreting cell in the interstitial area in the testes of males. They are named after Franz Leydig, a German anatomist who discovered these cells in 1850. Uniquely situated within the soft connective tissue surrounding the seminiferous tubules, Leydig cells form an integral part of the male reproductive system. They are usually polygonal cells characterized by well developed smooth endoplasmic reticulum, high lipid content and a large round nucleus. They are found across mammalian species, including humans. \nThe primary function of Leydig cells is the production of androgens, the male sex hormones, the most notable of which is testosterone. Leydig cells synthesize testosterone from cholesterol through a series of enzymatic reactions. The production and release of testosterone are mainly regulated by the luteinizing hormone (LH) released by the anterior pituitary gland. In response to LH, Leydig cells convert cholesterol into testosterone, which then plays a crucial role in the development and maintenance of primary and secondary male sexual characteristics. These include the formation and maturation of male reproductive organs, onset of spermatogenesis, and the presentation of male secondary sexual traits such as the deepening of the voice, growth of facial hair, development of muscles, and a broadening of shoulders.\nApart from testosterone production, Leydig cells also secrete insulin-like factor 3 (INSL3) that is essential for testicular descent during embryonic development in males. Dysregulation or loss of Leydig cells can lead to numerous conditions like testosterone deficiency, infertility, and certain forms of testicular cancer. Although not typical, Leydig cells can regenerate if they are damaged, ensuring the continuous production of testosterone and maintaining male reproductive health. They provide an excellent model to study cell differentiation and hormone regulation, thereby enhancing our understanding of reproductive biology and associated disorders." xsd:string {xref="DOI:10.1016/j.coemr.2019.03.001", xref="DOI:10.1093/biolre/ioy059", xref="DOI:10.1210/clinem/dgaa603", xref="DOI:10.3389/fendo.2014.00006", xref="https://www.ncbi.nlm.nih.gov/books/NBK556007/#:~:text=Leydig%20cells%20are%20the%20primary,secondary%20sexual%20characteristics%20and%20behaviors."} [Term] id: CL:0000179 @@ -2540,6 +2585,7 @@ name: progesterone secreting cell def: "Any secretory cell that is capable of some progesterone secretion." [FBC:Autogenerated] xref: ZFA:0009109 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000174 ! steroid hormone secreting cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000151 ! secretory cell intersection_of: capable_of GO:0042701 ! progesterone secretion relationship: capable_of GO:0042701 ! progesterone secretion @@ -2572,6 +2618,7 @@ subset: human_reference_atlas xref: BTO:0000575 xref: CALOHA:TS-0454 xref: FMA:14515 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000182 xref: ZFA:0009111 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000066 ! epithelial cell @@ -2581,6 +2628,7 @@ relationship: capable_of GO:0098754 ! detoxification relationship: part_of UBERON:0002107 ! liver relationship: RO:0002202 CL:0005026 ! develops from hepatoblast property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nHepatocytes are the major cell type constituting 70-80% of the liver's cytoplasmic mass, playing crucial roles in maintaining the body's metabolic homeostasis. Dimensions of mature hepatocytes typically range from 20 to 30 μm in humans, but size may vary depending on their location within the liver lobule. Hepatocytes are characterized by high biosynthetic, enzymatic, and endocytic activity. They contain abundant mitochondria, smooth and rough endoplasmic reticulum, peroxisomes, lysosomes, and a large nucleus that is often binucleate. \nThe liver consists of three zones - the periportal Zone 1, midzone 2, and pericentral Zone 3 - which have differential nutrient and oxygen status, and damage susceptibility; hepatocytes in the different zones show signifcant functional heterogeneity ('hepatocyte functional zonation'). Hepatocytes are involved in a multitude of critical functions including the metabolism of lipids, carbohydrates, and proteins, the synthesis of serum proteins (e.g., albumin, transferrin, and lipoproteins), the detoxification and excretion of endogenous and exogenous substances, the storage of vitamins and minerals, and the production and secretion of bile. \nHeterocytes demonstrate a remarkable regenerative capacity, which enables the liver to recover from injury and loss of tissue mass. Notably, hepatocytes perform biotransformation with both phase I and phase II enzymes, which modify drugs, xenobiotics, and various substances for elimination from the body. Phase I enzymes, such as cytochrome P450, catalyze both oxidative and reductive reactions of many xenobiotics; many of the products of phase I enzymes are substrates for the phase II enzymes, which catalyze conjugation reactions. \nAlterations in hepatocyte function have significant implications for overall human health and disease. Certain conditions, such as hepatitis, cirrhosis, and liver cancer, can profoundly affect hepatocyte structure and function, thereby disrupting the liver's ability to perform its vital roles within the body. As the primary site for drug metabolism, changes in hepatocyte function can also impact the effectiveness and toxicity of pharmaceuticals. The regenerative ability of hepatocytes makes them valuable cells for liver regenerative medicine and bioartificial liver support systems, and their study has provided significant insights into liver biology and disease." xsd:string {xref="DOI:10.1016/j.biocel.2011.11.011", xref="DOI:10.1055/s-2007-1007096", xref="DOI:10.1083/jcb.201903090", xref="DOI:10.1111/j.1439-0396.2007.00752.x"} [Term] id: CL:0000183 @@ -2631,6 +2679,7 @@ xref: WBbt:0003675 xref: ZFA:0009114 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000183 ! contractile cell +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000393 ! electrically responsive cell relationship: RO:0002202 CL:0000056 ! develops from myoblast property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI @@ -2647,7 +2696,7 @@ xref: BTO:0004392 xref: CALOHA:TS-2158 xref: FMA:9727 xref: ZFA:0009115 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001134 ! skeletal muscle tissue relationship: part_of UBERON:0001134 ! skeletal muscle tissue @@ -2728,7 +2777,7 @@ name: sensory receptor cell def: "A cell that is capable of detection of a stimulus involved in sensory perception." [] synonym: "receptor cell" EXACT [] xref: MESH:D011984 -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0050906 ! detection of stimulus involved in sensory perception intersection_of: part_of UBERON:0001032 ! sensory system @@ -2854,17 +2903,18 @@ relationship: capable_of GO:0050912 ! detection of chemical stimulus involved in [Term] id: CL:0000210 name: photoreceptor cell -def: "A cell specialized to detect and transduce light." [MESH:D010786] +def: "A cell specialized in detecting light stimuli that are involved in visual perception." [MESH:D010786] subset: cellxgene_subset xref: BTO:0001060 xref: CALOHA:TS-0868 xref: FBbt:00004211 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:86740 xref: ZFA:0009127 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000006 {is_inferred="true"} ! neuronal receptor cell +is_a: CL:0000101 ! sensory neuron +is_a: CL:0008028 ! visual system neuron intersection_of: CL:0000540 ! neuron -intersection_of: capable_of GO:0050962 ! detection of light stimulus involved in sensory perception -relationship: capable_of GO:0050962 ! detection of light stimulus involved in sensory perception +intersection_of: capable_of GO:0050908 ! detection of light stimulus involved in visual perception +relationship: capable_of GO:0050908 ! detection of light stimulus involved in visual perception property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg" xsd:anyURI [Term] @@ -2972,6 +3022,7 @@ def: "A cell of the outer of the three germ layers of the embryo." [MESH:D004475 synonym: "ectoderm cell" EXACT [] xref: FMA:72549 xref: ZFA:0009137 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000924 ! ectoderm @@ -2984,6 +3035,7 @@ synonym: "mesoblast" EXACT [] synonym: "mesoderm cell" EXACT [] xref: FMA:72554 xref: ZFA:0009138 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000926 ! mesoderm @@ -2994,6 +3046,7 @@ def: "A cell of the inner of the three germ layers of the embryo." [MESH:D004707 synonym: "endoderm cell" EXACT [] xref: FMA:72555 xref: ZFA:0009139 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000925 ! endoderm @@ -3023,6 +3076,7 @@ relationship: bearer_of PATO:0001405 ! anucleate id: CL:0000226 name: single nucleate cell def: "A cell with a single nucleus." [FB:ma, GOC:tfm] +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002242 ! nucleate cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0001407 ! mononucleate @@ -3040,12 +3094,10 @@ relationship: bearer_of PATO:0001406 ! binucleate [Term] id: CL:0000228 name: multinucleate cell -def: "A cell with more than one nucleus." [FB:ma] -synonym: "syncitium" EXACT [] -synonym: "syncytial cell" EXACT [] -synonym: "syncytium" EXACT [] -xref: AEO:0000203 -xref: WBbt:0008074 +def: "A cell with more than one nucleus." [FB:ma, Wikipedia:Multinucleate] +synonym: "multinucleated cells" EXACT [Wikipedia:Multinucleate] +synonym: "polynuclear cells" EXACT [Wikipedia:Multinucleate] +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002242 ! nucleate cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0001908 ! multinucleate @@ -3217,19 +3269,27 @@ relationship: has_part GO:0005903 ! brush border [Term] id: CL:0000240 name: stratified squamous epithelial cell +def: "A stratified epithelial cell that is part of squamous epithelium, characterized by multiple layers of cells. The basal layer is directly attached to the basement membrane and the apical layer consists of flattened squamous cells. This provides a protective barrier, commonly found in areas subject to abrasion, such as the skin, oral cavity, and esophagus." [PMID:30422572, Wikipedia:Epithelium, Wikipedia:Stratified_squamous_epithelium] subset: human_reference_atlas xref: ZFA:0009144 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000076 ! squamous epithelial cell is_a: CL:0000079 ! stratified epithelial cell +intersection_of: CL:0000079 ! stratified epithelial cell +intersection_of: part_of UBERON:0006915 ! stratified squamous epithelium +relationship: part_of UBERON:0006915 ! stratified squamous epithelium property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000241 name: stratified cuboidal epithelial cell +def: "A stratified epithelial cell that is part of cuboidal epithelium, characterized by multiple layers of cuboidal cells forming the apical layer. This provides a protective lining for ducts in large glands, such as sweat glands." [PMID:30422572, Wikipedia:Stratified_cuboidal_epithelium] subset: human_reference_atlas xref: ZFA:0009145 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000075 ! columnar/cuboidal epithelial cell is_a: CL:0000079 ! stratified epithelial cell +intersection_of: CL:0000079 ! stratified epithelial cell +intersection_of: part_of UBERON:0010077 ! cuboidal epithelium +relationship: part_of UBERON:0010077 ! cuboidal epithelium property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -3346,14 +3406,14 @@ replaced_by: PO:0020094 [Term] id: CL:0000255 name: eukaryotic cell -def: "Any cell that only exists in Eukaryota." [FBC:Autogenerated] +def: "Any cell that in taxon some Eukaryota." [FBC:Autogenerated] subset: cellxgene_subset xref: MESH:D005057 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell -intersection_of: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +intersection_of: RO:0002162 NCBITaxon:2759 ! in taxon Eukaryota disjoint_from: CL:0000520 ! prokaryotic cell -relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 ! in taxon Eukaryota [Term] id: CL:0000256 @@ -3363,11 +3423,11 @@ is_a: CL:0000325 ! stuff accumulating cell [Term] id: CL:0000257 name: Eumycetozoan cell -def: "Any cell that only exists in Eumycetozoa." [FBC:Autogenerated] +def: "Any cell that in taxon some Eumycetozoa." [FBC:Autogenerated] is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell -intersection_of: RO:0002160 NCBITaxon:142796 ! only in taxon Eumycetozoa -relationship: RO:0002160 NCBITaxon:142796 ! only in taxon Eumycetozoa +intersection_of: RO:0002162 NCBITaxon:142796 ! in taxon Eumycetozoa +relationship: RO:0002162 NCBITaxon:142796 ! in taxon Eumycetozoa [Term] id: CL:0000258 @@ -3562,6 +3622,7 @@ subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas xref: ZFA:0009154 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000006 ! neuronal receptor cell is_a: CL:0000210 ! photoreceptor cell intersection_of: CL:0000210 ! photoreceptor cell intersection_of: part_of UBERON:0000970 ! eye @@ -3859,14 +3920,21 @@ name: pulmonary alveolar epithelial cell def: "An epithelial cell that lines the peripheral gas exchange region of the lungs of air-breathing vertebrates." [GOC:tfm, PMID:20054144, PMID:29463737] subset: cellxgene_subset synonym: "alveolar epithelial cell" EXACT [] +synonym: "alveolus of lung epithelial cell" EXACT [] +synonym: "epithelial cell of alveolus of lung" EXACT [] synonym: "pneumocyte" EXACT [PMID:32491474] synonym: "pneumonocyte" EXACT [] xref: BTO:0000395 xref: CALOHA:TS-2168 xref: FMA:62499 +xref: MESH:D056809 +is_a: CL:0000076 ! squamous epithelial cell is_a: CL:0000082 ! epithelial cell of lung -is_a: CL:0010003 ! epithelial cell of alveolus of lung +intersection_of: CL:0000066 ! epithelial cell +intersection_of: part_of UBERON:0004821 ! pulmonary alveolus epithelium relationship: part_of UBERON:0004821 ! pulmonary alveolus epithelium +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2024-09-02T08:27:21Z" xsd:dateTime [Term] id: CL:0000323 @@ -3978,8 +4046,7 @@ def: "A neural precursor of the central nervous system." [PMID:1295739] synonym: "neuroblast" BROAD [] xref: FBbt:00005146 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000047 ! neural stem cell -is_a: CL:0000255 ! eukaryotic cell -relationship: RO:0002160 NCBITaxon:33317 ! only in taxon Protostomia +relationship: RO:0002162 NCBITaxon:33317 ! in taxon Protostomia [Term] id: CL:0000339 @@ -4013,7 +4080,7 @@ def: "Any animal cell containing pigment granules." [GOC:tfm, ISBN:0721662544] xref: ZFA:0009170 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000147 ! pigment cell is_a: CL:0000255 ! eukaryotic cell -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata [Term] id: CL:0000343 @@ -4062,6 +4129,7 @@ def: "A cell of the sclera of the eye." [GOC:add] subset: eye_upper_slim xref: ZFA:0009174 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000293 ! structural cell intersection_of: CL:0000293 ! structural cell intersection_of: part_of UBERON:0001773 ! sclera @@ -4075,6 +4143,7 @@ def: "A structural cell that is part of optic choroid." [GOC:add] subset: eye_upper_slim xref: ZFA:0009175 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000293 ! structural cell intersection_of: CL:0000293 ! structural cell intersection_of: part_of UBERON:0001776 ! optic choroid @@ -4087,7 +4156,7 @@ name: extraembryonic cell def: "Any cell that is part of some extraembryonic structure." [FBC:Autogenerated] subset: general_cell_types_upper_slim xref: ZFA:0009176 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0000478 ! extraembryonic structure relationship: part_of UBERON:0000478 ! extraembryonic structure @@ -4104,7 +4173,7 @@ relationship: part_of UBERON:0010302 ! amnioserosa [Term] id: CL:0000351 name: trophoblast cell -def: "An extraembryonic cell that develops from a trophectodermal cell. This cell is found in the outer layer of the blastocyst and can invade other structures in the uterus once the blastocyst implants into the uterine wall. A trophoblast cell is involved in the implantation of the embryo into the uterine wall, placental formation, remodelling of maternal vasculature in the uterus, nutrient and gas exchange, hormone production, and immune modulation to support fetal development." [GOC:tfm, MESH:D014327, PMID:37630754] {comment="doi:10.1007/978-3-030-84725-8"} +def: "An extraembryonic cell that develops from a trophectodermal cell. This cell is found in the outer layer of the blastocyst and can invade other structures in the uterus once the blastocyst implants into the uterine wall. A trophoblast cell is involved in the implantation of the embryo into the uterine wall, placental formation, remodelling of maternal vasculature in the uterus, nutrient and gas exchange, hormone production, and immune modulation to support fetal development." [doi:10.1007/978-3-030-84725-8, GOC:tfm, MESH:D014327, PMID:37630754] synonym: "trophoblastic cell" EXACT [doi:10.1007/978-3-030-84725-8] xref: FMA:83028 is_a: BFO:0000002 @@ -4188,6 +4257,7 @@ id: CL:0000360 name: morula cell def: "A cell of the early embryo at the developmental stage in which the blastomeres, resulting from repeated mitotic divisions of the fertilized ovum (zygote), form a compact cell mass." [MESH:D009028] is_a: CL:0000007 ! early embryonic cell (metazoa) +is_a: CL:0000255 ! eukaryotic cell relationship: part_of UBERON:0000085 ! morula [Term] @@ -4241,8 +4311,8 @@ is_a: CL:0000007 ! early embryonic cell (metazoa) is_a: CL:0000255 ! eukaryotic cell is_a: CL:0010017 ! zygote intersection_of: CL:0010017 ! zygote -intersection_of: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa -relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +intersection_of: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa [Term] id: CL:0000366 @@ -4296,9 +4366,8 @@ id: CL:0000373 name: histoblast def: "A progenitor cell found in the larval epidermis of insects and that gives rise to the adult abdominal epidermis." [doi:10.1016/j.cub.2022.01.045] xref: FBbt:00001789 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} -is_a: CL:0000255 ! eukaryotic cell is_a: CL:0011026 ! progenitor cell -relationship: RO:0002160 NCBITaxon:50557 ! only in taxon Insecta +relationship: RO:0002162 NCBITaxon:50557 ! in taxon Insecta [Term] id: CL:0000374 @@ -4360,6 +4429,7 @@ name: scolopale cell def: "A cell that is part of a scolopidium and surrounds the dendrite of a scolopidial neuron." [doi:10.1016/B978-012369493-5.50012-2, doi:10.1017/CBO9780511818202.024] synonym: "scolopidial sheath cell" EXACT [ISBN:978-087969828-7] xref: FBbt:00005219 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000378 ! supporting cell (sensu Nematoda and Protostomia) relationship: part_of UBERON:0001038 ! chordotonal organ @@ -4398,7 +4468,7 @@ xref: FBbt:00005063 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ is_a: BFO:0000002 is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000390 ! blood cell (sensu Nematoda and Protostomia) -relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda +relationship: RO:0002162 NCBITaxon:6656 ! in taxon Arthropoda relationship: RO:0002202 CL:0000385 ! develops from prohemocyte (sensu Nematoda and Protostomia) [Term] @@ -4550,6 +4620,7 @@ id: CL:0000407 name: scolopidial ligament cell def: "A cell that anchors the cell body of a scolopidial neuron to the integument." [doi:10.1016/B978-0-12-408088-1.00002-6, doi:10.1023/a\:1018564904170] xref: FBbt:00005221 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000378 ! supporting cell (sensu Nematoda and Protostomia) relationship: part_of UBERON:0001038 ! chordotonal organ @@ -4654,8 +4725,10 @@ is_a: CL:0000036 ! epithelial fate stem cell [Term] id: CL:0000420 name: syncytial epithelial cell +def: "An epithelial cell that forms a syncytium, which is a multinucleated cell resulting from the fusion of multiple cells." [] +xref: Wikipedia:Syncytium is_a: CL:0000066 ! epithelial cell -is_a: CL:0000228 ! multinucleate cell +is_a: CL:4052002 ! syncytial cell [Term] id: CL:0000421 @@ -4717,9 +4790,8 @@ def: "A columnar epithelial cell that is part of an insect imaginal disc." [doi: comment: This term does not encompass all the cell types that may be found in an epithelial disc (such as the peripodial or adepithelial cells), only the cells that form the disc epithelium proper. xref: FBbt:00007108 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000146 ! simple columnar epithelial cell -is_a: CL:0000255 ! eukaryotic cell relationship: part_of UBERON:0000939 ! imaginal disc -relationship: RO:0002160 NCBITaxon:50557 ! only in taxon Insecta +relationship: RO:0002162 NCBITaxon:50557 ! in taxon Insecta [Term] id: CL:0000430 @@ -4729,6 +4801,7 @@ synonym: "xanthophore" RELATED [] xref: ZFA:0009198 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000147 ! pigment cell +is_a: CL:0000255 ! eukaryotic cell relationship: RO:0002202 CL:0005002 ! develops from xanthoblast [Term] @@ -4739,6 +4812,7 @@ synonym: "guanophore" RELATED [] xref: ZFA:0009199 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000147 ! pigment cell +is_a: CL:0000255 ! eukaryotic cell relationship: RO:0002202 CL:0005001 ! develops from iridoblast [Term] @@ -4779,6 +4853,7 @@ is_a: CL:0000151 ! secretory cell id: CL:0000436 name: vaginal lubricant secreting cell is_a: CL:0000151 ! secretory cell +is_a: CL:0000255 ! eukaryotic cell relationship: part_of UBERON:0000996 ! vagina [Term] @@ -4839,8 +4914,7 @@ def: "A stem cell that gives rise to the follicle cells that surround the oocyte synonym: "somatic stem cell" BROAD [doi:10.1016/j.devcel.2005.08.012] xref: FBbt:00004903 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000036 ! epithelial fate stem cell -is_a: CL:0000255 ! eukaryotic cell -relationship: RO:0002160 NCBITaxon:6656 {IAO:0000233="https://github.com/obophenotype/cell-ontology/issues/1943"} ! only in taxon Arthropoda +relationship: RO:0002162 NCBITaxon:6656 {IAO:0000233="https://github.com/obophenotype/cell-ontology/issues/1943"} ! in taxon Arthropoda [Term] id: CL:0000442 @@ -4940,6 +5014,7 @@ xref: MESH:D003713 xref: ZFA:0009209 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000113 ! mononuclear phagocyte is_a: CL:0000145 ! professional antigen presenting cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000738 ! leukocyte intersection_of: bearer_of PATO:0001407 ! mononucleate intersection_of: capable_of GO:0001816 ! cytokine production @@ -5065,9 +5140,8 @@ id: CL:0000462 name: adepithelial cell def: "A cell of mesodermal origin that is closely associated with the epithelium of an imaginal disc. It is a precursor of some of the insect's adult muscles." [doi:10.1016/S0925-4773(97)00654-0] xref: FBbt:00003219 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} -is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000680 ! muscle precursor cell -relationship: RO:0002160 NCBITaxon:50557 ! only in taxon Insecta +relationship: RO:0002162 NCBITaxon:50557 ! in taxon Insecta [Term] id: CL:0000463 @@ -5075,10 +5149,9 @@ name: epidermal cell (sensu Arthropoda) def: "An epidermal cell that secretes chitinous cuticle from its apical side." [FlyBase:ds, ISBN:ISBN\:978-0801481253] comment: While insect epidermis is generally columnar/cuboidal, there are certainly well studied cases where it is not (e.g.- Rhodnius prolixus when starved). So it would be safer to add this as a differentium for particular species where this is known. -DSJ. xref: FBbt:00007325 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} -is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000362 ! epidermal cell is_a: CL:0000710 ! neurecto-epithelial cell -relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda +relationship: RO:0002162 NCBITaxon:6656 ! in taxon Arthropoda relationship: RO:0002202 CL:0000464 ! develops from epidermoblast [Term] @@ -5095,9 +5168,8 @@ id: CL:0000465 name: cardioblast (sensu Arthropoda) def: "A precursor of the cells that form the dorsal vessel of arthropods." [doi:10.1007/BF00360522] xref: FBbt:00001666 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} -is_a: CL:0000255 ! eukaryotic cell is_a: CL:0010021 ! cardiac myoblast -relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda +relationship: RO:0002162 NCBITaxon:6656 ! in taxon Arthropoda [Term] id: CL:0000467 @@ -5123,8 +5195,7 @@ synonym: "neuro-glioblast" EXACT [] synonym: "neuroglioblast" EXACT [] xref: FBbt:00005147 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000047 ! neural stem cell -is_a: CL:0000255 ! eukaryotic cell -relationship: RO:0002160 NCBITaxon:33317 ! only in taxon Protostomia +relationship: RO:0002162 NCBITaxon:33317 ! in taxon Protostomia [Term] id: CL:0000469 @@ -5132,6 +5203,7 @@ name: ganglion mother cell def: "A neural progenitor cell that is the daughter of a neuroblast (sensu arthopoda). The progeny of ganglion mother cells develop into neurons, glia and (occasionally) epithelial cells." [] xref: FBbt:00005149 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: BFO:0000002 +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0011020 ! neural progenitor cell relationship: RO:0002202 CL:0000338 ! develops from neuroblast (sensu Nematoda and Protostomia) @@ -5191,10 +5263,9 @@ synonym: "follicle cell" BROAD [] synonym: "ovarian follicle cell" BROAD [] xref: FBbt:00004904 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: BFO:0000002 -is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000500 ! follicular epithelial cell is_a: CL:2000064 ! ovarian surface epithelial cell -relationship: RO:0002160 NCBITaxon:50557 {source="https://github.com/obophenotype/cell-ontology/issues/589"} ! only in taxon Insecta +relationship: RO:0002162 NCBITaxon:50557 {source="https://github.com/obophenotype/cell-ontology/issues/589"} ! in taxon Insecta relationship: RO:0002202 CL:0000441 ! develops from follicle stem cell (sensu Arthropoda) [Term] @@ -5288,7 +5359,7 @@ comment: Oenocytes are highly variable in size, shape, cluster formation and ana xref: FBbt:00004995 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000151 ! secretory cell is_a: CL:0000255 ! eukaryotic cell -relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda +relationship: RO:0002162 NCBITaxon:6656 ! in taxon Arthropoda [Term] id: CL:0000488 @@ -5415,10 +5486,12 @@ synonym: "granulosa cell of ovary" EXACT [] xref: BTO:0000542 xref: CALOHA:TS-0729 xref: FMA:18718 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000501 xref: ZFA:0009227 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000174 ! steroid hormone secreting cell is_a: CL:0002174 ! follicular cell of ovary -relationship: RO:0002207 CL:4033066 ! directly develops from pre-granulosa cell +relationship: RO:0002202 CL:4033066 ! develops from pre-granulosa cell +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nGranulosa cells are a type of somatic cell most commonly known for their crucial role within the ovarian follicles of female mammalian species. Named for their grainy appearance, they are situated in the follicular epithelium, lining the inner part of the follicle and directly surrounding the oocyte. These cells stand as an integral part of the ovarian structure and function.\nOne of the primary roles of granulosa cells is to aid in the production and secretion of sex hormones, particularly estrogen. They achieve this by working in tandem with theca cells, which stay attached to the external layer of the follicle. Theca cells produce androstenedione (a type of androgen) which granulosa cells then convert into estradiol, a form of estrogen, with the help of the enzyme aromatase. Moreover, granulosa cells participate in luteinization, transforming into luteal granulosa cells as a response to the luteinizing hormone during ovulation. This allows the formation of the corpus luteum, responsible for the secretion of progesterone necessary to maintain pregnancy.\nGranulosa cells also play a significant role in follicular development and oocyte maturation, involving close communication with the contained oocyte. They support the oocyte through the provision of nutrients and growth factors, control its meiotic cycle and ensure it is appropriately oriented and instructed for impending ovulation. Furthermore, granulosa cells contribute to the formation of the zona pellucida and the follicular fluid, providing an optimal environment for the oocyte's growth and maturation. These cells, thus, perform multiple vital roles, underscoring their importance in fertility and reproductive health." xsd:string {xref="DOI:10.1016/j.ejogrb.2004.01.010", xref="DOI:10.1093/humrep/del408", xref="DOI:10.1093/humupd/6.3.279", xref="DOI:10.1210/jcem-28-3-355", xref="DOI:10.3389/fendo.2019.00832/full"} [Term] id: CL:0000502 @@ -5427,9 +5500,11 @@ def: "A cell found throughout the gastrointestinal tract and in the pancreas. Th subset: cellxgene_subset synonym: "D cell" EXACT [] xref: FMA:62935 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000502 xref: ZFA:0009228 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0000172 ! somatostatin secreting cell +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nType D enteroendocrine cells, also known as D or delta cells, are specialized hormone-releasing cells found in the pancreas and also scattered throughout the lining of the gastrointestinal tract in mammals, notably within the stomach and the upper part of the small intestine known as the duodenum. The primary role of D cells is to produce and secrete somatostatin, a potent paracrine inhibitor. \nIn the gastrointestinal tract, somatostatin slows down digestion. It reduces gastric acid secretion and slows down the rate of gastric emptying, thereby prolonging and controling the digestive p. Functionally, these effects are aimed at sustaining nutrient absorption to optimize energy extraction from consumed food.\nIn the pancreas, D cells maintain a vital role in endocrine regulation. D cells in the pancreatic islands secrete somatostatin to inhibit the release of both insulin and glucagon from type A cells and B cells, glucoregulatory hormones that control blood sugar levels. Hence, D cells contribute considerably to the homeostasis of the body's metabolic processes. It is also noteworthy that dysfunctional D cells or irregular somatostatin signaling has been associated with certain pathologies such as neuroendocrine tumors and gastric ulcers." xsd:string {xref="DOI:10.1016/j.pharmthera.2015.05.007", xref="DOI:10.1038/s41574-018-0020-6", xref="DOI:10.1093/annonc/mdh216", xref="https://www.sciencedirect.com/topics/neuroscience/somatostatin-cell"} [Term] id: CL:0000503 @@ -5504,10 +5579,12 @@ def: "An epithelial cell found in the basal part of the intestinal glands (crypt subset: cellxgene_subset xref: BTO:0000993 xref: FMA:62897 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000510 is_a: CL:0000150 {is_inferred="true"} ! glandular epithelial cell is_a: CL:0000323 ! lysozyme secreting cell is_a: CL:0002563 ! intestinal epithelial cell relationship: part_of UBERON:0001983 ! crypt of Lieberkuhn +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nPaneth cells are specialized epithelial cells that are primarily located at the bottom of the crypts of Lieberkühn in the small intestine, where they play a pivotal role in maintaining gut homeostasis. They have also been found in smaller numbers in the colonic crypts and other parts of the gastrointestinal tract. Paneth cells are characterized by large acidophilic granules, which take up most of the cytoplasmic volume, causing the nucleus to be pushed toward the base of the cell.\nPaneth cells function as a part of the innate immune system. The large granules inside the cells are filled with antimicrobial peptides, such as defensins and lysozymes. Upon bacterial intrusion or cellular signaling indicating a potential infection, Paneth cells release the granules containing the antimicrobial substances into the crypt lumen, effectively serving as the first line of defense against bacterial invasion within the gastrointestinal tract. In essence, Paneth cells serve as guardians, protecting the intestinal stem cells from harmful pathogens that may disturb the gut ecosystem.\nIn addition to their primary role in immunity, Paneth cells are also crucial for supporting the stem cell niche in the intestinal crypts. They are located adjacent to Lgr5+ stem cells and secrete various growth factors such as EGF, TGF-alpha, Wnt3, and Notch ligand Dll4. These factors regulate the self-renewal and differentiation of these stem cells, which continuously replenish the intestinal epithelium. Consequently, any abnormality or dysfunction in Paneth cells could lead to a disturbance in gut homeostasis, possibly resulting in various illnesses such as inflammatory bowel disease." xsd:string {xref="DOI:10.1007/s00018-002-8412-z", xref="DOI:10.1038/nature09637", xref="DOI:10.1038/nrmicro2546", xref="DOI:10.1146/annurev-physiol-030212-183744", xref="DOI:10.3389/fimmu.2020.00587"} [Term] id: CL:0000511 @@ -5587,6 +5664,7 @@ name: macrophage derived foam cell def: "A type of foam cell derived from a macrophage containing lipids in small vacuoles and typically seen in atherolosclerotic lesions, as well as other conditions." [GOC:add, PMID:20213546] synonym: "lipophage" EXACT [] is_a: BFO:0000002 +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000891 ! foam cell relationship: RO:0002202 CL:0000235 ! develops from macrophage @@ -5596,7 +5674,7 @@ name: phagocyte (sensu Vertebrata) def: "A phagocyte in vertebrates that is able to phagocytosis." [GOC:tfm] is_a: CL:0000234 ! phagocyte is_a: CL:0000255 ! eukaryotic cell -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata [Term] id: CL:0000519 @@ -5615,11 +5693,11 @@ property_value: RO:0002161 NCBITaxon:2759 [Term] id: CL:0000521 name: fungal cell -def: "Any cell that only exists in Fungi." [FBC:Autogenerated] +def: "Any cell that in taxon some Fungi." [FBC:Autogenerated] is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell -intersection_of: RO:0002160 NCBITaxon:4751 ! only in taxon Fungi -relationship: RO:0002160 NCBITaxon:4751 ! only in taxon Fungi +intersection_of: RO:0002162 NCBITaxon:4751 ! in taxon Fungi +relationship: RO:0002162 NCBITaxon:4751 ! in taxon Fungi [Term] id: CL:0000522 @@ -5654,8 +5732,8 @@ synonym: "syncytial trophoblast cell" EXACT [PMID:11787150] synonym: "syncytiotrophoblastic cell" EXACT [PMID:21733368] synonym: "syntrophoblast cell" RELATED [] xref: FMA:83043 -is_a: CL:0000228 ! multinucleate cell is_a: CL:0000351 ! trophoblast cell +is_a: CL:4052002 ! syncytial cell intersection_of: CL:0000351 ! trophoblast cell intersection_of: bearer_of PATO:0001908 ! multinucleate relationship: part_of UBERON:0000371 ! syncytiotrophoblast @@ -5702,9 +5780,8 @@ name: primary neuron (sensu Teleostei) def: "A neuron that develops during the early segmentation stages in teleosts, before the neural tube is formed." [doi:10.1242/dev.108.1.121, PMID:1842357] xref: ZFA:0009242 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 -is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000540 ! neuron -relationship: RO:0002160 NCBITaxon:32443 {IAO:0000233="https://github.com/obophenotype/cell-ontology/pull/1950"} ! only in taxon Teleostei +relationship: RO:0002162 NCBITaxon:32443 {IAO:0000233="https://github.com/obophenotype/cell-ontology/pull/1950"} ! in taxon Teleostei [Term] id: CL:0000531 @@ -5744,9 +5821,8 @@ name: secondary neuron (sensu Teleostei) def: "A neuron of teleosts that develops later than a primary neuron, typically during the larval stages." [doi:10.1242/dev.108.1.121, PMID:1842357] xref: ZFA:0009246 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 -is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000540 ! neuron -relationship: RO:0002160 NCBITaxon:32443 {IAO:0000233="https://github.com/obophenotype/cell-ontology/pull/1950"} ! only in taxon Teleostei +relationship: RO:0002162 NCBITaxon:32443 {IAO:0000233="https://github.com/obophenotype/cell-ontology/pull/1950"} ! in taxon Teleostei [Term] id: CL:0000536 @@ -5923,6 +5999,7 @@ synonym: "rubriblast" EXACT [ISBN:0721601464] xref: FMA:83518 is_a: CL:0000764 {is_inferred="true"} ! erythroid lineage cell is_a: CL:0002242 ! nucleate cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000764 ! erythroid lineage cell intersection_of: bearer_of PATO:0002505 ! nucleated intersection_of: bearer_of PATO:0040072 ! high nuclear/cytoplasmic ratio @@ -5980,6 +6057,7 @@ synonym: "prorubricyte" EXACT [ISBN:0721601464] xref: FMA:83505 xref: ZFA:0005236 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000765 {is_inferred="true"} ! erythroblast +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017503 ! basophilic cytoplasm intersection_of: has_part GO:0000792 ! heterochromatin @@ -6001,6 +6079,7 @@ synonym: "rubricyte" EXACT [ISBN:0721601464] xref: FMA:83506 xref: ZFA:0005241 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000765 {is_inferred="true"} ! erythroblast +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017504 ! polychromatophilic cytoplasm intersection_of: has_part GO:0000792 ! heterochromatin @@ -6139,6 +6218,7 @@ is_a: CL:0000763 ! myeloid cell is_a: CL:0001012 ! CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor is_a: CL:0011026 ! progenitor cell is_a: CL:1001610 ! bone marrow hematopoietic cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002032 ! hematopoietic oligopotent progenitor cell intersection_of: capable_of GO:0030225 ! macrophage differentiation intersection_of: capable_of GO:0030851 ! granulocyte differentiation @@ -6168,6 +6248,7 @@ xref: CALOHA:TS-0864 xref: MESH:D012156 xref: ZFA:0009252 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000764 {is_inferred="true"} ! erythroid lineage cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000764 ! erythroid lineage cell intersection_of: capable_of GO:0071971 ! extracellular exosome assembly intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -6209,6 +6290,7 @@ xref: FMA:83551 xref: ZFA:0009253 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0002194 {is_inferred="true"} ! monopoietic cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002194 ! monopoietic cell intersection_of: capable_of GO:0030224 ! monocyte differentiation intersection_of: has_part GO:0042582 ! azurophil granule @@ -6337,6 +6419,7 @@ synonym: "chondroplast" EXACT [] xref: ZFA:0009258 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000134 {is_inferred="true"} ! mesenchymal stem cell is_a: CL:0011026 ! progenitor cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: RO:0002104 PR:000001444 ! has plasma membrane part cadherin-5 intersection_of: RO:0002104 PR:000002112 ! has plasma membrane part vascular endothelial growth factor receptor 2 @@ -6388,6 +6471,7 @@ xref: ZFA:0009260 {sssom:mapping_justification="https://w3id.org/semapv/vocab/Un is_a: CL:0000443 {is_inferred="true"} ! calcitonin secreting cell is_a: CL:0000458 ! serotonin secreting cell is_a: CL:0000710 {is_inferred="true"} ! neurecto-epithelial cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000710 ! neurecto-epithelial cell intersection_of: capable_of GO:0001820 ! serotonin secretion intersection_of: capable_of GO:0014046 ! dopamine secretion @@ -6405,6 +6489,7 @@ def: "A pigment cell derived from the neural crest. Contains uric acid or other xref: ZFA:0009261 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000147 ! pigment cell +is_a: CL:0000255 ! eukaryotic cell relationship: RO:0002202 CL:0005003 ! develops from leucoblast [Term] @@ -6429,6 +6514,7 @@ def: "A pigment cell derived from the neural crest. Contains pteridine and/or ca xref: ZFA:0009263 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000147 ! pigment cell +is_a: CL:0000255 ! eukaryotic cell relationship: RO:0002202 CL:0005004 ! develops from pigment erythroblast [Term] @@ -6490,6 +6576,7 @@ synonym: "enterochromaffin cell" EXACT [] synonym: "Kulchitsky cell" EXACT [] xref: FMA:62934 xref: FMA:83132 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000577 xref: MESH:D004759 is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0000166 ! chromaffin cell @@ -6498,6 +6585,7 @@ is_a: CL:0000506 ! enkephalin secreting cell is_a: CL:0002251 ! epithelial cell of alimentary canal relationship: part_of UBERON:0004786 ! gastrointestinal system mucosa property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nType EC enteroendocrine cells, also known as enterochromaffin cells, are a vital hormone-secreting cell type found in the gastrointestinal tract. These cells are named after their location in the intestines (“entero”) and because they are stainable by chromium salts (“chromaffin”). \nThe primary function of type EC enteroendocrine cells is to act as chemosensors and lies in their capacity to produce and secrete serotonin, also known as 5-hydroxytryptamine (5-HT). Serotonin is a neurotransmitter that plays a significant role in modulating motility, secretion, vasodilation, perception of pain, and appetite in the gastrointestinal system. However, its function is not limited to the gastrointestinal tract; once secreted, serotonin is distributed via the bloodstream and contributes to regulating mood, appetite, and sleep in the brain. \nVia specific chemosensory receptors type EC enteroendocrine cells are able to respond to various environmental, metabolic, and homeostatic stimuli and transduce information from the gut to the nervous system: Food intake, particularly the ingestion of fats and carbohydrates, prompts these cells to produce and release serotonin; the mechanical stimulus of food in the lumen can also trigger release. The distribution, function, and responsiveness of type EC cells reveal them as a crucial link between the intestinal environment, the nervous system, and the regulation of numerous bodily functions." xsd:string {xref="DOI:10.1016/0166-4328(96)00075-7", xref="DOI:10.1016/j.cell.2017.05.034", xref="DOI:10.1038/s41574-019-0168-8", xref="DOI:10.1073/pnas.1804938115"} [Term] id: CL:0000578 @@ -6564,6 +6652,7 @@ xref: BTO:0001034 xref: FMA:83025 xref: ZFA:0009267 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000864 {is_inferred="true"} ! tissue-resident macrophage +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000864 ! tissue-resident macrophage intersection_of: capable_of GO:0042742 ! defense response to bacterium intersection_of: CL:4030046 GO:0042613 ! lacks_plasma_membrane_part MHC class II protein complex @@ -6644,8 +6733,10 @@ synonym: "MF.Lu" RELATED [] xref: BTO:0000802 xref: CALOHA:TS-0030 xref: FMA:83023 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000583 is_a: CL:0000864 {is_inferred="true"} ! tissue-resident macrophage is_a: CL:1001603 ! lung macrophage +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000864 ! tissue-resident macrophage intersection_of: capable_of GO:0019882 ! antigen processing and presentation intersection_of: CL:4030046 PR:000001206 ! lacks_plasma_membrane_part CX3C chemokine receptor 1 @@ -6667,6 +6758,7 @@ relationship: RO:0002104 PR:000002064 ! has plasma membrane part macrosialin relationship: RO:0002104 PR:000002972 ! has plasma membrane part macrophage mannose receptor 1 relationship: RO:0015016 PR:000001012 ! has low plasma membrane amount integrin alpha-M property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nAlveolar macrophages are unique tissue-resident macrophages found in the lungs, specifically in the air sacs or alveoli where gas exchange occurs. They are characterized by specific surface markers including: F4/80-positive, CD11b-/low, CD11c-positive, CD68-positive, sialoadhesin-positive, dectin-1-positive, MR-positive, CX3CR1-negative. These specialized immune cells form a crucial part of the body's defense mechanism, playing important roles in pulmonary health and homeostasis. They are the first line of defense in the pulmonary immune response, acting as scavengers that patrol the alveoli and engulf foreign particles like bacteria, dust, and other debris that enter the lungs through inhalation.\nThe primary function of these alveolar macrophages is phagocytosis, whereby they consume and digest foreign substances, dead cells, and other particulates. In the lung, alveolar macrophages are also responsible for clearing surfactant. Additionally, alveolar macrophages also play an integral role in initiating the immune response, as they secrete several pro-inflammatory cytokines and chemokines that recruit other immune cells to the site of infection or inflammation.\nBeyond their role in host defense, alveolar macrophages contribute to tissue remodeling and wound repair in the lungs, aiding in maintaining lung integrity. They also regulate local inflammation and control the immune response to prevent excessive inflammation that may be harmful. However, an imbalance in the function of alveolar macrophages can contribute to various lung diseases. Abnormal alveolar macrophage activation has been implicated in chronic inflammatory diseases such as emphysema, asthma, and fibrosis." xsd:string {xref="DOI:10.1007/s00424-017-1965-3", xref="DOI:10.1016/j.cellimm.2018.01.005", xref="DOI:10.1038/nri3600", xref="DOI:10.14348/molcells.2021.0058"} [Term] id: CL:0000584 @@ -6932,6 +7024,7 @@ synonym: "EoP" RELATED OMO:0003000 [PMCID:PMC2212039, PMCID:PMC2626675] synonym: "eosinophil stem cell" RELATED [] is_a: CL:0000763 ! myeloid cell is_a: CL:0002191 {is_inferred="true"} ! granulocytopoietic cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002191 ! granulocytopoietic cell intersection_of: capable_of GO:0030222 ! eosinophil differentiation intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -7014,6 +7107,7 @@ synonym: "CFU-Bas" RELATED [] synonym: "colony forming unit basophil" RELATED [] is_a: CL:0000763 ! myeloid cell is_a: CL:0002191 {is_inferred="true"} ! granulocytopoietic cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002191 ! granulocytopoietic cell intersection_of: capable_of GO:0030221 ! basophil differentiation intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -7145,11 +7239,13 @@ subset: cellxgene_subset synonym: "acinic cell" EXACT [] synonym: "acinous cell" EXACT [] xref: FMA:83625 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000622 xref: MESH:D061354 xref: ZFA:0009277 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000150 ! glandular epithelial cell is_a: CL:0000154 ! protein secreting cell relationship: part_of UBERON:0009842 ! glandular acinus +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nAcinar cells are specialized exocrine gland cells that secrete specific enzymes and fluids to aid in digestion. Found primarily in the pancreas and salivary glands, the term acinar is derived from the Latin word 'acinus' which means 'grape'; this is because acinar cells are arranged in a grape-like cluster around small ducts, formulating an acinus structure. \nIn the salivary glands, acinar cells secrete digestive enzymes as well as other substances such as mucus and water. These secretions service the initial stages of the digestive process, preparing the consumed food for onward digestion in the stomach and intestines by lubricating and partially breaking it down. \nIn the pancreas, acinar cells are responsible for synthesizing and secreting a significant amount of digestive enzymes, such as trypsin, chymotrypsin, and amylase. These enzymes are stored in zymogen granules inside the acinar cells until they are dispatched into the small intestine. Once within the small intestine, they break down proteins, carbohydrates, and fats into substances that can be absorbed. This is vital to the effective and efficient digestion and absorption of nutrients from the food we consume. \nAcinar cells have high protein synthesis rates and are susceptible to accumulation of misfolded proteins; the subsequential induction of ER stress is thought to be involved in the development of pancreatitis, a serious inflammatory disease of the exocrine pancreas." xsd:string {xref="DOI:10.1007/BF00710764", xref="DOI:10.1038/nrgastro.2013.36", xref="DOI:10.1097/MOG.0b013e32832ebfac", xref="DOI:10.1111/prd.12116", xref="DOI:10.1152/physrev.00011.2011"} [Term] id: CL:0000623 @@ -7293,6 +7389,7 @@ xref: FMA:67763 xref: ZFA:0009279 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000057 ! fibroblast is_a: CL:0000327 ! extracellular matrix secreting cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002320 ! connective tissue cell intersection_of: part_of UBERON:0002107 ! liver intersection_of: RO:0002104 PR:000007939 ! has plasma membrane part glial fibrillary acidic protein @@ -7440,19 +7537,20 @@ property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000647 name: multinucleated giant cell -def: "A phagocytic cell formed by the fusion of macrophages, occurs in chronic inflammatory responses to persistent microorganism such as M.tuberculosis, component of granulomas. Sometimes used to refer to megakaryocytes." [GOC:add, GOC:tfm, ISBN:0702022918, ISBN:0702024783] +def: "A phagocytic syncytial cell formed by the fusion of macrophages, occurs in chronic inflammatory responses to persistent microorganism such as M.tuberculosis, component of granulomas. Sometimes used to refer to megakaryocytes." [GOC:add, GOC:tfm, ISBN:0702022918, ISBN:0702024783, PMID:33348900, Wikipedia:Giant_cell] comment: Role or process: Chronic infection, granulomatous inflammation. Consider also megakaryocyte (CL:0000556) as sometimes multinucleated giant cell is used to refer to this. subset: blood_and_immune_upper_slim synonym: "foreign body giant cell" EXACT [ISBN:0702022918, ISBN:0702024783] synonym: "Langerhans giant cell" EXACT [ISBN:0702022918, ISBN:0702024783] synonym: "macrophage polykaryon" EXACT [ISBN:0702022918, ISBN:0702024783] +synonym: "MGC" RELATED OMO:0003000 [PMID:33348900] synonym: "multinucleate giant cell" EXACT [ISBN:0702022918, ISBN:0702024783] synonym: "syncytial giant cell" EXACT [ISBN:0702022918, ISBN:0702024783] xref: BTO:0003107 xref: FMA:83035 xref: MESH:D015726 -is_a: CL:0000228 ! multinucleate cell is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte +is_a: CL:4052002 ! syncytial cell intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: bearer_of PATO:0001908 ! multinucleate intersection_of: participates_in GO:0002432 ! granuloma formation @@ -7545,6 +7643,7 @@ synonym: "kidney podocyte" EXACT [] synonym: "renal podocyte" EXACT [] xref: BTO:0002295 xref: FMA:70967 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000653 xref: ZFA:0009285 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0002522 ! renal filtration cell is_a: CL:1000450 ! epithelial cell of glomerular capsule @@ -7553,6 +7652,7 @@ intersection_of: part_of UBERON:0005751 ! glomerular visceral epithelium relationship: part_of UBERON:0005751 ! glomerular visceral epithelium property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/1460" xsd:string +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nPodocytes are highly specialized, terminally differentiated glomerular visceral epithelial cells that wrap around the capillaries in the kidneys. They play an essential role in kidney function, particularly in the filtration selectivity of the glomerulus. Each podocyte is characterized by a unique architecture with a large cell body, ‘major processes’ extending outwardly from the cell body and ‘foot processes’, also known as pedicels, which surround. the glomerular capillary loops\nPodocytes represent the last barrier of the glomerular filtration membrane in the kidney. This barrier prevents the leakage of plasma proteins from the blood into the urine, hence maintaining protein homeostasis in the body. The foot processes of the podocytes interdigitate with those from neighboring cells. The cell-cell junctions between the foot processes, the slit-diaphragms, are thought to create a molecular sensor of renal filtration that prevents the passage of macromolecules while allowing water and small solutes to pass.\nPodocytes also contribute to the glomerular basement membrane by secreting collagen and maintain glomerular endothelial cell fenestration by secreting VEGFA. They have been shown to play a role in inducing cytoskeletal regulation, cell adhesion, and inflammatory response, consistent with their essential function in the kidney. \nThe importance of podocytes is further emphasized by the effects of their damage or loss. Abnormalities in podocytes often result in severe kidney diseases (podocytopathies), including focal segmental glomerulosclerosis (FSGS) and minimal change disease (MCD). Injury to the podocytes can result in \"effacement\" or flattening of foot processes, leading to increased permeability of the filtration barrier and proteinuria (an excess of serum protein in urine) which is a common symptom of kidney diseases." xsd:string {xref="DOI:10.1038/s41467-022-33748-1", xref="DOI:10.1038/s41572-020-0196-7", xref="DOI:10.1146/annurev-physiol-020911-153238", xref="DOI:10.1159/000481633", xref="DOI:10.3389/fcell.2021.771931"} [Term] id: CL:0000654 @@ -7590,6 +7690,7 @@ xref: BTO:0001115 xref: CALOHA:TS-2194 xref: FMA:72292 is_a: CL:0000017 ! spermatocyte +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000017 ! spermatocyte intersection_of: bearer_of PATO:0001394 ! diploid intersection_of: capable_of GO:0007140 ! male meiotic nuclear division @@ -7605,6 +7706,7 @@ xref: CALOHA:TS-2195 xref: FBbt:00004941 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:72293 is_a: CL:0000017 ! spermatocyte +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000413 ! haploid cell intersection_of: CL:0000017 ! spermatocyte intersection_of: bearer_of PATO:0001375 ! haploid @@ -7669,11 +7771,13 @@ name: fenestrated endothelial cell def: "An endothelial cell that has small pores, or fenestrations, which allow for the efficient exchange of substances between the blood and surrounding tissues." [DOI:10.1007/978-3-211-99390-3_133] subset: cellxgene_subset synonym: "window cell" EXACT [] +xref: https://cellxgene.cziscience.com/cellguide/CL_0000666 xref: ZFA:0009286 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000115 ! endothelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: bearer_of PATO:0002064 ! fenestrated relationship: bearer_of PATO:0002064 ! fenestrated +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nFenestrated cells are specialized epithelial cells that are characterized by a distinctive structural feature, fenestrations or tiny pores, which allow an exchange of substances such as fluids, nutrients, and waste between blood vessels and the surrounding tissue environments. These cells are present in various types of epithelial tissues in the human body, including the intestinal tract, endocrine glands, and certain parts of the renal system. \nThere are multiple types of endothelial cell fenestrations. The most common type is found in systemic capillaries of the endocrine tissue (e.g., pancreatic islets), gastrointestinal mucosa, and renal peritubular capillaries. Here, the fenestrated cells have fenestrations in their peripheral cytoplasm with a unique thin and permeable diaphragm that provides a high degree of selectivity, blocking the passage of larger molecules while allowing the free movement of smaller ones. In contrast, other types of fenestrations, such as the discontinuous epithelium of the liver sinusoidal endothelial cells, do not have diaphragms. \nCharacteristically, fenestrated cells play a vital role in the filtering process of body systems. They are a key part of the glomeruli in the kidneys where blood is filtered under high pressure. The fenestrations present in the endothelial cells lining the capillaries of the glomerulus allow the free passage of water and small solute molecules towards the Bowman's capsule, leaving behind larger proteins and cells in the blood, thereby aiding in the filtration and waste removal process. \nIn the endocrine system, fenestrated cells in glandular capillaries allow the prompt release of hormones into the bloodstream. These cells have tightly clustered fenestrations which increase the surface area available for passive diffusion, improving the efficiency of hormone secretion. In villi of the small intestine, these cells increase absorption efficiency, permitting the exchange of water, electrolytes, and nutrients.\nOverall, fenestrated cells contribute immensely to important physiological processes of filtration, absorption, and secretion, primarily connecting our body's circulation system with the surrounding tissues and organs." xsd:string {xref="DOI:10.1002/ar.1092200109", xref="DOI:10.1016/0306-4522(86)90162-4", xref="DOI:10.1016/j.devcel.2012.11.003", xref="DOI:10.1038/s41467-022-31571-2", xref="DOI:10.1152/ajprenal.90601.2008"} [Term] id: CL:0000667 @@ -7784,7 +7888,7 @@ name: gut absorptive cell def: "Cell of the intestinal epithelium with a brush border made up of many parallel packed microvilli; associated with absorption, particularly of macromolecules." [JB:jb] subset: cellxgene_subset xref: ZFA:0009289 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell relationship: part_of UBERON:0001277 ! intestinal epithelium [Term] @@ -7816,6 +7920,7 @@ subset: cellxgene_subset xref: ZFA:0009291 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000055 ! non-terminally differentiated cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0011115 ! precursor cell intersection_of: RO:0002203 CL:0000187 ! develops into muscle cell relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell @@ -7844,12 +7949,14 @@ synonym: "M-cell" EXACT [] synonym: "microfold cell" EXACT [] xref: BTO:0003600 xref: FMA:62929 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000682 xref: ZFA:0009293 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000473 ! defensive cell is_a: CL:0000627 ! transporting cell is_a: CL:0002251 ! epithelial cell of alimentary canal relationship: part_of UBERON:0003929 ! digestive tract epithelium property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nM cells, or microfold cells, of the gut are specialized epithelial cells found in the lining of the gut, specifically in the follicle-associated epithelium of mucosa-associated lymphoid tissue, where they function as sentries against toxins and pathogens. M cells are characterized by apical microfolds (hence their alternate name) which express unique adhesion molecules that enable them to sample the luminal macromolecules. \nOther morphological features that distinguish M cells from other intestinal mucosal cells include sparse microvilli and a reduced thickness of the glycocalyx, which permits adhesion while not hindering the transport of molecules. They also have unique intraepithelial invaginations on the basolateral side which are filled with macrophages and other immune cells that can process the engulfed macromolecules quickly. \nThese morphological characteristics enable M cells to serve a dual role in immune responses. They initiate the immune response by transporting antigens (such as toxic or pathogenic substances) across the epithelial layer to lymphocytes and antigen-presenting cells in the underlying lymphoid tissue. This specialized transport process is called 'transcytosis.' They also have specialized molecules like glycoprotein-2 for bacterial uptake. Simultaneously, M cells help maintain immune tolerance to food antigens and commensal bacteria, preventing unnecessary reactions to non-pathogenic substances and hypersensitivity conditions. While these functions are crucial for well-being, M cell dysfunction can lead to serious conditions like Crohn's disease and other inflammatory bowel diseases." xsd:string {xref="DOI:10.1038/nature08529", xref="DOI:10.1093/jb/mvv121", xref="DOI:10.1136/gut.47.5.735", xref="https://www.ncbi.nlm.nih.gov/books/NBK534232/", xref="https://www.sciencedirect.com/topics/medicine-and-dentistry/microfold-cell"} [Term] id: CL:0000683 @@ -7988,8 +8095,10 @@ subset: cellxgene_subset synonym: "type F enteroendocrine cell" EXACT [] xref: FMA:62938 xref: FMA:83409 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000696 is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0000167 ! peptide hormone secreting cell +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nPP cells, also known as pancreatic polypeptide cells (and previously called F cells or gamma cells), are enteroendocrine cells predominantly found in the islets of Langerhans in the head of the pancreas. They are one of the four main endocrine cell types present in the pancreatic islets, along with type A, B and D cells. PP cells are notable for their production of pancreatic polypeptide, an anorexigenic hormone that modulates food intake and energy homeostasis. \nBy secreting pancreatic polypeptide, PP cells play a significant role in the management of both digestive and appetite regulation. Upon ingestion of food, there is a significant increase in the secretion of pancreatic polypeptide, which then reduces biliary secretion and helps slow down the movement of food through the digestive tract. This allows more time for digestion to take place and nutrients to be absorbed, promoting the efficient use of dietary intake. The pancreatic polypeptide further reduces appetite by interacting with the hypothalamus, the area of the brain responsible for control of hunger.\nGiven their important role in digestion, malfunction or damage to PP cells can lead to a disturbance in the digestive process and contribute to some disease conditions. For example, an overproduction of pancreatic polypeptide can result in conditions such as pancreatic tumors and diabetes. Conversely, an under secretion might contribute to obesity due to impaired dietary control. Furthermore, PP cells may also play a role in the body's energy balance, suggesting their implication in conditions related to energy metabolism." xsd:string {xref="DOI:10.1016/j.febslet.2014.07.005", xref="DOI:10.1016/j.mce.2015.06.028", xref="DOI:10.1038/s41580-020-00317-7", xref="DOI:10.1210/jc.2003-030630", xref="DOI:10.1369/00221554155835"} [Term] id: CL:0000697 @@ -8072,7 +8181,8 @@ relationship: part_of UBERON:0000971 ! ommatidium id: CL:0000706 name: choroid plexus epithelial cell alt_id: CL:1000430 -def: "Specialized ependymal cell that produces the cerebrospinal fluid from the blood and secretes it into the lumen of the brain and spinal chord." [GOC:add, GOC:tfm, JB:jb, PMID:9550134] +def: "A specialized ependymal cell that is part of the choroid plexus epithelium, responsible for producing cerebrospinal fluid (CSF) by selectively filtering and modifying blood plasma components before secreting it into the brain and spinal cord. This cell is characterized by a brush border on its apical surface, which enhances the secretion of CSF." [GOC:add, GOC:tfm, JB:jb, PMID:15561411, PMID:9550134] +comment: A choroid plexus epithelial cell possesses non-motile 9+0 cilia. While these cilia can exhibit transient motility during development, they generally do not contribute significantly to the directional flow of cerebrospinal fluid (CSF). Instead, they are primarily involved in sensory functions. {xref="PMID:25729351"} subset: cellxgene_subset subset: human_reference_atlas synonym: "choroid plexus cell" BROAD [DOI:10.1101/2022.10.12.511898] @@ -8080,11 +8190,12 @@ synonym: "epithelial cell of choroid plexus" EXACT [] xref: FMA:70549 xref: ZFA:0009304 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000065 ! ependymal cell +is_a: CL:0000239 ! brush border epithelial cell is_a: CL:0000627 ! transporting cell -is_a: CL:0002319 ! neural cell intersection_of: CL:0000065 ! ependymal cell -intersection_of: part_of UBERON:0001886 ! choroid plexus -relationship: part_of UBERON:0001886 ! choroid plexus +intersection_of: part_of UBERON:0003911 ! choroid plexus epithelium +relationship: capable_of GO:0033326 ! cerebrospinal fluid secretion +relationship: part_of UBERON:0003911 ! choroid plexus epithelium property_value: RO:0002175 NCBITaxon:9606 property_value: terms:date "2023-08-04T08:48:30Z" xsd:dateTime @@ -8141,8 +8252,9 @@ subset: human_reference_atlas xref: BTO:0002236 xref: MESH:D054885 is_a: CL:0000154 ! protein secreting cell -is_a: CL:0002174 ! follicular cell of ovary -relationship: RO:0002202 CL:0000501 ! develops from granulosa cell +is_a: CL:0000501 ! granulosa cell +is_a: UBERON:0004120 ! mesoderm-derived structure +relationship: RO:0002202 CL:4033084 ! develops from cuboidal granulosa cell property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -8215,7 +8327,7 @@ id: CL:0000722 name: cystoblast is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000586 ! germ cell -relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda +relationship: RO:0002162 NCBITaxon:6656 ! in taxon Arthropoda [Term] id: CL:0000723 @@ -8287,11 +8399,13 @@ def: "A cell of a layer of transitional epithelium in the wall of the proximal u subset: cellxgene_subset synonym: "urinary tract transitional epithelial cell" NARROW [] xref: FMA:84127 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000731 xref: ZFA:0009308 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000244 ! transitional epithelial cell intersection_of: CL:0000244 ! transitional epithelial cell intersection_of: part_of UBERON:0000365 ! urothelium relationship: part_of UBERON:0000365 ! urothelium +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nUrothelial cells are a unique type of epithelial cell found lining the urinary tract system. They form the urothelium, a specialized, multi-layered epithelium that lines major portions of the urinary tract, including the renal pelvis, ureters, bladder, and the proximal part of the urethra. The distinct characteristic of urothelial cells is their ability to stretch and contract depending on the volume of liquid they contain - a feature that facilitates the essential role they play in maintaining the functionality and integrity of the urinary system.\nThe primary function of urothelial cells is to provide an impermeable barrier to urine, preventing the toxic components present in the urine from seeping back into the body's bloodstream. The urothelium consists of a superficial umbrella cell layer, 1–2 layers of intermediate cells, and a basal cell layer. The umbrella layer is composed of large, mostly binucleated cells that are covered in an asymmetrical unit membrane, the uroplakin plaques. These plaques function to seal the apical membrane of the bladder from the toxic and highly variable contents of urine. The lipid bilayer structure of uroplakin plaques has an exceptionally high concentration of uroplakins that contribute to the barrier function of the urothelium.\nBeyond their mechanical function, urothelial cells also play a role in sensing and signaling changes in the urinary system. They express a number of sensor molecules or respond to thermal, mechanical and chemical stimuli and can release chemical mediators. This allows them to act as sensory transducers because they detect changes in the filling state of the bladder and transmit this information to the nervous system. Moreover, these versatile cells contribute to the defense mechanism against urinary tract pathogens. They respond to bacterial infections by releasing chemical messengers, cytokines and chemokines, to attract immune cells, and also can engulf pathogens via endocytosis." xsd:string {xref="DOI:10.1002/nau.22195", xref="DOI:10.1038/ki.2009.73", xref="DOI:10.1038/ncpuro0672", xref="DOI:10.1038/s41579-020-0324-0", xref="DOI:10.1152/physrev.00041.2019"} [Term] id: CL:0000732 @@ -8367,7 +8481,7 @@ intersection_of: bearer_of PATO:0002505 ! nucleated intersection_of: capable_of GO:0001667 ! ameboidal-type cell migration relationship: capable_of GO:0001667 ! ameboidal-type cell migration relationship: part_of UBERON:0002405 ! immune system -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002202 CL:0000037 ! develops from hematopoietic stem cell property_value: RO:0002175 NCBITaxon:9606 @@ -8477,6 +8591,7 @@ synonym: "blue chromatophore" RELATED [] xref: ZFA:0009317 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000147 ! pigment cell +is_a: CL:0000255 ! eukaryotic cell relationship: RO:0002202 CL:0005005 ! develops from cyanoblast [Term] @@ -8527,13 +8642,11 @@ subset: cellxgene_subset subset: human_reference_atlas xref: FMA:67750 xref: ZFA:0009321 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: BFO:0000002 -is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000749 ! ON-bipolar cell relationship: RO:0002102 UBERON:0008925 ! axon synapses in sublaminar layer S4 relationship: RO:0002102 UBERON:0008926 ! axon synapses in sublaminar layer S5 relationship: RO:0002103 CL:0000604 ! synapsed by retinal rod cell -relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia +property_value: RO:0002175 NCBITaxon:32443 {xref="PMID:38627529"} property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -8655,6 +8768,7 @@ xref: CALOHA:TS-0647 xref: MESH:D022423 xref: ZFA:0009324 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000988 {is_inferred="true"} ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: RO:0002202 CL:0000049 ! develops from common myeloid progenitor @@ -8973,11 +9087,12 @@ intersection_of: bearer_of PATO:0001407 ! mononucleate [Term] id: CL:0000779 name: multinuclear osteoclast -def: "A specialized multinuclear osteoclast associated with the absorption and removal of bone." [GOC:add, PMID:12713016, PMID:9415452] +def: "A specialized multinuclear osteoclast, forming a syncytium through the fusion of mononuclear precursor cells, associated with the absorption and removal of bone." [GOC:add, PMID:12713016, PMID:29379067, PMID:38903088, PMID:9415452] comment: Morphology: multinucleated, highly vesicular. synonym: "multinucleated osteoclast" EXACT [] is_a: CL:0000092 {is_inferred="true"} ! osteoclast is_a: CL:0000783 ! multinucleated phagocyte +is_a: CL:4052002 ! syncytial cell intersection_of: CL:0000092 ! osteoclast intersection_of: bearer_of PATO:0001908 ! multinucleate relationship: RO:0002202 CL:0000778 ! develops from mononuclear osteoclast @@ -9098,6 +9213,7 @@ xref: FMA:70574 xref: MESH:D010950 xref: ZFA:0009332 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000946 {is_inferred="true"} ! antibody secreting cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000946 ! antibody secreting cell intersection_of: CL:4030046 GO:0019814 ! lacks_plasma_membrane_part immunoglobulin complex intersection_of: CL:4030046 GO:0042613 ! lacks_plasma_membrane_part MHC class II protein complex @@ -9173,6 +9289,7 @@ synonym: "alpha-beta T-cell" EXACT [] synonym: "alpha-beta T-lymphocyte" EXACT [] xref: ZFA:0009335 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000084 {is_inferred="true"} ! T cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000084 ! T cell intersection_of: RO:0002104 GO:0042105 ! has plasma membrane part alpha-beta T cell receptor complex disjoint_from: CL:0000798 ! gamma-delta T cell @@ -9349,6 +9466,7 @@ synonym: "gammadelta T cell" EXACT [] synonym: "gd T cell" RELATED OMO:0003000 [] xref: ZFA:0009336 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000084 {is_inferred="true"} ! T cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000084 ! T cell intersection_of: RO:0002104 GO:0042106 ! has plasma membrane part gamma-delta T cell receptor complex relationship: RO:0002104 GO:0042106 ! has plasma membrane part gamma-delta T cell receptor complex @@ -9446,6 +9564,7 @@ synonym: "immature single positive T-lymphocyte" EXACT [] synonym: "ISP" EXACT [] synonym: "T.ISP.th" EXACT [] is_a: CL:0000893 {is_inferred="true"} ! thymocyte +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000893 ! thymocyte intersection_of: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecule intersection_of: CL:4030046 PR:000001307 ! lacks_plasma_membrane_part CD44 molecule @@ -9476,6 +9595,7 @@ synonym: "preT.DN2.Th" EXACT [] synonym: "TN2 cell" EXACT [] synonym: "TN2 thymocyte" EXACT [] is_a: CL:0002489 ! double negative thymocyte +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000893 ! thymocyte intersection_of: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecule intersection_of: CL:4030046 PR:000025402 ! lacks_plasma_membrane_part T cell receptor co-receptor CD8 @@ -9502,6 +9622,7 @@ synonym: "preT.DN3.Th" EXACT [] synonym: "TN3 cell" EXACT [] synonym: "TN3 thymocyte" EXACT [] is_a: CL:0002489 ! double negative thymocyte +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000893 ! thymocyte intersection_of: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecule intersection_of: CL:4030046 PR:000001307 ! lacks_plasma_membrane_part CD44 molecule @@ -9528,6 +9649,7 @@ synonym: "double negative 4" EXACT [] synonym: "early cortical thymocyte" BROAD [] synonym: "T.DN4.th" EXACT [] is_a: CL:0002489 ! double negative thymocyte +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000893 ! thymocyte intersection_of: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecule intersection_of: CL:4030046 PR:000001307 ! lacks_plasma_membrane_part CD44 molecule @@ -9876,6 +9998,7 @@ synonym: "preNK cell" RELATED [PMID:11532393] synonym: "pro-natural killer cell" EXACT [] xref: ZFA:0009348 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000838 {is_inferred="true"} ! lymphoid lineage restricted progenitor cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: CL:4030046 PR:000001874 ! lacks_plasma_membrane_part KLRB1-like protein intersection_of: CL:4030046 PR:000002065 ! lacks_plasma_membrane_part mast/stem cell growth factor receptor @@ -9910,6 +10033,7 @@ synonym: "progenitor B-lymphocyte" EXACT [] xref: BTO:0003104 xref: ZFA:0009349 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000838 {is_inferred="true"} ! lymphoid lineage restricted progenitor cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: has_part PR:000001903 ! paired box protein PAX-5 intersection_of: has_part PR:000006611 ! DNA nucleotidylexotransferase @@ -9984,6 +10108,7 @@ synonym: "colony forming unit mast cell" RELATED [] synonym: "MCP" EXACT [] is_a: CL:0000763 ! myeloid cell is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: capable_of GO:0060374 ! mast cell differentiation intersection_of: CL:4030045 PR:000005307 ! lacks_part CCAAT/enhancer-binding protein alpha @@ -10100,6 +10225,7 @@ xref: CALOHA:TS-0825 xref: FMA:83530 is_a: CL:0000763 ! myeloid cell is_a: CL:0002191 ! granulocytopoietic cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: bearer_of PATO:0040072 ! high nuclear/cytoplasmic ratio intersection_of: CL:4030046 PR:000001012 ! lacks_plasma_membrane_part integrin alpha-M @@ -10136,7 +10262,9 @@ xref: BTO:0000725 xref: CALOHA:TS-0448 xref: ZFA:0009354 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001402 ! multipotent intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -10412,6 +10540,7 @@ name: neuromast mantle cell def: "Neuromast mantle cell is a non-sensory cell. Neuromast mantle cells surround the neuromast support cells and neuromast hair cells, separating the neuromast from the epidermis, and secrete cupula in which the ciliary bundles of all the hair cells are embedded." [ISBN:0125296509] xref: ZFA:0009362 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell +is_a: CL:0000255 ! eukaryotic cell disjoint_from: CL:0000855 ! sensory hair cell relationship: part_of UBERON:0008904 ! neuromast @@ -10421,6 +10550,7 @@ name: neuromast supporting cell def: "Neuromast support cell is a non-sensory cell of the neuromast that extend between the sensory hair cells from the basement membrane to the apical surface; neuromast support cells are surrounded by neuromast mantle cells." [ISBN:0125296509] synonym: "neuromast support cell" EXACT [] xref: ZFA:0009363 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000630 ! supporting cell disjoint_from: CL:0000855 ! sensory hair cell relationship: part_of UBERON:0008904 ! neuromast @@ -10498,7 +10628,9 @@ comment: Markers: CCR2+CXCCR1 (human, mouse, rat). subset: cellxgene_subset subset: human_reference_atlas synonym: "inflammatory monocyte" EXACT [] +xref: https://cellxgene.cziscience.com/cellguide/CL_0000860 is_a: CL:0000576 {is_inferred="true"} ! monocyte +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000576 ! monocyte intersection_of: capable_of GO:0002548 ! monocyte chemotaxis intersection_of: capable_of GO:0006909 ! phagocytosis @@ -10514,6 +10646,7 @@ relationship: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon relationship: CL:4030046 PR:000001289 ! lacks_plasma_membrane_part membrane-spanning 4-domains subfamily A member 1 relationship: RO:0015015 PR:000001199 ! has high plasma membrane amount C-C chemokine receptor type 2 property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nClassical monocytes are a subtype of monocytes that are characterized by high CD14 but no CD16 expression. Emerging from the bone marrow and entering the bloodstream, these cells play central roles in immune responses and regulation of inflammation. CD14-positive CD16-negative monocytes form the majority of circulating monocytes in the body, typically contributing to around 80-90% of the total monocyte pool. \nThe primary function of the classical monocytes is to serve in the frontline of host defense against infections. They are primed to migrate to sites of infection, and they express pattern recognition receptors that help them identify and phagocytose pathogens, leading to their destruction. Classical monocytes also contribute to inflammation by producing several pro-inflammatory cytokines including interleukins and tumor necrosis factors. \nIn response to specific signals from tissues under pathological conditions, such as infection or injury, classical monocytes can leave the bloodstream and migrate towards the affected sites. Following their arrival, these cells differentiate into diverse cell types including macrophages and dendritic cells to combat specific pathogens or injury. Dysregulated monocyte activity can lead to the development of many human diseases including inflammation, infection, tissue injury, and various autoimmune diseases." xsd:string {xref="DOI:10.1038/nri.2017.28", xref="DOI:10.1111/sji.12883", xref="DOI:10.1182/blood-2009-07-235028", xref="DOI:10.3389/fimmu.2015.00423/full", xref="DOI:10.3389/fimmu.2019.02035"} [Term] id: CL:0000861 @@ -10526,6 +10659,7 @@ synonym: "wandering histiocyte" EXACT [] xref: FMA:84643 xref: FMA:84645 is_a: CL:0000235 {is_inferred="true"} ! macrophage +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000235 ! macrophage intersection_of: participates_in GO:0006954 ! inflammatory response intersection_of: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M @@ -10555,6 +10689,7 @@ comment: Markers: Express: TNFa, IL1b, IL6, iNOS, NADPH-oxidase; produce: reacti subset: cellxgene_subset synonym: "classically activated macrophage" EXACT [] synonym: "M1 macrophage" RELATED [PMID:28923980] +xref: https://cellxgene.cziscience.com/cellguide/CL_0000863 is_a: CL:0000861 {is_inferred="true"} ! elicited macrophage intersection_of: CL:0000861 ! elicited macrophage intersection_of: capable_of GO:0032611 ! interleukin-1 beta production @@ -10569,6 +10704,7 @@ relationship: capable_of GO:0032640 ! tumor necrosis factor production relationship: capable_of GO:0042554 ! superoxide anion generation relationship: capable_of GO:0042742 ! defense response to bacterium relationship: capable_of GO:0051767 ! nitric-oxide synthase biosynthetic process +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nInflammatory macrophages, also sometimes referred to as M1 or classically activated macrophages, play an important role in the inflammatory response. The M1/M2 classification is based upon macrophage polarization rather than macrophage location and refers to macrophage activation towards either a more inflammatory or more resolving phenotype, respectively, although the functional diversity of macrophages is more nuanced than such a dichotomy suggests.\nInflammatory macrophages are derived from monocytes recruited to a site of infection or injury. M1 macrophages are classically activated, typically by IFN-γ or lipopolysaccharide (LPS). Upon sensing signs of inflammation, they quickly respond by increasing their pro-inflammatory activity. They achieve this by producing a range of signaling molecules, such as nitric oxide, reactive oxygen species, and numerous cytokines such as tumor necrosis factor-alpha (TNF-alpha) and interleukin-1, -6 and -12. The release of these potent molecules helps to recruit other immune cells to the site, killing off pathogenic organisms and facilitation inflammation. At the same time, M1 macrophages can also present antigens to T cells, thereby helping to induce an adaptive immune response. Over time, these macrophages may transition in phenotype and function to help resolve the inflammation and promote tissue repair.\nDespite the beneficial role of inflammatory macrophages in dealing with pathogens, chronic activation of these cells can lead to harmful effects. Over time, continuous production of pro-inflammatory molecules can cause damage to tissues and organs. This is seen in certain chronic inflammatory diseases, such as atherosclerosis, diabetes, obesity, asthma, and various autoimmune disorders. In such situations, the normally protective function of inflammatory macrophages is not properly controlled, which can contribute to disease pathology." xsd:string {xref="DOI:10.1038/s41392-023-01452-1", xref="DOI:10.1186/s12935-021-02089-2", xref="DOI:10.3389/fimmu.2015.00263", xref="DOI:10.3389/fimmu.2020.583084"} [Term] id: CL:0000864 @@ -10623,6 +10759,7 @@ def: "A secondary lymphoid organ macrophage found in a lymph node. This cell is comment: Marker was observed on rat cells. synonym: "MF.LN" EXACT [] is_a: CL:0000867 {is_inferred="true"} ! secondary lymphoid organ macrophage +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000867 ! secondary lymphoid organ macrophage intersection_of: part_of UBERON:0000029 ! lymph node intersection_of: RO:0015015 PR:000001931 ! has high plasma membrane amount sialoadhesin @@ -10673,6 +10810,7 @@ def: "A splenic macrophage found in the marginal zone of the spleen, involved in comment: Markers: Mouse: F4/80-, MARCO+, SR-A+, SIGN-R1+, Dectin2+. subset: human_reference_atlas is_a: CL:0000871 {is_inferred="true"} ! splenic macrophage +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000871 ! splenic macrophage intersection_of: CL:4030046 PR:000001012 ! lacks_plasma_membrane_part integrin alpha-M intersection_of: part_of UBERON:0001251 ! marginal zone of spleen @@ -10694,6 +10832,7 @@ name: splenic metallophillic macrophage def: "A splenic macrophage found in the areas surrounding the white pulp of the spleen, adjacent to the marginal sinus. Markers include F4/80-negative, Dectin2-low, sialoadhesin-positive." [GO_REF:0000031, GOC:ana, PMID:20018690] comment: Markers: Mouse: F4/80-, Dectin2-low, sialoadhesin+. is_a: CL:0000871 {is_inferred="true"} ! splenic macrophage +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000871 ! splenic macrophage intersection_of: adjacent_to UBERON:0001959 ! white pulp of spleen intersection_of: CL:4030046 PR:000001813 ! lacks_plasma_membrane_part adhesion G protein-coupled receptor E1 @@ -10713,6 +10852,7 @@ def: "A splenic macrophage found in the red-pulp of the spleen, and involved in comment: Markers: Mouse: F4/80+, CD68+, MR+, Dectin2+, macrosialin+, sialoadhesin-low; role or process: immune, clearance of senescent erythrocytes. subset: human_reference_atlas is_a: CL:0000871 {is_inferred="true"} ! splenic macrophage +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000871 ! splenic macrophage intersection_of: capable_of GO:0006955 ! immune response intersection_of: capable_of GO:0034102 ! erythrocyte clearance @@ -10745,6 +10885,7 @@ subset: human_reference_atlas synonym: "patrolling monocyte" EXACT [] synonym: "resident monocyte" EXACT [] is_a: CL:0000576 {is_inferred="true"} ! monocyte +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000576 ! monocyte intersection_of: bearer_of PATO:0000587 ! decreased size intersection_of: capable_of GO:0031294 ! lymphocyte costimulation @@ -10770,6 +10911,7 @@ def: "A splenic macrophage found in the white pulp of the spleen. Markers includ comment: Markers: Mouse: F4/80-, CD68+, macrosialin+. subset: human_reference_atlas is_a: CL:0000871 {is_inferred="true"} ! splenic macrophage +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000871 ! splenic macrophage intersection_of: CL:4030046 PR:000001813 ! lacks_plasma_membrane_part adhesion G protein-coupled receptor E1 intersection_of: part_of UBERON:0001959 ! white pulp of spleen @@ -10841,6 +10983,7 @@ def: "A border associated macrophage that is adjacent to a small blood vessel of synonym: "pvMΦ" RELATED OMO:0003000 [PMID:37232741] is_a: CL:4033054 ! perivascular cell is_a: CL:4042003 {is_inferred="true"} ! border associated macrophage +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:4042003 ! border associated macrophage intersection_of: part_of UBERON:0001981 ! blood vessel intersection_of: RO:0002104 PR:000001483 ! has plasma membrane part low affinity immunoglobulin gamma Fc region receptor III @@ -10941,6 +11084,7 @@ def: "An immature myeloid leukocyte of heterogeneous phenotype found particularl comment: Markers: Mouse: CD11b+GR1+CD31+; Human: CD34+ CD33+CD15-CD13+. (According to some reports in humans these cells are iNOS+ARG1+IL13+IFNg+); location: In cancerous tissue; in the blood and lymphoid organs in sepsis. subset: blood_and_immune_upper_slim is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: bearer_of PATO:0001501 ! immature intersection_of: capable_of GO:0050777 ! negative regulation of immune response @@ -10958,12 +11102,14 @@ def: "An elicited macrophage characterized by low production of pro-inflammatory comment: Role or process: tissue remodeling. subset: cellxgene_subset synonym: "M2 macrophage" RELATED [PMID:28923980] +xref: https://cellxgene.cziscience.com/cellguide/CL_0000890 is_a: CL:0000861 {is_inferred="true"} ! elicited macrophage intersection_of: CL:0000861 ! elicited macrophage intersection_of: capable_of GO:0048771 ! tissue remodeling intersection_of: has_part PR:000001844 ! arginase-1 relationship: capable_of GO:0048771 ! tissue remodeling relationship: has_part PR:000001844 ! arginase-1 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nAlternatively activated macrophages, also referred to as M2 macrophages, are immune cells originating from monocytes. The M1/M2 classification is based upon macrophage polarization rather than macrophage location and refers to macrophage activation towards either a more inflammatory or more resolving phenotype, respectively, although the functional diversity of macrophages is more nuanced than such a dichotomy suggests.\nM2 macrophages cells are differentiated from their precursors generally in response to Th2 cytokines, such as interleukin-4 (IL-4), interleukin-10 (IL-10), and interleukin-13 (IL-13). Tissue-resident macrophages are also sometimes said to have an “M2-like” phenotype. M2 macrophages play key roles in immunoregulation and disease resolution.\nFunctionally, alternatively activated macrophages are essential in wound healing and tissue repair and remodeling, largely due to their potent anti-inflammatory actions and their ability to promote angiogenesis. They achieve these functions by the production of specific growth factors and signaling proteins including Arg1, Ym1/2, Fizz1, and TGF-β. Additionally, they provide defense against specific categories of pathogens, particularly parasites, through specific communication with Th2 cells. \nHowever, dysfunction of M2 macrophages can be harmful. Alternatively activated macrophages have been associated with several pathological conditions such as asthma, fibrosis, and tumor progression. This is due to their capacity to inhibit inflammatory responses, promote unneeded wound healing processes, and support tumour growth and spreading. Furthermore, complex roles have been observed in metabolic disorders, cardiovascular diseases, and neurodegenerative diseases, showing the diverse functional spectrum of these cells." xsd:string {xref="DOI:10.1038/s41392-023-01452-1", xref="DOI:10.1186/s12935-021-02089-2", xref="DOI:10.3389/fimmu.2015.00263", xref="DOI:10.3389/fimmu.2020.583084"} [Term] id: CL:0000891 @@ -10979,6 +11125,7 @@ id: CL:0000892 name: smooth muscle cell derived foam cell def: "A type of foam cell derived from a smooth muscle cell containing lipids in small vacuoles and typically seen in atherolosclerotic lesions, as well as other conditions." [GOC:add, PMID:30664015] is_a: BFO:0000002 +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000891 ! foam cell relationship: RO:0002202 CL:0000192 ! develops from smooth muscle cell @@ -11016,6 +11163,7 @@ synonym: "DN1 thymocyte" EXACT [] synonym: "double negative 1" EXACT [] synonym: "preT.DN1.Th" EXACT [] is_a: CL:0000827 {is_inferred="true"} ! pro-T cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000827 ! pro-T cell intersection_of: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecule intersection_of: CL:4030046 PR:000001084 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD8 alpha chain @@ -11887,6 +12035,7 @@ comment: These cells are also reportedly CD7-low, CD10-negative, CD45RA-positive subset: cellxgene_subset synonym: "pre-NK cell" EXACT [] is_a: CL:0000623 ! natural killer cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000623 ! natural killer cell intersection_of: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule intersection_of: RO:0002104 PR:000001381 ! has plasma membrane part interleukin-2 receptor subunit beta @@ -11907,6 +12056,7 @@ synonym: "CD16-negative, CD56-bright NK cell" EXACT [] synonym: "CD56-bright cytokine secreting natural killer cell" EXACT [] synonym: "CD56-bright cytokine secreting NK cell" EXACT [] is_a: CL:0000824 ! mature natural killer cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000824 ! mature natural killer cell intersection_of: capable_of GO:0032609 ! type II interferon production intersection_of: CL:4030046 PR:000001483 ! lacks_plasma_membrane_part low affinity immunoglobulin gamma Fc region receptor III @@ -11936,6 +12086,7 @@ synonym: "CD16-positive, CD56-positive NK cell" EXACT [] synonym: "cytotoxic CD56-dim natural killer cell" EXACT [] synonym: "cytotoxic CD56-dim NK cell" EXACT [] is_a: CL:0000824 ! mature natural killer cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000824 ! mature natural killer cell intersection_of: capable_of GO:0001816 ! cytokine production intersection_of: capable_of GO:0042267 ! natural killer cell mediated cytotoxicity @@ -13054,6 +13205,7 @@ comment: Cell markers are associated with mouse hematopoietic stem cell. Origina synonym: "LSK stem cell" EXACT [] synonym: "Sca1-positive hematopoietic stem cell" EXACT [] is_a: CL:0000037 {is_inferred="true"} ! hematopoietic stem cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000037 ! hematopoietic stem cell intersection_of: CL:4030046 PR:000001014 ! lacks_plasma_membrane_part receptor-type tyrosine-protein phosphatase C isoform CD45RABC intersection_of: CL:4030046 PR:000001084 ! lacks_plasma_membrane_part T-cell surface glycoprotein CD8 alpha chain @@ -13231,6 +13383,7 @@ synonym: "CD10-positive common lymphocyte progenitor" EXACT [] synonym: "CD10-positive common lymphoid precursor" EXACT [] is_a: CL:0000051 {is_inferred="true"} ! common lymphoid progenitor is_a: CL:0000995 ! CD34-positive, CD38-positive common myeloid progenitor OR CD34-positive, CD38-positive common lymphoid progenitor +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000051 ! common lymphoid progenitor intersection_of: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule intersection_of: RO:0002104 PR:000001015 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RA @@ -13251,6 +13404,7 @@ comment: These markers are associated with human cells. Originally described in is_a: CL:0000576 {is_inferred="true"} ! monocyte is_a: CL:0000839 ! myeloid lineage restricted progenitor cell is_a: CL:0001019 ! CD115-positive monocyte OR common dendritic progenitor +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000576 ! monocyte intersection_of: RO:0002104 PR:000001012 ! has plasma membrane part integrin alpha-M intersection_of: RO:0002104 PR:000002062 ! has plasma membrane part macrophage colony-stimulating factor 1 receptor @@ -13289,6 +13443,7 @@ subset: cellxgene_subset synonym: "CD133-positive hematopoietic stem cell" EXACT [PMID:16140871] xref: CALOHA:TS-0448 is_a: CL:0000037 {is_inferred="true"} ! hematopoietic stem cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000037 ! hematopoietic stem cell intersection_of: CL:4030046 PR:000001024 ! lacks_plasma_membrane_part neural cell adhesion molecule 1 intersection_of: CL:4030046 PR:000001408 ! lacks_plasma_membrane_part ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 @@ -13318,6 +13473,7 @@ synonym: "CD217-positive common lymphocyte progenitor" EXACT [] synonym: "CD217-positive common lymphoid precursor" EXACT [] is_a: CL:0000051 {is_inferred="true"} ! common lymphoid progenitor is_a: CL:0001030 ! CD117-positive common myeloid progenitor OR CD217-positive common lymphoid progenitor +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000051 ! common lymphoid progenitor intersection_of: CL:4030046 PR:000001014 ! lacks_plasma_membrane_part receptor-type tyrosine-protein phosphatase C isoform CD45RABC intersection_of: RO:0002104 PR:000001869 ! has plasma membrane part interleukin-7 receptor subunit alpha @@ -13366,6 +13522,7 @@ comment: These markers are associated with human cells. Originally described in synonym: "CD7-negative lymphoid precursor" EXACT [] is_a: CL:0000051 {is_inferred="true"} ! common lymphoid progenitor is_a: CL:0001012 ! CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000051 ! common lymphoid progenitor intersection_of: CL:4030046 PR:000001015 ! lacks_plasma_membrane_part receptor-type tyrosine-protein phosphatase C isoform CD45RA intersection_of: CL:4030046 PR:000001836 ! lacks_plasma_membrane_part CD7 molecule @@ -13382,6 +13539,7 @@ def: "CD7-positive lymphoid progenitor cell is a lymphoid progenitor cell that i comment: These markers are associated with human cells. Originally described in the dendritic cell ontology (DC_CL:0000040)(PMID:19243617). synonym: "CD7-positive lymphoid precursor" EXACT [] is_a: CL:0000051 {is_inferred="true"} ! common lymphoid progenitor +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000051 ! common lymphoid progenitor intersection_of: CL:4030046 PR:000001015 ! lacks_plasma_membrane_part receptor-type tyrosine-protein phosphatase C isoform CD45RA intersection_of: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule @@ -13402,6 +13560,7 @@ synonym: "common dendritic precursor" EXACT [] synonym: "pro-DCs" EXACT [PMID:21219184] is_a: CL:0000763 ! myeloid cell is_a: CL:0001019 ! CD115-positive monocyte OR common dendritic progenitor +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002031 ! hematopoietic lineage restricted progenitor cell intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule intersection_of: CL:4030046 PR:000001004 ! lacks_plasma_membrane_part CD4 molecule @@ -13493,7 +13652,7 @@ name: bone cell def: "A connective tissue cell found in bone." [GO_REF:0000034, GOC:add] subset: general_cell_types_upper_slim subset: human_reference_atlas -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001474 ! bone element relationship: part_of UBERON:0001474 ! bone element @@ -13630,9 +13789,9 @@ is_a: CL:0002678 ! memory regulatory T cell intersection_of: CL:0002678 ! memory regulatory T cell intersection_of: RO:0002104 PR:000001017 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RO intersection_of: RO:0002104 PR:000001200 ! has plasma membrane part C-C chemokine receptor type 4 -intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens +intersection_of: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens relationship: RO:0002104 PR:000001017 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RO -relationship: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens +relationship: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens [Term] id: CL:0001047 @@ -13754,6 +13913,7 @@ subset: cellxgene_subset subset: human_reference_atlas synonym: "monocyte" NARROW [PMID:22343568] is_a: CL:0000576 ! monocyte +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000576 ! monocyte intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule intersection_of: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon @@ -13839,6 +13999,7 @@ synonym: "myeloid stem cell" RELATED [ISBN:0878932437] synonym: "pluripotent stem cell (bone marrow)" RELATED [ISBN:0878932437] is_a: CL:0000049 ! common myeloid progenitor is_a: CL:0011026 ! progenitor cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000049 ! common myeloid progenitor intersection_of: capable_of GO:0002573 ! myeloid leukocyte differentiation intersection_of: capable_of GO:0043011 ! myeloid dendritic cell differentiation @@ -13992,6 +14153,7 @@ synonym: "colony forming unit erythroid" RELATED [] synonym: "erythroid stem cell" RELATED [] xref: BTO:0004911 is_a: CL:0000038 ! erythroid progenitor cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000038 ! erythroid progenitor cell intersection_of: capable_of GO:0030218 ! erythrocyte differentiation intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -14082,6 +14244,7 @@ subset: cellxgene_subset subset: human_reference_atlas synonym: "ILC3" EXACT [] is_a: CL:0001065 ! innate lymphoid cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0001065 ! innate lymphoid cell intersection_of: has_part PR:000003455 ! nuclear receptor ROR-gamma isoform 2 relationship: has_part PR:000003455 ! nuclear receptor ROR-gamma isoform 2 @@ -14097,6 +14260,7 @@ synonym: "CD34-negative, CD117-positive ILC" EXACT [] synonym: "CD34-negative, CD117-positive ILCP" EXACT [] synonym: "CD34-negative, CD117-positive innate lymphoid cell precusor" EXACT [] is_a: CL:0001082 ! immature innate lymphoid cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0001065 ! innate lymphoid cell intersection_of: bearer_of PATO:0001501 ! immature intersection_of: CL:4030046 PR:P28906 ! lacks_plasma_membrane_part hematopoietic progenitor cell antigen CD34 (human) @@ -14128,6 +14292,7 @@ def: "An innate lymphoid cell precursor in the human with the phenotype CD34-pos subset: cellxgene_subset synonym: "CD34-positive, CD56-positive, CD117-positive CILP" EXACT [] is_a: CL:0001082 ! immature innate lymphoid cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0001065 ! innate lymphoid cell intersection_of: bearer_of PATO:0001501 ! immature intersection_of: RO:0002104 PR:P10721 ! has plasma membrane part mast/stem cell growth factor receptor Kit (human) @@ -14169,6 +14334,7 @@ def: "An ILC1 cell in the human with the phenotype CD56-negative, IL-7Ralpha-pos subset: cellxgene_subset synonym: "innate lymphoid cell 1, human" EXACT [] is_a: CL:0001068 ! ILC1 +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0001068 ! ILC1 intersection_of: has_part PR:Q9UL17 ! T-box transcription factor TBX21 (human) intersection_of: RO:0002104 PR:P16871 ! has plasma membrane part interleukin-7 receptor subunit alpha (human) @@ -14223,6 +14389,7 @@ def: "A group 2 innate lymphoid cell in the human with the phenotype CD25-positi subset: cellxgene_subset synonym: "ILC2, human" EXACT [] is_a: CL:0001069 ! group 2 innate lymphoid cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0001069 ! group 2 innate lymphoid cell intersection_of: has_part PR:P23771 ! trans-acting T-cell-specific transcription factor GATA-3 (human) intersection_of: RO:0002104 PR:P01589 ! has plasma membrane part interleukin-2 receptor subunit alpha (human) @@ -14280,6 +14447,7 @@ name: lymphocyte of B lineage, CD19-positive def: "A lymphocyte of B lineage that is CD19-positive." [GOC:add] comment: Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells). Lymphocytes of B cell lineage can be distinguished from those of T cell lineage by their lack of CD3e (as part of the T cell receptor complex). is_a: CL:0000945 ! lymphocyte of B lineage +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000945 ! lymphocyte of B lineage intersection_of: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon intersection_of: RO:0002104 PR:000001002 ! has plasma membrane part CD19 molecule @@ -14303,7 +14471,6 @@ is_a: CL:0001200 ! lymphocyte of B lineage, CD19-positive intersection_of: CL:0001200 ! lymphocyte of B lineage, CD19-positive intersection_of: capable_of GO:0019724 ! B cell mediated immunity intersection_of: RO:0002104 PR:000001002 ! has plasma membrane part CD19 molecule -intersection_of: RO:0002162 NCBITaxon:40674 ! in taxon Mammalia property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 [Term] @@ -14333,13 +14500,13 @@ intersection_of: CL:4030046 PR:000001380 ! lacks_plasma_membrane_part interleuki intersection_of: output_of GO:0043379 ! memory T cell differentiation intersection_of: RO:0002104 PR:000001017 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RO intersection_of: RO:0002104 PR:000001869 ! has plasma membrane part interleukin-7 receptor subunit alpha -intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens +intersection_of: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens intersection_of: RO:0015015 PR:000001307 ! has high plasma membrane amount CD44 molecule intersection_of: RO:0015015 PR:000001381 ! has high plasma membrane amount interleukin-2 receptor subunit beta relationship: CL:4030046 PR:000001380 ! lacks_plasma_membrane_part interleukin-2 receptor subunit alpha relationship: RO:0002104 PR:000001017 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RO relationship: RO:0002104 PR:000001869 ! has plasma membrane part interleukin-7 receptor subunit alpha -relationship: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens +relationship: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens relationship: RO:0002202 CL:0000906 ! develops from activated CD8-positive, alpha-beta T cell relationship: RO:0015015 PR:000001307 ! has high plasma membrane amount CD44 molecule relationship: RO:0015015 PR:000001381 ! has high plasma membrane amount interleukin-2 receptor subunit beta @@ -14358,13 +14525,13 @@ intersection_of: CL:4030046 PR:000001380 ! lacks_plasma_membrane_part interleuki intersection_of: output_of GO:0043379 ! memory T cell differentiation intersection_of: RO:0002104 PR:000001017 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RO intersection_of: RO:0002104 PR:000001869 ! has plasma membrane part interleukin-7 receptor subunit alpha -intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens +intersection_of: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens intersection_of: RO:0015015 PR:000001307 ! has high plasma membrane amount CD44 molecule intersection_of: RO:0015015 PR:000001381 ! has high plasma membrane amount interleukin-2 receptor subunit beta relationship: CL:4030046 PR:000001380 ! lacks_plasma_membrane_part interleukin-2 receptor subunit alpha relationship: RO:0002104 PR:000001017 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C isoform CD45RO relationship: RO:0002104 PR:000001869 ! has plasma membrane part interleukin-7 receptor subunit alpha -relationship: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens +relationship: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens relationship: RO:0002202 CL:0000896 ! develops from activated CD4-positive, alpha-beta T cell relationship: RO:0015015 PR:000001307 ! has high plasma membrane amount CD44 molecule relationship: RO:0015015 PR:000001381 ! has high plasma membrane amount interleukin-2 receptor subunit beta @@ -14484,6 +14651,7 @@ name: CD34-positive, CD38-positive megakaryocyte erythroid progenitor cell def: "A megakaryocyte erythroid progenitor cell is CD34-positive, CD38-positive and is IL3-receptor alpha-negative and CD45RA-negative." [GOC:tfm, PMID:12615892, PMID:190227700] comment: Markers are associated with human cell type. is_a: CL:0000050 {is_inferred="true"} ! megakaryocyte-erythroid progenitor cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000050 ! megakaryocyte-erythroid progenitor cell intersection_of: CL:4030046 PR:000001015 ! lacks_plasma_membrane_part receptor-type tyrosine-protein phosphatase C isoform CD45RA intersection_of: CL:4030046 PR:000001865 ! lacks_plasma_membrane_part interleukin-3 receptor class 2 alpha chain @@ -14502,6 +14670,7 @@ name: Kit-positive, CD34-negative megakaryocyte erythroid progenitor cell def: "A megakaryocyte erythroid progenitor cell that is Kit-positive and is Sca1-negative, CD34-negative, CD90-negative, IL7r-alpha-negative and Fcgr II/III-low." [GOC:tfm, http://www.immgen.org/index_content.html, PMID:12615892, PMID:19022770] comment: Markers are associated with mouse cells. is_a: CL:0000050 {is_inferred="true"} ! megakaryocyte-erythroid progenitor cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000050 ! megakaryocyte-erythroid progenitor cell intersection_of: CL:4030046 PR:000001003 ! lacks_plasma_membrane_part CD34 molecule intersection_of: CL:4030046 PR:000001479 ! lacks_plasma_membrane_part low affinity immunoglobulin gamma Fc region receptor II @@ -14577,6 +14746,7 @@ def: "A lin-negative, MHC-II-negative, CD11c-positive, FLT3-positive cell with i subset: cellxgene_subset is_a: CL:0000763 ! myeloid cell is_a: CL:0002031 {is_inferred="true"} ! hematopoietic lineage restricted progenitor cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002031 ! hematopoietic lineage restricted progenitor cell intersection_of: CL:4030046 GO:0042613 ! lacks_plasma_membrane_part MHC class II protein complex intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -14620,6 +14790,7 @@ def: "A progenitor cell that can give rise to plasmacytoid and myeloid dendritic comment: Markers are associated with mouse cells. synonym: "murine MDP" EXACT [] is_a: CL:0002009 {is_inferred="true"} ! macrophage dendritic cell progenitor +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002009 ! macrophage dendritic cell progenitor intersection_of: RO:0002104 PR:000001206 ! has plasma membrane part CX3C chemokine receptor 1 intersection_of: RO:0002104 PR:000002001 ! has plasma membrane part receptor-type tyrosine-protein kinase FLT3 @@ -14728,6 +14899,7 @@ name: Kit-negative, Ly-76 high orthochromatophilic erythroblasts def: "An orthochromatophilic erythroblast that is ter119-high, CD71-low, and Kit-negative." [GOC:ak, GOC:tfm, PMID:19805084] comment: Cell surface markers associated with mouse cells. is_a: CL:0000552 {is_inferred="true"} ! orthochromatic erythroblast +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000552 ! orthochromatic erythroblast intersection_of: CL:4030046 PR:000001869 ! lacks_plasma_membrane_part interleukin-7 receptor subunit alpha intersection_of: CL:4030046 PR:000002065 ! lacks_plasma_membrane_part mast/stem cell growth factor receptor @@ -14749,6 +14921,7 @@ name: CD71-negative, GlyA-positive orthochromatic erythroblast def: "An erythroblast that is GlyA-positive and CD71-negative." [GOC:ak, GOC:tfm, PMID:1638021] comment: Markers associated with human cells. is_a: CL:0000552 {is_inferred="true"} ! orthochromatic erythroblast +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000552 ! orthochromatic erythroblast intersection_of: CL:4030046 PR:000001945 ! lacks_plasma_membrane_part transferrin receptor protein 1 intersection_of: RO:0002104 PR:000001460 ! has plasma membrane part glycophorin-A @@ -14790,6 +14963,7 @@ name: GlyA-positive erythrocyte def: "An enucleate erythrocyte that is GlyA-positive." [GOC:ak, GOC:tfm, PMID:20134094] comment: Marker is associated with human cell types. is_a: CL:0000595 {is_inferred="true"} ! enucleate erythrocyte +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000595 ! enucleate erythrocyte intersection_of: RO:0002104 PR:000001460 ! has plasma membrane part glycophorin-A relationship: RO:0002104 PR:000001460 ! has plasma membrane part glycophorin-A @@ -14803,6 +14977,7 @@ name: Ly-76 high positive erythrocyte def: "An enucleate erythrocyte that is Lyg-76-high." [GOC:ak, GOC:tfm, PMID:19805084] comment: Marker is associated with mouse cell types. is_a: CL:0000595 {is_inferred="true"} ! enucleate erythrocyte +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000595 ! enucleate erythrocyte intersection_of: RO:0015015 PR:000002981 ! has high plasma membrane amount lymphocyte antigen 76 (mouse) relationship: RO:0002202 CL:0002019 ! develops from Ly-76 high reticulocyte @@ -14816,6 +14991,7 @@ name: CD34-positive, CD41-positive, CD42-positive megakaryocyte progenitor cell def: "A megakaroycotye progenitor cell that is CD34-positive, CD41-positive and CD42-positive on the cell surface." [GOC:ak, GOC:tfm, PMID:15232614] comment: Markers are associated with human cell type. is_a: CL:0000553 {is_inferred="true"} ! megakaryocyte progenitor cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000553 ! megakaryocyte progenitor cell intersection_of: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule intersection_of: RO:0002104 PR:000001907 ! has plasma membrane part platelet glycoprotein Ib alpha chain @@ -14833,6 +15009,7 @@ name: Kit-positive megakaryocyte progenitor cell def: "A megakaryocyte progenitor cell that is Kit-positive, CD41-positive, CD9-positive, Sca-1-negative, IL7ralpha-negative, CD150-negative, and Fcgamma receptor II/III-low." [GOC:ak, GOC:tfm, PMID:16951553] comment: Markers are associated with mouse cells. is_a: CL:0000553 {is_inferred="true"} ! megakaryocyte progenitor cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000553 ! megakaryocyte progenitor cell intersection_of: CL:4030046 PR:000001833 ! lacks_plasma_membrane_part SLAM family member 1 intersection_of: CL:4030046 PR:000001869 ! lacks_plasma_membrane_part interleukin-7 receptor subunit alpha @@ -14858,6 +15035,7 @@ name: CD34-positive, CD41-positive, CD42-negative megakaryocyte progenitor cell def: "A megakaryocyte progenitor cell that is CD34-positive, CD41-positive, and CD42-negative." [GOC:ak, GOC:tfm, PMID:15232614] comment: Markers are commonly associated with human cells. is_a: CL:0000553 {is_inferred="true"} ! megakaryocyte progenitor cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000553 ! megakaryocyte progenitor cell intersection_of: CL:4030046 PR:000001907 ! lacks_plasma_membrane_part platelet glycoprotein Ib alpha chain intersection_of: RO:0002104 PR:000001003 ! has plasma membrane part CD34 molecule @@ -14875,6 +15053,7 @@ name: CD34-negative, CD41-positive, CD42-positive megakaryocyte cell def: "A megakaryocyte progenitor cell that is CD34-negative, CD41-positive and CD42-positive." [GOC:ak, GOC:tfm, PMID:15232614] comment: Markers are commonly associated with human cells. is_a: CL:0000556 {is_inferred="true"} ! megakaryocyte +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000556 ! megakaryocyte intersection_of: CL:4030046 PR:000001003 ! lacks_plasma_membrane_part CD34 molecule intersection_of: RO:0002104 PR:000001907 ! has plasma membrane part platelet glycoprotein Ib alpha chain @@ -14892,6 +15071,7 @@ name: CD9-positive, CD41-positive megakaryocyte cell def: "A megakaryocyte cell with is CD9-positive and CD41-positive." [GOC:tfm] comment: Markers are commonly associated with mouse cells. is_a: CL:0000556 {is_inferred="true"} ! megakaryocyte +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000556 ! megakaryocyte intersection_of: RO:0002104 PR:000005178 ! has plasma membrane part CD9 molecule intersection_of: RO:0002104 PR:000009127 ! has plasma membrane part integrin alpha-IIb @@ -14910,6 +15090,7 @@ subset: cellxgene_subset synonym: "BMCP" EXACT [] is_a: CL:0000763 ! myeloid cell is_a: CL:0002191 ! granulocytopoietic cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: capable_of GO:0030221 ! basophil differentiation intersection_of: capable_of GO:0060374 ! mast cell differentiation @@ -14972,6 +15153,7 @@ name: hematopoietic lineage restricted progenitor cell def: "A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells." [GOC:tfm, PMID:19022770] subset: blood_and_immune_upper_slim is_a: BFO:0000002 +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001400 ! unipotent @@ -14988,6 +15170,7 @@ def: "A hematopoietic oligopotent progenitor cell that has the ability to differ comment: This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). subset: blood_and_immune_upper_slim is_a: BFO:0000002 +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001401 ! oligopotent @@ -15664,6 +15847,7 @@ synonym: "acinar cell of pancreas" EXACT [] xref: BTO:0000028 xref: CALOHA:TS-0737 xref: FMA:63032 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002064 xref: ZFA:0005739 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000622 {is_inferred="true"} ! acinar cell is_a: CL:1001599 ! pancreas exocrine glandular cell @@ -15673,6 +15857,7 @@ relationship: has_part GO:0042589 ! zymogen granule membrane relationship: part_of UBERON:0001263 ! pancreatic acinus property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nPancreatic acinar cells are the functional units of the exocrine pancreas. These cells are structurally arranged in small clusters - or acini - with a small central lumen, and their primary function is to produce and secrete enzymes that facilitate digestion of proteins, carbohydrates, and fats within the small intestine.\nSome of the most important digestive enzymes synthesized by the pancreatic acinar cells include amylase, which digests carbohydrates, lipase, which breaks down fats, and several proteases such as trypsin and chymotrypsin which are vital for the digestion of proteins. Importantly, these enzymes are produced as proenzymes or zymogens to avoid autolysis, or the breakdown of the pancreas itself.\nThe release of these enzymes by the pancreatic acinar cells is strictly regulated by hormones and neurochemicals. Cholecystokinin (CCK) released from the enteroendocrine cells in the duodenum cause the release of these enzymes. Moreover, acinar cells also respond to another hormone, secretin, by releasing bicarbonate-rich fluid which helps to neutralize the gastric acid in the duodenum. \nDysregulation in the function of pancreatic acinar cells can lead to severe health issues, including pancreatitis, which is characterized by inflammatory damage to the organ due to the premature activation of digestive enzymes." xsd:string {xref="DOI:10.1016/0165-6147(89)90192-2", xref="DOI:10.1038/nrgastro.2013.36", xref="DOI:10.1097/01.mog.0000239863.96833.c0", xref="https://www.ncbi.nlm.nih.gov/books/NBK54134/"} creation_date: 2010-06-24T03:16:29Z [Term] @@ -15693,11 +15878,13 @@ id: CL:0002067 name: type A enteroendocrine cell def: "An enteroendocrine cell that produces glucagon." [GOC:tfm, ISBN:0412046911] xref: FMA:62939 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002067 is_a: CL:0000164 ! enteroendocrine cell is_a: CL:0000170 ! glucagon secreting cell intersection_of: CL:0000164 ! enteroendocrine cell intersection_of: capable_of GO:0070091 ! glucagon secretion property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nType A enteroendocrine cells, also known as alpha cells or A cells, are a species of endocrine cells primarily located in the pancreatic islets of Langerhans; they have also been identified within the lining of the stomach. Functionally, these cells are pivotal in glucose metabolism and homeostasis, accounting for about 20% of the total population of cells in the pancreatic islets. \nThe primary role of type A enteroendocrine cells involves the synthesis, storage, and secretion of the peptide hormone glucagon, which is critical in energy regulation throughout the body. In response to a decrease in blood glucose levels, the pancreatic A cells are stimulated to secrete glucagon into the bloodstream. Glucagon acts on its target cells, mainly in the liver, to stimulate glycogenolysis and gluconeogenesis processes, thereby increasing blood glucose levels back to normal. In this way, pancreatic A cells play an integral role in maintaining glucose homeostasis and preventing hypoglycemia.\nPancreatic A cells also participate in the local regulation of islet activities as glucagon acts through glucagon receptors on A, B and D type cells within the islets. Recent studies have also shown that Pancreatic A cells play a role in the generation and regeneration of B type cells. Following beta cell injuries pancreatic A cells increase in numbers and produce Glucagon-like peptide-1 (GLP-1), which increases the proliferation and cytoprotection of beta cells. In response to extreme injury of B type cells pancreatic A cells can transform (transdifferentiate) into functioning B type cells.\nUntil recently, glucagon has been considered a pancreas-specific hormone; however, extrapancreatic glucagon has been reported in patients who had undergone complete, and glucagon-positive cells been identified in the human stomach, indicating that Type A enteroendocrine cells are not restricted to the pancreas." xsd:string {xref="DOI:10.1016/j.diabres.2018.06.013", xref="DOI:10.1210/en.2016-1748", xref="DOI:10.2337/db15-1541", xref="DOI:10.2337/dbi19-0002", xref="DOI:10.3389/fphys.2012.00349/full"} creation_date: 2010-09-10T10:48:54Z [Term] @@ -15943,12 +16130,13 @@ creation_date: 2010-07-14T03:22:02Z id: CL:0002085 name: tanycyte alt_id: CL:0000643 -def: "Specialized elongated ventricular ependymal cell that has processes that extend to the outer, or pial, surface of the CNS. Resemble spongioblasts seen in developing brain. Found in the adult brain in the third ventricle, cerebral aqueduct, spinal canal and floor of the fourth ventricle." [GOC:tfm, http://neurolex.org/wiki/Category\:Tanycyte] +def: "A specialized elongated ventricular ependymal cell that has processes that extend to the outer, or pial, surface of the CNS. A tanycyte is found in the adult brain, specifically in the third ventricle, cerebral aqueduct, spinal canal, and floor of the fourth ventricle. This cell type is involved in hormonal regulation, gatekeeping molecules between the bloodstream and cerebrospinal fluid, metabolic sensing, and regulating food intake." [GOC:tfm, http://neurolex.org/wiki/Category\:Tanycyte] subset: cellxgene_subset -synonym: "stretch cell" EXACT [] +synonym: "stretch cell" EXACT [PMID:29351662] xref: BTO:0001953 xref: FMA:54560 is_a: CL:0000683 ! ependymoglial cell +relationship: part_of UBERON:0004670 ! ependyma property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-07-15T11:21:11Z @@ -16000,6 +16188,7 @@ name: group 2 innate lymphoid cell, mouse def: "A group 2 innate lymphoid cell in the mouse capable of secreting IL-13 in response to a helminth infection. This cell is lineage-negative, ICOS-positive, IL1RL1-positive, IL7Ralpha-positive, and IL17Br-positive." [GOC:add, GOC:tfm, PMID:20200518] synonym: "nuocyte" BROAD [] is_a: CL:0001069 ! group 2 innate lymphoid cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0001069 ! group 2 innate lymphoid cell intersection_of: capable_of GO:0002830 ! positive regulation of type 2 immune response intersection_of: capable_of GO:0032616 ! interleukin-13 production @@ -16784,13 +16973,14 @@ comment: These cells possess numerous cilia on their surface, typically ranging subset: cellxgene_subset subset: human_reference_atlas xref: FMA:70542 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002145 is_a: CL:0002202 ! epithelial cell of tracheobronchial tree is_a: CL:0005012 ! multi-ciliated epithelial cell is_a: CL:4030034 ! respiratory ciliated cell -relationship: has_part GO:0031514 ! motile cilium relationship: RO:0002202 CL:0002209 ! develops from intermediate epitheliocyte property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nCiliated columnar cells of the tracheobronchial tree compose the inner lining of the tracheobronchial tree, the system of airways consisting of trachea, bronchi and bronchioles that allow passage of air into the lungs, where gas exchange occurs. A defining feature of these endo-epithelial cells are the tiny hair-like structures covering their surface, known as cilia. The nucleus is located at the base of the cell, and the area above it is rich in mitochondria and well-developed endoplasmic reticulum, both crucial for the energy-intensive process of cilia operation.\nThe primary function of these ciliated cells is to keep the respiratory tract clean via mucociliary clearance or the respiratory escalator. These cells create a two-layered 'coat': The lower \"sol\" layer is watery where the cilia can beat in coordinated waves, and the upper \"gel\" layer is thick and sticky, trapping inhaled particles, such as dust, bacteria, viruses, and other potentially harmful substances. This rhythmical beating of the cilia then moves the mucus and trapped particles upwards and out of the respiratory tract, which is then either coughed out or swallowed.\nDamage or dysfunction of these ciliated cells, as seen in diseases such as primary ciliary dyskinesia, cystic fibrosis, or chronic bronchitis, may lead to reduced or ineffective mucociliary clearance and an increased susceptibility to respiratory infections." xsd:string {xref="DOI:10.1101/cshperspect.a028241", xref="DOI:10.1146/annurev-physiol-021014-071931", xref="DOI:10.1152/ajplung.00329.2019", xref="DOI:10.1159/000196486"} creation_date: 2010-08-24T03:38:29Z [Term] @@ -16889,6 +17079,7 @@ xref: BTO:0001943 xref: FMA:68650 is_a: BFO:0000002 is_a: CL:0000225 ! anucleate cell +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000311 ! keratin accumulating cell relationship: part_of UBERON:0002027 ! stratum corneum of epidermis relationship: RO:0002202 CL:0000312 ! develops from keratinocyte @@ -17111,6 +17302,8 @@ xref: EMAPA:31247 xref: FMA:70589 is_a: CL:0000500 ! follicular epithelial cell is_a: CL:0002078 ! meso-epithelial cell +is_a: CL:2000064 ! ovarian surface epithelial cell +relationship: part_of UBERON:0001305 ! ovarian follicle property_value: RO:0002161 NCBITaxon:50557 {source="https://github.com/obophenotype/cell-ontology/issues/589"} property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-08-25T03:01:27Z @@ -17262,6 +17455,7 @@ xref: BTO:0004632 xref: FMA:70970 is_a: CL:0000666 ! fenestrated endothelial cell is_a: CL:0002681 ! kidney cortical cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0000074 ! renal glomerulus relationship: has_part GO:0036053 ! glomerular endothelium fenestra @@ -17468,8 +17662,10 @@ synonym: "fibrillovesicular cell" EXACT [] synonym: "multivesicular cell" EXACT [] synonym: "tuft cell" EXACT [] xref: FMA:67978 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002204 is_a: CL:0002076 ! endo-epithelial cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nBrush cells, also referred to as tuft cells or multivesicular cells, are a specialized type of epithelial cell mainly noted for their characteristic 'brush border' composed of microvilli. These cells reside in the epithelial lining of tissue organs such as the respiratory tract, gastrointestinal tract, and the bile ducts. The name derives from their distinct appearance under the microscope, which resembles a brush due to the dense layer of microvilli protruding into the lumen.\nA key function of brush cells is chemosensation: They express a variety of signaling molecules and receptors that enable them to detect specific chemical stimuli in the environment and act as sensory transducers. Many of these receptors are responsive to luminal content, which makes brush cells vital for regulating and coordinating appropriate physiological responses to changes in these substances. \nRecent research has also elucidated an important role for these cells in immunity. Intestinal brush cells have been found to be the source of a cytokine called interleukin-25, which can initiate type 2 immune responses during parasitic infections. This immune function, along with the chemosensing abilities, signifies that brush cells could serve crucial roles in health and disease, although much research is still required to fully elucidate their myriad roles in physiology and pathology. Overall, brush cells are a versatile cell type, whose distinct morphology and functional capabilities allow them to perform a unique set of functions within the body." xsd:string {xref="DOI:10.1007/978-3-211-99390-3_83", xref="DOI:10.1038/nature16161", xref="DOI:10.1111/j.1469-7580.2005.00403.x", xref="DOI:10.3389/fphys.2015.00087", xref="DOI:10.5114/ceji.2022.124416"} creation_date: 2010-09-02T02:28:53Z [Term] @@ -17726,11 +17922,13 @@ def: "A lens fiber cell that develops from primary lens fiber; located towards t subset: cellxgene_subset subset: human_reference_atlas synonym: "secondary lens fibre" EXACT [] +xref: https://cellxgene.cziscience.com/cellguide/CL_0002225 is_a: BFO:0000002 is_a: CL:0011004 ! lens fiber cell relationship: RO:0002202 CL:0002228 ! develops from primary lens fiber property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nSecondary lens fibers are a specialized type of elongated cells located within the structure of the eye's lens. They play an essential role in vision by enabling light transmission and focus on the retina, which allows for clear, distinct vision. These cells are characterized by their lack of nuclei and organelles, their orderly alignment, and their high protein content, particularly crystallins. \nLens fibers are differentiated from equatorial epithelial cells of the lens in a process that involves cell elongation, denucleation and tight packing, which serve to reduce light scattering occurrences in the eye. This differentiation accelerates substantially after birth in comparison to during embryogenesis and continues throughout life, contributing to the growth of the eye lens. Secondary lens fibers are specifically those cells that are newly differentiated and cover the old lens fiber core. This process also leads to the removal of light-obstructing cellular components, mainly nuclei and organelles, making these fibers transparent and ideal for their function. \nThe fibers carry out their primary function of light refraction via a high concentration of specialized proteins known as crystallins, which form a gradient of refractive index together with the cytoplasm. This index manipulation facilitates precise light focus onto the retina. Secondary lens fibers also contribute to the lens's shape and biomechanical properties through intercellular interactions, particularly at the sutures where the ends of the fibers meet. Any disruption to secondary lens fibers can lead to vision problems, including cataracts, which is the clouding of the lens resulting from the aggregation of crystallin proteins." xsd:string {xref="DOI:10.1016/B978-1-4377-1926-0.10005-0", xref="DOI:10.1016/j.biocel.2007.10.034", xref="DOI:10.1098/rstb.2010.0324", xref="DOI:10.1136/bmjophth-2020-000459", xref="https://www.sciencedirect.com/topics/immunology-and-microbiology/lens-fiber"} creation_date: 2010-09-07T10:53:39Z [Term] @@ -17903,6 +18101,7 @@ xref: EMAPA:17965 xref: FMA:84772 xref: ISBN:0721662544 xref: VHOG:0000661 +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000670 ! primordial germ cell relationship: part_of UBERON:0000992 ! ovary property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -18039,12 +18238,14 @@ def: "A cell that is found in a zone occupying the bottom region of the crypt; p subset: cellxgene_subset synonym: "stem cell of intestinal crypt of Lieberkuhn" EXACT [] xref: FMA:63379 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002250 is_a: CL:0000048 ! multi fate stem cell is_a: CL:0002563 ! intestinal epithelial cell intersection_of: CL:0000034 ! stem cell intersection_of: part_of UBERON:0001983 ! crypt of Lieberkuhn relationship: part_of UBERON:0001983 ! crypt of Lieberkuhn property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nIntestinal crypt stem cells, also known as crypt base columnar cells, are a unique type of cell, characterized by the highly specific marker LGR5, found in the intestinal epithelium. Situated at the bottom of the minute pockets known as crypts of Lieberkühn, these are undifferentiated cells that have the ability to perpetually self-renew, as well as differentiate into various other cell types that constitute the epithelial lining of the intestine. \nThe fundamental role of intestinal crypt stem cells is to provide a constant supply of new cells to maintain the cellular turnover of the intestinal epithelium, a tissue known for rapid self-renewal. These stem cells are nurtured and protected by specialized epithelial and mesenchymal cells, and together constitute the intestinal stem cell niche. \nAn important function of intestinal crypt stem cells is to sustain the balance between cell division and programmed cell death, called apoptosis, to ensure the integrity of the intestinal lining. Given their active proliferation rate, these stem cells initiate the creation of diverse differentiated cell types, including enterocytes (the primary absorptive cells in the intestinal lumen), goblet cells (that produce mucus to protect the epithelial layer), enteroendocrine cells (involved in producing gastrointestinal hormones), and Paneth cells (involved in secreting antimicrobial peptides). This diversity in output regulates the physiological activities of the gut ranging from nutrient absorption, hormone secretion, bacterial balance, to immunity.\nResearch studies suggest that dysregulation in intestinal crypt stem cell proliferation and differentiation is associated with several intestinal disorders including intestinal cancer, and various enteropathies." xsd:string {xref="DOI:10.1016/j.cell.2013.07.004", xref="DOI:10.1038/s41575-018-0081-y", xref="DOI:10.1038/s41580-020-0278-0", xref="DOI:10.1101/gad.1674008", xref="DOI:10.1111/j.1365-2184.2009.00642.x"} creation_date: 2010-09-08T09:21:22Z [Term] @@ -18359,6 +18560,7 @@ synonym: "PP cell of pancreatic islet" EXACT [] synonym: "PP-cell of pancreatic islet" EXACT [] xref: BTO:0000805 xref: FMA:70588 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002275 xref: MESH:D050418 xref: ZFA:0005742 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000696 ! PP cell @@ -18369,6 +18571,7 @@ intersection_of: part_of UBERON:0001264 ! pancreas relationship: part_of UBERON:0000006 ! islet of Langerhans property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nPancreatic polypeptide (PP) cells (also called F or gamma cells) are unique endocrine cells located within the Islets of Langerhans in the pancreas. PP cells are one of the rarer pancreatic cell types and are more prevalent in the head and neck of the pancreas. They are critical in normal pancreatic physiological functions and are involved in the development of pancreatic endocrine disorders.\nThe primary function of PP cells is the production and secretion of the pancreatic polypeptide hormone (PP). This hormone plays a crucial role in several gastrointestinal functions and metabolic responses. The release of the PP hormone is stimulated after eating, especially in protein-rich meals, leading to it being present in large amounts during digestion. The fundamental role of PP is to self-regulate pancreatic secretion activities ensuring its exocrine and endocrine functions are under control.\nThe pancreatic polypeptide hormone from PP cells also aids in adapting to low physical activity and fasting by reducing the production of insulin and glucagon and inhibiting the hepatic glucose production. Additionally, this hormone influences gut motility by slowing down the gastric emptying and reducing small intestinal transit, thereby controlling the pace at which nutritional substances are absorbed. Because of these functions, any malfunction or irregularity in PP cells can result in various disorders such as diabetes and pancreatic diseases." xsd:string {xref="DOI:10.1016/B978-0-12-819402-7.00001-2", xref="DOI:10.1016/B978-012369442-3/50154-9", xref="DOI:10.1016/j.mce.2015.06.028", xref="DOI:10.1038/s42255-019-0148-2", xref="DOI:10.3389/fendo.2023.1192311"} creation_date: 2010-09-10T03:30:31Z [Term] @@ -18659,12 +18862,13 @@ creation_date: 2010-09-13T03:23:25Z [Term] id: CL:0002301 name: type B synovial cell -def: "A resident stromal cell located in the synovial membrane and responsible for the production of immune-related cytokines and chemokines. This cell type secretes glycoproteins and hyaluronic acid, has abundant granular endoplasmic reticulum, but contains fewer vacuoles and vesicles." [GOC:tfm, ISBN:0517223651, PMID:34433485, PMID:34772990] {terms:contributor="https://orcid.org/0000-0002-0819-0473"} +def: "A resident stromal cell located in the synovial membrane and responsible for the production of immune-related cytokines and chemokines. This cell type secretes glycoproteins and hyaluronic acid, has abundant granular endoplasmic reticulum, but contains fewer vacuoles and vesicles." [GOC:tfm, ISBN:0517223651, PMID:34433485, PMID:34772990] comment: Type B synovial cells play a key role in the pathogenesis of chronic inflammatory diseases, such as rheumatoid arthritis, and are essential for the maintenance of normal joint functions. Fibroblast-like synoviocytes from different joints have different properties, which may contribute to the characteristic pattern of joint involvement in different types of arthritis. {xref="https://en.wikipedia.org/wiki/Fibroblast-like_synoviocyte", xref="PMID:34433485"} synonym: "fibroblast-like synoviocyte" EXACT [] synonym: "synovial fibroblast" EXACT [PMID:23147896] xref: BTO:0003652 xref: FMA:66788 +is_a: CL:0000076 ! squamous epithelial cell is_a: CL:0000214 ! synovial cell is_a: CL:0000499 ! stromal cell intersection_of: CL:0000499 ! stromal cell @@ -18672,6 +18876,7 @@ intersection_of: part_of UBERON:0002018 ! synovial membrane of synovial joint relationship: capable_of GO:0030213 ! hyaluronan biosynthetic process relationship: part_of UBERON:0002018 ! synovial membrane of synovial joint relationship: produces UBERON:0001090 ! synovial fluid +property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-13T03:39:14Z @@ -18682,6 +18887,7 @@ def: "A synovial cell that is macrophage-like, characterized by surface ruffles comment: Type A cells are usually round and located in the upper part of the synovial intima. {xref="PMID:10770586"} synonym: "type A synoviocyte" EXACT [] xref: FMA:66787 +is_a: CL:0000076 ! squamous epithelial cell is_a: CL:0000214 ! synovial cell is_a: CL:0000234 ! phagocyte relationship: part_of UBERON:0002018 ! synovial membrane of synovial joint @@ -18699,10 +18905,12 @@ subset: eye_upper_slim subset: human_reference_atlas synonym: "PE cell" EXACT [https://doi.org/10.1016/j.exer.2003.09.021] xref: FMA:70606 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002303 is_a: CL:0000529 ! pigmented epithelial cell relationship: part_of UBERON:0001778 ! ciliary epithelium property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nPigmented ciliary epithelial cells, which are a type of pigment cell, have a crucial function within the eye's ciliary body. The ciliary body, located behind the iris, is one of the eye’s most vital structures and consists of two types of epithelial cells: the pigmented and the non-pigmented ciliary epithelial cells. The pigmented ciliary epithelial cells form the outer layer of the ciliary body and exhibit a black or brown pigmentation due to the melanin they contain.\nOne key function of pigmented ciliary epithelial cells is to aid in the formation of aqueous humor, an intraocular fluid that nourishes the cornea and lens, and maintains intraocular pressure which is essential for the eye’s shape and light refraction. These cells facilitate this function in conjunction with the non-pigmented ciliary epithelial cells. Together, the pigmented and non-pigmented ciliary epithelial cells form a bilayer epithelium that allows the secretion of aqueous humor through a bi-directional fluid transport mechanism.\nPigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, a physiological frontier that controls the entry and exit of various substances from the blood to the aqueous humor and vice versa. The pigmentation in these cells, intensified by melanin, helps to absorb scattered light coming into the eye, reducing any potential damage and glare." xsd:string {xref="DOI:10.1016/S1569-2590(05)10005-6", xref="DOI:10.1111/j.1444-0938.2002.tb02384.x"} creation_date: 2010-09-13T04:09:27Z [Term] @@ -18904,6 +19112,7 @@ def: "A mesothelial cell capable of circulating in the blood by first losing its xref: FMA:86712 is_a: BFO:0000002 is_a: CL:0000081 ! blood cell +is_a: CL:0000255 ! eukaryotic cell relationship: RO:0002202 CL:0000077 ! develops from mesothelial cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-15T10:47:11Z @@ -18915,7 +19124,7 @@ def: "A cell that is part of the nervous system." [GOC:tfm, ISBN:0618947256] subset: cellxgene_subset xref: CALOHA:TS-2040 xref: FMA:70333 -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001016 ! nervous system relationship: part_of UBERON:0001016 ! nervous system @@ -18932,7 +19141,7 @@ xref: CALOHA:TS-2096 xref: FMA:63875 xref: MESH:D003239 xref: ZFA:0009392 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0002384 ! connective tissue relationship: part_of UBERON:0002384 ! connective tissue @@ -19081,9 +19290,11 @@ name: basal epithelial cell of tracheobronchial tree def: "An epithelial cell type that lacks the columnar shape typical for other respiratory epithelial cells. This cell type is able to differentiate into other respiratory epithelial cells in response to injury." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas +xref: https://cellxgene.cziscience.com/cellguide/CL_0002329 is_a: CL:0002202 ! epithelial cell of tracheobronchial tree property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nThe basal epithelial cells of the tracheobronchial tree are critical components found in the lining of the airway passages, including the trachea and bronchi. They are keratin-5-positive, nonciliated, cuboidal cells and typically tightly attached to the basement membrane. In humans, the proportion of basal cells in the respiratory epithelium gradually decreases going down the tracheobronchial tree: they represent approximately 34% of the cells in the trachea, 27% in the large airways, and 10% in the small airways, although it is worth noting that there are differences in the compositions of the tracheobronchial epithelia between different species.\nBasal epithelial cells serve as the basal layer of the tracheobronchial epithelium, providing both structural and regenerative support for the epithelial tissue that lines the upper regions of the respiratory tract. They serve as progenitor or stem cells that are capable of differentiating into multiple cell types, such as ciliated and secretory cells. This gives them a central role in homeostatic maintenance of the epithelium, and in repairing damaged epithelium after an injury or during disease. This regenerative capacity is crucial in maintaining the integrity of the tracheobronchial surface, especially given its continual exposure to inhaled irritants and microorganisms. \nIn addition to their primary restorative function, basal epithelial cells are also involved in the initial immune response within the tracheobronchial tree. Equipped with pattern recognition receptors, these cells can identify and respond to pathogenic organisms, triggering an immune response and producing a range of inflammatory mediators, such as cytokines and chemokines, to help combat infections." xsd:string {xref="DOI:10.1165/rcmb.2013-0049OC", xref="DOI:10.1186/s12931-014-0160-8", xref="DOI:10.2353/ajpath.2010.090870"} creation_date: 2010-09-20T02:10:36Z [Term] @@ -19103,7 +19314,7 @@ subset: human_reference_atlas is_a: CL:0002145 ! ciliated columnar cell of tracheobronchial tree is_a: CL:0002328 ! bronchial epithelial cell intersection_of: CL:0000064 ! ciliated cell -intersection_of: part_of UBERON:0002185 ! bronchus +intersection_of: part_of UBERON:0002031 ! epithelium of bronchus property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-20T02:21:12Z @@ -19166,6 +19377,7 @@ comment: Human markers; killer cell immunoglobulin-like receptor 2DL1 is used as subset: cellxgene_subset synonym: "p-NK" RELATED [PMID:12457618] is_a: CL:0000823 ! immature natural killer cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000823 ! immature natural killer cell intersection_of: CL:4030046 PR:000001003 ! lacks_plasma_membrane_part CD34 molecule intersection_of: RO:0002104 PR:000001024 ! has plasma membrane part neural cell adhesion molecule 1 @@ -19234,6 +19446,7 @@ subset: human_reference_atlas synonym: "decidual NK cell" EXACT [] synonym: "dNK cell" EXACT [] is_a: CL:0000824 ! mature natural killer cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000824 ! mature natural killer cell intersection_of: CL:4030046 PR:000001483 ! lacks_plasma_membrane_part low affinity immunoglobulin gamma Fc region receptor III intersection_of: RO:0002104 PR:000009766 ! has plasma membrane part galectin-1 @@ -19254,6 +19467,7 @@ def: "A natural killer cell that is developmentally immature, has the phenotype comment: Human markers; killer cell immunoglobulin-like receptor 2DL1 is used as a representative example (PRO at this time lacks a KIR superfamily). synonym: "p-NK" RELATED [PMID:12457618] is_a: CL:0000823 ! immature natural killer cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000823 ! immature natural killer cell intersection_of: CL:4030046 PR:000001003 ! lacks_plasma_membrane_part CD34 molecule intersection_of: CL:4030046 PR:000001024 ! lacks_plasma_membrane_part neural cell adhesion molecule 1 @@ -19277,6 +19491,7 @@ def: "An immature natural killer cell that is NK1.1-positive, DX5-positive, Ly49 comment: Markers are associated with mouse cells. synonym: "preNK.BM" BROAD [] is_a: CL:0000823 ! immature natural killer cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000823 ! immature natural killer cell intersection_of: RO:0002104 PR:000001008 ! has plasma membrane part integrin alpha-2 intersection_of: RO:0002104 PR:000002977 ! has plasma membrane part killer cell lectin-like receptor subfamily B member 1C @@ -19299,6 +19514,7 @@ id: CL:0002346 name: Dx5-negative, NK1.1-positive immature natural killer cell, mouse def: "An immature natural killer cell that is NK1.1-positive and DX-5 negative." [GOC:tfm, PMID:12766763] is_a: CL:0000823 ! immature natural killer cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000823 ! immature natural killer cell intersection_of: CL:4030046 PR:000001008 ! lacks_plasma_membrane_part integrin alpha-2 intersection_of: RO:0002104 PR:000002977 ! has plasma membrane part killer cell lectin-like receptor subfamily B member 1C @@ -19314,6 +19530,7 @@ id: CL:0002347 name: CD27-high, CD11b-high natural killer cell, mouse def: "A mature natural killer cell that is CD27-high and CD11b-high. This cell type is capable of interferon-gamma secretion." [GOC:tfm, PMID:19949422] is_a: CL:0000824 ! mature natural killer cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000824 ! mature natural killer cell intersection_of: capable_of GO:0032609 ! type II interferon production intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus @@ -19331,6 +19548,7 @@ id: CL:0002348 name: CD27-low, CD11b-high natural killer cell, mouse def: "A CD27-low, CD11b-high natural killer cell that has a higher threshold of activation due to higher expression of inhibitory receptors." [GOC:tfm, PMID:1994922] is_a: CL:0000824 ! mature natural killer cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000824 ! mature natural killer cell intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus intersection_of: RO:0015015 PR:000001012 ! has high plasma membrane amount integrin alpha-M @@ -19347,6 +19565,7 @@ id: CL:0002349 name: CD27-high, CD11b-low natural killer cell, mouse def: "A natural killer cell that is CD27-high and CD11b-low." [GOC:tfm, PMID:1994922] is_a: CL:0000824 ! mature natural killer cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000824 ! mature natural killer cell intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus intersection_of: RO:0015015 PR:000001963 ! has high plasma membrane amount CD27 molecule @@ -19403,6 +19622,7 @@ id: CL:0002353 name: fetal liver hematopoietic progenitor cell def: "A hematopoietic stem cell that resides in the fetal liver. In mice, this cell type is first observed at E10.5. This cell type is MHC-positive, HSA-positive, AA4.1-positive, CD45-positive, Sca-1 positive, CD150-positive, CD48-negative and CD244-negative." [GOC:tfm, ISBN:978-1-60327-346-6, PMID:16569764] is_a: CL:0002352 {is_inferred="true"} ! gestational hematopoietic stem cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002352 ! gestational hematopoietic stem cell intersection_of: CL:4030046 PR:000001308 ! lacks_plasma_membrane_part CD48 molecule intersection_of: CL:4030046 PR:000001896 ! lacks_plasma_membrane_part natural killer cell receptor 2B4 @@ -19430,6 +19650,7 @@ name: yolk sac hematopoietic stem cell def: "A hematopoietic stem found in the yolk sac. In mice, this cell type is Sca-1-negative, CD45-negative, MHC-negative, HSA-positive, AA4.1-positive, CD44-positive." [doi:10.1097/MOH.0b013e3282f97ae1, GOC:tfm] synonym: "hemangioblast precursor" EXACT [] is_a: CL:0002352 {is_inferred="true"} ! gestational hematopoietic stem cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002352 ! gestational hematopoietic stem cell intersection_of: CL:4030046 GO:0042611 ! lacks_plasma_membrane_part MHC protein complex intersection_of: CL:4030046 PR:000001006 ! lacks_plasma_membrane_part receptor-type tyrosine-protein phosphatase C @@ -19456,6 +19677,7 @@ synonym: "primitive erythroblast" EXACT [] synonym: "primitive erythrocyte" EXACT [] synonym: "primitive erythroid cell" EXACT [] is_a: CL:0002417 {is_inferred="true"} ! primitive erythroid lineage cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002417 ! primitive erythroid lineage cell intersection_of: bearer_of PATO:0000586 ! increased size intersection_of: has_part PR:000008467 ! hemoglobin subunit zeta @@ -19489,6 +19711,7 @@ name: fetal derived definitive erythrocyte def: "A fetal liver derived enucleated erythrocyte. This erythrocyte resembles adult erythrocytes in that they are small (3- to 6- times smaller than primitive erythrocytes) and produce adult hemaglobins." [GOC:tfm, PMID:11495698] synonym: "macrocyte" EXACT [] is_a: CL:0000595 {is_inferred="true"} ! enucleate erythrocyte +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000595 ! enucleate erythrocyte intersection_of: has_part PR:000008857 ! hemoglobin subunit beta-1 intersection_of: part_of UBERON:0000922 ! embryo @@ -19537,6 +19760,7 @@ def: "A progenitor cell that is capable of forming colonies of primitive erythro synonym: "EryP-CFC" EXACT [] synonym: "inner blood island hemangioblast" EXACT [] is_a: CL:0002417 {is_inferred="true"} ! primitive erythroid lineage cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002417 ! primitive erythroid lineage cell intersection_of: RO:0002104 PR:000009127 ! has plasma membrane part integrin alpha-IIb relationship: RO:0002104 PR:000009127 ! has plasma membrane part integrin alpha-IIb @@ -19659,11 +19883,13 @@ name: respiratory goblet cell def: "A simple columnar epithelial cell that secretes mucin. Rough endoplasmic reticulum, mitochondria, the nucleus, and other organelles are concentrated in the basal portion. The apical plasma membrane projects microvilli to increase surface area for secretion." [GOC:tfm, ISBN:0721662544] subset: cellxgene_subset synonym: "respiratory mucosa goblet cells" EXACT [MP:0010863] +xref: https://cellxgene.cziscience.com/cellguide/CL_0002370 is_a: CL:0000160 ! goblet cell is_a: CL:0002368 ! respiratory epithelial cell intersection_of: CL:0000160 ! goblet cell intersection_of: part_of UBERON:0004802 ! respiratory tract epithelium property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nThe respiratory goblet cell is a highly specialized cell type found primarily within the respiratory tract, including the nose, trachea, and lungs. Named because their shape resembles a goblet - a drinking vessel with a wide body and narrow neck - these cells form a vital part of the respiratory system's protective mechanisms. They are found within the columnar epithelium lining these organs, which forms a barrier between the internal body and the exterior environment.\nA principal function of the respiratory goblet cell is the production and secretion of mucus, a carbohydrate-rich, viscous and gel-like substance that plays a critical role in trapping dust, bacteria, viruses, and other airborne particles that are inhaled. The mucus secreted by the goblet cells covers the lining of the respiratory tract, effectively catching these particles and preventing them from reaching the lungs and causing infection. Mucus also provides hydration and lubrication to the respiratory tract surfaces, which is important in maintaining the tissue's health and functioning.\nIn addition to their mucus-secreting capabilities, respiratory goblet cells also play a significant role in the body's inflammatory responses. When the respiratory system is exposed to irritants or pathogens, the number and activity of goblet cells often increase, leading to a higher production of mucus. This is a protective response designed to trap and neutralize the harmful substances more effectively. However, in conditions like chronic obstructive pulmonary disease (COPD) and asthma, an overproliferation of goblet cells, also known as goblet cell hyperplasia, can lead to excessive mucus production and airway obstruction." xsd:string {xref="DOI:10.1016/S1357-2725(02)00083-3", xref="DOI:10.1111/febs.15731", xref="DOI:10.1165/ajrcmb.25.5.f218", xref="DOI:10.2147/COPD.S38938", xref="DOI:10.3109/01902148.2013.791733"} creation_date: 2010-09-23T04:42:27Z [Term] @@ -19685,12 +19911,12 @@ creation_date: 2010-09-24T09:44:42Z id: CL:0002372 name: myotube alt_id: CL:0000369 -def: "A transversely striated, synctial muscle cell, formed by the fusion of myoblasts." [GOC:dos, GOC:tfm, ISBN:0323052908, PMID:22274696] -synonym: "myotubule" EXACT [] -synonym: "single cell sarcomere" EXACT [] +def: "A transversely striated, multinucleated syncytial muscle cell, formed by the fusion of myoblasts during muscle development." [GOC:dos, GOC:tfm, ISBN:0323052908, PMID:22274696] +synonym: "myofiber" EXACT [FBbt:00005812] +synonym: "myofibril" EXACT [FBbt:00005812] xref: FBbt:00005812 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} -is_a: CL:0000228 ! multinucleate cell is_a: CL:0000737 ! striated muscle cell +is_a: CL:4052002 ! syncytial cell intersection_of: CL:0000187 ! muscle cell intersection_of: bearer_of PATO:0001908 ! multinucleate intersection_of: bearer_of PATO:0002478 ! transversely striated @@ -19725,12 +19951,15 @@ creation_date: 2010-09-24T01:49:31Z [Term] id: CL:0002375 name: Schwann cell precursor -def: "A glioblast cell that develops from a migratory neural crest cell. The SCP is embedded among neurons (axons) with minimal extracellular spaces separating them from nerve cell membranes and has no basal lamina. In rodents SCPs are the only cells in the Schwann cell linage that expresses Cdh19." [GOC:tfm] +def: "A multipotent progenitor cell that develops from a migratory neural crest cell. The schwann cell precursor is embedded among axons, with minimal extracellular space separating them from nerve cell membranes. This cell lacks a basal lamina, which distinguishes it from more mature Schwann cells. In rodents, cadherin-19 (Cdh19) serves as a specific marker for this developmental stage." [GOC:tfm, PMID:15580626, PMID:30971890, PMID:35815410] +comment: Schwann cell precursor are capable of differentiating into Schwann cells and other cell types such as melanocytes, neurons, and mesenchymal cells. {xref="PMID:35815410"} subset: cellxgene_subset synonym: "Schwann cell precursor cell" EXACT [] -is_a: CL:0000030 ! glioblast +synonym: "SCP" RELATED OMO:0003000 [PMID:35815410] is_a: CL:0011026 ! progenitor cell +relationship: bearer_of PATO:0001402 ! multipotent relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell +relationship: RO:0002387 CL:0002573 ! has potential to develop into Schwann cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-09-24T02:06:10Z @@ -20001,7 +20230,7 @@ creation_date: 2010-10-04T12:49:49Z [Term] id: CL:0002399 name: CD1c-positive myeloid dendritic cell -def: "A myeloid dendritic cell found in the blood that is CD1c-positive." [GOC:dsd, GOC:tfm, PMID:20204387, PMID:20628149] +def: "A myeloid dendritic cell that is CD1c-positive." [GOC:dsd, GOC:tfm, PMID:20204387, PMID:20628149] comment: Normally represent 10-20% of peripheral blood mDCs (human). They are also CD281-positive (TLR1), CD282-positive (TLR2), CD283-positive (TLR3), CD284-positive (TLR4), CD285-positive (TLR5), CD286-positive (TLR6), CD288-positive (TLR8), and CD290-positive (TLR10) [PMID:20204387]. Upon TLR stimulation, these cells were potent producers of CXCL8 (IL-8), while producing little TNF-alpha. subset: cellxgene_subset subset: human_reference_atlas @@ -20241,6 +20470,7 @@ synonym: "CD3e-positive T cell" EXACT [] synonym: "CD3epsilon T cell" RELATED [] synonym: "mature T-cell" EXACT [] is_a: CL:0000084 {is_inferred="true"} ! T cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000084 ! T cell intersection_of: output_of GO:0045058 ! T cell selection intersection_of: RO:0002104 GO:0042101 ! has plasma membrane part T cell receptor complex @@ -20327,6 +20557,7 @@ subset: human_reference_atlas synonym: "ETP" EXACT [] synonym: "preT.ETP.Th" EXACT [] is_a: CL:0000827 {is_inferred="true"} ! pro-T cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000827 ! pro-T cell intersection_of: CL:4030046 PR:000001380 ! lacks_plasma_membrane_part interleukin-2 receptor subunit alpha intersection_of: RO:0002104 PR:000001307 ! has plasma membrane part CD44 molecule @@ -20548,6 +20779,7 @@ comment: Note: Nk1.1 expression is restricted to C57BL strains of laboratory mic synonym: "NK.sp" EXACT [] synonym: "NK1.1-positive NK cell" EXACT [] is_a: CL:0000824 ! mature natural killer cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000824 ! mature natural killer cell intersection_of: RO:0002104 PR:000002977 ! has plasma membrane part killer cell lectin-like receptor subfamily B member 1C intersection_of: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus @@ -20727,7 +20959,6 @@ creation_date: 2010-11-10T01:46:51Z id: CL:0002453 name: oligodendrocyte precursor cell def: "A progenitor cell of the central nervous system that can differentiate into oligodendrocytes or type-2 astrocytes. This cell originates from multiple structures within the developing brain including the medial ganglion eminence and the lateral ganglionic eminence. These cells migrate throughout the central nervous system and persist into adulthood where they play an important role in remyelination of injured neurons." [GOC:tfm, PMID:10704434, PMID:11756508, PMID:20142420, PMID:2182078, PMID:24133281, PMID:9826671] -comment: This cell type can be purified from optic nerves and other regions of the embryonic, postnatal and adult rat CNS and can be differentiated in vitro to oligodendrocytes and type-2 astrocytes. Some references use the terms 'oligodendrocyte precursor cell' and 'oligodendrocyte type-2 astrocyte (O-2A) progenitor' to refer to the same entity (e.g., PMID:10704434), while others describe an oligodendrocyte type-2 astrocyte (O-2A) progenitor cell as the precurosr to oligodendrocyte- and type-2 astrocyte- progenitor cells (e.g, ISBN:9780702028991). {xref="PMID:10704434", xref="ISBN:9780702028991", xref="PMID:2182078"} subset: cellxgene_subset subset: human_reference_atlas synonym: "O-2A/OPC" RELATED OMO:0003000 [PMID:24133281] @@ -20739,6 +20970,7 @@ is_a: CL:0011026 ! progenitor cell relationship: RO:0002202 CL:0000339 ! develops from glioblast (sensu Vertebrata) property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This cell type can be purified from optic nerves and other regions of the embryonic, postnatal and adult rat CNS and can be differentiated in vitro to oligodendrocytes and type-2 astrocytes. Some references use the terms 'oligodendrocyte precursor cell' and 'oligodendrocyte type-2 astrocyte (O-2A) progenitor' to refer to the same entity (e.g., PMID:10704434), while others describe an oligodendrocyte type-2 astrocyte (O-2A) progenitor cell as the precurosr to oligodendrocyte- and type-2 astrocyte- progenitor cells (e.g, ISBN:9780702028991)." xsd:string {xref="ISBN:9780702028991", xref="PMID:10704434", xref="PMID:2182078"} creation_date: 2010-11-10T02:51:34Z [Term] @@ -21050,6 +21282,7 @@ synonym: "MF.BM" RELATED OMO:0003000 [] xref: BTO:0004732 is_a: CL:0000864 {is_inferred="true"} ! tissue-resident macrophage is_a: CL:0010004 ! mononuclear cell of bone marrow +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000864 ! tissue-resident macrophage intersection_of: CL:4030046 PR:000001014 ! lacks_plasma_membrane_part receptor-type tyrosine-protein phosphatase C isoform CD45RABC intersection_of: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon @@ -21069,6 +21302,7 @@ id: CL:0002477 name: adipose macrophage def: "A macrophage located in adipose tissue that is CD45-positive, CD11c-positive, and SIRPa-positive." [GOC:tfm] is_a: CL:0000864 {is_inferred="true"} ! tissue-resident macrophage +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000864 ! tissue-resident macrophage intersection_of: RO:0002104 PR:000001006 ! has plasma membrane part receptor-type tyrosine-protein phosphatase C intersection_of: RO:0002104 PR:000001013 ! has plasma membrane part integrin alpha-X @@ -21284,7 +21518,7 @@ xref: BTO:0001539 xref: CALOHA:TS-0115 xref: FMA:83808 xref: FMA:84791 -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0007100 ! primary circulatory organ relationship: part_of UBERON:0007100 ! primary circulatory organ @@ -21606,9 +21840,8 @@ id: CL:0002520 name: nephrocyte def: "An insect excretory cell that regulates hemolymph composition by filtration and filtrate endocytosis." [GOC:tfm, PMID:19783135] xref: BTO:0004597 -is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002522 ! renal filtration cell -relationship: RO:0002160 NCBITaxon:50557 ! only in taxon Insecta +relationship: RO:0002162 NCBITaxon:50557 ! in taxon Insecta property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-08T01:34:56Z @@ -21631,6 +21864,7 @@ creation_date: 2011-02-21T02:51:22Z id: CL:0002522 name: renal filtration cell def: "A renal filtration cell is a specialized cell of the renal system that filter fluids by charge, size or both." [GOC:tfm] +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000424 ! excretory cell relationship: part_of UBERON:0001008 ! renal system property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 @@ -21639,12 +21873,13 @@ creation_date: 2011-02-08T01:37:59Z [Term] id: CL:0002523 name: mesonephric podocyte -def: "A specialized epithelial cell that contains \"feet\" that interdigitate with the \"feet\" of other glomerular epithelial cells in the mesonephros." [GOC:tfm] {terms:contributor="https://orcid.org/0000-0002-2244-7917"} +def: "A specialized epithelial cell that contains \"feet\" that interdigitate with the \"feet\" of other glomerular epithelial cells in the mesonephros." [GOC:tfm] synonym: "mesonephric glomerular visceral epithelial cell" EXACT [ZFA:0001674] is_a: CL:0000653 ! podocyte intersection_of: CL:0000653 ! podocyte intersection_of: part_of UBERON:0000080 ! mesonephros relationship: part_of UBERON:0000080 ! mesonephros +property_value: terms:contributor https://orcid.org/0000-0002-2244-7917 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-08T01:58:30Z @@ -21834,12 +22069,14 @@ name: intrahepatic cholangiocyte def: "An epithelial cell of the intrahepatic portion of the bile duct. These cells are flattened or cuboidal in shape, and have a small nuclear-to-cytoplasmic ratio relative to large/extrahepatic cholangiocytes." [GOC:tfm, PMID:23720296] subset: cellxgene_subset synonym: "small bile duct cholangiocyte" EXACT [PMID:23720296] +xref: https://cellxgene.cziscience.com/cellguide/CL_0002538 xref: ZFA:0009379 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:1000488 {is_inferred="true"} ! cholangiocyte intersection_of: CL:1000488 ! cholangiocyte intersection_of: part_of UBERON:0004823 ! intrahepatic bile duct epithelium relationship: part_of UBERON:0004823 ! intrahepatic bile duct epithelium property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nIntrahepatic cholangiocytes represent a subset of the biliary epithelial cells that form a network of tubes in the liver called the biliary tree The intrahepatic cholangiocytes reside specifically in the intrahepatic bile ducts and play a crucial role in liver physiology and bile production and secretion, thereby aiding in the digestion and absorption of fats in the small intestine. These specific cholangiocytes arise from bipotent hepatoblasts, whereas extrahepatic cholangiocytes share an embryologic origin with the ventral pancreas.\nRecent research suggests that there is also heterogeneity within populations of intrahepatic cholangiocytes with different transcriptional profiles, proliferative capacity, and biological function; for example, subpopulations differ in calcium-mobilizing receptors.\nThe primary function of intrahepatic cholangiocytes is related to bile formation and maintenance of its flow. In addition to their secretory and absorptive activities, they are involved in the regulation of bile composition, volume, and alkalinization, contributing to the neutralization of the acidic chyme (partly digested food) that enters the intestine from the stomach. Intrahepatic cholangiocytes are also recognized for their role in liver regeneration and repair, often proliferating in response to injury. \nIntrahepatic cholangiocytes take part in certain pathological conditions, like primary biliary cirrhosis and cholangiocarcinoma. Changes in these cells often lead to abnormalities in bile formation and transport, causing cholestatic liver diseases. Overall, the primary and secondary functional activities of intrahepatic cholangiocytes are vital in maintaining liver function, digestive processes, and contributing to the body's response to liver injury." xsd:string {xref="DOI:10.1002/hep.31252", xref="DOI:10.1016/j.ajpath.2023.02.012", xref="DOI:10.1016/j.biocel.2010.06.020", xref="DOI:10.1016/j.gastha.2022.07.015"} creation_date: 2011-02-28T01:20:20Z [Term] @@ -21887,6 +22124,7 @@ subset: human_reference_atlas synonym: "endothelial cell of vein" EXACT [] synonym: "venous endothelial cell" EXACT [] xref: FMA:62104 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002543 xref: KUPO:0001099 is_a: CL:0000071 {is_inferred="true"} ! blood vessel endothelial cell intersection_of: CL:0000071 ! blood vessel endothelial cell @@ -21894,6 +22132,7 @@ intersection_of: part_of UBERON:0001638 ! vein relationship: part_of UBERON:0001638 ! vein property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nVein endothelial cells form a thin layer of squamous cells, the endothelium, lining the interior surface of veins throughout the body. They shape the inner cellular lining of the entire vascular system, including the heart, playing a crucial role in blood circulation. The unique characteristic compact arrangement of these cells enables veins to act as a barrier between the blood (that can contain foreign substances) and the surrounding venous tissue and maintain the integrity of the vascular system.\nThe primary function of vein endothelial cells is to control the exchange of substances between the bloodstream and the surrounding tissues. They facilitate selective transportation of molecules depending on their size and solubility, including gases, nutrients, hormones, and waste products. Vein endothelial cells also play a protective role by inhibiting the translocation of toxins or pathogens from blood to tissues. Additionally, these cells are involved in blood coagulation and inflammation response, primarily by producing substances that inhibit blood clot formation under normal conditions and initiating clotting when necessary.\nAnother significant function of vein endothelial cells is the regulation of blood flow and blood pressure. They produce and release several substances, including nitric oxide and prostacyclin, which help in controlling vasodilation and vasoconstriction, thereby regulating blood pressure. These cells are also responsible for angiogenesis, the formation of new blood vessels, which is crucial during wound healing and in the formation of granulation tissue. Consequently, any dysfunction in vein endothelial cells can lead to severe health problems like atherosclerosis, hypertension, and thrombosis." xsd:string {xref="DOI:10.1007/s00441-008-0706-5", xref="DOI:10.1038/s41569-022-00770-1", xref="DOI:10.1038/s41598-021-01360-w", xref="DOI:10.3390/ijms20184411"} creation_date: 2011-02-28T03:48:11Z [Term] @@ -22074,7 +22313,7 @@ creation_date: 2011-02-28T05:24:28Z id: CL:0002559 name: hair follicle cell def: "An animal cell that is part of a hair follicle." [GOC:tfm] -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0002073 ! hair follicle relationship: part_of UBERON:0002073 ! hair follicle @@ -22207,11 +22446,13 @@ name: mesenchymal stem cell of adipose tissue def: "A mesenchymal stem cell of adipose tissue." [GOC:tfm] subset: cellxgene_subset synonym: "mesenchymal stem cell of adipose" EXACT [] +xref: https://cellxgene.cziscience.com/cellguide/CL_0002570 is_a: CL:0000134 ! mesenchymal stem cell intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: part_of UBERON:0001013 ! adipose tissue relationship: part_of UBERON:0001013 ! adipose tissue property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nMesenchymal stem cells of adipose tissue, also known commonly as adipose-derived stem cells (ADSCs), are a population of adult stem cells that can be obtained easily from adipose tissues. They have many of the same regenerative properties as other mesenchymal stem cells, but are more easily accessible than bone marrow-derived stem cells.\nAdipose-derived stem cells show immense promise in the field of regenerative medicine due to their ability to differentiate into adipocytes, chondrocytes, myocytes, osteoblasts, and other cell types. ADSCs also possess immunomodulatory and homeostatic functions: they have the ability to suppress immune responses and provide a therapeutic environment for tissue repair and regeneration, as well as supporting the proliferation of adipocytes and the overall expansion of adipose tissue and contributing to the tissue's ability to react to demands of energy storage and mobilization. Dysfunction of these cells may contribute to metabolic complications observed in obesity and diabetes. \nADSCs have been used for therapeutic applications such as pathological wound healing, severe refractory acute graft-versus-host disease, and idiopathic thrombocytopenic purpura." xsd:string {xref="DOI:10.1016/j.biopha.2019.108765", xref="DOI:10.1016/j.tibtech.2006.01.010", xref="DOI:10.1038/s41536-019-0083-6", xref="DOI:10.1096/fj.202100332R", xref="DOI:10.1111/dgd.12049"} creation_date: 2011-03-01T09:57:17Z [Term] @@ -22247,11 +22488,13 @@ subset: human_reference_atlas synonym: "neurolemmocyte" EXACT [PMID:32119275, PMID:38638689] xref: BTO:0001220 xref: CALOHA:TS-0898 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002573 xref: MESH:D012583 is_a: CL:0000125 ! glial cell relationship: part_of UBERON:0000010 ! peripheral nervous system property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nSchwann cells, also known as neurolemmocytes, are a type of glial cell located in the peripheral nervous system. These cells play a significant role in the healthy functioning of nerves by producing myelin, a fatty substance that forms a coating around nerve fibers. Myelin serves as an insulator and enhances the speed and efficiency of electrical nerve impulses; a single Schwann cell can myelinate a single axon. Myelination starts by the elongation and envelopment of the Schwann cell around the axon, followed by the synthesis and deposition of myelin layers. Some studies suggest that Schwann cells may regulate neuronal action potential, muscular contraction, and the sensitive response. \nWhile Schwann cells are most commonly known for the formation of the myelin sheath, some Schwann cells do not form myelin: Remak Schwann cells, a class of nonmyelinating Schwann cells, ensheath axons with smaller diameter, such as C fiber nociceptors in sciatic nerves and form Remak bundles.\nSchwann cells are found along both motor and sensory neurons and are crucial for the advancement and recovery of peripheral nerve injuries, due to their capacity to support nerve regeneration. In cases of nerve injury, Schwann cells play a vital role in recovery by initiating Wallerian degeneration, a process in which the part of the axon distal to the injury site degrades and is then cleared away. Following this, Schwann cells can guide the regrowth of the nerve, providing a conducive environment for axon regeneration. They remodel themselves into a regenerative phenotype, proliferate, and organize themselves into bands of Büngner that provide physical and chemical guidance for the regrowths of axons. This function of Schwann cells in the repair and regeneration of nervous system highlights their therapeutic potential in peripheral nerve injury treatments." xsd:string {xref="DOI:10.1002/glia.23892", xref="DOI:10.1016/B978-0-444-52902-2.00005-9", xref="DOI:10.1016/j.biocel.2006.05.007", xref="DOI:10.1186/1742-2094-8-110", xref="DOI:10.1186/s13064-020-00140-y"} creation_date: 2011-03-02T01:19:27Z [Term] @@ -22282,7 +22525,7 @@ creation_date: 2011-03-02T02:54:18Z [Term] id: CL:0002576 name: perineurial cell -def: "A glial cell that is part of the perineurium. This cell type has thin long bipolar cytoplasmic processes, pinocytotic vesicles, fragments of external lamina and/or external lamina-like material, attachment plaques, and desmosome-like junctions. Perineurial cells historically have been referred to as fibroblasts because of shape; however, unlike fibroblasts, a perineurial cell: does not have a compact nucleus and large endoplasmic reticulum; does have a double basement membrane opposed to a single basal lamina; is carefully joined to other perineurial cells by tight junctions into a single sheet as opposed to arranged in a large mass; and finally, can surround a small axon bundle at a nerve terminal whereas a fibroblast cannot." [GO:tfm, http://en.wikipedia.org/wiki/Perineurium, NCIT:C41442, PMID:25818566] {comment="https://orcid.org/0000-0001-7655-4833"} +def: "A glial cell that is part of the perineurium. This cell type has thin long bipolar cytoplasmic processes, pinocytotic vesicles, fragments of external lamina and/or external lamina-like material, attachment plaques, and desmosome-like junctions. Perineurial cells historically have been referred to as fibroblasts because of shape; however, unlike fibroblasts, a perineurial cell: does not have a compact nucleus and large endoplasmic reticulum; does have a double basement membrane opposed to a single basal lamina; is carefully joined to other perineurial cells by tight junctions into a single sheet as opposed to arranged in a large mass; and finally, can surround a small axon bundle at a nerve terminal whereas a fibroblast cannot." [GO:tfm, http://en.wikipedia.org/wiki/Perineurium, NCIT:C41442, PMID:25818566] comment: There are studies that largely accept the idea that the perineurial cell is a modified fibroblast with myofibroblastic features. {xref="PMID:36244793"} subset: human_reference_atlas synonym: "perineurial glial cell" EXACT [PMID:25818566] @@ -22290,6 +22533,7 @@ is_a: CL:0000125 ! glial cell is_a: CL:0002320 ! connective tissue cell relationship: part_of UBERON:0000121 ! perineurium property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0001-7655-4833 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-03-02T03:03:58Z @@ -22385,6 +22629,7 @@ def: "A blood vessel endothelial cell that is part of the retina." [GOC:tfm] subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +xref: https://cellxgene.cziscience.com/cellguide/CL_0002585 is_a: CL:0000071 {is_inferred="true"} ! blood vessel endothelial cell is_a: CL:0009004 ! retinal cell intersection_of: CL:0000071 ! blood vessel endothelial cell @@ -22392,6 +22637,7 @@ intersection_of: part_of UBERON:0000966 ! retina relationship: part_of UBERON:0000966 ! retina property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nRetinal blood vessel endothelial cells constitute the innermost lining of the blood vessels found in the retina, the light-sensitive layer of tissue at the back of the eye. The primary role of these cells revolves around their location within the retinal vascular system, forming the structure of the blood-retinal barrier, a subset of the larger blood-ocular barrier system. \nThe endothelial cells are particularly involved in the growth of new retinal blood vessels from pre-existing ones (angiogenesis); this is critical in managing the amount of oxygen and essential nutrients delivered to the ocular tissues. They are crucial for maintaining homeostasis in the retinal environment by controlling the exchange of molecules between the blood and the retina. Furthermore, they mediate immune cell trafficking, supporting the immune privilege of the eye by preventing the unrestricted infiltration of inflammatory cells into the retina, thus maintaining ocular health and normal vision.\nThe malfunction or dysfunction of retinal blood vessel endothelial cells is implicated in numerous ocular pathologies, particularly diabetic retinopathy, which is one of the leading causes of blindness worldwide. In such conditions, the compromise in the integrity of the blood-retinal barrier and excess angiogenesis can lead to retinal edema and pathological neovascularization, resulting in vision loss." xsd:string {xref="DOI:0.1016/j.preteyeres.2015.08.001", xref="DOI:10.1016/j.preteyeres.2012.08.004", xref="DOI:10.1038/nature04482", xref="DOI:10.5301/EJO.2010.6049"} creation_date: 2011-03-06T03:28:27Z [Term] @@ -22403,6 +22649,7 @@ subset: eye_upper_slim subset: human_reference_atlas xref: BTO:0004910 xref: FMA:75802 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002586 is_a: CL:0000066 ! epithelial cell is_a: CL:0000149 ! visual pigment cell is_a: CL:0009004 ! retinal cell @@ -22412,6 +22659,7 @@ relationship: has_part GO:0042470 ! melanosome relationship: part_of UBERON:0001782 ! pigmented layer of retina property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nRetinal pigment epithelial (RPE) cells form a single layer of cells at the back of the eye sandwiched between the neurosensory retina and the choroid, playing a significant role in maintaining vision health. These pigment-laden cells are highly specialized and perform an array of metabolic and transport functions essential for the maintenance of the photoreceptor cells (rods and cones) in the retina. The pigmentation of RPE cells actively aids in the absorption of excess light and the prevention of light scattering, thus enhancing the eye's optical properties.\nThe retinal pigment epithelium forms a key part of the blood/retina barrier. The cells have long sheet-like microvilli on their apical membrane that project into the light-sensitive outer segments of the photoreceptors, forming a close structural interaction. The basolateral membrane of the RPE interacts with the underlying Bruch’s membrane, which separates the RPE cells from fenestrated endothelium of the choriocapillaris. \nRPE cells support the photoreceptor by providing them with oxygen and nutrients (such as glucose, retinol and fatty acids) and removing waste products. They also recycle the visual pigment, in a process called the \"visual cycle\", where the RPE cells play a vital role in the regeneration of visual pigment (11-cis retinol) following the absorption of light. This is essential for the maintenance of photoreceptor excitability.\nBeyond this, RPE cells take part in the phagocytosis process, where they digest the shed ends of photoreceptor outer segments, thus, preventing the build-up of waste residue that could otherwise harm retinal health. They also secrete various factors, including growth factors required to maintain the structural integrity of choriocapillaris endothelium and photoreceptors, as well as immunosuppressive factors that play an important role in establishing the immune privilege of the eye." xsd:string {xref="DOI:10.1111/febs.16018", xref="DOI:10.1152/physrev.00021.2004", xref="DOI:10.3389/fphar.2021.727870/full", xref="https://www.sciencedirect.com/topics/chemistry/retinal-pigment"} creation_date: 2011-03-06T03:37:09Z [Term] @@ -22628,7 +22876,7 @@ creation_date: 2011-03-06T06:57:33Z [Term] id: CL:0002605 name: astrocyte of the cerebral cortex -def: "An astrocyte of the cerebral cortex." [GOC:tfm] +def: "A transcriptomically distinct astrocyte that is found in the cerebral cortex." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas is_a: CL:0012000 ! astrocyte of the forebrain @@ -22777,11 +23025,13 @@ id: CL:0002618 name: endothelial cell of umbilical vein def: "An endothelial cell of the umbilical vein." [GOC:tfm] xref: BTO:0004296 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002618 is_a: CL:0002543 ! vein endothelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0002066 ! umbilical vein relationship: part_of UBERON:0002066 ! umbilical vein property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nEndothelial cells of the umbilical vein form the inner lining of the veins found in the umbilical cord. They are involved in tube formation and migration which are essential for angiogenesis, the process of generating new blood vessels; this is critical during the fetal stage for the development of the circulatory system. Endothelial cells of the umbilical vein also play a role in controlling the passage of white blood cells into tissues during inflammatory responses.\nBecause human umbilical vein endothelial cells (HUVECs) can easily be derived from the umbilical cord, and because they express common endothelial cell markers, they have been used as an epithelial cell model for studies on cell proliferation, migration, angiogenesis, and inflammation. They have been used as models for vascular diseases like atherosclerosis, for investigating how tumor cells infiltrate blood vessels and form metastases. \nThus, while endothelial cells of the umbilical vein play a critical role in vascular biology, they also represent a powerful tool in disease studies and potential treatment strategies." xsd:string {xref="DOI:10.1002/cyto.a.20952", xref="DOI:10.1007/s12015-006-0015-x", xref="DOI:10.1172/JCI107470", xref="DOI:10.3390/app10030938", xref="https://www.ncbi.nlm.nih.gov/books/NBK53254/"} creation_date: 2011-03-14T11:36:51Z [Term] @@ -22818,7 +23068,7 @@ creation_date: 2011-03-14T12:31:49Z id: CL:0002621 name: gingival epithelial cell def: "Any epithelial cell that is part of some gingival epithelium." [FBC:Autogenerated] -is_a: CL:0002251 ! epithelial cell of alimentary canal +is_a: CL:1001576 ! oral mucosa squamous cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001949 ! gingival epithelium relationship: part_of UBERON:0001949 ! gingival epithelium @@ -22958,11 +23208,13 @@ def: "A basal cell in the respiratory tract." [GOC:tfm, PMID:20699479] subset: cellxgene_subset synonym: "airway basal cell" EXACT [] synonym: "airway basal stem cell" EXACT [] +xref: https://cellxgene.cziscience.com/cellguide/CL_0002633 is_a: CL:0000646 ! basal cell intersection_of: CL:0000646 ! basal cell intersection_of: part_of UBERON:0004802 ! respiratory tract epithelium relationship: part_of UBERON:0004802 ! respiratory tract epithelium property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nRespiratory basal cells are highly specialized cells that serve a crucial role in the human airway epithelium, predominantly found lining the surfaces of the trachea and bronchi. These cells exhibit a distinctive columnar shape and are attached directly to the basal lamina. They are characterized by the presence of high amounts of cytoplasmic keratins, predominantly keratin 5 and 14, and transcription factor tumor protein (tp63), which set them apart from other types of lung epithelial cells such as ciliated cells and secretory cells. \nBasal cells are essential for maintaining airway integrity. They make up one third of all respiratory epithelial cells and serve as stem cells as they can transform into different cell types, like goblet cells, ciliated cells, and club cells, when needed for homeostatic maintenance of the epithelial barrier or to repair and restore a healthy cellular environment after injury.\nTheir position at the interface between the internal environment and the external atmosphere makes these cells a first line of defense against air-borne irritants, allergens, and pathogens. Their robust, intrinsic reparative properties facilitate effective recovery from such adversities. However, damage to respiratory basal cells or abnormalities in their function are associated with several respiratory pathologies such as asthma, chronic obstructive pulmonary disease, and lung cancer. Therefore, understanding these cells' function, and their role in disease, is crucial for the development of new therapeutic strategies for respiratory disorders." xsd:string {xref="DOI:10.1186/s12931-022-02042-5", xref="DOI:10.3389/falgy.2021.787128", xref="DOI:110.1038/s41385-020-00370-7"} creation_date: 2011-06-21T03:11:10Z [Term] @@ -23348,8 +23600,10 @@ id: CL:0002671 name: endothelial stalk cell def: "An endothelial stalk cell is a specialized endothelial cell that follows behind the tip cell of an angiogenic sprout." [GOC:tfm, PMID:21521739] subset: cellxgene_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_0002671 is_a: CL:0000071 ! blood vessel endothelial cell property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nEndothelial stalk cells are specialized vascular cells vital in angiogenesis, a process through which new blood vessels are formed from pre-existing ones; specifically, endothelial stalk cells are involved in sprouting angiogenesis, where they help form the body of new blood vessels. \nVascular sprouting relies on the coordinated activity of migrating endothelial tip cells at the forefront and proliferating stalk cells that elongate the sprout. The process is tightly controlled by different growths factors: Vascular Endothelial Growth Factor acts on endothelial cells, inducing them to become endothelial tip cells that initiate sprouting. After sprouting initiation, activation of Notch signaling suppresses differentiation toward a tip cell phenotype and some of the endothelial cells differentiate into stalk cells, which follow tip cells, multiply, and elongate to provide a structural backbone to the growing vessel sprout. \nIn contrast to endothelial tip cells, which migrate and lead the angiogenic sprout, endothelial stalk cells behind the sprouts continue forming the tube or lumen for blood flow and facilitate maturation and stability of the new vessel. The delicate balance between the activities of stalk and tip cells during angiogenesis is crucial to build a functional vascular network. Dysfunctions in endothelial stalk cells can lead to pathological conditions such as impaired wound healing, unregulated tumor growth, and metastasis due to abnormal angiogenesis." xsd:string {xref="DOI:10.1007/s12079-019-00511-z", xref="DOI:10.1016/j.cmet.2013.08.001", xref="DOI:10.1101/cshperspect.a006569", xref="DOI:10.3389/fcell.2021.642352"} creation_date: 2011-08-16T01:49:32Z [Term] @@ -23438,6 +23692,7 @@ name: natural helper lymphocyte def: "A lymphocyte found in adipose tissue that lacks lineage markers of other lymphocytes but is capable of mediating TH2 cytokine responses. This cell type is found in fat associated lymphoid clusters, proliferates in response to IL2 and produce large amounts of TH2 cytokines such as IL5, IL6 and IL13" [GOC:tfm, PMID:20023630] subset: blood_and_immune_upper_slim is_a: CL:0000542 {is_inferred="true"} ! lymphocyte +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000542 ! lymphocyte intersection_of: CL:4030046 GO:0042105 ! lacks_plasma_membrane_part alpha-beta T cell receptor complex intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -23999,6 +24254,7 @@ synonym: "long wavelength sensitive cone" EXACT [PMID:31117170] synonym: "long- (L) wavelength-sensitive cone" EXACT [https://doi.org/10.7554/eLife.39166] synonym: "long-wavelength cone" EXACT [https://doi.org/10.1038/323623a0] is_a: CL:0000573 ! retinal cone cell +is_a: PR:000050567 ! protein-containing material entity relationship: has_part PR:000001244 ! long-wave-sensitive opsin 1 property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string @@ -24013,6 +24269,7 @@ synonym: "middle wavelength sensitive cone" EXACT [PMID:31117170] synonym: "middle- (M) wavelength-sensitive cone" EXACT [https://doi.org/10.7554/eLife.39166] synonym: "middle-wavelength-sensitive (M) cone" EXACT [https://opg.optica.org/josaa/abstract.cfm?URI=josaa-6-1-153] is_a: CL:0000573 ! retinal cone cell +is_a: PR:000050567 ! protein-containing material entity relationship: has_part PR:000001224 ! medium-wave-sensitive opsin property_value: terms:contributor "https://orcid.org/0000-0002-5260-9315" xsd:string @@ -24740,9 +24997,11 @@ name: ionocyte def: "Specialized epithelial cells involved in the maintenance of osmotic homeostasis. They are characterized by abundant mitochondria and ion transporters. In amniotes, they are present in the renal system. In freshwater fish, ionocytes in the skin and gills help maintain osmotic homeostasis by absorbing salt from the external environment." [PMID:17555741, PMID:19268451] subset: cellxgene_subset subset: human_reference_atlas +xref: https://cellxgene.cziscience.com/cellguide/CL_0005006 xref: ZFA:0005323 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nIonocytes are specialized cells predominantly found in the mammalian respiratory and renal systems as well as in the gills, skin, and intestinal tract of fish. These cells play crucial roles in maintaining ion and acid-base homeostasis. Ionocytes demonstrate remarkable plasticity and are able to adapt themselves in response to changes in environmental conditions such as pH, salinity, ion concentration, and temperature.\nThese cells work by selectively absorbing specific ions from the environment, thus maintaining the body's internal ionic balance. The most commonly absorbed ions include sodium (Na+), chloride (Cl-), calcium (Ca2+), and hydrogen (H+). Moreover, ionocytes contribute to acid-base regulation. In response to acidosis or alkalosis, ionocytes can either excrete or retain hydrogen (H+) and bicarbonate (HCO3-) ions to readjust the blood pH. Further, experimental evidence suggests a functional complexity of ionocytes, implying diverse roles beyond ion regulation. Recent research highlights ionocytes' involvement in ammonia excretion and the regulation of extracellular fluid volume, highlighting their contribution to the overall homeostatic process.\nMalfunctioning ionocytes have been implicated in various diseases, including cystic fibrosis which is caused by mutations in the chloride channel CFTR, an ionocyte marker." xsd:string {xref="DOI:10.1016/j.jcf.2019.09.010", xref="DOI:10.1038/s41586-018-0393-7", xref="DOI:10.1038/s41598-023-30603-1", xref="DOI:10.1146/annurev-pathol-042420-094031", xref="DOI:10.3389/fmars.2020.00709"} [Term] id: CL:0005007 @@ -24771,9 +25030,11 @@ id: CL:0005009 name: renal principal cell def: "A cuboidal epithelial cell of the kidney which regulates sodium and potassium balance. The activity of sodium and potassium channels on the apical membrane of the cell is regulated by aldosterone and vasopressin. In mammals this cell type is located in the renal collecting duct system." [CL:CVS] subset: cellxgene_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_0005009 xref: ZFA:0005322 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000075 ! columnar/cuboidal epithelial cell is_a: CL:0002518 ! kidney epithelial cell +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nRenal principal cells are the major cell type in the initial collecting tubule and the cortical and outer medullary collecting ducts, as well as the connecting tubule, in the nephrons of the kidneys.\nA key function of renal principal cells is the regulation of water balance in the body. These cells express aquaporin-2 (AQP2) water channels, which facilitate the reabsorption of water from the fluid within the renal tubule lumen back into the blood. The translocation of AQP2 to the cell membrane is controlled by the hormone vasopressin: In response to high vasopressin levels, AQP2 moves to the cell membrane, allowing water to pass through effectively and be reabsorbed, therefore concentrating the urine. Conversely, in low vasopressin conditions, AQP2 is removed from the membrane, reducing water reabsorption and diluting the urine. \nRenal principal cells are also involved in the regulation of sodium and potassium levels in the body. They have sodium channels (ENaC) in their luminal membranes which permit the reabsorption of sodium ions from the tubule fluid back into the blood, resulting in a net reabsorption of sodium ions into the systemic circulation. This process is controlled, in part, by the hormone aldosterone. Additionally, renal principal cells contain potassium channels that facilitate the secretion of potassium ions into the urine. The activities of these channels, in coordination with other cell types in the nephron, are critical for maintaining electrolyte balance and overall body homeostasis." xsd:string {xref="DOI:10.1016/j.krcp.2013.07.005", xref="DOI:10.2215/CJN.05760513", xref="DOI:10.2215/CJN.08580813"} [Term] id: CL:0005010 @@ -24783,10 +25044,12 @@ comment: Intercalated cells are also called “mitochondria-rich cells”, refle subset: cellxgene_subset synonym: "intercalated cell" EXACT [] xref: FMA:86560 +xref: https://cellxgene.cziscience.com/cellguide/CL_0005010 xref: ZFA:0009375 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000075 ! columnar/cuboidal epithelial cell is_a: CL:0002078 ! meso-epithelial cell is_a: CL:1000449 ! epithelial cell of nephron +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nRenal intercalated cells are specialized cells located in the collecting duct system of the kidneys. The primary role of intercalated cells is to reabsorb bicarbonate ions and secrete hydrogen ions, thereby maintaining the acid-base homeostasis in the blood. They comprise two main subtypes primarily distinguished by their functional and morphological attributes: alpha and beta intercalated cells.\nAlpha intercalated cells are more predominant when the body is in a state of acidosis, a condition characterized by an increased acidity of the blood. These cells are specialized in secreting excessive hydrogen ions into the urine through a mechanism involving vacuolar H+-ATPase and H+/K+-ATPase pumps on their apical membranes. They simultaneously reabsorb bicarbonate ions from the tubular fluid and return them to the bloodstream via mechanisms involving carbonic anhydrase II and bicarbonate/chloride exchangers on the basolateral membrane. This dual process helps to increase blood pH towards normal levels.\nWhen the body is in a state of alkalosis, a condition characterized by lowered levels of hydrogen ions in the blood, beta intercalated cells are more predominant. They primarily reabsorb hydrogen ions from the tubular fluid through vacuolar H+-ATPase and H+/K+-ATPase pumps on their basolateral membranes, while secreting bicarbonate ions into the urine via pendrin, a bicarbonate/chloride exchanger in the apical membrane. These mechanisms work together to decrease blood pH towards normal levels. \nIn summary, renal intercalated cells play a critical role in the delicate balance of the body’s pH, safeguarding the body from potential harm caused by acidemia or alkalemia." xsd:string {xref="DOI:10.1152/ajprenal.2000.279.1.F195", xref="DOI:10.1161/HYPERTENSIONAHA.121.16492", xref="DOI:10.1681/ASN.V1011", xref="DOI:10.2215/CJN.08880914"} [Term] id: CL:0005011 @@ -24796,21 +25059,32 @@ comment: Type A intercalated cells are the more abundant type of intercalated ce subset: cellxgene_subset synonym: "type A intercalated cell" EXACT [PMID:25632105] synonym: "type A-IC" EXACT [PMID:25632105] +xref: https://cellxgene.cziscience.com/cellguide/CL_0005011 xref: ZFA:0009376 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0005010 ! renal intercalated cell relationship: capable_of GO:0046717 ! acid secretion +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nRenal alpha-intercalated cells are located within the connecting tubules and collecting ducts of the kidneys, which are components of the kidney's complex nephron system. Along with beta-intercalated cells, they play a critical role in the body’s acid-base balance. \nRenal alpha-intercalated cells contain an abundance of proton pumps and enzymes like carbonic anhydrase, which aid in the transport of hydrogen ions for secretion in the urine. The bicarbonate/chloride transporters on their apical membrane meanwhile take up bicarbonate ions from the urine and supply them back into the blood. Through this mechanism, these cells contribute significantly to the neutrality of blood pH, and dysfunction of renal alpha-intercalated cells often leads to distal renal tubular acidosis, a condition resulting in acidic blood and alkaline urine." xsd:string {xref="DOI:10.1016/j.semnephrol.2019.04.005", xref="DOI:10.1152/physiol.00008.2011", xref="DOI:10.1172/JCI63492", xref="DOI:10.3390/diseases2020071"} [Term] id: CL:0005012 name: multi-ciliated epithelial cell -def: "A ciliated epithelial cell with many cilia." [CL:CVS] +def: "A columnar/cuboidal epithelial cell with multiple motile cilia on its apical surface. These cells facilitate the movement of liquids such as mucus or cerebrospinal fluid across the epithelial surface." [CL:CVS, PMID:28400610, PMID:30422572, PMID:38032388] +comment: While the term 'multi-ciliated epithelial cell' refers to cells with multiple motile cilia, there are exceptions where epithelial cells may have multiple non-motile cilia. Examples include olfactory sensory neurons, which have non-motile cilia for sensory detection, and choroid plexus epithelial cells, which possess multiple non-motile cilia with transient motility during development. Multiciliated cells are essential for human health, and their dysfunction can lead to various diseases known as ciliopathies, such as primary ciliary dyskinesia. This condition affects the respiratory system, brain ventricles, and reproductive system, leading to chronic respiratory infections, hydrocephalus, and infertility {xref="PMID:22118931", xref="PMID:23959957", xref="PMID:26378583", xref="PMID:25729351"} subset: cellxgene_subset synonym: "MCC" RELATED OMO:0003000 [] synonym: "multi-ciliated cell" BROAD [] synonym: "multiciliated cell" BROAD [] synonym: "multiciliated epithelial cell" EXACT [] +xref: https://cellxgene.cziscience.com/cellguide/CL_0005012 xref: ZFA:0005242 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000067 ! ciliated epithelial cell +is_a: CL:0000075 ! columnar/cuboidal epithelial cell +intersection_of: CL:0000075 ! columnar/cuboidal epithelial cell +intersection_of: bearer_of PATO:0010007 ! multiciliated +intersection_of: has_part GO:0031514 ! motile cilium +relationship: bearer_of PATO:0010007 ! multiciliated +relationship: has_part GO:0031514 ! motile cilium +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nThe multi-ciliated epithelial cell are terminally differentiated epithelia that line brain ventricles, the respiratory tract and parts of the female and male reproductive organs in animals, playing critical roles in the maintenance of homeostasis through ciliary motion. They are characterized by the presence of hundreds of motile cilia, hair-like microtubule-based organelles that beat in a coordinated fashion to direct fluid flow over the cell surface.\nMulti-ciliated epithelial cells have fundamental roles in the proper functioning of many organ systems. In the respiratory system, they line the airways and orchestrate the coordinated movement of mucus, effectively clearing the airways of inhaled particles and pathogens. These cells are also vital in the ventricular system of the brain where they facilitate cerebrospinal fluid circulation, thus contributing to the maintenance of the brain's microenvironment. In the fallopian tube, multi-ciliated epithelial cells aid in the transport of oocytes from the ovary to the uterus, a process crucial to reproduction.\nThe formation and function of multi-ciliated epithelial cells is a highly regulated process that involves several stages of development including cell specification, centriole multiplication, and ciliogenesis. Any disruption in these processes can result in dysfunctional or decreased numbers of cilia, which can lead to a myriad of health issues, ranging from chronic respiratory infections to infertility." xsd:string {xref="DOI:10.1016/j.cub.2014.08.047", xref="DOI:10.1038/nrm.2017.21", xref="DOI:10.1101/cshperspect.a028233"} [Term] id: CL:0005013 @@ -24868,12 +25142,14 @@ comment: In mammals the endocrine pancreas is called the Islets of Langerhans. subset: cellxgene_subset subset: human_reference_atlas synonym: "pancreatic E cell" EXACT [] +xref: https://cellxgene.cziscience.com/cellguide/CL_0005019 xref: ZFA:0005598 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0005018 ! ghrelin secreting cell is_a: CL:0008024 ! pancreatic endocrine cell intersection_of: CL:0008024 ! pancreatic endocrine cell intersection_of: capable_of GO:0036321 ! ghrelin secretion property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nPancreatic epsilon cells are a specialized type of endocrine cell found in the islets of Langerhans, a region of the pancreas responsible for hormone production. These clusters of cells constitute only about 1% of the pancreatic islet cell population, making them a relatively small yet significant component of the pancreas. Pancreatic epsilon cells have a round or ovoid shape with occasional cytoplasmic extensions and are characterized by small and spherical granules. \nThe principal function of pancreatic epsilon cells involves the synthesis and release of the hormone ghrelin, a peptide hormone predominantly produced in the stomach; pancreatic epsilon cells are one of the few sites outside the gastrointestinal tract known to produce this hormone. Ghrelin has multiple vital roles, playing a significant part in generating hunger sensations, promoting fat storage, and influencing various metabolic processes. It also stimulates the release of Growth Hormone (GH) from the anterior pituitary gland.\nDuring fetal development, when they form a layer around the islet, epsilon cells are an important source of ghrelin, likely secreting the hormone into the circulation; their numbers decrease in adults. While research on pancreatic epsilon cells is still ongoing, these cells have been implicated in several disease states, most notably Type 2 diabetes and metabolic syndrome. The dysfunction or reduction in the number of pancreatic epsilon cells can lead to anomalies in ghrelin production, impacting overall metabolic homeostasis and glucose regulation." xsd:string {xref="DOI:10.1007/s00125-008-1238-y", xref="DOI:10.1152/physrev.00012.2004", xref="DOI:10.1210/en.2018-00833", xref="DOI:10.3389/fendo.2022.904004", xref="DOI:10.3390/ijms20081867"} [Term] id: CL:0005020 @@ -24955,8 +25231,10 @@ id: CL:0005026 name: hepatoblast def: "Multi fate stem cell that gives rise to both hepatocytes and cholangiocytes as descendants. The term often refers to fetal precursors of hepatocytes (differently from 'hepatic stem cell', usually applied to the self-renewing pool of hepatocyte precursors in the adult liver). Hepatoblasts may also be endogenous, as some stem cells found in the liver come from the bone marrow via blood circulation." [GOC:CVS, https://orcid.org/0000-0003-1940-6740, PMID:18356246, PMID:20483998, PMID:26798363] subset: cellxgene_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_0005026 is_a: CL:0000048 ! multi fate stem cell property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/800" xsd:string +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nHepatoblasts are immature precursor cells that predominate during the early stages of liver development, specifically in the embryonic phase of life. They first arise from the endoderm, one of the three primary germ layers in the very early embryo, and then differentiate into two distinct mature liver cell types - the hepatocytes and cholangiocytes. \nDuring liver organogenesis hepatoblasts proliferate and migrate into the septum transversum to form the liver bud. Proliferation and differentiation of these cells are regulated by several soluble factors, such as hepatocyte growth factor, which is a mitogen of both hepatoblasts and mature hepatocytes. As they start to differentiate into hepatocytes and cholangiocytes, the cells begin to express hepatic markers like albumin and alpha-fetoprotein. \nAlthough hepatoblasts are specified embryonic liver cells that are bipotential for hepatocytes and cholangiocytes, a subset of liver cells (called oval cells) has been identified in adults that express stem cell markers, such as CD133 and cKIT, and has been suggested to have the same potential as hepatoblasts to differentiate into hepatocytes and cholangiocytes." xsd:string {xref="DOI:10.1016/j.stem.2014.04.010", xref="DOI:10.1093/jb/mvr001", xref="DOI:10.1242/dev.031369", xref="DOI:10.1242/dev.114215", xref="DOI:10.5966/sctm.2015-0051"} [Term] id: CL:0007000 @@ -24965,6 +25243,7 @@ def: "Skeletogenic cell that has the potential to develop into an ameloblast. Lo comment: unsure of neural crest contribution. In VSAO we have develops_from CL:0000008 is_a: BFO:0000002 is_a: CL:0000055 ! non-terminally differentiated cell +is_a: CL:0000255 ! eukaryotic cell relationship: adjacent_to UBERON:0001763 ! odontogenic papilla relationship: part_of UBERON:0005176 ! tooth enamel organ relationship: RO:0002202 CL:0002077 ! develops from ecto-epithelial cell @@ -24986,6 +25265,7 @@ id: CL:0007002 name: precementoblast def: "Skeletogenic cell that has the potential to develop into a cementoblast." [GO_REF:0000034] is_a: CL:0000055 ! non-terminally differentiated cell +is_a: CL:0000255 ! eukaryotic cell relationship: part_of UBERON:0005176 ! tooth enamel organ property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 creation_date: 2012-06-15T04:37:13Z @@ -25019,7 +25299,7 @@ name: notochordal cell def: "Cell that is part of the notochord." [GO_REF:0000034] comment: NOTE: TO DO, notochord development still needs work. is_a: BFO:0000002 -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell relationship: part_of UBERON:0002328 ! notochord relationship: RO:0002202 CL:0007006 ! develops from chordamesodermal cell property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 @@ -25182,6 +25462,7 @@ synonym: "alarm substance secreting cell" EXACT [] synonym: "club cell" RELATED [https://github.com/obophenotype/cell-ontology/issues/583, ISBN-10:0412429403] synonym: "club cell (zebrafish)" EXACT [https://github.com/obophenotype/cell-ontology/issues/583] is_a: CL:0000151 ! secretory cell +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000473 ! defensive cell relationship: part_of UBERON:0001003 ! skin epidermis property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 @@ -25192,7 +25473,7 @@ name: micropylar cell def: "A specialized pore forming cell of the follicle, located adjacent to the animal pole of the oocyte. The micropylar cell makes the single micropyle (pore) through the chorion through which the sperm fertilizes the egg." [PMID:18582455, ZFA:0005239] synonym: "plug cell" EXACT [] xref: ZFA:0005239 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell relationship: part_of UBERON:0001305 ! ovarian follicle property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 @@ -25200,7 +25481,7 @@ property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 id: CL:0007023 name: flask cell def: "Epidermal cell rich in mitochondria. In amphibians, appears during metamorphosis." [DOI:10.1007/BF00717048] -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell relationship: part_of UBERON:0001003 ! skin epidermis property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 @@ -25253,12 +25534,12 @@ is_a: CL:0000187 ! muscle cell [Term] id: CL:0008005 name: obliquely striated somatic muscle cell -def: "A somatic muscle cell that is oblquely striated. Examples include the somatic muscles of nematodes." [PMID:8720463] -is_a: CL:0000228 ! multinucleate cell +def: "A somatic muscle cell that is obliquely striated and mononucleated. Examples include the somatic muscles of nematodes." [doi:10.3908/wormatlas.1.7, PMID:8720463] +is_a: CL:0000226 ! single nucleate cell is_a: CL:0000444 ! obliquely striated muscle cell is_a: CL:0008004 ! somatic muscle cell intersection_of: CL:0008004 ! somatic muscle cell -intersection_of: bearer_of PATO:0001908 ! multinucleate +intersection_of: bearer_of PATO:0001407 ! mononucleate intersection_of: bearer_of PATO:0002479 ! obliquely striated intersection_of: has_part GO:0030017 ! sarcomere @@ -25386,6 +25667,7 @@ subset: cellxgene_subset subset: human_reference_atlas synonym: "mesenchyme cell" EXACT [] is_a: CL:0000219 ! motile cell +is_a: CL:0000255 ! eukaryotic cell relationship: capable_of GO:0016477 ! cell migration relationship: part_of UBERON:0003104 ! mesenchyme property_value: RO:0002175 NCBITaxon:9606 @@ -25510,10 +25792,9 @@ name: rosehip neuron def: "A GABAergic interneuron in human cortical layer 1 that has large rosehip-shaped axonal boutons and compact arborization." [doi:10.1038/s41593-018-0205-2] comment: A rosehip cell has been shown to have an immunohistochemical profile GAD1+CCK+, CNR1–SST–CALB2–PVALB– that matches a single transcriptomically defined cell type whose specific molecular marker signature is not seen in mouse cortex. {xref="doi:10.1038/s41593-018-0205-2"} is_a: BFO:0000002 -is_a: CL:0000255 ! eukaryotic cell is_a: CL:0010011 ! cerebral cortex GABAergic interneuron relationship: RO:0002100 UBERON:0005390 ! has soma location cortical layer I -relationship: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens +relationship: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens relationship: RO:0002292 PR:000005110 ! expresses cholecystokinin relationship: RO:0002292 PR:000007785 ! expresses glutamate decarboxylase 1 relationship: RO:0002292 PR:000011467 ! expresses netrin-G1 @@ -25606,7 +25887,7 @@ creation_date: 2020-09-23T20:22:07Z [Term] id: CL:0008040 name: squamous endothelial cell of venule -def: "An endothelial cell of the venule that is squamous shaped. This is in contrast to the cubodial shape of high endothelial venule cells." [] {comment="GOC:tfm"} +def: "An endothelial cell of the venule that is squamous shaped. This is in contrast to the cubodial shape of high endothelial venule cells." [GOC:tfm] is_a: CL:0002653 ! squamous endothelial cell is_a: CL:1000414 ! endothelial cell of venule property_value: dc:date "2024-07-03T19:52:47Z" xsd:string @@ -25698,7 +25979,7 @@ name: larval midgut cell def: "Any cell in the midgut (middle subdivision of a digestive tract) of an insect larva." [] xref: GOC:pr xref: http://en.wikipedia.org/wiki/Insect#Midgut -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell relationship: part_of UBERON:0001555 ! digestive tract relationship: part_of UBERON:0002548 ! larva relationship: RO:0002162 NCBITaxon:50557 ! in taxon Insecta @@ -25722,7 +26003,7 @@ def: "Any cell in a salivary gland." [] subset: cellxgene_subset xref: GOC:pr xref: http://en.wikipedia.org/wiki/Salivary_gland -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell relationship: part_of UBERON:0001044 ! saliva-secreting gland [Term] @@ -25792,7 +26073,7 @@ synonym: "transient amplifying cell" EXACT [] synonym: "transit amplifying progenitor cell" EXACT [PMID:30827895] synonym: "transit-amplifying cell" EXACT [] is_a: BFO:0000002 -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell relationship: RO:0002202 CL:0000034 ! develops from stem cell property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 @@ -25865,6 +26146,7 @@ id: CL:0009015 name: Peyer's patch follicular dendritic cell def: "A follicular dendritic cell located in the Peyer's patch. These cells from a meshwork in which Peyer's patch B cells reside." [https://orcid.org/0000-0003-4183-8865, PMID:24437401] subset: location_grouping +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000442 ! follicular dendritic cell intersection_of: CL:0000442 ! follicular dendritic cell intersection_of: part_of UBERON:0001211 ! Peyer's patch @@ -25896,12 +26178,14 @@ subset: cellxgene_subset subset: location_grouping synonym: "crypt stem cell of small intestine" BROAD [] synonym: "stem cell of small intestine crypt of Lieberkuhn" EXACT [] +xref: https://cellxgene.cziscience.com/cellguide/CL_0009017 is_a: CL:0002250 ! intestinal crypt stem cell is_a: CL:0002254 ! epithelial cell of small intestine intersection_of: CL:0002250 ! intestinal crypt stem cell intersection_of: part_of UBERON:0001241 ! crypt of Lieberkuhn of small intestine relationship: part_of UBERON:0001241 ! crypt of Lieberkuhn of small intestine property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nIntestinal crypt stem cells of the small intestine are a type of adult stem cell intimately involved in the continuous replenishment of the intestinal epithelium, the innermost layer of the intestine responsible for nutrient absorption. These cells, located within the crypts of Lieberkühn, are the origin of various cell lineages that make up the functional units of the small intestine. They possess self-renewal ability, an essential feature of stem cells, which allows them to maintain a steady population in the small intestine.\nOne of the critical roles of intestinal crypt stem cells is to drive the continual renewal process taking place in the small intestine every 3-5 days. By proliferating intensively, these cells produce transient amplifying (TA) cells that are characterized by quick division and progressive differentiation. These cells eventually differentiate into specialized cell types, encompassing absorptive enterocytes, mucin-secreting goblet cells, hormone-secreting enteroendocrine cells, and Paneth cells, all of which have essential roles in digestion and nutrient absorption in the small intestine.\nIntestinal crypt stem cells of the small intestine are also play a significant part in injury recovery. Under regular conditions, these cells primarily exist in an active state, facilitating the constant renovation of the gut lining. However, upon injury or loss of regular intestinal crypt stem cells reserve intestinal stem cells, a slow-cycling and radio-resistant population, can be stimulated to take over the duties of active crypt stem cells. Such plasticity provides a powerful regenerative mechanism that ensures the intestinal epithelium's function and structural integrity amidst diverse conditions." xsd:string {xref="DOI:10.1016/j.celrep.2020.107952", xref="DOI:10.1038/s41575-018-0081-y", xref="DOI:10.1073/pnas.1607327113"} [Term] id: CL:0009018 @@ -26253,11 +26537,13 @@ name: intestinal crypt stem cell of colon def: "An intestinal crypt stem cell that is located in the colon." [http://orcid.org/0000-0003-3440-1876] subset: cellxgene_subset subset: location_grouping +xref: https://cellxgene.cziscience.com/cellguide/CL_0009043 is_a: CL:0002250 ! intestinal crypt stem cell is_a: CL:0011108 ! colon epithelial cell intersection_of: CL:0002250 ! intestinal crypt stem cell intersection_of: part_of UBERON:0001155 ! colon property_value: terms:contributor https://orcid.org/0000-0002-2825-0621 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nIntestinal crypt stem cells of the colon, also known as colon crypt base columnar (CBC) cells, are highly specialized cells primarily responsible for the constant self-renewal of the colonic epithelium. These cells are found in the crypts of Lieberkühn - deeply invaginated sections of the colon's mucosal layer. \nThe prime function of intestinal crypt stem cells of the colon is to serve as the source of constant cell regeneration in the colon. Every few days, these stem cells divide and differentiate into the various other types of intestinal cells, such as enterocytes, goblet cells, and enteroendocrine cells. \nA constant renewal cycle is necessary due to the harsh environment of the colon where cells continuously encounter abrasive food matter and potential pathogens, leading to a high turnover rate. When the colon's mucosal layer suffers damage, a rapid response is triggered whereby colon crypt stem cells divide faster and are directed to injured sites to repair the epithelial layer. Dysregulation of these cells' function or proliferation can contribute to disorders such as colorectal cancer." xsd:string {xref="DOI:10.1016/j.cell.2013.07.004", xref="DOI:10.1038/s41575-018-0081-y", xref="DOI:10.1073/pnas.1607327113", xref="DOI:10.1111/j.1365-2184.2009.00642.x", xref="DOI:10.1186/s12943-019-0962-x"} [Term] id: CL:0009044 @@ -26973,6 +27259,7 @@ property_value: terms:date "2022-03-17T12:00:44Z" xsd:dateTime id: CL:0009101 name: fibroblastic reticular cell def: "A reticular cell involved in directing B cells and T cells to specific regions within a tissue." [] +synonym: "FRC" RELATED OMO:0003000 [PMID:35440118] is_a: CL:0000186 ! myofibroblast cell is_a: CL:0000432 ! reticular cell property_value: seeAlso "https://github.com/obophenotype/cell-ontology/issues/1472" xsd:string @@ -27206,17 +27493,16 @@ property_value: terms:contributor https://orcid.org/0000-0002-6601-2165 [Term] id: CL:0010003 -name: epithelial cell of alveolus of lung -def: "An epithelial cell that is part_of a alveolus of lung." [] -comment: May be merged with pneumocyte in future +name: obsolete epithelial cell of alveolus of lung +def: "OBSOLETE. An epithelial cell that is part_of a alveolus of lung." [] +comment: This cell type is exactly the same as 'pulmonary alveolar epithelial cell'. subset: cellxgene_subset synonym: "alveolus of lung epithelial cell" EXACT [] xref: MESH:D056809 -is_a: CL:0000066 ! epithelial cell -intersection_of: CL:0000066 ! epithelial cell -intersection_of: part_of UBERON:0002299 ! alveolus of lung -relationship: part_of UBERON:0002299 ! alveolus of lung +relationship: term_tracker_item https://github.com/obophenotype/cell-ontology/issues/2429 property_value: terms:contributor https://orcid.org/0000-0002-6601-2165 +is_obsolete: true +replaced_by: CL:0000322 [Term] id: CL:0010004 @@ -27495,8 +27781,10 @@ id: CL:0011012 name: neural crest cell def: "A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells." [https://orcid.org/0000-0001-5208-3432, https://orcid.org/0000-0002-9900-7880] subset: cellxgene_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_0011012 is_a: CL:0000048 ! multi fate stem cell is_a: CL:0002321 ! embryonic cell (metazoa) +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." xsd:string {xref="DOI:10.1002/dvg.23276", xref="DOI:10.1242/dev.193193", xref="DOI:10.3389/fcell.2020.00635/full", xref="https://doi.org/10.1016/j.ydbio.2011.12.042"} [Term] id: CL:0011013 @@ -27597,6 +27885,7 @@ def: "A mast cell that is CD25+." [] comment: Mast cells do not normally express CD25, but neoplastic mast cells may be CD25-positive. synonym: "CD25+ neoplastic mast cell" EXACT [] is_a: CL:0001063 ! neoplastic cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0001063 ! neoplastic cell intersection_of: RO:0001000 CL:0000097 ! derives from mast cell intersection_of: RO:0002104 PR:000001380 ! has plasma membrane part interleukin-2 receptor subunit alpha @@ -27633,6 +27922,7 @@ name: progenitor cell def: "A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses." [https://doi.org/10.1016/B978-0-12-409503-8.00002-0, ISBN:978-1-62808-994-3] subset: cellxgene_subset is_a: BFO:0000002 +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0011115 ! precursor cell intersection_of: CL:0011115 ! precursor cell intersection_of: RO:0002202 CL:0000034 ! develops from stem cell @@ -27667,6 +27957,7 @@ def: "An explosive cell containing one giant secretory organelle called a cnidoc synonym: "cnidoblast" EXACT [] synonym: "nematocyte" EXACT [] is_a: CL:0000151 ! secretory cell +is_a: CL:0000255 ! eukaryotic cell relationship: has_part GO:0042151 ! nematocyst relationship: RO:0002162 NCBITaxon:6073 ! in taxon Cnidaria property_value: terms:contributor https://orcid.org/0000-0001-5208-3432 @@ -27910,12 +28201,14 @@ name: pulmonary ionocyte def: "An ionocyte that is part of the lung epithelium. The cells from this type are major sources of the CFTR protein in human and mice." [PMID:30069044, PMID:30069046] subset: cellxgene_subset subset: human_reference_atlas +xref: https://cellxgene.cziscience.com/cellguide/CL_0017000 is_a: CL:0000082 ! epithelial cell of lung is_a: CL:0005006 ! ionocyte intersection_of: CL:0005006 ! ionocyte intersection_of: part_of UBERON:0000115 ! lung epithelium property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-2473-2313 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nThe pulmonary ionocyte is a relatively newly identified, specific epithelial cell type found primarily in the pulmonary or respiratory system. Discovered through novel mapping techniques in 2018, these cells are surprisingly rare, making up less than 2% of the cells in the lung's airway, yet they play an essential role in the airway surface liquid and mucus regulation, a crucial factor in lung health.\nThe main responsibility of the pulmonary ionocyte pertains to the regulation and mobilization of chloride ions. They express a high level of CFTR (Cystic Fibrosis Transmembrane Conductance Regulator) gene, which encodes a protein channel across the membrane of cells that produce mucus, sweat, saliva, tears, and digestive enzymes. The activity of CFTR regulates the movement of chloride ions and fluids in and out of cells, which helps maintain a balance of fluid in the organs they are expressed in. If CFTR is dysfunctional, it can cause conditions such as cystic fibrosis, characterized by thick, sticky mucus that can clog the lungs and obstruct the pancreas, leading to respiratory and digestive issues.\nThe discovery of this cell type offers new doors to the treatment and further understanding of diseases like cystic fibrosis. Increased understanding of pulmonary ionocytes could contribute to the development of novel therapeutic approaches to manipulate the function of CFTR in the lungs and other organs affected by dysfunctional CFTR." xsd:string {xref="DOI:10.1038/s41586-018-0393-7", xref="DOI:10.1146/annurev-pathol-042420-094031", xref="DOI:10.1172/JCI171268"} [Term] id: CL:0017001 @@ -28134,6 +28427,7 @@ def: "Any serous secreting cell that is part of the tracheobronchial epithelium. subset: added_for_HCA subset: cellxgene_subset synonym: "serous cell of tracheobronchial tree" EXACT [] +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000313 ! serous secreting cell intersection_of: CL:0000313 ! serous secreting cell intersection_of: part_of UBERON:0007196 ! tracheobronchial tree @@ -28445,10 +28739,12 @@ id: CL:1000143 name: lung goblet cell def: "Any goblet cell that is part of some lung epithelium." [FBC:Autogenerated] subset: cellxgene_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_1000143 is_a: CL:0000082 ! epithelial cell of lung is_a: CL:0002370 ! respiratory goblet cell intersection_of: CL:0000160 ! goblet cell intersection_of: part_of UBERON:0000115 ! lung epithelium +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nLung goblet cells are critical components of the respiratory tract, specifically found in the bronchial segments. They are secretory epithelial cells known for their signature \"goblet\" or cup-like shape. Their primary function is to produce and secrete mucus that aids in trapping airborne particles and pathogens, preventing them from reaching the delicate environment of the lung. As part of the lung's epithelial lining, they act as frontline defenders, maintaining lung health and function.\nThe lung goblet cells are densely packed with granules containing mucin glycoproteins, the primary component of mucus. As mucus is produced and secreted, it moves towards the lumen of the lungs where the cilia, hair-like structures of the neighboring ciliated epithelial cells, help to navigate it upwards and out of the respiratory tract. This coordinated action ensures the expulsion of unwanted particles and pathogens, effectively cleaning the respiratory tract.\nDysfunction or abnormal proliferation of lung goblet cells can result in pathological conditions such as chronic obstructive pulmonary disorder (COPD) and asthma, where excessive mucus production leads to airway obstruction. Furthermore, lung goblet cells respond to a variety of stimuli, including toxins, allergens, irritants, and infections, adjusting their mucus production accordingly." xsd:string {xref="DOI:10.1038/s41385-018-0039-y", xref="DOI:10.1038/s41385-020-00370-7", xref="DOI:10.1159/000512268", xref="DOI:10.1513/AnnalsATS.201802-128AW", xref="https://www.ncbi.nlm.nih.gov/books/NBK553208/"} [Term] id: CL:1000147 @@ -28469,12 +28765,14 @@ def: "A specialized epithelial secretory cell that moves chloride ions and water synonym: "Malpighian tubule Type II cell" EXACT [FBbt:00005797] xref: FBbt:00005797 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: CL:0000151 ! secretory cell +is_a: CL:0000255 ! eukaryotic cell relationship: part_of UBERON:0001054 ! Malpighian tubule [Term] id: CL:1000182 name: malpighian tubule tip cell def: "Any tip cell that is part of some Malpighian tubule." [FBC:Autogenerated] +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000423 ! tip cell intersection_of: CL:0000423 ! tip cell intersection_of: part_of UBERON:0001054 ! Malpighian tubule @@ -28518,6 +28816,7 @@ subset: cellxgene_subset subset: human_reference_atlas synonym: "PNEC" RELATED OMO:0003000 [PMID:33355253] synonym: "pulmonary neuroendocrine cell" EXACT [PMID:33355253] +xref: https://cellxgene.cziscience.com/cellguide/CL_1000223 is_a: CL:0000006 ! neuronal receptor cell is_a: CL:0000098 ! sensory epithelial cell is_a: CL:0000165 ! neuroendocrine cell @@ -28529,6 +28828,7 @@ intersection_of: part_of UBERON:0002048 ! lung relationship: capable_of GO:0070483 ! detection of hypoxia relationship: has_part GO:0031045 ! dense core granule property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nLung neuroendocrine cells, also commonly known as pulmonary neuroendocrine cells (PNECs), are predominantly located in the respiratory epithelium of the bronchial and bronchiolar airways in the lungs. These cells, characterised by their small size and granular appearance, have a distinctive morphology that sets them apart from other lung cells. They are considered part of the diffuse neuroendocrine system due to their scattered distribution through the epithelium and have been classified into solitary cells and clustered forms known as neuroepithelial bodies.\nThe primary function of PNECs is linked to regulation and maintenance of the lung environment. They are sensory in nature and can secrete various bioactive substances such as serotonin, calcitonin, calcitonin gene-related peptides, and bombesin-like peptides which modulate airway smooth muscle tone and influence gut motility. For example, they act as oxygen sensors in response to hypoxia and are responsible for releasing neuropeptides that can induce responses. Moreover, PNECs provide an afferent function as they are equipped with long microvilli that project into the lumen of the bronchus and react to changes in the chemical composition of the luminal content." xsd:string {xref="DOI:10.1016/bs.ctdb.2018.12.002", xref="DOI:10.1016/j.devcel.2020.09.024", xref="DOI:10.1242/dmm.046920"} [Term] id: CL:1000236 @@ -28560,13 +28860,14 @@ relationship: RO:0002100 UBERON:2001314 ! has soma location posterior lateral li [Term] id: CL:1000271 name: lung ciliated cell -def: "Any ciliated cell that is part of some lung." [FBC:Autogenerated] +def: "An epithelial cell that is part of the lung epithelium. This cell is characterised by the presence of cilia on its apical surface." [PMID:27864314] subset: cellxgene_subset subset: human_reference_atlas +is_a: CL:0000067 ! ciliated epithelial cell +is_a: CL:0000082 ! epithelial cell of lung is_a: CL:4030034 ! respiratory ciliated cell -intersection_of: CL:0000064 ! ciliated cell -intersection_of: part_of UBERON:0002048 ! lung -relationship: part_of UBERON:0002048 ! lung +intersection_of: CL:0000067 ! ciliated epithelial cell +intersection_of: part_of UBERON:0000115 ! lung epithelium property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -28575,6 +28876,7 @@ name: lung secretory cell def: "Any secretory cell that is part of some lung." [FBC:Autogenerated] subset: cellxgene_subset is_a: CL:0000151 ! secretory cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000151 ! secretory cell intersection_of: part_of UBERON:0002048 ! lung relationship: part_of UBERON:0002048 ! lung @@ -29173,11 +29475,13 @@ name: enterocyte of epithelium of small intestine def: "An enterocyte that is part of the epithelium of small intestine." [GOC:tfm] subset: cellxgene_subset xref: FMA:263086 +xref: https://cellxgene.cziscience.com/cellguide/CL_1000334 is_a: CL:0000584 {is_inferred="true"} ! enterocyte is_a: CL:0002254 ! epithelial cell of small intestine intersection_of: CL:0000584 ! enterocyte intersection_of: part_of UBERON:0001902 ! epithelium of small intestine relationship: part_of UBERON:0001902 ! epithelium of small intestine +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nEnterocytes of the epithelium of the small intestine are specialized cells that reside in the lining of the small intestine, and are primarily responsible for the essential process of nutrient absorption. These cells are columnar epithelial cells with an apical surface lined with microvilli, a feature referred to as the 'brush border', to maximize the surface area available for absorption.\nEnterocytes play a critical role in both the digestion and absorption of nutrients from food. Their extensive brush border contains enzymes that further assist in nutrient breakdown and transport proteins that transfer nutrients, such as glucose, amino acids, lipids, and vitamins, across the cell membrane. \nThe enterocytes of the small intestine also participate in the barrier function of the gut lining. Enterocytes are connected by tight junctions, which act as a primary defense line against pathogenic invasion by maintaining intestinal barrier integrity. Additionally, their cell surface is coated in glycocalyx and mucus which forms a defensive barrier preventing the penetration of harmful bacteria into the systemic circulation." xsd:string {xref="DOI:10.1038/nrgastro.2013.35", xref="DOI:10.1038/nri3738", xref="DOI:10.1084/jem.20191130", xref="DOI:10.3389/fphys.2021.699152/full"} [Term] id: CL:1000335 @@ -29236,7 +29540,9 @@ name: enterocyte of epithelium proper of ileum def: "An enterocyte that is part of the epithelium proper of ileum." [GOC:tfm] subset: cellxgene_subset xref: FMA:263102 +xref: https://cellxgene.cziscience.com/cellguide/CL_1000342 is_a: CL:1000339 ! enterocyte of epithelium proper of small intestine +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nEnterocytes of the epithelium proper of the ileum, commonly known as ileal enterocytes, are specialized epithelial cells found lining the inner surface of the ileum, the final section of the small intestine in the human body. They play a pivotal role in nutrient absorption, digestive metabolic functions, and the maintenance of the host’s immune response. \nLike enterocytes in other parts of the intestine, ileal enterocytes exhibit distinct characteristics specific to their function and role. They have microvilli on their apical surfaces to increase absorption and are important in the absorption of vitamins and the reabsorption of bile salts. These cells also produce enzymes that metabolize lipids and xenobiotics." xsd:string {xref="DOI:10.1038/nri3738", xref="DOI:10.1084/jem.20191130", xref="DOI:10.1111/j.1365-2249.2011.04523.x"} [Term] id: CL:1000343 @@ -29277,16 +29583,19 @@ is_a: CL:0002071 ! enterocyte of epithelium of large intestine [Term] id: CL:1000347 -name: enterocyte of colon +name: colonocyte def: "A columnar cell of the colon that is part of the colonic epithelium." [GOC:tfm] subset: cellxgene_subset synonym: "colonocyte" EXACT [PMID:34497389] +synonym: "enterocyte of colon" EXACT [] synonym: "vacuolar absorptive cell of epithelium of colon" NARROW [] xref: FMA:263114 +xref: https://cellxgene.cziscience.com/cellguide/CL_1000347 is_a: CL:0002071 {is_inferred="true"} ! enterocyte of epithelium of large intestine is_a: CL:0011108 ! colon epithelial cell intersection_of: CL:0002071 ! enterocyte of epithelium of large intestine intersection_of: part_of UBERON:0000397 ! colonic epithelium +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nEnterocytes of the colon are specialized epithelial cells located in the lining of the colon, the largest part of the large intestine. These cells play a critical role in absorbing water, electrolytes, and certain vitamins from the food material passed on from the small intestine. With a unique structure of finger-like protrusions referred to as microvilli, the enterocytes increase their surface area for effective absorption. The colon is the last part of the digestive system, and as such, it is responsible for compacting undigested food materials and forming fecal matter. Enterocytes of the colon facilitate this process effectively through absorption of water.\nEnterocytes are known for their high regeneration potential, replenishing every 4-5 days, enabling the healthy functioning of the colon. They originate from stem cells located in the crypt of the colon and differentiate into mature enterocytes as they migrate upwards towards the luminal surface. This constant turnover aids in maintaining the intestinal barrier, preventing the entry of detrimental substances into the systemic circulation. Their tight junctions with other epithelial cells provide a robust barrier against invasive pathogens.\nEnterocytes of the colon are involved in the communication with the gut microbiota. These cells harbor enzymes necessary for the metabolism of short-chain fatty acids, which are the byproducts of the fermentation process by gut bacteria. Short-chain fatty acids serve as a major energy source for colonocytes and are important for maintaining colonic health. The dysfunction of enterocytes, therefore, could lead to disorders such as inflammatory bowel disease or colorectal cancer." xsd:string {xref="DOI:10.1007/s11894-010-0130-3", xref="DOI:10.1038/nrgastro.2013.35", xref="DOI:10.1038/nri3738", xref="DOI:10.1084/jem.20191130", xref="DOI:10.3389/fimmu.2019.00277"} [Term] id: CL:1000348 @@ -29786,12 +30095,14 @@ subset: human_reference_atlas synonym: "arterial endothelial cell" EXACT [] xref: BTO:0004758 xref: FMA:67761 +xref: https://cellxgene.cziscience.com/cellguide/CL_1000413 xref: KUPO:0001095 is_a: CL:0000071 ! blood vessel endothelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0001637 ! artery relationship: part_of UBERON:0001917 ! endothelium of artery property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nEndothelial cells of the artery, also referred to as arterial endothelial cells, form an integral part of the arterial system. They form a single layer, known as the endothelium, lining the interior surface of arteries, and are able to respond to the high-pressure and flow conditions present in arteries. The primary role of these cells is to provide a barrier between the vessel wall and the blood, exhibiting selective permeability to regulate the movement of liquids, gases, and blood-borne substances across the vascular wall.\nArterial endothelial cells significantly contribute to maintaining vascular homeostasis. They are at the forefront of sensations and responses to mechanical stimuli, like shear stress and blood pressure changes. An additional key function pertains to the production of nitric oxide, which helps to regulate vascular tone and blood pressure, prevents platelet aggregation, limits leukocyte adhesion to the endothelium, and inhibits smooth muscle cell proliferation. These varied but connected functions help to preclude the development of atherosclerosis, ensuring normal circulation and arterial health.\nMoreover, these cells play a pivotal role in inflammation and coagulation processes. During inflammatory events, they express various adhesion molecules, aiding in leukocyte recruitment and rolling onto the vessel walls for immune response. They also produce anticoagulant and procoagulant substances, involved in blood clotting and clot dissolution, respectively. Dysregulation of the usual functions of arterial endothelial cells can result in serious pathophysiological conditions, such as atherosclerosis, hypertension, and other cardiovascular diseases." xsd:string {xref="DOI:10.1007/s00441-008-0706-5", xref="DOI:10.1007/s10456-021-09785-7", xref="DOI:10.1016/j.ccm.2021.08.005", xref="DOI:10.1016/j.jvs.2004.03.043", xref="DOI:10.1177/153857440303700107"} [Term] id: CL:1000414 @@ -29974,10 +30285,12 @@ name: epithelial cell of lacrimal sac def: "An epithelial cell that is part of the lacrimal sac." [GOC:tfm] subset: cellxgene_subset xref: FMA:70560 +xref: https://cellxgene.cziscience.com/cellguide/CL_1000436 is_a: CL:1000437 ! epithelial cell of nasolacrimal duct intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001351 ! lacrimal sac relationship: part_of UBERON:0001351 ! lacrimal sac +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nEpithelial cells of the lacrimal sac play a significant role in the physiology of tear drainage, acting as an integral part of the lacrimal drainage system. The lacrimal sac is part of the nasolacrimal duct system, a conduit which connects the eye to the nasal cavity, and is lined by multilayered, non-keratinizing, squamous epithelial cells. \nThe epithelial cells of the lacrimal sac are specialized for the purpose of maintaining a moist environment and protecting the surface of the eye. They form a barrier that traps and removes potential contaminants from the tear film during the drainage process. These cells also actively contribute to tear turnover by expediting the drainage of excess tears. Dysfunctional epithelial cells of the lacrimal sac can lead to dacryocystitis, a condition characterized by inflammation of the lacrimal sac.\nEpithelial cells of the lacrimal sac also perform various other tasks which ensure the overall health of the eye. They are involved in the regulation of immune responses within the lacrimal apparatus and may have a possible role in host-microbiome interactions. Thus, epithelial cells of the lacrimal sac play a multifaceted role in tear drainage and ocular surface defence, directly translating to eye health and vision quality." xsd:string {xref="DOI:10.1007/s004290050160", xref="DOI:10.1111/j.1442-9071.2012.02818.x", xref="DOI:10.1167/tvst.8.4.32", xref="DOI:10.2147/OPTH.S26048", xref="DOI:10.3389/fimmu.2022.918619"} [Term] id: CL:1000437 @@ -30110,6 +30423,7 @@ subset: human_reference_atlas synonym: "epithelial cell of parietal layer of glomerular capsule" EXACT [FMA:70968] xref: FMA:70968 xref: KUPO:0001035 +is_a: CL:0000076 ! squamous epithelial cell is_a: CL:1000450 ! epithelial cell of glomerular capsule intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0005750 ! glomerular parietal epithelium @@ -30135,6 +30449,7 @@ subset: human_reference_atlas subset: kidney_upper_slim synonym: "epithelial cell of renal collecting tubule" EXACT [FMA:70982] xref: FMA:70982 +xref: https://cellxgene.cziscience.com/cellguide/CL_1000454 xref: KUPO:0001059 is_a: CL:0000072 {is_inferred="true"} ! non-branched duct epithelial cell is_a: CL:1000449 ! epithelial cell of nephron @@ -30142,6 +30457,7 @@ is_a: CL:1001225 {is_inferred="true"} ! kidney collecting duct cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001232 ! collecting duct of renal tubule property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nKidney collecting duct epithelial cells are a specialized type of cells that form an integral part of the renal system. Located in the collecting duct system of the kidneys, these cells are responsible for one of the final steps in the process of urine formation, and they are instrumental in the fine tuning of the volume and composition of urine by reabsorbing water and certain solutes back into the bloodstream.\nThese cells express specific channels and carriers that actively and passively transport ions and water. They also have channels on their membranes, such as sodium channels and potassium channels, involved in reabsorbing or secreting these electrolytes depending upon the body's needs. The function of renal collecting duct epithelial cells can be regulated by a variety of hormones, including vasopressin (antidiuretic hormone), which can modulate the ion channels and carriers and hence indirectly influence body fluid homeostasis.\nAside from their function in ion and water balance, kidney collecting duct epithelial cells also aid in maintaining the body's acid-base balance. They have specialized functionality to secret hydrogen ions into the tubular lumen, which contributes to acid excretion. Any dysfunction may have serious implications and lead to various renal or systemic diseases, exemplifying the importance of these cells in maintaining overall body homeostasis." xsd:string {xref="DOI:10.1016/j.ajpath.2014.01.014", xref="DOI:10.1016/j.semnephrol.2019.04.005", xref="DOI:10.2215/CJN.05760513", xref="DOI:10.2215/CJN.08880914"} [Term] id: CL:1000456 @@ -30377,6 +30693,7 @@ def: "An epithelial cell that is part of the bile duct. Cholangiocytes contribut subset: cellxgene_subset synonym: "epithelial cell of bile duct" EXACT [] xref: FMA:86481 +xref: https://cellxgene.cziscience.com/cellguide/CL_1000488 xref: ZFA:0009397 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: BFO:0000002 is_a: CL:0000069 {is_inferred="true"} ! branched duct epithelial cell @@ -30385,6 +30702,7 @@ intersection_of: capable_of GO:0015106 ! bicarbonate transmembrane transporter a intersection_of: part_of UBERON:0002394 ! bile duct relationship: part_of UBERON:0002394 ! bile duct relationship: RO:0002202 CL:0005026 ! develops from hepatoblast +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nCholangiocytes, also known as biliary epithelial cells, are specialized epithelial cells that line the biliary tract, which constitutes the gall bladder and bile ducts inside the liver. Crucial to the maintenance of the liver's health and function, cholangiocytes have a key role in the modification and secretion of bile, a fluid produced by hepatocytes that is essential to digestion and the absorption of fats and vitamins.\nCholangiocytes accomplish their primary function through the expression of a variety of transport proteins located on their apical and basolateral membranes, which propel bile acids and other contents of the bile into the biliary lumen. The hepatic bile, once secreted by the hepatocytes, is further modified by cholangiocytes via secretion and absorption processes. These processes help in the regulation of bile volume and composition, which is fundamental in ensuring the efficient digestion of dietary fats and fat-soluble vitamins and the excretion of cholesterol.\nIn addition to their role in bile modification, cholangiocytes also perform several other integral functions. For instance, these cells express Toll-like receptors (TLRs) which allow cholangiocytes to initiate an immune response against pathogens in the biliary lumen. When functioning normally, these cells contribute to biliary integrity, hepatic architecture, and overall hepatic physiology. However, when they become pathological, they are involved in the progression of liver diseases, such as primary biliary cirrhosis and cholangiocarcinoma – the malignancy of the biliary tract." xsd:string {xref="DOI:10.1016/j.jcmgh.2015.05.005", xref="DOI:10.1016/j.jhep.2012.10.011", xref="DOI:10.1038/s41575-019-0125-y", xref="DOI:10.1152/ajpgi.00227.2012", xref="DOI:10.5009/gnl16033"} [Term] id: CL:1000489 @@ -30417,10 +30735,12 @@ def: "A mesothelial cell that is part of the pleura." [GOC:tfm] subset: cellxgene_subset synonym: "pleural mesothelial cell" EXACT [FMA:86737] xref: FMA:86737 +xref: https://cellxgene.cziscience.com/cellguide/CL_1000491 is_a: CL:0000077 ! mesothelial cell intersection_of: CL:0000077 ! mesothelial cell intersection_of: part_of UBERON:0000977 ! pleura relationship: part_of UBERON:0000977 ! pleura +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nMesothelial cells of the pleura form a significant part of the pleural membrane, a thin, double-layered serous membrane that lines the thoracic cavity and encompasses the lungs. These specialized cells contribute to the pleura's key function of producing a lubricating serous fluid, which reduces friction between the lung's outer surface (visceral pleura) and the inner lining of the thoracic cavity (parietal pleura) during respiration. \nThe cellular structure of mesothelial cells, characterized by microvilli on their surface, aids in the secretion and absorption of the pleural fluid, effectively supporting the smooth expansion and contraction of the lungs. Dysregulation in mesothelial cells can lead to pathologies, including pleural effusion and malignant mesothelioma.\nMesothelial cells of the pleura display unique immunologic properties. They act as a first line of defense against infection because they are able to recognize pathogens and respond by secreting various cytokines and chemokines. Additionally, these cells are directly involved in the translocation of immune cells into the pleural cavity during inflammatory response, thereby playing an active role in the immune response within the pleural environment. \nIn the event of pleural injury, these cells are also involved in the mesothelial-mesenchymal transition, a process that allows mesothelial cells to transdifferentiate into myofibroblasts and promote tissue repair." xsd:string {xref="DOI:10.1016/j.ccm.2021.08.005", xref="DOI:10.1016/j.coi.2020.04.005", xref="DOI:10.1152/ajplung.90587.2008", xref="DOI:10.3389/fphys.2014.00284"} [Term] id: CL:1000492 @@ -30439,11 +30759,13 @@ def: "A mesothelial cell that is part of the visceral pleura." [GOC:tfm] subset: cellxgene_subset subset: human_reference_atlas xref: FMA:86739 +xref: https://cellxgene.cziscience.com/cellguide/CL_1000493 is_a: CL:1000491 ! mesothelial cell of pleura intersection_of: CL:0000077 ! mesothelial cell intersection_of: part_of UBERON:0002401 ! visceral pleura relationship: part_of UBERON:0002401 ! visceral pleura property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nMesothelial cells of visceral pleura are specialized epithelial cells that line the inner layer of the pleura, the membrane that envelops the lungs. Positioned adjacent to the lung tissue, these cells form a protective barrier and contribute to the structure of the visceral pleura. They are characterized by their cuboidal to squamous epithelial shape and the presence of microvilli on their surface, a feature aiding in fluid and solute exchange between the pleura and the lungs.\nThe primary function of mesothelial cells of visceral pleura is to secrete a lubricating serous fluid to facilitate smooth, frictionless lung movement within the thoracic cavity during respiration. This helps in the prevention of trauma or damage stemming from the constant rubbing of the lung tissue against the chest wall, hence playing a pivotal role in maintaining respiratory function. Besides fluid secretion, these cells have an essential role in the transportation of fluids and particles across the pleura, as well as in inflammation, wound healing, and tissue repair processes within the pleura.\nMesothelial cells of visceral pleura are notably implicated in the development of pleural diseases such as pleural effusion and pleural mesothelioma, a rare and aggressive form of cancer primarily linked with exposure to asbestos. Alterations, such as hyperplasia or metaplasia, may occur in these mesothelial cells under pathological conditions." xsd:string {xref="DOI:10.1016/S1357-2725(03)00242-5", xref="DOI:10.1152/physrev.00026.2003", xref="DOI:10.1371/journal.pone.0276978", xref="DOI:10.3389/fphys.2014.00221", xref="DOI:10.3390/jdb7020007"} [Term] id: CL:1000494 @@ -30482,7 +30804,7 @@ def: "A cell that is part of a kidney." [] subset: cellxgene_subset xref: KUPO:0001010 xref: ZFA:0009389 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0002113 ! kidney relationship: part_of UBERON:0002113 ! kidney @@ -30630,7 +30952,7 @@ id: CL:1000600 name: lower urinary tract cell def: "Any cell that is part of some lower urinary tract." [FBC:Autogenerated] xref: KUPO:0001115 -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001556 ! lower urinary tract relationship: part_of UBERON:0001556 ! lower urinary tract @@ -30640,7 +30962,7 @@ id: CL:1000601 name: ureteral cell def: "Any cell that is part of some ureter." [FBC:Autogenerated] xref: KUPO:0001116 -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0000056 ! ureter relationship: part_of UBERON:0000056 ! ureter @@ -31137,6 +31459,7 @@ name: glomerular capillary endothelial cell def: "An endothelial cell that is part of the glomerular capillary of the kidney." [] subset: cellxgene_subset subset: human_reference_atlas +xref: https://cellxgene.cziscience.com/cellguide/CL_1001005 xref: KUPO:0001037 is_a: CL:0002188 ! glomerular endothelial cell is_a: CL:1000892 ! kidney capillary endothelial cell @@ -31144,6 +31467,7 @@ intersection_of: CL:1000892 ! kidney capillary endothelial cell intersection_of: part_of UBERON:0004294 ! glomerular capillary endothelium relationship: part_of UBERON:0004294 ! glomerular capillary endothelium property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nThe glomerular capillary endothelial cell comprises an intrinsic component of the glomerulus in the kidney. Glomeruli contain a network of capillaries where the first step of blood filtration takes place, with glomerular capillary endothelial cells acting as an integral part of this process. Unlike regular endothelial cells that line the vasculature, unique fenestrations (openings) characterize these cells, allowing for enhanced permeability and filtration efficacy.\nTogether with the glomerular basement membrane and podocytes, the glomerular endothelial cells form the glomerular filtration barrier, which is responsible for blood filtration and therefore critical for removal of waste products, such as urea and creatinine, and excess substances, such as glucose and ions, from the bloodstream. The glomerular capillary endothelial cells' fenestrations permit the free flow of a variety of particles, barring larger, negatively charged proteins like serum albumin, enabling the formation of an ultrafiltrate. This ultrafiltrate is the primitive form of urine, which then passes through the proximal tubule for further processing and ultimately helps maintain systemic fluid and electrolyte balance.\nMoreover, the glomerular capillary endothelial cells are also believed to play a crucial role in renal pathologies. Any compromise to their structural integrity or functional performance can lead to kidney diseases, including but not limited to, diabetic nephropathy and glomerulonephritis. For instance, in diabetes, persistent hyperglycemia can injure these cells, leading to a compromised glomerular filtration barrier and proteinuria, indicating the loss of proteins in the urine." xsd:string {xref="DOI:10.1016/j.biocel.2010.05.015", xref="DOI:10.1016/j.yexcr.2012.02.032", xref="DOI:10.1111/j.1523-1755.2005.00260.x", xref="DOI:10.2337/diacare.28.1.164", xref="DOI:10.3389/fphys.2021.689083"} [Term] id: CL:1001006 @@ -31271,6 +31595,7 @@ name: kidney afferent arteriole endothelial cell def: "An endothelial cell that lines the interior surface of the afferent arteriole and maintains vascular tone. This cell responds to changing ion concentrations and blood pressure by releasing vasoactive substances, in order to regulate blood flow into the glomeruli, which is essential for glomerular filtration." [PMID:16990493, PMID:22733355, PMID:24066938, PMID:25834230] subset: cellxgene_subset subset: human_reference_atlas +xref: https://cellxgene.cziscience.com/cellguide/CL_1001096 xref: KUPO:0001039 is_a: CL:1000412 ! endothelial cell of arteriole is_a: CL:1000413 ! endothelial cell of artery @@ -31278,6 +31603,7 @@ is_a: CL:1001006 ! kidney afferent arteriole cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0004639 ! renal afferent arteriole property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nKidney afferent arteriole endothelial cells are a specialized type of cell located within the kidneys, forming the inner lining of the afferent arterioles, which are responsible for delivering blood to the glomeruli - capillary networks responsible for filtration - from where the process of urine formation begins in the nephrons.\nThe endothelial cells in the kidney afferent arterioles have a key function in regulating the blood flow and filtration. They have autocrine and paracrine signaling capabilities, meaning they can signal to themselves and other nearby cells. They produce nitric oxide, prostacyclin, and endothelin, which are powerful vasodilators and vasoconstrictors that regulate renal blood flow. These cells also engage in the mitigation of kidney injury and inflammation by promoting repair and regeneration, demonstrating the multifaceted roles these cells play in maintaining renal health." xsd:string {xref="DOI:10.1046/j.0001-6772.2003.01205.x", xref="DOI:10.1093/ndt/gfl308"} [Term] id: CL:1001097 @@ -31296,12 +31622,14 @@ name: kidney efferent arteriole endothelial cell def: "Any endothelial cell that is part of some renal efferent arteriole." [FBC:Autogenerated] subset: cellxgene_subset subset: human_reference_atlas +xref: https://cellxgene.cziscience.com/cellguide/CL_1001099 xref: KUPO:0001042 is_a: CL:1000412 ! endothelial cell of arteriole is_a: CL:1001009 ! kidney efferent arteriole cell intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0004640 ! renal efferent arteriole property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nKidney efferent arteriole endothelial cells constitute a vital component of the kidney's microvascular system. They are unique endothelial cells found lining the walls of efferent arterioles, which transport blood away from the glomeruli in the kidney.\nThe primary responsibilities of the kidney efferent arteriole endothelial cells involve controling renal blood flow, regulating glomerular filtration rate (GFR), and managing perfusion pressure. They do this by contracting and relaxing, effectively narrowing and widening the arteriole's lumen thereby controling the volume and rate of blood flow to the peritubular capillaries and creating the pressure gradient necessary for filtration in the glomerulus. \nFurthermore, kidney efferent arteriole endothelial cells show a high degree of plasticity in response to pathophysiological stimuli and can undergo structural and functional changes based on local needs. In conditions like hypertension and diabetes, these cells can experience hypertrophy and endothelial dysfunction, contributing to the progression of renal disease." xsd:string {xref="DOI:10.1016/j.semcdb.2014.08.002", xref="DOI:10.1016/j.semnephrol.2015.01.010", xref="DOI:10.1038/s41581-021-00411-9", xref="DOI:10.1681/ASN.2019111179"} [Term] id: CL:1001100 @@ -31437,12 +31765,14 @@ def: "A cell that is part of some vasa recta ascending limb." [] comment: It is known in some mammalian species that this cell may express PV-1, a component of the fenestral diaphragm. {xref="PMID:20392799", xref="PMID:20392798", xref="PMID:26062876"} subset: cellxgene_subset subset: human_reference_atlas +xref: https://cellxgene.cziscience.com/cellguide/CL_1001131 xref: KUPO:0001074 is_a: CL:1001036 {is_inferred="true"} ! vasa recta cell intersection_of: CL:1001036 ! vasa recta cell intersection_of: part_of UBERON:0009091 ! vasa recta ascending limb relationship: part_of UBERON:0009091 ! vasa recta ascending limb property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nThe vasa recta ascending limb cells are specialized epithelial cells that are part of the vasa recta in the kidney, a crucial component of the renal medulla that functions as a counter-current exchanger to maintain the concentration gradient required for water reabsorption. These particular cells are located in the ascending limb of the vasa recta, which takes blood flow from the medulla back to the cortex. \nThe primary function of vasa recta ascending limb cells is to preserve the renal medulla's hypertonicity, necessary for the kidney's urine concentration mechanism. Unlike the vasa recta descending limb cells, the venous-like epithelial cells of the ascending vasa recta are highly fenestrated and lack pericyte coverage, which facilitates water reuptake. \nAs the blood flows through the ascending limb, it loses solutes and gains water, which is driven by the high solute concentration in the surrounding interstitium. This process acts in concert with cellular action in the descending limb and contributions from the so-called Loop of Henle, which helps with water and sodium chloride retrieval from the urine.\nIn the context of normal physiological processes, the function of the vasa recta ascending limb cells is essential in maintaining the body's overall fluid balance, electrolyte concentration, and systemic blood pressure. Any dysfunction in these cells may lead to impaired urine concentration or dilution capability of the kidney, potentially resulting in conditions like diabetes insipidus or hyponatremia." xsd:string {xref="DOI:10.1016/B978-0-323-35515-5.00009-9", xref="DOI:10.1053/j.ajkd.2005.01.008", xref="DOI:10.1081/jdi-100101958", xref="DOI:10.1111/apha.12026", xref="DOI:10.1152/ajpregu.00657.2002"} [Term] id: CL:1001135 @@ -31605,12 +31935,14 @@ def: "A cell that is part of some vasa recta descending limb." [] comment: It is known in some mammalian species that this cell may express the urea transporter B. {xref="PMID:20392799", xref="PMID:20392798", xref="PMID:26062876"} subset: cellxgene_subset subset: human_reference_atlas +xref: https://cellxgene.cziscience.com/cellguide/CL_1001285 xref: KUPO:0001071 is_a: CL:1001036 {is_inferred="true"} ! vasa recta cell intersection_of: CL:1001036 ! vasa recta cell intersection_of: part_of UBERON:0009202 ! vasa recta descending limb relationship: part_of UBERON:0009202 ! vasa recta descending limb property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nVasa recta descending limb cells are specialized epithelial cells found in the vasa recta, a network of blood vessels in the renal medulla. These cells line the interior surface of the descending limb of the vasa recta and play a crucial role in the filtering and regulation of substances within the blood.\nIn contrast to vasa recta ascending limb cells, the arterial-like epithelial cells of the descending vasa recta are non-fenestrated and covered by a pericyte layer that regulates the medullary blood flow. They help keeping the body’s fluid and electrolyte balance in check through a process known as countercurrent exchange system, in which the cells of the descending limb are permeable to water but relatively impermeable to solutes, such as sodium and urea. As the blood descends into the medulla along its descending limb, water passively diffuses out of the vasa recta, concentrating the blood in solutes.\nIn addition to their central role in water and solute exchange, these cells contribute to maintaining the medullary osmotic gradient, a critical function to concentrate urine. The osmotic gradient is created by the counterflow of water and solutes between the descending and ascending limbs of the vasa recta and the adjacent Loop of Henle. The selective permeability of the descending limb cells allows them to maintain this gradient, which in turn helps to conserve water, a vital role in the overall function of the renal system. Thus, vasa recta descending limb cells have a significant function in renal physiology, particularly in osmoregulation and fluid balance." xsd:string {xref="DOI:10.1053/j.ajkd.2005.01.008", xref="DOI:10.1081/jdi-100101958", xref="DOI:10.1111/apha.12026#apha12026-bib-0039", xref="DOI:10.1152/ajpregu.00657.2002"} [Term] id: CL:1001286 @@ -31705,12 +32037,14 @@ name: kidney collecting duct principal cell def: "Any renal principal cell that is part of some collecting duct of renal tubule." [FBC:Autogenerated] subset: cellxgene_subset subset: human_reference_atlas +xref: https://cellxgene.cziscience.com/cellguide/CL_1001431 xref: KUPO:0001128 is_a: CL:0005009 {is_inferred="true"} ! renal principal cell is_a: CL:1000454 ! kidney collecting duct epithelial cell intersection_of: CL:0005009 ! renal principal cell intersection_of: part_of UBERON:0001232 ! collecting duct of renal tubule property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nThe kidney collecting duct principal cell is a highly specialized type of cell found in the late distal convoluted tubule and collecting duct of the kidney's nephron. Principal cells are located at the final segments of the renal tubules, where they play a pivotal role in key homeostatic processes.\nOne of their fundamental functions of kidney collecting duct principal cells is the regulation of water reabsorption, which is mediated by aquaporins (water channel proteins). Antidiuretic hormones, such as vasopressin, can stimulate the redistribution of these water channels from an intracellular pools to the apical plasma membrane of the principal cell; translocation of aquaporin (specifically, AQP2) is associated with an increase of osmotic water permeability. The water reabsorption affects the concentration of the final urine; these cells are therefore directly involved in the maintenance of the body's fluid balance.\nKidney collecting duct principal cells also participate in sodium and potassium ions regulation. They reabsorb sodium ions from the tubular fluid back into the bloodstream, a process facilitated by the action of aldosterone, a hormone released by the adrenal glands. Similarly, the principal cells secrete potassium ions into the tubular fluid in response to aldosterone, contributing to the regulation of potassium levels in the body. Impaired function of cells can lead to various renal diseases and disorders, highlighting the vital role of kidney collecting duct principal cells in the body's homeostatic processes." xsd:string {xref="DOI:10.1007/s11906-015-0538-0", xref="DOI:10.1016/B978-0-12-386456-7.05402-2", xref="DOI:10.1016/j.biocel.2022.106261", xref="DOI:10.1073/pnas.1710964114"} [Term] id: CL:1001432 @@ -32216,6 +32550,7 @@ xref: CALOHA:TS-1282 is_a: CL:0000150 ! glandular epithelial cell is_a: CL:0000152 ! exocrine cell is_a: CL:0002251 ! epithelial cell of alimentary canal +is_a: CL:0009005 ! salivary gland cell intersection_of: CL:0000150 ! glandular epithelial cell intersection_of: part_of UBERON:0001044 ! saliva-secreting gland relationship: part_of UBERON:0004809 ! salivary gland epithelium @@ -32227,11 +32562,13 @@ def: "Glandular cell of seminal vesicle epithelium." [NPX:PDR] subset: cellxgene_subset synonym: "seminal vesicle glandular cells" RELATED [CALOHA:TS-1283] xref: CALOHA:TS-1283 +xref: https://cellxgene.cziscience.com/cellguide/CL_1001597 is_a: CL:0000068 ! duct epithelial cell is_a: CL:0000150 ! glandular epithelial cell intersection_of: CL:0000150 ! glandular epithelial cell intersection_of: part_of UBERON:0000998 ! seminal vesicle relationship: part_of UBERON:0004805 ! seminal vesicle epithelium +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nSeminal vesicle glandular cells belong to a specialized group of epithelial cells that form the internal lining of the seminal vesicles, a pair of male reproductive organs. These cells are located within the complex tubuloalveolar glands that make up the seminal vesicles and are known for their unique pseudostratified columnar epithelium structure. \nThe primary function of these cells is the secretion of a variety of substances that ultimately constitute around 70% of the fluid volume of semen. Seminal cells produce a high-fructose fluid that serves as an energy source for the spermatozoa and promotes their motility. They also secrete other essential substances like proteins, enzymes, vitamin C, prostaglandins, and various other compounds. Collectively, these substances help in the nourishment, protection, and transportation of the spermatozoa throughout the male reproductive system and during the ejaculation process.\nSecondary to the production of seminal fluid, the seminal vesicle glandular cells also play a role in the contraction of the seminal vesicles during ejaculation. The contraction of these glands, induced by sympathetic nerves, ensures the efficient propulsion of the seminal fluid mixed with spermatozoa into the ejaculatory ducts and subsequently to the urethra. Notably, any malfunction or pathological condition affecting these cells can impact male fertility, emphasizing the importance of understanding the intricate functions of seminal vesicle glandular cells in maintaining the healthy physiological function of male reproduction." xsd:string {xref="DOI:10.1007/978-3-030-32300-4_26", xref="DOI:10.1007/s00265-006-0178-0", xref="DOI:10.1111/j.1439-0272.1992.tb02636.x", xref="https://www.ncbi.nlm.nih.gov/books/NBK499854/", xref="https://www.sciencedirect.com/topics/veterinary-science-and-veterinary-medicine/seminal-vesicle"} [Term] id: CL:1001598 @@ -32281,7 +32618,7 @@ relationship: part_of UBERON:0001235 ! adrenal cortex [Term] id: CL:1001602 name: cerebral cortex endothelial cell -def: "Endothelial cells forming the walls of the capillaries within the cerebral cortex." [NPX:PDR] +def: "A distinct endothelial cell forming the walls of the capillaries within the cerebral cortex." [NPX:PDR] subset: cellxgene_subset synonym: "cerebral cortex endothelial cells" RELATED [CALOHA:TS-2372] synonym: "endothelial cells of cerebral cortex" RELATED [CALOHA:TS-2372] @@ -32599,7 +32936,7 @@ creation_date: 2014-06-24T23:16:45Z id: CL:2000020 name: inner cell mass cell def: "Any native cell that is part of a inner cell mass." [GOC:TermGenie] -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0000087 ! inner cell mass relationship: part_of UBERON:0000087 ! inner cell mass @@ -32611,7 +32948,7 @@ id: CL:2000021 name: sebaceous gland cell def: "Any native cell that is part of a sebaceous gland." [GOC:TermGenie] subset: cellxgene_subset -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001821 ! sebaceous gland relationship: part_of UBERON:0001821 ! sebaceous gland @@ -33742,11 +34079,11 @@ property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023011 name: lamp5 GABAergic cortical interneuron -def: "A GABAergic neuron located in the cerebral cortex that expresses Lamp5" [PMID:30382198, PMID:37824655] +def: "A transcriptomically distinct GABAergic neuron located in the cerebral cortex that expresses Lamp5. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_subclass', clusters Lamp5." [https://cellxgene.cziscience.com/e/e4ddac12-f48f-4455-8e8d-c2a48a683437.cxg/, PMID:30382198, PMID:37824655] subset: BDS_subset subset: cellxgene_subset xref: ILX:0770149 -is_a: CL:4023064 ! caudal ganglionic eminence derived interneuron +is_a: CL:4023064 ! caudal ganglionic eminence derived cortical interneuron intersection_of: CL:0000099 ! interneuron intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neurotransmission intersection_of: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex @@ -33808,11 +34145,11 @@ property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023015 name: sncg GABAergic cortical interneuron -def: "A GABAergic neuron located in the cerebral cortex that expresses Gamma-synuclein" [PMID:33186530, PMID:37824655] +def: "A transcriptomically distinct GABAergic neuron located in the cerebral cortex that expresses Gamma-synuclein. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_subclass', clusters Sncg." [https://cellxgene.cziscience.com/e/e4ddac12-f48f-4455-8e8d-c2a48a683437.cxg/, PMID:33186530, PMID:37824655] subset: BDS_subset subset: cellxgene_subset xref: ILX:0770150 -is_a: CL:4023064 ! caudal ganglionic eminence derived interneuron +is_a: CL:4023064 ! caudal ganglionic eminence derived cortical interneuron intersection_of: CL:0000099 ! interneuron intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neurotransmission intersection_of: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex @@ -33824,11 +34161,19 @@ property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023016 name: VIP GABAergic cortical interneuron -def: "A GABAergic neuron located in the cerebral cortex that expresses vasoactive intestinal polypeptide" [PMID:33186530, PMID:37824655] +def: "A transcriptomically distinct cortical GABAergic neuron that expresses the vasocactive intestinal polypeptide and that has its soma located in the cerebral cortex. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_subclass', cluster Vip." [https://cellxgene.cziscience.com/e/e4ddac12-f48f-4455-8e8d-c2a48a683437.cxg/, PMID:33186530, PMID:37824655] subset: BDS_subset subset: cellxgene_subset +synonym: "cortical VIP neuron" RELATED [PMID:36384143] +synonym: "Vip" RELATED [ILX:0770151] +synonym: "Vip GABAergic neuron" BROAD [ILX:0770151] +synonym: "VIP interneuron" BROAD [PMID:33108272] +synonym: "VIP neuron" BROAD [PMID:33108272] +synonym: "VIP type" RELATED [PMID:37824655] +synonym: "VIP-Expressing GABAergic Neuron" BROAD [PMID:35221922] +synonym: "VIP-IN" RELATED [PMID:33794534] xref: ILX:0770151 -is_a: CL:4023064 ! caudal ganglionic eminence derived interneuron +is_a: CL:4023064 ! caudal ganglionic eminence derived cortical interneuron intersection_of: CL:0000099 ! interneuron intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neurotransmission intersection_of: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex @@ -33836,17 +34181,21 @@ intersection_of: RO:0002292 PR:000017299 ! expresses VIP peptides relationship: RO:0002292 PR:000017299 ! expresses VIP peptides property_value: IAO:0000028 "VIP cortical interneuron" xsd:string property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 +property_value: terms:description "This neuronal type is distinguished by its heterogeneous morphology and electrophysiological characteristics (Pronneke et al., 2015,2020; Apicella and Marchionni, 2022). Variations in morphology and firing patterns are observed in human cortical VIP interneurons. In a study by Lee et al., 2023, four distinct subtypes of VIP neurons were identified, each exhibiting unique morphologies, soma locations, and electrophysiological properties. These subtypes are defined according to their transcriptomic markers: LBH-VIP and CCD184-VIP, both of which display a bipolar morphology with axons and dendrites extending across cortical layers; and SY16-VIP and ADAMTSL1-VIP, characterized by a dendritic arbor that spreads horizontally within the same layer as the soma (Lee et al., 2023). Disruption or malfunction of VIP cortical interneuron is implicated in neurodevelopmental disorders such as Rett Syndrome and Dravet Syndrome (Goff and Goldberg 2021)." xsd:string {xref="PMID:26420784", xref="PMID:31210267", xref="PMID:33794534", xref="PMID:35221922"} [Term] id: CL:4023017 name: sst GABAergic cortical interneuron -def: "A GABAergic neuron located in the cerebral cortex that expresses somatostatin (sst)" [PMID:27477017, PMID:37824655] +def: "A transcriptomically distinct GABAergic neuron located in the cerebral cortex that expresses somatostatin (sst). The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: MGE-derived interneurons', Author Categories: 'CrossArea_subclass', cluster Sst." [https://cellxgene.cziscience.com/e/9c63201d-bfd9-41a8-bbbc-18d947556f3d.cxg/, PMID:27477017, PMID:33742131, PMID:37824655] +comment: In the mouse cortex, sst GABAergic cortical interneurons show heterogeneous electrophysiological signatures varying between low-threshold spiking (LTS), regular-spiking and fast-spiking (Song, Y. H., Yoon, J., & Lee, S. H. 2021). Sst GABAergic cortical interneurons have multiple functional roles in the brain. In the mouse, they involved in the generation of slow-waves during the sleep phase of non-rapid eye-movement (NREM) (Funk, C. M. et al., 2017), they maintain synaptic plasticity during motor learning (Adler, A., Zhao, R., et al., 2021), they enhance visual perception in the V1 cortical area by suppressing the activity of pyramidal excitatory neurons (Song, YH. et al., 2020). In humans, malfunctioning of sst GABAergic cortical interneurons is associated with neurodegenerative and psychiatric disorders such as Parkinson's disease, Alzheimer's disease, major depressive disorder, bipolar disorder and schizophrenia as individuals affected by these pathologies show a decrease of expression of SST in the brain (Song YH., Yoon J. et al., 2021). {xref="PMID:30792151", xref="PMID:33742131", xref="PMID:28821651", xref="PMID:32494634"} subset: BDS_subset subset: cellxgene_subset +synonym: "SOM+ inhibitory interneuron" RELATED [PMID:30001424] +synonym: "somatostatin-expressing inhibitory interneuron" RELATED [PMID:30001424] +synonym: "SST+ IN" RELATED [PMID:33742131] xref: ILX:0770152 -is_a: BFO:0000002 -is_a: CL:0010011 ! cerebral cortex GABAergic interneuron -intersection_of: CL:0000099 ! interneuron +is_a: CL:4023069 ! medial ganglionic eminence derived GABAergic cortical interneuron +intersection_of: CL:4023069 ! medial ganglionic eminence derived GABAergic cortical interneuron intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neurotransmission intersection_of: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex intersection_of: RO:0002292 PR:000015665 ! expresses somatostatin @@ -33857,13 +34206,12 @@ property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023018 name: pvalb GABAergic cortical interneuron -def: "A GABAergic interneuron located in the cerebral cortex that expresses Parvalbumin." [PMID:27477017, PMID:37824655] +def: "A transcriptomically distinct GABAergic interneuron with a soma located in a cerebral cortex and it expresses Parvalbumin. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: MGE-derived interneurons', Author Categories: 'CrossArea_subclass', cluster Pvalb." [https://cellxgene.cziscience.com/e/9c63201d-bfd9-41a8-bbbc-18d947556f3d.cxg/, PMID:27477017, PMID:37824655] subset: BDS_subset subset: cellxgene_subset xref: ILX:0770154 -is_a: BFO:0000002 -is_a: CL:0010011 ! cerebral cortex GABAergic interneuron -intersection_of: CL:0000099 ! interneuron +is_a: CL:4023069 ! medial ganglionic eminence derived GABAergic cortical interneuron +intersection_of: CL:4023069 ! medial ganglionic eminence derived GABAergic cortical interneuron intersection_of: capable_of GO:0061534 ! gamma-aminobutyric acid secretion, neurotransmission intersection_of: RO:0002100 UBERON:0000956 ! has soma location cerebral cortex intersection_of: RO:0002292 PR:000013502 ! expresses parvalbumin alpha @@ -33966,7 +34314,8 @@ name: L5 sst T-Martinotti interneuron (Mmus) def: "A sst GABAergic cortical interneuron with a soma found in L5 and possesses 'T-shaped' Martinotti morphologies with local axonal plexus in L5a and translaminar axons restricted to the uppermost part of L1. They show low-threshold spiking patterns with strong rebound firing, and inhibit the L1 apical tuft of nearby pyramidal cells." [PMID:28254942, PMID:29326172] subset: BDS_subset synonym: "L5 T Martinotti SST (Mus musculus)" EXACT [] -is_a: CL:4023017 ! sst GABAergic cortical interneuron +is_a: BFO:0000002 +is_a: CL:0010011 ! cerebral cortex GABAergic interneuron is_a: CL:4023086 ! T Martinotti neuron relationship: RO:0002100 UBERON:0005394 ! has soma location cortical layer V relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus @@ -33980,7 +34329,8 @@ name: L5 non-Martinotti sst GABAergic interneuron (Mmus) def: "A sst GABAergic cortical interneuron with a soma found in lower L5 with mostly local axonal arborization but with some sparse ascending axons. L5 non-Martinotti sst cells show somatic localization and local axon plexus in L5b and L5b/6 and substantial innervation of L3 and L4, and receive thalamic input from the ventral posteromedial nucleus and specifically target L4 neurons, avoiding L5 pyramidal cells. L5 non-Martinotti sst cells tend to show a higher input resistance and seem to be less stuttering." [PMID:28254942, PMID:29326172] subset: BDS_subset synonym: "L5 non-Martinotti SST (Mus musculus)" EXACT [] -is_a: CL:4023017 ! sst GABAergic cortical interneuron +is_a: BFO:0000002 +is_a: CL:0010011 ! cerebral cortex GABAergic interneuron relationship: RO:0002100 UBERON:0005394 ! has soma location cortical layer V relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002292 PR:P60041 ! expresses somatostatin (mouse) @@ -34006,7 +34356,8 @@ def: "A sst GABAergic cortical interneuron that has \"fanning-out' Martinotti mo comment: L2/3/5 fan Martionotti SST cells have an adapting firing pattern and non-zero afterdepolarization (ADP). {xref="PMID:33184512"} subset: BDS_subset synonym: "L2/3/5 fan Martinotti SST (Mus musculus)" EXACT [] -is_a: CL:4023017 ! sst GABAergic cortical interneuron +is_a: BFO:0000002 +is_a: CL:0010011 ! cerebral cortex GABAergic interneuron is_a: CL:4023087 ! fan Martinotti neuron relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002292 PR:P60041 ! expresses somatostatin (mouse) @@ -34019,7 +34370,8 @@ name: L4 sst Martinotti interneuron (Mmus) def: "A sst GABAergic cortical interneuron with a soma found in lower L2/3 and upper 5, L4 Sst cells have Martinotti morphology with ascending axons but denser local axons and sparser ‘fanning-out’ projections to L1. L4 sst cells have smaller membrane time constant to calb2 (L2/3/5 fan Martinotti Cell) and non-zero afterdepolarization (ADP)." [PMID:33184512] subset: BDS_subset synonym: "L4 SST (Mus musculus)" EXACT [] -is_a: CL:4023017 ! sst GABAergic cortical interneuron +is_a: BFO:0000002 +is_a: CL:0010011 ! cerebral cortex GABAergic interneuron is_a: CL:4023076 ! Martinotti neuron relationship: RO:0002100 UBERON:0005393 ! has soma location cortical layer IV relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus @@ -34070,7 +34422,7 @@ property_value: terms:contributor "https://orcid.org/0000-0002-7073-9172" xsd:st [Term] id: CL:4023036 name: chandelier pvalb GABAergic cortical interneuron -def: "A pvalb GABAergic cortical interneuron that is recognizable by the straight terminal axonal 'cartridges' of vertically oriented strings of synaptic boutons. Chandelier PV cells' boutons target exclusively the axon initial segment (AIS) of pyramidal cells, with a single cell innervating hundreds of pyramidal cells in a clustered manner." [PMID:27477017] +def: "A transcriptomically distinct pvalb GABAergic cortical interneuron that is recognizable by the straight terminal axonal 'cartridges' of vertically oriented strings of synaptic boutons. Chandelier PV cells' boutons target exclusively the axon initial segment (AIS) of pyramidal cells, with a single cell innervating hundreds of pyramidal cells in a clustered manner. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_subclass', clusters Chandelier." [https://cellxgene.cziscience.com/e/9c63201d-bfd9-41a8-bbbc-18d947556f3d.cxg/, PMID:27477017] comment: In mice, Chandelier PV cells have soma found in in upper L2/3, with some in deep L5 and exhibit fast-spiking but lower firing rate compared to basket cells, and have practically absent hyperpolarization sag. {xref="PMID:27477017"} subset: BDS_subset subset: cellxgene_subset @@ -34084,9 +34436,10 @@ property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023038 name: L6b glutamatergic cortical neuron -def: "A glutamatergic neuron with a soma found in cortical layer 6b. They are transcriptomically related to corticothalamic-projecting neurons but have differential projections to the thalamus or anterior cingulate." [DOI:10.1101/2020.10.19.34312, PMID:30382198, PMID:37824655] +def: "A glutamatergic neuron with a soma found in cortical layer 6b. They are transcriptomically related to corticothalamic-projecting neurons but have differential projections to the thalamus or anterior cingulate. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: Deep layer (non-IT) excitatory neuron', Author Categories: 'CrossArea_subclass', cluster L6b." [DOI:10.1101/2020.10.19.34312, https://cellxgene.cziscience.com/e/d01c9dff-abd1-4825-bf30-2eb2ba74597e.cxg/, PMID:30382198, PMID:37824655] subset: BDS_subset subset: cellxgene_subset +subset: human_reference_atlas xref: ILX:0770163 is_a: CL:0000679 ! glutamatergic neuron is_a: CL:0010012 ! cerebral cortex neuron @@ -34094,6 +34447,7 @@ intersection_of: CL:0000679 ! glutamatergic neuron intersection_of: RO:0002100 UBERON:8440003 ! has soma location cortical layer VIb relationship: RO:0002100 UBERON:8440003 ! has soma location cortical layer VIb property_value: IAO:0000028 "L6b glut" xsd:string +property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] @@ -34125,7 +34479,7 @@ property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023041 name: L5 extratelencephalic projecting glutamatergic cortical neuron -def: "A glutamatergic neuron, with a soma found in the deeper portion of L5, that has long-range axonal projections including deep subcortical targets outside of the telencephalon and, in some cases, the spinal cord. While the L5 ET neuron projections are not limited to ET targets, they are clearly differentiated from the neuron subclasses whose projections are constrained to intratelencephalic (IT) targets. L5 ET neurons are generally the largest excitatory cortical neurons, typically having a thick apical dendrite with a prominent dendritic tuft in layer 1 and displaying burst-firing physiological characteristics." [PMID:34616075, PMID:37824655] +def: "A transcriptomically distinct glutamatergic neuron, with a soma found in the deeper portion of L5, that has long-range axonal projections including deep subcortical targets outside of the telencephalon and, in some cases, the spinal cord. While the L5 ET neuron projections are not limited to ET targets, they are clearly differentiated from the neuron subclasses whose projections are constrained to intratelencephalic (IT) targets. L5 ET neurons are generally the largest excitatory cortical neurons, typically having a thick apical dendrite with a prominent dendritic tuft in layer 1 and displaying burst-firing physiological characteristics. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: Deep layer (non-IT) excitatory neurons ', Author Categories: 'CrossArea_subclass', clusters L5 ET." [https://cellxgene.cziscience.com/e/d01c9dff-abd1-4825-bf30-2eb2ba74597e.cxg/, PMID:34616075, PMID:37824655] subset: BDS_subset subset: cellxgene_subset synonym: "burst-firing layer 5 neuron" EXACT [DOI:10.3389/fncel.2011.00001] @@ -34145,7 +34499,7 @@ property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023042 name: L6 corticothalamic-projecting glutamatergic cortical neuron -def: "A corticothalamic-projecting neuron with a soma found in cortical layer 6." [PMID:34616075, PMID:37824655] +def: "A transcriptomically distinct corticothalamic-projecting neuron with a soma found in cortical layer 6. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: Deep layer (non-IT) excitatory neurons', Author Categories: 'CrossArea_subclass', clusters L6 CT." [https://cellxgene.cziscience.com/e/d01c9dff-abd1-4825-bf30-2eb2ba74597e.cxg/, PMID:34616075, PMID:37824655] subset: BDS_subset subset: cellxgene_subset synonym: "L6 CT" EXACT [PMID:28625486, PMID:34616075] @@ -34160,7 +34514,7 @@ property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023043 name: L5/6 near-projecting glutamatergic neuron of the primary motor cortex -def: "A near-projecting glutamatergic neuron with a soma found in layer 5/6 of the primary motor cortex." [PMID:31209381, PMID:34616075] +def: "A transcriptomically distinct near-projecting glutamatergic neuron with a soma found in layer 5/6 of the primary motor cortex. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: Deep layer (non-IT) excitatory neurons', Author Categories: 'CrossArea_subclass', cluster L5/6 NP." [https://cellxgene.cziscience.com/e/d01c9dff-abd1-4825-bf30-2eb2ba74597e.cxg/, PMID:31209381, PMID:34616075] subset: BDS_subset subset: cellxgene_subset synonym: "L5/6 NP M1" EXACT [] @@ -34277,7 +34631,7 @@ property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023051 name: vascular leptomeningeal cell -def: "A type of mesothelial fibroblast that is derived from the neural crest, is localized on blood vessels, and is a key component of the pia and arachnoid membranes surrounding the brain." [PMID:27284195, PMID:29443965, PMID:30096314, PMID:37824655] +def: "A transcriptomically distinct type of mesothelial fibroblast that is derived from the neural crest, is localized on blood vessels, and is a key component of the pia and arachnoid membranes surrounding the brain. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: Non-neuronal cells', Author Categories: 'CrossArea_subclass', clusters VLMC." [https://cellxgene.cziscience.com/e/5346f9c6-755e-4336-94cc-38706ec00c2f.cxg/, PMID:27284195, PMID:29443965, PMID:30096314, PMID:37824655] subset: BDS_subset subset: cellxgene_subset synonym: "VLMC" EXACT [] @@ -34431,12 +34785,11 @@ property_value: terms:contributor http://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023064 -name: caudal ganglionic eminence derived interneuron +name: caudal ganglionic eminence derived cortical interneuron def: "An interneuron that is derived from the caudal ganglionic eminence." [PMID:20130169, PMID:37824655, PMID:37824663] subset: human_reference_atlas synonym: "caudal ganglionic eminence derived GABAergic cortical interneuron" EXACT [PMID:20130169] synonym: "CGE cortical interneuron" RELATED OMO:0003000 [PMID:20130169] -synonym: "CGE interneuron" EXACT OMO:0003000 [PMID:37824663] synonym: "CGE interneuron" RELATED OMO:0003000 [PMID:37824663] synonym: "CGE-derived cell" RELATED OMO:0003000 [PMID:27034423] synonym: "CGE-derived GABAergic IN" RELATED OMO:0003000 [PMID:27034423] @@ -34581,7 +34934,8 @@ def: "A sst GABAergic cortical interneuron found in L6 that expresses tyrosine h subset: BDS_subset synonym: "L6 Th+ SST (Mus musculus)" EXACT [] synonym: "L6 tyrosine hydroxylase positive sst expressing GABAergic cortical interneuron (Mus musculus)" EXACT [] -is_a: CL:4023017 ! sst GABAergic cortical interneuron +is_a: BFO:0000002 +is_a: CL:0010011 ! cerebral cortex GABAergic interneuron relationship: RO:0002100 UBERON:0005395 ! has soma location cortical layer VI relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002292 PR:P24529 ! expresses tyrosine 3-monooxygenase (mouse) @@ -35013,7 +35367,8 @@ comment: L5/6 non-Martinotti SST cells have strongly facilitating excitatory inp subset: BDS_subset synonym: "L5/6 non-Martinotti morphology sst expressing GABAergic cortical interneuron (Mus musculus)" EXACT [] synonym: "L5/6 non-Martinotti SST (Mus musculus)" EXACT [] -is_a: CL:4023017 ! sst GABAergic cortical interneuron +is_a: BFO:0000002 +is_a: CL:0010011 ! cerebral cortex GABAergic interneuron relationship: RO:0002100 UBERON:8440002 ! has soma location cortical layer V/VI relationship: RO:0002162 NCBITaxon:10090 ! in taxon Mus musculus relationship: RO:0002292 PR:P60041 ! expresses somatostatin (mouse) @@ -35048,7 +35403,7 @@ property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 [Term] id: CL:4023121 name: sst chodl GABAergic cortical interneuron -def: "A sst GABAergic cortical interneuron that also expresses Chodl. These neurons are rare and correspond to the only known cortical interneurons with long-range projection." [PMID:15845086, PMID:31209381, PMID:33372656, PMID:37824655] +def: "A transcriptomically distinct sst GABAergic cortical interneuron that also expresses Chodl. These neurons are rare and correspond to the only known cortical interneurons with long-range projection. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: MGE-derived interneurons', Author Categories: 'CrossArea_subclass', clusters Sst Chodl." [https://cellxgene.cziscience.com/e/9c63201d-bfd9-41a8-bbbc-18d947556f3d.cxg/, PMID:15845086, PMID:31209381, PMID:33372656, PMID:37824655] subset: cellxgene_subset synonym: "long-range GABAergic interneuron" BROAD [] is_a: CL:4023017 ! sst GABAergic cortical interneuron @@ -35062,8 +35417,10 @@ name: oxytocin receptor sst GABAergic cortical interneuron def: "An interneuron located in the cerebral cortex that expresses the oxytocin receptor. These interneurons also express somatostatin." [PMID:25303526] comment: These cells were first identified in mouse. {xref="PMID:25303526"} synonym: "OxtrINs" RELATED OMO:0003000 [PMID:25303526] -is_a: CL:4023017 ! sst GABAergic cortical interneuron +is_a: BFO:0000002 +is_a: CL:0010011 ! cerebral cortex GABAergic interneuron relationship: RO:0002292 PR:000001635 ! expresses oxytocin receptor +relationship: RO:0002292 PR:000015665 ! expresses somatostatin property_value: RO:0002175 NCBITaxon:10090 {xref="PMID:25303526"} property_value: terms:contributor https://orcid.org/0000-0001-7258-9596 @@ -35276,11 +35633,13 @@ id: CL:4023181 name: hypendymal cell def: "A neurecto-epithelial cell that is part of the basal layer of the subcommissural organ and specializes in the secretion of proteins into the subarachnoid space. Hypendymal cells have similar characteristics to ependymal cells and express SCO-spondin." [https://orcid.org/0000-0001-7258-9596, PMID:26778959, PMID:9579598] subset: cellxgene_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_4023181 is_a: CL:0000710 ! neurecto-epithelial cell is_a: CL:0002319 ! neural cell relationship: part_of UBERON:0002139 ! subcommissural organ relationship: RO:0002292 PR:000015658 ! expresses SCO-spondin property_value: terms:contributor http://orcid.org/0000-0002-2105-0715 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nHypendymal cells are secretory cells located between the ependymal layer and the posterior commissure, forming the hypendmal layer of the subcommissural organ (SCO), a highly conserved gland that is part of the circumventricular system within the brain. \nHypendymal cells are bipolar cells with a thin apical pole and basal process. Most of the ultrastructural characteristics of these cells are similar to those described for the ependymal cells (which are arranged into another layer – the ependyma). However, ependymal cells release their secretion into the ventricular cerebrospinal fluid whereas hypendymal cells project processes to the local blood vessels and to the subarachnoidal space." xsd:string {xref="DOI:10.1002/(SICI)1097-0029(19980415)41:2<98::AID-JEMT2>3.0.CO;2-M", xref="DOI:10.1111/joa.13709", xref="DOI:10.3389/fncel.2015.00480"} [Term] id: CL:4023187 @@ -35488,8 +35847,9 @@ property_value: terms:date "2022-07-08T11:48:36Z" xsd:dateTime [Term] id: CL:4030004 name: thymic nurse cell -def: "A large epithelial cell found in the thymus. This cell type may internalize thymocytes through extensions of plasma membrane. The cell surface and cytoplasmic vacuoles of a thymic nurse cell express MHC Class I and MHC Class II antigens. The interaction of these antigens with a developing thymocyte determines whether the thymocyte undergoes positive or negative selection." [https://en.wikipedia.org/wiki/Thymic_nurse_cell] {terms:contributor="https://orcid.org/0000-0002-0819-0473"} +def: "A large epithelial cell found in the thymus. This cell type may internalize thymocytes through extensions of plasma membrane. The cell surface and cytoplasmic vacuoles of a thymic nurse cell express MHC Class I and MHC Class II antigens. The interaction of these antigens with a developing thymocyte determines whether the thymocyte undergoes positive or negative selection." [https://en.wikipedia.org/wiki/Thymic_nurse_cell] is_a: CL:0002293 ! epithelial cell of thymus +property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 property_value: terms:date "2022-02-18T12:43:20Z" xsd:dateTime [Term] @@ -35507,7 +35867,7 @@ property_value: terms:date "2022-09-14T16:19:11Z" xsd:dateTime [Term] id: CL:4030006 name: fallopian tube secretory epithelial cell -def: "An epithelial cell that is part of the fallopian tube epithelium that secretes mucous fluid and oviduct-specific products through the stimulation of estrogen and luteinizing hormone. The fallopian tube secretory cell has approximately the same height as the ciliated cell and is usually a more narrow columnar cell. The nucleus is ovoid and perpendicular to the long axis of the cell. The chromatin is more dense and the nucleolus smaller than that seen in the ciliated cell." [https://doi.org/10.1186/1477-7827-7-129, https://doi.org/10.3390/cells8080933, https://www.proteinatlas.org/learn/dictionary/normal/fallopian+tube] {terms:contributor="https://orcid.org/0000-0002-0819-0473"} +def: "An epithelial cell that is part of the fallopian tube epithelium that secretes mucous fluid and oviduct-specific products through the stimulation of estrogen and luteinizing hormone. The fallopian tube secretory cell has approximately the same height as the ciliated cell and is usually a more narrow columnar cell. The nucleus is ovoid and perpendicular to the long axis of the cell. The chromatin is more dense and the nucleolus smaller than that seen in the ciliated cell." [https://doi.org/10.1186/1477-7827-7-129, https://doi.org/10.3390/cells8080933, https://www.proteinatlas.org/learn/dictionary/normal/fallopian+tube] comment: The other cell types of the fallopian tube epithelium include the ciliated cell and the intercalary cell, or peg cell. The fallopian tube secretory epithelial cell type has been implicated as a source of high-grade serous ovarian carcinoma. {xref="https://doi.org/10.1016/j.ccr.2013.10.013", xref="https://www.proteinatlas.org/learn/dictionary/normal/fallopian+tube"} subset: human_reference_atlas synonym: "oviduct secretory epithelial cell" BROAD [] @@ -35515,12 +35875,13 @@ synonym: "uterine tube secretory epithelial cell" EXACT [] is_a: CL:1001591 ! oviduct glandular cell relationship: part_of UBERON:0003889 ! fallopian tube property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 property_value: terms:date "2022-03-03T10:39:31Z" xsd:dateTime [Term] id: CL:4030007 name: fallopian tube ciliated cell -def: "An epithelial ciliated cell that is part of the fallopian tube. This cell type is found mainly on the apex of the mucosal folds and contributes, together with peristaltic contractions, to the self-propulsion of spermatozoa, the transport of ovum during ovulation and the transport of the fertilized ovum to the intramural fallopian tube. A fallopian tube ciliated cell has a columnar shape and contains an oval or round nucleus, often located perpendicular or parallel to the long axis of the cell." [PMID:16565155] {terms:contributor="https://orcid.org/0000-0002-0819-0473"} +def: "An epithelial ciliated cell that is part of the fallopian tube. This cell type is found mainly on the apex of the mucosal folds and contributes, together with peristaltic contractions, to the self-propulsion of spermatozoa, the transport of ovum during ovulation and the transport of the fertilized ovum to the intramural fallopian tube. A fallopian tube ciliated cell has a columnar shape and contains an oval or round nucleus, often located perpendicular or parallel to the long axis of the cell." [PMID:16565155] subset: human_reference_atlas synonym: "oviduct ciliated cell" BROAD [] synonym: "uterine tube ciliated epithelial cell" EXACT [] @@ -35528,17 +35889,19 @@ is_a: CL:0005012 ! multi-ciliated epithelial cell relationship: part_of UBERON:0003889 ! fallopian tube relationship: part_of UBERON:0007589 ! ciliated columnar oviduct epithelium property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 property_value: terms:date "2022-03-08T12:40:19Z" xsd:dateTime [Term] id: CL:4030008 name: pronephric podocyte -def: "A specialized epithelial cell that contains \"feet\" that interdigitate with the \"feet\" of other glomerular epithelial cells in the pronephros." [PMID:10322630] {terms:contributor="https://orcid.org/0000-0002-2244-7917"} +def: "A specialized epithelial cell that contains \"feet\" that interdigitate with the \"feet\" of other glomerular epithelial cells in the pronephros." [PMID:10322630] synonym: "pronephric glomerular visceral epithelial cell" EXACT [ZFA:0001673] is_a: CL:0000653 ! podocyte intersection_of: CL:0000653 ! podocyte intersection_of: part_of UBERON:0002120 ! pronephros relationship: part_of UBERON:0002120 ! pronephros +property_value: terms:contributor https://orcid.org/0000-0002-2244-7917 property_value: terms:date "2022-03-11T14:38:32Z" xsd:dateTime [Term] @@ -35589,14 +35952,16 @@ property_value: terms:date "2022-05-10T13:31:06Z" xsd:dateTime [Term] id: CL:4030012 name: kidney loop of Henle short descending thin limb epithelial cell -def: "Epithelial cell of the descending thin limb of the short loop (cortical) nephron limited to the outer medulla (mainly inner strip). It is known in some mammalian species that the short descending limb of the loop of Henle selectively expresses the serine protease Corin, the homeobox TF Uncx, and the urea channel Slc14a2." [PMID:33769951] {terms:contributor="https://orcid.org/0000-0003-2804-127X"} +def: "Epithelial cell of the descending thin limb of the short loop (cortical) nephron limited to the outer medulla (mainly inner strip). It is known in some mammalian species that the short descending limb of the loop of Henle selectively expresses the serine protease Corin, the homeobox TF Uncx, and the urea channel Slc14a2." [PMID:33769951] subset: human_reference_atlas synonym: "epithelial cell of the descending thin limb of the short loop of Henle" EXACT [] +is_a: CL:0000076 ! squamous epithelial cell is_a: CL:1001111 ! kidney loop of Henle thin descending limb epithelial cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0005099 ! short descending thin limb relationship: part_of UBERON:0005099 ! short descending thin limb property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-2804-127X property_value: terms:date "2022-05-13T11:00:29Z" xsd:dateTime [Term] @@ -35624,7 +35989,7 @@ property_value: terms:date "2022-05-13T11:16:54Z" xsd:dateTime [Term] id: CL:4030015 name: kidney collecting duct alpha-intercalated cell -def: "A renal alpha-intercalated cell that is part of the collecting duct of the renal tubule." [PMID:31249312, PMID:9890303] {terms:contributor="https://orcid.org/0000-0003-2804-127X"} +def: "A renal alpha-intercalated cell that is part of the collecting duct of the renal tubule." [PMID:31249312, PMID:9890303] subset: human_reference_atlas synonym: "kidney collecting duct intercalated cell type A" EXACT [PMID:9890303] is_a: CL:0005011 ! renal alpha-intercalated cell @@ -35632,6 +35997,7 @@ is_a: CL:1001432 ! kidney collecting duct intercalated cell intersection_of: CL:0005011 ! renal alpha-intercalated cell intersection_of: part_of UBERON:0001232 ! collecting duct of renal tubule property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:contributor https://orcid.org/0000-0003-2804-127X property_value: terms:date "2022-05-31T11:15:10Z" xsd:dateTime [Term] @@ -35761,13 +36127,13 @@ property_value: terms:date "2022-07-05T15:50:17Z" xsd:dateTime [Term] id: CL:4030026 -name: BEST4+ intestinal epithelial cell, human -def: "An absorptive epithelial cell of the human intestine expressing bestrophin-4 (BEST4) calcium-activated ion channels." [https://orcid.org/0000-0002-7431-4139, PMID:24223998, PMID:35176508] +name: BEST4+ enteroycte +def: "An enterocyte of the human intestine expressing bestrophin-4 (BEST4) calcium-activated ion channels." [https://orcid.org/0000-0002-7431-4139, PMID:24223998, PMID:35176508] subset: cellxgene_subset -is_a: BFO:0000002 -is_a: CL:0000255 ! eukaryotic cell -is_a: CL:0000677 ! gut absorptive cell -relationship: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens +is_a: CL:0000584 ! enterocyte +intersection_of: CL:0000584 ! enterocyte +intersection_of: RO:0002292 PR:Q8NFU0 ! expresses bestrophin-4 (human) +relationship: RO:0002162 NCBITaxon:9606 ! in taxon Homo sapiens relationship: RO:0002292 PR:Q8NFU0 ! expresses bestrophin-4 (human) property_value: terms:date "2022-09-07T12:34:20Z" xsd:dateTime @@ -35786,7 +36152,7 @@ property_value: terms:date "2022-10-17T12:35:11Z" xsd:dateTime [Term] id: CL:4030028 name: glycinergic amacrine cell -def: "An amacrine cell that uses glycine as a neurotransmitter." [] {def="https://doi.org/10.1016/j.cell.2020.08.013"} +def: "An amacrine cell that uses glycine as a neurotransmitter." [https://doi.org/10.1016/j.cell.2020.08.013] subset: cellxgene_subset subset: human_reference_atlas synonym: "amacrine cell, glycinergic" EXACT [] @@ -35822,7 +36188,7 @@ property_value: terms:date "2022-11-14T10:08:14Z" xsd:dateTime id: CL:4030031 name: interstitial cell def: "Any cell that is located within the interstitium between the cells most prominent in defining a given tissue. \"Interstitial cell\" is a morphological term and refers to a variety of cells with differing origins and phenotypes." [PMID:24987007] -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0005169 ! interstitial tissue relationship: part_of UBERON:0005169 ! interstitial tissue @@ -36124,6 +36490,7 @@ synonym: "T cell receptor positive macrophage" EXACT [PMID:26074923] synonym: "TCR+ macrophage" EXACT [PMID:26074923] synonym: "TCR.macs" RELATED [PMID:37500727] {synonymtypedef="OMO:0003000"} is_a: CL:0000235 ! macrophage +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000235 ! macrophage intersection_of: RO:0002104 GO:0042101 ! has plasma membrane part T cell receptor complex relationship: RO:0002104 GO:0042101 ! has plasma membrane part T cell receptor complex @@ -37083,6 +37450,7 @@ synonym: "LumHR" RELATED OMO:0003000 [PMID:37380767] synonym: "luminal hormone-responsive cell" BROAD [PMID:37380767] synonym: "luminal mature cell" BROAD [PMID:20346151] is_a: CL:0002326 ! luminal epithelial cell of mammary gland +is_a: PR:000050567 ! protein-containing material entity relationship: RO:0002104 PR:000007204 ! has plasma membrane part estrogen receptor property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 property_value: terms:contributor https://orcid.org/0000-0003-4969-670X @@ -37190,9 +37558,10 @@ def: "A supporting cell that is part of the ovary and differentiates into a gran synonym: "ovarian pregranulosa cell" EXACT [PMID:32759216] synonym: "PG cell" RELATED OMO:0003000 [PMID:32759216] synonym: "pregranulosa cell" EXACT [PMID:17639032, PMID:32759216] +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000630 ! supporting cell relationship: part_of UBERON:0000992 ! ovary -relationship: RO:0002210 CL:0000501 ! directly develops into granulosa cell +relationship: RO:0002210 CL:4033083 ! directly develops into squamous granulosa cell property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 property_value: terms:contributor https://orcid.org/0000-0001-7655-4833 property_value: terms:date "2024-06-07T12:04:57Z" xsd:dateTime @@ -37200,13 +37569,13 @@ property_value: terms:date "2024-06-07T12:04:57Z" xsd:dateTime [Term] id: CL:4033067 name: mural granulosa cell -def: "A follicular cell of ovary that differentiates from a granulosa cell during the secondary follicle stage. Mural granulosa cells line the inner surface of the follicle wall, surrounding the fluid-filled antral cavity. These cells produce oestrogen during the follicular phase in response to follicle-stimulating hormone (FSH), and progesterone after ovulation in response to luteinizing hormone (LH)." [PMID:27815559, PMID:33970370, PMID:34198768] +def: "A follicular cell of ovary that differentiates from a cuboidal granulosa cell during the secondary follicle stage. Mural granulosa cells line the inner surface of the follicle wall, surrounding the fluid-filled antral cavity. These cells produce oestrogen during the follicular phase in response to follicle-stimulating hormone (FSH), and progesterone after ovulation in response to luteinizing hormone (LH)." [PMID:27815559, PMID:33970370, PMID:34198768] synonym: "MGC" RELATED OMO:0003000 [doi:10.1530/REP-16-0500] synonym: "mural GC" RELATED OMO:0003000 [PMID:34198768] xref: EFO:0005289 -is_a: CL:0002174 ! follicular cell of ovary -is_a: CL:2000064 ! ovarian surface epithelial cell -relationship: RO:0002207 CL:0000501 ! directly develops from granulosa cell +is_a: CL:0000501 ! granulosa cell +is_a: UBERON:0004120 ! mesoderm-derived structure +relationship: RO:0002202 CL:4033084 ! develops from cuboidal granulosa cell property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 property_value: terms:contributor https://orcid.org/0000-0001-7655-4833 property_value: terms:date "2024-06-07T12:15:13Z" xsd:dateTime @@ -37417,6 +37786,35 @@ relationship: RO:0000086 PATO:0002354 ! has quality active property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 property_value: terms:date "2024-07-02T09:14:23Z" xsd:string +[Term] +id: CL:4033083 +name: squamous granulosa cell +def: "A granulosa cell that has a squamous morphology and form a single layer around the oocyte in primordial follicles. This cell develops directly into a cuboidal granulosa cell during the primordial-to-primary follicle transition." [PMID:28892263] +comment: Often in literature squamous granulosa cell and pre-granulosa cell are used as synonyms. However, this term only makes reference to the quiescent granulosa cells that surround the primordial ovarian follicle, while a pre-granulosa cell proliferates to form the primordial follicle (and thus cells become the squamous granulosa cells). {xref="https://orcid.org/0000-0001-6677-8489"} +synonym: "flattened granulosa cell" EXACT [PMID:22402964] +synonym: "pre-granulosa cell" RELATED [PMID:33914868] +synonym: "squamous GC" RELATED OMO:0003000 [PMID:33914868] +is_a: CL:0000501 ! granulosa cell +relationship: part_of UBERON:0003981 ! primordial ovarian follicle +relationship: RO:0002207 CL:4033066 ! directly develops from pre-granulosa cell +relationship: RO:0002210 CL:4033084 ! directly develops into cuboidal granulosa cell +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2024-09-24T13:13:24Z" xsd:dateTime + +[Term] +id: CL:4033084 +name: cuboidal granulosa cell +def: "A granulosa cell that has a cuboidal morphology and develops from squamous granulosa cell during the transition between primordial follicle to primary follicle. Cuboidal granulosa cells proliferate to form a second layer within secondary follicles." [PMID:28892263] +synonym: "columnar GC" RELATED OMO:0003000 [PMID:19001500] +synonym: "columnar granulosa cell" EXACT [PMID:19001500] +synonym: "cuboidal epithelial granulosa cell" EXACT [PMID:31849844] +synonym: "cuboidal GC" RELATED OMO:0003000 [PMID:33914868] +is_a: CL:0000501 ! granulosa cell +is_a: UBERON:0004120 ! mesoderm-derived structure +relationship: RO:0002207 CL:4033083 ! directly develops from squamous granulosa cell +property_value: terms:contributor https://orcid.org/0000-0001-6677-8489 +property_value: terms:date "2024-09-24T13:14:57Z" xsd:dateTime + [Term] id: CL:4040000 name: glial restricted tripotential precursor cell @@ -37499,6 +37897,7 @@ id: CL:4040006 name: dermal chromatophore def: "A chromatophore that is part of the dermis." [PMID:28553007] is_a: CL:0000147 ! pigment cell +is_a: CL:0000255 ! eukaryotic cell relationship: part_of UBERON:0002067 ! dermis property_value: terms:contributor https://orcid.org/0000-0002-0819-0473 property_value: terms:date "2024-03-07T09:37:14Z" xsd:dateTime @@ -37506,10 +37905,11 @@ property_value: terms:date "2024-03-07T09:37:14Z" xsd:dateTime [Term] id: CL:4042001 name: TAC3-positive striatal interneuron -def: "A GABAergic interneuron that has its soma located in the striatum and that has an enriched expression of the gene TAC3." [PMID:32999462, PMID:34727523] +def: "A GABAergic interneuron that has its soma located in the striatum and that has an enriched expression of the genes TAC3 and LHX6." [PMID:32999462, PMID:34727523] synonym: "TAC3 interneuron" EXACT [PMID:34727523] is_a: CL:0000402 ! CNS interneuron is_a: CL:0011005 ! GABAergic interneuron +is_a: PR:000050567 ! protein-containing material entity relationship: RO:0002100 UBERON:0002435 ! has soma location striatum relationship: RO:0002104 PR:000016004 ! has plasma membrane part tachykinin-3 property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 @@ -37524,6 +37924,7 @@ synonym: "D1Sh TAC3 archetype" RELATED OMO:0003000 [PMID:34727523] synonym: "TAC3-positive D1Sh-MSN" RELATED OMO:0003000 [PMID:34727523] synonym: "TAC3-positive MSN" RELATED OMO:0003000 [PMID:34727523] is_a: CL:4030051 ! nucleus accumbens shell and olfactory tubercle D1 medium spiny neuron +is_a: PR:000050567 ! protein-containing material entity relationship: RO:0002104 PR:000016004 ! has plasma membrane part tachykinin-3 property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 property_value: terms:date "2024-03-05T13:36:54Z" xsd:dateTime @@ -37646,7 +38047,6 @@ name: Lamp5 Lhx6 neuron def: "A transcriptomically distinct lamp5 GABAergic cortical interneuron located in the cerebral cortex that expresses Lamp5 and Lhx6. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_subclass', Lamp5 Lhx6." [https://cellxgene.cziscience.com/e/e4ddac12-f48f-4455-8e8d-c2a48a683437.cxg/, PMID:34004146, PMID:36007006, PMID:37824655, PMID:37824669] synonym: "Ivy cell" EXACT [PMID:36007006] synonym: "Lamp5-Lhx6 type" EXACT [PMID:30382198] -is_a: CL:4023011 ! lamp5 GABAergic cortical interneuron property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 property_value: terms:date "2024-04-23T09:37:55Z" xsd:dateTime @@ -37687,6 +38087,146 @@ relationship: part_of UBERON:0011148 ! submucosal gland property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 property_value: terms:date "2024-07-12T10:58:06Z" xsd:dateTime +[Term] +id: CL:4042017 +name: alpha1-tanycyte +def: "A tanycyte cell found in the ventromedial and dorsomedial nuclei of the hypothalamus. This type of tanycyte extends its protrusions close to parenchymal neurons without contacting blood vessels. It expresses the glial marker S-100β." [PMID:16344112, PMID:26578855, wikipedia:Tanycyte] +comment: In rodents, a1 tanycytes are known to express DARPP-32, GPR50, NA Vimentin, Connexin 43, GLT-1, GLUT1(+) (Goodman and Hajihosseini 2015; Prevot et al., 2018). {xref="PMID:26578855"} +synonym: "DMH tanycyte" RELATED [PMID:29351662] +synonym: "VMH tanycyte" RELATED [PMID:29351662] +is_a: CL:0002085 ! tanycyte +is_a: CL:0012000 ! astrocyte of the forebrain +relationship: part_of UBERON:0004642 ! third ventricle ependyma +relationship: RO:0002292 PR:000014419 ! expresses +property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 +property_value: terms:date "2024-08-19T13:06:16Z" xsd:dateTime + +[Term] +id: CL:4042018 +name: alpha2-tanycyte +def: "A type of tanycyte found in the dorsomedial arcuate nucleus of the hypothalamus. This mono-ciliated tanycyte extends its protrusion to the arcuate nucleus and expresses the glial marker S-100β." [PMID:16344112, PMID:26578855, PMID:29351662, wikipedia:Tanycyte] +comment: In rodents, this type of tanycyte is more developmentally advanced than alpha1 tanycytes, shows a high neurogenic competence and expresses the following markers DARPP-32, Vimentin, GPR50, Connexin-43, GLT-1, GLUT1(+) (Goodman and Hajihosseini 2015; Prevot et al., 2018) {xref="PMID:26578855"} +synonym: "dmARH tanycyte" RELATED [PMID:29351662] +is_a: CL:0002085 ! tanycyte +relationship: overlaps UBERON:0001932 ! arcuate nucleus of hypothalamus +relationship: RO:0002292 PR:000014419 ! expresses +property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 +property_value: terms:date "2024-08-19T13:13:20Z" xsd:dateTime + +[Term] +id: CL:4042019 +name: beta1-tanycyte +def: "A type of tanycyte found in the lateral infundibular recess of the brain. This tanycyte has an elongated morphology with multiple microvilli extending to the third ventricle in the lateral zones of the median eminence. This type of tanycyte expresses FGF receptors 1 and 2, is in contact with GnRH neurons, and is involved in the release of gonadotropin-releasing hormone (GnRH)." [PMID:16344112, PMID:26578855, PMID:29351662, Wikipedia:Tanycyte] +synonym: "vmARH tanycyte" RELATED [PMID:29351662] +is_a: CL:0000151 ! secretory cell +is_a: CL:0002085 ! tanycyte +is_a: CL:0012000 ! astrocyte of the forebrain +relationship: capable_of GO:0032274 ! gonadotropin secretion +relationship: overlaps UBERON:0002197 ! median eminence of neurohypophysis +relationship: part_of UBERON:0006250 ! infundibular recess of 3rd ventricle +relationship: RO:0002292 PR:000007479 ! expresses fibroblast growth factor 1 +relationship: RO:0002292 PR:000007489 ! expresses fibroblast growth factor 2 +property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 +property_value: terms:date "2024-08-19T13:17:32Z" xsd:dateTime + +[Term] +id: CL:4042020 +name: beta2-tanycyte +def: "A type of tanycyte found in the floor of the infundibular recess in the brain. This tanycyte has an elongated morphology with multiple microvilli extending medially and ventrally to the median eminence, contacting the pial surface and blood vessels. This type of tanycyte expresses FGF receptors 1 and 2, is in contact with GnRH neurons, and is involved in the release of gonadotropin-releasing hormone (GnRH)." [PMID:16344112, PMID:26578855, PMID:29351662, wikipedia:Tanycyte] +synonym: "ME tanycyte" RELATED [PMID:29351662] +is_a: CL:0002085 ! tanycyte +is_a: CL:0012000 ! astrocyte of the forebrain +relationship: overlaps UBERON:0002197 ! median eminence of neurohypophysis +relationship: part_of UBERON:0006250 ! infundibular recess of 3rd ventricle +relationship: RO:0002292 PR:000007479 ! expresses fibroblast growth factor 1 +relationship: RO:0002292 PR:000007489 ! expresses fibroblast growth factor 2 +property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 +property_value: terms:date "2024-08-19T13:21:39Z" xsd:dateTime + +[Term] +id: CL:4042021 +name: neuronal-restricted precursor +def: "A progenitor cell of the central nervous system that differentiates exclusively onto neurons. This progenitor cell is found in a hippocampus subventricular zone, developing cortex and spinal cord of the central nervous system." [PMID:10467245] +comment: In vitro cultures of embryonic mouse neural tubes show that neuronal-restricted precursors (NRPs) are derived from multipotent neuroepithelial cells to give rise to neurons. This progression suggests a linear relationship between multipotent progenitors and neuronal-restricted differentiation. (Mayer-Proschel et al., 1997). In the spinal cord of rats, neural-restricted precursor cells give rise cholinergic, GABAergic, glutametergic neurons (Cao and Howard et al., 2002). {xref="PMID:9354325", xref="PMID:12429182"} +synonym: "NRP" RELATED [PMID:12429182] {synonymtypedef="OMO:0003000"} +is_a: CL:0000123 ! neuron associated cell (sensu Vertebrata) +is_a: CL:0011026 ! progenitor cell +relationship: part_of UBERON:0001017 ! central nervous system +property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 +property_value: terms:date "2024-09-02T11:42:12Z" xsd:dateTime + +[Term] +id: CL:4042022 +name: astrocyte-restricted precursor +def: "A progenitor cell of the central nervous system that differentiates exclusively onto astrocytes. This progenitor cell expresses CD44 and S100 calcium-binding protein B." [PMID:15531362, PMID:33052610] +comment: In vitro, this progenitor cell can differentiate from glial-restricted precursor cells. {xref="PMID:33052610"} +synonym: "ARP" RELATED [PMID:33052610] {synonymtypedef="OMO:0003000"} +synonym: "astrocyte precursor cell" RELATED [PMID:33052610] +is_a: CL:0000123 ! neuron associated cell (sensu Vertebrata) +is_a: CL:0011026 ! progenitor cell +relationship: part_of UBERON:0001017 ! central nervous system +relationship: RO:0002203 CL:0000127 ! develops into astrocyte +relationship: RO:0002292 PR:000001307 ! expresses CD44 molecule +property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 +property_value: terms:date "2024-09-02T11:44:45Z" xsd:dateTime + +[Term] +id: CL:4042023 +name: striatal pthlh-expressing interneuron +def: "A GABAergic interneuron expressing PTHLH and PVALB that has its soma in a striatum. This GABAergic interneuron type presents a spatial expression gradient of PVALB in the mouse striatum." [PMID:30134177, PMID:37292997] +comment: According to spatial transcriptomic data in the human striatum, pthlh-expressing interneurons are one of the most abundant population of interneurons in the striatum (Leonardo D. Garma, et al., 2024). {xref="PMID:37292997"} +synonym: "PTHLH/PVALB cell" RELATED [PMID:37292997] +synonym: "PTHLH +/PVALB+ interneuron" RELATED [PMID:37292997] +is_a: BFO:0000002 +is_a: CL:0000402 ! CNS interneuron +is_a: CL:0011005 ! GABAergic interneuron +relationship: RO:0002100 UBERON:0002435 ! has soma location striatum +relationship: RO:0002292 PR:000013433 ! expresses parathyroid hormone-related protein +relationship: RO:0002292 PR:000013502 ! expresses parvalbumin alpha +property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 +property_value: terms:date "2024-09-17T10:20:15Z" xsd:dateTime + +[Term] +id: CL:4042024 +name: striatal PTHLH MOXD1 expressing interneuron +def: "A pthlh-expressing interneuron that expresses MOXD1 and has its soma in a striatum." [PMID:30134177] +is_a: CL:4042023 ! striatal pthlh-expressing interneuron +relationship: RO:0002292 PR:000010529 ! expresses +property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 +property_value: terms:date "2024-09-17T10:26:57Z" xsd:dateTime + +[Term] +id: CL:4042025 +name: substantia nigra dopaminergic neuron +def: "A midbrain dopaminergic neuron that has its soma located in a substantia nigra. This dopaminergic neuron type is highly metabolically active and it is involved in the regulation of movement, cognition, motivation and reward. Neurodegeneration of this dopaminergic neuronal type causes loss in fine motor control in Parkinson's Disease." [PMID:32826893, PMID:35308118] +synonym: "SNpc dopaminergic neuron" NARROW [PMID:35308118] +is_a: CL:0002614 ! neuron of the substantia nigra +is_a: CL:2000097 ! midbrain dopaminergic neuron +property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 +property_value: terms:date "2024-09-16T13:09:29Z" xsd:dateTime + +[Term] +id: CL:4042026 +name: GABAergic interneuron of the anterior substantia nigra pars reticulata +def: "A GABAergic interneuron that has its soma in the anterior section of the substantia nigra pars reticulata. This GABAergic interneuron is characterized by the expression of Six3 and Foxp1 and it develops from Nkx6-2 expressing neuronal progenitors in the ventrolateral midbrain-diencephalon region." [PMID:36148148] +synonym: "aSNpr" RELATED OMO:0003000 [PMID:36148148] +is_a: CL:0002614 ! neuron of the substantia nigra +relationship: RO:0002292 PR:000007643 ! expresses forkhead box protein P1 +relationship: RO:0002292 PR:000013047 ! expresses POU domain, class 6, transcription factor 2 +relationship: RO:0002292 PR:000014898 ! expresses homeobox protein SIX3 +property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 +property_value: terms:date "2024-09-23T13:56:01Z" xsd:dateTime + +[Term] +id: CL:4042027 +name: GABAergic interneuron of the posterior substantia nigra pars reticulata +def: "A GABAergic interneuron that has its soma in the posterior section of the substantia nigra pars reticulata. This GABAergic interneuron is characterised by the expression of the transcription factors Pax5, Ctip2 and Pou6f2 and it develops from the ventrolateral r1 neuroepithelium expresing NKX61." [PMID:36148148] +synonym: "pSNpr" RELATED [PMID:36148148] +is_a: CL:0002614 ! neuron of the substantia nigra +relationship: RO:0002292 PR:000001903 ! expresses paired box protein PAX-5 +property_value: terms:contributor https://orcid.org/0000-0002-0098-8958 +property_value: terms:date "2024-09-23T14:49:11Z" xsd:dateTime + [Term] id: CL:4047001 name: cycling stromal cell @@ -37758,6 +38298,264 @@ relationship: RO:0000086 PATO:0002354 ! has quality active property_value: terms:contributor https://orcid.org/0009-0005-7919-4905 property_value: terms:date "2024-07-19T09:14:23Z" xsd:string +[Term] +id: CL:4047006 +name: fetal artery endothelial cell +def: "An endothelial cell that lines an artery in the fetal circulatory system." [PMID:34497389] +synonym: "endothelial cell of fetal artery" EXACT [PMID:34497389] +synonym: "fetal arterial EC" EXACT [PMID:34497389] +synonym: "fetal artery EC" EXACT [PMID:34497389] +is_a: CL:1000413 ! endothelial cell of artery +property_value: terms:contributor https://orcid.org/0009-0005-7919-4905 +property_value: terms:date "2024-08-16T13:52:25Z" xsd:dateTime + +[Term] +id: CL:4047007 +name: immature pericyte +def: "A pericyte that is in an early stage of development, found in newly forming or remodeling blood vessels. An immature pericyte is characterized by it's mesenchymal stem cell-like properties and high proliferative capacity, which allows it to differentiate into various types of pericytes and contribute to the structural and functional maturation of the vasculature. Immature pericytes are stellate in new vessels and elongated with less protrusions in remodeling vessels." [PMID:21839917, PMID:28564607, PMID:32466671, PMID:34497389, PMID:36685855] +synonym: "immature PCs" RELATED OMO:0003000 [PMID:28564607] +synonym: "imPCs" RELATED OMO:0003000 [PMID:28564607] +is_a: CL:0000669 ! pericyte +property_value: terms:contributor https://orcid.org/0009-0005-7919-4905 +property_value: terms:date "2024-08-19T11:32:32Z" xsd:dateTime + +[Term] +id: CL:4047011 +name: fetal vein endothelial cell +def: "An endothelial cell that lines the veins in the fetal circulatory system." [doi:10.1101/2021.04.07.438755] +synonym: "fetal vein EC" RELATED OMO:0003000 [doi:10.1101/2021.04.07.438755] +synonym: "fetal venous EC" RELATED OMO:0003000 [doi:10.1101/2021.04.07.438755] +synonym: "fetal venous endothelial cell" EXACT [doi:10.1101/2021.04.07.438755] +is_a: CL:0002543 ! vein endothelial cell +property_value: terms:contributor https://orcid.org/0009-0005-7919-4905 +property_value: terms:date "2024-09-05T15:45:32Z" xsd:dateTime + +[Term] +id: CL:4047012 +name: angiogenic pericyte +def: "A specialized pericyte that actively participates in the formation of new blood vessels during angiogenesis by undergoing phenotypic changes, increasing proliferation, and interacting closely with endothelial cells." [PMID:24853910, PMID:34497389] +is_a: CL:0000669 ! pericyte +property_value: terms:contributor https://orcid.org/0009-0005-7919-4905 +property_value: terms:date "2024-09-06T08:41:39Z" xsd:dateTime + +[Term] +id: CL:4047018 +name: early colonocyte +def: "An enterocyte that is part of the colon, in the early stages of differentiation, located in the intestinal crypt-villus axis." [PMID:28049136, PMID:36060223] +synonym: "early enterocyte of colon" EXACT [doi:10.1101/2021.01.13.426602] +is_a: CL:1000347 ! colonocyte +is_a: CL:4047019 ! early enterocyte +intersection_of: CL:4047019 ! early enterocyte +intersection_of: part_of UBERON:0001155 ! colon +property_value: terms:contributor https://orcid.org/0009-0005-7919-4905 +property_value: terms:date "2024-09-24T11:50:13Z" xsd:dateTime + +[Term] +id: CL:4047019 +name: early enterocyte +def: "An enterocyte in the early stages of development, located above the transit-amplifying cell zone in the intestinal crypt-villus axis." [PMID:20683682, PMID:35235783] +is_a: CL:0000584 ! enterocyte +intersection_of: CL:0000584 ! enterocyte +intersection_of: part_of UBERON:0013740 ! wall of crypt of Lieberkuhn +relationship: part_of UBERON:0013740 ! wall of crypt of Lieberkuhn +property_value: terms:contributor https://orcid.org/0009-0005-7919-4905 +property_value: terms:date "2024-09-24T12:11:09Z" xsd:dateTime + +[Term] +id: CL:4047051 +name: small intestine BEST4+ enterocyte +def: "An enterocyte of the human small intestine expressing bestrophin-4 (BEST4) calcium-activated ion channels. These enterocytes have a disinctive transcriptomic profile and are scattered through the small intestine epithelium." [PMID:24223998, PMID:34497389] +is_a: CL:1000334 ! enterocyte of epithelium of small intestine +is_a: CL:4030026 ! BEST4+ enteroycte +intersection_of: CL:0000584 ! enterocyte +intersection_of: part_of UBERON:0001902 ! epithelium of small intestine +intersection_of: RO:0002292 PR:Q8NFU0 ! expresses bestrophin-4 (human) +property_value: terms:contributor https://orcid.org/0009-0005-7919-4905 +property_value: terms:date "2024-07-25T13:05:50Z" xsd:dateTime + +[Term] +id: CL:4047052 +name: BEST4+ colonocyte +def: "An enterocyte of the human colon expressing bestrophin-4 (BEST4) calcium-activated ion channels. These cells have a distinct transcriptomic profile compared to other enterocytes and are scattered through the colon epithelium." [PMID:24223998, PMID:34497389] +is_a: CL:1000347 ! colonocyte +is_a: CL:4030026 ! BEST4+ enteroycte +intersection_of: CL:1000347 ! colonocyte +intersection_of: RO:0002292 PR:Q8NFU0 ! expresses bestrophin-4 (human) +property_value: terms:contributor https://orcid.org/0009-0005-7919-4905 +property_value: terms:date "2024-07-25T13:21:19Z" xsd:dateTime + +[Term] +id: CL:4052001 +name: multiciliated ependymal cell +def: "An ependymal cell that lines the lateral, third, and fourth ventricles of the brain. The cell is characterized by multiple motile cilia on its apical surface, which beats in a coordinated manner to facilitate the movement of cerebrospinal fluid (CSF), contributing to brain homeostasis." [PMID:25045600, PMID:28067220, PMID:37008045] +comment: multiciliated ependymal cell, with an average of 16 motile cilia per cell, exhibits two types of planar cell polarity (PCP): rotational polarity, with unidirectional cilia orientation, and translational polarity, with asymmetric cilia positioning in the apical area. This location-specific PCP varies across the ventricular wall, aligning with the direction of CSF flow. These cells are interconnected by adherens and gap junctions, which support intercellular communication and maintain the structural integrity of the ependymal layer. Unlike some other cell types, these cells lack tight junctions. {xref="PMID:25045600", xref="PMID:27311928"} +synonym: "E1" RELATED OMO:0003000 [PMID:28067220, PMID:37008045] +synonym: "multiciliated ependymal cells" BROAD [PMID:25045600] +is_a: CL:0000065 ! ependymal cell +is_a: CL:0005012 ! multi-ciliated epithelial cell +relationship: part_of UBERON:0005357 ! brain ependyma +property_value: terms:contributor https://orcid.org/0009-0000-8480-9277 +property_value: terms:date "2024-08-20T10:06:15Z" xsd:dateTime + +[Term] +id: CL:4052002 +name: syncytial cell +def: "A multinucleate cell formed by the fusion of multiple uninuclear cells through plasma membrane fusion. This process leads to a single large cell containing multiple nuclei within a shared cytoplasm." [PMID:20851884, Wikipedia:Syncytium] +synonym: "SC" RELATED OMO:0003000 [PMID:9067520] +synonym: "syncytium" EXACT [WBbt:0008074] +is_a: BFO:0000002 +is_a: CL:0000228 ! multinucleate cell +intersection_of: CL:0000000 ! cell +intersection_of: bearer_of PATO:0001908 ! multinucleate +intersection_of: output_of GO:0000768 ! syncytium formation by plasma membrane fusion +relationship: output_of GO:0000768 ! syncytium formation by plasma membrane fusion +property_value: terms:contributor https://orcid.org/0009-0000-8480-9277 +property_value: terms:date "2024-08-15T10:38:46Z" xsd:dateTime + +[Term] +id: CL:4052003 +name: intestinal villus capillary endothelial cell +def: "A capillary endothelial cell that is part of the intestinal villus. This cell is highly fenestrated, with fenestrations most numerous at the villus tips, and plays a vital role in nutrient absorption and maintaining the selective permeability of the intestinal barrier." [PMID:18480313, PMID:35810168, PMID:38051275] +synonym: "villus blood capillary endothelial cells" BROAD [PMID:35810168] +synonym: "villus tip endothelial cell" RELATED [PMID:38051275] +is_a: CL:0000666 ! fenestrated endothelial cell +is_a: CL:0002144 ! capillary endothelial cell +intersection_of: CL:0002144 ! capillary endothelial cell +intersection_of: part_of UBERON:0001213 ! intestinal villus +relationship: part_of UBERON:0001213 ! intestinal villus +property_value: terms:contributor https://orcid.org/0009-0000-8480-9277 +property_value: terms:date "2024-09-17T10:03:25Z" xsd:dateTime + +[Term] +id: CL:4052004 +name: intestinal fibroblastic reticular cell +def: "A specialized fibroblastic reticular cell that is part of gut-associated lymphoid tissue (GALT), responsible for forming a structural network that facilitates immune cell interactions. This cell is found in Peyer's patches, cryptopatches, and isolated lymphoid follicles. It plays crucial roles in maintaining intestinal immunity by controlling innate lymphoid cell homeostasis and function, organizing lymphoid structures, and contributing to intestinal microbiome balance." [PMID:33707780, PMID:35440118] +synonym: "Ccl19-expressing fibroblastic reticular cell" NARROW [PMID:35440118] +synonym: "gut-associated secondary lymphoid organs fibroblastic reticular cell" RELATED [PMID:35440118] +synonym: "solitary intestinal lymphoid tissue fibroblastic reticular cell" NARROW [PMID:35440118] +is_a: CL:0009101 ! fibroblastic reticular cell +relationship: part_of UBERON:0001962 ! gut-associated lymphoid tissue +property_value: terms:contributor https://orcid.org/0009-0000-8480-9277 +property_value: terms:date "2024-09-19T11:22:18Z" xsd:dateTime +property_value: terms:description "Intestinal fibroblastic reticular cells develop from both perivascular and subepithelial progenitors during Peyer's patch formation. Intestinal fibroblastic reticular cells express key markers such as CCL19, CCL21, CXCL13, TNFSF13B (also known as BAFF), and produce IL-7, which are important for their immune regulatory functions and the organization of lymphoid structures." xsd:string {xref="PMID:33707780", xref="PMID:35440118"} + +[Term] +id: CL:4052005 +name: intestinal subserosal fibroblast +def: "A fibroblast that is part of the subserosa of intestine. This cell interacts with immune cells and play roles in inflammation and fibrosis. In certain conditions, such as Crohn's disease, subserosal fibroblast may differentiate into myofibroblasts." [PMID:23143399, PMID:26694715, PMID:38877292] +is_a: CL:0000057 ! fibroblast +relationship: part_of UBERON:0001243 ! serosa of intestine +relationship: part_of UBERON:0012375 ! subserosa +property_value: terms:contributor https://orcid.org/0009-0000-8480-9277 +property_value: terms:date "2024-09-19T12:58:29Z" xsd:dateTime + +[Term] +id: CL:4052006 +name: intestinal enteroendocrine progenitor +def: "An epithelial cell that is part of the crypt of Lieberkuhn, originating from intestinal stem cells and giving rise to enteroendocrine cells (EECs). In mouse and human, this cell can be characterized by the expression of Neurog3, and has the ability to proliferate and differentiate into multiple EEC subtypes. Its proliferative potential contributes to crypt growth, distinguishing it from fully differentiated EECs." [doi:/10.1038/s41467-021-27901-5, PMID:31756561, PMID:32531023, PMID:35913117, PMID:38260422] +comment: The EEC progenitor is also present in other organisms; for example, flies have EEC progenitors but lack intestinal crypts and do not express the same markers. Instead, they are Dl+ and Pros+. {xref="PMID:25670791"} +synonym: "EEC Progenitor" RELATED OMO:0003000 [PMID:31756561] +is_a: CL:0002563 ! intestinal epithelial cell +is_a: CL:0011026 ! progenitor cell +relationship: part_of UBERON:0011184 ! epithelium of crypt of Lieberkuhn +relationship: RO:0002202 CL:0002250 ! develops from intestinal crypt stem cell +property_value: terms:contributor https://orcid.org/0009-0000-8480-9277 +property_value: terms:date "2024-09-20T12:13:26Z" xsd:dateTime + +[Term] +id: CL:4052007 +name: subepithelial intestinal fibroblast +def: "A fibroblast located adjacent to the intestinal epithelium in both the small intestine and colon, specifically around the crypts. This cell is characterized by the expression of PDGFRα and various collagen isoforms, including COL4A5 and COL4A6. It secretes signalling molecules like TGF-β, Wnt ligands, and BMPs, which are crucial for epithelial homeostasis, intestinal stem cell support, and basement membrane formation." [PMID:30270042, PMID:33430285, PMID:33916891, PMID:37080817] +comment: The S2 fibroblast population has been identified as a subset of intestinal fibroblasts located near the epithelial lining. This population is divided into two subtypes: S2a and S2b. S2a is involved in epithelial differentiation, while S2b, located at the top of the crypt, regulates intestinal stem cell proliferation, niche formation, and wound healing. {xref="PMID:30270042", xref="PMID:33916891", xref="PMID:37495570"} +synonym: "S2 fibroblast" RELATED [PMID:30270042, PMID:33916891] +synonym: "S2 mesenchymal cells" RELATED [PMID:33916891] +is_a: CL:0000057 ! fibroblast +relationship: adjacent_to UBERON:0001277 ! intestinal epithelium +property_value: terms:contributor https://orcid.org/0009-0000-8480-9277 +property_value: terms:date "2024-09-23T09:59:27Z" xsd:dateTime + +[Term] +id: CL:4052008 +name: crypt-bottom fibroblast +def: "A subepithelial intestinal fibroblast that is located adjacent to the base of the crypt of Lieberkühn, near the intestinal stem cells. Characterized by low PDGFRα expression, this cell is crucial for maintaining the intestinal stem cell niche. Crypt-bottom fibroblast secretes key signaling molecules including canonical Wnt ligands (Wnt2, Wnt2b), Wnt potentiators (Rspo3), and BMP inhibitors (Grem1), which collectively regulate intestinal stem cell function and epithelial homeostasis." [doi:/10.1371/journal.pbio.3001032, PMID:33916891] +synonym: "bottom pericryptic-associated fibroblasts" RELATED [PMID:33916891] +synonym: "CBFs" RELATED OMO:0003000 [doi:/10.1371/journal.pbio.3001032] +is_a: CL:4052007 ! subepithelial intestinal fibroblast +relationship: adjacent_to CL:0002250 ! intestinal crypt stem cell +relationship: adjacent_to UBERON:0013739 ! base of crypt of Lieberkuhn +property_value: terms:contributor https://orcid.org/0009-0000-8480-9277 +property_value: terms:date "2024-09-23T10:23:18Z" xsd:dateTime + +[Term] +id: CL:4052009 +name: crypt-top fibroblast +def: "A subepithelial intestinal fibroblast that is located adjacent to the top of the crypt of Lieberkuhn. Characterized by high experession of PDGFRα, this cell secretes a range of signaling factors, including WNTs and BMPs, that drive epithelial differentiation, creating a gradient that regulates the balance between stem cell maintenance and differentiation." [doi:/10.1371/journal.pbio.3001032, PMID:33916891] +comment: S2b fibroblasts are located at the top of the crypt and express NRG1 and NPY. {xref="PMID:37495570"} +synonym: "CTFs" RELATED OMO:0003000 [doi:/10.1371/journal.pbio.3001032] +synonym: "S2b fibroblast" RELATED [PMID:37495570] +synonym: "top pericryptic fibroblast" RELATED [PMID:33916891] +is_a: CL:4052007 ! subepithelial intestinal fibroblast +relationship: adjacent_to UBERON:0013740 ! wall of crypt of Lieberkuhn +property_value: terms:contributor https://orcid.org/0009-0000-8480-9277 +property_value: terms:date "2024-09-23T11:14:04Z" xsd:dateTime + +[Term] +id: CL:4052010 +name: pre-theca cell +def: "A stromal cell that serves as a precursor to the theca cell layers in the ovary growing follicles. This cell is present in the early stages of follicular growth, particularly in smaller follicles. Unlike mature theca cell, a pre-theca cell is initially non-steroidogenic and lacks luteinizing hormone receptors." [PMID:20628033, PMID:31320652, PMID:36205477] +synonym: "early theca cell" EXACT [PMID:36205477] +synonym: "progenitor theca cell" EXACT [PMID:31320652] +is_a: CL:0002132 ! stromal cell of ovary +relationship: part_of UBERON:0012186 ! ovary growing follicle +relationship: RO:0002203 CL:0000503 ! develops into theca cell +property_value: terms:contributor https://orcid.org/0009-0000-8480-9277 +property_value: terms:date "2024-09-25T11:15:57Z" xsd:dateTime + +[Term] +id: CL:4052011 +name: follicle associated enterocyte +def: "An enterocyte found in the follicle-associated epithelium (FAE) that covers Peyer's patches and other mucosa-associated lymphoid tissues. This cell has reduced absorptive capacity and expresses higher levels of chemokines CCL20 and CXCL16, compared to regular villus enterocytes. It contributes to antigen sampling and immune interactions, supporting the specialized function of the FAE in mucosal immunity." [PMID:29339448, PMID:34634036, PMID:7107724] +synonym: "FAE enterocyte" RELATED OMO:0003000 [PMID:7107724] +synonym: "follicle-associated epithelium enterocyte" EXACT [PMID:7107724] +synonym: "follicular enterocyte" RELATED [PMID:7107724] +is_a: CL:0000584 ! enterocyte +property_value: terms:contributor https://orcid.org/0009-0000-8480-9277 +property_value: terms:date "2024-09-25T15:28:25Z" xsd:dateTime + +[Term] +id: CL:4052048 +name: intercalated cell of salivary gland +def: "A cuboidal epithelial cell that is part of the intercalated duct of salivary gland. This cell expresses proteins commonly associated with acinar cells and displays calcium signaling characteristics similar to secretory cells, indicating an active role in the secretory process rather than ion reabsorption." [PMID:30855909, PMID:35799078, PMID:36726292, PMID:37724716] +synonym: "Id cell" RELATED [PMID:35799078] +synonym: "intercalated duct cell" BROAD [PMID:37724716] +synonym: "salivary intercalated duct cells" EXACT [PMID:37724716] +is_a: CL:0000068 ! duct epithelial cell +is_a: CL:1001596 ! salivary gland glandular cell +relationship: part_of UBERON:0014727 ! intercalated duct of salivary gland +relationship: part_of UBERON:0015766 ! epithelium of duct of salivary gland +property_value: terms:contributor https://orcid.org/0000-0003-4389-9821 +property_value: terms:contributor https://orcid.org/0009-0000-8480-9277 +property_value: terms:date "2024-09-11T09:55:55Z" xsd:dateTime + +[Term] +id: CL:4052049 +name: striated cell of salivary gland +def: "An columnar/cuboidal epithelial cell that is part of the striated duct of salivary gland, characterized by basal striations formed by infoldings of the plasma membrane. This cell play a crucial role in modifying the electrolyte composition and concentration of saliva through active ion transport, particularly the absorption of sodium and secretion of potassium." [PMID:30855909, PMID:34147989, PMID:36726292] +synonym: "SD cells" BROAD [PMID:11590591] +synonym: "striated duct cells" BROAD [PMID:11590591] +is_a: CL:0000068 ! duct epithelial cell +is_a: CL:0000075 ! columnar/cuboidal epithelial cell +is_a: CL:1001596 ! salivary gland glandular cell +intersection_of: CL:0000075 ! columnar/cuboidal epithelial cell +intersection_of: part_of UBERON:0014729 ! striated duct of salivary gland +relationship: capable_of GO:0036376 ! sodium ion export across plasma membrane +relationship: capable_of GO:1990573 ! potassium ion import across plasma membrane +relationship: part_of UBERON:0014729 ! striated duct of salivary gland +relationship: part_of UBERON:0015766 ! epithelium of duct of salivary gland +property_value: terms:contributor https://orcid.org/0000-0003-4389-9821 +property_value: terms:contributor https://orcid.org/0009-0000-8480-9277 +property_value: terms:date "2024-09-11T10:00:25Z" xsd:dateTime + [Term] id: CP:0000000 name: obsolete CP:0000000 @@ -38129,9 +38927,9 @@ synonym: "chromosome scaffold" RELATED [] synonym: "cytoplasmic chromatin" NARROW [] synonym: "nuclear chromatin" NARROW [] xref: NIF_Subcellular:sao1615953555 -is_a: BFO:0000004 -is_a: GO:0032993 ! protein-DNA complex +is_a: GO:0110165 ! cellular anatomical entity relationship: part_of GO:0005694 ! chromosome +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28301" xsd:anyURI [Term] id: GO:0000791 @@ -38592,7 +39390,7 @@ namespace: biological_process def: "The process in which a subpopulation of granulosa cells surrounding the oocyte acquires the specialized features of an ovarian cumulus cell." [PMID:30010832] synonym: "ovarian cumulus cell differentiation" EXACT [] is_a: GO:0003006 ! developmental process involved in reproduction -is_a: GO:0030855 ! epithelial cell differentiation +is_a: GO:0060014 ! granulosa cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0000711 ! cumulus cell relationship: part_of GO:0001547 ! antral ovarian follicle growth @@ -40144,18 +40942,21 @@ id: GO:0001932 name: regulation of protein phosphorylation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of addition of phosphate groups into an amino acid in a protein." [GOC:hjd] +subset: gocheck_obsoletion_candidate synonym: "regulation of protein amino acid phosphorylation" EXACT [GOC:bf] is_a: GO:0031399 ! regulation of protein modification process is_a: GO:0042325 ! regulation of phosphorylation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0006468 ! protein phosphorylation relationship: regulates GO:0006468 ! protein phosphorylation +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28278" xsd:anyURI [Term] id: GO:0001933 name: negative regulation of protein phosphorylation namespace: biological_process def: "Any process that stops, prevents or reduces the rate of addition of phosphate groups to amino acids within a protein." [GOC:hjd] +subset: gocheck_obsoletion_candidate synonym: "down regulation of protein amino acid phosphorylation" EXACT [] synonym: "down-regulation of protein amino acid phosphorylation" EXACT [] synonym: "downregulation of protein amino acid phosphorylation" EXACT [] @@ -40167,13 +40968,14 @@ is_a: GO:0042326 ! negative regulation of phosphorylation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0006468 ! protein phosphorylation relationship: negatively_regulates GO:0006468 ! protein phosphorylation +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28278" xsd:anyURI [Term] id: GO:0001934 name: positive regulation of protein phosphorylation namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein." [GOC:hjd] -comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. +subset: gocheck_obsoletion_candidate synonym: "activation of protein amino acid phosphorylation" NARROW [] synonym: "positive regulation of protein amino acid phosphorylation" EXACT [GOC:bf] synonym: "stimulation of protein amino acid phosphorylation" NARROW [] @@ -40187,6 +40989,7 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0006468 ! protein phosphorylation relationship: positively_regulates GO:0006468 ! protein phosphorylation property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27189" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28278" xsd:anyURI [Term] id: GO:0001935 @@ -40461,7 +41264,7 @@ id: GO:0001977 name: renal system process involved in regulation of blood volume namespace: biological_process def: "A slow mechanism of blood pressure regulation that responds to changes in pressure resulting from fluid and salt intake by modulating the quantity of blood in the circulatory system." [GOC:dph, GOC:tb, ISBN:0721643949] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "renal blood volume control of blood pressure" RELATED [] synonym: "renal regulation of blood volume" RELATED [GOC:dph, GOC:tb] is_a: GO:0003071 ! renal system process involved in regulation of systemic arterial blood pressure @@ -40553,6 +41356,18 @@ synonym: "regulation of heart contraction rate" EXACT [] synonym: "regulation of rate of heart contraction" EXACT [] is_a: GO:0008016 ! regulation of heart contraction +[Term] +id: GO:0002028 +name: regulation of sodium ion transport +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:dph] +synonym: "regulation of Na+ transport" EXACT [] +synonym: "regulation of sodium transport" EXACT [] +is_a: GO:0051049 ! regulation of transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006814 ! sodium ion transport +relationship: regulates GO:0006814 ! sodium ion transport + [Term] id: GO:0002036 name: regulation of L-glutamate import across plasma membrane @@ -43056,13 +43871,15 @@ is_a: GO:0002532 ! production of molecular mediator involved in inflammatory res [Term] id: GO:0002538 -name: arachidonic acid metabolite production involved in inflammatory response +name: arachidonate metabolite production involved in inflammatory response namespace: biological_process def: "The synthesis or release of products of arachidonic acid metabolism following a stimulus as part of an inflammatory response, resulting in an increase in their intracellular or extracellular levels." [GOC:add, ISBN:0781735149] synonym: "arachidonic acid metabolite production involved in acute inflammatory response" BROAD [GOC:mah] +synonym: "arachidonic acid metabolite production involved in inflammatory response" EXACT [] synonym: "production of arachidonic acid metabolites involved in acute inflammatory response" BROAD [] synonym: "production of arachidonic acid metabolites involved in inflammatory response" EXACT [] is_a: GO:0002532 ! production of molecular mediator involved in inflammatory response +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28648" xsd:anyURI [Term] id: GO:0002539 @@ -43070,7 +43887,7 @@ name: prostaglandin production involved in inflammatory response namespace: biological_process def: "The synthesis or release of any prostaglandin following a stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels." [GOC:add, ISBN:0781735149] synonym: "prostaglandin production involved in acute inflammatory response" BROAD [] -is_a: GO:0002538 ! arachidonic acid metabolite production involved in inflammatory response +is_a: GO:0002538 ! arachidonate metabolite production involved in inflammatory response [Term] id: GO:0002540 @@ -43078,7 +43895,7 @@ name: leukotriene production involved in inflammatory response namespace: biological_process def: "The synthesis or release of any leukotriene following a stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels." [GOC:add, ISBN:0781735149] synonym: "leukotriene production involved in acute inflammatory response" BROAD [] -is_a: GO:0002538 ! arachidonic acid metabolite production involved in inflammatory response +is_a: GO:0002538 ! arachidonate metabolite production involved in inflammatory response [Term] id: GO:0002544 @@ -46437,6 +47254,17 @@ intersection_of: GO:0097205 ! renal filtration intersection_of: occurs_in UBERON:0000074 ! renal glomerulus relationship: occurs_in UBERON:0000074 ! renal glomerulus +[Term] +id: GO:0003096 +name: renal sodium ion transport +namespace: biological_process +def: "The directed movement of sodium ions (Na+) by the renal system." [GOC:mtg_cardio] +is_a: GO:0003014 ! renal system process +is_a: GO:0006814 ! sodium ion transport +intersection_of: GO:0006814 ! sodium ion transport +intersection_of: occurs_in UBERON:0001008 ! renal system +relationship: occurs_in UBERON:0001008 ! renal system + [Term] id: GO:0003097 name: renal water transport @@ -48465,7 +49293,8 @@ subset: goslim_yeast synonym: "lamin/chromatin binding" NARROW [] synonym: "microtubule/chromatin interaction" NARROW [] synonym: "nuclear membrane vesicle binding to chromatin" NARROW [] -is_a: GO:0044877 ! protein-containing complex binding +is_a: BFO:0000003 +is_a: GO:0005488 ! binding intersection_of: GO:0005488 ! binding intersection_of: has_primary_input GO:0000785 ! chromatin relationship: has_primary_input GO:0000785 ! chromatin @@ -48703,7 +49532,8 @@ namespace: molecular_function alt_id: GO:0004718 def: "Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate." [RHEA:10596] synonym: "protein-tyrosine kinase activity" EXACT [] -xref: EC:2.7.10.2 {source="skos:narrowMatch"} +xref: EC:2.7.10.- {source="skos:exactMatch"} +xref: MetaCyc:2.7.10.1-RXN xref: Reactome:R-HSA-112333 "SRC autophosphorylation is positively regulated by InlA-bound CDH1" xref: Reactome:R-HSA-114600 "Fyn/Lyn-mediated phosphorylation of FcR1 gamma" xref: Reactome:R-HSA-1168394 "STAT5 tyrosine phosphorylation" @@ -49096,7 +49926,6 @@ def: "Combining with a signal and transmitting the signal from one side of the m synonym: "receptor protein tyrosine kinase activity" RELATED [EC:2.7.10.1] synonym: "receptor protein-tyrosine kinase activity" RELATED [EC:2.7.10.1] xref: EC:2.7.10.1 {source="skos:exactMatch"} -xref: MetaCyc:2.7.10.1-RXN xref: Reactome:R-HSA-166544 "TrkA receptor autophosphorylates" xref: Reactome:R-HSA-167019 "SHC, complexed with TrkA, is tyrosine-phosphorylated" xref: Reactome:R-HSA-167683 "TrkA phosphorylates PLCG1" @@ -49142,6 +49971,7 @@ xref: Reactome:R-HSA-8987202 "IFNL1:IFNLR1:JAK1:IL10RB:TYK2 phosphorylates JAK1, xref: Reactome:R-HSA-8987255 "IL26:IL10RB:p-TYK2:IL20RA:p-JAK1:STAT1,STAT3 phosphorylates STAT1,STAT3" is_a: GO:0004713 ! protein tyrosine kinase activity is_a: GO:0019199 ! transmembrane receptor protein kinase activity +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28176" xsd:anyURI [Term] id: GO:0004879 @@ -49424,6 +50254,7 @@ name: insulin receptor activity namespace: molecular_function def: "Combining with insulin receptor ligand and transmitting the signal across the plasma membrane to initiate a change in cell activity." [ISBN:0198506732] synonym: "insulin-activated receptor activity" EXACT [] +xref: EC:2.7.10.1 {source="skos:broadMatch"} xref: Reactome:R-HSA-74715 "Autophosphorylation of insulin receptor" is_a: GO:0004714 ! transmembrane receptor protein tyrosine kinase activity is_a: GO:0016500 ! protein-hormone receptor activity @@ -49435,6 +50266,7 @@ relationship: part_of GO:0008286 ! insulin receptor signaling pathway relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa relationship: RO:0002162 NCBITaxon:6072 {all_only="true"} ! in taxon Eumetazoa property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23056" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28520" xsd:anyURI [Term] id: GO:0005044 @@ -49635,6 +50467,44 @@ is_a: GO:0015267 ! channel activity intersection_of: GO:0015267 ! channel activity intersection_of: has_primary_input CHEBI:29108 +[Term] +id: GO:0005267 +name: potassium channel activity +namespace: molecular_function +def: "Enables the energy-independent facilitated diffusion of a potassium ion through a transmembrane aqueous pore or channel." [GOC:BHF, GOC:mtg_transport, GOC:pr, ISBN:0815340729] +xref: Reactome:R-HSA-1296024 "Activation of ATP sensitive Potassium channels in neuroendocrine cells" +xref: Reactome:R-HSA-1296035 "Activation of Ca2+ activated Potassium channels with Intermediate conductance" +xref: Reactome:R-HSA-1296037 "Activation of Ca2+ activated Potassium channels with large conductance" +xref: Reactome:R-HSA-1296039 "Activation of Ca2+ activated Potassium channels with small conductance" +xref: Reactome:R-HSA-1296348 "Activation of TWIK-related K+ channel (TREK)" +xref: Reactome:R-HSA-1299297 "Activation of THIK" +xref: Reactome:R-HSA-1299304 "Activation of tandem pore domain in a weak inwardly rectifying K+ channels" +xref: Reactome:R-HSA-1299318 "Activation of TASK" +xref: Reactome:R-HSA-1299338 "Activation of TRESK" +xref: Reactome:R-HSA-1299359 "Activation of TALK" +xref: Reactome:R-HSA-2534365 "Slo3 Potassium Transport" +xref: Reactome:R-HSA-5578910 "KCNK dimers transport K+ from cytosol to extracellular region" +is_a: GO:0005261 ! monoatomic cation channel activity +is_a: GO:0015079 ! potassium ion transmembrane transporter activity +intersection_of: GO:0015267 ! channel activity +intersection_of: has_primary_input CHEBI:29103 + +[Term] +id: GO:0005272 +name: sodium channel activity +namespace: molecular_function +def: "Enables the energy-independent facilitated diffusion of a sodium ion through a transmembrane aqueous pore or channel." [GOC:BHF, GOC:mtg_transport, GOC:pr, ISBN:0815340729] +xref: Reactome:R-HSA-2730664 "UNC79:UNC80:NALCN transports Na+ extracellular region to cytosol" +xref: Reactome:R-HSA-3295580 "TRPM4,5 transport extracellular Na+ to cytosol" +xref: Reactome:R-HSA-9717374 "SCN3A:SCN2B,4B transports Na+ from the extracellular region to the cytosol" +xref: Reactome:R-HSA-9717382 "SCN9A:SCN1B,2B,4B transports Na+ from the extracellular region to the cytosol" +xref: Reactome:R-HSA-9717395 "TRPM5 transports Na+ from the extracellular region to the cytosol" +xref: Reactome:R-HSA-9717396 "SCN2A:SCN1B,2B,4B transports Na+ from the extracellular region to the cytosol" +is_a: GO:0015081 ! sodium ion transmembrane transporter activity +is_a: GO:0015267 ! channel activity +intersection_of: GO:0015267 ! channel activity +intersection_of: has_primary_input CHEBI:29101 + [Term] id: GO:0005275 name: amine transmembrane transporter activity @@ -49734,7 +50604,7 @@ is_a: GO:0005215 ! transporter activity intersection_of: GO:0005215 ! transporter activity intersection_of: has_primary_input CHEBI:18059 relationship: has_primary_input CHEBI:18059 -relationship: part_of GO:0006869 ! lipid transport +relationship: part_of GO:0006869 {source="GO_REF:0000090"} ! lipid transport [Term] id: GO:0005326 @@ -49744,7 +50614,7 @@ def: "Enables the directed movement of a neurotransmitter into, out of or within synonym: "neurotransmitter transporter activity" RELATED [] xref: Reactome:R-HSA-374896 "Uptake of Noradrenaline" xref: Reactome:R-HSA-374919 "Noradrenaline clearance from the synaptic cleft" -relationship: part_of GO:0006836 ! neurotransmitter transport +relationship: part_of GO:0006836 {source="GO_REF:0000090"} ! neurotransmitter transport relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa relationship: RO:0002162 NCBITaxon:6072 {all_only="true"} ! in taxon Eumetazoa @@ -49772,23 +50642,6 @@ intersection_of: has_primary_input CHEBI:30616 relationship: has_primary_input CHEBI:30616 relationship: part_of GO:0015867 ! ATP transport -[Term] -id: GO:0005355 -name: glucose transmembrane transporter activity -namespace: molecular_function -alt_id: GO:0015579 -def: "Enables the transfer of the hexose monosaccharide glucose from one side of a membrane to the other." [GOC:ai, GOC:mtg_transport, ISBN:0815340729] -synonym: "galactose/glucose (methylgalactoside) porter activity" RELATED [] -synonym: "glucose permease activity" EXACT [] -synonym: "lactose/glucose efflux transporter activity" NARROW [] -xref: Reactome:R-HSA-499981 "Transport of Extracellular Glucose to the Cytosol by GLUT1 and GLUT2" -xref: Reactome:R-HSA-5653873 "SLC2A1 tetramer transports Glc from cytosol to Golgi lumen" -is_a: GO:0022857 ! transmembrane transporter activity -intersection_of: GO:0022857 ! transmembrane transporter activity -intersection_of: has_primary_input CHEBI:4167 -relationship: has_primary_input CHEBI:4167 -relationship: part_of GO:1904659 ! glucose transmembrane transport - [Term] id: GO:0005372 name: water transmembrane transporter activity @@ -49833,7 +50686,6 @@ id: GO:0005488 name: binding namespace: molecular_function def: "The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule." [GOC:ceb, GOC:mah, ISBN:0198506732] -comment: Note that this term is in the subset of terms that should not be used for direct, manual gene product annotation. Please choose a more specific child term, or request a new one if no suitable term is available. For ligands that bind to signal transducing receptors, consider the molecular function term 'receptor binding ; GO:0005102' and its children. subset: goslim_pir subset: goslim_plant synonym: "ligand" NARROW [] @@ -50413,9 +51265,9 @@ synonym: "ribosomal RNA" RELATED [] xref: NIF_Subcellular:sao1429207766 xref: Wikipedia:Ribosome is_a: GO:0043232 ! intracellular non-membrane-bounded organelle +is_a: PR:000050567 ! protein-containing material entity relationship: capable_of_part_of GO:0006412 ! translation relationship: has_part CHEBI:33697 -relationship: has_part PR:000000001 ! protein [Term] id: GO:0005856 @@ -50650,6 +51502,7 @@ xref: NIF_Subcellular:sao787716553 xref: Wikipedia:Cilium is_a: GO:0043227 ! membrane-bounded organelle is_a: GO:0120025 ! plasma membrane bounded cell projection +is_a: PR:000050567 ! protein-containing material entity relationship: has_part GO:0030990 ! intraciliary transport particle relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota relationship: RO:0002162 NCBITaxon:2759 {all_only="true"} ! in taxon Eukaryota @@ -50765,15 +51618,16 @@ synonym: "glycogen anabolism" EXACT [] synonym: "glycogen biosynthesis" EXACT [] synonym: "glycogen formation" EXACT [] synonym: "glycogen synthesis" EXACT [] -xref: MetaCyc:GLYCOGENSYNTH-PWY -xref: MetaCyc:PWY-5067 -xref: MetaCyc:PWY-7900 +xref: MetaCyc:GLYCOGENSYNTH-PWY {source="skos:narrowMatch"} +xref: MetaCyc:PWY-5067 {source="skos:narrowMatch"} +xref: MetaCyc:PWY-7900 {source="skos:narrowMatch"} is_a: GO:0005977 ! glycogen metabolic process is_a: GO:0009250 ! glucan biosynthetic process intersection_of: GO:0009058 ! biosynthetic process intersection_of: has_primary_output CHEBI:28087 relationship: has_primary_output CHEBI:28087 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27107" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28527" xsd:anyURI [Term] id: GO:0005979 @@ -50799,15 +51653,16 @@ synonym: "glycogen breakdown" EXACT [] synonym: "glycogen catabolism" EXACT [] synonym: "glycogen degradation" EXACT [] synonym: "glycogenolysis" EXACT [GOC:sl] -xref: MetaCyc:GLYCOCAT-PWY -xref: MetaCyc:PWY-5941 -xref: MetaCyc:PWY-7662 +xref: MetaCyc:GLYCOCAT-PWY {source="skos:narrowMatch"} +xref: MetaCyc:PWY-5941 {source="skos:narrowMatch"} +xref: MetaCyc:PWY-7662 {source="skos:narrowMatch"} is_a: GO:0005977 ! glycogen metabolic process is_a: GO:0009056 ! catabolic process intersection_of: GO:0009056 ! catabolic process intersection_of: has_primary_input CHEBI:28087 relationship: has_primary_input CHEBI:28087 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27107" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28527" xsd:anyURI [Term] id: GO:0005981 @@ -51126,7 +51981,7 @@ synonym: "DNA replication-independent nuclesome assembly" NARROW [] synonym: "establishment of chromatin architecture" EXACT [GOC:mah] synonym: "establishment or maintenance of chromatin architecture" EXACT [GOC:mah] synonym: "transcription-coupled nucleosome assembly" NARROW [] -is_a: GO:0071824 ! protein-DNA complex organization +is_a: GO:0016043 ! cellular component organization intersection_of: GO:0016043 ! cellular component organization intersection_of: results_in_organization_of GO:0000785 ! chromatin relationship: results_in_organization_of GO:0000785 ! chromatin @@ -51412,7 +52267,7 @@ id: GO:0006468 name: protein phosphorylation namespace: biological_process def: "The process of introducing a phosphate group on to a protein." [GOC:hb] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate subset: goslim_yeast synonym: "protein amino acid phosphorylation" EXACT [GOC:bf] is_a: GO:0016310 ! phosphorylation @@ -51423,7 +52278,7 @@ id: GO:0006469 name: negative regulation of protein kinase activity namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity." [GOC:go_curators] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "down regulation of protein kinase activity" EXACT [] synonym: "down-regulation of protein kinase activity" EXACT [] synonym: "downregulation of protein kinase activity" EXACT [] @@ -51652,8 +52507,8 @@ synonym: "cellular amino acid derivative metabolism" EXACT [] synonym: "cellular modified amino acid metabolism" EXACT [GOC:mah] synonym: "modified amino acid metabolic process" EXACT [GOC:mah] synonym: "modified amino acid metabolism" EXACT [GOC:mah] +is_a: BFO:0000003 is_a: GO:0044237 ! cellular metabolic process -is_a: GO:1901564 ! organonitrogen compound metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:83821 relationship: has_primary_input_or_output CHEBI:83821 @@ -52107,6 +52962,48 @@ intersection_of: GO:0006810 ! transport intersection_of: has_primary_input CHEBI:23906 relationship: has_primary_input CHEBI:23906 +[Term] +id: GO:0006813 +name: potassium ion transport +namespace: biological_process +alt_id: GO:0015458 +alt_id: GO:0071804 +def: "The directed movement of potassium ions (K+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] +synonym: "cellular potassium ion transport" EXACT [] +synonym: "K+ conductance" RELATED [] +synonym: "low voltage-dependent potassium channel auxiliary protein activity" RELATED [GOC:mah] +synonym: "low voltage-gated potassium channel auxiliary protein activity" RELATED [GOC:mah] +synonym: "potassium conductance" NARROW [] +synonym: "potassium ion conductance" NARROW [] +synonym: "potassium transport" RELATED [] +synonym: "sodium/potassium transport" BROAD [] +is_a: BFO:0000003 +is_a: GO:0006810 ! transport +intersection_of: GO:0006810 ! transport +intersection_of: has_primary_input CHEBI:29103 +relationship: has_primary_input CHEBI:29103 +created_by: mah +creation_date: 2010-09-03T02:39:22Z + +[Term] +id: GO:0006814 +name: sodium ion transport +namespace: biological_process +alt_id: GO:0006834 +alt_id: GO:0016974 +def: "The directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] +synonym: "mitochondrial sodium/calcium ion exchange" NARROW [] +synonym: "sodium channel auxiliary protein activity" RELATED [GOC:mah] +synonym: "sodium transport" EXACT [] +synonym: "sodium/potassium transport" BROAD [] +synonym: "sodium:calcium exchange" NARROW [] +synonym: "sodium:solute transport" NARROW [] +is_a: BFO:0000003 +is_a: GO:0006810 ! transport +intersection_of: GO:0006810 ! transport +intersection_of: has_primary_input CHEBI:29101 +relationship: has_primary_input CHEBI:29101 + [Term] id: GO:0006816 name: calcium ion transport @@ -52294,6 +53191,19 @@ intersection_of: GO:0055082 ! intracellular chemical homeostasis intersection_of: regulates_levels_of CHEBI:24875 relationship: regulates_levels_of CHEBI:24875 +[Term] +id: GO:0006883 +name: intracellular sodium ion homeostasis +namespace: biological_process +def: "A homeostatic process involved in the maintenance of a steady state level of sodium ions within a cell." [GOC:ai, GOC:mah] +synonym: "cellular sodium ion homeostasis" EXACT [] +is_a: GO:0030003 ! intracellular monoatomic cation homeostasis +is_a: GO:0055078 ! sodium ion homeostasis +is_a: GO:0055080 ! monoatomic cation homeostasis +is_a: GO:0055082 ! intracellular chemical homeostasis +intersection_of: GO:0055082 ! intracellular chemical homeostasis +intersection_of: regulates_levels_of CHEBI:29101 + [Term] id: GO:0006884 name: cell volume homeostasis @@ -52615,7 +53525,6 @@ id: GO:0006950 name: response to stress namespace: biological_process def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." [GOC:mah] -comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: goslim_candida subset: goslim_chembl subset: goslim_drosophila @@ -52625,6 +53534,7 @@ subset: goslim_plant_ribbon synonym: "response to abiotic stress" RELATED [] synonym: "response to biotic stress" RELATED [] is_a: GO:0050896 ! response to stimulus +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26810" xsd:anyURI [Term] id: GO:0006952 @@ -53484,6 +54394,9 @@ def: "The generation and maintenance of gametes in a multicellular organism. A g synonym: "gametogenesis" RELATED [] is_a: GO:0048609 ! multicellular organismal reproductive process relationship: part_of GO:0019953 ! sexual reproduction +property_value: RO:0002161 NCBITaxon:2 +property_value: RO:0002161 NCBITaxon:2157 +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0007277 @@ -53939,6 +54852,17 @@ intersection_of: results_in_development_of UBERON:0001017 ! central nervous syst relationship: part_of GO:0007399 ! nervous system development relationship: results_in_development_of UBERON:0001017 ! central nervous system +[Term] +id: GO:0007418 +name: ventral midline development +namespace: biological_process +def: "The process whose specific outcome is the progression of the ventral midline over time, from its formation to the mature structure. In protostomes (such as insects, snails and worms) as well as deuterostomes (vertebrates), the midline is an embryonic region that functions in patterning of the adjacent nervous tissue. The ventral midline in insects is a cell population extending along the ventral surface of the embryo and is the region from which cells detach to form the ventrally located nerve cords. In vertebrates, the midline is originally located dorsally. During development, it folds inwards and becomes the ventral part of the dorsally located neural tube and is then called the ventral midline, or floor plate." [GOC:bf, GOC:go_curators, PMID:12075342] +is_a: GO:0048856 ! anatomical structure development +intersection_of: GO:0048856 ! anatomical structure development +intersection_of: results_in_development_of UBERON:0009571 ! ventral midline +relationship: part_of GO:0007417 ! central nervous system development +relationship: results_in_development_of UBERON:0009571 ! ventral midline + [Term] id: GO:0007420 name: brain development @@ -54640,6 +55564,8 @@ intersection_of: GO:0046907 ! intracellular transport intersection_of: occurs_in GO:0043005 ! neuron projection intersection_of: results_in_transport_along GO:0005874 ! microtubule relationship: occurs_in GO:0043005 ! neuron projection +relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {all_only="true"} ! in taxon Metazoa [Term] id: GO:0008089 @@ -55134,7 +56060,7 @@ is_a: GO:0140318 ! protein transporter activity intersection_of: GO:0005215 ! transporter activity intersection_of: has_primary_input PR:000000001 ! protein intersection_of: results_in_transport_across GO:0016020 ! membrane -relationship: part_of GO:0071806 ! protein transmembrane transport +relationship: part_of GO:0071806 {source="GO_REF:0000090"} ! protein transmembrane transport [Term] id: GO:0008324 @@ -55297,7 +56223,7 @@ intersection_of: GO:0022857 ! transmembrane transporter activity intersection_of: has_primary_input CHEBI:28938 relationship: has_participant CHEBI:28938 relationship: has_primary_input CHEBI:28938 -relationship: part_of GO:0072488 ! ammonium transmembrane transport +relationship: part_of GO:0072488 {source="GO_REF:0000090"} ! ammonium transmembrane transport property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22368" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23129" xsd:anyURI property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26941" xsd:anyURI @@ -56808,21 +57734,6 @@ def: "The directed movement of substances, into, out of or within a cell, either is_a: GO:0003018 ! vascular process in circulatory system is_a: GO:0006810 ! transport -[Term] -id: GO:0010243 -name: response to organonitrogen compound -namespace: biological_process -def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond." [PMID:9869419] -comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. -subset: gocheck_do_not_annotate -synonym: "response to organic nitrogen" EXACT [] -is_a: BFO:0000003 -is_a: GO:0050896 ! response to stimulus -intersection_of: GO:0050896 ! response to stimulus -intersection_of: has_primary_input CHEBI:35352 -relationship: has_primary_input CHEBI:35352 -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27194" xsd:anyURI - [Term] id: GO:0010256 name: endomembrane system organization @@ -56947,7 +57858,7 @@ id: GO:0010469 name: regulation of signaling receptor activity namespace: biological_process def: "Any process that modulates the frequency, rate or extent of a signaling receptor activity. Receptor activity is when a molecule combines with an extracellular or intracellular messenger to initiate a change in cell activity." [GOC:dph, GOC:tb] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "regulation of receptor activity" BROAD [] synonym: "regulation of signalling receptor activity" EXACT [] is_a: GO:0009966 ! regulation of signal transduction @@ -57941,6 +58852,28 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0010761 ! fibroblast migration relationship: negatively_regulates GO:0010761 ! fibroblast migration +[Term] +id: GO:0010765 +name: positive regulation of sodium ion transport +namespace: biological_process +def: "Any process that increases the frequency, rate or extent of the directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:dph, GOC:tb] +is_a: GO:0002028 ! regulation of sodium ion transport +is_a: GO:0051050 ! positive regulation of transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006814 ! sodium ion transport +relationship: positively_regulates GO:0006814 ! sodium ion transport + +[Term] +id: GO:0010766 +name: negative regulation of sodium ion transport +namespace: biological_process +def: "Any process that decreases the frequency, rate or extent of the directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:dph, GOC:tb] +is_a: GO:0002028 ! regulation of sodium ion transport +is_a: GO:0051051 ! negative regulation of transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006814 ! sodium ion transport +relationship: negatively_regulates GO:0006814 ! sodium ion transport + [Term] id: GO:0010770 name: positive regulation of cell morphogenesis @@ -58018,38 +58951,41 @@ relationship: positively_regulates GO:0010818 ! T cell chemotaxis [Term] id: GO:0010827 -name: regulation of glucose transmembrane transport +name: regulation of D-glucose transmembrane transport namespace: biological_process def: "Any process that modulates the frequency, rate or extent of glucose transport across a membrane. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:dph, GOC:tb] +synonym: "regulation of glucose transmembrane transport" EXACT [] synonym: "regulation of glucose transport" RELATED [] is_a: GO:0034762 ! regulation of transmembrane transport intersection_of: GO:0065007 ! biological regulation -intersection_of: regulates GO:1904659 ! glucose transmembrane transport -relationship: regulates GO:1904659 ! glucose transmembrane transport +intersection_of: regulates GO:1904659 ! D-glucose transmembrane transport +relationship: regulates GO:1904659 ! D-glucose transmembrane transport [Term] id: GO:0010828 -name: positive regulation of glucose transmembrane transport +name: positive regulation of D-glucose transmembrane transport namespace: biological_process def: "Any process that increases the frequency, rate or extent of glucose transport across a membrane. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:BHF, GOC:dph, GOC:tb] +synonym: "positive regulation of glucose transmembrane transport" EXACT [] synonym: "positive regulation of glucose transport" RELATED [] -is_a: GO:0010827 ! regulation of glucose transmembrane transport +is_a: GO:0010827 ! regulation of D-glucose transmembrane transport is_a: GO:0034764 ! positive regulation of transmembrane transport intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:1904659 ! glucose transmembrane transport -relationship: positively_regulates GO:1904659 ! glucose transmembrane transport +intersection_of: positively_regulates GO:1904659 ! D-glucose transmembrane transport +relationship: positively_regulates GO:1904659 ! D-glucose transmembrane transport [Term] id: GO:0010829 -name: negative regulation of glucose transmembrane transport +name: negative regulation of D-glucose transmembrane transport namespace: biological_process def: "Any process that decreases the frequency, rate or extent of glucose transport across a membrane. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:BHF, GOC:dph, GOC:tb] +synonym: "negative regulation of glucose transmembrane transport" EXACT [] synonym: "negative regulation of glucose transport" RELATED [] -is_a: GO:0010827 ! regulation of glucose transmembrane transport +is_a: GO:0010827 ! regulation of D-glucose transmembrane transport is_a: GO:0034763 ! negative regulation of transmembrane transport intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:1904659 ! glucose transmembrane transport -relationship: negatively_regulates GO:1904659 ! glucose transmembrane transport +intersection_of: negatively_regulates GO:1904659 ! D-glucose transmembrane transport +relationship: negatively_regulates GO:1904659 ! D-glucose transmembrane transport [Term] id: GO:0010830 @@ -59845,7 +60781,7 @@ is_a: GO:0022857 ! transmembrane transporter activity intersection_of: GO:0022857 ! transmembrane transporter activity intersection_of: has_primary_input CHEBI:24867 relationship: has_primary_input CHEBI:24867 -relationship: part_of GO:0034220 ! monoatomic ion transmembrane transport +relationship: part_of GO:0034220 {source="GO_REF:0000090"} ! monoatomic ion transmembrane transport property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24479" xsd:anyURI [Term] @@ -59866,7 +60802,41 @@ intersection_of: GO:0005215 ! transporter activity intersection_of: has_primary_input CHEBI:15378 intersection_of: results_in_transport_across GO:0016020 ! membrane relationship: has_primary_input CHEBI:15378 -relationship: part_of GO:1902600 ! proton transmembrane transport +relationship: part_of GO:1902600 {source="GO_REF:0000090"} ! proton transmembrane transport + +[Term] +id: GO:0015079 +name: potassium ion transmembrane transporter activity +namespace: molecular_function +alt_id: GO:0015388 +alt_id: GO:0022817 +def: "Enables the transfer of potassium ions (K+) from one side of a membrane to the other." [GOC:ai] +synonym: "potassium transporter activity" EXACT [] +synonym: "potassium uptake permease activity" RELATED [] +synonym: "potassium uptake transmembrane transporter activity" RELATED [] +xref: RHEA:29463 +is_a: GO:0022857 ! transmembrane transporter activity +intersection_of: GO:0022857 ! transmembrane transporter activity +intersection_of: has_primary_input CHEBI:29103 +relationship: has_participant CHEBI:29103 +relationship: has_primary_input CHEBI:29103 +relationship: part_of GO:0071805 {source="GO_REF:0000090"} ! potassium ion transmembrane transport + +[Term] +id: GO:0015081 +name: sodium ion transmembrane transporter activity +namespace: molecular_function +alt_id: GO:0022816 +def: "Enables the transfer of sodium ions (Na+) from one side of a membrane to the other." [GOC:ai, GOC:BHF, RHEA:34963] +synonym: "sodium transporter activity" EXACT [] +xref: RHEA:34963 +is_a: GO:0022857 ! transmembrane transporter activity +intersection_of: GO:0022857 ! transmembrane transporter activity +intersection_of: has_primary_input CHEBI:29101 +relationship: has_participant CHEBI:29101 +relationship: has_primary_input CHEBI:29101 +relationship: part_of GO:0035725 ! sodium ion transmembrane transport +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24076" xsd:anyURI [Term] id: GO:0015085 @@ -59929,7 +60899,7 @@ is_a: GO:0022857 ! transmembrane transporter activity intersection_of: GO:0022857 ! transmembrane transporter activity intersection_of: has_primary_input CHEBI:16646 relationship: has_primary_input CHEBI:16646 -relationship: part_of GO:0034219 ! carbohydrate transmembrane transport +relationship: part_of GO:0034219 {source="GO_REF:0000090"} ! carbohydrate transmembrane transport [Term] id: GO:0015149 @@ -59942,7 +60912,7 @@ is_a: GO:0022857 ! transmembrane transporter activity intersection_of: GO:0022857 ! transmembrane transporter activity intersection_of: has_primary_input CHEBI:18133 relationship: has_primary_input CHEBI:18133 -relationship: part_of GO:0008645 ! hexose transmembrane transport +relationship: part_of GO:0008645 {source="GO_REF:0000090"} ! hexose transmembrane transport [Term] id: GO:0015159 @@ -60016,7 +60986,7 @@ is_a: GO:0022857 ! transmembrane transporter activity intersection_of: GO:0022857 ! transmembrane transporter activity intersection_of: has_primary_input CHEBI:35238 relationship: has_primary_input CHEBI:35238 -relationship: part_of GO:0003333 ! amino acid transmembrane transport +relationship: part_of GO:0003333 {source="GO_REF:0000090"} ! amino acid transmembrane transport [Term] id: GO:0015172 @@ -60150,6 +61120,20 @@ xref: Reactome:R-HSA-8953430 "PXMP2 trimer transports glycolate from cytosol to xref: TC:1 is_a: GO:0022803 ! passive transmembrane transporter activity +[Term] +id: GO:0015269 +name: calcium-activated potassium channel activity +namespace: molecular_function +def: "Enables the calcium concentration-regulatable energy-independent passage of potassium ions across a lipid bilayer down a concentration gradient." [GOC:dph, GOC:mtg_transport] +xref: Reactome:R-HSA-9663752 "KCNN2 transports K+ from the cytosol to the extracellular region" +xref: Reactome:R-HSA-9667809 "KCNMA1:KCNMB1 transports potassium ions from the cytosol to the extracellular region" +is_a: GO:0005227 ! calcium-activated cation channel activity +is_a: GO:0005267 ! potassium channel activity +intersection_of: GO:0022836 ! gated channel activity +intersection_of: has_primary_input CHEBI:29103 +intersection_of: has_small_molecule_activator CHEBI:29108 +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24605" xsd:anyURI + [Term] id: GO:0015276 name: ligand-gated monoatomic ion channel activity @@ -60168,6 +61152,37 @@ intersection_of: GO:0022836 ! gated channel activity intersection_of: has_primary_input CHEBI:24867 intersection_of: has_small_molecule_activator CHEBI:24431 +[Term] +id: GO:0015277 +name: kainate selective glutamate receptor activity +namespace: molecular_function +def: "An ionotropic glutamate receptor activity that exhibits fast gating by glutamate, acts by opening a cation channel permeable to sodium and potassium, and for which kainate is an agonist." [GOC:mah, PMID:10049997, PMID:8804111] +comment: Note that this term represents an activity and not a gene product. Consider also annotating to the molecular function terms 'ionotropic glutamate receptor activity ; GO:0004970' and 'cation channel activity ; GO:0005261'. +is_a: GO:0004970 ! glutamate-gated receptor activity +is_a: GO:0005267 ! potassium channel activity +is_a: GO:0015280 ! ligand-gated sodium channel activity +is_a: GO:0099094 ! ligand-gated monoatomic cation channel activity +intersection_of: GO:0022836 ! gated channel activity +intersection_of: has_primary_input CHEBI:29101 +intersection_of: has_primary_input CHEBI:29103 +intersection_of: has_small_molecule_activator CHEBI:14321 + +[Term] +id: GO:0015280 +name: ligand-gated sodium channel activity +namespace: molecular_function +def: "Enables the transmembrane transfer of a sodium ion by a channel that opens when a specific ligand has been bound by the channel complex or one of its constituent parts." [GOC:mah] +synonym: "acid-sensing ion channel activity" NARROW [GOC:fj] +synonym: "amiloride-sensitive sodium channel activity" NARROW [GOC:fj] +synonym: "ASIC activity" NARROW [GOC:fj] +synonym: "epithelial sodium channel" NARROW [GOC:fj] +xref: Reactome:R-HSA-2672334 "SCNN channels transport extracellular Na+ to cytosol" +is_a: GO:0005272 ! sodium channel activity +is_a: GO:0022834 ! ligand-gated channel activity +intersection_of: GO:0022836 ! gated channel activity +intersection_of: has_primary_input CHEBI:29101 +intersection_of: has_small_molecule_activator CHEBI:24431 + [Term] id: GO:0015291 name: secondary active transmembrane transporter activity @@ -60425,19 +61440,6 @@ intersection_of: GO:0006810 ! transport intersection_of: has_primary_input CHEBI:30616 relationship: has_primary_input CHEBI:30616 -[Term] -id: GO:0015869 -name: protein-DNA complex transport -namespace: biological_process -def: "The directed movement of protein-DNA complexes into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:ai] -synonym: "DNA-protein complex transport" EXACT [GOC:mah] -is_a: GO:0006886 ! intracellular protein transport -is_a: GO:0015931 ! nucleobase-containing compound transport -is_a: GO:0031503 ! protein-containing complex localization -intersection_of: GO:0006810 ! transport -intersection_of: has_primary_input GO:0032993 ! protein-DNA complex -relationship: has_primary_input GO:0032993 ! protein-DNA complex - [Term] id: GO:0015870 name: acetylcholine transport @@ -60829,7 +61831,7 @@ id: GO:0016310 name: phosphorylation namespace: biological_process def: "The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide." [ISBN:0198506732] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate subset: goslim_chembl subset: goslim_metagenomics xref: Wikipedia:Phosphorylation @@ -61056,7 +62058,7 @@ relationship: has_primary_input CHEBI:35238 id: GO:0016740 name: transferase activity namespace: molecular_function -def: "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [ISBN:0198506732] +def: "Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [EC:2.-.-.-] subset: goslim_candida subset: goslim_chembl subset: goslim_drosophila @@ -61088,7 +62090,7 @@ is_a: GO:0016740 ! transferase activity id: GO:0016773 name: phosphotransferase activity, alcohol group as acceptor namespace: molecular_function -def: "Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor)." [GOC:jl] +def: "Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor)." [EC:2.7.1.-] subset: goslim_drosophila xref: EC:2.7.1.- xref: Reactome:R-HSA-2161193 "abacavir + AMP => abacavir monophosphate + adenosine" @@ -61246,6 +62248,9 @@ synonym: "ligand-dependent nuclear receptor interactor activity" RELATED [] synonym: "nuclear hormone receptor binding" EXACT [] synonym: "steroid hormone receptor binding" BROAD [] is_a: GO:0061629 ! RNA polymerase II-specific DNA-binding transcription factor binding +property_value: RO:0002161 NCBITaxon:2 +property_value: RO:0002161 NCBITaxon:2157 +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0017046 @@ -61337,6 +62342,9 @@ is_a: GO:0051301 ! cell division intersection_of: GO:0051301 ! cell division intersection_of: has_primary_input CL:0000034 ! stem cell relationship: has_primary_input CL:0000034 ! stem cell +property_value: RO:0002161 NCBITaxon:2 +property_value: RO:0002161 NCBITaxon:2157 +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0017148 @@ -61378,7 +62386,7 @@ id: GO:0018108 name: peptidyl-tyrosine phosphorylation namespace: biological_process def: "The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine." [RESID:AA0039] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate xref: RESID:AA0039 is_a: GO:0006468 ! protein phosphorylation is_a: GO:0018212 ! peptidyl-tyrosine modification @@ -61416,7 +62424,7 @@ id: GO:0018212 name: peptidyl-tyrosine modification namespace: biological_process def: "The modification of peptidyl-tyrosine." [GOC:go_curators] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate is_a: GO:0018193 ! peptidyl-amino acid modification [Term] @@ -61909,6 +62917,19 @@ intersection_of: results_in_formation_of UBERON:0003063 ! prechordal plate relationship: part_of GO:0007399 ! nervous system development relationship: results_in_formation_of UBERON:0003063 ! prechordal plate +[Term] +id: GO:0021508 +name: floor plate formation +namespace: biological_process +def: "The formation of a ventral region of glial cells in the neural tube that provides inductive signals for the specification of neuronal cell types. The floor plate is evident at the ventral midline by the neural fold stage." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, PMID:11262869] +is_a: BFO:0000003 +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +intersection_of: GO:0048646 ! anatomical structure formation involved in morphogenesis +intersection_of: results_in_formation_of UBERON:0003079 ! floor plate +relationship: part_of GO:0007418 ! ventral midline development +relationship: part_of GO:0033505 ! floor plate morphogenesis +relationship: results_in_formation_of UBERON:0003079 ! floor plate + [Term] id: GO:0021510 name: spinal cord development @@ -63026,6 +64047,17 @@ intersection_of: results_in_development_of UBERON:0001021 ! nerve relationship: part_of GO:0007399 ! nervous system development relationship: results_in_development_of UBERON:0001021 ! nerve +[Term] +id: GO:0021678 +name: third ventricle development +namespace: biological_process +def: "The process whose specific outcome is the progression of the third ventricle over time, from its formation to the mature structure. The third ventricle is the narrow cleft inferior to the corpus callosum, within the diencephalon, between the paired thalami. Its floor is formed by the hypothalamus, its anterior wall by the lamina terminalis, and its roof by ependyma, and it communicates with the fourth ventricle by the cerebral aqueduct, and with the lateral ventricles by the interventricular foramina." [GO_REF:0000021, GOC:cls, GOC:dgh, GOC:dph, GOC:jid, ISBN:0838580343] +is_a: GO:0048856 ! anatomical structure development +intersection_of: GO:0048856 ! anatomical structure development +intersection_of: results_in_development_of UBERON:0002286 ! third ventricle +relationship: part_of GO:0021591 ! ventricular system development +relationship: results_in_development_of UBERON:0002286 ! third ventricle + [Term] id: GO:0021679 name: cerebellar molecular layer development @@ -64834,7 +65866,7 @@ id: GO:0022898 name: regulation of transmembrane transporter activity namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transmembrane transporter activity." [GOC:dph, GOC:mtg_cardio, GOC:mtg_transport] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate is_a: GO:0032409 ! regulation of transporter activity is_a: GO:0034762 ! regulation of transmembrane transport intersection_of: GO:0065007 ! biological regulation @@ -64977,6 +66009,20 @@ intersection_of: regulates_levels_of CHEBI:23906 relationship: regulates_levels_of CHEBI:23906 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/24455" xsd:anyURI +[Term] +id: GO:0030007 +name: intracellular potassium ion homeostasis +namespace: biological_process +alt_id: GO:0017079 +def: "A homeostatic process involved in the maintenance of a steady state level of potassium ions within a cell." [GOC:mah] +synonym: "cellular potassium ion homeostasis" EXACT [] +is_a: GO:0030003 ! intracellular monoatomic cation homeostasis +is_a: GO:0055075 ! potassium ion homeostasis +is_a: GO:0055080 ! monoatomic cation homeostasis +is_a: GO:0055082 ! intracellular chemical homeostasis +intersection_of: GO:0055082 ! intracellular chemical homeostasis +intersection_of: regulates_levels_of CHEBI:29103 + [Term] id: GO:0030010 name: establishment of cell polarity @@ -65565,14 +66611,15 @@ synonym: "chondroitin sulfate catabolism" EXACT [] synonym: "chondroitin sulfate degradation" EXACT [] synonym: "chondroitin sulphate catabolic process" EXACT [] synonym: "chondroitin sulphate catabolism" EXACT [] -xref: MetaCyc:PWY-6572 -xref: MetaCyc:PWY-6573 +xref: MetaCyc:PWY-6572 {source="skos:narrowMatch"} +xref: MetaCyc:PWY-6573 {source="skos:narrowMatch"} is_a: GO:0009056 ! catabolic process is_a: GO:0030204 ! chondroitin sulfate metabolic process intersection_of: GO:0009056 ! catabolic process intersection_of: has_primary_input CHEBI:37397 relationship: has_primary_input CHEBI:37397 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27107" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28527" xsd:anyURI [Term] id: GO:0030210 @@ -66879,6 +67926,18 @@ synonym: "cytoskeleton polarization" RELATED [] is_a: GO:0007010 ! cytoskeleton organization is_a: GO:0007163 ! establishment or maintenance of cell polarity +[Term] +id: GO:0030955 +name: potassium ion binding +namespace: molecular_function +def: "Binding to a potassium ion (K+)." [GOC:mah] +synonym: "K ion binding" EXACT [] +is_a: BFO:0000003 +is_a: GO:0005488 ! binding +intersection_of: GO:0005488 ! binding +intersection_of: has_primary_input CHEBI:29103 +relationship: has_primary_input CHEBI:29103 + [Term] id: GO:0030990 name: intraciliary transport particle @@ -67824,6 +68883,18 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0036211 ! protein modification process relationship: positively_regulates GO:0036211 ! protein modification process +[Term] +id: GO:0031402 +name: sodium ion binding +namespace: molecular_function +def: "Binding to a sodium ion (Na+)." [GOC:mah] +synonym: "Na+ ion binding" EXACT [] +is_a: BFO:0000003 +is_a: GO:0005488 ! binding +intersection_of: GO:0005488 ! binding +intersection_of: has_primary_input CHEBI:29101 +relationship: has_primary_input CHEBI:29101 + [Term] id: GO:0031406 name: carboxylic acid binding @@ -68444,7 +69515,7 @@ id: GO:0032069 name: regulation of nuclease activity namespace: biological_process def: "Any process that modulates the frequency, rate or extent of nuclease activity, the hydrolysis of ester linkages within nucleic acids." [GOC:mah] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "nuclease regulator activity" RELATED [] is_a: GO:0051336 ! regulation of hydrolase activity is_a: GO:0060255 ! regulation of macromolecule metabolic process @@ -68457,7 +69528,7 @@ id: GO:0032070 name: regulation of deoxyribonuclease activity namespace: biological_process def: "Any process that modulates the frequency, rate or extent of deoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid." [GOC:mah] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "deoxyribonuclease regulator" RELATED [] synonym: "DNase regulator" RELATED [] is_a: GO:0032069 ! regulation of nuclease activity @@ -68471,7 +69542,7 @@ id: GO:0032074 name: negative regulation of nuclease activity namespace: biological_process def: "Any process that stops or reduces the rate of nuclease activity, the hydrolysis of ester linkages within nucleic acids." [GOC:mah] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "down regulation of nuclease activity" EXACT [] synonym: "down-regulation of nuclease activity" EXACT [] synonym: "downregulation of nuclease activity" EXACT [] @@ -68489,7 +69560,7 @@ id: GO:0032075 name: positive regulation of nuclease activity namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of nuclease activity, the hydrolysis of ester linkages within nucleic acids." [GOC:mah] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "activation of nuclease activity" NARROW [] synonym: "nuclease activator" RELATED [] synonym: "stimulation of nuclease activity" NARROW [] @@ -68508,7 +69579,7 @@ id: GO:0032076 name: negative regulation of deoxyribonuclease activity namespace: biological_process def: "Any process that stops or reduces the rate of deoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid." [GOC:mah] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "deoxyribonuclease inhibitor" RELATED [] synonym: "DNase inhibitor" RELATED [] synonym: "down regulation of deoxyribonuclease activity" EXACT [] @@ -68527,7 +69598,7 @@ id: GO:0032077 name: positive regulation of deoxyribonuclease activity namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of deoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid." [GOC:mah] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "activation of deoxyribonuclease activity" NARROW [] synonym: "deoxyribonuclease activator" RELATED [] synonym: "DNase activator" RELATED [] @@ -69505,7 +70576,7 @@ id: GO:0032409 name: regulation of transporter activity namespace: biological_process def: "Any process that modulates the activity of a transporter." [GOC:mah] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate is_a: GO:0065009 ! regulation of molecular function intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0005215 ! transporter activity @@ -69516,7 +70587,7 @@ id: GO:0032410 name: negative regulation of transporter activity namespace: biological_process def: "Any process that stops or reduces the activity of a transporter." [GOC:mah] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "down regulation of transporter activity" EXACT [] synonym: "down-regulation of transporter activity" EXACT [] synonym: "downregulation of transporter activity" EXACT [] @@ -69533,7 +70604,7 @@ id: GO:0032411 name: positive regulation of transporter activity namespace: biological_process def: "Any process that activates or increases the activity of a transporter." [GOC:mah] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "activation of transporter activity" NARROW [] synonym: "stimulation of transporter activity" NARROW [] synonym: "up regulation of transporter activity" EXACT [] @@ -69551,7 +70622,7 @@ id: GO:0032412 name: regulation of monoatomic ion transmembrane transporter activity namespace: biological_process def: "Any process that modulates the activity of an ion transporter." [GOC:mah, GOC:tb] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "regulation of ion transmembrane transporter activity" BROAD [] synonym: "regulation of ion transporter activity" EXACT [GOC:tb] is_a: GO:0022898 ! regulation of transmembrane transporter activity @@ -69564,7 +70635,7 @@ id: GO:0032413 name: negative regulation of ion transmembrane transporter activity namespace: biological_process def: "Any process that stops or reduces the activity of an ion transporter." [GOC:mah, GOC:tb] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "down regulation of ion transporter activity" EXACT [] synonym: "down-regulation of ion transporter activity" EXACT [] synonym: "downregulation of ion transporter activity" EXACT [] @@ -69582,7 +70653,7 @@ id: GO:0032414 name: positive regulation of ion transmembrane transporter activity namespace: biological_process def: "Any process that activates or increases the activity of an ion transporter." [GOC:mah, GOC:tb] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "activation of ion transporter activity" NARROW [] synonym: "positive regulation of ion transporter activity" EXACT [GOC:tb] synonym: "stimulation of ion transporter activity" NARROW [] @@ -70967,7 +72038,7 @@ id: GO:0032780 name: negative regulation of ATP-dependent activity namespace: biological_process def: "Any process that stops or reduces the rate of an ATP-dependent activity." [GOC:mah] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "down regulation of ATPase activity" EXACT [] synonym: "down-regulation of ATPase activity" EXACT [] synonym: "downregulation of ATPase activity" EXACT [] @@ -70986,7 +72057,7 @@ id: GO:0032781 name: positive regulation of ATP-dependent activity namespace: biological_process def: "Any process that activates or increases the rate of an ATP-dependent activity." [GOC:mah] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "activation of ATPase activity" NARROW [] synonym: "positive regulation of adenosinetriphosphatase activity" EXACT [] synonym: "positive regulation of ATPase activity" EXACT [] @@ -71949,6 +73020,18 @@ intersection_of: has_primary_input CL:0000312 ! keratinocyte relationship: has_primary_input CL:0000312 ! keratinocyte property_value: RO:0002161 NCBITaxon:6656 +[Term] +id: GO:0032983 +name: kainate selective glutamate receptor complex +namespace: cellular_component +def: "An assembly of four or five subunits which form a structure with an extracellular N-terminus and a large loop that together form the ligand binding domain. The C-terminus is intracellular. The ionotropic glutamate receptor complex itself acts as a ligand gated ion channel; on binding glutamate, charged ions pass through a channel in the center of the receptor complex. Kainate receptors are multimeric assemblies of GluK1-3 (also called GluR5-7), GluK4 (KA1) and GluK5 (KA2) subunits." [GOC:bf, PMID:18655795] +is_a: GO:0008328 ! ionotropic glutamate receptor complex +is_a: GO:0034705 ! potassium channel complex +is_a: GO:0034706 ! sodium channel complex +intersection_of: GO:0032991 ! protein-containing complex +intersection_of: capable_of GO:0015277 ! kainate selective glutamate receptor activity +relationship: capable_of GO:0015277 ! kainate selective glutamate receptor activity + [Term] id: GO:0032984 name: protein-containing complex disassembly @@ -71968,18 +73051,6 @@ intersection_of: results_in_disassembly_of GO:0032991 ! protein-containing compl relationship: results_in_disassembly_of GO:0032991 ! protein-containing complex property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22580" xsd:anyURI -[Term] -id: GO:0032986 -name: protein-DNA complex disassembly -namespace: biological_process -def: "The disaggregation of a protein-DNA complex into its constituent components." [GOC:mah] -synonym: "DNA-protein complex disassembly" EXACT [GOC:mah] -is_a: GO:0032984 ! protein-containing complex disassembly -is_a: GO:0071824 ! protein-DNA complex organization -intersection_of: GO:0022411 ! cellular component disassembly -intersection_of: results_in_disassembly_of GO:0032993 ! protein-DNA complex -relationship: results_in_disassembly_of GO:0032993 ! protein-DNA complex - [Term] id: GO:0032987 name: protein-lipid complex disassembly @@ -72037,19 +73108,8 @@ synonym: "protein complex" NARROW [] synonym: "protein containing complex" EXACT [] synonym: "protein-protein complex" NARROW [] is_a: GO:0005575 ! cellular_component +is_a: PR:000050567 ! protein-containing material entity disjoint_from: GO:0110165 ! cellular anatomical entity -relationship: has_part PR:000000001 ! protein - -[Term] -id: GO:0032993 -name: protein-DNA complex -namespace: cellular_component -def: "A macromolecular complex containing both protein and DNA molecules." [GOC:mah] -comment: Note that this term is intended to classify complexes that have DNA as one of the members of the complex, that is, the complex does not exist if DNA is not present. Protein complexes that interact with DNA e.g. transcription factor complexes should not be classified here. -subset: goslim_pir -synonym: "DNA-protein complex" EXACT [GOC:mah] -is_a: GO:0032991 ! protein-containing complex -relationship: has_part CHEBI:16991 [Term] id: GO:0032994 @@ -73028,6 +74088,29 @@ intersection_of: GO:0048878 ! chemical homeostasis intersection_of: regulates_levels_of CHEBI:16646 relationship: regulates_levels_of CHEBI:16646 +[Term] +id: GO:0033504 +name: floor plate development +namespace: biological_process +def: "The progression of the floor plate over time from its initial formation until its mature state." [GOC:dh] +is_a: GO:0048856 ! anatomical structure development +intersection_of: GO:0048856 ! anatomical structure development +intersection_of: results_in_development_of UBERON:0003306 ! floor plate of neural tube +relationship: part_of GO:0021915 ! neural tube development +relationship: results_in_development_of UBERON:0003306 ! floor plate of neural tube + +[Term] +id: GO:0033505 +name: floor plate morphogenesis +namespace: biological_process +def: "The process in which the anatomical structure of the floor plate is generated and organized." [GOC:dh] +is_a: GO:0048598 ! embryonic morphogenesis +is_a: GO:0048729 ! tissue morphogenesis +intersection_of: GO:0009653 ! anatomical structure morphogenesis +intersection_of: results_in_morphogenesis_of UBERON:0003079 ! floor plate +relationship: part_of GO:0033504 ! floor plate development +relationship: results_in_morphogenesis_of UBERON:0003079 ! floor plate + [Term] id: GO:0033568 name: lactoferrin receptor activity @@ -73142,7 +74225,7 @@ id: GO:0033673 name: negative regulation of kinase activity namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [GOC:mah] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "down regulation of kinase activity" EXACT [] synonym: "down-regulation of kinase activity" EXACT [] synonym: "downregulation of kinase activity" EXACT [] @@ -73160,7 +74243,7 @@ id: GO:0033674 name: positive regulation of kinase activity namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [GOC:mah] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "kinase activator" NARROW [] synonym: "stimulation of kinase activity" NARROW [] synonym: "up regulation of kinase activity" EXACT [] @@ -73986,6 +75069,26 @@ intersection_of: GO:0032991 ! protein-containing complex intersection_of: capable_of GO:0005262 ! calcium channel activity relationship: capable_of GO:0005262 ! calcium channel activity +[Term] +id: GO:0034705 +name: potassium channel complex +namespace: cellular_component +def: "An ion channel complex through which potassium ions pass." [GOC:mah] +is_a: GO:0034703 ! cation channel complex +intersection_of: GO:0032991 ! protein-containing complex +intersection_of: capable_of GO:0005267 ! potassium channel activity +relationship: capable_of GO:0005267 ! potassium channel activity + +[Term] +id: GO:0034706 +name: sodium channel complex +namespace: cellular_component +def: "An ion channel complex through which sodium ions pass." [GOC:mah] +is_a: GO:0034703 ! cation channel complex +intersection_of: GO:0032991 ! protein-containing complex +intersection_of: capable_of GO:0005272 ! sodium channel activity +relationship: capable_of GO:0005272 ! sodium channel activity + [Term] id: GO:0034755 name: iron ion transmembrane transport @@ -75337,6 +76440,20 @@ relationship: has_primary_input CL:0000546 ! T-helper 2 cell created_by: bf creation_date: 2011-03-02T03:05:59Z +[Term] +id: GO:0035725 +name: sodium ion transmembrane transport +namespace: biological_process +def: "A process in which a sodium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore." [GOC:vw] +comment: Note that this term is not intended for use in annotating lateral movement within membranes. +synonym: "sodium ion membrane transport" EXACT [] +is_a: GO:0006814 ! sodium ion transport +is_a: GO:0034220 ! monoatomic ion transmembrane transport +intersection_of: GO:0055085 ! transmembrane transport +intersection_of: has_primary_input CHEBI:29101 +created_by: bf +creation_date: 2011-03-10T02:52:36Z + [Term] id: GO:0035733 name: hepatic stellate cell activation @@ -75784,6 +76901,35 @@ relationship: results_in_development_of CL:0000556 ! megakaryocyte created_by: bf creation_date: 2011-05-13T01:28:06Z +[Term] +id: GO:0035864 +name: response to potassium ion +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a potassium ion stimulus." [GOC:yaf] +synonym: "response to K+ ion" EXACT [GOC:bf] +synonym: "response to potassium" EXACT [GOC:bf] +is_a: BFO:0000003 +is_a: GO:0050896 ! response to stimulus +intersection_of: GO:0050896 ! response to stimulus +intersection_of: has_primary_input CHEBI:29103 +relationship: has_primary_input CHEBI:29103 +created_by: bf +creation_date: 2011-05-25T02:58:45Z + +[Term] +id: GO:0035865 +name: cellular response to potassium ion +namespace: biological_process +def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a potassium ion stimulus." [GOC:yaf] +synonym: "cellular response to K+ ion" EXACT [GOC:bf] +synonym: "cellular response to potassium" EXACT [GOC:bf] +is_a: GO:0035864 ! response to potassium ion +is_a: GO:0070887 ! cellular response to chemical stimulus +intersection_of: GO:0070887 ! cellular response to chemical stimulus +intersection_of: has_primary_input CHEBI:29103 +created_by: bf +creation_date: 2011-05-25T02:59:11Z + [Term] id: GO:0035869 name: ciliary transition zone @@ -76225,6 +77371,9 @@ def: "A large plasma membrane-lined circular pore that perforates the flattened synonym: "GEnC fenestration" EXACT [PMID:19129259] synonym: "glomerular endothelial cell fenestration" EXACT [PMID:19129259] is_a: GO:0046930 ! pore complex +property_value: RO:0002161 NCBITaxon:2 +property_value: RO:0002161 NCBITaxon:2157 +property_value: RO:0002161 NCBITaxon:4751 created_by: bf creation_date: 2011-12-12T10:53:24Z @@ -76629,6 +77778,26 @@ relationship: results_in_maturation_of CL:0000233 ! platelet created_by: bf creation_date: 2012-09-11T15:23:11Z +[Term] +id: GO:0036376 +name: sodium ion export across plasma membrane +namespace: biological_process +alt_id: GO:0071436 +alt_id: GO:0098667 +def: "The directed movement of sodium ions from inside of a cell, across the plasma membrane and into the extracellular region." [GOC:vw, PMID:14674689] +synonym: "sodium export" RELATED [GOC:mah] +synonym: "sodium ion export" RELATED [] +synonym: "sodium ion export from cell" EXACT [] +is_a: GO:0035725 ! sodium ion transmembrane transport +is_a: GO:0140115 ! export across plasma membrane +intersection_of: GO:0006810 ! transport +intersection_of: has_primary_input CHEBI:29101 +intersection_of: has_target_end_location GO:0005576 ! extracellular region +intersection_of: has_target_start_location GO:0005829 ! cytosol +intersection_of: results_in_transport_across GO:0005886 ! plasma membrane +created_by: mah +creation_date: 2009-12-16T11:13:55Z + [Term] id: GO:0036379 name: myofilament @@ -78042,7 +79211,7 @@ name: regulation of phosphorylation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of addition of phosphate groups into a molecule." [GOC:jl] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate is_a: GO:0019220 ! regulation of phosphate metabolic process intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0016310 ! phosphorylation @@ -78055,7 +79224,7 @@ name: negative regulation of phosphorylation namespace: biological_process def: "Any process that stops, prevents or decreases the rate of addition of phosphate groups to a molecule." [GOC:jl] comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "down regulation of phosphorylation" EXACT [] synonym: "down-regulation of phosphorylation" EXACT [] synonym: "downregulation of phosphorylation" EXACT [] @@ -78451,7 +79620,8 @@ synonym: "indole derivative metabolism" NARROW [] synonym: "indole-containing compound metabolism" EXACT [] synonym: "ketole metabolic process" EXACT [] synonym: "ketole metabolism" EXACT [] -is_a: GO:1901564 ! organonitrogen compound metabolic process +is_a: BFO:0000003 +is_a: GO:0008152 ! metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:24828 relationship: has_primary_input_or_output CHEBI:24828 @@ -79688,7 +80858,7 @@ name: positive regulation of catalytic activity namespace: biological_process alt_id: GO:0048554 def: "Any process that activates or increases the activity of an enzyme." [GOC:ebc, GOC:jl, GOC:tb, GOC:vw] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate subset: goslim_chembl synonym: "activation of enzyme activity" NARROW [] synonym: "activation of metalloenzyme activity" NARROW [] @@ -79714,7 +80884,7 @@ name: negative regulation of catalytic activity namespace: biological_process alt_id: GO:0048553 def: "Any process that stops or reduces the activity of an enzyme." [GOC:ebc, GOC:jl, GOC:tb, GOC:vw] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "down regulation of enzyme activity" EXACT [] synonym: "down regulation of metalloenzyme activity" NARROW [] synonym: "down-regulation of enzyme activity" EXACT [] @@ -79977,6 +81147,7 @@ id: GO:0043227 name: membrane-bounded organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane." [GOC:go_curators] +subset: gocheck_do_not_annotate synonym: "membrane-enclosed organelle" EXACT [] xref: NIF_Subcellular:sao414196390 is_a: GO:0043226 ! organelle @@ -79984,30 +81155,35 @@ intersection_of: GO:0043226 ! organelle intersection_of: has_part GO:0016020 ! membrane disjoint_from: GO:0043228 ! non-membrane-bounded organelle relationship: has_part GO:0016020 ! membrane +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI [Term] id: GO:0043228 name: non-membrane-bounded organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:go_curators] +subset: gocheck_do_not_annotate subset: goslim_mouse synonym: "biological condensate" RELATED [] synonym: "non-membrane-enclosed organelle" EXACT [] xref: NIF_Subcellular:sao1456184038 is_a: GO:0043226 ! organelle property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21881" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI [Term] id: GO:0043229 name: intracellular organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:go_curators] +subset: gocheck_do_not_annotate subset: goslim_pir is_a: GO:0043226 ! organelle intersection_of: GO:0043226 ! organelle intersection_of: part_of GO:0005622 ! intracellular anatomical structure disjoint_from: GO:0043230 ! extracellular organelle relationship: part_of GO:0005622 ! intracellular anatomical structure +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI [Term] id: GO:0043230 @@ -80162,6 +81338,63 @@ is_a: GO:0043230 ! extracellular organelle intersection_of: GO:0043228 ! non-membrane-bounded organelle intersection_of: part_of GO:0005576 ! extracellular region +[Term] +id: GO:0043266 +name: regulation of potassium ion transport +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the directed movement of potassium ions (K+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:jl] +synonym: "regulation of K+ conductance" NARROW [] +synonym: "regulation of K+ transport" EXACT [] +synonym: "regulation of potassium conductance" NARROW [] +synonym: "regulation of potassium ion conductance" NARROW [] +synonym: "regulation of potassium transport" EXACT [] +is_a: GO:0051049 ! regulation of transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0006813 ! potassium ion transport +relationship: regulates GO:0006813 ! potassium ion transport + +[Term] +id: GO:0043267 +name: negative regulation of potassium ion transport +namespace: biological_process +def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the directed movement of potassium ions (K+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:jl] +synonym: "down regulation of potassium ion transport" EXACT [] +synonym: "down-regulation of potassium ion transport" EXACT [] +synonym: "downregulation of potassium ion transport" EXACT [] +synonym: "inhibition of potassium ion transport" NARROW [] +synonym: "negative regulation of K+ transport" EXACT [] +synonym: "negative regulation of potassium ion conductance" NARROW [] +synonym: "negative regulation of potassium transport" EXACT [] +synonym: "regulation of K+ conductance" NARROW [] +synonym: "regulation of potassium conductance" NARROW [] +synonym: "transmembrane conductance regulator activity" RELATED [] +is_a: GO:0043266 ! regulation of potassium ion transport +is_a: GO:0051051 ! negative regulation of transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0006813 ! potassium ion transport +relationship: negatively_regulates GO:0006813 ! potassium ion transport + +[Term] +id: GO:0043268 +name: positive regulation of potassium ion transport +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the directed movement of potassium ions (K+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:jl] +synonym: "activation of potassium ion transport" NARROW [] +synonym: "positive regulation of K+ conductance" NARROW [] +synonym: "positive regulation of K+ transport" EXACT [] +synonym: "positive regulation of potassium conductance" NARROW [] +synonym: "positive regulation of potassium ion conductance" NARROW [] +synonym: "positive regulation of potassium transport" EXACT [] +synonym: "stimulation of potassium ion transport" NARROW [] +synonym: "up regulation of potassium ion transport" EXACT [] +synonym: "up-regulation of potassium ion transport" EXACT [] +synonym: "upregulation of potassium ion transport" EXACT [] +is_a: GO:0043266 ! regulation of potassium ion transport +is_a: GO:0051050 ! positive regulation of transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0006813 ! potassium ion transport +relationship: positively_regulates GO:0006813 ! potassium ion transport + [Term] id: GO:0043269 name: regulation of monoatomic ion transport @@ -81092,7 +82325,7 @@ id: GO:0043412 name: macromolecule modification namespace: biological_process def: "The covalent alteration of one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological macromolecule, resulting in a change in its properties." [GOC:go_curators] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate subset: goslim_pir is_a: GO:0043170 ! macromolecule metabolic process property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI @@ -81148,7 +82381,7 @@ namespace: biological_process alt_id: GO:1904168 alt_id: GO:2000824 def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription." [GOC:jl] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "down regulation of transcription factor activity" EXACT [] synonym: "down-regulation of transcription factor activity" EXACT [] synonym: "downregulation of transcription factor activity" EXACT [] @@ -81211,7 +82444,7 @@ id: GO:0043462 name: regulation of ATP-dependent activity namespace: biological_process def: "Any process that modulates the rate of an ATP-dependent activity." [GOC:jl] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "regulation of adenosinetriphosphatase activity" EXACT [] synonym: "regulation of ATPase activity" EXACT [] is_a: GO:0065009 ! regulation of molecular function @@ -81420,7 +82653,7 @@ id: GO:0043549 name: regulation of kinase activity namespace: biological_process def: "Any process that modulates the frequency, rate or extent of kinase activity, the catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule." [GOC:bf] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate is_a: GO:0042325 ! regulation of phosphorylation is_a: GO:0051338 ! regulation of transferase activity intersection_of: GO:0065007 ! biological regulation @@ -81877,9 +83110,11 @@ name: cellular component biogenesis namespace: biological_process alt_id: GO:0071843 def: "A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component." [GOC:jl, GOC:mah] +subset: gocheck_do_not_annotate subset: goslim_pir synonym: "cellular component biogenesis at cellular level" EXACT [] is_a: GO:0071840 ! cellular component organization or biogenesis +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27194" xsd:anyURI [Term] id: GO:0044087 @@ -81956,7 +83191,7 @@ id: GO:0044093 name: positive regulation of molecular function namespace: biological_process def: "Any process that activates or increases the rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding." [GO:jl] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate is_a: GO:0065009 ! regulation of molecular function intersection_of: GO:0065007 ! biological regulation intersection_of: positively_regulates GO:0003674 ! molecular_function @@ -82497,6 +83732,9 @@ synonym: "nonspecific immune response" EXACT [] xref: Wikipedia:Innate_immune_system is_a: GO:0006955 ! immune response is_a: GO:0140546 ! defense response to symbiont +property_value: RO:0002161 NCBITaxon:2 +property_value: RO:0002161 NCBITaxon:2157 +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0045088 @@ -85731,7 +86969,7 @@ id: GO:0045859 name: regulation of protein kinase activity namespace: biological_process def: "Any process that modulates the frequency, rate or extent of protein kinase activity." [GOC:go_curators] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate is_a: GO:0001932 ! regulation of protein phosphorylation is_a: GO:0043549 ! regulation of kinase activity intersection_of: GO:0065007 ! biological regulation @@ -85743,7 +86981,7 @@ id: GO:0045860 name: positive regulation of protein kinase activity namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of protein kinase activity." [GOC:go_curators] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "stimulation of protein kinase activity" NARROW [] synonym: "up regulation of protein kinase activity" EXACT [] synonym: "up-regulation of protein kinase activity" EXACT [] @@ -91666,10 +92904,12 @@ id: GO:0050730 name: regulation of peptidyl-tyrosine phosphorylation namespace: biological_process def: "Any process that modulates the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine." [GOC:ai] +subset: gocheck_obsoletion_candidate is_a: GO:0001932 ! regulation of protein phosphorylation intersection_of: GO:0065007 ! biological regulation intersection_of: regulates GO:0018108 ! peptidyl-tyrosine phosphorylation relationship: regulates GO:0018108 ! peptidyl-tyrosine phosphorylation +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28278" xsd:anyURI [Term] id: GO:0050731 @@ -91692,6 +92932,7 @@ id: GO:0050732 name: negative regulation of peptidyl-tyrosine phosphorylation namespace: biological_process def: "Any process that stops, prevents, or reduces the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine." [GOC:ai] +subset: gocheck_obsoletion_candidate synonym: "down regulation of peptidyl-tyrosine phosphorylation" EXACT [] synonym: "down-regulation of peptidyl-tyrosine phosphorylation" EXACT [] synonym: "downregulation of peptidyl-tyrosine phosphorylation" EXACT [] @@ -91701,6 +92942,7 @@ is_a: GO:0050730 ! regulation of peptidyl-tyrosine phosphorylation intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0018108 ! peptidyl-tyrosine phosphorylation relationship: negatively_regulates GO:0018108 ! peptidyl-tyrosine phosphorylation +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28278" xsd:anyURI [Term] id: GO:0050746 @@ -91986,7 +93228,7 @@ name: regulation of catalytic activity namespace: biological_process alt_id: GO:0048552 def: "Any process that modulates the activity of an enzyme." [GOC:ai, GOC:ebc, GOC:vw] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate subset: goslim_chembl synonym: "regulation of enzyme activity" EXACT [] synonym: "regulation of metalloenzyme activity" NARROW [] @@ -92681,7 +93923,6 @@ synonym: "sensory transduction of light stimulus during visual perception" EXACT synonym: "visual perception, detection of light stimulus" EXACT [] synonym: "visual perception, sensory transduction during perception of light" EXACT [] synonym: "visual perception, sensory transduction of light stimulus" EXACT [] -is_a: GO:0009584 ! detection of visible light is_a: GO:0050962 ! detection of light stimulus involved in sensory perception intersection_of: GO:0009583 ! detection of light stimulus intersection_of: part_of GO:0007601 ! visual perception @@ -93590,7 +94831,7 @@ namespace: biological_process alt_id: GO:1904167 alt_id: GO:2000823 def: "Any process that modulates the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription." [GOC:ai] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "regulation of androgen receptor activity" NARROW [] synonym: "regulation of DNA binding transcription factor activity" EXACT [] synonym: "regulation of sequence-specific DNA binding transcription factor activity" EXACT [] @@ -93608,7 +94849,7 @@ name: positive regulation of DNA-binding transcription factor activity namespace: biological_process alt_id: GO:1904169 def: "Any process that activates or increases the frequency, rate or extent of activity of a transcription factor, any factor involved in the initiation or regulation of transcription." [GOC:ai] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "activation of transcription factor activity" NARROW [] synonym: "positive regulation of DNA binding transcription factor activity" EXACT [] synonym: "positive regulation of sequence-specific DNA binding transcription factor activity" EXACT [] @@ -94772,7 +96013,7 @@ id: GO:0051336 name: regulation of hydrolase activity namespace: biological_process def: "Any process that modulates the frequency, rate or extent of hydrolase activity, the catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3." [GOC:ai] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "hydrolase regulator" EXACT [] is_a: GO:0050790 ! regulation of catalytic activity intersection_of: GO:0065007 ! biological regulation @@ -94785,7 +96026,7 @@ name: regulation of transferase activity namespace: biological_process def: "Any process that modulates the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2." [GOC:ai] comment: This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "transferase regulator" EXACT [] is_a: GO:0050790 ! regulation of catalytic activity intersection_of: GO:0065007 ! biological regulation @@ -94797,7 +96038,7 @@ id: GO:0051345 name: positive regulation of hydrolase activity namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of hydrolase activity, the catalysis of the hydrolysis of various bonds." [GOC:ai] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "activation of hydrolase activity" NARROW [] synonym: "hydrolase activator" EXACT [] synonym: "stimulation of hydrolase activity" NARROW [] @@ -94815,7 +96056,7 @@ id: GO:0051346 name: negative regulation of hydrolase activity namespace: biological_process def: "Any process that stops or reduces the rate of hydrolase activity, the catalysis of the hydrolysis of various bonds." [GOC:ai] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "down regulation of hydrolase activity" EXACT [] synonym: "down-regulation of hydrolase activity" EXACT [] synonym: "downregulation of hydrolase activity" EXACT [] @@ -94833,7 +96074,7 @@ name: positive regulation of transferase activity namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor." [GOC:ai] comment: This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "activation of transferase activity" NARROW [] synonym: "stimulation of transferase activity" NARROW [] synonym: "transferase activator" EXACT [] @@ -94852,7 +96093,7 @@ name: negative regulation of transferase activity namespace: biological_process def: "Any process that stops or reduces the rate of transferase activity, the catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from a donor compound to an acceptor." [GOC:ai] comment: This term is useful for grouping, but is too general for manual annotation. Please use a child term instead. -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "down regulation of transferase activity" EXACT [] synonym: "down-regulation of transferase activity" EXACT [] synonym: "downregulation of transferase activity" EXACT [] @@ -95937,7 +97178,7 @@ id: GO:0051767 name: nitric-oxide synthase biosynthetic process namespace: biological_process alt_id: GO:0051768 -def: "The chemical reactions and pathways resulting in the formation of a nitric-oxide synthase, an enzyme which catalyzes the reaction L-arginine + n NADPH + n H+ + m O2 = citrulline + nitric oxide + n NADP+." [EC:1.14.13.39, GOC:ai] +def: "The chemical reactions and pathways resulting in the formation of a nitric-oxide synthase, an enzyme which catalyzes the reaction L-arginine + n NADPH + n H+ + m O2 = citrulline + nitric oxide + n NADP+." [GOC:ai] synonym: "brain nitric-oxide synthase biosynthetic process" NARROW [GOC:bf] synonym: "endothelial nitric-oxide synthase biosynthetic process" NARROW [GOC:bf] synonym: "inducible nitric-oxide synthase biosynthetic process" NARROW [GOC:bf] @@ -95960,6 +97201,7 @@ synonym: "NOS2 synthase biosynthetic process" NARROW [] synonym: "NOS3 biosynthesis" NARROW [GOC:bf] is_a: GO:0009059 ! macromolecule biosynthetic process property_value: RO:0002161 NCBITaxon:4751 +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28860" xsd:anyURI [Term] id: GO:0051769 @@ -96669,7 +97911,8 @@ name: imidazole-containing compound metabolic process namespace: biological_process def: "The chemical reactions and pathways involving imidazoles, five-membered organic heterocycle containing two nitrogen atoms at positions 1 and 3, or any of its derivatives; compounds containing an imidazole skeleton." [GOC:curators] synonym: "imidazole metabolism" EXACT [] -is_a: GO:1901564 ! organonitrogen compound metabolic process +is_a: BFO:0000003 +is_a: GO:0008152 ! metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:24780 relationship: has_primary_input_or_output CHEBI:24780 @@ -96993,6 +98236,29 @@ intersection_of: GO:0065007 ! biological regulation intersection_of: negatively_regulates GO:0048738 ! cardiac muscle tissue development relationship: negatively_regulates GO:0048738 ! cardiac muscle tissue development +[Term] +id: GO:0055056 +name: D-glucose transmembrane transporter activity +namespace: molecular_function +alt_id: GO:0015579 +def: "Enables the transfer of the D-enantiomer of the hexose monosaccharide glucose from one side of a membrane to the other." [GOC:jid, GOC:jsg, GOC:mah] +xref: Reactome:R-HSA-429094 "SLC2A6,8,10,12 transport Glc from extracellular region to cytosol" +xref: Reactome:R-HSA-450095 "GLUT2 (SLC2A2) transports Glc from cytosol to extracellular region" +xref: Reactome:R-HSA-499981 "Transport of Extracellular Glucose to the Cytosol by GLUT1 and GLUT2" +xref: Reactome:R-HSA-5339524 "GLUT1 (SLC2A1) tetramer transports Glc from extracellular region to cytosol" +xref: Reactome:R-HSA-5632804 "SLC2A1 tetramer does not transport Glc from extracellular region to cytosol" +xref: Reactome:R-HSA-5632871 "Defective SLC2A10 does not transport Glc from extracellular region to cytosol" +xref: Reactome:R-HSA-5653873 "SLC2A1 tetramer transports Glc from cytosol to Golgi lumen" +xref: Reactome:R-HSA-8981553 "GLUT14 (SLC2A14) tetramer transports Glc from extracellular region to cytosol" +xref: Reactome:R-HSA-8981564 "GLUT3 (SLC2A3) tetramer transports Glc from extracellular region to cytosol" +xref: Reactome:R-HSA-8981570 "GLUT4 (SLC2A4) tetramer transports Glc from extracellular region to cytosol" +xref: Reactome:R-HSA-8981574 "GLUT2 (SLC2A2) tetramer transports Glc from extracellular region to cytosol" +is_a: GO:0022857 ! transmembrane transporter activity +intersection_of: GO:0022857 ! transmembrane transporter activity +intersection_of: has_primary_input CHEBI:4167 +relationship: has_primary_input CHEBI:4167 +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27326" xsd:anyURI + [Term] id: GO:0055057 name: neuroblast division @@ -97041,6 +98307,26 @@ intersection_of: GO:0048878 ! chemical homeostasis intersection_of: regulates_levels_of CHEBI:29108 relationship: regulates_levels_of CHEBI:29108 +[Term] +id: GO:0055075 +name: potassium ion homeostasis +namespace: biological_process +def: "Any process involved in the maintenance of an internal steady state of potassium ions within an organism or cell." [GOC:jid, GOC:mah] +is_a: GO:0048878 ! chemical homeostasis +intersection_of: GO:0048878 ! chemical homeostasis +intersection_of: regulates_levels_of CHEBI:29103 +relationship: regulates_levels_of CHEBI:29103 + +[Term] +id: GO:0055078 +name: sodium ion homeostasis +namespace: biological_process +def: "Any process involved in the maintenance of an internal steady state of sodium ions within an organism or cell." [GOC:ai, GOC:jid, GOC:mah] +is_a: GO:0048878 ! chemical homeostasis +intersection_of: GO:0048878 ! chemical homeostasis +intersection_of: regulates_levels_of CHEBI:29101 +relationship: regulates_levels_of CHEBI:29101 + [Term] id: GO:0055080 name: monoatomic cation homeostasis @@ -97636,8 +98922,8 @@ subset: goslim_plant_ribbon subset: goslim_prokaryote subset: goslim_prokaryote_ribbon synonym: "binding, bridging" EXACT [] -synonym: "protein complex scaffold activity" RELATED [] -synonym: "protein-containing complex scaffold activity" RELATED [] +synonym: "protein complex scaffold activity" BROAD [] +synonym: "protein-containing complex scaffold activity" BROAD [] is_a: GO:0003674 ! molecular_function relationship: has_part GO:0005488 ! binding @@ -102493,7 +103779,7 @@ id: GO:0061097 name: regulation of protein tyrosine kinase activity namespace: biological_process def: "Any process that modulates the rate, frequency, or extent of protein tyrosine kinase activity." [GOC:dph, GOC:tb] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate is_a: GO:0045859 ! regulation of protein kinase activity is_a: GO:0050730 ! regulation of peptidyl-tyrosine phosphorylation intersection_of: GO:0065007 ! biological regulation @@ -102507,7 +103793,7 @@ id: GO:0061098 name: positive regulation of protein tyrosine kinase activity namespace: biological_process def: "Any process that increases the rate, frequency, or extent of protein tyrosine kinase activity." [GOC:dph, GOC:tb] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate is_a: GO:0045860 ! positive regulation of protein kinase activity is_a: GO:0050731 ! positive regulation of peptidyl-tyrosine phosphorylation is_a: GO:0061097 ! regulation of protein tyrosine kinase activity @@ -102522,7 +103808,7 @@ id: GO:0061099 name: negative regulation of protein tyrosine kinase activity namespace: biological_process def: "Any process that decreases the rate, frequency, or extent of protein tyrosine kinase activity." [GOC:dph, GOC:tb] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate is_a: GO:0006469 ! negative regulation of protein kinase activity is_a: GO:0050732 ! negative regulation of peptidyl-tyrosine phosphorylation is_a: GO:0061097 ! regulation of protein tyrosine kinase activity @@ -105594,18 +106880,6 @@ intersection_of: results_in_assembly_of GO:0032991 ! protein-containing complex relationship: results_in_assembly_of GO:0032991 ! protein-containing complex property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/22580" xsd:anyURI -[Term] -id: GO:0065004 -name: protein-DNA complex assembly -namespace: biological_process -def: "The aggregation, arrangement and bonding together of proteins and DNA molecules to form a protein-DNA complex." [GOC:jl] -synonym: "DNA-protein complex assembly" EXACT [GOC:mah] -is_a: GO:0065003 ! protein-containing complex assembly -is_a: GO:0071824 ! protein-DNA complex organization -intersection_of: GO:0022607 ! cellular component assembly -intersection_of: results_in_assembly_of GO:0032993 ! protein-DNA complex -relationship: results_in_assembly_of GO:0032993 ! protein-DNA complex - [Term] id: GO:0065005 name: protein-lipid complex assembly @@ -105642,7 +106916,7 @@ id: GO:0065009 name: regulation of molecular function namespace: biological_process def: "Any process that modulates the frequency, rate or extent of a molecular function, an elemental biological activity occurring at the molecular level, such as catalysis or binding." [GOC:isa_complete] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate subset: goslim_pir subset: goslim_plant synonym: "regulation of a molecular function" EXACT [] @@ -107462,20 +108736,6 @@ relationship: has_primary_input GO:1990777 ! lipoprotein particle created_by: mah creation_date: 2009-12-14T02:48:51Z -[Term] -id: GO:0071417 -name: cellular response to organonitrogen compound -namespace: biological_process -def: "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organonitrogen stimulus. An organonitrogen compound is formally a compound containing at least one carbon-nitrogen bond." [GOC:mah] -synonym: "cellular response to organic nitrogen" EXACT [GOC:mah] -is_a: GO:0010243 ! response to organonitrogen compound -is_a: GO:0070887 ! cellular response to chemical stimulus -is_a: GO:0071495 ! cellular response to endogenous stimulus -intersection_of: GO:0070887 ! cellular response to chemical stimulus -intersection_of: has_primary_input CHEBI:35352 -created_by: mah -creation_date: 2009-12-14T04:07:27Z - [Term] id: GO:0071418 name: cellular response to amine stimulus @@ -107872,7 +109132,7 @@ id: GO:0071705 name: nitrogen compound transport namespace: biological_process def: "The directed movement of nitrogen-containing compounds into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore." [GOC:mah] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate is_a: BFO:0000003 is_a: GO:0006810 ! transport intersection_of: GO:0006810 ! transport @@ -108103,6 +109363,25 @@ relationship: results_in_organization_of GO:0005640 ! nuclear outer membrane created_by: mah creation_date: 2010-03-29T04:03:37Z +[Term] +id: GO:0071805 +name: potassium ion transmembrane transport +namespace: biological_process +alt_id: GO:0010163 +def: "A process in which a potassium ion is transported from one side of a membrane to the other." [GOC:mah] +comment: Note that this term is not intended for use in annotating lateral movement within membranes. +synonym: "high affinity potassium ion import" NARROW [] +synonym: "high affinity potassium ion uptake" NARROW [GOC:dph, GOC:tb] +synonym: "high-affinity potassium ion import" NARROW [] +synonym: "high-affinity potassium ion uptake" NARROW [GOC:dph, GOC:tb] +synonym: "potassium ion membrane transport" EXACT [] +is_a: GO:0006813 ! potassium ion transport +is_a: GO:0034220 ! monoatomic ion transmembrane transport +intersection_of: GO:0055085 ! transmembrane transport +intersection_of: has_primary_input CHEBI:29103 +created_by: mah +creation_date: 2010-09-03T02:43:49Z + [Term] id: GO:0071806 name: protein transmembrane transport @@ -108145,21 +109424,6 @@ relationship: has_primary_input GO:0032994 ! protein-lipid complex created_by: mah creation_date: 2010-09-06T04:26:27Z -[Term] -id: GO:0071824 -name: protein-DNA complex organization -namespace: biological_process -def: "Any process in which macromolecules aggregate, disaggregate, or are modified, resulting in the formation, disassembly, or alteration of a protein-DNA complex." [GOC:mah] -synonym: "DNA-protein complex subunit organization" EXACT [GOC:mah] -synonym: "protein-DNA complex subunit organisation" EXACT [GOC:mah] -synonym: "protein-DNA complex subunit organization" EXACT [] -is_a: GO:0043933 ! protein-containing complex organization -intersection_of: GO:0016043 ! cellular component organization -intersection_of: results_in_organization_of GO:0032993 ! protein-DNA complex -relationship: results_in_organization_of GO:0032993 ! protein-DNA complex -created_by: mah -creation_date: 2010-09-08T10:03:26Z - [Term] id: GO:0071825 name: protein-lipid complex organization @@ -114239,16 +115503,19 @@ creation_date: 2013-12-12T11:07:09Z [Term] id: GO:0097545 -name: axonemal outer doublet +name: axonemal doublet microtubule namespace: cellular_component -def: "Part of an axoneme consisting in a doublet microtubule. Nine of these outer doublets form the 9+0 axoneme, while the 9+2 axoneme also contains a central pair. Dynein arms attached to the doublets provide the mechanism of movement of the cilium." [GOC:cilia, GOC:krc, GOC:pr, PMID:5044758, PMID:5664206, Wikipedia:Axoneme] +def: "A cellular anatomical entity that is part of an axoneme consisting of a doublet microtubule." [GOC:cilia, GOC:krc, GOC:pr, https://github.com/geneontology/go-ontology/issues/26128, PMID:5044758, PMID:5664206, Wikipedia:Axoneme] +synonym: "axonemal outer doublet" EXACT [] synonym: "axoneme outer doublet" EXACT [] +synonym: "DMT" RELATED [] synonym: "outer doublet" BROAD [] synonym: "outer-doublet microtubules" RELATED [] is_a: GO:0110165 ! cellular anatomical entity relationship: has_part GO:0097649 ! A axonemal microtubule relationship: has_part GO:0097650 ! B axonemal microtubule relationship: part_of GO:0005930 ! axoneme +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26128" xsd:anyURI created_by: pr creation_date: 2013-12-12T11:19:29Z @@ -114283,6 +115550,28 @@ relationship: results_in_fusion_of GO:0005773 ! vacuole created_by: pr creation_date: 2014-02-28T09:49:31Z +[Term] +id: GO:0097623 +name: potassium ion export across plasma membrane +namespace: biological_process +alt_id: GO:0071435 +alt_id: GO:0098668 +def: "The directed movement of potassium ions from inside of a cell, across the plasma membrane and into the extracellular region." [GOC:vw, PMID:11932440] +synonym: "potassium export" BROAD [GOC:mah] +synonym: "potassium export across plasma membrane" EXACT [] +synonym: "potassium ion export" BROAD [] +synonym: "potassium ion export from cell" EXACT [] +is_a: GO:0071805 ! potassium ion transmembrane transport +is_a: GO:0140115 ! export across plasma membrane +intersection_of: GO:0006810 ! transport +intersection_of: has_primary_input CHEBI:29103 +intersection_of: has_target_end_location GO:0005576 ! extracellular region +intersection_of: has_target_start_location GO:0005829 ! cytosol +intersection_of: results_in_transport_across GO:0005886 ! plasma membrane +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/14265" xsd:anyURI +created_by: pr +creation_date: 2009-12-16T11:10:45Z + [Term] id: GO:0097628 name: distal tip cell migration @@ -114331,7 +115620,7 @@ namespace: cellular_component def: "A complete microtubule with 13 protofilaments that fuses with an incomplete microtubule called B tubule (containing 10 protofilaments only) to form an axonemal outer doublet. Inner and outer dynein arms, as well as the radial spoke, are attached to the A tubule." [GOC:cilia, ISBN:0716731363] synonym: "A tubule" BROAD [] is_a: GO:0005879 ! axonemal microtubule -relationship: part_of GO:0097545 ! axonemal outer doublet +relationship: part_of GO:0097545 ! axonemal doublet microtubule created_by: pr creation_date: 2014-09-10T20:41:28Z @@ -114342,7 +115631,7 @@ namespace: cellular_component def: "An incomplete microtubule containing 10 protofilaments that fuses with a complete microtubule called A tubule (containing 13 protofilaments) to form an axonemal outer doublet." [GOC:cilia, ISBN:0716731363] synonym: "B tubule" BROAD [] is_a: GO:0005879 ! axonemal microtubule -relationship: part_of GO:0097545 ! axonemal outer doublet +relationship: part_of GO:0097545 ! axonemal doublet microtubule created_by: pr creation_date: 2014-09-10T20:43:18Z @@ -114424,7 +115713,7 @@ relationship: has_part GO:0001534 ! radial spoke relationship: has_part GO:0036156 ! inner dynein arm relationship: has_part GO:0036157 ! outer dynein arm relationship: has_part GO:0097540 ! axonemal central pair -relationship: has_part GO:0097545 ! axonemal outer doublet +relationship: has_part GO:0097545 ! axonemal doublet microtubule created_by: pr creation_date: 2016-09-27T15:26:34Z @@ -114760,6 +116049,7 @@ def: "A complex of collagen trimers such as a fibril or collagen network." [GOC: synonym: "Supramolecular aggregate of collagen" EXACT [PMID:19693541] synonym: "Supramolecular collagen assembly" EXACT [PMID:21421911] is_a: GO:0099080 ! supramolecular complex +is_a: PR:000050567 ! protein-containing material entity relationship: has_part GO:0005581 ! collagen trimer relationship: part_of GO:0062023 ! collagen-containing extracellular matrix @@ -114934,15 +116224,16 @@ creation_date: 2012-05-31T02:45:02Z [Term] id: GO:0098708 -name: glucose import across plasma membrane +name: D-glucose import across plasma membrane namespace: biological_process alt_id: GO:0061490 alt_id: GO:1990821 -def: "The directed movement of glucose from outside of a cell, across the plasma membrane and into the cytosol." [GOC:dos] +def: "The directed movement of D-glucose from outside of a cell, across the plasma membrane and into the cytosol." [GOC:dos] +synonym: "glucose import across plasma membrane" EXACT [] synonym: "glucose import into cell" EXACT [] synonym: "high affinity glucose import" NARROW [] is_a: GO:0098739 ! import across plasma membrane -is_a: GO:1904659 ! glucose transmembrane transport +is_a: GO:1904659 ! D-glucose transmembrane transport intersection_of: GO:0006810 ! transport intersection_of: has_primary_input CHEBI:4167 intersection_of: has_target_end_location GO:0005829 ! cytosol @@ -114995,6 +116286,26 @@ intersection_of: results_in_transport_across GO:0005886 ! plasma membrane created_by: mah creation_date: 2013-06-12T12:32:47Z +[Term] +id: GO:0098719 +name: sodium ion import across plasma membrane +namespace: biological_process +alt_id: GO:0097369 +alt_id: GO:1990118 +def: "The directed movement of sodium ions from outside of a cell, across the plasma membrane and into the cytosol." [GOC:dos] +synonym: "sodium import" EXACT [] +synonym: "sodium ion import" RELATED [] +synonym: "sodium ion import into cell" EXACT [] +is_a: GO:0035725 ! sodium ion transmembrane transport +is_a: GO:0098739 ! import across plasma membrane +intersection_of: GO:0006810 ! transport +intersection_of: has_primary_input CHEBI:29101 +intersection_of: has_target_end_location GO:0005829 ! cytosol +intersection_of: has_target_start_location GO:0005576 ! extracellular region +intersection_of: results_in_transport_across GO:0005886 ! plasma membrane +created_by: pr +creation_date: 2012-08-03T16:55:52Z + [Term] id: GO:0098722 name: asymmetric stem cell division @@ -115604,7 +116915,7 @@ id: GO:0098962 name: regulation of postsynaptic neurotransmitter receptor activity namespace: biological_process def: "Any process that modulates the frequency, rate or extent of neurotransmitter receptor activity involved in synaptic transmission. Modulation may be via an effect on ligand affinity, or effector function such as ion selectivity or pore opening/closing in ionotropic receptors." [GOC:dos] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate subset: goslim_synapse is_a: GO:0031644 ! regulation of nervous system process is_a: GO:0050804 ! modulation of chemical synaptic transmission @@ -115732,6 +117043,17 @@ is_a: GO:0008066 ! glutamate receptor activity intersection_of: GO:0004930 ! G protein-coupled receptor activity intersection_of: has_primary_input CHEBI:14321 +[Term] +id: GO:0098991 +name: kainate selective glutamate receptor signaling pathway +namespace: biological_process +def: "The series of molecular signals initiated by glutamate binding to an kainate-selective glutamate receptor on the surface of the target cell, followed by the movement of ions through a channel in the receptor complex, ending with the regulation of a downstream cellular process, e.g. transcription." [GOC:signaling, ISBN:9780071120005] +subset: goslim_synapse +is_a: GO:0035235 ! ionotropic glutamate receptor signaling pathway +intersection_of: GO:0007165 ! signal transduction +intersection_of: starts_with GO:0015277 ! kainate selective glutamate receptor activity +relationship: starts_with GO:0015277 ! kainate selective glutamate receptor activity + [Term] id: GO:0098992 name: neuronal dense core vesicle @@ -116370,7 +117692,7 @@ id: GO:0099531 name: presynaptic process involved in chemical synaptic transmission namespace: biological_process def: "The pathway leading to secretion of a neurotransmitter from the presynapse as part of synaptic transmission." [GOC:dos] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate subset: goslim_synapse is_a: GO:0050877 ! nervous system process intersection_of: GO:0050877 ! nervous system process @@ -116685,7 +118007,7 @@ id: GO:0099601 name: regulation of neurotransmitter receptor activity namespace: biological_process def: "Any process that modulates the frequency, rate or extent of neurotransmitter receptor activity. Modulation may be via an effect on ligand affinity, or effector function such as ion selectivity or pore opening/closing in ionotropic receptors." [GOC:dos] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate subset: goslim_synapse is_a: GO:0010469 ! regulation of signaling receptor activity intersection_of: GO:0065007 ! biological regulation @@ -116999,6 +118321,42 @@ relationship: positively_regulates GO:0048280 ! vesicle fusion with Golgi appara created_by: hjd creation_date: 2019-06-27T15:20:59Z +[Term] +id: GO:0106426 +name: regulation of kainate selective glutamate receptor signaling pathway +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of the kainate selective glutamate receptor signaling pathway." [PMID:12597860] +is_a: GO:1900449 ! regulation of glutamate receptor signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0098991 ! kainate selective glutamate receptor signaling pathway +relationship: regulates GO:0098991 ! kainate selective glutamate receptor signaling pathway +created_by: hjd + +[Term] +id: GO:0106427 +name: negative regulation of kainate selective glutamate receptor signaling pathway +namespace: biological_process +def: "Any process that stops, prevents or reduces the frequency, rate or extent of the kainate selective glutamate receptor signaling pathway." [PMID:12597860] +is_a: GO:0048519 ! negative regulation of biological process +is_a: GO:0106426 ! regulation of kainate selective glutamate receptor signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0106426 ! regulation of kainate selective glutamate receptor signaling pathway +relationship: negatively_regulates GO:0106426 ! regulation of kainate selective glutamate receptor signaling pathway +created_by: hjd + +[Term] +id: GO:0106428 +name: positive regulation of kainate selective glutamate receptor signaling pathway +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of the kainate selective glutamate receptor signaling pathway." [PMID:12597860] +is_a: GO:0048518 ! positive regulation of biological process +is_a: GO:0106426 ! regulation of kainate selective glutamate receptor signaling pathway +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0106426 ! regulation of kainate selective glutamate receptor signaling pathway +relationship: positively_regulates GO:0106426 ! regulation of kainate selective glutamate receptor signaling pathway +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/23558" xsd:anyURI +created_by: hjd + [Term] id: GO:0110011 name: regulation of basement membrane organization @@ -117297,7 +118655,7 @@ id: GO:0110112 name: regulation of lipid transporter activity namespace: biological_process def: "Any process that modulates the frequency, rate, or extent of lipid transporter activity." [GOC:BHF, GOC:BHF_miRNA, GOC:rph, PMID:27365390] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate is_a: GO:0032368 ! regulation of lipid transport is_a: GO:0032409 ! regulation of transporter activity intersection_of: GO:0065007 ! biological regulation @@ -117311,7 +118669,7 @@ id: GO:0110113 name: positive regulation of lipid transporter activity namespace: biological_process def: "Any process that increases the frequency, rate, or extent of lipid transporter activity." [GOC:BHF, GOC:BHF_miRNA, GOC:rph, PMID:27365390] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate is_a: GO:0032370 ! positive regulation of lipid transport is_a: GO:0032411 ! positive regulation of transporter activity is_a: GO:0110112 ! regulation of lipid transporter activity @@ -117326,7 +118684,7 @@ id: GO:0110114 name: negative regulation of lipid transporter activity namespace: biological_process def: "Any process that decreases the frequency, rate, or extent of lipid transporter activity." [GOC:BHF, GOC:BHF_miRNA, GOC:rph, PMID:27365390] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate is_a: GO:0032369 ! negative regulation of lipid transport is_a: GO:0032410 ! negative regulation of transporter activity is_a: GO:0110112 ! regulation of lipid transporter activity @@ -118032,9 +119390,9 @@ synonym: "outer doublet assembly" BROAD [] synonym: "outer-doublet microtubule assembly" BROAD [] is_a: GO:0022607 ! cellular component assembly intersection_of: GO:0009987 ! cellular process -intersection_of: results_in_assembly_of GO:0097545 ! axonemal outer doublet +intersection_of: results_in_assembly_of GO:0097545 ! axonemal doublet microtubule relationship: part_of GO:0035082 ! axoneme assembly -relationship: results_in_assembly_of GO:0097545 ! axonemal outer doublet +relationship: results_in_assembly_of GO:0097545 ! axonemal doublet microtubule property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21154" xsd:anyURI created_by: krc creation_date: 2021-03-23T16:28:18Z @@ -121183,12 +122541,75 @@ relationship: positively_regulates GO:1903804 ! glycine import across plasma mem created_by: al creation_date: 2012-06-13T07:40:40Z +[Term] +id: GO:1901016 +name: regulation of potassium ion transmembrane transporter activity +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of potassium ion transmembrane transporter activity." [GOC:BHF, GOC:TermGenie] +subset: gocheck_obsoletion_candidate +synonym: "regulation of potassium transporter activity" EXACT [GOC:TermGenie] +is_a: GO:0022898 ! regulation of transmembrane transporter activity +is_a: GO:1901379 ! regulation of potassium ion transmembrane transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0015079 ! potassium ion transmembrane transporter activity +relationship: regulates GO:0015079 ! potassium ion transmembrane transporter activity +created_by: rl +creation_date: 2012-06-15T01:13:49Z + +[Term] +id: GO:1901017 +name: negative regulation of potassium ion transmembrane transporter activity +namespace: biological_process +def: "Any process that stops, prevents or reduces the frequency, rate or extent of potassium ion transmembrane transporter activity." [GOC:BHF, GOC:TermGenie] +subset: gocheck_obsoletion_candidate +synonym: "down regulation of potassium ion transmembrane transporter activity" EXACT [GOC:TermGenie] +synonym: "down regulation of potassium transporter activity" EXACT [GOC:TermGenie] +synonym: "down-regulation of potassium ion transmembrane transporter activity" EXACT [GOC:TermGenie] +synonym: "down-regulation of potassium transporter activity" EXACT [GOC:TermGenie] +synonym: "downregulation of potassium ion transmembrane transporter activity" EXACT [GOC:TermGenie] +synonym: "downregulation of potassium transporter activity" EXACT [GOC:TermGenie] +synonym: "inhibition of potassium ion transmembrane transporter activity" NARROW [GOC:TermGenie] +synonym: "inhibition of potassium transporter activity" EXACT [GOC:TermGenie] +synonym: "negative regulation of potassium transporter activity" EXACT [GOC:TermGenie] +is_a: GO:0032410 ! negative regulation of transporter activity +is_a: GO:1901016 ! regulation of potassium ion transmembrane transporter activity +is_a: GO:1901380 ! negative regulation of potassium ion transmembrane transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0015079 ! potassium ion transmembrane transporter activity +relationship: negatively_regulates GO:0015079 ! potassium ion transmembrane transporter activity +created_by: rl +creation_date: 2012-06-15T01:14:10Z + +[Term] +id: GO:1901018 +name: positive regulation of potassium ion transmembrane transporter activity +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of potassium ion transmembrane transporter activity." [GOC:BHF, GOC:TermGenie] +subset: gocheck_obsoletion_candidate +synonym: "activation of potassium ion transmembrane transporter activity" NARROW [GOC:TermGenie] +synonym: "activation of potassium transporter activity" EXACT [GOC:TermGenie] +synonym: "positive regulation of potassium transporter activity" EXACT [GOC:TermGenie] +synonym: "up regulation of potassium ion transmembrane transporter activity" EXACT [GOC:TermGenie] +synonym: "up regulation of potassium transporter activity" EXACT [GOC:TermGenie] +synonym: "up-regulation of potassium ion transmembrane transporter activity" EXACT [GOC:TermGenie] +synonym: "up-regulation of potassium transporter activity" EXACT [GOC:TermGenie] +synonym: "upregulation of potassium ion transmembrane transporter activity" EXACT [GOC:TermGenie] +synonym: "upregulation of potassium transporter activity" EXACT [GOC:TermGenie] +is_a: GO:0032411 ! positive regulation of transporter activity +is_a: GO:1901016 ! regulation of potassium ion transmembrane transporter activity +is_a: GO:1901381 ! positive regulation of potassium ion transmembrane transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0015079 ! potassium ion transmembrane transporter activity +relationship: positively_regulates GO:0015079 ! potassium ion transmembrane transporter activity +created_by: rl +creation_date: 2012-06-15T01:14:18Z + [Term] id: GO:1901019 name: regulation of calcium ion transmembrane transporter activity namespace: biological_process def: "Any process that modulates the frequency, rate or extent of calcium ion transmembrane transporter activity." [GOC:BHF, GOC:TermGenie] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate is_a: GO:0022898 ! regulation of transmembrane transporter activity is_a: GO:1903169 ! regulation of calcium ion transmembrane transport intersection_of: GO:0065007 ! biological regulation @@ -121202,7 +122623,7 @@ id: GO:1901020 name: negative regulation of calcium ion transmembrane transporter activity namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of calcium ion transmembrane transporter activity." [GOC:BHF, GOC:TermGenie] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "down regulation of calcium ion transmembrane transporter activity" EXACT [GOC:TermGenie] synonym: "down-regulation of calcium ion transmembrane transporter activity" EXACT [GOC:TermGenie] synonym: "downregulation of calcium ion transmembrane transporter activity" EXACT [GOC:TermGenie] @@ -121221,7 +122642,7 @@ id: GO:1901021 name: positive regulation of calcium ion transmembrane transporter activity namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of calcium ion transmembrane transporter activity." [GOC:BHF, GOC:TermGenie] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "activation of calcium ion transmembrane transporter activity" NARROW [GOC:TermGenie] synonym: "up regulation of calcium ion transmembrane transporter activity" EXACT [GOC:TermGenie] synonym: "up-regulation of calcium ion transmembrane transporter activity" EXACT [GOC:TermGenie] @@ -121296,7 +122717,10 @@ is_a: GO:0019538 ! protein metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output PR:000009054 ! insulin gene translation product relationship: has_primary_input_or_output PR:000009054 ! insulin gene translation product +property_value: RO:0002161 NCBITaxon:2 +property_value: RO:0002161 NCBITaxon:2157 property_value: RO:0002161 NCBITaxon:33090 +property_value: RO:0002161 NCBITaxon:4751 created_by: pm creation_date: 2012-07-13T12:32:40Z @@ -121374,7 +122798,8 @@ name: primary amino compound metabolic process namespace: biological_process def: "The chemical reactions and pathways involving primary amino compound." [GOC:TermGenie] synonym: "primary amino compound metabolism" EXACT [GOC:TermGenie] -is_a: GO:1901564 ! organonitrogen compound metabolic process +is_a: BFO:0000003 +is_a: GO:0008152 ! metabolic process intersection_of: GO:0008152 ! metabolic process intersection_of: has_primary_input_or_output CHEBI:50994 relationship: has_primary_input_or_output CHEBI:50994 @@ -121977,6 +123402,58 @@ relationship: negatively_regulates GO:0001944 ! vasculature development created_by: bf creation_date: 2012-09-06T09:17:24Z +[Term] +id: GO:1901379 +name: regulation of potassium ion transmembrane transport +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of potassium ion transmembrane transport." [GOC:BHF, GOC:TermGenie] +synonym: "regulation of potassium ion membrane transport" EXACT [] +is_a: GO:0034765 ! regulation of monoatomic ion transmembrane transport +is_a: GO:0043266 ! regulation of potassium ion transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0071805 ! potassium ion transmembrane transport +relationship: regulates GO:0071805 ! potassium ion transmembrane transport +created_by: rl +creation_date: 2012-09-28T15:58:00Z + +[Term] +id: GO:1901380 +name: negative regulation of potassium ion transmembrane transport +namespace: biological_process +def: "Any process that stops, prevents or reduces the frequency, rate or extent of potassium ion transmembrane transport." [GOC:BHF, GOC:TermGenie] +synonym: "down regulation of potassium ion transmembrane transport" EXACT [GOC:TermGenie] +synonym: "down-regulation of potassium ion transmembrane transport" EXACT [GOC:TermGenie] +synonym: "downregulation of potassium ion transmembrane transport" EXACT [GOC:TermGenie] +synonym: "inhibition of potassium ion transmembrane transport" NARROW [GOC:TermGenie] +synonym: "negative regulation of potassium ion membrane transport" EXACT [] +is_a: GO:0034766 ! negative regulation of monoatomic ion transmembrane transport +is_a: GO:0043267 ! negative regulation of potassium ion transport +is_a: GO:1901379 ! regulation of potassium ion transmembrane transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0071805 ! potassium ion transmembrane transport +relationship: negatively_regulates GO:0071805 ! potassium ion transmembrane transport +created_by: rl +creation_date: 2012-09-28T15:59:08Z + +[Term] +id: GO:1901381 +name: positive regulation of potassium ion transmembrane transport +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of potassium ion transmembrane transport." [GOC:BHF, GOC:TermGenie] +synonym: "activation of potassium ion transmembrane transport" NARROW [GOC:TermGenie] +synonym: "positive regulation of potassium ion membrane transport" EXACT [] +synonym: "up regulation of potassium ion transmembrane transport" EXACT [GOC:TermGenie] +synonym: "up-regulation of potassium ion transmembrane transport" EXACT [GOC:TermGenie] +synonym: "upregulation of potassium ion transmembrane transport" EXACT [GOC:TermGenie] +is_a: GO:0034767 ! positive regulation of monoatomic ion transmembrane transport +is_a: GO:0043268 ! positive regulation of potassium ion transport +is_a: GO:1901379 ! regulation of potassium ion transmembrane transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0071805 ! potassium ion transmembrane transport +relationship: positively_regulates GO:0071805 ! potassium ion transmembrane transport +created_by: rl +creation_date: 2012-09-28T15:59:25Z + [Term] id: GO:1901382 name: regulation of chorionic trophoblast cell proliferation @@ -122102,7 +123579,7 @@ is_a: GO:0022857 ! transmembrane transporter activity intersection_of: GO:0022857 ! transmembrane transporter activity intersection_of: has_primary_input CHEBI:63299 relationship: has_primary_input CHEBI:63299 -relationship: part_of GO:1901264 ! carbohydrate derivative transport +relationship: part_of GO:1901264 {source="GO_REF:0000090"} ! carbohydrate derivative transport created_by: pr creation_date: 2012-10-17T10:31:22Z @@ -122245,59 +123722,6 @@ relationship: positively_regulates GO:0001885 ! endothelial cell development created_by: pr creation_date: 2012-10-30T12:59:58Z -[Term] -id: GO:1901564 -name: organonitrogen compound metabolic process -namespace: biological_process -def: "The chemical reactions and pathways involving organonitrogen compound." [GOC:pr, GOC:TermGenie] -subset: gocheck_do_not_annotate -synonym: "organonitrogen compound metabolism" EXACT [GOC:TermGenie] -is_a: BFO:0000003 -is_a: GO:0008152 ! metabolic process -intersection_of: GO:0008152 ! metabolic process -intersection_of: has_primary_input_or_output CHEBI:35352 -relationship: has_primary_input_or_output CHEBI:35352 -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -created_by: pr -creation_date: 2012-11-04T15:17:52Z - -[Term] -id: GO:1901565 -name: organonitrogen compound catabolic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the breakdown of organonitrogen compound." [GOC:pr, GOC:TermGenie] -subset: gocheck_do_not_annotate -synonym: "organonitrogen compound breakdown" EXACT [GOC:TermGenie] -synonym: "organonitrogen compound catabolism" EXACT [GOC:TermGenie] -synonym: "organonitrogen compound degradation" EXACT [GOC:TermGenie] -is_a: GO:0009056 ! catabolic process -is_a: GO:1901564 ! organonitrogen compound metabolic process -intersection_of: GO:0009056 ! catabolic process -intersection_of: has_primary_input CHEBI:35352 -relationship: has_primary_input CHEBI:35352 -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -created_by: pr -creation_date: 2012-11-04T15:17:56Z - -[Term] -id: GO:1901566 -name: organonitrogen compound biosynthetic process -namespace: biological_process -def: "The chemical reactions and pathways resulting in the formation of organonitrogen compound." [GOC:pr, GOC:TermGenie] -subset: gocheck_do_not_annotate -synonym: "organonitrogen compound anabolism" EXACT [GOC:TermGenie] -synonym: "organonitrogen compound biosynthesis" EXACT [GOC:TermGenie] -synonym: "organonitrogen compound formation" EXACT [GOC:TermGenie] -synonym: "organonitrogen compound synthesis" EXACT [GOC:TermGenie] -is_a: GO:0009058 ! biosynthetic process -is_a: GO:1901564 ! organonitrogen compound metabolic process -intersection_of: GO:0009058 ! biosynthetic process -intersection_of: has_primary_output CHEBI:35352 -relationship: has_primary_output CHEBI:35352 -property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26424" xsd:anyURI -created_by: pr -creation_date: 2012-11-04T15:18:00Z - [Term] id: GO:1901588 name: dendritic microtubule @@ -124325,6 +125749,66 @@ relationship: regulates GO:0006325 ! chromatin organization created_by: bf creation_date: 2013-07-01T13:21:52Z +[Term] +id: GO:1902305 +name: regulation of sodium ion transmembrane transport +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of sodium ion transmembrane transport." [GOC:BHF, GOC:mtg_cardiac_conduct_nov11, GOC:rl, GOC:TermGenie, PMID:18591664] +synonym: "regulation of sodium ion membrane transport" EXACT [GOC:TermGenie] +is_a: GO:0002028 ! regulation of sodium ion transport +is_a: GO:0034765 ! regulation of monoatomic ion transmembrane transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0035725 ! sodium ion transmembrane transport +relationship: regulates GO:0035725 ! sodium ion transmembrane transport +created_by: rl +creation_date: 2013-07-18T13:33:53Z + +[Term] +id: GO:1902306 +name: negative regulation of sodium ion transmembrane transport +namespace: biological_process +def: "Any process that stops, prevents or reduces the frequency, rate or extent of sodium ion transmembrane transport." [GOC:BHF, GOC:mtg_cardiac_conduct_nov11, GOC:rl, GOC:TermGenie, PMID:18591664] +synonym: "down regulation of sodium ion membrane transport" EXACT [GOC:TermGenie] +synonym: "down regulation of sodium ion transmembrane transport" EXACT [GOC:TermGenie] +synonym: "down-regulation of sodium ion membrane transport" EXACT [GOC:TermGenie] +synonym: "down-regulation of sodium ion transmembrane transport" EXACT [GOC:TermGenie] +synonym: "downregulation of sodium ion membrane transport" EXACT [GOC:TermGenie] +synonym: "downregulation of sodium ion transmembrane transport" EXACT [GOC:TermGenie] +synonym: "inhibition of sodium ion membrane transport" NARROW [GOC:TermGenie] +synonym: "inhibition of sodium ion transmembrane transport" NARROW [GOC:TermGenie] +synonym: "negative regulation of sodium ion membrane transport" EXACT [GOC:TermGenie] +is_a: GO:0010766 ! negative regulation of sodium ion transport +is_a: GO:0034766 ! negative regulation of monoatomic ion transmembrane transport +is_a: GO:1902305 ! regulation of sodium ion transmembrane transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0035725 ! sodium ion transmembrane transport +relationship: negatively_regulates GO:0035725 ! sodium ion transmembrane transport +created_by: rl +creation_date: 2013-07-18T13:34:01Z + +[Term] +id: GO:1902307 +name: positive regulation of sodium ion transmembrane transport +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of sodium ion transmembrane transport." [GOC:BHF, GOC:mtg_cardiac_conduct_nov11, GOC:rl, GOC:TermGenie, PMID:18591664] +synonym: "activation of sodium ion membrane transport" NARROW [GOC:TermGenie] +synonym: "activation of sodium ion transmembrane transport" NARROW [GOC:TermGenie] +synonym: "positive regulation of sodium ion membrane transport" EXACT [GOC:TermGenie] +synonym: "up regulation of sodium ion membrane transport" EXACT [GOC:TermGenie] +synonym: "up regulation of sodium ion transmembrane transport" EXACT [GOC:TermGenie] +synonym: "up-regulation of sodium ion membrane transport" EXACT [GOC:TermGenie] +synonym: "up-regulation of sodium ion transmembrane transport" EXACT [GOC:TermGenie] +synonym: "upregulation of sodium ion membrane transport" EXACT [GOC:TermGenie] +synonym: "upregulation of sodium ion transmembrane transport" EXACT [GOC:TermGenie] +is_a: GO:0010765 ! positive regulation of sodium ion transport +is_a: GO:0034767 ! positive regulation of monoatomic ion transmembrane transport +is_a: GO:1902305 ! regulation of sodium ion transmembrane transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0035725 ! sodium ion transmembrane transport +relationship: positively_regulates GO:0035725 ! sodium ion transmembrane transport +created_by: rl +creation_date: 2013-07-18T13:34:18Z + [Term] id: GO:1902337 name: regulation of apoptotic process involved in morphogenesis @@ -124513,7 +125997,7 @@ id: GO:1902427 name: regulation of water channel activity namespace: biological_process def: "Any process that modulates the frequency, rate or extent of water channel activity." [GOC:nhn, GOC:TermGenie, PMID:22095752] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "regulation of aquaporin" NARROW [GOC:TermGenie] synonym: "regulation of aquaporin permeability" NARROW [PMID:22095752] is_a: GO:0022898 ! regulation of transmembrane transporter activity @@ -124523,36 +126007,12 @@ relationship: regulates GO:0015250 ! water channel activity created_by: bf creation_date: 2013-09-23T12:56:31Z -[Term] -id: GO:1902428 -name: negative regulation of water channel activity -namespace: biological_process -def: "Any process that stops, prevents or reduces the frequency, rate or extent of water channel activity." [GOC:TermGenie] -subset: gocheck_do_not_annotate -synonym: "down regulation of aquaporin" NARROW [GOC:TermGenie] -synonym: "down regulation of water channel activity" EXACT [GOC:TermGenie] -synonym: "down-regulation of aquaporin" NARROW [GOC:TermGenie] -synonym: "down-regulation of water channel activity" EXACT [GOC:TermGenie] -synonym: "downregulation of aquaporin" NARROW [GOC:TermGenie] -synonym: "downregulation of water channel activity" EXACT [GOC:TermGenie] -synonym: "inhibition of aquaporin" NARROW [GOC:TermGenie] -synonym: "inhibition of water channel activity" NARROW [GOC:TermGenie] -synonym: "negative regulation of aquaporin" NARROW [GOC:TermGenie] -is_a: GO:0032410 ! negative regulation of transporter activity -is_a: GO:0034763 ! negative regulation of transmembrane transport -is_a: GO:1902427 ! regulation of water channel activity -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0015250 ! water channel activity -relationship: negatively_regulates GO:0015250 ! water channel activity -created_by: bf -creation_date: 2013-09-23T12:56:40Z - [Term] id: GO:1902429 name: positive regulation of water channel activity namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of water channel activity." [GOC:nhn, GOC:TermGenie, PMID:22095752] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "activation of aquaporin" NARROW [GOC:TermGenie] synonym: "activation of water channel activity" NARROW [GOC:TermGenie] synonym: "aquaporin activation" NARROW [PMID:22095752] @@ -126878,7 +128338,7 @@ id: GO:1903048 name: regulation of acetylcholine-gated cation channel activity namespace: biological_process def: "Any process that modulates the frequency, rate or extent of acetylcholine-gated cation channel activity." [GO_REF:0000059, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:21718690] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate is_a: GO:0032412 ! regulation of monoatomic ion transmembrane transporter activity is_a: GO:0098815 ! modulation of excitatory postsynaptic potential is_a: GO:0098962 ! regulation of postsynaptic neurotransmitter receptor activity @@ -126889,26 +128349,6 @@ relationship: regulates GO:0022848 ! acetylcholine-gated monoatomic cation-selec created_by: bf creation_date: 2014-05-22T14:46:53Z -[Term] -id: GO:1903049 -name: negative regulation of acetylcholine-gated cation channel activity -namespace: biological_process -def: "Any process that stops, prevents or reduces the frequency, rate or extent of acetylcholine-gated cation channel activity." [GO_REF:0000059, GOC:bf, GOC:PARL, GOC:TermGenie, PMID:21718690] -subset: gocheck_do_not_annotate -synonym: "down regulation of acetylcholine-gated cation channel activity" EXACT [GOC:TermGenie] -synonym: "down-regulation of acetylcholine-gated cation channel activity" EXACT [GOC:TermGenie] -synonym: "downregulation of acetylcholine-gated cation channel activity" EXACT [GOC:TermGenie] -synonym: "inhibition of acetylcholine-gated cation channel activity" NARROW [GOC:TermGenie] -is_a: GO:0032413 ! negative regulation of ion transmembrane transporter activity -is_a: GO:1903048 ! regulation of acetylcholine-gated cation channel activity -is_a: GO:2000272 ! negative regulation of signaling receptor activity -is_a: GO:2001258 ! negative regulation of cation channel activity -intersection_of: GO:0065007 ! biological regulation -intersection_of: negatively_regulates GO:0022848 ! acetylcholine-gated monoatomic cation-selective channel activity -relationship: negatively_regulates GO:0022848 ! acetylcholine-gated monoatomic cation-selective channel activity -created_by: bf -creation_date: 2014-05-22T14:47:00Z - [Term] id: GO:1903050 name: regulation of proteolysis involved in protein catabolic process @@ -127581,13 +129021,157 @@ name: multi-ciliated epithelial cell differentiation namespace: biological_process def: "The process in which a relatively unspecialized cell acquires the specialized features of a multi-ciliated epithelial cell." [GO_REF:0000086, GOC:sp, GOC:TermGenie, PMID:22231168, PMID:24934224] synonym: "multiciliate cell differentiation" BROAD [] -is_a: GO:0030855 ! epithelial cell differentiation +is_a: GO:0002065 ! columnar/cuboidal epithelial cell differentiation intersection_of: GO:0030154 ! cell differentiation intersection_of: results_in_acquisition_of_features_of CL:0005012 ! multi-ciliated epithelial cell relationship: results_in_acquisition_of_features_of CL:0005012 ! multi-ciliated epithelial cell created_by: tb creation_date: 2014-08-05T19:21:21Z +[Term] +id: GO:1903276 +name: regulation of sodium ion export across plasma membrane +namespace: biological_process +alt_id: GO:1903273 +def: "Any process that modulates the frequency, rate or extent of sodium ion export across the plasma membrane." [GO_REF:0000058, GOC:BHF, GOC:rl, GOC:TermGenie, PMID:17095720] +synonym: "regulation of sodium export" RELATED [GOC:TermGenie] +synonym: "regulation of sodium ion export" RELATED [] +synonym: "regulation of sodium ion export from cell" EXACT [] +is_a: GO:1902305 ! regulation of sodium ion transmembrane transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0036376 ! sodium ion export across plasma membrane +relationship: regulates GO:0036376 ! sodium ion export across plasma membrane +created_by: rl +creation_date: 2014-08-08T17:06:46Z + +[Term] +id: GO:1903277 +name: negative regulation of sodium ion export across plasma membrane +namespace: biological_process +alt_id: GO:1903274 +def: "Any process that stops, prevents or reduces the frequency, rate or extent of sodium ion export across the plasma membrane." [GO_REF:0000058, GOC:BHF, GOC:rl, GOC:TermGenie, PMID:17095720] +synonym: "down regulation of sodium export" RELATED [GOC:TermGenie] +synonym: "down regulation of sodium ion export" RELATED [GOC:TermGenie] +synonym: "down regulation of sodium ion export from cell" EXACT [GOC:TermGenie] +synonym: "down-regulation of sodium export" RELATED [GOC:TermGenie] +synonym: "down-regulation of sodium ion export" RELATED [GOC:TermGenie] +synonym: "down-regulation of sodium ion export from cell" EXACT [GOC:TermGenie] +synonym: "downregulation of sodium export" RELATED [GOC:TermGenie] +synonym: "downregulation of sodium ion export" RELATED [GOC:TermGenie] +synonym: "downregulation of sodium ion export from cell" EXACT [GOC:TermGenie] +synonym: "inhibition of sodium export" NARROW [GOC:TermGenie] +synonym: "inhibition of sodium ion export" NARROW [GOC:TermGenie] +synonym: "inhibition of sodium ion export from cell" NARROW [GOC:TermGenie] +synonym: "negative regulation of sodium export" RELATED [GOC:TermGenie] +synonym: "negative regulation of sodium ion export" RELATED [] +synonym: "negative regulation of sodium ion export from cell" EXACT [] +is_a: GO:1902306 ! negative regulation of sodium ion transmembrane transport +is_a: GO:1903276 ! regulation of sodium ion export across plasma membrane +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0036376 ! sodium ion export across plasma membrane +relationship: negatively_regulates GO:0036376 ! sodium ion export across plasma membrane +created_by: rl +creation_date: 2014-08-08T17:10:22Z + +[Term] +id: GO:1903278 +name: positive regulation of sodium ion export across plasma membrane +namespace: biological_process +alt_id: GO:1903275 +def: "Any process that activates or increases the frequency, rate or extent of sodium ion export across the plasma membrane." [GO_REF:0000058, GOC:BHF, GOC:rl, GOC:TermGenie, PMID:17095720] +synonym: "activation of sodium export" NARROW [GOC:TermGenie] +synonym: "activation of sodium ion export" NARROW [GOC:TermGenie] +synonym: "activation of sodium ion export from cell" NARROW [GOC:TermGenie] +synonym: "positive regulation of sodium export" RELATED [GOC:TermGenie] +synonym: "positive regulation of sodium ion export" RELATED [] +synonym: "positive regulation of sodium ion export from cell" EXACT [] +synonym: "up regulation of sodium export" RELATED [GOC:TermGenie] +synonym: "up regulation of sodium ion export" RELATED [GOC:TermGenie] +synonym: "up regulation of sodium ion export from cell" EXACT [GOC:TermGenie] +synonym: "up-regulation of sodium export" RELATED [GOC:TermGenie] +synonym: "up-regulation of sodium ion export" RELATED [GOC:TermGenie] +synonym: "up-regulation of sodium ion export from cell" EXACT [GOC:TermGenie] +synonym: "upregulation of sodium export" RELATED [GOC:TermGenie] +synonym: "upregulation of sodium ion export" RELATED [GOC:TermGenie] +synonym: "upregulation of sodium ion export from cell" EXACT [GOC:TermGenie] +is_a: GO:1902307 ! positive regulation of sodium ion transmembrane transport +is_a: GO:1903276 ! regulation of sodium ion export across plasma membrane +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0036376 ! sodium ion export across plasma membrane +relationship: positively_regulates GO:0036376 ! sodium ion export across plasma membrane +created_by: rl +creation_date: 2014-08-08T17:10:30Z + +[Term] +id: GO:1903286 +name: regulation of potassium ion import +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of potassium ion import." [GO_REF:0000058, GOC:BHF, GOC:mtg_cardiac_conduct_nov11, GOC:rl, GOC:TermGenie, PMID:10636900] +synonym: "regulation of potassium import" EXACT [GOC:TermGenie] +synonym: "regulation of potassium ion uptake" EXACT [GOC:TermGenie] +is_a: GO:1901379 ! regulation of potassium ion transmembrane transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:1990573 ! potassium ion import across plasma membrane +relationship: regulates GO:1990573 ! potassium ion import across plasma membrane +created_by: rl +creation_date: 2014-08-11T14:26:16Z + +[Term] +id: GO:1903287 +name: negative regulation of potassium ion import across plasma membrane +namespace: biological_process +def: "Any process that stops, prevents or reduces the frequency, rate or extent of potassium ion import across the plasma membrane." [GO_REF:0000058, GOC:BHF, GOC:mtg_cardiac_conduct_nov11, GOC:rl, GOC:TermGenie, PMID:10636900] +synonym: "down regulation of potassium import" BROAD [GOC:TermGenie] +synonym: "down regulation of potassium ion import" BROAD [GOC:TermGenie] +synonym: "down regulation of potassium ion uptake" BROAD [GOC:TermGenie] +synonym: "down-regulation of potassium import" BROAD [GOC:TermGenie] +synonym: "down-regulation of potassium ion import" BROAD [GOC:TermGenie] +synonym: "down-regulation of potassium ion uptake" BROAD [GOC:TermGenie] +synonym: "downregulation of potassium import" BROAD [GOC:TermGenie] +synonym: "downregulation of potassium ion import" BROAD [GOC:TermGenie] +synonym: "downregulation of potassium ion uptake" BROAD [GOC:TermGenie] +synonym: "inhibition of potassium import" NARROW [GOC:TermGenie] +synonym: "inhibition of potassium ion import" NARROW [GOC:TermGenie] +synonym: "inhibition of potassium ion uptake" NARROW [GOC:TermGenie] +synonym: "negative regulation of potassium import" BROAD [GOC:TermGenie] +synonym: "negative regulation of potassium ion import" BROAD [] +synonym: "negative regulation of potassium ion uptake" BROAD [GOC:TermGenie] +is_a: GO:1901380 ! negative regulation of potassium ion transmembrane transport +is_a: GO:1903286 ! regulation of potassium ion import +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:1990573 ! potassium ion import across plasma membrane +relationship: negatively_regulates GO:1990573 ! potassium ion import across plasma membrane +created_by: rl +creation_date: 2014-08-11T14:26:24Z + +[Term] +id: GO:1903288 +name: positive regulation of potassium ion import across plasma membrane +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of potassium ion import across the plasma membrane." [GO_REF:0000058, GOC:BHF, GOC:mtg_cardiac_conduct_nov11, GOC:rl, GOC:TermGenie, PMID:10636900] +synonym: "activation of potassium import" NARROW [GOC:TermGenie] +synonym: "activation of potassium ion import" NARROW [GOC:TermGenie] +synonym: "activation of potassium ion uptake" NARROW [GOC:TermGenie] +synonym: "positive regulation of potassium import" EXACT [GOC:TermGenie] +synonym: "positive regulation of potassium ion import" BROAD [] +synonym: "positive regulation of potassium ion uptake" EXACT [GOC:TermGenie] +synonym: "up regulation of potassium import" EXACT [GOC:TermGenie] +synonym: "up regulation of potassium ion import" EXACT [GOC:TermGenie] +synonym: "up regulation of potassium ion uptake" EXACT [GOC:TermGenie] +synonym: "up-regulation of potassium import" EXACT [GOC:TermGenie] +synonym: "up-regulation of potassium ion import" EXACT [GOC:TermGenie] +synonym: "up-regulation of potassium ion uptake" EXACT [GOC:TermGenie] +synonym: "upregulation of potassium import" EXACT [GOC:TermGenie] +synonym: "upregulation of potassium ion import" EXACT [GOC:TermGenie] +synonym: "upregulation of potassium ion uptake" EXACT [GOC:TermGenie] +is_a: GO:1901381 ! positive regulation of potassium ion transmembrane transport +is_a: GO:1903286 ! regulation of potassium ion import +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:1990573 ! potassium ion import across plasma membrane +relationship: positively_regulates GO:1990573 ! potassium ion import across plasma membrane +created_by: rl +creation_date: 2014-08-11T14:26:32Z + [Term] id: GO:1903292 name: protein localization to Golgi membrane @@ -129327,6 +130911,78 @@ relationship: regulates GO:0007009 ! plasma membrane organization created_by: al creation_date: 2014-12-10T18:59:44Z +[Term] +id: GO:1903764 +name: regulation of potassium ion export across plasma membrane +namespace: biological_process +alt_id: GO:1902302 +def: "Any process that modulates the frequency, rate or extent of potassium ion export across the plasma membrane." [GO_REF:0000058, GOC:BHF, GOC:mtg_cardiac_conduct_nov11, GOC:rl, GOC:TermGenie, PMID:19646991] +synonym: "regulation of potassium export" BROAD [GOC:TermGenie] +synonym: "regulation of potassium export across plasma membrane" BROAD [GOC:TermGenie] +synonym: "regulation of potassium ion export" BROAD [] +is_a: GO:1901379 ! regulation of potassium ion transmembrane transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0097623 ! potassium ion export across plasma membrane +relationship: regulates GO:0097623 ! potassium ion export across plasma membrane +created_by: rl +creation_date: 2013-07-17T16:39:53Z + +[Term] +id: GO:1903765 +name: negative regulation of potassium ion export across plasma membrane +namespace: biological_process +alt_id: GO:1902303 +def: "Any process that stops, prevents or reduces the frequency, rate or extent of potassium ion export across the plasma membrane." [GO_REF:0000058, GOC:BHF, GOC:mtg_cardiac_conduct_nov11, GOC:rl, GOC:TermGenie, PMID:19646991] +synonym: "down regulation of potassium export" BROAD [GOC:TermGenie] +synonym: "down regulation of potassium ion export" BROAD [GOC:TermGenie] +synonym: "down regulation of potassium ion export across plasma membrane" EXACT [GOC:TermGenie] +synonym: "down-regulation of potassium export" BROAD [GOC:TermGenie] +synonym: "down-regulation of potassium ion export" BROAD [GOC:TermGenie] +synonym: "down-regulation of potassium ion export across plasma membrane" EXACT [GOC:TermGenie] +synonym: "downregulation of potassium export" BROAD [GOC:TermGenie] +synonym: "downregulation of potassium ion export" BROAD [GOC:TermGenie] +synonym: "downregulation of potassium ion export across plasma membrane" EXACT [GOC:TermGenie] +synonym: "inhibition of potassium export" NARROW [GOC:TermGenie] +synonym: "inhibition of potassium ion export" RELATED [GOC:TermGenie] +synonym: "inhibition of potassium ion export across plasma membrane" EXACT [GOC:TermGenie] +synonym: "negative regulation of potassium export" BROAD [GOC:TermGenie] +synonym: "negative regulation of potassium ion export" BROAD [] +is_a: GO:1901380 ! negative regulation of potassium ion transmembrane transport +is_a: GO:1903764 ! regulation of potassium ion export across plasma membrane +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0097623 ! potassium ion export across plasma membrane +relationship: negatively_regulates GO:0097623 ! potassium ion export across plasma membrane +created_by: rl +creation_date: 2013-07-17T16:40:02Z + +[Term] +id: GO:1903766 +name: positive regulation of potassium ion export across plasma membrane +namespace: biological_process +alt_id: GO:1902304 +def: "Any process that activates or increases the frequency, rate or extent of potassium ion export across the plasma membrane." [GO_REF:0000058, GOC:BHF, GOC:mtg_cardiac_conduct_nov11, GOC:rl, GOC:TermGenie, PMID:19646991] +synonym: "activation of potassium export" RELATED [GOC:TermGenie] +synonym: "activation of potassium ion export" RELATED [GOC:TermGenie] +synonym: "activation of potassium ion export across plasma membrane" RELATED [GOC:TermGenie] +synonym: "positive regulation of potassium export" BROAD [GOC:TermGenie] +synonym: "positive regulation of potassium ion export" BROAD [] +synonym: "up regulation of potassium export" BROAD [GOC:TermGenie] +synonym: "up regulation of potassium ion export" BROAD [GOC:TermGenie] +synonym: "up regulation of potassium ion export across plasma membrane" EXACT [GOC:TermGenie] +synonym: "up-regulation of potassium export" BROAD [GOC:TermGenie] +synonym: "up-regulation of potassium ion export" BROAD [GOC:TermGenie] +synonym: "up-regulation of potassium ion export across plasma membrane" EXACT [GOC:TermGenie] +synonym: "upregulation of potassium export" BROAD [GOC:TermGenie] +synonym: "upregulation of potassium ion export" BROAD [GOC:TermGenie] +synonym: "upregulation of potassium ion export across plasma membrane" EXACT [GOC:TermGenie] +is_a: GO:1901381 ! positive regulation of potassium ion transmembrane transport +is_a: GO:1903764 ! regulation of potassium ion export across plasma membrane +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0097623 ! potassium ion export across plasma membrane +relationship: positively_regulates GO:0097623 ! potassium ion export across plasma membrane +created_by: rl +creation_date: 2013-07-17T16:40:10Z + [Term] id: GO:1903778 name: protein localization to vacuolar membrane @@ -129389,6 +131045,52 @@ relationship: positively_regulates GO:0061337 ! cardiac conduction created_by: rph creation_date: 2015-01-07T13:20:28Z +[Term] +id: GO:1903782 +name: regulation of sodium ion import across plasma membrane +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of sodium ion import across the plasma membrane." [GO_REF:0000058, GOC:BHF, GOC:mtg_cardiac_conduct_nov11, GOC:nc, GOC:TermGenie, PMID:19376779] +is_a: GO:1902305 ! regulation of sodium ion transmembrane transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0098719 ! sodium ion import across plasma membrane +relationship: regulates GO:0098719 ! sodium ion import across plasma membrane +created_by: nc +creation_date: 2015-01-07T16:48:43Z + +[Term] +id: GO:1903783 +name: negative regulation of sodium ion import across plasma membrane +namespace: biological_process +def: "Any process that stops, prevents or reduces the frequency, rate or extent of sodium ion import across the plasma membrane." [GO_REF:0000058, GOC:BHF, GOC:mtg_cardiac_conduct_nov11, GOC:nc, GOC:TermGenie, PMID:19376779] +synonym: "down regulation of sodium ion import across plasma membrane" EXACT [GOC:TermGenie] +synonym: "down-regulation of sodium ion import across plasma membrane" EXACT [GOC:TermGenie] +synonym: "downregulation of sodium ion import across plasma membrane" EXACT [GOC:TermGenie] +synonym: "inhibition of sodium ion import across plasma membrane" NARROW [GOC:TermGenie] +is_a: GO:1902306 ! negative regulation of sodium ion transmembrane transport +is_a: GO:1903782 ! regulation of sodium ion import across plasma membrane +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0098719 ! sodium ion import across plasma membrane +relationship: negatively_regulates GO:0098719 ! sodium ion import across plasma membrane +created_by: nc +creation_date: 2015-01-07T16:48:51Z + +[Term] +id: GO:1903784 +name: positive regulation of sodium ion import across plasma membrane +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of sodium ion import across the plasma membrane." [GO_REF:0000058, GOC:BHF, GOC:mtg_cardiac_conduct_nov11, GOC:nc, GOC:TermGenie, PMID:19376779] +synonym: "activation of sodium ion import across plasma membrane" NARROW [GOC:TermGenie] +synonym: "up regulation of sodium ion import across plasma membrane" EXACT [GOC:TermGenie] +synonym: "up-regulation of sodium ion import across plasma membrane" EXACT [GOC:TermGenie] +synonym: "upregulation of sodium ion import across plasma membrane" EXACT [GOC:TermGenie] +is_a: GO:1902307 ! positive regulation of sodium ion transmembrane transport +is_a: GO:1903782 ! regulation of sodium ion import across plasma membrane +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0098719 ! sodium ion import across plasma membrane +relationship: positively_regulates GO:0098719 ! sodium ion import across plasma membrane +created_by: nc +creation_date: 2015-01-07T16:49:00Z + [Term] id: GO:1903789 name: regulation of amino acid transmembrane transport @@ -130159,7 +131861,10 @@ is_a: GO:0006915 ! apoptotic process intersection_of: GO:0006915 ! apoptotic process intersection_of: occurs_in CL:0000066 ! epithelial cell relationship: occurs_in CL:0000066 ! epithelial cell +property_value: RO:0002161 NCBITaxon:2 +property_value: RO:0002161 NCBITaxon:2157 property_value: RO:0002161 NCBITaxon:33090 +property_value: RO:0002161 NCBITaxon:4751 created_by: sl creation_date: 2015-03-06T22:27:17Z @@ -131316,7 +133021,7 @@ id: GO:1904254 name: regulation of iron ion transmembrane transporter activity namespace: biological_process def: "Any process that modulates the frequency, rate or extent of an iron transmembrane transporter activity." [GO_REF:0000059, GOC:BHF, GOC:kom, GOC:TermGenie, PMID:15514116] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "regulation of iron cation channel activity" EXACT [GOC:TermGenie] synonym: "regulation of iron channel activity" EXACT [] synonym: "regulation of iron-specific channel activity" EXACT [GOC:TermGenie] @@ -131333,7 +133038,7 @@ id: GO:1904255 name: negative regulation of iron ion transmembrane transporter activity namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of an iron transmembrane transporter activity." [GO_REF:0000059, GOC:BHF, GOC:kom, GOC:TermGenie, PMID:15514116] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "down regulation of iron cation channel activity" EXACT [GOC:TermGenie] synonym: "down regulation of iron channel activity" EXACT [GOC:TermGenie] synonym: "down regulation of iron-specific channel activity" EXACT [GOC:TermGenie] @@ -131358,37 +133063,6 @@ relationship: negatively_regulates GO:0005381 ! iron ion transmembrane transport created_by: kom creation_date: 2015-05-20T14:05:06Z -[Term] -id: GO:1904256 -name: positive regulation of iron ion transmembrane transporter activity -namespace: biological_process -def: "Any process that activates or increases the frequency, rate or extent of an iron transmembrane transporter activity." [GO_REF:0000059, GOC:BHF, GOC:kom, GOC:TermGenie, PMID:15514116] -subset: gocheck_do_not_annotate -synonym: "activation of iron cation channel activity" NARROW [GOC:TermGenie] -synonym: "activation of iron channel activity" NARROW [GOC:TermGenie] -synonym: "activation of iron-specific channel activity" NARROW [GOC:TermGenie] -synonym: "positive regulation of iron cation channel activity" EXACT [GOC:TermGenie] -synonym: "positive regulation of iron channel activity" EXACT [] -synonym: "positive regulation of iron transmembrane transporter activity" EXACT [] -synonym: "positive regulation of iron-specific channel activity" EXACT [GOC:TermGenie] -synonym: "up regulation of iron cation channel activity" EXACT [GOC:TermGenie] -synonym: "up regulation of iron channel activity" EXACT [GOC:TermGenie] -synonym: "up regulation of iron-specific channel activity" EXACT [GOC:TermGenie] -synonym: "up-regulation of iron cation channel activity" EXACT [GOC:TermGenie] -synonym: "up-regulation of iron channel activity" EXACT [GOC:TermGenie] -synonym: "up-regulation of iron-specific channel activity" EXACT [GOC:TermGenie] -synonym: "upregulation of iron cation channel activity" EXACT [GOC:TermGenie] -synonym: "upregulation of iron channel activity" EXACT [GOC:TermGenie] -synonym: "upregulation of iron-specific channel activity" EXACT [GOC:TermGenie] -is_a: GO:0032411 ! positive regulation of transporter activity -is_a: GO:0034761 ! positive regulation of iron ion transmembrane transport -is_a: GO:1904254 ! regulation of iron ion transmembrane transporter activity -intersection_of: GO:0065007 ! biological regulation -intersection_of: positively_regulates GO:0005381 ! iron ion transmembrane transporter activity -relationship: positively_regulates GO:0005381 ! iron ion transmembrane transporter activity -created_by: kom -creation_date: 2015-05-20T14:05:12Z - [Term] id: GO:1904266 name: regulation of Schwann cell chemotaxis @@ -132930,10 +134604,11 @@ creation_date: 2015-09-03T22:44:56Z [Term] id: GO:1904659 -name: glucose transmembrane transport +name: D-glucose transmembrane transport namespace: biological_process alt_id: GO:0015758 -def: "The process in which glucose is transported across a membrane." [GO_REF:0000069, GOC:TermGenie, PMID:9090050] +def: "The process in which D-glucose is transported across a membrane." [GO_REF:0000069, GOC:TermGenie, PMID:9090050] +synonym: "glucose transmembrane transport" EXACT [] synonym: "glucose transport" RELATED [] is_a: GO:0055085 ! transmembrane transport intersection_of: GO:0006810 ! transport @@ -139597,6 +141272,25 @@ relationship: results_in_maturation_of GO:0031045 ! dense core granule created_by: kmv creation_date: 2014-09-30T20:35:11Z +[Term] +id: GO:1990573 +name: potassium ion import across plasma membrane +namespace: biological_process +alt_id: GO:0010107 +def: "The directed movement of potassium ions from outside of a cell, across the plasma membrane and into the cytosol." [PMID:9139127] +synonym: "potassium import" BROAD [] +synonym: "potassium ion import" BROAD [] +synonym: "potassium ion uptake" BROAD [GOC:dph, GOC:tb] +is_a: GO:0071805 ! potassium ion transmembrane transport +is_a: GO:0098739 ! import across plasma membrane +intersection_of: GO:0006810 ! transport +intersection_of: has_primary_input CHEBI:29103 +intersection_of: has_target_end_location GO:0005829 ! cytosol +intersection_of: has_target_start_location GO:0005576 ! extracellular region +intersection_of: results_in_transport_across GO:0005886 ! plasma membrane +created_by: vw +creation_date: 2014-12-04T09:48:12Z + [Term] id: GO:1990580 name: regulation of cytoplasmic translational termination @@ -141122,7 +142816,7 @@ id: GO:2000272 name: negative regulation of signaling receptor activity namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of a signaling receptor activity." [GOC:obol] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "negative regulation of receptor activity" BROAD [] synonym: "negative regulation of signalling receptor activity" EXACT [] is_a: GO:0010469 ! regulation of signaling receptor activity @@ -141138,7 +142832,7 @@ id: GO:2000273 name: positive regulation of signaling receptor activity namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of signaling receptor activity." [GOC:obol] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "positive regulation of signalling receptor activity" EXACT [] is_a: GO:0010469 ! regulation of signaling receptor activity is_a: GO:0044093 ! positive regulation of molecular function @@ -141371,6 +143065,23 @@ relationship: positively_regulates GO:0016079 ! synaptic vesicle exocytosis created_by: dph creation_date: 2011-01-03T08:21:14Z +[Term] +id: GO:2000312 +name: regulation of kainate selective glutamate receptor activity +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of kainate selective glutamate receptor activity." [GOC:BHF] +subset: gocheck_obsoletion_candidate +is_a: GO:0032412 ! regulation of monoatomic ion transmembrane transporter activity +is_a: GO:0099601 ! regulation of neurotransmitter receptor activity +is_a: GO:1901016 ! regulation of potassium ion transmembrane transporter activity +is_a: GO:2000649 ! regulation of sodium ion transmembrane transporter activity +is_a: GO:2001257 ! regulation of cation channel activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0015277 ! kainate selective glutamate receptor activity +relationship: regulates GO:0015277 ! kainate selective glutamate receptor activity +created_by: bf +creation_date: 2011-01-18T10:14:16Z + [Term] id: GO:2000316 name: regulation of T-helper 17 type immune response @@ -143026,6 +144737,53 @@ relationship: positively_regulates GO:0072089 ! stem cell proliferation created_by: dph creation_date: 2011-04-27T01:04:25Z +[Term] +id: GO:2000649 +name: regulation of sodium ion transmembrane transporter activity +namespace: biological_process +def: "Any process that modulates the frequency, rate or extent of sodium ion transmembrane transporter activity." [GOC:obol] +subset: gocheck_obsoletion_candidate +synonym: "regulation of sodium transporter activity" EXACT [GOC:obol] +is_a: GO:0022898 ! regulation of transmembrane transporter activity +is_a: GO:1902305 ! regulation of sodium ion transmembrane transport +intersection_of: GO:0065007 ! biological regulation +intersection_of: regulates GO:0015081 ! sodium ion transmembrane transporter activity +relationship: regulates GO:0015081 ! sodium ion transmembrane transporter activity +created_by: yaf +creation_date: 2011-04-28T08:42:53Z + +[Term] +id: GO:2000650 +name: negative regulation of sodium ion transmembrane transporter activity +namespace: biological_process +def: "Any process that stops, prevents or reduces the frequency, rate or extent of sodium ion transmembrane transporter activity." [GOC:obol] +subset: gocheck_obsoletion_candidate +synonym: "negative regulation of sodium transporter activity" EXACT [GOC:obol] +is_a: GO:0032410 ! negative regulation of transporter activity +is_a: GO:1902306 ! negative regulation of sodium ion transmembrane transport +is_a: GO:2000649 ! regulation of sodium ion transmembrane transporter activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: negatively_regulates GO:0015081 ! sodium ion transmembrane transporter activity +relationship: negatively_regulates GO:0015081 ! sodium ion transmembrane transporter activity +created_by: yaf +creation_date: 2011-04-28T08:42:57Z + +[Term] +id: GO:2000651 +name: positive regulation of sodium ion transmembrane transporter activity +namespace: biological_process +def: "Any process that activates or increases the frequency, rate or extent of sodium ion transmembrane transporter activity." [GOC:obol] +subset: gocheck_obsoletion_candidate +synonym: "positive regulation of sodium transporter activity" EXACT [GOC:obol] +is_a: GO:0032411 ! positive regulation of transporter activity +is_a: GO:1902307 ! positive regulation of sodium ion transmembrane transport +is_a: GO:2000649 ! regulation of sodium ion transmembrane transporter activity +intersection_of: GO:0065007 ! biological regulation +intersection_of: positively_regulates GO:0015081 ! sodium ion transmembrane transporter activity +relationship: positively_regulates GO:0015081 ! sodium ion transmembrane transporter activity +created_by: yaf +creation_date: 2011-04-28T08:43:00Z + [Term] id: GO:2000654 name: regulation of cellular response to testosterone stimulus @@ -143651,7 +145409,7 @@ id: GO:2000825 name: positive regulation of androgen receptor activity namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of androgen receptor activity." [GOC:obol] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate is_a: GO:0006357 ! regulation of transcription by RNA polymerase II is_a: GO:0051091 ! positive regulation of DNA-binding transcription factor activity is_a: GO:2000273 ! positive regulation of signaling receptor activity @@ -144951,7 +146709,7 @@ id: GO:2001257 name: regulation of cation channel activity namespace: biological_process def: "Any process that modulates the frequency, rate or extent of cation channel activity." [GOC:BHF] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "regulation of cation diffusion facilitator activity" EXACT [GOC:obol] synonym: "regulation of nonselective cation channel activity" EXACT [GOC:obol] is_a: GO:0022898 ! regulation of transmembrane transporter activity @@ -144967,7 +146725,7 @@ id: GO:2001258 name: negative regulation of cation channel activity namespace: biological_process def: "Any process that stops, prevents or reduces the frequency, rate or extent of cation channel activity." [GOC:BHF] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "negative regulation of cation diffusion facilitator activity" EXACT [GOC:obol] synonym: "negative regulation of nonselective cation channel activity" EXACT [GOC:obol] is_a: GO:0032410 ! negative regulation of transporter activity @@ -144984,7 +146742,7 @@ id: GO:2001259 name: positive regulation of cation channel activity namespace: biological_process def: "Any process that activates or increases the frequency, rate or extent of cation channel activity." [GOC:BHF] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "positive regulation of cation diffusion facilitator activity" EXACT [GOC:obol] synonym: "positive regulation of nonselective cation channel activity" EXACT [GOC:obol] is_a: GO:0032411 ! positive regulation of transporter activity @@ -145100,6 +146858,7 @@ name: Ecdysozoa namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:33317 ! Protostomia +disjoint_from: NCBITaxon:2697495 ! Spiralia [Term] id: NCBITaxon:1206795 @@ -145119,6 +146878,7 @@ synonym: "gamophytes" EXACT OMO:0003003 [] synonym: "Zygnematophyceae" RELATED synonym [] xref: GC_ID:1 is_a: NCBITaxon:131221 ! Streptophytina +disjoint_from: NCBITaxon:3193 ! Embryophyta [Term] id: NCBITaxon:131221 @@ -145183,6 +146943,7 @@ name: Acrogymnospermae namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:58024 ! Spermatophyta +disjoint_from: NCBITaxon:3398 ! Magnoliopsida [Term] id: NCBITaxon:1445966 @@ -145293,6 +147054,8 @@ xref: PMID:8590690 xref: PMID:9103655 xref: PMID:9336922 is_a: NCBITaxon:131567 ! cellular organisms +disjoint_from: NCBITaxon:2157 ! Archaea +disjoint_from: NCBITaxon:2759 ! Eukaryota [Term] id: NCBITaxon:2058185 @@ -145361,6 +147124,7 @@ xref: PMID:8590690 xref: PMID:9103655 xref: PMID:9336922 is_a: NCBITaxon:131567 ! cellular organisms +disjoint_from: NCBITaxon:2759 ! Eukaryota [Term] id: NCBITaxon:2301116 @@ -145389,6 +147153,11 @@ name: Discoba namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:2759 ! Eukaryota +disjoint_from: NCBITaxon:2698737 ! Sar +disjoint_from: NCBITaxon:33090 ! Viridiplantae +disjoint_from: NCBITaxon:33154 ! Opisthokonta +disjoint_from: NCBITaxon:38254 ! Glaucocystophyceae +disjoint_from: NCBITaxon:554915 ! Amoebozoa [Term] id: NCBITaxon:2684882 @@ -145411,6 +147180,10 @@ namespace: ncbi_taxonomy synonym: "SAR supergroup" RELATED synonym [] xref: GC_ID:1 is_a: NCBITaxon:2759 ! Eukaryota +disjoint_from: NCBITaxon:33090 ! Viridiplantae +disjoint_from: NCBITaxon:33154 ! Opisthokonta +disjoint_from: NCBITaxon:38254 ! Glaucocystophyceae +disjoint_from: NCBITaxon:554915 ! Amoebozoa [Term] id: NCBITaxon:2759 @@ -145437,6 +147210,7 @@ xref: PMID:11214318 xref: PMID:11214319 xref: PMID:12878460 is_a: NCBITaxon:1437010 ! Boreoeutheria +disjoint_from: NCBITaxon:314146 ! Euarchontoglires [Term] id: NCBITaxon:314146 @@ -145459,6 +147233,7 @@ xref: PMID:11214319 xref: PMID:12082125 xref: PMID:15522813 is_a: NCBITaxon:314146 ! Euarchontoglires +disjoint_from: NCBITaxon:9443 ! Primates [Term] id: NCBITaxon:314293 @@ -145565,6 +147340,9 @@ xref: GC_ID:1 xref: PMID:16248873 xref: PMID:30257078 is_a: NCBITaxon:2759 ! Eukaryota +disjoint_from: NCBITaxon:33154 ! Opisthokonta +disjoint_from: NCBITaxon:38254 ! Glaucocystophyceae +disjoint_from: NCBITaxon:554915 ! Amoebozoa [Term] id: NCBITaxon:3312 @@ -145573,6 +147351,7 @@ namespace: ncbi_taxonomy synonym: "conifers" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:1437180 ! Acrogymnospermae +disjoint_from: NCBITaxon:3372 ! Gnetopsida [Term] id: NCBITaxon:33154 @@ -145582,6 +147361,8 @@ synonym: "Fungi/Metazoa group" RELATED synonym [] synonym: "opisthokonts" RELATED synonym [] xref: GC_ID:1 is_a: NCBITaxon:2759 ! Eukaryota +disjoint_from: NCBITaxon:38254 ! Glaucocystophyceae +disjoint_from: NCBITaxon:554915 ! Amoebozoa [Term] id: NCBITaxon:33208 @@ -145593,6 +147374,7 @@ synonym: "metazoans" EXACT genbank_common_name [] synonym: "multicellular animals" EXACT OMO:0003003 [] xref: GC_ID:1 is_a: NCBITaxon:33154 ! Opisthokonta +disjoint_from: NCBITaxon:4751 ! Fungi [Term] id: NCBITaxon:33213 @@ -145600,6 +147382,7 @@ name: Bilateria namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:6072 ! Eumetazoa +disjoint_from: NCBITaxon:6073 ! Cnidaria [Term] id: NCBITaxon:33317 @@ -145607,6 +147390,7 @@ name: Protostomia namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:33213 ! Bilateria +disjoint_from: NCBITaxon:33511 ! Deuterostomia [Term] id: NCBITaxon:33511 @@ -145624,6 +147408,7 @@ synonym: "carnivores" EXACT genbank_common_name [] synonym: "carnivores" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:314145 ! Laurasiatheria +disjoint_from: NCBITaxon:9787 ! Perissodactyla [Term] id: NCBITaxon:33630 @@ -145724,6 +147509,7 @@ synonym: "Glaucophyceae" RELATED synonym [] synonym: "Glaucophyta" RELATED synonym [] xref: GC_ID:1 is_a: NCBITaxon:2759 ! Eukaryota +disjoint_from: NCBITaxon:554915 ! Amoebozoa [Term] id: NCBITaxon:39107 @@ -145741,6 +147527,7 @@ synonym: "mammals" EXACT genbank_common_name [] synonym: "mammals" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:32524 ! Amniota +disjoint_from: NCBITaxon:8457 ! Sauropsida [Term] id: NCBITaxon:41665 @@ -145798,6 +147585,7 @@ name: Taphrinomycotina namespace: ncbi_taxonomy xref: GC_ID:1 is_a: NCBITaxon:4890 ! Ascomycota +disjoint_from: NCBITaxon:716545 ! saccharomyceta [Term] id: NCBITaxon:4751 @@ -146001,6 +147789,7 @@ synonym: "roundworm" EXACT OMO:0003003 [] synonym: "roundworms" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:1206794 ! Ecdysozoa +disjoint_from: NCBITaxon:88770 ! Panarthropoda [Term] id: NCBITaxon:6236 @@ -146063,6 +147852,7 @@ synonym: "echinoderms" EXACT genbank_common_name [] synonym: "echinoderms" RELATED blast_name [] xref: GC_ID:1 is_a: NCBITaxon:33511 ! Deuterostomia +disjoint_from: NCBITaxon:7711 ! Chordata [Term] id: NCBITaxon:7711 @@ -146112,6 +147902,7 @@ synonym: "Osteichthyes" RELATED in_part [] synonym: "ray-finned fishes" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:117571 ! Euteleostomi +disjoint_from: NCBITaxon:8287 ! Sarcopterygii [Term] id: NCBITaxon:8287 @@ -146199,6 +147990,7 @@ synonym: "monkeys" EXACT OMO:0003003 [] synonym: "New World monkeys" EXACT genbank_common_name [] xref: GC_ID:1 is_a: NCBITaxon:314293 ! Simiiformes +disjoint_from: NCBITaxon:9526 ! Catarrhini [Term] id: NCBITaxon:9480 @@ -146409,6 +148201,7 @@ is_a: PATO:0000051 ! morphology id: PATO:0000068 name: qualitative namespace: quality +def: "A quality of an entity that is descriptive or observational, typically not represented numerically." [https://libguides.macalester.edu/c.php?g=527786&p=3608639, https://www.ncbi.nlm.nih.gov/books/NBK470395/] comment: TODO: define this or obsolete it and move children somewhere else. is_a: PATO:0000001 ! quality @@ -146916,9 +148709,9 @@ is_a: PATO:0002505 ! nucleated [Term] id: PATO:0001408 -name: ciliatedness +name: ciliated namespace: quality -def: "A cellular quality inhering in a bearer by virtue of the bearer's having thin, tail-like projections extending outwards from the cell body." [Wikipedia:http\://en.wikipedia.org/wiki/Ciliated] +def: "A cellular quality inhering in a bearer by virtue of the bearer's having one or more cilia as a part." [PMID:36924208, wikipedia:Cilium] subset: cell_quality subset: value_slim is_a: PATO:0001396 ! cellular quality @@ -147785,12 +149578,21 @@ creation_date: 2014-12-12T08:43:17Z id: PATO:0010006 name: cell morphology namespace: quality -def: "A quality of a single cell inhering in the bearer by virtue of the bearer's size or shape or structure." [ORCID:0000-0002-7073-9172] +def: "A quality of a single cell inhering in the bearer by virtue of the bearer's size or shape or structure." [https://orcid.org/0000-0002-7073-9172] comment: Use this term for morphologies that can *only* inhere in a cell, e.g. morphological qualities inhering in a cell by virtue of the presence, location or shape of one or more cell parts. is_a: PATO:0000051 ! morphology property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 creation_date: 2021-01-23T11:31:53Z +[Term] +id: PATO:0010007 +name: multiciliated +namespace: quality +def: "A cellular quality inhering in a bearer by virtue of the bearer's having multiple cilia." [PMID:36924208] +is_a: PATO:0001408 ! ciliated +property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 +property_value: terms:date "2024-07-23T10:43:20Z" xsd:dateTime + [Term] id: PATO:0015006 name: polymeric @@ -148273,7 +150075,7 @@ synonym: "native protein" NARROW [IEDB:BP] synonym: "natural protein" EXACT [PRO:DAN] is_a: BFO:0000002 is_a: PR:000018263 ! amino acid chain -is_a: PR:000064867 ! protein-containing molecular entity +is_a: PR:000050567 ! protein-containing material entity relationship: output_of GO:0006412 ! translation [Term] @@ -149800,6 +151602,7 @@ name: prominin namespace: protein def: "A protein with core architecture consisting of one Prominin (Pfam:PF05478) domain. The prominins are an emerging family of proteins that, among the multispan membrane proteins, display a novel topology. Mouse and human prominin and prominin-like 1 are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain." [InterPro:IPR008795, PMID:11467842] comment: Category=family. +xref: PANTHER:PTHR22730 xref: PIRSF:PIRSF017831 is_a: CHEBI:36080 is_a: PR:000000001 ! protein @@ -151365,6 +153168,23 @@ xref: IUPHARobj:1835 is_a: CHEBI:36080 is_a: PR:000000001 ! protein +[Term] +id: PR:000004691 +name: B-cell lymphoma/leukemia 11B +namespace: protein +def: "A protein that is a translation product of the human BCL11B gene or a 1:1 ortholog thereof." [PRO:DNx] +comment: Category=gene. +synonym: "B-cell CLL/lymphoma 11B" EXACT [] +synonym: "BCL-11B" EXACT [] +synonym: "BCL11B" EXACT PRO-short-label [PRO:DNx] +synonym: "COUP-TF-interacting protein 2" EXACT [] +synonym: "CTIP2" RELATED Gene-based [] +synonym: "radiation-induced tumor suppressor gene 1 protein" EXACT [] +synonym: "RIT1" RELATED Gene-based [] +synonym: "Rit1" EXACT [] +is_a: CHEBI:36080 +is_a: PR:000000001 ! protein + [Term] id: PR:000004724 name: bestrophin-4 @@ -151546,6 +153366,40 @@ synonym: "IgE Fc receptor subunit alpha" EXACT [] xref: IUPHARobj:2933 is_a: PR:000001355 ! immunoglobulin gamma Fc receptor II/III/IV +[Term] +id: PR:000007479 +name: fibroblast growth factor 1 +namespace: protein +def: "A protein that is a translation product of the human FGF1 gene or a 1:1 ortholog thereof." [PRO:DNx] +comment: Category=gene. +synonym: "acidic fibroblast growth factor" EXACT [] +synonym: "aFGF" EXACT [] +synonym: "beta-endothelial cell growth factor" EXACT [] +synonym: "ECGF-beta" EXACT [] +synonym: "Fgf-1" RELATED Gene-based [] +synonym: "FGF1" EXACT PRO-short-label [PRO:DNx] +synonym: "FGFA" RELATED Gene-based [] +synonym: "HBGF-1" EXACT [] +synonym: "heparin-binding growth factor 1" EXACT [] +is_a: CHEBI:36080 +is_a: PR:000000001 ! protein + +[Term] +id: PR:000007489 +name: fibroblast growth factor 2 +namespace: protein +def: "A protein that is a translation product of the human FGF2 gene or a 1:1 ortholog thereof." [PRO:DNx] +comment: Category=gene. +synonym: "basic fibroblast growth factor" EXACT [] +synonym: "BFGF" EXACT [] +synonym: "Fgf-2" RELATED Gene-based [] +synonym: "FGF2" EXACT PRO-short-label [PRO:DNx] +synonym: "FGFB" RELATED Gene-based [] +synonym: "HBGF-2" EXACT [] +synonym: "heparin-binding growth factor 2" EXACT [] +is_a: CHEBI:36080 +is_a: PR:000000001 ! protein + [Term] id: PR:000007499 name: fibroblast growth factor 8 @@ -151595,6 +153449,18 @@ xref: IUPHARobj:2958 is_a: CHEBI:36080 is_a: PR:000000001 ! protein +[Term] +id: PR:000007643 +name: forkhead box protein P1 +namespace: protein +def: "A protein that is a translation product of the human FOXP1 gene or a 1:1 ortholog thereof." [PRO:DNx] +comment: Category=gene. +synonym: "forkhead-related transcription factor 1" RELATED [] +synonym: "FOXP1" EXACT PRO-short-label [PRO:DNx] +synonym: "HSPC215" RELATED Gene-based [] +is_a: CHEBI:36080 +is_a: PR:000000001 ! protein + [Term] id: PR:000007785 name: glutamate decarboxylase 1 @@ -152065,6 +153931,19 @@ synonym: "preprodynorphin" EXACT [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein +[Term] +id: PR:000013047 +name: POU domain, class 6, transcription factor 2 +namespace: protein +def: "A protein that is a translation product of the human POU6F2 gene or a 1:1 ortholog thereof." [PRO:DNx] +comment: Category=gene. +synonym: "POU6F2" EXACT PRO-short-label [PRO:DNx] +synonym: "retina-derived POU domain factor 1" EXACT [] +synonym: "RPF-1" EXACT [] +synonym: "RPF1" RELATED Gene-based [] +is_a: CHEBI:36080 +is_a: PR:000000001 ! protein + [Term] id: PR:000013206 name: bone marrow proteoglycan @@ -152088,6 +153967,21 @@ comment: Category=gene. synonym: "PRL" EXACT PRO-short-label [PRO:DNx] is_a: PR:000029968 ! somatotropin hormone family member +[Term] +id: PR:000013433 +name: parathyroid hormone-related protein +namespace: protein +def: "A protein that is a translation product of the human PTHLH gene or a 1:1 ortholog thereof." [PRO:DNx] +comment: Category=gene. +synonym: "parathyroid hormone-like protein" EXACT [] +synonym: "PLP" RELATED [] +synonym: "PTH-rP" EXACT [] +synonym: "PTHLH" EXACT PRO-short-label [PRO:DNx] +synonym: "PTHRP" RELATED Gene-based [] +synonym: "PTHrP" EXACT [] +is_a: CHEBI:36080 +is_a: PR:000000001 ! protein + [Term] id: PR:000013502 name: parvalbumin alpha @@ -152218,6 +154112,17 @@ synonym: "ShhNC" EXACT [] is_a: CHEBI:36080 is_a: PR:000000001 ! protein +[Term] +id: PR:000014898 +name: homeobox protein SIX3 +namespace: protein +def: "A protein that is a translation product of the human SIX3 gene or a 1:1 ortholog thereof." [PRO:DNx] +comment: Category=gene. +synonym: "sine oculis homeobox homolog 3" EXACT [] +synonym: "SIX3" EXACT PRO-short-label [PRO:DNx] +is_a: CHEBI:36080 +is_a: PR:000000001 ! protein + [Term] id: PR:000015325 name: gamma-synuclein @@ -152246,6 +154151,20 @@ synonym: "SOX2" EXACT PRO-short-label [PRO:DNx] is_a: CHEBI:36080 is_a: PR:000000001 ! protein +[Term] +id: PR:000015557 +name: spondin-1 +namespace: protein +def: "A protein that is a translation product of the human SPON1 gene or a 1:1 ortholog thereof." [PRO:DNx] +comment: Category=gene. +synonym: "F-spondin" EXACT [] +synonym: "KIAA0762" RELATED Gene-based [] +synonym: "SPON1" EXACT PRO-short-label [PRO:DNx] +synonym: "vascular smooth muscle cell growth-promoting factor" EXACT [] +synonym: "VSGP" RELATED Gene-based [] +is_a: CHEBI:36080 +is_a: PR:000000001 ! protein + [Term] id: PR:000015658 name: SCO-spondin @@ -152592,6 +154511,30 @@ is_a: PR:000018264 ! proteolytic cleavage product intersection_of: PR:000007152 ! eosinophil peroxidase intersection_of: output_of GO:0016485 ! protein processing +[Term] +id: PR:000019879 +name: fibroblast growth factor 1 proteolytic cleavage product +namespace: protein +def: "A fibroblast growth factor 1 that has been processed by proteolytic cleavage." [PRO:DNx] +comment: Category=modification. +synonym: "FGF1/ClvPrd" EXACT PRO-short-label [PRO:DNx] +is_a: PR:000007479 ! fibroblast growth factor 1 +is_a: PR:000018264 ! proteolytic cleavage product +intersection_of: PR:000007479 ! fibroblast growth factor 1 +intersection_of: output_of GO:0016485 ! protein processing + +[Term] +id: PR:000019882 +name: fibroblast growth factor 2 proteolytic cleavage product +namespace: protein +def: "A fibroblast growth factor 2 that has been processed by proteolytic cleavage." [PRO:DNx] +comment: Category=modification. +synonym: "FGF2/ClvPrd" EXACT PRO-short-label [PRO:DNx] +is_a: PR:000007489 ! fibroblast growth factor 2 +is_a: PR:000018264 ! proteolytic cleavage product +intersection_of: PR:000007489 ! fibroblast growth factor 2 +intersection_of: output_of GO:0016485 ! protein processing + [Term] id: PR:000020329 name: integrin alpha-IIb proteolytic cleavage product @@ -152685,6 +154628,18 @@ is_a: PR:000018264 ! proteolytic cleavage product intersection_of: PR:000013206 ! bone marrow proteoglycan intersection_of: output_of GO:0016485 ! protein processing +[Term] +id: PR:000021172 +name: parathyroid hormone-related protein proteolytic cleavage product +namespace: protein +def: "A parathyroid hormone-related protein that has been processed by proteolytic cleavage." [PRO:DNx] +comment: Category=modification. +synonym: "PTHLH/ClvPrd" EXACT PRO-short-label [PRO:DNx] +is_a: PR:000013433 ! parathyroid hormone-related protein +is_a: PR:000018264 ! proteolytic cleavage product +intersection_of: PR:000013433 ! parathyroid hormone-related protein +intersection_of: output_of GO:0016485 ! protein processing + [Term] id: PR:000021468 name: sonic hedgehog protein proteolytic cleavage product @@ -152958,7 +154913,6 @@ synonym: "fam:GPCR" EXACT PRO-short-label [PRO:DAN] synonym: "seven-transmembrane receptor" BROAD [IUPHARfam:694] xref: IUPHARfam:694 is_a: BFO:0000004 -is_a: BFO:0000040 is_a: CHEBI:36080 is_a: PR:000000001 ! protein intersection_of: PR:000000001 ! protein @@ -153105,7 +155059,6 @@ synonym: "nonselective channel protein" EXACT [PRO:XQ] synonym: "pore class transporter protein" EXACT [PRO:XQ] synonym: "pore protein" EXACT [PRO:XQ] is_a: BFO:0000004 -is_a: BFO:0000040 is_a: CHEBI:36080 is_a: PR:000000001 ! protein intersection_of: PR:000000001 ! protein @@ -153205,17 +155158,17 @@ union_of: PR:P0DN77 ! medium-wave-sensitive opsin 2 (human) union_of: PR:P0DN78 ! medium-wave-sensitive opsin 3 (human) [Term] -id: PR:000064867 -name: protein-containing molecular entity +id: PR:000050567 +name: protein-containing material entity namespace: protein -def: "A molecular entity that minimally consists of a protein." [PRO:DAN] -comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). +def: "A material entity that minimally consists of a protein." [PRO:DAN] +comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566). synonym: "protein" NARROW [PRO:DAN] synonym: "protein aggregate" NARROW [PRO:DAN] synonym: "protein complex" NARROW [PRO:DAN] synonym: "protein-containing complex" NARROW [PRO:DAN] -is_a: CHEBI:23367 -intersection_of: CHEBI:23367 +is_a: BFO:0000040 +intersection_of: BFO:0000040 intersection_of: has_part PR:000000001 ! protein relationship: has_part PR:000000001 ! protein @@ -153448,7 +155401,7 @@ intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus id: PR:O54707 name: natural killer cells antigen CD94 (mouse) namespace: protein -def: "A killer cell lectin-like receptor subfamily D member 1 that is encoded in the genome of mouse." [OMA:O54707, PRO:DNx] +def: "A killer cell lectin-like receptor subfamily D member 1 that is encoded in the genome of mouse." [OMA:O54707, PANTHER:PTHR22800\:SF15, PRO:DNx] comment: Category=organism-gene. synonym: "Cd94" RELATED Gene-based [UniProtKB:O54707] synonym: "CD94 (mouse)" EXACT [UniProtKB:O54707] @@ -153544,7 +155497,7 @@ intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens id: PR:O88324 name: CD83 antigen (mouse) namespace: protein -def: "A CD83 molecule that is encoded in the genome of mouse." [OMA:O88324, PRO:DNx] +def: "A CD83 molecule that is encoded in the genome of mouse." [OMA:O88324, PANTHER:PTHR15193\:SF0, PRO:DNx] comment: Category=organism-gene. synonym: "Cd83" RELATED Gene-based [UniProtKB:O88324] synonym: "CD83 (mouse)" EXACT [UniProtKB:O88324] @@ -153617,6 +155570,21 @@ is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000002037 ! complement component C1q receptor intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus +[Term] +id: PR:O95343 +name: homeobox protein SIX3 (human) +namespace: protein +def: "A homeobox protein SIX3 that is encoded in the genome of human." [PRO:DNx, UniProtKB:O95343] +comment: Category=organism-gene. +synonym: "hSIX3" EXACT PRO-short-label [PRO:DNx] +synonym: "sine oculis homeobox homolog 3 (human)" EXACT [UniProtKB:O95343] +synonym: "SIX3" RELATED Gene-based [UniProtKB:O95343] +xref: UniProtKB:O95343 +is_a: PR:000014898 ! homeobox protein SIX3 +is_a: PR:000029067 ! Homo sapiens protein +intersection_of: PR:000014898 ! homeobox protein SIX3 +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens + [Term] id: PR:O95936 name: eomesodermin homolog (human) @@ -153629,7 +155597,6 @@ synonym: "T-box brain protein 2 (human)" EXACT [UniProtKB:O95936] synonym: "T-brain-2 (human)" EXACT [UniProtKB:O95936] synonym: "TBR-2 (human)" EXACT [UniProtKB:O95936] synonym: "TBR2" RELATED Gene-based [UniProtKB:O95936] -xref: Reactome:R-HSA-452232 "PR:O95936 located_in GO:0005654" xref: UniProtKB:O95936 is_a: PR:000003463 ! eomesodermin is_a: PR:000029067 ! Homo sapiens protein @@ -154169,6 +156136,28 @@ is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000010543 ! myeloperoxidase intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens +[Term] +id: PR:P05230 +name: fibroblast growth factor 1 (human) +namespace: protein +def: "A fibroblast growth factor 1 that is encoded in the genome of human." [PRO:DNx, UniProtKB:P05230] +comment: Category=organism-gene. +synonym: "acidic fibroblast growth factor (human)" EXACT [UniProtKB:P05230] +synonym: "aFGF (human)" EXACT [UniProtKB:P05230] +synonym: "ECGF (human)" EXACT [UniProtKB:P05230] +synonym: "endothelial cell growth factor (human)" EXACT [UniProtKB:P05230] +synonym: "FGF-1 (human)" EXACT [UniProtKB:P05230] +synonym: "FGF1" RELATED Gene-based [UniProtKB:P05230] +synonym: "FGFA" RELATED Gene-based [UniProtKB:P05230] +synonym: "HBGF-1 (human)" EXACT [UniProtKB:P05230] +synonym: "heparin-binding growth factor 1 (human)" EXACT [UniProtKB:P05230] +synonym: "hFGF1" EXACT PRO-short-label [PRO:DNx] +xref: UniProtKB:P05230 +is_a: PR:000007479 ! fibroblast growth factor 1 +is_a: PR:000029067 ! Homo sapiens protein +intersection_of: PR:000007479 ! fibroblast growth factor 1 +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens + [Term] id: PR:P05532 name: mast/stem cell growth factor receptor Kit (mouse) @@ -154734,6 +156723,26 @@ is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001083 ! CD2 molecule intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus +[Term] +id: PR:P09038 +name: fibroblast growth factor 2 (human) +namespace: protein +def: "A fibroblast growth factor 2 that is encoded in the genome of human." [PRO:DNx, UniProtKB:P09038] +comment: Category=organism-gene. +synonym: "basic fibroblast growth factor (human)" EXACT [UniProtKB:P09038] +synonym: "bFGF (human)" EXACT [UniProtKB:P09038] +synonym: "FGF-2 (human)" EXACT [UniProtKB:P09038] +synonym: "FGF2" RELATED Gene-based [UniProtKB:P09038] +synonym: "FGFB" RELATED Gene-based [UniProtKB:P09038] +synonym: "HBGF-2 (human)" EXACT [UniProtKB:P09038] +synonym: "heparin-binding growth factor 2 (human)" EXACT [UniProtKB:P09038] +synonym: "hFGF2" EXACT PRO-short-label [PRO:DNx] +xref: UniProtKB:P09038 +is_a: PR:000007489 ! fibroblast growth factor 2 +is_a: PR:000029067 ! Homo sapiens protein +intersection_of: PR:000007489 ! fibroblast growth factor 2 +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens + [Term] id: PR:P09240 name: cholecystokinin (mouse) @@ -155370,6 +157379,24 @@ is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001858 ! immunoglobulin iota chain intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens +[Term] +id: PR:P12272 +name: parathyroid hormone-related protein (human) +namespace: protein +def: "A parathyroid hormone-related protein that is encoded in the genome of human." [PRO:DNx, UniProtKB:P12272] +comment: Category=organism-gene. +synonym: "hPTHLH" EXACT PRO-short-label [PRO:DNx] +synonym: "parathyroid hormone-like protein (human)" EXACT [UniProtKB:P12272] +synonym: "PLP (human)" BROAD [UniProtKB:P12272] +synonym: "PTH-rP (human)" EXACT [UniProtKB:P12272] +synonym: "PTHLH" RELATED Gene-based [UniProtKB:P12272] +synonym: "PTHRP" RELATED Gene-based [UniProtKB:P12272] +xref: UniProtKB:P12272 +is_a: PR:000013433 ! parathyroid hormone-related protein +is_a: PR:000029067 ! Homo sapiens protein +intersection_of: PR:000013433 ! parathyroid hormone-related protein +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens + [Term] id: PR:P12314 name: high affinity immunoglobulin gamma Fc receptor I (human) @@ -155777,6 +157804,26 @@ is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001002 ! CD19 molecule intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens +[Term] +id: PR:P15655 +name: fibroblast growth factor 2 (mouse) +namespace: protein +def: "A fibroblast growth factor 2 that is encoded in the genome of mouse." [OMA:P15655, PRO:DNx] +comment: Category=organism-gene. +synonym: "basic fibroblast growth factor (mouse)" EXACT [UniProtKB:P15655] +synonym: "bFGF (mouse)" EXACT [UniProtKB:P15655] +synonym: "Fgf-2" RELATED Gene-based [UniProtKB:P15655] +synonym: "FGF-2 (mouse)" EXACT [UniProtKB:P15655] +synonym: "Fgf2" RELATED Gene-based [UniProtKB:P15655] +synonym: "HBGF-2 (mouse)" EXACT [UniProtKB:P15655] +synonym: "heparin-binding growth factor 2 (mouse)" EXACT [UniProtKB:P15655] +synonym: "mFGF2" EXACT PRO-short-label [PRO:DNx] +xref: UniProtKB:P15655 +is_a: PR:000007489 ! fibroblast growth factor 2 +is_a: PR:000029032 ! Mus musculus protein +intersection_of: PR:000007489 ! fibroblast growth factor 2 +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus + [Term] id: PR:P15702 name: leukosialin (mouse) @@ -156722,6 +158769,25 @@ is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001020 ! CD3 epsilon intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus +[Term] +id: PR:P22858 +name: parathyroid hormone-related protein (mouse) +namespace: protein +def: "A parathyroid hormone-related protein that is encoded in the genome of mouse." [OMA:P22858, PRO:DNx] +comment: Category=organism-gene. +synonym: "mPTHLH" EXACT PRO-short-label [PRO:DNx] +synonym: "parathyroid hormone-like protein (mouse)" EXACT [UniProtKB:P22858] +synonym: "PLP (mouse)" RELATED [UniProtKB:P22858] +synonym: "PTH-rP (mouse)" EXACT [UniProtKB:P22858] +synonym: "Pthlh" RELATED Gene-based [UniProtKB:P22858] +synonym: "Pthrp" RELATED Gene-based [UniProtKB:P22858] +synonym: "PTHrP (mouse)" EXACT [UniProtKB:P22858] +xref: UniProtKB:P22858 +is_a: PR:000013433 ! parathyroid hormone-related protein +is_a: PR:000029032 ! Mus musculus protein +intersection_of: PR:000013433 ! parathyroid hormone-related protein +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus + [Term] id: PR:P22897 name: macrophage mannose receptor 1 (human) @@ -157140,7 +159206,7 @@ synonym: "2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferas synonym: "2'-phospho-cyclic-ADP-ribose transferase (human)" EXACT [UniProtKB:P28907] synonym: "ADP-ribosyl cyclase 1 (human)" EXACT [] synonym: "ADPRC 1 (human)" EXACT [UniProtKB:P28907] -synonym: "cADPR hydrolase 1 (human)" EXACT [UniProtKB:P28907] +synonym: "cADPr hydrolase 1 (human)" EXACT [UniProtKB:P28907] synonym: "CD38" RELATED Gene-based [UniProtKB:P28907] synonym: "cyclic ADP-ribose hydrolase 1 (human)" EXACT [UniProtKB:P28907] synonym: "hCD38" EXACT PRO-short-label [PRO:DNx] @@ -158491,7 +160557,7 @@ synonym: "2'-phospho-ADP-ribosyl cyclase/2'-phospho-cyclic-ADP-ribose transferas synonym: "2'-phospho-cyclic-ADP-ribose transferase (mouse)" EXACT [UniProtKB:P56528] synonym: "ADP-ribosyl cyclase 1 (mouse)" EXACT [UniProtKB:P56528] synonym: "ADPRC 1 (mouse)" EXACT [UniProtKB:P56528] -synonym: "cADPR hydrolase 1 (mouse)" EXACT [UniProtKB:P56528] +synonym: "cADPr hydrolase 1 (mouse)" EXACT [UniProtKB:P56528] synonym: "Cd38" RELATED Gene-based [UniProtKB:P56528] synonym: "CD38 (mouse)" EXACT [UniProtKB:P56528] synonym: "cyclic ADP-ribose hydrolase 1 (mouse)" EXACT [UniProtKB:P56528] @@ -158504,6 +160570,21 @@ is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001408 ! ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1 intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus +[Term] +id: PR:P58462 +name: forkhead box protein P1 (mouse) +namespace: protein +def: "A forkhead box protein P1 that is encoded in the genome of mouse." [OMA:P58462, PRO:DNx] +comment: Category=organism-gene. +synonym: "forkhead-related transcription factor 1 (mouse)" RELATED [UniProtKB:P58462] +synonym: "Foxp1" RELATED Gene-based [UniProtKB:P58462] +synonym: "mFOXP1" EXACT PRO-short-label [PRO:DNx] +xref: UniProtKB:P58462 +is_a: PR:000007643 ! forkhead box protein P1 +is_a: PR:000029032 ! Mus musculus protein +intersection_of: PR:000007643 ! forkhead box protein P1 +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus + [Term] id: PR:P59901 name: leukocyte immunoglobulin-like receptor subfamily A member 4 (human) @@ -158569,6 +160650,27 @@ is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001208 ! C-X-C chemokine receptor type 4 intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens +[Term] +id: PR:P61148 +name: fibroblast growth factor 1 (mouse) +namespace: protein +def: "A fibroblast growth factor 1 that is encoded in the genome of mouse." [OMA:P61148, PRO:DNx] +comment: Category=organism-gene. +synonym: "acidic fibroblast growth factor (mouse)" EXACT [UniProtKB:P61148] +synonym: "aFGF (mouse)" EXACT [UniProtKB:P61148] +synonym: "Fgf-1" RELATED Gene-based [UniProtKB:P61148] +synonym: "FGF-1 (mouse)" EXACT [UniProtKB:P61148] +synonym: "Fgf1" RELATED Gene-based [UniProtKB:P61148] +synonym: "Fgfa" RELATED Gene-based [UniProtKB:P61148] +synonym: "HBGF-1 (mouse)" EXACT [UniProtKB:P61148] +synonym: "heparin-binding growth factor 1 (mouse)" EXACT [UniProtKB:P61148] +synonym: "mFGF1" EXACT PRO-short-label [PRO:DNx] +xref: UniProtKB:P61148 +is_a: PR:000007479 ! fibroblast growth factor 1 +is_a: PR:000029032 ! Mus musculus protein +intersection_of: PR:000007479 ! fibroblast growth factor 1 +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus + [Term] id: PR:P61168 name: D(2) dopamine receptor (mouse) @@ -158679,6 +160781,23 @@ is_a: PR:000029562 ! iroquois-class homeodomain protein IRX-6 intersection_of: PR:000029562 ! iroquois-class homeodomain protein IRX-6 intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens +[Term] +id: PR:P78424 +name: POU domain, class 6, transcription factor 2 (human) +namespace: protein +def: "A POU domain, class 6, transcription factor 2 that is encoded in the genome of human." [PRO:DNx, UniProtKB:P78424] +comment: Category=organism-gene. +synonym: "hPOU6F2" EXACT PRO-short-label [PRO:DNx] +synonym: "POU6F2" RELATED Gene-based [UniProtKB:P78424] +synonym: "retina-derived POU domain factor 1 (human)" EXACT [UniProtKB:P78424] +synonym: "RPF-1 (human)" EXACT [UniProtKB:P78424] +synonym: "RPF1" RELATED Gene-based [UniProtKB:P78424] +xref: UniProtKB:P78424 +is_a: PR:000013047 ! POU domain, class 6, transcription factor 2 +is_a: PR:000029067 ! Homo sapiens protein +intersection_of: PR:000013047 ! POU domain, class 6, transcription factor 2 +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens + [Term] id: PR:P78509 name: reelin (human) @@ -159828,6 +161947,21 @@ is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001931 ! sialoadhesin intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus +[Term] +id: PR:Q62233 +name: homeobox protein SIX3 (mouse) +namespace: protein +def: "A homeobox protein SIX3 that is encoded in the genome of mouse." [OMA:Q62233, PRO:DNx] +comment: Category=organism-gene. +synonym: "mSIX3" EXACT PRO-short-label [PRO:DNx] +synonym: "sine oculis homeobox homolog 3 (mouse)" EXACT [UniProtKB:Q62233] +synonym: "Six3" RELATED Gene-based [UniProtKB:Q62233] +xref: UniProtKB:Q62233 +is_a: PR:000014898 ! homeobox protein SIX3 +is_a: PR:000029032 ! Mus musculus protein +intersection_of: PR:000014898 ! homeobox protein SIX3 +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus + [Term] id: PR:Q62351 name: transferrin receptor protein 1 (mouse) @@ -160085,6 +162219,20 @@ is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001925 ! scavenger receptor cysteine-rich type 1 protein M130 intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens +[Term] +id: PR:Q8BJI4 +name: POU domain, class 6, transcription factor 2 (mouse) +namespace: protein +def: "A POU domain, class 6, transcription factor 2 that is encoded in the genome of mouse." [PRO:DNx] +comment: Category=organism-gene. +synonym: "mPOU6F2" EXACT PRO-short-label [PRO:DNx] +synonym: "Pou6f2" RELATED Gene-based [UniProtKB:Q8BJI4] +xref: UniProtKB:Q8BJI4 +is_a: PR:000013047 ! POU domain, class 6, transcription factor 2 +is_a: PR:000029032 ! Mus musculus protein +intersection_of: PR:000013047 ! POU domain, class 6, transcription factor 2 +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus + [Term] id: PR:Q8C567 name: natural cytotoxicity triggering receptor 1 (mouse) @@ -160241,6 +162389,21 @@ is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001293 ! C-type lectin domain family 4 member K intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus +[Term] +id: PR:Q8VCC9 +name: spondin-1 (mouse) +namespace: protein +def: "A spondin-1 that is encoded in the genome of mouse." [OMA:Q8VCC9, PRO:DNx] +comment: Category=organism-gene. +synonym: "F-spondin (mouse)" EXACT [UniProtKB:Q8VCC9] +synonym: "mSPON1" EXACT PRO-short-label [PRO:DNx] +synonym: "Spon1" RELATED Gene-based [UniProtKB:Q8VCC9] +xref: UniProtKB:Q8VCC9 +is_a: PR:000015557 ! spondin-1 +is_a: PR:000029032 ! Mus musculus protein +intersection_of: PR:000015557 ! spondin-1 +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus + [Term] id: PR:Q8WTT0 name: C-type lectin domain family 4 member C (human) @@ -160346,6 +162509,27 @@ is_a: PR:000029032 ! Mus musculus protein intersection_of: PR:000001350 ! forkhead box protein P3 intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus +[Term] +id: PR:Q99PV8 +name: B-cell lymphoma/leukemia 11B (mouse) +namespace: protein +def: "A B-cell lymphoma/leukemia 11B that is encoded in the genome of mouse." [OMA:Q99PV8, PRO:DNx] +comment: Category=organism-gene. +synonym: "B-cell CLL/lymphoma 11B (mouse)" EXACT [UniProtKB:Q99PV8] +synonym: "BCL-11B (mouse)" EXACT [UniProtKB:Q99PV8] +synonym: "Bcl11b" RELATED Gene-based [UniProtKB:Q99PV8] +synonym: "COUP-TF-interacting protein 2 (mouse)" EXACT [UniProtKB:Q99PV8] +synonym: "Ctip2" RELATED Gene-based [UniProtKB:Q99PV8] +synonym: "mBCL11B" EXACT PRO-short-label [PRO:DNx] +synonym: "mRit1" EXACT [UniProtKB:Q99PV8] +synonym: "radiation-induced tumor suppressor gene 1 protein (mouse)" EXACT [UniProtKB:Q99PV8] +synonym: "Rit1" RELATED Gene-based [UniProtKB:Q99PV8] +xref: UniProtKB:Q99PV8 +is_a: PR:000004691 ! B-cell lymphoma/leukemia 11B +is_a: PR:000029032 ! Mus musculus protein +intersection_of: PR:000004691 ! B-cell lymphoma/leukemia 11B +intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus + [Term] id: PR:Q9BXN2 name: C-type lectin domain family 7 member A (human) @@ -160430,6 +162614,27 @@ is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001931 ! sialoadhesin intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens +[Term] +id: PR:Q9C0K0 +name: B-cell lymphoma/leukemia 11B (human) +namespace: protein +def: "A B-cell lymphoma/leukemia 11B that is encoded in the genome of human." [PRO:DNx, UniProtKB:Q9C0K0] +comment: Category=organism-gene. +synonym: "B-cell CLL/lymphoma 11B (human)" EXACT [UniProtKB:Q9C0K0] +synonym: "BCL-11B (human)" EXACT [UniProtKB:Q9C0K0] +synonym: "BCL11B" RELATED Gene-based [UniProtKB:Q9C0K0] +synonym: "COUP-TF-interacting protein 2 (human)" EXACT [UniProtKB:Q9C0K0] +synonym: "CTIP2" RELATED Gene-based [UniProtKB:Q9C0K0] +synonym: "hBCL11B" EXACT PRO-short-label [PRO:DNx] +synonym: "hRit1" EXACT [UniProtKB:Q9C0K0] +synonym: "radiation-induced tumor suppressor gene 1 protein (human)" EXACT [UniProtKB:Q9C0K0] +synonym: "RIT1" RELATED Gene-based [UniProtKB:Q9C0K0] +xref: UniProtKB:Q9C0K0 +is_a: PR:000004691 ! B-cell lymphoma/leukemia 11B +is_a: PR:000029067 ! Homo sapiens protein +intersection_of: PR:000004691 ! B-cell lymphoma/leukemia 11B +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens + [Term] id: PR:Q9CXM0 name: chondrolectin (mouse) @@ -160481,6 +162686,23 @@ is_a: PR:000029562 ! iroquois-class homeodomain protein IRX-6 intersection_of: PR:000029562 ! iroquois-class homeodomain protein IRX-6 intersection_of: RO:0002160 NCBITaxon:10090 ! only in taxon Mus musculus +[Term] +id: PR:Q9H334 +name: forkhead box protein P1 (human) +namespace: protein +def: "A forkhead box protein P1 that is encoded in the genome of human." [PRO:DNx, UniProtKB:Q9H334] +comment: Category=organism-gene. +synonym: "FOXP1" RELATED Gene-based [UniProtKB:Q9H334] +synonym: "hFOXP1" EXACT PRO-short-label [PRO:DNx] +synonym: "HSPC215" RELATED Gene-based [UniProtKB:Q9H334] +synonym: "Mac-1-regulated forkhead (human)" EXACT [UniProtKB:Q9H334] +synonym: "MFH (human)" EXACT [UniProtKB:Q9H334] +xref: UniProtKB:Q9H334 +is_a: PR:000007643 ! forkhead box protein P1 +is_a: PR:000029067 ! Homo sapiens protein +intersection_of: PR:000007643 ! forkhead box protein P1 +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens + [Term] id: PR:Q9H9P2 name: chondrolectin (human) @@ -160518,6 +162740,24 @@ is_a: PR:000029067 ! Homo sapiens protein intersection_of: PR:000001666 ! relaxin receptor 1 intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens +[Term] +id: PR:Q9HCB6 +name: spondin-1 (human) +namespace: protein +def: "A spondin-1 that is encoded in the genome of human." [PRO:DNx, UniProtKB:Q9HCB6] +comment: Category=organism-gene. +synonym: "F-spondin (human)" EXACT [UniProtKB:Q9HCB6] +synonym: "hSPON1" EXACT PRO-short-label [PRO:DNx] +synonym: "KIAA0762" RELATED Gene-based [UniProtKB:Q9HCB6] +synonym: "SPON1" RELATED Gene-based [UniProtKB:Q9HCB6] +synonym: "vascular smooth muscle cell growth-promoting factor (human)" EXACT [UniProtKB:Q9HCB6] +synonym: "VSGP" RELATED Gene-based [UniProtKB:Q9HCB6] +xref: UniProtKB:Q9HCB6 +is_a: PR:000015557 ! spondin-1 +is_a: PR:000029067 ! Homo sapiens protein +intersection_of: PR:000015557 ! spondin-1 +intersection_of: RO:0002160 NCBITaxon:9606 ! only in taxon Homo sapiens + [Term] id: PR:Q9JIP3 name: interleukin-17 receptor B (mouse) @@ -161142,7 +163382,7 @@ intersection_of: part_of UBERON:0005725 ! olfactory system intersection_of: RO:0002176 UBERON:0001707 ! connects nasal cavity relationship: part_of UBERON:0000033 {source="ZFA"} ! head relationship: part_of UBERON:0005725 ! olfactory system -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002176 UBERON:0001707 ! connects nasal cavity [Term] @@ -161187,7 +163427,7 @@ is_a: UBERON:0004121 ! ectoderm-derived structure relationship: capable_of_part_of GO:0007608 ! sensory perception of smell relationship: part_of UBERON:0001004 {gci_relation="part_of", gci_filler="NCBITaxon:32523", source="PMID:25312359"} ! respiratory system relationship: part_of UBERON:0001456 {source="FMA", source="ZFA-def"} ! face -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002202 UBERON:0003050 {source="ZFA"} ! develops from olfactory placode relationship: RO:0002433 UBERON:0001004 ! contributes to morphology of respiratory system relationship: RO:0002433 UBERON:0001456 ! contributes to morphology of face @@ -161308,7 +163548,7 @@ relationship: has_part CL:0000440 {source="ZFA"} ! melanocyte stimulating hormon relationship: has_part CL:0000642 {source="ZFA"} ! folliculostellate cell relationship: has_part UBERON:0002196 ! adenohypophysis relationship: has_part UBERON:0002198 ! neurohypophysis -relationship: RO:0002160 NCBITaxon:7742 {source="PMID:19084529"} ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 {source="PMID:19084529"} ! in taxon Vertebrata relationship: RO:0002433 UBERON:0001894 ! contributes to morphology of diencephalon relationship: RO:0002495 UBERON:0034875 {source="https://orcid.org/0000-0003-3308-6245"} ! immediate transformation of future pituitary gland property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/97/Gray1180.png" xsd:anyURI @@ -161336,7 +163576,7 @@ xref: UMLS:C0225344 {source="ncithesaurus:Submucosa"} xref: Wikipedia:Submucosa is_a: UBERON:0004923 ! organ component layer relationship: BSPO:0001107 UBERON:0000344 ! mucosa -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002473 UBERON:0002384 ! composed primarily of connective tissue property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png" xsd:anyURI property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png" xsd:anyURI @@ -161513,6 +163753,7 @@ xref: MIAA:0000284 xref: SCTID:20795001 xref: VHOG:0000860 xref: Wikipedia:Skin +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0034944 {source="FMA"} ! zone of organ relationship: has_part UBERON:0001003 ! skin epidermis @@ -161641,7 +163882,7 @@ xref: Wikipedia:Compound_eye is_a: UBERON:0015165 ! multi-unit eye intersection_of: UBERON:0000970 ! eye intersection_of: RO:0002473 UBERON:0000971 ! composed primarily of ommatidium -relationship: RO:0002160 NCBITaxon:6656 {source="PMID:21062451"} ! only in taxon Arthropoda +relationship: RO:0002162 NCBITaxon:6656 {source="PMID:21062451"} ! in taxon Arthropoda relationship: RO:0002473 UBERON:0000971 ! composed primarily of ommatidium property_value: seeAlso "https://github.com/obophenotype/uberon/issues/457" xsd:anyURI @@ -161788,7 +164029,7 @@ xref: VSAO:0000075 xref: Wikipedia:Appendage xref: XAO:0000218 is_a: UBERON:0000475 ! organism subdivision -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0000029 @@ -161929,7 +164170,7 @@ xref: XAO:0003024 xref: ZFA:0001114 is_a: UBERON:0011676 ! subdivision of organism along main body axis relationship: part_of UBERON:0007811 ! craniocervical region -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria relationship: RO:0002551 UBERON:0003129 {gci_relation="part_of", gci_filler="NCBITaxon:7776"} ! has skeleton skull [Term] @@ -161951,6 +164192,7 @@ xref: EMAPA:35631 xref: FMA:18634 xref: MA:0002907 xref: SCTID:258665002 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0001305 ! ovarian follicle intersection_of: UBERON:0001305 ! ovarian follicle intersection_of: has_component UBERON:0005170 {cardinality="1"} ! granulosa cell layer @@ -161977,6 +164219,7 @@ synonym: "secondary follicle of ovary" EXACT [] xref: EMAPA:35632 xref: FMA:18637 xref: MA:0002908 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0001305 ! ovarian follicle intersection_of: UBERON:0001305 ! ovarian follicle intersection_of: has_component UBERON:0005170 {minCardinality="2"} ! granulosa cell layer @@ -162012,6 +164255,7 @@ xref: MA:0002909 xref: NCIT:C32692 xref: SCTID:362261008 xref: UMLS:C0600225 {source="ncithesaurus:Graafian_Follicle"} +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0001305 ! ovarian follicle intersection_of: UBERON:0001305 ! ovarian follicle intersection_of: has_component UBERON:0005170 {minCardinality="2"} ! granulosa cell layer @@ -162096,6 +164340,7 @@ xref: TAO:0005425 xref: UMLS:C0036760 {source="ncithesaurus:Serosa"} xref: Wikipedia:Serous_membrane xref: ZFA:0005425 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004120 ! mesoderm-derived structure relationship: has_part UBERON:0001136 ! mesothelium @@ -162135,7 +164380,7 @@ xref: ZFA:0005647 is_a: UBERON:0007846 {source="VSAO"} ! dense regular connective tissue relationship: has_part CL:0000327 {source="AEO"} ! extracellular matrix secreting cell relationship: part_of UBERON:0002204 {source="OG"} ! musculoskeletal system -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002176 UBERON:0001474 ! connects bone element relationship: RO:0002176 UBERON:0001630 ! connects muscle organ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg" xsd:anyURI @@ -162337,6 +164582,7 @@ id: UBERON:0000054 name: macula namespace: uberon def: "Thickened areas of the saccule or utricle where the termination of the vestibular nerve occurs[MESH,modified]." [MESH:A09.246.631.909.625.125] +subset: human_reference_atlas subset: pheno_slim subset: uberon_slim synonym: "acoustic macula" RELATED [MESH:A09.246.631.909.625.125] @@ -162353,6 +164599,7 @@ is_a: UBERON:0000479 ! tissue is_a: UBERON:0004121 ! ectoderm-derived structure relationship: has_part GO:0070451 ! cell hair relationship: part_of UBERON:0001846 ! internal ear +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000055 @@ -162473,6 +164720,7 @@ xref: UMLS:C0687028 {source="ncithesaurus:Duct"} xref: Wikipedia:Duct_(anatomy) xref: XAO:0004000 xref: ZFA:0005171 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000063 ! organ subunit relationship: has_part UBERON:0034969 ! epithelial layer of duct relationship: RO:0000086 PATO:0002299 ! has quality tubular @@ -162511,7 +164759,7 @@ is_a: UBERON:0004921 {source="cjm"} ! subdivision of digestive tract is_a: UBERON:0013765 ! digestive system element relationship: part_of UBERON:0000160 ! intestine relationship: part_of UBERON:0004907 ! lower digestive tract -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002433 UBERON:0000160 ! contributes to morphology of intestine property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/large-intestine-female/v1.3/assets/3d-sbu-f-large-intestine.glb" xsd:anyURI property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/large-intestine-male/v1.3/assets/3d-sbu-m-large-intestine.glb" xsd:anyURI @@ -162872,7 +165120,7 @@ xref: SCTID:118966000 xref: UMLS:C1519343 {source="ncithesaurus:Skeletal_System_Part"} is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision relationship: part_of UBERON:0001434 ! skeletal system -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002473 UBERON:0004765 ! composed primarily of skeletal element [Term] @@ -163282,6 +165530,7 @@ def: "Nonparenchymatous organ that primarily consists of dense connective tissue synonym: "membrane" BROAD [] synonym: "membrane of organ" EXACT [] xref: FMA:7145 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000062 ! organ relationship: RO:0002473 UBERON:0011823 {source="FMA-def"} ! composed primarily of dense connective tissue property_value: terms:contributor https://orcid.org/0000-0002-6601-2165 @@ -163510,7 +165759,7 @@ is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000108 {source="BILS"} ! blastula stage relationship: RO:0002082 GO:0007369 ! simultaneous with gastrulation -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0000110 @@ -163527,7 +165776,7 @@ is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000109 ! gastrula stage relationship: RO:0002082 GO:0001841 ! simultaneous with neural tube formation -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: seeAlso "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/343" xsd:anyURI @@ -163549,7 +165798,7 @@ is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000110 {gci_relation="part_of", gci_filler="NCBITaxon:32523"} ! neurula stage relationship: RO:0002082 GO:0048513 ! simultaneous with animal organ development -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: seeAlso "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/533" xsd:anyURI @@ -163656,6 +165905,7 @@ synonym: "segment of tracheobronchial tree" NARROW [FMA:12224] synonym: "tracheobronchial tree segment" NARROW [FMA:12224] xref: EMAPA:37946 {source="MA:th"} xref: FMA:12224 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000025 ! tube is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0000025 ! tube @@ -163793,7 +166043,7 @@ xref: NCIT:C13197 xref: NLX:28443 xref: Wikipedia:Nucleus_(neuroanatomy) is_a: UBERON:0011215 ! central nervous system cell part cluster -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002473 UBERON:0002020 ! composed primarily of gray matter [Term] @@ -163857,14 +166107,14 @@ namespace: uberon is_a: UBERON:0000475 ! organism subdivision disjoint_from: UBERON:0000154 {source="lexical"} ! posterior region of body relationship: BSPO:0000096 UBERON:0000154 ! posterior region of body -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria [Term] id: UBERON:0000154 name: posterior region of body namespace: uberon is_a: UBERON:0000475 ! organism subdivision -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria [Term] id: UBERON:0000155 @@ -164029,7 +166279,7 @@ xref: ZFA:0005781 is_a: UBERON:0013522 ! subdivision of tube relationship: part_of UBERON:0001555 {source="ZFA"} ! digestive tract relationship: part_of UBERON:0004122 {source="AAO"} ! genitourinary system -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata property_value: IAO:0000116 "adding df link to embryonic cloaca leads to a cycle in uberon-simple, as cloaca is a suberclass of embryonic cloaca" xsd:string [Term] @@ -164072,7 +166322,7 @@ xref: Wikipedia:Definitive_urogenital_sinus is_a: BFO:0000002 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0000163 {source="MP-def"} ! embryonic cloaca -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002202 UBERON:0003064 ! develops from intermediate mesoderm relationship: RO:0002433 UBERON:0000163 ! contributes to morphology of embryonic cloaca property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png" xsd:anyURI @@ -164135,7 +166385,7 @@ is_a: UBERON:0004921 ! subdivision of digestive tract intersection_of: UBERON:0004921 ! subdivision of digestive tract intersection_of: BSPO:0001106 UBERON:0001555 ! digestive tract relationship: BSPO:0001106 UBERON:0001555 ! digestive tract -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002202 UBERON:0035804 ! develops from future mouth property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/661" xsd:anyURI @@ -164280,7 +166530,7 @@ xref: UMLS:C0002638 {source="ncithesaurus:Amniotic_Fluid"} xref: VHOG:0001267 is_a: UBERON:0000463 ! organism substance relationship: RO:0001025 UBERON:0000305 ! located in amnion -relationship: RO:0002160 NCBITaxon:32524 ! only in taxon Amniota +relationship: RO:0002162 NCBITaxon:32524 ! in taxon Amniota relationship: RO:0002221 UBERON:0000922 ! surrounds embryo relationship: RO:0002328 GO:0001701 ! functionally related to in utero embryonic development @@ -164343,6 +166593,7 @@ xref: Wikipedia:Blood xref: XAO:0000124 xref: ZFA:0000007 is_a: BFO:0000002 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000179 ! haemolymphatic fluid relationship: has_part CL:0000232 {source="CL:tm"} ! erythrocyte relationship: has_part UBERON:0001969 ! blood plasma @@ -164363,7 +166614,7 @@ is_a: UBERON:0006314 ! bodily fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: part_of UBERON:0002193 ! hemolymphoid system relationship: part_of UBERON:0002193 ! hemolymphoid system -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: terms:contributor https://orcid.org/0000-0002-6601-2165 creation_date: 2009-04-08T04:38:19Z @@ -164393,7 +166644,7 @@ xref: Wikipedia:Gyrus is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0034768 ! morphological feature relationship: part_of UBERON:0000956 ! cerebral cortex -relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia +relationship: RO:0002162 NCBITaxon:40674 ! in taxon Mammalia relationship: RO:0002219 UBERON:0013118 ! surrounded by sulcus of brain property_value: seeAlso "https://github.com/obophenotype/uberon/issues/573" xsd:anyURI @@ -164538,7 +166789,7 @@ xref: XAO:0004031 xref: ZFA:0001675 is_a: UBERON:0000062 ! organ relationship: has_part UBERON:0002384 ! connective tissue -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/9/9a/Knee_diagram.svg" xsd:anyURI [Term] @@ -164611,6 +166862,7 @@ xref: SCTID:361885006 xref: UMLS:C0224856 {source="ncithesaurus:Tendon_Sheath"} xref: Wikipedia:Tendon_sheath is_a: BFO:0000002 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004923 ! organ component layer intersection_of: UBERON:0004923 ! organ component layer intersection_of: bounding_layer_of UBERON:0000043 ! tendon @@ -164641,11 +166893,12 @@ xref: SCTID:181457005 xref: UMLS:C0002630 {source="ncithesaurus:Amnion"} xref: VHOG:0000721 xref: Wikipedia:Amnion +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005631 ! extraembryonic membrane relationship: has_part UBERON:0003254 ! amniotic ectoderm relationship: has_part UBERON:0003262 ! amniotic mesoderm -relationship: RO:0002160 NCBITaxon:32524 {source="Hymans"} ! only in taxon Amniota +relationship: RO:0002162 NCBITaxon:32524 {source="Hymans"} ! in taxon Amniota relationship: RO:0002202 UBERON:0005971 {source="ISBN:0073040584"} ! develops from amniotic fold relationship: RO:0002221 UBERON:0000922 ! surrounds embryo relationship: RO:0002254 UBERON:0000924 {source="ISBN:0073040584-table5.4"} ! has developmental contribution from ectoderm @@ -165069,10 +167322,11 @@ xref: NCIT:C13166 xref: SCTID:361693009 xref: UMLS:C0026724 {source="ncithesaurus:Mucosa"} xref: Wikipedia:Mucous_membrane +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004923 ! organ component layer relationship: has_part UBERON:0000483 ! epithelium relationship: has_part UBERON:0002384 ! connective tissue -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/4/4e/Ens.png" xsd:anyURI property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/en/thumb/4/4e/Ens.png/200px-Ens.png" xsd:anyURI @@ -165205,7 +167459,7 @@ xref: Wikipedia:Parenchyma is_a: UBERON:0000064 ! organ part disjoint_from: UBERON:0003891 ! stroma relationship: capable_of GO:0032501 ! multicellular organismal process -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0000355 @@ -165259,7 +167513,7 @@ is_a: UBERON:0002050 ! embryonic structure relationship: has_part UBERON:0000087 ! inner cell mass relationship: has_part UBERON:0000088 ! trophoblast relationship: part_of UBERON:0000307 ! blastula -relationship: RO:0002160 NCBITaxon:32525 ! only in taxon Theria +relationship: RO:0002162 NCBITaxon:32525 ! in taxon Theria relationship: RO:0002202 UBERON:0000085 ! develops from morula relationship: RO:0002491 UBERON:0000108 ! existence starts and ends during blastula stage property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/7/72/Blastocyst_English.svg" xsd:anyURI @@ -165662,7 +167916,7 @@ is_a: UBERON:0011216 ! organ system subdivision intersection_of: UBERON:0011216 ! organ system subdivision intersection_of: RO:0002473 UBERON:0001015 ! composed primarily of musculature relationship: capable_of GO:0003012 ! muscle system process -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002473 UBERON:0001015 ! composed primarily of musculature property_value: IAO:0000116 "consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77" xsd:string property_value: RO:0002161 NCBITaxon:6040 @@ -165899,6 +168153,7 @@ xref: SCTID:181480002 xref: UMLS:C0036270 {source="ncithesaurus:Scalp"} xref: Wikipedia:Scalp is_a: BFO:0000002 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0034921 ! multi organ part structure relationship: has_part UBERON:0000014 ! zone of skin relationship: has_part UBERON:0002384 ! connective tissue @@ -165996,6 +168251,7 @@ id: UBERON:0000412 name: dermal papilla namespace: uberon def: "A mesodermal signaling center of the hair follicle consisting of closely packed specialized mesenchymal fibroblasts. Framed by the enlarged bulb matrix in anagen." [DOI:10.1016/j.cub.2008.12.005] +subset: human_reference_atlas subset: pheno_slim synonym: "dermal papilla cell" RELATED [BTO:0001858] synonym: "dermal papillae" EXACT OMO:0003004 [] @@ -166023,6 +168279,7 @@ relationship: part_of UBERON:0001992 ! papillary layer of dermis relationship: RO:0002473 CL:0000057 ! composed primarily of fibroblast property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/34/Skin.jpg" xsd:anyURI property_value: IAO:0000116 "consider adding grouping class for TAO:0001995 ! papilla" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0000414 @@ -166208,6 +168465,7 @@ synonym: "trabecula arachnoideum" RELATED OMO:0003011 [] xref: BTO:0002500 xref: FMA:83979 xref: Wikipedia:Arachnoid_trabeculae +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000440 ! trabecula is_a: UBERON:0010313 ! neural crest-derived structure intersection_of: UBERON:0000440 ! trabecula @@ -166400,6 +168658,7 @@ xref: FMA:86485 xref: NCIT:C12309 xref: SCTID:264460007 xref: UMLS:C0227837 {source="ncithesaurus:Endocervix"} +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000064 ! organ part is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0000064 ! organ part @@ -167007,6 +169266,7 @@ xref: VHOG:0000387 xref: Wikipedia:Epithelium xref: XAO:0003045 xref: ZFA:0001486 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: RO:0002473 CL:0000066 ! composed primarily of epithelial cell @@ -167014,7 +169274,7 @@ union_of: UBERON:0000486 ! multilaminar epithelium union_of: UBERON:0000490 ! unilaminar epithelium relationship: has_part GO:0005911 ! cell-cell junction relationship: has_part UBERON:0005769 ! basement membrane of epithelium -relationship: RO:0002160 NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! in taxon Metazoa relationship: RO:0002473 CL:0000066 ! composed primarily of epithelial cell property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI @@ -167236,7 +169496,7 @@ xref: NCIT:C120839 xref: Wikipedia:Interstitial_fluid is_a: UBERON:0000463 ! organism substance relationship: part_of UBERON:0000479 ! tissue -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002221 CL:0000000 ! surrounds cell [Term] @@ -167289,7 +169549,7 @@ xref: SCTID:302553009 xref: Wikipedia:Abdomen is_a: UBERON:0009569 ! subdivision of trunk relationship: part_of UBERON:0002417 {source="MA"} ! abdominal segment of trunk -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata property_value: IAO:0000116 "Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class" xsd:string [Term] @@ -167370,7 +169630,7 @@ xref: Wikipedia:Germ_layer xref: XAO:0003011 xref: ZFA:0001122 is_a: UBERON:0010316 ! germ layer / neural crest -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0000924 @@ -167524,7 +169784,7 @@ xref: ZFA:0001290 is_a: UBERON:0013522 ! subdivision of tube relationship: part_of UBERON:0000924 ! ectoderm relationship: part_of UBERON:0035804 ! future mouth -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI property_value: IAO:0000116 "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" xsd:string @@ -167554,7 +169814,7 @@ is_a: BFO:0000002 is_a: UBERON:0016566 {source="EHDAA2"} ! pit relationship: part_of UBERON:0007026 ! presumptive gut relationship: RO:0001025 UBERON:0012469 {source="EHDAA2"} ! located in external anal region -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002202 UBERON:0000924 ! develops from ectoderm relationship: RO:0002387 UBERON:0001353 ! has potential to develop into anal region property_value: IAO:0000116 "removed WBbt:0006795 'proctodeum' - junction between the alimentary and genital tracts in the male." xsd:string @@ -167612,7 +169872,7 @@ xref: MIAA:0000064 xref: Wikipedia:Imaginal_disc is_a: UBERON:0000481 {source="FBbt text definition"} ! multi-tissue structure relationship: part_of UBERON:0002548 ! larva -relationship: RO:0002160 NCBITaxon:50557 {source="Wikipedia"} ! only in taxon Insecta +relationship: RO:0002162 NCBITaxon:50557 {source="Wikipedia"} ! in taxon Insecta [Term] id: UBERON:0000941 @@ -167718,7 +169978,7 @@ is_a: UBERON:0004921 {source="cjm"} ! subdivision of digestive tract is_a: UBERON:0010039 {source="cjm"} ! food storage organ relationship: capable_of GO:0001696 ! gastric acid secretion relationship: part_of UBERON:0001041 ! foregut -relationship: RO:0002160 NCBITaxon:7776 ! only in taxon Gnathostomata +relationship: RO:0002162 NCBITaxon:7776 ! in taxon Gnathostomata relationship: RO:0002433 UBERON:0001007 ! contributes to morphology of digestive system property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/e/e0/Stomach_diagram.svg" xsd:anyURI property_value: RO:0002161 NCBITaxon:7864 {source="Wikipedia"} @@ -167858,7 +170118,7 @@ intersection_of: UBERON:0007100 ! primary circulatory organ intersection_of: has_part UBERON:0004151 ! cardiac chamber relationship: has_part UBERON:0004151 ! cardiac chamber relationship: part_of UBERON:0015410 {source="MA"} ! heart plus pericardium -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002202 UBERON:0004141 ! develops from heart tube relationship: RO:0002433 UBERON:0004535 ! contributes to morphology of cardiovascular system property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/heart-female/v1.3/assets/3d-vh-f-heart.glb" xsd:anyURI @@ -167916,7 +170176,7 @@ disjoint_from: UBERON:0002416 ! integumental system disjoint_from: UBERON:0002423 ! hepatobiliary system disjoint_from: UBERON:0004456 ! entire sense organ system disjoint_from: UBERON:8450002 ! excretory system -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002473 UBERON:0002368 ! composed primarily of endocrine gland relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage @@ -168091,7 +170351,7 @@ synonym: "medulla" EXACT [FMA:61108] xref: FMA:61108 xref: galen:Medulla is_a: UBERON:0000471 ! compound organ component -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002219 UBERON:0001851 ! surrounded by cortex [Term] @@ -168251,6 +170511,7 @@ xref: VHOG:0000164 xref: Wikipedia:Cornea xref: XAO:0000180 xref: ZFA:0000640 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0010000 ! multicellular anatomical structure is_a: UBERON:0010313 ! neural crest-derived structure relationship: has_part UBERON:0001772 ! corneal epithelium @@ -168479,7 +170740,7 @@ xref: Wikipedia:Sternum is_a: UBERON:0005181 ! thoracic segment organ is_a: UBERON:0010363 {source="ISBN:0073040584"} ! endochondral element relationship: part_of UBERON:0003252 {source="FMA"} ! thoracic rib cage -relationship: RO:0002160 NCBITaxon:32523 {source="ISBN:0073040584"} ! only in taxon Tetrapoda +relationship: RO:0002162 NCBITaxon:32523 {source="ISBN:0073040584"} ! in taxon Tetrapoda relationship: RO:0002170 UBERON:0002228 ! connected to rib relationship: RO:0002170 UBERON:0007831 ! connected to pectoral girdle skeleton relationship: RO:0002170 UBERON:0008255 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to right clavicle @@ -168565,7 +170826,7 @@ relationship: has_part UBERON:0002400 ! parietal pleura relationship: has_part UBERON:0002401 ! visceral pleura relationship: part_of UBERON:0009778 {source="https://github.com/obophenotype/uberon/issues/86"} ! pleural sac relationship: RO:0000086 PATO:0001748 ! has quality invaginated -relationship: RO:0002160 NCBITaxon:32524 ! only in taxon Amniota +relationship: RO:0002162 NCBITaxon:32524 ! in taxon Amniota relationship: RO:0002202 UBERON:0003081 ! develops from lateral plate mesoderm relationship: RO:0002433 UBERON:0001004 ! contributes to morphology of respiratory system property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/ab/Gray965.png" xsd:anyURI @@ -168821,7 +171082,7 @@ xref: Wikipedia:Pons is_a: UBERON:0002616 ! regional part of brain relationship: part_of UBERON:0001895 {source="neuronames"} ! metencephalon relationship: part_of UBERON:0002298 ! brainstem -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002433 UBERON:0001895 ! contributes to morphology of metencephalon relationship: RO:0002433 UBERON:0002298 ! contributes to morphology of brainstem property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/36/Gray768.png" xsd:anyURI @@ -169042,7 +171303,7 @@ intersection_of: UBERON:0000991 ! gonad intersection_of: part_of UBERON:0000474 ! female reproductive system disjoint_from: UBERON:0009117 ! indifferent gonad relationship: BSPO:0000126 UBERON:0003975 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="FMA-abduced-lr"} ! internal female genitalia -relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa relationship: RO:0002202 UBERON:0009117 ! develops from indifferent gonad property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/d4/Gray589.png" xsd:anyURI property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png" xsd:anyURI @@ -169083,7 +171344,7 @@ xref: ZFA:0000560 is_a: UBERON:0000025 ! tube is_a: UBERON:0005156 ! reproductive structure relationship: part_of UBERON:0000474 ! female reproductive system -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002176 UBERON:0000992 ! connects ovary relationship: RO:0002176 UBERON:0013514 ! connects space surrounding organism @@ -169117,7 +171378,7 @@ xref: Wikipedia:Uterus is_a: BFO:0000002 is_a: UBERON:0013515 {source="cjm"} ! subdivision of oviduct relationship: part_of UBERON:0004175 ! internal genitalia -relationship: RO:0002160 NCBITaxon:32525 ! only in taxon Theria +relationship: RO:0002162 NCBITaxon:32525 ! in taxon Theria relationship: RO:0002495 UBERON:0005795 ! immediate transformation of embryonic uterus property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/6a/Female_reproductive_system_lateral_nolabel.png" xsd:anyURI property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/uterus-female/v1.2/assets/3d-vh-f-uterus.glb" xsd:anyURI @@ -169196,7 +171457,7 @@ xref: Wikipedia:Vulva is_a: UBERON:0000062 ! organ is_a: UBERON:0005156 ! reproductive structure relationship: part_of UBERON:0005056 ! external female genitalia -relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia +relationship: RO:0002162 NCBITaxon:40674 ! in taxon Mammalia property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/da/Female_unshaved_genitalia.jpg" xsd:anyURI [Term] @@ -169279,7 +171540,7 @@ relationship: channel_for UBERON:0010143 ! seminal vesicle fluid relationship: channels_from UBERON:0000998 ! seminal vesicle relationship: channels_from UBERON:0001000 ! vas deferens relationship: channels_into UBERON:0000057 ! urethra -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/prostate-male/v1.2/assets/3d-vh-m-prostate.glb" xsd:anyURI property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/3/35/Male_anatomy.png" xsd:anyURI @@ -169320,7 +171581,7 @@ relationship: channels_from UBERON:0001301 ! epididymis relationship: channels_into UBERON:0000999 ! ejaculatory duct relationship: part_of UBERON:0005352 {source="FMA"} ! spermatic cord relationship: part_of UBERON:0006947 ! male genital duct -relationship: RO:0002160 NCBITaxon:32524 ! only in taxon Amniota +relationship: RO:0002162 NCBITaxon:32524 ! in taxon Amniota relationship: RO:0002433 UBERON:0004054 ! contributes to morphology of internal male genitalia property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/d1/Male_anatomy_en.svg" xsd:anyURI @@ -169423,7 +171684,7 @@ disjoint_from: UBERON:0004456 ! entire sense organ system disjoint_from: UBERON:8450002 ! excretory system relationship: capable_of GO:0003016 ! respiratory system process relationship: capable_of GO:0007585 ! respiratory gaseous exchange by respiratory system -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/5e/Respiratory_system_complete_en.svg" xsd:anyURI property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/lung-female/v1.4/assets/3d-vh-f-lung.glb" xsd:anyURI @@ -169552,7 +171813,7 @@ is_a: UBERON:8450002 ! excretory system intersection_of: UBERON:8450002 ! excretory system intersection_of: capable_of GO:0097254 ! renal tubular secretion relationship: capable_of GO:0097254 ! renal tubular secretion -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage property_value: RO:0002161 NCBITaxon:110815 {source="Wikipedia"} property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} @@ -169584,7 +171845,7 @@ disjoint_from: UBERON:0002423 ! hepatobiliary system disjoint_from: UBERON:0004456 ! entire sense organ system disjoint_from: UBERON:8450002 ! excretory system relationship: capable_of GO:0003013 ! circulatory system process -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} @@ -169682,7 +171943,6 @@ namespace: uberon def: "The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]." [BIRNLEX:844, ISBN:0-14-051288-8, ISBN:3110148986, NLM:nervous+system, WB:rynl, Wikipedia:Nervous_system, ZFIN:curator] subset: cumbo subset: efo_slim -subset: human_reference_atlas subset: pheno_slim subset: uberon_slim subset: vertebrate_core @@ -169731,14 +171991,13 @@ disjoint_from: UBERON:0004456 ! entire sense organ system disjoint_from: UBERON:8450002 ! excretory system relationship: capable_of GO:0050877 ! nervous system process relationship: has_part CL:0000540 ! neuron -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002473 CL:0002319 ! composed primarily of neural cell relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage relationship: RO:0002495 UBERON:0016880 {source="Bgee:AN"} ! immediate transformation of future nervous system property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:6040 -property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001017 @@ -169785,7 +172044,7 @@ xref: ZFA:0000012 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0011216 {source="FBbt", source="cjm"} ! organ system subdivision relationship: part_of UBERON:0001016 ! nervous system -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria relationship: RO:0002495 UBERON:0016879 {source="Bgee:AN"} ! immediate transformation of future central nervous system property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} property_value: RO:0002175 NCBITaxon:9606 @@ -169987,7 +172246,7 @@ disjoint_from: UBERON:0002423 ! hepatobiliary system disjoint_from: UBERON:0004456 ! entire sense organ system disjoint_from: UBERON:8450002 ! excretory system relationship: capable_of_part_of GO:0050912 ! detection of chemical stimulus involved in sensory perception of taste -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage [Term] @@ -170028,7 +172287,7 @@ is_a: UBERON:0004121 ! ectoderm-derived structure relationship: has_part GO:0045095 ! keratin filament relationship: part_of UBERON:0001003 {source="FMA"} ! skin epidermis relationship: part_of UBERON:0011932 {source="FMA"} ! pilosebaceous unit -relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia +relationship: RO:0002162 NCBITaxon:40674 ! in taxon Mammalia relationship: RO:0002202 UBERON:0002073 ! develops from hair follicle property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/25/Gray945.png" xsd:anyURI property_value: IAO:0000116 "TODO for now we treat vibrissa/whisker as a syonym, but these have different follicles. We could introduce subclasses (see also: Pangolin scales)" xsd:string @@ -170050,7 +172309,7 @@ xref: MAT:0000209 xref: MIAA:0000209 xref: Wikipedia:Chordotonal_organ is_a: UBERON:0000020 ! sense organ -relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda +relationship: RO:0002162 NCBITaxon:6656 ! in taxon Arthropoda [Term] id: UBERON:0001040 @@ -170152,7 +172411,7 @@ is_a: UBERON:0006562 ! pharynx relationship: distally_connected_to UBERON:0001043 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! esophagus relationship: part_of UBERON:0001004 ! respiratory system relationship: RO:0002150 UBERON:0001043 {gci_relation="part_of", gci_filler="NCBITaxon:7742"} ! continuous with esophagus -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002202 UBERON:0009145 {source="EHDAA2"} ! develops from pharyngeal region of foregut relationship: RO:0002551 UBERON:0008895 {gci_relation="part_of", gci_filler="NCBITaxon:89593"} ! has skeleton splanchnocranium @@ -170242,7 +172501,7 @@ intersection_of: produces UBERON:0001836 ! saliva relationship: capable_of GO:0046541 ! saliva secretion relationship: produces UBERON:0001836 ! saliva relationship: RO:0001025 UBERON:0000167 ! located in oral cavity -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria relationship: RO:0002433 UBERON:0001007 ! contributes to morphology of digestive system property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/51/Illu_quiz_hn_02.jpg" xsd:anyURI @@ -170444,7 +172703,7 @@ xref: TADS:0000163 xref: TGMA:0001038 xref: Wikipedia:Malpighian_tubule is_a: UBERON:0009773 {source="GO"} ! renal tubule -relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda +relationship: RO:0002162 NCBITaxon:6656 ! in taxon Arthropoda [Term] id: UBERON:0001058 @@ -170468,7 +172727,7 @@ is_a: UBERON:0000477 ! anatomical cluster relationship: capable_of_part_of GO:0007613 {source="Wikipedia"} ! memory relationship: capable_of_part_of GO:0008355 {source="Wikipedia"} ! olfactory learning relationship: part_of UBERON:0000955 ! brain -relationship: RO:0002160 NCBITaxon:33317 ! only in taxon Protostomia +relationship: RO:0002162 NCBITaxon:33317 ! in taxon Protostomia property_value: RO:0002161 NCBITaxon:6217 property_value: RO:0002175 NCBITaxon:6340 property_value: RO:0002175 NCBITaxon:6656 @@ -170568,6 +172827,7 @@ xref: NCIT:C49571 xref: SCTID:244570000 xref: UMLS:C0021815 {source="ncithesaurus:Intervertebral_Disc"} xref: Wikipedia:Intervertebral_disk +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0011135 ! intervertebral cartilage intersection_of: UBERON:0011135 ! intervertebral cartilage intersection_of: has_part UBERON:0002242 ! nucleus pulposus @@ -170707,7 +172967,7 @@ is_a: UBERON:8410024 ! intestinal junction intersection_of: UBERON:0007651 ! anatomical junction intersection_of: RO:0002176 UBERON:0000059 ! connects large intestine intersection_of: RO:0002176 UBERON:0002108 ! connects small intestine -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002176 UBERON:0000059 ! connects large intestine relationship: RO:0002176 UBERON:0002108 ! connects small intestine @@ -171301,7 +173561,7 @@ xref: Wikipedia:Thoracid_diaphragm is_a: UBERON:0003830 ! thoracic segment muscle is_a: UBERON:0003831 ! respiratory system muscle relationship: RO:0002005 UBERON:0001884 ! innervated_by phrenic nerve -relationship: RO:0002160 NCBITaxon:40674 {source="PMID:23586979"} ! only in taxon Mammalia +relationship: RO:0002162 NCBITaxon:40674 {source="PMID:23586979"} ! in taxon Mammalia relationship: RO:0002495 UBERON:0010084 ! immediate transformation of future diaphragm property_value: RO:0002161 NCBITaxon:8782 {source="Wikipedia:Thoracic_diaphragm#Comparative_anatomy_and_evolution"} @@ -171614,7 +173874,7 @@ intersection_of: UBERON:0000075 ! subdivision of skeletal system intersection_of: RO:0002473 UBERON:0010913 ! composed primarily of vertebral element relationship: part_of UBERON:0011138 {source="cjm"} ! postcranial axial skeletal system relationship: protects UBERON:0002240 ! spinal cord -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002473 UBERON:0010913 ! composed primarily of vertebral element property_value: IAO:0000116 "Note that in contrast to VSAO, this is a subset of the skeletal system, and thus includes intervertebral joints, cartilage and ligaments etc. Some ontologies such as AAO seem to purely refer to the skeleton" xsd:string property_value: RO:0002161 NCBITaxon:7762 @@ -171676,7 +173936,7 @@ xref: XAO:0000167 is_a: UBERON:0002368 ! endocrine gland relationship: capable_of GO:0035898 ! parathyroid hormone secretion relationship: capable_of_part_of GO:0055074 {source="Wikipedia"} ! calcium ion homeostasis -relationship: RO:0002160 NCBITaxon:32523 {source="PMID:16313389"} ! only in taxon Tetrapoda +relationship: RO:0002162 NCBITaxon:32523 {source="PMID:16313389"} ! in taxon Tetrapoda relationship: RO:0002202 UBERON:0007124 {gci_relation="part_of", gci_filler="NCBITaxon:10090", source="PMID:16313389"} ! develops from pharyngeal pouch 3 [Term] @@ -171863,7 +174123,7 @@ xref: SCTID:123961009 xref: UMLS:C0004600 {source="ncithesaurus:Back"} xref: Wikipedia:Dorsum_(anatomy) is_a: UBERON:0000475 ! organism subdivision -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/432px-Gray-back.PNG" xsd:anyURI [Term] @@ -172207,7 +174467,7 @@ is_a: BFO:0000002 is_a: UBERON:0009854 ! digestive tract diverticulum relationship: part_of UBERON:0001155 {source="EHDAA2"} ! colon relationship: RO:0002150 UBERON:0001156 {source="Wikipedia"} ! continuous with ascending colon -relationship: RO:0002160 NCBITaxon:7776 ! only in taxon Gnathostomata +relationship: RO:0002162 NCBITaxon:7776 ! in taxon Gnathostomata relationship: RO:0002202 UBERON:0001045 {source="Wikipedia"} ! develops from midgut relationship: RO:0002433 UBERON:0000059 ! contributes to morphology of large intestine property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/82/Stomach_colon_rectum_diagram.svg" xsd:anyURI @@ -172298,7 +174558,7 @@ xref: XAO:0000243 xref: ZFA:0000706 is_a: UBERON:0004921 ! subdivision of digestive tract relationship: part_of UBERON:0000059 {source="FMA"} ! large intestine -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002433 UBERON:0000059 ! contributes to morphology of large intestine property_value: IAO:0000116 "Some references do not consider the caecum to be part of the colon." xsd:string {xref="http://orcid.org/0000-0002-1572-1316"} property_value: IAO:0000116 "TODO - abstract this such that it legitimately covers all vertebrates" xsd:string @@ -172464,6 +174724,7 @@ xref: UMLS:C0017129 {source="ncithesaurus:Fundus_of_the_Stomach"} xref: VHOG:0000421 xref: Wikipedia:Fundus_(stomach) is_a: BFO:0000002 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0009870 ! zone of stomach relationship: has_part UBERON:0010038 ! fundic gastric gland relationship: RO:0002433 UBERON:0000945 ! contributes to morphology of stomach @@ -172522,13 +174783,14 @@ xref: NCIT:C12256 xref: SCTID:362138004 xref: UMLS:C0007144 {source="ncithesaurus:Cardia"} xref: Wikipedia:Cardia +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0009870 ! zone of stomach intersection_of: UBERON:0009870 ! zone of stomach intersection_of: has_part UBERON:0008859 ! cardiac gastric gland relationship: has_part UBERON:0008859 ! cardiac gastric gland relationship: RO:0002150 UBERON:0001043 ! continuous with esophagus relationship: RO:0002150 UBERON:0001161 ! continuous with body of stomach -relationship: RO:0002160 NCBITaxon:40674 {source="ISBN:0073040584"} ! only in taxon Mammalia +relationship: RO:0002162 NCBITaxon:40674 {source="ISBN:0073040584"} ! in taxon Mammalia relationship: RO:0002433 UBERON:0000945 ! contributes to morphology of stomach property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/3/33/Illu_stomach.jpg" xsd:anyURI property_value: IAO:0000116 "There were previously conflicting statements in the academic anatomy community[10][11][12] over whether the cardia is part of the stomach, part of the esophagus or a distinct entity. Modern surgical and medical textbooks have agreed that 'The gastric cardia is now clearly considered to be part of the stomach'[13][14]. Classical anatomy textbooks, and some other resources[15], describe the cardia as the first of 4 regions of the stomach. This makes sense histologically because the mucosa of the cardia is the same as that of the stomach[WP]" xsd:string @@ -172599,6 +174861,7 @@ xref: UMLS:C0034196 {source="ncithesaurus:Pylorus"} xref: VHOG:0000420 xref: Wikipedia:Pylorus is_a: BFO:0000002 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0009870 ! zone of stomach intersection_of: UBERON:0009870 ! zone of stomach intersection_of: has_part UBERON:0001165 ! pyloric antrum @@ -172747,6 +175010,7 @@ xref: SCTID:181267003 xref: UMLS:C0005423 {source="ncithesaurus:Biliary_Tract"} xref: Wikipedia:Biliary_tract xref: XAO:0000455 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0013765 ! digestive system element intersection_of: UBERON:0000062 ! organ @@ -173666,7 +175930,7 @@ xref: Wikipedia:Peyer's_patch is_a: UBERON:0001962 {source="FMA", source="MA"} ! gut-associated lymphoid tissue relationship: part_of UBERON:0000030 {comment="EDITOR_NOTE check this"} ! lamina propria relationship: part_of UBERON:0001242 ! intestinal mucosa -relationship: RO:0002160 NCBITaxon:32524 {source="PMID:PMID:20181529"} ! only in taxon Amniota +relationship: RO:0002162 NCBITaxon:32524 {source="PMID:PMID:20181529"} ! in taxon Amniota property_value: RO:0002161 NCBITaxon:8459 {source="PMID:PMID:20181529"} [Term] @@ -173698,7 +175962,7 @@ intersection_of: UBERON:0011148 ! submucosal gland intersection_of: part_of UBERON:0002114 ! duodenum relationship: part_of UBERON:0002114 ! duodenum relationship: RO:0001025 UBERON:0003332 {source="FMA, modified"} ! located in submucosa of duodenum -relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia +relationship: RO:0002162 NCBITaxon:40674 ! in taxon Mammalia property_value: IAO:0000116 "currently defined as equivalent to any submucosal gland in the duodenum." xsd:string [Term] @@ -173731,6 +175995,7 @@ xref: UMLS:C1519988 {source="ncithesaurus:Villus"} xref: Wikipedia:Intestinal_villus xref: ZFA:0005125 is_a: BFO:0000002 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004923 {source="FMA"} ! organ component layer relationship: has_part CL:0000066 ! epithelial cell relationship: has_part UBERON:0001981 ! blood vessel @@ -175016,7 +177281,7 @@ is_a: BFO:0000002 is_a: UBERON:0002075 ! viscus relationship: has_part UBERON:0000016 ! endocrine pancreas relationship: has_part UBERON:0000017 {gci_relation="part_of", gci_filler="NCBITaxon:89593"} ! exocrine pancreas -relationship: RO:0002160 NCBITaxon:7742 {source="PMID:16417468"} ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 {source="PMID:16417468"} ! in taxon Vertebrata relationship: RO:0002254 UBERON:0003923 {source="Wikipedia"} ! has developmental contribution from dorsal pancreatic bud relationship: RO:0002254 UBERON:0003924 {source="Wikipedia"} ! has developmental contribution from ventral pancreatic bud property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/pancreas-female/v1.3/assets/3d-vh-f-pancreas.glb" xsd:anyURI @@ -175321,6 +177586,7 @@ xref: NCIT:C33342 xref: SCTID:362192000 xref: UMLS:C0227514 {source="ncithesaurus:Portal_Triad"} xref: Wikipedia:Portal_triad +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0034921 ! multi organ part structure relationship: has_part UBERON:0001193 ! hepatic artery @@ -175743,7 +178009,7 @@ xref: FMA:17734 xref: MA:0001652 is_a: UBERON:0000064 ! organ part relationship: part_of UBERON:0000362 ! renal medulla -relationship: RO:0002160 NCBITaxon:40674 {source="GO:0072053"} ! only in taxon Mammalia +relationship: RO:0002162 NCBITaxon:40674 {source="GO:0072053"} ! in taxon Mammalia relationship: RO:0002433 UBERON:0000362 ! contributes to morphology of renal medulla property_value: RO:0002175 NCBITaxon:9606 @@ -175781,7 +178047,7 @@ is_a: UBERON:0019042 ! reproductive system mucosa intersection_of: UBERON:0000344 ! mucosa intersection_of: part_of UBERON:0000995 ! uterus relationship: part_of UBERON:0000459 {source="FMA"} ! uterine wall -relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia +relationship: RO:0002162 NCBITaxon:40674 ! in taxon Mammalia relationship: RO:0002433 UBERON:0000995 ! contributes to morphology of uterus property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cervix.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 @@ -175912,7 +178178,7 @@ relationship: channel_for CL:0000019 ! sperm relationship: channels_from UBERON:0006946 ! efferent duct relationship: channels_into UBERON:0001000 ! vas deferens relationship: part_of UBERON:0006947 {source="FMA"} ! male genital duct -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002202 UBERON:0003074 {source="Wikipedia"} ! develops from mesonephric duct relationship: RO:0002433 UBERON:0004054 ! contributes to morphology of internal male genitalia property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c3/Illu_testis_surface.jpg" xsd:anyURI @@ -176495,7 +178761,6 @@ id: UBERON:0001335 name: prostatic urethra namespace: uberon def: "The widest and most dilatable part of the male urethra canal which runs almost vertically through the prostate from its base to its apex, lying nearer its anterior than its posterior surface; this portion of the urethral canal is spindle-shaped, being wider in the middle than at either extremity, and narrowest below, where it joins the membranous portion; it is lined by transitional epithelium and contains in its posterior wall, or floor, the orifices of the prostatic utricle, ejaculatory ducts, and prostatic ducts, collectively known as the seminal colliculus (aka verumontanum)." [MGI:anna, MP:0011777] -subset: human_reference_atlas subset: pheno_slim subset: uberon_slim synonym: "male prostatic urethra" EXACT [MP:0011777] @@ -176517,7 +178782,6 @@ relationship: part_of UBERON:0001333 {source="FMA", source="MA"} ! male urethra relationship: RO:0001025 UBERON:0002367 {source="FMA"} ! located in prostate gland relationship: RO:0002433 UBERON:0001333 ! contributes to morphology of male urethra property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/d7/Gray1142.png" xsd:anyURI -property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001338 @@ -176540,7 +178804,7 @@ is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0000057 ! urethra relationship: part_of UBERON:0000057 ! urethra -relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia +relationship: RO:0002162 NCBITaxon:40674 ! in taxon Mammalia relationship: RO:0002433 UBERON:0000057 ! contributes to morphology of urethra [Term] @@ -178018,7 +180282,7 @@ is_a: UBERON:0000475 ! organism subdivision relationship: has_part UBERON:0016884 ! shoulder joint relationship: overlaps UBERON:0001421 {source="FMA-modified"} ! pectoral girdle region relationship: part_of UBERON:0010708 ! pectoral complex -relationship: RO:0002160 NCBITaxon:32523 ! only in taxon Tetrapoda +relationship: RO:0002162 NCBITaxon:32523 ! in taxon Tetrapoda property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/90/Shoulderjoint.PNG" xsd:anyURI [Term] @@ -178228,7 +180492,7 @@ intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue disjoint_from: UBERON:0001630 ! muscle organ disjoint_from: UBERON:0005090 ! muscle structure disjoint_from: UBERON:0010538 ! paired limb/fin segment -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002473 UBERON:0002481 {source="VSAO-modified"} ! composed primarily of bone tissue [Term] @@ -179445,7 +181709,7 @@ xref: ZFA:0000112 is_a: BFO:0000002 is_a: UBERON:0000025 ! tube relationship: part_of UBERON:0001007 ! digestive system -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002176 UBERON:0000165 ! connects mouth relationship: RO:0002495 UBERON:0007026 {source="NCBIBook:NBK10107"} ! immediate transformation of presumptive gut property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} @@ -179522,7 +181786,7 @@ subset: non_informative synonym: "organ neck" EXACT [] xref: FMA:45733 is_a: UBERON:0034944 {source="FMA"} ! zone of organ -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0001568 @@ -180779,7 +183043,7 @@ intersection_of: RO:0002134 UBERON:0000378 ! innervates tongue muscle relationship: extends_fibers_into UBERON:0002871 ! hypoglossal nucleus relationship: RO:0002134 UBERON:0001571 ! innervates genioglossus muscle relationship: RO:0002134 UBERON:0001572 ! innervates hyoglossus muscle -relationship: RO:0002160 NCBITaxon:32523 ! only in taxon Tetrapoda +relationship: RO:0002162 NCBITaxon:32523 ! in taxon Tetrapoda property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/ef/Gray794.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 @@ -180998,7 +183262,7 @@ is_a: UBERON:0011164 ! neurocranium bone relationship: overlaps UBERON:0002241 ! chondrocranium relationship: overlaps UBERON:0003113 ! dermatocranium relationship: part_of UBERON:0005902 {source="FMA"} ! occipital region -relationship: RO:0002160 NCBITaxon:117570 {source="WP"} ! only in taxon Teleostomi +relationship: RO:0002162 NCBITaxon:117570 {source="WP"} ! in taxon Teleostomi relationship: RO:0002170 UBERON:0001092 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to vertebral bone 1 relationship: RO:0002170 UBERON:0001677 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! connected to sphenoid bone relationship: RO:0002202 UBERON:0003089 {source="PMID:11523816"} ! develops from sclerotome @@ -181257,7 +183521,7 @@ is_a: UBERON:0001444 ! subdivision of head is_a: UBERON:0015212 ! lateral structure relationship: BSPO:0000126 UBERON:0000033 ! head relationship: part_of UBERON:0001690 ! ear -relationship: RO:0002160 NCBITaxon:32523 ! only in taxon Tetrapoda +relationship: RO:0002162 NCBITaxon:32523 ! in taxon Tetrapoda relationship: RO:0002433 UBERON:0000033 ! contributes to morphology of head relationship: RO:0002433 UBERON:0001690 ! contributes to morphology of ear property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Gray907.png" xsd:anyURI @@ -181548,7 +183812,7 @@ intersection_of: RO:0002576 UBERON:0011595 ! skeleton of jaw region relationship: overlaps UBERON:0008895 ! splanchnocranium relationship: part_of UBERON:0011156 {source="cjm"} ! facial skeleton relationship: part_of UBERON:0011595 ! jaw region -relationship: RO:0002160 NCBITaxon:7776 ! only in taxon Gnathostomata +relationship: RO:0002162 NCBITaxon:7776 ! in taxon Gnathostomata relationship: RO:0002576 UBERON:0011595 ! skeleton of jaw region property_value: IAO:0000116 "TODO - move ZFA:0001227 (it is the entire jaw skeleton)." xsd:string @@ -182041,7 +184305,7 @@ is_a: BFO:0000002 is_a: UBERON:0034769 {source="FMA"} ! lymphomyeloid tissue relationship: has_part CL:0000542 ! lymphocyte relationship: part_of UBERON:0002465 ! lymphoid system -relationship: RO:0002160 NCBITaxon:7742 {source="NCBIBook:NBK27108"} ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 {source="NCBIBook:NBK27108"} ! in taxon Vertebrata [Term] id: UBERON:0001745 @@ -182100,6 +184364,7 @@ xref: EMAPA:37769 {source="MA:th"} xref: FMA:55515 xref: MA:0000730 xref: SCTID:371402001 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000353 ! parenchyma is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest @@ -182121,6 +184386,7 @@ xref: FMA:55566 xref: MA:0002676 xref: NCIT:C33265 xref: UMLS:C0927176 {source="ncithesaurus:Parathyroid_Gland_Capsule"} +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0003893 ! capsule intersection_of: UBERON:0003893 ! capsule intersection_of: bounding_layer_of UBERON:0001132 ! parathyroid gland @@ -182171,7 +184437,7 @@ is_a: UBERON:0000467 ! anatomical system is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0010409 {source="MA"} ! ocular surface region relationship: part_of UBERON:0035639 {source="HPO:pr"} ! ocular adnexa -relationship: RO:0002160 NCBITaxon:32523 ! only in taxon Tetrapoda +relationship: RO:0002162 NCBITaxon:32523 ! in taxon Tetrapoda relationship: RO:0002202 UBERON:0000076 {source="ISBN:0781772214"} ! develops from external ectoderm relationship: RO:0002433 UBERON:0000019 ! contributes to morphology of camera-type eye property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/cf/Gray896.png" xsd:anyURI @@ -182206,7 +184472,7 @@ xref: XAO:0004051 xref: ZFA:0005143 is_a: UBERON:0010365 {source="VSAO"} ! odontoid tissue is_a: UBERON:4000013 ! mineralized skeletal tissue -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002494 UBERON:0011587 {source="VSAO"} ! transformation of pre-dentine [Term] @@ -182235,7 +184501,7 @@ xref: Wikipedia:Enamel_organ xref: XAO:0004198 is_a: UBERON:0010365 {source="VSAO"} ! odontoid tissue is_a: UBERON:4000013 ! mineralized skeletal tissue -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002202 UBERON:0011588 {source="VSAO"} ! develops from pre-enamel relationship: RO:0002473 CHEBI:52255 ! composed primarily of property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/66/Enamelorgan11-17-05.jpg" xsd:anyURI @@ -182365,7 +184631,7 @@ is_a: UBERON:0001444 ! subdivision of head relationship: part_of UBERON:0001691 ! external ear relationship: RO:0000086 PATO:0001297 ! has quality reflectivity relationship: RO:0002150 UBERON:0001352 ! continuous with external acoustic meatus -relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia +relationship: RO:0002162 NCBITaxon:40674 ! in taxon Mammalia relationship: RO:0002202 UBERON:0006208 ! develops from auditory hillocks [Term] @@ -183135,7 +185401,7 @@ relationship: has_part CHEBI:27547 relationship: has_part CHEBI:28838 relationship: has_part CL:0000573 ! retinal cone cell relationship: part_of UBERON:0000053 ! macula lutea -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg" xsd:anyURI [Term] @@ -183728,6 +185994,7 @@ xref: UMLS:C0229232 {source="ncithesaurus:Lens_Capsule"} xref: VHOG:0000550 xref: Wikipedia:Lens_(anatomy)#Lens_capsule xref: ZFA:0005574 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0005764 ! acellular membrane intersection_of: UBERON:0000476 ! acellular anatomical structure @@ -184090,6 +186357,7 @@ id: UBERON:0001820 name: sweat gland namespace: uberon def: "Any of the coil glands of the skin that secrete sweat." [ISBN:0-683-40008-8, MP:0000674] +subset: human_reference_atlas subset: organ_slim subset: pheno_slim subset: uberon_slim @@ -184115,10 +186383,11 @@ intersection_of: UBERON:0002530 ! gland intersection_of: produces UBERON:0001089 ! sweat relationship: produces UBERON:0001089 ! sweat relationship: RO:0000086 PATO:0002299 ! has quality tubular -relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia +relationship: RO:0002162 NCBITaxon:40674 ! in taxon Mammalia relationship: RO:0002202 UBERON:0005089 ! develops from sweat gland placode property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Skin.svg" xsd:anyURI property_value: IAO:0000116 "TODO - check if all sweat glands are epidermal - see EMAPA:29743" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001821 @@ -184150,7 +186419,7 @@ is_a: UBERON:0012344 {source="Wikipedia"} ! holocrine gland is_a: UBERON:0019319 ! exocrine gland of integumental system relationship: part_of UBERON:0011932 ! pilosebaceous unit relationship: produces UBERON:0001866 ! sebum -relationship: RO:0002160 NCBITaxon:40674 {source="VHOG"} ! only in taxon Mammalia +relationship: RO:0002162 NCBITaxon:40674 {source="VHOG"} ! in taxon Mammalia relationship: RO:0002202 UBERON:0005088 ! develops from sebaceous gland placode property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/4/49/HairFollicle.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 @@ -184262,6 +186531,7 @@ xref: MESH:D013666 xref: NCIT:C33739 xref: UMLS:C0039409 {source="ncithesaurus:Tear"} xref: Wikipedia:Tear +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000456 ! secretion of exocrine gland intersection_of: UBERON:0000456 ! secretion of exocrine gland intersection_of: produced_by UBERON:0001817 ! lacrimal gland @@ -184696,7 +186966,7 @@ is_a: UBERON:0004111 ! anatomical conduit is_a: UBERON:0004121 ! ectoderm-derived structure relationship: channel_for UBERON:0001827 ! secretion of lacrimal gland relationship: part_of UBERON:0001750 {source="FMA"} ! lacrimal apparatus -relationship: RO:0002160 NCBITaxon:32523 {source="ISBN:9780674021839"} ! only in taxon Tetrapoda +relationship: RO:0002162 NCBITaxon:32523 {source="ISBN:9780674021839"} ! in taxon Tetrapoda relationship: RO:0002176 UBERON:0001707 ! connects nasal cavity relationship: RO:0002176 UBERON:0010284 ! connects lacrimal punctum property_value: RO:0002161 NCBITaxon:8459 {source="PMID:7559104"} @@ -186216,7 +188486,7 @@ intersection_of: UBERON:0002530 ! gland intersection_of: capable_of GO:0007595 ! lactation relationship: capable_of GO:0007595 ! lactation relationship: produces UBERON:0001913 ! milk -relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia +relationship: RO:0002162 NCBITaxon:40674 ! in taxon Mammalia relationship: RO:0002202 UBERON:0005333 ! develops from mammary bud property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Illu_breast_anatomy.jpg" xsd:anyURI property_value: IAO:0000116 "Originally this was classified as a female reproductive structure, as it was in the MP in 2011" xsd:string @@ -186271,6 +188541,7 @@ xref: UMLS:C1511310 {source="ncithesaurus:Breast_Fluid_or_Secretion"} xref: VHOG:0001263 xref: Wikipedia:Breast_milk is_a: BFO:0000002 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0006314 ! bodily fluid is_a: UBERON:0006539 ! mammary gland fluid/secretion relationship: has_part CHEBI:18059 @@ -186681,7 +188952,7 @@ xref: UMLS:C0175173 {source="BIRNLEX:2547"} xref: Wikipedia:Neocortex is_a: UBERON:0002616 ! regional part of brain relationship: part_of UBERON:0000956 ! cerebral cortex -relationship: RO:0002160 NCBITaxon:7742 {source="Wikipedia"} ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 {source="Wikipedia"} ! in taxon Vertebrata relationship: RO:0002433 UBERON:0000956 ! contributes to morphology of cerebral cortex property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/77/Neocortex.jpg" xsd:anyURI @@ -186772,7 +189043,7 @@ relationship: capable_of_part_of GO:0007613 {source="Wikipedia"} ! memory relationship: part_of UBERON:0000349 {source="FMA"} ! limbic system relationship: part_of UBERON:0002421 {source="ABA"} ! hippocampal formation relationship: part_of UBERON:0002600 {source="FMA"} ! limbic lobe -relationship: RO:0002160 NCBITaxon:40674 {source="Wikipedia:Hippocampus"} ! only in taxon Mammalia +relationship: RO:0002162 NCBITaxon:40674 {source="Wikipedia:Hippocampus"} ! in taxon Mammalia property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/2e/Gray739-emphasizing-hippocampus.png" xsd:anyURI [Term] @@ -186820,6 +189091,7 @@ xref: MA:0001835 xref: NCIT:C49209 xref: SCTID:278980009 xref: UMLS:C0225604 {source="ncithesaurus:Bronchus_Cartilage"} +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0003603 ! lower respiratory tract cartilage intersection_of: UBERON:0007844 ! cartilage element intersection_of: part_of UBERON:0002185 ! bronchus @@ -187054,6 +189326,7 @@ xref: MIAA:0000052 xref: NCIT:C13356 xref: UMLS:C0032105 {source="ncithesaurus:Plasma"} xref: Wikipedia:Blood_plasma +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000179 ! haemolymphatic fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: has_part GO:0005577 ! fibrinogen complex @@ -187363,6 +189636,7 @@ xref: VHOG:0001250 xref: Wikipedia:Blood_vessel xref: XAO:0001011 xref: ZFA:0005314 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000055 ! vessel is_a: UBERON:0004120 ! mesoderm-derived structure relationship: capable_of_part_of GO:0008015 ! blood circulation @@ -187446,7 +189720,7 @@ xref: UMLS:C1621887 {source="ncithesaurus:Crypts_of_the_Lieberkuhn"} xref: Wikipedia:Intestinal_crypt is_a: UBERON:0000333 ! intestinal gland relationship: RO:0000086 PATO:0002299 {source="Wikipedia:Tubular_gland"} ! has quality tubular -relationship: RO:0002160 NCBITaxon:32523 ! only in taxon Tetrapoda +relationship: RO:0002162 NCBITaxon:32523 ! in taxon Tetrapoda relationship: RO:0002433 UBERON:0001242 ! contributes to morphology of intestinal mucosa property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/38/Small_intestine_low_mag.jpg" xsd:anyURI property_value: seeAlso UBERON:2005256 @@ -187532,7 +189806,7 @@ is_a: UBERON:0000487 {source="FMA-text-def", source="https://github.com/obopheno is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: RO:0002473 CL:0000115 ! composed primarily of endothelial cell -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002473 CL:0000115 ! composed primarily of endothelial cell property_value: RO:0002175 NCBITaxon:9606 @@ -187570,7 +189844,7 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005156 ! reproductive structure relationship: part_of UBERON:0000474 ! female reproductive system relationship: part_of UBERON:0016887 ! entire extraembryonic component -relationship: RO:0002160 NCBITaxon:32525 {source="https://github.com/obophenotype/uberon/issues/1376"} ! only in taxon Theria +relationship: RO:0002162 NCBITaxon:32525 {source="https://github.com/obophenotype/uberon/issues/1376"} ! in taxon Theria relationship: RO:0002202 UBERON:0000995 {source="ISBN:0073040584"} ! develops from uterus relationship: RO:0002202 UBERON:0003124 {source="Wikipedia"} ! develops from chorion membrane relationship: RO:0002202 UBERON:0004340 {source="ISBN:0073040584"} ! develops from allantois @@ -187659,6 +189933,7 @@ xref: NCIT:C94819 xref: UMLS:C0221930 {source="ncithesaurus:Stratum_Papillare"} xref: UMLS:C0682598 {source="ncithesaurus:Papillary_Dermis"} xref: Wikipedia:Papillary_dermis +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0013754 ! integumentary system layer relationship: part_of UBERON:0002067 ! dermis @@ -187714,6 +189989,7 @@ xref: UMLS:C0225362 {source="ncithesaurus:Hyaline_Cartilage"} xref: VSAO:0000094 xref: Wikipedia:Hyaline_cartilage xref: XAO:0004029 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002418 {source="FMA"} ! cartilage tissue relationship: RO:0002473 GO:0005585 {source="VSAO-text-def"} ! composed primarily of collagen type II trimer property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/2a/Gray292.png" xsd:anyURI @@ -187738,6 +190014,7 @@ xref: UMLS:C0684077 {source="ncithesaurus:Fibrocartilage"} xref: VSAO:0000103 xref: Wikipedia:Fibrocartilage xref: XAO:0004028 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002418 ! cartilage tissue relationship: has_part GO:0005584 ! collagen type I trimer property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/2e/Gray295.png" xsd:anyURI @@ -188222,7 +190499,7 @@ is_a: UBERON:0035642 ! laryngeal nerve intersection_of: UBERON:0001021 ! nerve intersection_of: extends_fibers_into UBERON:0020358 ! accessory XI nerve nucleus relationship: extends_fibers_into UBERON:0020358 ! accessory XI nerve nucleus -relationship: RO:0002160 NCBITaxon:32523 ! only in taxon Tetrapoda +relationship: RO:0002162 NCBITaxon:32523 ! in taxon Tetrapoda property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/5e/Gray791.png" xsd:anyURI [Term] @@ -188333,6 +190610,7 @@ xref: NCIT:C12850 xref: SCTID:420086000 xref: UMLS:C0221924 {source="ncithesaurus:Stratum_Spinosum"} xref: Wikipedia:Stratum_spinosum +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0013754 ! integumentary system layer intersection_of: UBERON:0013754 ! integumentary system layer @@ -188420,7 +190698,7 @@ xref: XAO:0000015 xref: ZFA:0000029 is_a: UBERON:0002616 ! regional part of brain relationship: overlaps UBERON:0002298 ! brainstem -relationship: RO:0002160 NCBITaxon:89593 ! only in taxon Craniata +relationship: RO:0002162 NCBITaxon:89593 ! in taxon Craniata relationship: RO:0002433 UBERON:0000955 ! contributes to morphology of brain relationship: RO:0002495 UBERON:0007277 {source="Bgee:AN"} ! immediate transformation of presumptive hindbrain property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI @@ -188487,7 +190765,7 @@ is_a: UBERON:0000475 ! organism subdivision is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0000310 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! breast relationship: part_of UBERON:0001911 ! mammary gland -relationship: RO:0002160 NCBITaxon:32525 ! only in taxon Theria +relationship: RO:0002162 NCBITaxon:32525 ! in taxon Theria relationship: RO:0002202 UBERON:0008425 {source="Stedmans"} ! develops from mammary ridge property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/59/Female_nipple_profile.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/1873" xsd:string @@ -188531,6 +190809,7 @@ id: UBERON:0002033 name: arrector muscle of hair namespace: uberon def: "A tiny smooth muscle that connects the hair follicle with the dermis." [DOI:10.1016/j.cub.2008.12.005] +subset: human_reference_atlas subset: pheno_slim subset: uberon_slim synonym: "arectores pilorum" RELATED [BTO:0005132] @@ -188553,6 +190832,7 @@ xref: Wikipedia:Arrector_pili_muscle is_a: UBERON:0001135 {source="FMA"} ! smooth muscle tissue relationship: part_of UBERON:0011932 {source="FMA"} ! pilosebaceous unit relationship: RO:0002371 UBERON:0002073 ! attached to hair follicle +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002036 @@ -188625,7 +190905,7 @@ xref: XAO:0003098 xref: ZFA:0000100 is_a: UBERON:0002616 ! regional part of brain relationship: part_of UBERON:0001895 {source="FMA", source="MA"} ! metencephalon -relationship: RO:0002160 NCBITaxon:7742 {source="ISBN:0471888893"} ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 {source="ISBN:0471888893"} ! in taxon Vertebrata relationship: RO:0002202 UBERON:0006215 ! develops from rhombic lip relationship: RO:0002433 UBERON:0001895 ! contributes to morphology of metencephalon property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/a/a7/Cerebellum_NIH.png" xsd:anyURI @@ -188782,7 +191062,7 @@ is_a: UBERON:0010314 ! structure with developmental contribution from neural cre relationship: BFO:0000067 GO:0006590 ! contains process thyroid hormone generation relationship: capable_of GO:0036161 {source="Wikipedia"} ! calcitonin secretion relationship: capable_of_part_of GO:0055074 {source="Wikipedia"} ! calcium ion homeostasis -relationship: RO:0002160 NCBITaxon:7711 {source="Wikipedia:Endostyle"} ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {source="Wikipedia:Endostyle"} ! in taxon Chordata relationship: RO:0002494 UBERON:0007689 ! transformation of thyroid diverticulum property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/a3/Illu_thyroid_parathyroid.jpg" xsd:anyURI property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c6/Illu_endocrine_system.jpg" xsd:anyURI @@ -188859,7 +191139,7 @@ is_a: UBERON:0005178 ! thoracic cavity element is_a: UBERON:0015212 ! lateral structure relationship: BSPO:0000126 UBERON:0000170 ! pair of lungs relationship: part_of UBERON:0000170 {note="some species only have a single lung"} ! pair of lungs -relationship: RO:0002160 NCBITaxon:7776 ! only in taxon Gnathostomata +relationship: RO:0002162 NCBITaxon:7776 ! in taxon Gnathostomata relationship: RO:0002202 UBERON:0000118 ! develops from lung bud relationship: RO:0002219 UBERON:0009778 {gci_relation="part_of", gci_filler="NCBITaxon:9606", source="FMA"} ! surrounded by pleural sac relationship: RO:0002433 UBERON:0001004 ! contributes to morphology of respiratory system @@ -188969,6 +191249,7 @@ xref: FMA:69087 xref: MA:0000117 xref: NCIT:C32050 xref: UMLS:C1181304 {source="ncithesaurus:Adrenal_Gland_Capsule"} +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0003893 ! capsule is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0010313 ! neural crest-derived structure @@ -189221,6 +191502,7 @@ xref: VHOG:0000108 xref: Wikipedia:Dermis xref: XAO:0000217 xref: ZFA:0001119 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0013754 ! integumentary system layer @@ -189289,6 +191571,7 @@ xref: TAO:0001136 xref: UMLS:C0278403 {source="ncithesaurus:Subcutis"} xref: Wikipedia:Hypodermis xref: ZFA:0001136 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0013754 ! integumentary system layer relationship: BSPO:0000107 UBERON:0002067 ! dermis @@ -189339,6 +191622,7 @@ id: UBERON:0002074 name: hair shaft namespace: uberon def: "The main part of the hair which is composed of trichocytes and is divided into the cortex and medulla." [DOI:10.1016/j.cub.2008.12.005] +subset: human_reference_atlas subset: pheno_slim synonym: "scapus pili" RELATED [BTO:0004672] synonym: "shaft of hair" EXACT [] @@ -189354,6 +191638,7 @@ is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001037 {source="DOI:10.1016/j.cub.2008.12.005"} ! strand of hair property_value: IAO:0000116 "TODO - add distinct subclasses for coat hair vs vibrissa hair" xsd:string property_value: IAO:0000116 "TODO - check definition of trichocyte in CL" xsd:string +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002075 @@ -189392,6 +191677,7 @@ id: UBERON:0002076 name: cuticle of hair namespace: uberon def: "Smooth and glossy outer protective cell layer of hair shaft." [MGI:llw2, MP:0003810] +subset: human_reference_atlas subset: pheno_slim synonym: "hair cuticle" EXACT [] xref: EMAPA:35388 @@ -189403,12 +191689,14 @@ intersection_of: UBERON:0000119 ! cell layer intersection_of: bounding_layer_of UBERON:0002074 ! hair shaft relationship: bounding_layer_of UBERON:0002074 ! hair shaft relationship: part_of UBERON:0002074 ! hair shaft +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002077 name: cortex of hair namespace: uberon def: "A cortex that is part of a hair [Automatically generated definition]." [OBOL:automatic] +subset: human_reference_atlas subset: pheno_slim synonym: "coat hair cortex" EXACT [OBOL:automatic] synonym: "coat/hair cortex" EXACT [OBOL:automatic] @@ -189424,6 +191712,7 @@ is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0001851 ! cortex intersection_of: part_of UBERON:0001037 ! strand of hair relationship: part_of UBERON:0002074 ! hair shaft +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0002078 @@ -189760,7 +192049,7 @@ xref: XAO:0003166 is_a: UBERON:0010912 ! subdivision of skeleton relationship: overlaps UBERON:0000026 ! appendage relationship: part_of UBERON:0011249 ! appendicular skeletal system -relationship: RO:0002160 NCBITaxon:7776 ! only in taxon Gnathostomata +relationship: RO:0002162 NCBITaxon:7776 ! in taxon Gnathostomata relationship: RO:0002433 UBERON:0001434 ! contributes to morphology of skeletal system property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/7c/Appendicular_skeleton_diagram.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 @@ -189875,7 +192164,7 @@ xref: SCTID:362707009 xref: UMLS:C0025474 {source="ncithesaurus:Mesentery"} xref: Wikipedia:Mesentery#Mesentery_.28general.29 is_a: UBERON:0000042 ! serous membrane -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/1/19/Gray1038.png" xsd:anyURI [Term] @@ -189909,6 +192198,7 @@ xref: SCTID:181469002 xref: UMLS:C1123023 {source="ncithesaurus:Skin"} xref: Wikipedia:Skin xref: XAO:0000023 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000062 ! organ is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0002199 ! integument @@ -190024,7 +192314,7 @@ xref: XAO:0003027 is_a: UBERON:0004708 ! paired limb/fin intersection_of: UBERON:0000475 ! organism subdivision intersection_of: RO:0002551 UBERON:0004381 ! has skeleton skeleton of limb -relationship: RO:0002160 NCBITaxon:32523 {note="extends to stem tetrapods such as Eusthenopteron"} ! only in taxon Tetrapoda +relationship: RO:0002162 NCBITaxon:32523 {note="extends to stem tetrapods such as Eusthenopteron"} ! in taxon Tetrapoda relationship: RO:0002202 UBERON:0004347 ! develops from limb bud relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage relationship: RO:0002551 UBERON:0004381 ! has skeleton skeleton of limb @@ -190221,7 +192511,7 @@ xref: ZFA:0000436 is_a: UBERON:0004177 ! hemopoietic organ is_a: UBERON:0005057 ! immune organ is_a: UBERON:0017672 ! abdominal viscera -relationship: RO:0002160 NCBITaxon:7776 {source="multiple sources - true spleen appear in jawed vertebrates"} ! only in taxon Gnathostomata +relationship: RO:0002162 NCBITaxon:7776 {source="multiple sources - true spleen appear in jawed vertebrates"} ! in taxon Gnathostomata relationship: RO:0002202 UBERON:0006293 ! develops from spleen primordium property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/spleen-female/v1.3/assets/3d-vh-f-spleen.glb" xsd:anyURI property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/spleen-male/v1.3/assets/3d-vh-m-spleen.glb" xsd:anyURI @@ -190273,7 +192563,7 @@ relationship: has_part UBERON:0004647 ! liver lobule relationship: overlaps UBERON:0002405 {source="ZFA-weakened"} ! immune system relationship: part_of UBERON:0002423 {source="ZFA"} ! hepatobiliary system relationship: produces UBERON:0001970 ! bile -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002202 UBERON:0004161 {source="EHDAA2"} ! develops from septum transversum relationship: RO:0002202 UBERON:0008836 {source="http://www.stembook.org/node/512"} ! develops from liver bud relationship: RO:0002433 UBERON:0002423 ! contributes to morphology of hepatobiliary system @@ -190326,7 +192616,7 @@ xref: ZFA:0001323 is_a: UBERON:0004921 ! subdivision of digestive tract is_a: UBERON:0013765 ! digestive system element relationship: part_of UBERON:0000160 ! intestine -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002433 UBERON:0000160 ! contributes to morphology of intestine property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/82/Stomach_colon_rectum_diagram.svg" xsd:anyURI property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/small-intestine-female/v1.2/assets/3d-vh-f-small-intestine.glb" xsd:anyURI @@ -190498,7 +192788,7 @@ is_a: UBERON:0005172 ! abdomen element is_a: UBERON:0015212 ! lateral structure relationship: BSPO:0000126 UBERON:0000468 ! multicellular organism relationship: part_of UBERON:0011143 {source="FMA"} ! upper urinary tract -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002202 UBERON:0003918 ! develops from kidney mesenchyme relationship: RO:0002202 UBERON:0005095 ! develops from kidney rudiment relationship: RO:0002433 UBERON:0001008 ! contributes to morphology of renal system @@ -190911,6 +193201,7 @@ xref: TAO:0000683 xref: UMLS:C0038533 {source="BIRNLEX:1028"} xref: Wikipedia:Subcommissural_organ xref: ZFA:0000683 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0010134 {source="MA"} ! secretory circumventricular organ relationship: has_part CL:0000065 ! ependymal cell relationship: part_of UBERON:0002314 {source="MA"} ! midbrain tectum @@ -191477,7 +193768,7 @@ xref: EMAPA:18765 xref: FMA:74562 xref: MA:0000013 is_a: UBERON:0000467 {source="MA"} ! anatomical system -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria [Term] id: UBERON:0002194 @@ -191587,11 +193878,57 @@ relationship: has_part CL:0000439 {source="ZFA"} ! prolactin secreting cell relationship: has_part CL:0000467 {source="ZFA"} ! adrenocorticotropic hormone secreting cell relationship: has_part CL:0002312 ! somatotroph relationship: part_of UBERON:0000007 ! pituitary gland -relationship: RO:0002160 NCBITaxon:7742 {source="PMID:19084529"} ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 {source="PMID:19084529"} ! in taxon Vertebrata relationship: RO:0002202 UBERON:0009122 {source="NCBIBook:NBK53175", source="ZFA"} ! develops from adenohypophyseal placode relationship: RO:0002433 UBERON:0000007 ! contributes to morphology of pituitary gland property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray1181.png" xsd:anyURI +[Term] +id: UBERON:0002197 +name: median eminence of neurohypophysis +namespace: uberon +def: "Elevation on the ventral surface of the brain located at the zone of attachment between the hypothalamic floor and the hypophysis (Butler and Hodos, Comparative Vertebrate Neuroanatomy, 2nd ed., 2005, pg. 446)." [BIRNLEX:925] +subset: pheno_slim +subset: uberon_slim +synonym: "eminentia medialis (Shantha)" RELATED OMO:0003011 [NeuroNames:402] +synonym: "eminentia mediana" RELATED OMO:0003011 [NeuroNames:402] +synonym: "eminentia mediana hypothalami" EXACT OMO:0003011 [FMA:74634, FMA:TA] +synonym: "eminentia mediana hypothalami" RELATED OMO:0003011 [Wikipedia:Median_eminence] +synonym: "eminentia postinfundibularis" RELATED OMO:0003011 [NeuroNames:402] +synonym: "ME" BROAD OMO:0003000 [BIRNLEX:925, NIFSTD:NeuroNames_abbrevSource] +synonym: "medial eminence" RELATED [NeuroNames:402] +synonym: "median eminence" EXACT [] +synonym: "median eminence of hypothalamus" EXACT [] +synonym: "median eminence of posterior lobe of pituitary gland" EXACT [] +synonym: "median eminence of tuber cinereum" EXACT [] +xref: AAO:0010539 +xref: BAMS:ME +xref: BIRNLEX:925 +xref: BM:ME +xref: BTO:0001954 +xref: DHBA:13338 +xref: DMBA:15689 +xref: EHDAA2:0001080 +xref: EHDAA:7540 +xref: EMAPA:17521 +xref: FMA:74634 +xref: GAID:463 +xref: HBA:12916 +xref: MA:0000859 +xref: MBA:10671 +xref: MESH:D008473 +xref: neuronames:402 {source="BIRNLEX:925"} +xref: SCTID:369121004 +xref: UMLS:C0025056 {source="BIRNLEX:925"} +xref: VHOG:0001179 +xref: Wikipedia:Median_eminence +is_a: UBERON:0003296 ! gland of diencephalon +is_a: UBERON:0003937 ! reproductive gland +is_a: UBERON:0010134 ! secretory circumventricular organ +relationship: part_of UBERON:0002198 ! neurohypophysis +relationship: RO:0002162 NCBITaxon:8287 {source="ISBN:0471888893"} ! in taxon Sarcopterygii +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/8c/HypothalamicNuclei.PNG" xsd:anyURI + [Term] id: UBERON:0002198 name: neurohypophysis @@ -191651,7 +193988,7 @@ is_a: UBERON:0010134 {source="MA"} ! secretory circumventricular organ relationship: capable_of GO:0001992 {source="Wikipedia"} ! regulation of systemic arterial blood pressure by vasopressin relationship: capable_of GO:0030103 {source="Wikipedia"} ! vasopressin secretion relationship: part_of UBERON:0000007 {source="ZFA"} ! pituitary gland -relationship: RO:0002160 NCBITaxon:7742 {source="PMID:19084529"} ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 {source="PMID:19084529"} ! in taxon Vertebrata relationship: RO:0002202 UBERON:0002346 ! develops from neurectoderm property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b9/Pituitary_gland_representation.PNG" xsd:anyURI property_value: IAO:0000116 "request magnocellular cell from CL. Request oxytocin secretion from GO. Notes: 'The hypophysis or pituitary gland is derived, in part from an ectodermal outpocketing of the stomodeum (Rathke's Pouch) and in part from the floor of the diencephalon'" xsd:string {source="http://syllabus.med.unc.edu/courseware/embryo_images/"} @@ -191686,12 +194023,13 @@ xref: VSAO:0000029 xref: Wikipedia:Integument xref: ZFA:0000368 is_a: BFO:0000002 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0011216 {source="FMA"} ! organ system subdivision relationship: bounding_layer_of UBERON:0000468 ! multicellular organism relationship: has_part UBERON:0002072 ! hypodermis relationship: has_part UBERON:0002097 ! skin of body relationship: part_of UBERON:0002416 {source="FMA"} ! integumental system -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -192049,6 +194387,7 @@ xref: FMA:7497 xref: MA:0001501 xref: SCTID:42903008 xref: Wikipedia:Synchondrosis +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002209 ! fibrous joint is_a: UBERON:0002213 ! cartilaginous joint intersection_of: UBERON:0002209 ! fibrous joint @@ -192103,7 +194442,7 @@ is_a: UBERON:0000982 ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: RO:0002219 UBERON:0001484 ! surrounded by articular capsule disjoint_from: UBERON:0011134 ! nonsynovial joint -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002219 UBERON:0001484 ! surrounded by articular capsule [Term] @@ -192201,7 +194540,7 @@ relationship: capable_of GO:0050910 ! detection of mechanical stimulus involved relationship: has_part CL:0000202 ! auditory hair cell relationship: part_of UBERON:0001855 {source="MA"} ! cochlear duct of membranous labyrinth relationship: RO:0001025 UBERON:0002295 {source="Wikipedia:Scala_media"} ! located in scala media -relationship: RO:0002160 NCBITaxon:32523 ! only in taxon Tetrapoda +relationship: RO:0002162 NCBITaxon:32523 ! in taxon Tetrapoda property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/c7/Cochlea-crosssection.png" xsd:anyURI property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/cb/Cochlea-crosssection.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:40674 @@ -192388,6 +194727,7 @@ xref: FMA:76703 xref: MA:0000112 xref: SCTID:316586000 xref: Wikipedia:Nucleus_pulposus +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000062 ! organ is_a: UBERON:0002384 ! connective tissue is_a: UBERON:0004120 ! mesoderm-derived structure @@ -192436,7 +194776,7 @@ relationship: capable_of GO:0043695 {source="Wikipedia"} ! detection of pheromon relationship: part_of UBERON:0000004 ! nose relationship: part_of UBERON:0009954 ! vomeronasal system relationship: RO:0000086 PATO:0000588 {gci_relation="part_of", gci_filler="NCBITaxon:314295"} ! has quality vestigial -relationship: RO:0002160 NCBITaxon:8287 ! only in taxon Sarcopterygii +relationship: RO:0002162 NCBITaxon:8287 ! in taxon Sarcopterygii relationship: RO:0002202 UBERON:0003050 {source="Wikipedia"} ! develops from olfactory placode relationship: RO:0002254 UBERON:0009714 {source="EHDAA2-abduced"} ! has developmental contribution from intermaxillary process property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/84/Gray51.png" xsd:anyURI @@ -192889,6 +195229,83 @@ relationship: RO:0002494 UBERON:0009676 ! transformation of early telencephalic property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray734.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 +[Term] +id: UBERON:0002286 +name: third ventricle +namespace: uberon +def: "Part of the ventricular system of the brain, forming a single large cavity in the midline of the diencephalon; it is continuous with the lateral ventricles through the interventricular foramen and the fourth ventricle through the cerebral aqueduct. (Maryann Martone)." [BIRNLEX:714] +subset: human_reference_atlas +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "3rd ventricle" EXACT [] +synonym: "diencephalic ventricle" RELATED [] +synonym: "diencephalic vesicle" NARROW [] +synonym: "ventriculus diencephali" EXACT [ZFA:0000161] +synonym: "ventriculus tertius cerebri" RELATED OMO:0003011 [Wikipedia:Third_ventricle] +xref: BAMS:3V +xref: BAMS:V3 +xref: BIRNLEX:714 +xref: BM:Die-3V +xref: CALOHA:TS-2058 +xref: DHBA:10602 +xref: EHDAA2:0000084 +xref: EMAPA:16900 +xref: EV:0100308 +xref: FMA:78454 +xref: GAID:614 +xref: HBA:9420 +xref: MA:0000182 +xref: MBA:129 +xref: MESH:D020542 +xref: NCIT:C12827 +xref: neuronames:446 +xref: SCTID:180931007 +xref: TAO:0000161 +xref: UMLS:C0149555 {source="ncithesaurus:Third_Ventricle_of_Brain", source="BIRNLEX:714"} +xref: VHOG:0000007 +xref: Wikipedia:Third_ventricle +xref: ZFA:0000161 +is_a: UBERON:0004086 ! brain ventricle +relationship: part_of UBERON:0001894 ! diencephalon +relationship: RO:0002202 UBERON:0006284 {source="EHDAA2"} ! develops from early prosencephalic vesicle +relationship: RO:0002433 UBERON:0001894 ! contributes to morphology of diencephalon +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/7d/Gray734.png" xsd:anyURI +property_value: IAO:0000116 "consider adding class for secondary vesicle precursor" xsd:string +property_value: RO:0002175 NCBITaxon:9606 + +[Term] +id: UBERON:0002288 +name: choroid plexus of third ventricle +namespace: uberon +def: "Part of choroid plexus contained in the third ventricle." [NLX:18606] +subset: vertebrate_core +synonym: "3rd ventricle choroid plexus" RELATED [] +synonym: "chorioid plexus of cerebral hemisphere of third ventricle" EXACT [OBOL:automatic] +synonym: "chorioid plexus of third ventricle" EXACT [] +synonym: "choroid plexus third ventricle" EXACT [ZFA:0001444] +synonym: "diencephalic choroid plexus" EXACT [ZFA:0001444] +synonym: "third ventricle chorioid plexus of cerebral hemisphere" EXACT [OBOL:automatic] +synonym: "third ventricle choroid plexus" EXACT [] +xref: BAMS:chp3 +xref: BAMS:cp3v +xref: EMAPA:18543 +xref: FMA:78462 +xref: HBA:9709 +xref: MA:0000879 +xref: NCIT:C49782 +xref: neuronames:452 +xref: NLX:18606 +xref: SCTID:61576002 +xref: TAO:0001444 +xref: UMLS:C0152291 {source="ncithesaurus:Choroid_Plexus_of_the_Third_Ventricle"} +xref: VHOG:0001374 +xref: ZFA:0001444 +is_a: UBERON:0001886 ! choroid plexus +intersection_of: UBERON:0001886 ! choroid plexus +intersection_of: part_of UBERON:0002286 ! third ventricle +relationship: part_of UBERON:0002286 ! third ventricle + [Term] id: UBERON:0002290 name: choroid plexus of fourth ventricle @@ -192985,6 +195402,7 @@ xref: NCIT:C12678 xref: SCTID:361354009 xref: Wikipedia:Biliary_system is_a: BFO:0000002 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0011216 ! organ system subdivision intersection_of: UBERON:0011216 ! organ system subdivision intersection_of: capable_of GO:0006699 ! bile acid biosynthetic process @@ -193023,32 +195441,6 @@ relationship: RO:0002433 UBERON:0001844 ! contributes to morphology of cochlea property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/bc/Gray928.png" xsd:anyURI property_value: IAO:0000116 "TODO - check cochlear duct vs cochlear aqueduct vs scala media" xsd:string -[Term] -id: UBERON:0002296 -name: dorsal mesentery -namespace: uberon -def: "The mesentery that originates from the dorsal side of the peritoneal cavity[ZFA]." [Wikipedia:Dorsal_mesentery, Wikipedia:Mesentery#Development, ZFIN:curator] -subset: uberon_slim -subset: vertebrate_core -synonym: "dorsal mesogastrium" RELATED [Wikipedia:Dorsal_mesentery] -synonym: "mesenterium dorsale commune" RELATED OMO:0003011 [Wikipedia:Dorsal_mesentery] -xref: EHDAA2:0004560 -xref: EHDAA:3019 -xref: EHDAA:3033 -xref: EHDAA:3921 -xref: EHDAA:3934 -xref: EHDAA:3957 -xref: EHDAA:3971 -xref: FMA:79795 -xref: SCTID:308823000 -xref: TAO:0005130 -xref: Wikipedia:Mesentery#Development -xref: ZFA:0005130 -is_a: UBERON:0006598 ! presumptive structure -relationship: part_of UBERON:0009664 {source="EHDAA2"} ! gut mesentery -relationship: RO:0002387 UBERON:0002095 ! has potential to develop into mesentery -property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/85/Gray985.png" xsd:anyURI - [Term] id: UBERON:0002298 name: brainstem @@ -193128,7 +195520,7 @@ intersection_of: part_of UBERON:0002048 ! lung relationship: BFO:0000067 GO:0007585 ! contains process respiratory gaseous exchange by respiratory system relationship: part_of UBERON:0006524 {source="MA"} ! alveolar system relationship: part_of UBERON:0008874 ! pulmonary acinus -relationship: RO:0002160 NCBITaxon:40674 {source="PMID:12625309", source="PMID:12869615"} ! only in taxon Mammalia +relationship: RO:0002162 NCBITaxon:40674 {source="PMID:12625309", source="PMID:12869615"} ! in taxon Mammalia relationship: RO:0002433 UBERON:0008874 ! contributes to morphology of pulmonary acinus property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/4/46/Alveolus_diagram.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 @@ -193198,6 +195590,7 @@ xref: SCTID:362219002 xref: UMLS:C0022445 {source="ncithesaurus:Juxtaglomerular_Apparatus"} xref: Wikipedia:Juxtaglomerular_apparatus is_a: BFO:0000002 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000061 ! anatomical structure relationship: capable_of GO:0003093 {source="GO"} ! regulation of glomerular filtration relationship: has_part CL:0000648 ! kidney granular cell @@ -193761,7 +196154,7 @@ relationship: BSPO:0000102 UBERON:0001049 ! neural tube relationship: part_of UBERON:0000922 {gci_relation="part_of", gci_filler="NCBITaxon:40674"} ! embryo relationship: part_of UBERON:0011137 ! axial skeletal system relationship: produces PR:000014841 ! sonic hedgehog protein -relationship: RO:0002160 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! in taxon Chordata relationship: RO:0002202 UBERON:0004880 {source="ZFA"} ! develops from chordamesoderm relationship: RO:0002202 UBERON:0006267 {source="EHDAA2"} ! develops from notochordal plate relationship: RO:0002488 UBERON:0000068 ! existence starts during embryo stage @@ -193805,7 +196198,7 @@ xref: ZFA:0000155 is_a: BFO:0000002 is_a: UBERON:0005423 ! developing anatomical structure is_a: UBERON:0007503 {source="EHDAA2"} ! epithelial vesicle -relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {source="GOTAX:0000352"} ! in taxon Chordata relationship: RO:0002202 UBERON:0003059 {source="ZFA"} ! develops from presomitic mesoderm property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:7712 {source="PMID:17237766"} @@ -193827,6 +196220,7 @@ xref: NCIT:C12957 xref: UMLS:C1516995 {source="ncithesaurus:Exocrine_System"} xref: Wikipedia:Exocrine_gland xref: WikipediaCategory:Exocrine_system +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000467 ! anatomical system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system @@ -193834,7 +196228,7 @@ disjoint_from: UBERON:0002416 ! integumental system disjoint_from: UBERON:0002423 ! hepatobiliary system disjoint_from: UBERON:0004456 ! entire sense organ system disjoint_from: UBERON:8450002 ! excretory system -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002473 UBERON:0002365 ! composed primarily of exocrine gland relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage @@ -194081,7 +196475,7 @@ is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0010316 ! germ layer / neural crest relationship: part_of UBERON:0002346 {source="XAO", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! neurectoderm -relationship: RO:0002160 NCBITaxon:89593 ! only in taxon Craniata +relationship: RO:0002162 NCBITaxon:89593 ! in taxon Craniata relationship: RO:0002202 UBERON:0003075 {source="BTO"} ! develops from neural plate relationship: RO:0002202 UBERON:0005062 {source="PMID:11523831"} ! develops from neural fold relationship: RO:0002473 CL:0000333 ! composed primarily of migratory neural crest cell @@ -194652,7 +197046,7 @@ xref: SCTID:362305004 xref: UMLS:C0031869 {source="ncithesaurus:Pia_Mater"} xref: Wikipedia:Pia_mater is_a: UBERON:0000391 ! leptomeninx -relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia +relationship: RO:0002162 NCBITaxon:40674 ! in taxon Mammalia relationship: RO:0002473 UBERON:0011825 ! composed primarily of loose connective tissue property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/31/Gray770-en.svg" xsd:anyURI property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/65/Gray770.png" xsd:anyURI @@ -194684,7 +197078,7 @@ xref: SCTID:362304000 xref: UMLS:C1510935 {source="ncithesaurus:Arachnoid_Membrane"} xref: Wikipedia:Arachnoid_mater is_a: UBERON:0000391 ! leptomeninx -relationship: RO:0002160 NCBITaxon:40674 {source="ISBN:0073040584"} ! only in taxon Mammalia +relationship: RO:0002162 NCBITaxon:40674 {source="ISBN:0073040584"} ! in taxon Mammalia relationship: RO:0002473 GO:0071953 ! composed primarily of elastic fiber property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/a0/Gray767.png" xsd:anyURI @@ -194781,6 +197175,7 @@ xref: NCIT:C12712 xref: SCTID:115976003 xref: UMLS:C0015282 {source="ncithesaurus:Exocrine_Gland"} xref: Wikipedia:Exocrine_gland +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002530 ! gland intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0002330 ! exocrine system @@ -194821,7 +197216,7 @@ xref: VHOG:0001261 xref: Wikipedia:Prostate is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0010147 ! male accessory sex gland -relationship: RO:0002160 NCBITaxon:40674 {source="Wikipedia"} ! only in taxon Mammalia +relationship: RO:0002162 NCBITaxon:40674 {source="Wikipedia"} ! in taxon Mammalia relationship: RO:0002202 UBERON:0003820 ! develops from prostate bud property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/a1/Prostatelead.jpg" xsd:anyURI property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/prostate-male/v1.2/assets/3d-vh-m-prostate.glb" xsd:anyURI @@ -194942,6 +197337,7 @@ xref: VHOG:0000253 xref: Wikipedia:Thymus xref: XAO:0000163 xref: ZFA:0001078 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0002368 {source="EHDAA2"} ! endocrine gland is_a: UBERON:0004177 ! hemopoietic organ @@ -194951,7 +197347,7 @@ relationship: BFO:0000067 GO:0030217 ! contains process T cell differentiation relationship: has_part UBERON:0003483 ! thymus lymphoid tissue relationship: has_part UBERON:0003846 ! thymus epithelium relationship: part_of UBERON:0000153 ! anterior region of body -relationship: RO:0002160 NCBITaxon:7776 {source="multiple sources - true thymus appears in jawed vertebrates"} ! only in taxon Gnathostomata +relationship: RO:0002162 NCBITaxon:7776 {source="multiple sources - true thymus appears in jawed vertebrates"} ! in taxon Gnathostomata relationship: RO:0002202 UBERON:0005562 {source="ZFA"} ! develops from thymus primordium property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/thymus-female/v1.3/assets/3d-vh-f-thymus.glb" xsd:anyURI property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/thymus-male/v1.3/assets/3d-vh-m-thymus.glb" xsd:anyURI @@ -195261,7 +197657,7 @@ xref: VSAO:0000017 xref: XAO:0001017 xref: ZFA:0001632 is_a: UBERON:0000479 ! tissue -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -195294,7 +197690,7 @@ intersection_of: RO:0002473 CL:0000187 ! composed primarily of muscle cell disjoint_from: UBERON:0003714 ! neural tissue relationship: capable_of GO:0006936 ! muscle contraction relationship: part_of UBERON:0001015 ! musculature -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002473 CL:0000187 ! composed primarily of muscle cell [Term] @@ -195486,7 +197882,7 @@ disjoint_from: UBERON:0002423 ! hepatobiliary system disjoint_from: UBERON:0004456 ! entire sense organ system disjoint_from: UBERON:8450002 ! excretory system relationship: part_of UBERON:0002193 {source="FMA"} ! hemolymphoid system -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002202 UBERON:0003061 ! develops from blood island property_value: RO:0002175 NCBITaxon:9606 @@ -195856,6 +198252,7 @@ xref: Wikipedia:Pericardium xref: XAO:0004182 xref: ZFA:0000054 is_a: BFO:0000002 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000481 ! multi-tissue structure relationship: has_part UBERON:0002359 ! fibrous pericardium relationship: has_part UBERON:0002406 ! pericardial sac @@ -195949,7 +198346,7 @@ xref: Wikipedia:Autonomic_nervous_system xref: ZFA:0001574 is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision relationship: part_of UBERON:0000010 {source="EMAPA", source="MA", source="NIFSTD", source="ZFA-modified-from-isa"} ! peripheral nervous system -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002433 UBERON:0001016 ! contributes to morphology of nervous system property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray839.png" xsd:anyURI @@ -195979,7 +198376,7 @@ is_a: UBERON:0000062 {source="Wikipedia"} ! organ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005156 ! reproductive structure relationship: part_of UBERON:0000997 {source="MA"} ! mammalian vulva -relationship: RO:0002160 NCBITaxon:40674 {source="Wikipedia"} ! only in taxon Mammalia +relationship: RO:0002162 NCBITaxon:40674 {source="Wikipedia"} ! in taxon Mammalia relationship: RO:0002202 UBERON:0005876 {source="EHDAA2", source="Wikipedia"} ! develops from undifferentiated genital tubercle relationship: RO:0002433 UBERON:0005056 ! contributes to morphology of external female genitalia property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/c/cf/Clitoris_anatomy_labeled-en.svg" xsd:anyURI @@ -196073,7 +198470,7 @@ xref: WBbt:0005741 xref: Wikipedia:Tail is_a: UBERON:0011676 ! subdivision of organism along main body axis relationship: part_of UBERON:0000154 ! posterior region of body -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria property_value: IAO:0000116 "Note we also have a subclass post-anal tail, for the chordate specific structure. currently defined very generally, inclusive of caudal fin" xsd:string property_value: RO:0002161 NCBITaxon:9606 @@ -196120,6 +198517,7 @@ xref: VHOG:0000403 xref: Wikipedia:Integumentary_system xref: XAO:0000176 is_a: BFO:0000002 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000467 ! anatomical system disjoint_from: UBERON:0002423 ! hepatobiliary system disjoint_from: UBERON:0004456 ! entire sense organ system @@ -196191,7 +198589,7 @@ is_a: UBERON:0004755 ! skeletal tissue disjoint_from: UBERON:0002481 {source="https://github.com/obophenotype/uberon/issues/117"} ! bone tissue relationship: has_part CHEBI:18085 relationship: has_part CL:0000138 ! chondrocyte -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria relationship: RO:0002433 UBERON:0001434 ! contributes to morphology of skeletal system property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/Hypertrophic_Zone_of_Epiphyseal_Plate.jpg" xsd:anyURI @@ -196275,7 +198673,7 @@ xref: UMLS:C0175202 {source="BIRNLEX:715"} xref: Wikipedia:Hippocampal_formation is_a: UBERON:0002616 ! regional part of brain relationship: part_of UBERON:0000956 {source="MBA-indirect", source="NIFSTD"} ! cerebral cortex -relationship: RO:0002160 NCBITaxon:40674 {source="Wikipedia:Hippocampus"} ! only in taxon Mammalia +relationship: RO:0002162 NCBITaxon:40674 {source="Wikipedia:Hippocampus"} ! in taxon Mammalia property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/brain-female/v1.4/assets/3d-allen-f-brain.glb" xsd:anyURI property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/brain-male/v1.4/assets/3d-allen-m-brain.glb" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 @@ -196369,6 +198767,7 @@ xref: Wikipedia:Hepatobiliary_system xref: XAO:0000132 xref: ZFA:0000036 is_a: BFO:0000002 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0011216 ! organ system subdivision disjoint_from: UBERON:0004456 ! entire sense organ system disjoint_from: UBERON:8450002 ! excretory system @@ -196376,7 +198775,7 @@ relationship: capable_of GO:0061007 ! hepaticobiliary system process relationship: has_part UBERON:0002107 ! liver relationship: has_part UBERON:0002294 ! biliary system relationship: part_of UBERON:0001007 ! digestive system -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage [Term] @@ -196935,7 +199334,7 @@ xref: ZFA:0000385 is_a: UBERON:0000467 ! anatomical system relationship: part_of UBERON:0002193 {source="FMA"} ! hemolymphoid system relationship: part_of UBERON:0002405 ! immune system -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b3/TE-Lymphatic_system_diagram.svg" xsd:anyURI [Term] @@ -197192,7 +199591,7 @@ xref: ZFA:0005621 is_a: UBERON:0004755 {source="VSAO"} ! skeletal tissue disjoint_from: UBERON:0005090 ! muscle structure relationship: part_of UBERON:0001474 ! bone element -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata property_value: IAO:0000116 "see https://github.com/obophenotype/uberon/issues/27" xsd:string [Term] @@ -197502,7 +199901,7 @@ is_a: UBERON:0005398 ! female reproductive gland relationship: capable_of GO:0042701 ! progesterone secretion relationship: has_part CL:0000175 ! luteal cell relationship: part_of UBERON:0000992 {source="MA"} ! ovary -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002202 UBERON:0001305 ! develops from ovarian follicle property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/57/Folliclesinovary.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:7762 {source="PMID:20959416"} @@ -197570,6 +199969,7 @@ xref: NCIT:C13184 xref: SCTID:33840008 xref: UMLS:C0031110 {source="ncithesaurus:Periosteum"} xref: Wikipedia:Periosteum +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000158 ! membranous layer relationship: part_of UBERON:0001474 ! bone element relationship: RO:0002473 UBERON:0011822 ! composed primarily of dense irregular connective tissue @@ -197698,6 +200098,7 @@ xref: SCTID:87483006 xref: UMLS:C0162864 {source="ncithesaurus:Tunica_Intima"} xref: Wikipedia:Tunica_intima is_a: BFO:0000002 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004923 {source="FMA"} ! organ component layer relationship: adjacent_to UBERON:0010161 {source="ISBN:0073040584"} ! lumen of blood vessel relationship: has_part UBERON:0001986 ! endothelium @@ -197786,7 +200187,7 @@ xref: WikipediaCategory:Glands is_a: UBERON:0000062 ! organ relationship: capable_of GO:0046903 ! secretion relationship: produces UBERON:0000463 ! organism substance -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/a1/Gray1026.png" xsd:anyURI [Term] @@ -197840,7 +200241,7 @@ xref: VHOG:0000201 xref: XAO:0000107 xref: ZFA:0000077 is_a: UBERON:0002050 ! embryonic structure -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata property_value: IAO:0000116 "See notes from https://github.com/obophenotype/uberon/wiki/The-neural-crest" xsd:string [Term] @@ -197861,7 +200262,7 @@ xref: TGMA:0000540 xref: Wikipedia:Sensillum is_a: UBERON:0000020 ! sense organ relationship: part_of UBERON:0001016 ! nervous system -relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda +relationship: RO:0002162 NCBITaxon:6656 ! in taxon Arthropoda property_value: IAO:0000116 "this term should be ceded to the arthropod anatomy ontology" xsd:string [Term] @@ -197924,7 +200325,7 @@ is_a: UBERON:0010188 {source="EHDAA2"} ! protuberance is_a: UBERON:0010314 ! structure with developmental contribution from neural crest relationship: part_of UBERON:0008814 ! pharyngeal arch system relationship: part_of UBERON:0008816 {source="PMID:16313389"} ! embryonic head -relationship: RO:0002160 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! in taxon Chordata relationship: RO:0002256 UBERON:0007690 {source="PMID:16313389"} ! developmentally induced by early pharyngeal endoderm property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/8b/Gray41.png" xsd:anyURI @@ -197953,7 +200354,7 @@ is_a: BFO:0000002 is_a: UBERON:0001032 ! sensory system relationship: has_part UBERON:0010202 ! lateral line relationship: overlaps UBERON:0000010 ! peripheral nervous system -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata property_value: IAO:0000116 "we model this as being potentially inclusive of lateral line scales, and thus overlapping with the skeletal system. This is to accomodate TAO" xsd:string property_value: RO:0002161 NCBITaxon:32524 {source="http://tolweb.org/Amniota"} @@ -197988,7 +200389,7 @@ intersection_of: part_of UBERON:0012354 ! acropodium region relationship: has_part UBERON:0015023 ! phalanx endochondral element relationship: part_of UBERON:0012354 ! acropodium region relationship: part_of UBERON:5002544 ! digit plus metapodial segment -relationship: RO:0002160 NCBITaxon:32523 ! only in taxon Tetrapoda +relationship: RO:0002162 NCBITaxon:32523 ! in taxon Tetrapoda relationship: RO:0002433 UBERON:0002470 ! contributes to morphology of autopod region [Term] @@ -198008,7 +200409,7 @@ xref: MIAA:0000369 xref: XAO:0000305 is_a: UBERON:0005085 {source="cjm"} ! ectodermal placode relationship: part_of UBERON:0000033 ! head -relationship: RO:0002160 NCBITaxon:7711 {source="PMID:11523831", source="PMID:22512454"} ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {source="PMID:11523831", source="PMID:22512454"} ! in taxon Chordata property_value: IAO:0000116 "Do not merge with neurogenic placode" xsd:string [Term] @@ -198418,7 +200819,7 @@ is_a: UBERON:0005844 ! spinal cord segment intersection_of: UBERON:0005844 ! spinal cord segment intersection_of: adjacent_to UBERON:0005434 ! cervical region relationship: adjacent_to UBERON:0005434 ! cervical region -relationship: RO:0002160 NCBITaxon:8287 ! only in taxon Sarcopterygii +relationship: RO:0002162 NCBITaxon:8287 ! in taxon Sarcopterygii property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -199674,7 +202075,7 @@ xref: ZFA:0001204 is_a: BFO:0000002 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0000926 ! mesoderm -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002202 UBERON:0000926 ! develops from mesoderm property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI @@ -199889,7 +202290,7 @@ xref: ZFA:0000132 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0016879 ! future central nervous system -relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {source="GOTAX:0000352"} ! in taxon Chordata relationship: RO:0002256 UBERON:0002328 {source="Wikipedia"} ! developmentally induced by notochord relationship: RO:0002495 UBERON:0007284 {source="Bgee:AN"} ! immediate transformation of presumptive neural plate property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI @@ -199961,6 +202362,40 @@ relationship: part_of UBERON:0000010 {source="ZFA"} ! peripheral nervous system relationship: RO:0002202 UBERON:0000076 {source="EHDAA2-abduced"} ! develops from external ectoderm relationship: RO:0002385 UBERON:0002410 ! has potential to developmentally contribute to autonomic nervous system +[Term] +id: UBERON:0003079 +name: floor plate +namespace: uberon +def: "The specialized glial structure (non-neuronal cells) situated at the ventral midline of the embryonic neural tube; this structure spans the anteroposterior axis from the midbrain to the tail regions, separating the left and right basal plates of the developing neural tube, and serves as an organizer to ventralize tissues in the embryo as well as to guide neuronal positioning and differentiation along the dorsoventral axis of the neural tube." [GO:0021508, MGI:anna, PMID:15738958, Wikipedia:Floor_plate] +comment: "A structure integral to the developing nervous system of vertebrate organisms. Located on the ventral midline of the embryonic neural tube, the floor plate is a specialized glial structure that spans the anteroposterior axis from the midbrain to the tail regions. It has been shown that the floor plate is conserved among vertebrates with homologous structures in invertebrates such as the fruit fly Drosophila and the nematode C. elegans. Functionally, the structure serves as an organizer to ventralize tissues in the embryo as well as to guide neuronal positioning and differentiation along the dorsoventral axis of the neural tube." {source="Wikipedia:Floor_plate"} +subset: efo_slim +subset: pheno_slim +subset: uberon_slim +subset: vertebrate_core +synonym: "bodenplatte" RELATED [BTO:0001720] +synonym: "floorplate" EXACT [] +synonym: "FP" RELATED [TAO:0000022] +synonym: "ventral plate" RELATED [BTO:0001720] +xref: AAO:0011041 +xref: BTO:0001720 +xref: EFO:0003473 +xref: EMAPA:32684 +xref: RETIRED_EHDAA2:0000545 +xref: TAO:0000022 +xref: Wikipedia:Floor_plate +xref: ZFA:0000022 +is_a: UBERON:0000119 ! cell layer +is_a: UBERON:0004120 ! mesoderm-derived structure +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0005291 ! embryonic tissue +relationship: BSPO:0015102 UBERON:0001049 ! neural tube +relationship: part_of UBERON:0001049 ! neural tube +relationship: produces PR:000015557 ! spondin-1 +relationship: RO:0002202 UBERON:0002328 {source="Wikipedia"} ! develops from notochord +relationship: RO:0002473 CL:0000125 ! composed primarily of glial cell +relationship: RO:0002495 UBERON:0007286 ! immediate transformation of presumptive floor plate +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/8/89/Gray642.png" xsd:anyURI + [Term] id: UBERON:0003080 name: anterior neural tube @@ -200007,7 +202442,7 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue relationship: part_of UBERON:0000926 {source="EHDAA2", source="VHOG"} ! mesoderm -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria relationship: RO:0002221 UBERON:0003887 ! surrounds intraembryonic coelom property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI @@ -200143,7 +202578,7 @@ xref: XAO:0000397 xref: ZFA:0001080 is_a: UBERON:0005856 {source="EHDAA2"} ! developing mesenchymal condensation is_a: UBERON:0007530 {source="EHDAA2"} ! migrating mesenchyme population -relationship: RO:0002160 NCBITaxon:7742 {source="VHOG:0000680"} ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 {source="VHOG:0000680"} ! in taxon Vertebrata relationship: RO:0002202 UBERON:0002329 {source="ZFA"} ! develops from somite property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI @@ -200349,7 +202784,7 @@ xref: ZFA:0000393 is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002254 UBERON:0000926 {gci_relation="part_of", gci_filler="NCBITaxon:7711"} ! has developmental contribution from mesoderm relationship: RO:0002328 GO:0032502 ! functionally related to developmental process relationship: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell @@ -200423,7 +202858,7 @@ xref: XAO:0003169 xref: ZFA:0000863 is_a: UBERON:0011159 ! primary subdivision of cranial skeletal system relationship: part_of UBERON:0010364 ! dermal skeleton -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata property_value: IAO:0000116 "wikipedia treats skull roof and dermatocranium as synonymous, but some sources treat the roof as being part of the dermatocranium - see UBERONREF:0000007" xsd:string property_value: RO:0002161 NCBITaxon:7777 {source="ISBN:0073040584"} @@ -200755,7 +203190,7 @@ is_a: UBERON:0005631 ! extraembryonic membrane relationship: adjacent_to UBERON:0000922 ! embryo relationship: has_part UBERON:0003265 ! chorionic mesenchyme relationship: has_part UBERON:0003374 ! chorionic ectoderm -relationship: RO:0002160 NCBITaxon:32524 {source="Hymans"} ! only in taxon Amniota +relationship: RO:0002162 NCBITaxon:32524 {source="Hymans"} ! in taxon Amniota relationship: RO:0002202 UBERON:0005971 {source="ISBN:0073040584"} ! develops from amniotic fold property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/51/Gray24.png" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 @@ -200797,7 +203232,7 @@ xref: XAO:0000118 is_a: UBERON:0000117 ! respiratory tube relationship: part_of UBERON:0007196 ! tracheobronchial tree relationship: RO:0001025 UBERON:0002224 ! located in thoracic cavity -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002202 UBERON:0008947 {source="EHDAA2"} ! develops from respiratory primordium relationship: RO:0002433 UBERON:0001004 ! contributes to morphology of respiratory system property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/9f/Illu_conducting_passages.svg" xsd:anyURI @@ -200817,10 +203252,11 @@ synonym: "trachea" BROAD SENSU [FBbt:00005043] xref: SPD:0000434 xref: TADS:0000315 xref: Wikipedia:Invertebrate_trachea +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0001005 ! respiratory airway relationship: has_part UBERON:0003914 ! epithelial tube relationship: part_of UBERON:0005155 ! open tracheal system -relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda +relationship: RO:0002162 NCBITaxon:6656 ! in taxon Arthropoda [Term] id: UBERON:0003128 @@ -200880,7 +203316,7 @@ relationship: has_part UBERON:0003128 ! cranium relationship: has_part UBERON:0003278 ! skeleton of lower jaw relationship: part_of UBERON:0000033 ! head relationship: part_of UBERON:0010323 ! cranial skeletal system -relationship: RO:0002160 NCBITaxon:89593 ! only in taxon Craniata +relationship: RO:0002162 NCBITaxon:89593 ! in taxon Craniata [Term] id: UBERON:0003133 @@ -200970,7 +203406,7 @@ is_a: UBERON:0000119 ! cell layer relationship: adjacent_to UBERON:0000179 ! haemolymphatic fluid relationship: adjacent_to UBERON:0001021 ! nerve relationship: part_of UBERON:0001016 ! nervous system -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata [Term] id: UBERON:0003210 @@ -200984,7 +203420,7 @@ is_a: UBERON:0004121 ! ectoderm-derived structure relationship: adjacent_to UBERON:0000178 ! blood relationship: adjacent_to UBERON:0001359 ! cerebrospinal fluid relationship: part_of UBERON:0001886 ! choroid plexus -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata [Term] id: UBERON:0003212 @@ -202082,6 +204518,185 @@ intersection_of: part_of UBERON:0000926 ! mesoderm relationship: part_of UBERON:0000926 ! mesoderm relationship: part_of UBERON:0007798 {source="EHDAA2"} ! vascular system +[Term] +id: UBERON:0003306 +name: floor plate of neural tube +namespace: uberon +def: "A floor plate that is part of a neural tube [Automatically generated definition]." [OBOL:automatic] +subset: efo_slim +subset: vertebrate_core +synonym: "floor plate neural tube" EXACT [ZFA:0001434] +synonym: "floorplate neural tube" RELATED [VHOG:0000300] +synonym: "floorplate of neural tube" EXACT [OBOL:automatic] +synonym: "neural tube floor plate" EXACT [OBOL:automatic] +synonym: "neural tube floorplate" EXACT [OBOL:automatic] +xref: EFO:0003688 +xref: EHDAA2:0001256 +xref: EHDAA:2871 +xref: EHDAA:910 +xref: EMAPA:16165 +xref: TAO:0001434 +xref: VHOG:0000300 +xref: ZFA:0001434 +is_a: UBERON:0000481 ! multi-tissue structure +is_a: UBERON:0004120 ! mesoderm-derived structure +is_a: UBERON:0004121 ! ectoderm-derived structure +intersection_of: UBERON:0000481 ! multi-tissue structure +intersection_of: part_of UBERON:0001049 ! neural tube +intersection_of: part_of UBERON:0003079 ! floor plate +relationship: part_of UBERON:0003079 ! floor plate + +[Term] +id: UBERON:0003307 +name: floor plate of midbrain +namespace: uberon +def: "A floor plate that is part of a midbrain [Automatically generated definition]." [OBOL:automatic] +subset: efo_slim +subset: vertebrate_core +synonym: "floor plate mesencephalon" RELATED [VHOG:0000780] +synonym: "floor plate midbrain" EXACT [VHOG:0000780] +synonym: "floor plate midbrain region" EXACT [ZFA:0001677] +synonym: "floorplate midbrain" RELATED [VHOG:0000780] +synonym: "floorplate of midbrain" EXACT [OBOL:automatic] +synonym: "midbrain floor plate" EXACT [OBOL:automatic] +synonym: "midbrain floorplate" EXACT [OBOL:automatic] +xref: DHBA:12325 +xref: EHDAA2:0001164 +xref: EHDAA:3698 +xref: EMAPA:16975 +xref: RETIRED_EHDAA2:0001106 +xref: TAO:0002196 +xref: VHOG:0000780 +xref: ZFA:0001677 +is_a: UBERON:0002616 ! regional part of brain +is_a: UBERON:0003306 ! floor plate of neural tube +intersection_of: UBERON:0000481 ! multi-tissue structure +intersection_of: part_of UBERON:0001891 ! midbrain +intersection_of: part_of UBERON:0003079 ! floor plate +relationship: part_of UBERON:0001891 ! midbrain + +[Term] +id: UBERON:0003308 +name: floor plate of telencephalon +namespace: uberon +def: "A floor plate that is part of a telencephalon [Automatically generated definition]." [OBOL:automatic] +subset: vertebrate_core +synonym: "floor plate telencephalic region" EXACT [ZFA:0000914] +synonym: "floor plate telencephalon" EXACT [VHOG:0000783] +synonym: "floorplate of telencephalon" EXACT [OBOL:automatic] +synonym: "floorplate telencephalon" EXACT [ZFA:0000914] +synonym: "telencephalon floor plate" EXACT [OBOL:automatic] +synonym: "telencephalon floorplate" EXACT [OBOL:automatic] +xref: EHDAA2:0001983 +xref: EHDAA:3498 +xref: EMAPA:16655 +xref: TAO:0000914 +xref: VHOG:0000783 +xref: ZFA:0000914 +is_a: UBERON:0002616 ! regional part of brain +is_a: UBERON:0003306 ! floor plate of neural tube +intersection_of: UBERON:0000481 ! multi-tissue structure +intersection_of: part_of UBERON:0001893 ! telencephalon +intersection_of: part_of UBERON:0003079 ! floor plate +relationship: part_of UBERON:0001893 ! telencephalon + +[Term] +id: UBERON:0003309 +name: floor plate of diencephalon +namespace: uberon +def: "A floor plate that is part of a diencephalon [Automatically generated definition]." [OBOL:automatic] +subset: vertebrate_core +synonym: "between brain floor plate" EXACT [OBOL:automatic] +synonym: "between brain floorplate" EXACT [OBOL:automatic] +synonym: "diencephalon floor plate" EXACT [OBOL:automatic] +synonym: "diencephalon floorplate" EXACT [OBOL:automatic] +synonym: "floor plate diencephalic region" EXACT [ZFA:0000871] +synonym: "floor plate diencephalon" EXACT [VHOG:0000782] +synonym: "floor plate of between brain" EXACT [OBOL:automatic] +synonym: "floor plate of interbrain" EXACT [OBOL:automatic] +synonym: "floor plate of mature diencephalon" EXACT [OBOL:automatic] +synonym: "floorplate diencephalon" EXACT [ZFA:0000871] +synonym: "floorplate of between brain" EXACT [OBOL:automatic] +synonym: "floorplate of diencephalon" EXACT [OBOL:automatic] +synonym: "floorplate of interbrain" EXACT [OBOL:automatic] +synonym: "floorplate of mature diencephalon" EXACT [OBOL:automatic] +synonym: "interbrain floor plate" EXACT [OBOL:automatic] +synonym: "interbrain floorplate" EXACT [OBOL:automatic] +synonym: "mature diencephalon floor plate" EXACT [OBOL:automatic] +synonym: "mature diencephalon floorplate" EXACT [OBOL:automatic] +xref: EHDAA2:0000388 +xref: EHDAA:1975 +xref: EHDAA:2651 +xref: EHDAA:3480 +xref: EMAPA:16903 +xref: TAO:0000871 +xref: VHOG:0000782 +xref: ZFA:0000871 +is_a: UBERON:0002616 ! regional part of brain +is_a: UBERON:0003306 ! floor plate of neural tube +intersection_of: UBERON:0000481 ! multi-tissue structure +intersection_of: part_of UBERON:0001894 ! diencephalon +intersection_of: part_of UBERON:0003079 ! floor plate +relationship: part_of UBERON:0001894 ! diencephalon + +[Term] +id: UBERON:0003310 +name: floor plate of metencephalon +namespace: uberon +def: "A floor plate that is part of a metencephalon [Automatically generated definition]." [OBOL:automatic] +synonym: "epencephalon-2 floor plate" EXACT [OBOL:automatic] +synonym: "epencephalon-2 floorplate" EXACT [OBOL:automatic] +synonym: "floor plate metencephalon" EXACT [VHOG:0000784] +synonym: "floor plate of epencephalon-2" EXACT [OBOL:automatic] +synonym: "floorplate metencephalon" RELATED [VHOG:0000784] +synonym: "floorplate of epencephalon-2" EXACT [OBOL:automatic] +synonym: "floorplate of metencephalon" EXACT [OBOL:automatic] +synonym: "metencephalon floor plate" EXACT [OBOL:automatic] +synonym: "metencephalon floorplate" EXACT [OBOL:automatic] +xref: EHDAA2:0001158 +xref: EHDAA:5500 +xref: EMAPA:17258 +xref: VHOG:0000784 +is_a: UBERON:0002616 ! regional part of brain +is_a: UBERON:0003306 ! floor plate of neural tube +intersection_of: UBERON:0000481 ! multi-tissue structure +intersection_of: part_of UBERON:0001895 ! metencephalon +intersection_of: part_of UBERON:0003079 ! floor plate +relationship: part_of UBERON:0001895 ! metencephalon + +[Term] +id: UBERON:0003311 +name: floor plate of medulla oblongata +namespace: uberon +def: "A floor plate that is part of a medulla oblongata [Automatically generated definition]." [OBOL:automatic] +synonym: "bulb floor plate" EXACT [OBOL:automatic] +synonym: "bulb floorplate" EXACT [OBOL:automatic] +synonym: "floor plate medulla oblongata" EXACT [VHOG:0000786] +synonym: "floor plate of bulb" EXACT [OBOL:automatic] +synonym: "floor plate of medulla oblonmgata" EXACT [OBOL:automatic] +synonym: "floor plate of metepencephalon" EXACT [OBOL:automatic] +synonym: "floorplate medulla oblongata" RELATED [VHOG:0000786] +synonym: "floorplate of bulb" EXACT [OBOL:automatic] +synonym: "floorplate of medulla oblongata" EXACT [OBOL:automatic] +synonym: "floorplate of medulla oblonmgata" EXACT [OBOL:automatic] +synonym: "floorplate of metepencephalon" EXACT [OBOL:automatic] +synonym: "medulla oblongata floor plate" EXACT [OBOL:automatic] +synonym: "medulla oblongata floorplate" EXACT [OBOL:automatic] +synonym: "medulla oblonmgata floor plate" EXACT [OBOL:automatic] +synonym: "medulla oblonmgata floorplate" EXACT [OBOL:automatic] +synonym: "metepencephalon floor plate" EXACT [OBOL:automatic] +synonym: "metepencephalon floorplate" EXACT [OBOL:automatic] +xref: EHDAA2:0001097 +xref: EHDAA:7590 +xref: EMAPA:17551 +xref: VHOG:0000786 +is_a: UBERON:0002616 ! regional part of brain +is_a: UBERON:0003306 ! floor plate of neural tube +intersection_of: UBERON:0000481 ! multi-tissue structure +intersection_of: part_of UBERON:0001896 ! medulla oblongata +intersection_of: part_of UBERON:0003079 ! floor plate +relationship: part_of UBERON:0001896 ! medulla oblongata + [Term] id: UBERON:0003312 name: mesenchyme of testis @@ -207718,7 +210333,7 @@ xref: Wikipedia:Recurrent_laryngeal_nerve is_a: BFO:0000002 is_a: UBERON:0011779 ! nerve of head region is_a: UBERON:0035642 ! laryngeal nerve -relationship: RO:0002160 NCBITaxon:32523 ! only in taxon Tetrapoda +relationship: RO:0002162 NCBITaxon:32523 ! in taxon Tetrapoda relationship: RO:0002202 UBERON:0003117 {source="Wikipedia"} ! develops from pharyngeal arch 6 relationship: RO:0002380 UBERON:0001759 ! branching part of vagus nerve property_value: RO:0002175 NCBITaxon:9606 @@ -208920,7 +211535,7 @@ is_a: UBERON:0013515 ! subdivision of oviduct is_a: UBERON:0015212 ! lateral structure relationship: BSPO:0000126 UBERON:0003975 {source="FMA-abduced-lr"} ! internal female genitalia relationship: part_of UBERON:0002355 ! pelvic region of trunk -relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia +relationship: RO:0002162 NCBITaxon:40674 ! in taxon Mammalia relationship: RO:0002176 UBERON:0000995 ! connects uterus relationship: RO:0002176 UBERON:0003984 ! connects uterine tube infundibulum relationship: RO:0002202 UBERON:0003890 ! develops from Mullerian duct @@ -208970,7 +211585,7 @@ xref: FMA:81494 xref: NCIT:C67387 xref: UMLS:C0927195 {source="ncithesaurus:Stroma_Connective_Tissue"} is_a: UBERON:0000064 ! organ part -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002473 UBERON:0002384 ! composed primarily of connective tissue [Term] @@ -209134,7 +211749,7 @@ is_a: UBERON:0003909 ! sinusoid intersection_of: UBERON:0003909 ! sinusoid intersection_of: part_of UBERON:0001250 ! red pulp of spleen relationship: part_of UBERON:0001250 ! red pulp of spleen -relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia +relationship: RO:0002162 NCBITaxon:40674 ! in taxon Mammalia relationship: RO:0002170 UBERON:0010400 ! connected to spleen trabecular vein property_value: RO:0002161 NCBITaxon:10088 {source="http://www.informatics.jax.org/greenbook/chapters/chapter13.shtml"} property_value: RO:0002161 NCBITaxon:9681 {source="http://www.informatics.jax.org/greenbook/chapters/chapter13.shtml"} @@ -209172,7 +211787,7 @@ synonym: "tooth-like organ" EXACT [http://orcid.org/0000-0002-6601-2165] xref: HAO:0001019 is_a: UBERON:0004765 ! skeletal element relationship: capable_of_part_of GO:0071626 ! mastication -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria [Term] id: UBERON:0003914 @@ -209725,7 +212340,7 @@ xref: SCTID:362262001 xref: Wikipedia:Infundibulum_of_uterine_tube is_a: UBERON:0013515 {source="FMA"} ! subdivision of oviduct relationship: part_of UBERON:0003889 {gci_relation="part_of", gci_filler="NCBITaxon:40674", source="FMA"} ! fallopian tube -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/6/66/Illu_cervix.jpg" xsd:anyURI property_value: RO:0002175 NCBITaxon:8782 property_value: RO:0002175 NCBITaxon:9606 @@ -209746,6 +212361,7 @@ synonym: "thymus cortico-medullary boundary" EXACT [MP:0009543] synonym: "thymus corticomedullary junction" EXACT [MP:0009543] synonym: "thymus corticomedullary zone" EXACT [MP:0009543] xref: EMAPA:37974 {source="MA:th"} +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000077 ! mixed endoderm/mesoderm-derived structure is_a: UBERON:0007651 ! anatomical junction intersection_of: UBERON:0007651 ! anatomical junction @@ -209845,7 +212461,7 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005156 ! reproductive structure is_a: UBERON:0005292 ! extraembryonic tissue relationship: part_of UBERON:0001987 ! placenta -relationship: RO:0002160 NCBITaxon:9989 {source="MP:0004255", source="PMID:11433360"} ! only in taxon Rodentia +relationship: RO:0002162 NCBITaxon:9989 {source="MP:0004255", source="PMID:11433360"} ! in taxon Rodentia relationship: RO:0002202 UBERON:0004364 {source="PMID:19829370"} ! develops from ectoplacental cone relationship: RO:0002473 CL:0002499 ! composed primarily of spongiotrophoblast cell @@ -209993,7 +212609,7 @@ xref: EMAPA:17545 xref: EMAPA:32712 is_a: BFO:0000002 is_a: UBERON:0014950 ! layer of developing cerebral cortex -relationship: RO:0002160 NCBITaxon:40674 {source="Wikipedia"} ! only in taxon Mammalia +relationship: RO:0002162 NCBITaxon:40674 {source="Wikipedia"} ! in taxon Mammalia relationship: RO:0002202 UBERON:0004061 ! develops from neural tube mantle layer [Term] @@ -210401,7 +213017,7 @@ xref: FMA:285406 xref: MA:0001910 is_a: UBERON:0001444 ! subdivision of head relationship: part_of UBERON:0001456 ! face -relationship: RO:0002160 NCBITaxon:89593 ! only in taxon Craniata +relationship: RO:0002162 NCBITaxon:89593 ! in taxon Craniata relationship: RO:0002433 UBERON:0001456 ! contributes to morphology of face property_value: IAO:0000116 "this class is currently a union of the snout (e.g. in mouse), the midface and the lower face. Note that in MA, snout includes the whole jaw and should thus be more alike the lower face than the midface, so its placement here is not strictly accurate. In future we might introduce specific classes for each of these, and include the full parthood relationships. if this is done, then care should be taken to preserve inferences such as an abnormality of the lower face being an abnormality of the midface." xsd:string @@ -210646,7 +213262,7 @@ is_a: UBERON:0003258 ! endoderm of foregut is_a: UBERON:0005291 ! embryonic tissue relationship: overlaps UBERON:0002539 ! pharyngeal arch relationship: part_of UBERON:0008814 ! pharyngeal arch system -relationship: RO:0002160 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! in taxon Chordata relationship: RO:0002202 UBERON:0007690 {source="EHDAA2", source="ZFA"} ! develops from early pharyngeal endoderm [Term] @@ -210843,7 +213459,7 @@ def: "Cartilage that will provide a scaffold for mineralization of endochondral synonym: "growth plate" RELATED [] is_a: UBERON:0002418 ! cartilage tissue relationship: part_of UBERON:0010363 ! endochondral element -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002221 UBERON:0004763 ! surrounds endochondral bone tissue relationship: site_of GO:0030282 ! bone mineralization @@ -211033,7 +213649,7 @@ synonym: "ventricular conduction system" EXACT [] is_a: UBERON:0010131 {source="cjm"} ! conducting tissue of heart is_a: UBERON:0018649 ! cardiac muscle tissue of ventricle relationship: part_of UBERON:0002350 {source="GO"} ! conducting system of heart -relationship: RO:0002160 NCBITaxon:32523 {source="PMID:12626327", source="PMID:21234997", source="github:michaelerice"} ! only in taxon Tetrapoda +relationship: RO:0002162 NCBITaxon:32523 {source="PMID:12626327", source="PMID:21234997", source="github:michaelerice"} ! in taxon Tetrapoda [Term] id: UBERON:0004148 @@ -211126,7 +213742,7 @@ xref: XAO:0004325 is_a: UBERON:0001630 ! muscle organ is_a: UBERON:0004120 ! mesoderm-derived structure relationship: RO:0002005 UBERON:0001785 {source="ISBN:0073040584"} ! innervated_by cranial nerve -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002202 UBERON:0010360 {source="PMID:21610022"} ! develops from pharyngeal arch mesenchyme from head mesenchyme relationship: RO:0002473 UBERON:0001134 ! composed primarily of skeletal muscle tissue @@ -212896,6 +215512,7 @@ namespace: uberon def: "A zone of skin that is part of a lower leg [Automatically generated definition]." [OBOL:automatic] synonym: "hind limb middle limb segment skin" EXACT [OBOL:automatic] synonym: "hind limb zeugopod skin" EXACT [OBOL:automatic] +synonym: "hindlimb zeugopod skin" EXACT [https://orcid.org/0000-0002-0819-0473] xref: EMAPA:18156 xref: MA:0000680 xref: SCTID:244180007 @@ -213068,6 +215685,34 @@ intersection_of: UBERON:0000483 ! epithelium intersection_of: part_of UBERON:0002307 ! choroid plexus of lateral ventricle relationship: part_of UBERON:0002307 ! choroid plexus of lateral ventricle +[Term] +id: UBERON:0004275 +name: third ventricle choroid plexus epithelium +namespace: uberon +def: "A choroid plexus epithelium that is part of a third ventricle [Automatically generated definition]." [OBOL:automatic] +synonym: "chorioid plexus of cerebral hemisphere epithelial tissue of third ventricle" EXACT [OBOL:automatic] +synonym: "chorioid plexus of cerebral hemisphere epithelium of third ventricle" EXACT [OBOL:automatic] +synonym: "choroid plexus epithelial tissue of third ventricle" EXACT [OBOL:automatic] +synonym: "choroid plexus epithelium of third ventricle" EXACT [OBOL:automatic] +synonym: "epithelial tissue of chorioid plexus of cerebral hemisphere of third ventricle" EXACT [OBOL:automatic] +synonym: "epithelial tissue of choroid plexus of third ventricle" EXACT [OBOL:automatic] +synonym: "epithelium of chorioid plexus of cerebral hemisphere of third ventricle" EXACT [OBOL:automatic] +synonym: "epithelium of choroid plexus of third ventricle" EXACT [OBOL:automatic] +synonym: "third ventricle chorioid plexus of cerebral hemisphere epithelial tissue" EXACT [OBOL:automatic] +synonym: "third ventricle chorioid plexus of cerebral hemisphere epithelium" EXACT [OBOL:automatic] +synonym: "third ventricle choroid plexus epithelial tissue" EXACT [OBOL:automatic] +synonym: "third ventricle epithelial tissue of chorioid plexus of cerebral hemisphere" EXACT [OBOL:automatic] +synonym: "third ventricle epithelial tissue of choroid plexus" EXACT [OBOL:automatic] +synonym: "third ventricle epithelium of chorioid plexus of cerebral hemisphere" EXACT [OBOL:automatic] +synonym: "third ventricle epithelium of choroid plexus" EXACT [OBOL:automatic] +xref: EMAPA:37055 {source="MA:th"} +xref: FMA:242821 +xref: MA:0000880 +is_a: UBERON:0003911 ! choroid plexus epithelium +intersection_of: UBERON:0003911 ! choroid plexus epithelium +intersection_of: part_of UBERON:0002286 ! third ventricle +relationship: part_of UBERON:0002288 ! choroid plexus of third ventricle + [Term] id: UBERON:0004276 name: fourth ventricle choroid plexus epithelium @@ -213377,7 +216022,7 @@ xref: Wikipedia:Allantois is_a: BFO:0000002 is_a: UBERON:0005631 ! extraembryonic membrane relationship: overlaps UBERON:0001008 {source="EHDAA2-modified"} ! renal system -relationship: RO:0002160 NCBITaxon:32524 {source="Hymans"} ! only in taxon Amniota +relationship: RO:0002162 NCBITaxon:32524 {source="Hymans"} ! in taxon Amniota relationship: RO:0002202 UBERON:0000162 {source="Hymans"} ! develops from cloaca relationship: RO:0002254 UBERON:0000925 ! has developmental contribution from endoderm relationship: RO:0002254 UBERON:0004872 {source="ISBN:0073040584"} ! has developmental contribution from splanchnic layer of lateral plate mesoderm @@ -213448,7 +216093,7 @@ xref: UMLS:C0282505 {source="ncithesaurus:Limb_Bud"} xref: Wikipedia:Limb_bud xref: XAO:0003161 is_a: UBERON:0004357 ! paired limb/fin bud -relationship: RO:0002160 NCBITaxon:32523 ! only in taxon Tetrapoda +relationship: RO:0002162 NCBITaxon:32523 ! in taxon Tetrapoda relationship: RO:0002254 UBERON:0005733 ! has developmental contribution from limb field relationship: RO:0002256 UBERON:0003081 {source="ISBN:9780878932504"} ! developmentally induced by lateral plate mesoderm relationship: RO:0002387 UBERON:0002101 ! has potential to develop into limb @@ -214967,6 +217612,7 @@ xref: XAO:0000100 xref: XAO:0001010 xref: ZFA:0000010 is_a: BFO:0000002 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000467 ! anatomical system intersection_of: UBERON:0000467 ! anatomical system intersection_of: has_part UBERON:0000948 ! heart @@ -215018,6 +217664,7 @@ synonym: "set of blood vessels" EXACT [] xref: TAO:0001079 xref: ZFA:0001079 is_a: BFO:0000002 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel @@ -215241,6 +217888,7 @@ xref: MA:0002719 xref: SCTID:362030008 xref: VHOG:0000273 is_a: BFO:0000002 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0007798 {source="MA"} ! vascular system relationship: RO:0002351 UBERON:0001637 ! has member artery property_value: RO:0002175 NCBITaxon:9606 @@ -215290,6 +217938,7 @@ xref: SCTID:362060003 xref: UMLS:C1267406 {source="ncithesaurus:Venous_System"} xref: VHOG:0000277 is_a: BFO:0000002 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0007798 {source="MA"} ! vascular system relationship: RO:0002473 UBERON:0001638 ! composed primarily of vein property_value: RO:0002175 NCBITaxon:9606 @@ -215445,6 +218094,22 @@ relationship: part_of UBERON:0002106 ! spleen relationship: RO:0002433 UBERON:0002106 ! contributes to morphology of spleen property_value: RO:0002175 NCBITaxon:9606 +[Term] +id: UBERON:0004642 +name: third ventricle ependyma +namespace: uberon +def: "An ependyma that is part of a third ventricle [Automatically generated definition]." [OBOL:automatic] +synonym: "3rd ventricle ependyma" EXACT [MA:0000882] +synonym: "ependyma of third ventricle" EXACT [MA:0000882] +xref: EMAPA:35100 +xref: FMA:242833 +xref: MA:0000882 +xref: SCTID:362316006 +is_a: UBERON:0005357 ! brain ependyma +intersection_of: UBERON:0004670 ! ependyma +intersection_of: part_of UBERON:0002286 ! third ventricle +relationship: part_of UBERON:0002286 ! third ventricle + [Term] id: UBERON:0004643 name: lateral ventricle ependyma @@ -216155,7 +218820,7 @@ is_a: BFO:0000003 is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000111 ! organogenesis stage relationship: preceded_by UBERON:0000110 ! neurula stage -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0004708 @@ -216173,6 +218838,7 @@ synonym: "pectoral or pelvic appendage" EXACT [https://orcid.org/0000-0002-6601- synonym: "pelvic/pectoral appendage" EXACT [https://orcid.org/0000-0002-6601-2165] xref: VSAO:0000067 is_a: BFO:0000002 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000026 {source="VSAO"} ! appendage intersection_of: UBERON:0000026 ! appendage intersection_of: part_of UBERON:0010707 ! appendage girdle complex @@ -216180,7 +218846,7 @@ relationship: has_part UBERON:0000014 ! zone of skin relationship: has_part UBERON:0001015 ! musculature relationship: has_part UBERON:0002049 ! vasculature relationship: part_of UBERON:0010707 {source="VSAO"} ! appendage girdle complex -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002170 UBERON:0007823 ! connected to appendage girdle region relationship: RO:0002202 UBERON:0004357 ! develops from paired limb/fin bud relationship: RO:0002551 UBERON:0011582 ! has skeleton paired limb/fin skeleton @@ -216409,7 +219075,7 @@ xref: UMLS:C0228280 {source="BIRNLEX:1097"} xref: Wikipedia:Piriform_cortex is_a: UBERON:0002616 ! regional part of brain relationship: part_of UBERON:0002894 ! olfactory cortex -relationship: RO:0002160 NCBITaxon:32523 {source="Wikipedia"} ! only in taxon Tetrapoda +relationship: RO:0002162 NCBITaxon:32523 {source="Wikipedia"} ! in taxon Tetrapoda relationship: RO:0002433 UBERON:0002894 ! contributes to morphology of olfactory cortex property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b1/Human_brainstem_anterior_view_2_description.JPG" xsd:anyURI property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/brain-female/v1.4/assets/3d-allen-f-brain.glb" xsd:anyURI @@ -216714,6 +219380,57 @@ intersection_of: RO:0002202 UBERON:0002067 ! develops from dermis relationship: has_part UBERON:0004755 ! skeletal tissue relationship: RO:0002202 UBERON:0002067 ! develops from dermis +[Term] +id: UBERON:0004757 +name: rectal salt gland +namespace: uberon +def: "An evagination of the terminal portion of the intestine that is capable of secreting high concentrations of excess sodium chloride." [http://www.briancoad.com/dictionary/complete%20dictionary.htm, UBERON:cjm] +subset: organ_slim +synonym: "digitiform gland" BROAD [http://www.briancoad.com/dictionary/complete%20dictionary.htm] +synonym: "glandula rectalis" BROAD OMO:0003011 [http://www.briancoad.com/dictionary/complete%20dictionary.htm] +synonym: "rectal gland" BROAD [] +xref: BTO:0001157 +xref: SCTID:80455007 +is_a: UBERON:0003408 ! gland of digestive tract +is_a: UBERON:0004758 ! salt gland +intersection_of: UBERON:0002530 ! gland +intersection_of: capable_of GO:0055078 ! sodium ion homeostasis +intersection_of: part_of UBERON:0001052 ! rectum +relationship: part_of UBERON:0001052 ! rectum +relationship: RO:0002162 NCBITaxon:7776 ! in taxon Gnathostomata +property_value: RO:0002161 NCBITaxon:32523 +property_value: RO:0002175 NCBITaxon:118072 +property_value: RO:0002175 NCBITaxon:119203 + +[Term] +id: UBERON:0004758 +name: salt gland +namespace: uberon +def: "An organ for excreting excess salts. It is found in elasmobranchs, seabirds, and some reptiles.[WP]." [Wikipedia:Salt_gland] +subset: functional_classification +subset: organ_slim +xref: BTO:0001204 +xref: GAID:1235 +xref: MESH:D012491 +xref: Wikipedia:Salt_gland +is_a: UBERON:0002530 ! gland +intersection_of: UBERON:0002530 ! gland +intersection_of: capable_of GO:0055078 ! sodium ion homeostasis +relationship: capable_of GO:0055078 ! sodium ion homeostasis +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata +property_value: RO:0002161 NCBITaxon:40674 + +[Term] +id: UBERON:0004759 +name: cranial salt gland +namespace: uberon +def: "A salt gland located in the cranium or head region." [OBOL:automatic] +subset: organ_slim +is_a: UBERON:0004758 ! salt gland +intersection_of: UBERON:0004758 ! salt gland +intersection_of: part_of UBERON:0000033 ! head +relationship: part_of UBERON:0000033 ! head + [Term] id: UBERON:0004760 name: gland of anal canal @@ -216764,7 +219481,7 @@ xref: XAO:0003059 is_a: BFO:0000002 is_a: UBERON:0000075 {source="FMA"} ! subdivision of skeletal system relationship: has_part UBERON:0002418 ! cartilage tissue -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002202 UBERON:0009617 {source="PMC1571569"} ! develops from head paraxial mesoderm [Term] @@ -216892,7 +219609,7 @@ is_a: UBERON:0034925 ! anatomical collection intersection_of: UBERON:0034925 ! anatomical collection intersection_of: RO:0002351 UBERON:0000982 ! has member skeletal joint relationship: part_of UBERON:0001434 {source="FMA"} ! skeletal system -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria relationship: RO:0002328 GO:0040011 ! functionally related to locomotion relationship: RO:0002351 UBERON:0000982 ! has member skeletal joint relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage @@ -218471,7 +221188,7 @@ xref: TAO:0000091 xref: ZFA:0000091 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0003068 ! axial mesoderm -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata [Term] id: UBERON:0004883 @@ -218913,7 +221630,7 @@ subset: upper_level xref: FMA:82485 is_a: UBERON:0000064 ! organ part relationship: part_of UBERON:0000060 ! anatomical wall -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0004924 @@ -220985,7 +223702,7 @@ xref: FMA:30316 is_a: BFO:0000002 is_a: UBERON:0000061 ! anatomical structure relationship: has_part CL:0000187 ! muscle cell -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0005092 @@ -221543,7 +224260,7 @@ xref: FBbt:00005024 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ xref: SPD:0000427 xref: TADS:0000043 is_a: UBERON:0001004 ! respiratory system -relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda +relationship: RO:0002162 NCBITaxon:6656 ! in taxon Arthropoda [Term] id: UBERON:0005156 @@ -221893,6 +224610,7 @@ id: UBERON:0005184 name: hair medulla namespace: uberon def: "Innermost layer of the hair shaft." [Wikipedia:Bone_marrow_of_ovary_(hair)] +subset: human_reference_atlas subset: pheno_slim synonym: "medulla of hair shaft" RELATED [BTO:0004671] xref: BTO:0004671 @@ -221905,6 +224623,7 @@ is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0000958 ! medulla of organ intersection_of: part_of UBERON:0001037 ! strand of hair relationship: part_of UBERON:0001037 ! strand of hair +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0005185 @@ -222106,6 +224825,7 @@ def: "Stromal matrix surrounding blood vessels within the choroid plexus." [PMCI synonym: "choroid plexus stromal matrix" EXACT [PMCID:PMC3496674] xref: EMAPA:36609 xref: MA:0000825 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0003891 ! stroma is_a: UBERON:0004121 ! ectoderm-derived structure intersection_of: UBERON:0003891 ! stroma @@ -222693,6 +225413,7 @@ xref: EMAPA:28136 xref: MA:0002608 xref: SCTID:243707006 xref: Wikipedia:Medullary_interstitium +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005215 ! kidney interstitium intersection_of: UBERON:0005169 ! interstitial tissue intersection_of: part_of UBERON:0001225 ! cortex of kidney @@ -222857,6 +225578,32 @@ intersection_of: UBERON:0005283 ! tela choroidea intersection_of: part_of UBERON:0002422 ! fourth ventricle relationship: part_of UBERON:0002422 ! fourth ventricle +[Term] +id: UBERON:0005288 +name: tela choroidea of third ventricle +namespace: uberon +def: "Tela chorioidea that lines the third ventricle[ZFA]. The part of the choroid plexus in relation to the body of the ventricle forms the vascular fringed margin of a triangular process of pia mater, named the tela chorioidea of the third ventricle, and projects from under cover of the lateral edge of the fornix. Blood is supplied by branches from the superior cerebellar artery[WP]." [Wikipedia:Tela_chorioidea_of_third_ventricle, ZFIN:curator] +subset: vertebrate_core +synonym: "choroid membrane of third ventricle" EXACT [FMA:78463] +synonym: "tela chorioidea of third ventricle" EXACT [] +synonym: "tela chorioidea third ventricle" EXACT [ZFA:0005159] +synonym: "tela choroidea third ventricle" EXACT [] +synonym: "tela choroidea ventriculi tertii" EXACT OMO:0003011 [FMA:78463, FMA:TA] +synonym: "tela choroidea ventriculi tertii" RELATED OMO:0003011 [Wikipedia:Tela_chorioidea_of_third_ventricle] +xref: BAMS:tc3v +xref: FMA:78463 +xref: neuronames:453 +xref: SCTID:362320005 +xref: TAO:0005159 +xref: Wikipedia:Tela_chorioidea_of_third_ventricle +xref: ZFA:0005159 +is_a: UBERON:0004121 ! ectoderm-derived structure +is_a: UBERON:0005283 ! tela choroidea +intersection_of: UBERON:0005283 ! tela choroidea +intersection_of: part_of UBERON:0002286 ! third ventricle +relationship: part_of UBERON:0002286 ! third ventricle +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/60/Gray723.png" xsd:anyURI + [Term] id: UBERON:0005289 name: tela choroidea of telencephalic ventricle @@ -223418,6 +226165,7 @@ xref: NCIT:C12329 xref: SCTID:181433005 xref: UMLS:C0037855 {source="ncithesaurus:Spermatic_Cord"} xref: Wikipedia:Spermatic_cord +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005156 ! reproductive structure is_a: UBERON:0034921 ! multi organ part structure relationship: has_part UBERON:0001000 ! vas deferens @@ -224265,7 +227013,7 @@ xref: MA:0002975 xref: SCTID:246901006 xref: Wikipedia:Adipose_capsule_of_kidney is_a: UBERON:0001013 ! adipose tissue -relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia +relationship: RO:0002162 NCBITaxon:40674 ! in taxon Mammalia property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg" xsd:anyURI property_value: IAO:0000116 "TODO - split perinephric / perirenal" xsd:string @@ -224671,7 +227419,7 @@ xref: FMA:24219 xref: SCTID:123958008 is_a: UBERON:0011676 ! subdivision of organism along main body axis relationship: part_of UBERON:0000974 ! neck -relationship: RO:0002160 NCBITaxon:8287 ! only in taxon Sarcopterygii +relationship: RO:0002162 NCBITaxon:8287 ! in taxon Sarcopterygii [Term] id: UBERON:0005436 @@ -225367,24 +228115,6 @@ intersection_of: UBERON:0002329 ! somite intersection_of: part_of UBERON:0002100 ! trunk relationship: part_of UBERON:0002100 ! trunk -[Term] -id: UBERON:0005602 -name: dorsal mesogastrium -namespace: uberon -def: "The portion of mesentery attached to the greater curvature of the stomach is named the dorsal mesentery (or dorsal mesogastrium, when referring to the portion at the stomach), and the part which suspends the colon is termed the mesocolon. The dorsal mesogastrium develops into the greater omentum." [Wikipedia:Dorsal_mesentery] -synonym: "dorsal mesentery" RELATED [Wikipedia:Dorsal_mesentery] -xref: EHDAA2:0000416 -xref: EHDAA:3001 -xref: EMAPA:17025 -xref: MA:0001618 -xref: NCIT:C34142 -xref: UMLS:C1512038 {source="ncithesaurus:Dorsal_Mesogastrium"} -xref: VHOG:0000352 -xref: Wikipedia:Dorsal_mesentery -is_a: UBERON:0003281 {source="MA"} ! mesentery of stomach -relationship: part_of UBERON:0002296 {source="EHDAA2"} ! dorsal mesentery -relationship: part_of UBERON:0003281 {source="EHDAA2"} ! mesentery of stomach - [Term] id: UBERON:0005604 name: extrahepatic part of hepatic duct @@ -225622,6 +228352,7 @@ xref: EMAPA:35904 xref: FMA:5900 xref: XAO:0004143 is_a: BFO:0000002 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002049 ! vasculature relationship: has_part UBERON:0001981 ! blood vessel @@ -225853,32 +228584,6 @@ intersection_of: UBERON:0002095 ! mesentery intersection_of: part_of UBERON:0001153 ! caecum relationship: part_of UBERON:0001153 ! caecum -[Term] -id: UBERON:0005685 -name: midgut dorsal mesentery -namespace: uberon -def: "A dorsal mesentery that is part of a midgut." [OBOL:automatic] -xref: EMAPA:16722 -xref: EMAPA:17040 -xref: EMAPA:18671 -xref: RETIRED_EHDAA2:0001187 -xref: SCTID:361434009 -is_a: UBERON:0002296 ! dorsal mesentery -intersection_of: UBERON:0002296 ! dorsal mesentery -intersection_of: part_of UBERON:0001045 ! midgut -relationship: part_of UBERON:0001045 ! midgut - -[Term] -id: UBERON:0005686 -name: caecum dorsal mesentery -namespace: uberon -def: "A dorsal mesentery that is part of a caecum." [OBOL:automatic] -xref: RETIRED_EHDAA2:0000208 -is_a: UBERON:0002296 ! dorsal mesentery -intersection_of: UBERON:0002296 ! dorsal mesentery -intersection_of: part_of UBERON:0001153 ! caecum -relationship: part_of UBERON:0001153 ! caecum - [Term] id: UBERON:0005687 name: orbitosphenoid cartilage element @@ -226063,6 +228768,28 @@ relationship: part_of UBERON:0003064 {source="ZFA"} ! intermediate mesoderm relationship: RO:0002387 UBERON:0002120 ! has potential to develop into pronephros relationship: RO:0002495 UBERON:0007297 {source="Bgee:AN"} ! immediate transformation of presumptive pronephric mesoderm +[Term] +id: UBERON:0005723 +name: floor plate spinal cord region +namespace: uberon +alt_id: UBERON:0005247 +def: "A multi-tissue structure that is part of a spinal cord and is part of a floor plate." [OBOL:automatic] +subset: vertebrate_core +synonym: "floor plate spinal cord" EXACT [VHOG:0000787] +synonym: "floorplate spinal cord" EXACT [ZFA:0000890] +synonym: "spinal cord floor" RELATED [VHOG:0000787] +xref: EMAPA:17578 +xref: TAO:0000890 +xref: VHOG:0000787 +xref: XAO:0000306 +xref: ZFA:0000890 +is_a: UBERON:0001948 ! regional part of spinal cord +is_a: UBERON:0003306 ! floor plate of neural tube +intersection_of: UBERON:0000481 ! multi-tissue structure +intersection_of: part_of UBERON:0002240 ! spinal cord +intersection_of: part_of UBERON:0003079 ! floor plate +relationship: RO:0002202 UBERON:0003306 ! develops from floor plate of neural tube + [Term] id: UBERON:0005725 name: olfactory system @@ -226199,6 +228926,7 @@ xref: NCIT:C33818 xref: SCTID:61066005 xref: UMLS:C0225342 {source="ncithesaurus:Tunica_Adventitia"} xref: Wikipedia:Tunica_externa_(vessels) +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004797 {source="cjm"} ! blood vessel layer is_a: UBERON:0005742 ! adventitia relationship: RO:0000086 PATO:0002462 ! has quality collagenous @@ -226421,7 +229149,7 @@ xref: Wikipedia:Urorectal_septum is_a: UBERON:0003037 ! septum relationship: part_of UBERON:0001008 {source="MA"} ! renal system relationship: part_of UBERON:0012361 {source="EHDAA2"} ! internal anal region -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/fb/Gray992.png" xsd:anyURI property_value: IAO:0000116 "todo - use to define cloacal septation in GO" xsd:string @@ -226455,11 +229183,12 @@ xref: NCIT:C13191 xref: SCTID:68989006 xref: UMLS:C0004799 {source="ncithesaurus:Basement_Membrane"} xref: Wikipedia:Basement_membrane +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005764 {source="FMA"} ! acellular membrane relationship: adjacent_to CL:0000066 ! epithelial cell relationship: has_part GO:0005587 ! collagen type IV trimer relationship: part_of UBERON:0000483 ! epithelium -relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa relationship: RO:0002473 GO:0005604 ! composed primarily of basement membrane property_value: RO:0002175 NCBITaxon:80999 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} @@ -227014,7 +229743,7 @@ xref: Wikipedia:Genital_tubercle is_a: BFO:0000002 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0009196 {source="EHDAA2"} ! indifferent external genitalia -relationship: RO:0002160 NCBITaxon:32524 {source="https://github.com/obophenotype/uberon/issues/1230"} ! only in taxon Amniota +relationship: RO:0002162 NCBITaxon:32524 {source="https://github.com/obophenotype/uberon/issues/1230"} ! in taxon Amniota relationship: RO:0002202 UBERON:0004874 ! develops from somatopleure relationship: RO:0002387 UBERON:0011757 ! has potential to develop into differentiated genital tubercle property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/d/d6/Gray1119.png" xsd:anyURI @@ -227247,6 +229976,7 @@ comment: See notes for serous membrane xref: FMA:9689 xref: SCTID:362890006 is_a: BFO:0000002 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000062 ! organ relationship: has_part UBERON:0000042 ! serous membrane relationship: has_part UBERON:0002553 ! anatomical cavity @@ -227336,6 +230066,7 @@ id: UBERON:0005932 name: bulb of hair follicle namespace: uberon def: "Thickening of the proximal end of the hair follicle. Contains rapidly proliferating, rather undifferentiated matrix cells (transient amplifying cells), melanocytes and outer root sheath cells." [DOI:10.1016/j.cub.2008.12.005] +subset: human_reference_atlas subset: pheno_slim synonym: "coat hair bulb" NARROW SENSU [MA:0000161] synonym: "hair bulb" EXACT [FMA:70666] @@ -227349,6 +230080,7 @@ xref: UMLS:C0221962 {source="ncithesaurus:Hair_Bulb"} is_a: UBERON:0000479 ! tissue is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0002073 ! hair follicle +property_value: RO:0002175 NCBITaxon:9606 property_value: seeAlso "https://github.com/obophenotype/mouse-anatomy-ontology/issues/56" xsd:anyURI [Term] @@ -227368,6 +230100,7 @@ id: UBERON:0005941 name: hair inner root sheath namespace: uberon def: "A multilayered tube composed of terminally differentiated hair follicle keratinocytes that is surrounded by the outer root sheath; the layers of the inner root sheath include the companion layer, Henle's layer, Huxley's layer and the inner root sheath cuticle[MP]." [https://github.com/obophenotype/mouse-anatomy-ontology/issues/56, MP:0010685] +subset: human_reference_atlas subset: pheno_slim synonym: "hair follicle inner root sheath" EXACT [MP:0010685] synonym: "inner root sheath" RELATED [BTO:0003971] @@ -227380,12 +230113,14 @@ xref: FMA:70935 xref: MA:0000779 is_a: UBERON:0005933 ! hair root sheath relationship: has_part CL:0000312 ! keratinocyte +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0005942 name: hair outer root sheath namespace: uberon def: "A stratified epithelium that surrounds the hair follicle that merges proximally with the basal layer of the interfollicular epidermis and distally with the hair bulb." [DOI:10.1016/j.cub.2008.12.005, http://www.keratin.com/aa/aa022.shtml, https://github.com/obophenotype/mouse-anatomy-ontology/issues/56] +subset: human_reference_atlas subset: pheno_slim synonym: "external root sheath of hair follicle" EXACT [FMA:70943] synonym: "hair follicle outer root sheath" EXACT [BTO:0003969] @@ -227402,6 +230137,7 @@ xref: SCTID:319224003 xref: Wikipedia:Outer_root_sheath is_a: UBERON:0005933 ! hair root sheath relationship: RO:0002150 UBERON:0005932 ! continuous with bulb of hair follicle +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0005944 @@ -227599,7 +230335,7 @@ synonym: "amnionic fold" EXACT [http://placentation.ucsd.edu/glossfs.html] xref: EMAPA:16076 is_a: BFO:0000002 is_a: UBERON:0000478 ! extraembryonic structure -relationship: RO:0002160 NCBITaxon:32524 ! only in taxon Amniota +relationship: RO:0002162 NCBITaxon:32524 ! in taxon Amniota relationship: RO:0002202 UBERON:0004874 {source="ISBN:0073040584"} ! develops from somatopleure [Term] @@ -228151,7 +230887,7 @@ intersection_of: UBERON:0006134 ! nerve fiber intersection_of: has_part GO:0043209 ! myelin sheath disjoint_from: UBERON:0006136 ! unmyelinated nerve fiber relationship: has_part GO:0043209 ! myelin sheath -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria property_value: IAO:0000116 "consider adding link to UBERON:0002316 ! white matter of neuraxis" xsd:string property_value: RO:0002161 NCBITaxon:117569 property_value: RO:0002161 NCBITaxon:7762 @@ -228789,6 +231525,41 @@ intersection_of: RO:0002473 UBERON:0005866 ! composed primarily of pre-cartilage relationship: RO:0002202 UBERON:0006210 {source="EHDAA2"} ! develops from body-wall mesenchyme relationship: RO:0002473 UBERON:0005866 ! composed primarily of pre-cartilage condensation +[Term] +id: UBERON:0006250 +name: infundibular recess of 3rd ventricle +namespace: uberon +def: "A funnel-shaped diverticulum that extends downward from the anterior aspect of the floor of the third ventricle into the infundibulum of the hypophysis; the embryonic structure gives rise the neural component of the pituitary (pas nervosa)." [https://sourceforge.net/p/obo/mammalian-phenotype-requests/1930/, MGI:anna] +subset: pheno_slim +synonym: "infundibular reccess" RELATED [BAMS:IRe] +synonym: "infundibular recess" EXACT [FMA:78456] +synonym: "infundibular recess of third ventricle" EXACT [FMA:78456] +synonym: "recessus infundibularis" EXACT OMO:0003011 [FMA:TA] +synonym: "recessus infundibuli" EXACT OMO:0003011 [FMA:TA] +synonym: "recessus infundibuli" RELATED OMO:0003011 [Wikipedia:Infundibular_recess] +synonym: "third ventricle infundibular recess" RELATED [BAMS:V3ir] +xref: BAMS:IRe +xref: BAMS:V3ir +xref: EHDAA2:0000827 +xref: EHDAA:4479 +xref: EMAPA:16899 +xref: EMAPA_RETIRED:16648 +xref: FMA:78456 +xref: neuronames:458 +xref: SCTID:369280006 +xref: Wikipedia:Infundibular_recess +is_a: UBERON:0002050 ! embryonic structure +is_a: UBERON:0005291 ! embryonic tissue +is_a: UBERON:0007499 {source="EHDAA2"} ! epithelial sac +is_a: UBERON:0010371 ! ecto-epithelium +is_a: UBERON:0012275 ! meso-epithelium +relationship: part_of UBERON:0002286 {source="EMAPA"} ! third ventricle +relationship: part_of UBERON:0034876 {source="EMAPA"} ! future neurohypophysis +relationship: RO:0002202 UBERON:0003309 {source="EHDAA2"} ! develops from floor plate of diencephalon +relationship: RO:0002202 UBERON:0034876 {source="EHDAA2"} ! develops from future neurohypophysis +property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/75/Gray654.png" xsd:anyURI +property_value: IAO:0000116 "in FMA this is a cavity, whereas in EHDAA2 it is an epithelial sac" xsd:string + [Term] id: UBERON:0006254 name: ischial cartilage element @@ -228951,7 +231722,7 @@ xref: UMLS:C1518430 {source="ncithesaurus:Notochordal_Process"} xref: VHOG:0001213 is_a: BFO:0000002 is_a: UBERON:0005423 ! developing anatomical structure -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002202 UBERON:0000924 {source="EHDAA2"} ! develops from ectoderm [Term] @@ -229008,7 +231779,7 @@ intersection_of: UBERON:0003914 ! epithelial tube intersection_of: RO:0002176 UBERON:0001179 ! connects peritoneal cavity intersection_of: RO:0002176 UBERON:0002402 ! connects pleural cavity relationship: part_of UBERON:0011997 {source="EHDAA2"} ! coelom -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002176 UBERON:0001179 ! connects peritoneal cavity relationship: RO:0002176 UBERON:0002402 ! connects pleural cavity @@ -229164,11 +231935,8 @@ xref: EHDAA:3003 xref: EMAPA:18535 xref: XAO:0000326 is_a: UBERON:0001048 {source="XAO"} ! primordium -is_a: UBERON:0002050 ! embryonic structure is_a: UBERON:0003104 ! mesenchyme is_a: UBERON:0004120 ! mesoderm-derived structure -is_a: UBERON:0005291 ! embryonic tissue -relationship: part_of UBERON:0005602 {source="EHDAA2-modified"} ! dorsal mesogastrium relationship: RO:0002202 UBERON:0004872 {source="XAO"} ! develops from splanchnic layer of lateral plate mesoderm [Term] @@ -229282,6 +232050,18 @@ intersection_of: part_of UBERON:0002285 ! telencephalic ventricle relationship: part_of UBERON:0002307 ! choroid plexus of lateral ventricle property_value: IAO:0000116 "definitions should be fixed to use generic stroma class" xsd:string +[Term] +id: UBERON:0006339 +name: third ventricle choroid plexus stroma +namespace: uberon +def: "A choroid plexus stroma that is part of a third ventricle." [OBOL:automatic] +xref: EMAPA:37056 {source="MA:th"} +xref: MA:0000881 +is_a: UBERON:0005206 ! choroid plexus stroma +intersection_of: UBERON:0005206 ! choroid plexus stroma +intersection_of: part_of UBERON:0002286 ! third ventricle +relationship: part_of UBERON:0002288 ! choroid plexus of third ventricle + [Term] id: UBERON:0006340 name: fourth ventricle choroid plexus stroma @@ -229372,7 +232152,7 @@ is_a: UBERON:0007719 ! bone of reproductive organ intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0000989 ! penis relationship: part_of UBERON:0000989 ! penis -relationship: RO:0002160 NCBITaxon:40674 {source="Wikipedia"} ! only in taxon Mammalia +relationship: RO:0002162 NCBITaxon:40674 {source="Wikipedia"} ! in taxon Mammalia property_value: RO:0002161 NCBITaxon:9606 [Term] @@ -229392,7 +232172,7 @@ is_a: UBERON:0007719 ! bone of reproductive organ intersection_of: UBERON:0001474 ! bone element intersection_of: part_of UBERON:0002411 ! clitoris relationship: part_of UBERON:0002411 ! clitoris -relationship: RO:0002160 NCBITaxon:40674 {source="Wikipedia"} ! only in taxon Mammalia +relationship: RO:0002162 NCBITaxon:40674 {source="Wikipedia"} ! in taxon Mammalia relationship: RO:0002433 UBERON:0001434 ! contributes to morphology of skeletal system relationship: RO:0002433 UBERON:0002411 ! contributes to morphology of clitoris relationship: sexually_homologous_to UBERON:0006435 ! os penis @@ -229698,7 +232478,7 @@ xref: MAT:0000049 xref: MESH:D010614 xref: MIAA:0000049 is_a: UBERON:0004921 ! subdivision of digestive tract -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria [Term] id: UBERON:0006563 @@ -229898,7 +232678,7 @@ intersection_of: UBERON:0006598 ! presumptive structure intersection_of: part_of UBERON:0000307 ! blastula intersection_of: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm relationship: part_of UBERON:0000307 ! blastula -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm [Term] @@ -229967,7 +232747,7 @@ intersection_of: UBERON:0006598 ! presumptive structure intersection_of: part_of UBERON:0000307 ! blastula intersection_of: RO:0002387 UBERON:0000924 ! has potential to develop into ectoderm relationship: part_of UBERON:0000307 ! blastula -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002387 UBERON:0000924 ! has potential to develop into ectoderm [Term] @@ -229985,7 +232765,7 @@ intersection_of: UBERON:0006598 ! presumptive structure intersection_of: part_of UBERON:0000307 ! blastula intersection_of: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm relationship: part_of UBERON:0000307 ! blastula -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm [Term] @@ -230297,7 +233077,7 @@ xref: UMLS:C0225358 {source="ncithesaurus:Muscle_Layer"} xref: Wikipedia:Muscular_layer is_a: UBERON:0018260 ! layer of muscle tissue relationship: adjacent_to UBERON:0000009 ! submucosa -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata property_value: IAO:0000116 "currently this class conflates a generic layer of muscle and a specific layer found lining the digestive tract (the muscularis externa), typically composed of circular and longitudinal layers (although this varies)" xsd:string [Term] @@ -230403,7 +233183,7 @@ is_a: UBERON:0013685 ! foramen of skull intersection_of: UBERON:0004111 ! anatomical conduit intersection_of: RO:0002570 UBERON:0001650 ! conduit for hypoglossal nerve relationship: part_of UBERON:0001676 ! occipital bone -relationship: RO:0002160 NCBITaxon:7776 ! only in taxon Gnathostomata +relationship: RO:0002162 NCBITaxon:7776 ! in taxon Gnathostomata relationship: RO:0002570 UBERON:0001650 ! conduit for hypoglossal nerve [Term] @@ -230762,7 +233542,7 @@ is_a: UBERON:0013522 ! subdivision of tube intersection_of: UBERON:0013522 ! subdivision of tube intersection_of: site_of GO:0009790 ! embryo development relationship: part_of UBERON:0000474 ! female reproductive system -relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa relationship: site_of GO:0009790 ! embryo development [Term] @@ -231567,7 +234347,7 @@ relationship: channel_for CL:0000019 ! sperm relationship: channels_from UBERON:0003959 ! rete testis relationship: channels_into UBERON:0001301 ! epididymis relationship: part_of UBERON:0006947 {source="FMA"} ! male genital duct -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b5/Hodenschema.svg" xsd:anyURI [Term] @@ -231728,6 +234508,7 @@ xref: EFO:0003709 xref: TAO:0005077 xref: ZFA:0005077 is_a: BFO:0000002 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005423 ! developing anatomical structure relationship: has_part CL:0000115 ! endothelial cell relationship: has_part CL:0000566 ! angioblastic mesenchymal cell @@ -232461,6 +235242,7 @@ synonym: "bone marrow stroma" EXACT [FMA:21426] xref: CALOHA:TS-0085 xref: FMA:21426 xref: Wikipedia:Bone_marrow#Stroma +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0003891 ! stroma is_a: UBERON:0004120 ! mesoderm-derived structure intersection_of: UBERON:0003891 ! stroma @@ -232485,6 +235267,7 @@ xref: FMA:7393 xref: NCIT:C117875 xref: SCTID:361384001 xref: Wikipedia:Tracheobronchial_tree +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000062 ! organ is_a: UBERON:0004119 ! endoderm-derived structure relationship: has_part UBERON:0002185 ! bronchus @@ -232920,7 +235703,7 @@ is_a: UBERON:0011582 ! paired limb/fin skeleton intersection_of: UBERON:0010912 ! subdivision of skeleton intersection_of: RO:0002576 UBERON:0004710 ! skeleton of pectoral appendage relationship: part_of UBERON:0004710 {source="VSAO"} ! pectoral appendage -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002576 UBERON:0004710 ! skeleton of pectoral appendage [Term] @@ -232932,7 +235715,7 @@ is_a: UBERON:0011582 ! paired limb/fin skeleton intersection_of: UBERON:0010912 ! subdivision of skeleton intersection_of: RO:0002576 UBERON:0004709 ! skeleton of pelvic appendage relationship: part_of UBERON:0004709 {source="VSAO"} ! pelvic appendage -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002576 UBERON:0004709 ! skeleton of pelvic appendage [Term] @@ -233064,6 +235847,20 @@ intersection_of: RO:0002387 UBERON:0003077 {source="https://github.com/obophenot relationship: part_of UBERON:0000307 ! blastula relationship: RO:0002387 UBERON:0003077 ! has potential to develop into paraxial mesoderm +[Term] +id: UBERON:0007286 +name: presumptive floor plate +namespace: uberon +def: "A presumptive structure that has the potential to develop into a floor plate." [OBOL:automatic] +subset: efo_slim +xref: EFO:0003454 +xref: TAO:0001218 +xref: ZFA:0001218 +is_a: UBERON:0006598 ! presumptive structure +intersection_of: UBERON:0006598 ! presumptive structure +intersection_of: RO:0002387 UBERON:0003079 ! has potential to develop into floor plate +relationship: RO:0002387 UBERON:0003079 ! has potential to develop into floor plate + [Term] id: UBERON:0007288 name: presumptive forebrain midbrain boundary @@ -233237,6 +236034,7 @@ synonym: "pancreatic lobule" EXACT [FMA:16012] xref: EMAPA:37710 {source="MA:th"} xref: FMA:16012 xref: MA:0000721 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000064 ! organ part is_a: UBERON:0004119 ! endoderm-derived structure relationship: has_part UBERON:0001263 ! pancreatic acinus @@ -233316,6 +236114,21 @@ intersection_of: BSPO:0015101 UBERON:0001723 ! tongue relationship: BSPO:0015101 UBERON:0001723 ! tongue property_value: IAO:0000116 "check superior/dorsal" xsd:string +[Term] +id: UBERON:0007373 +name: inferior surface of tongue +namespace: uberon +def: "The lower (inferior) side of the tongue." [http://orcid.org/0000-0002-6601-2165] +synonym: "ventral surface of tongue" EXACT [FMA:54648] +synonym: "ventrum linguae" EXACT [] +xref: FMA:54648 +xref: SCTID:362100003 +is_a: UBERON:0007367 ! surface of tongue +intersection_of: UBERON:0007367 ! surface of tongue +intersection_of: BSPO:0015102 UBERON:0001723 ! tongue +relationship: BSPO:0015102 UBERON:0001723 ! tongue +property_value: IAO:0000116 "check inferior/ventral" xsd:string + [Term] id: UBERON:0007375 name: roof of mouth @@ -233358,7 +236171,7 @@ intersection_of: UBERON:0000483 ! epithelium intersection_of: bounding_layer_of UBERON:0000468 ! multicellular organism intersection_of: RO:0002202 UBERON:0007383 ! develops from enveloping layer of ectoderm relationship: bounding_layer_of UBERON:0000468 ! multicellular organism -relationship: RO:0002160 NCBITaxon:6072 {source="Wikipedia:Epidermis_(zoology)"} ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 {source="Wikipedia:Epidermis_(zoology)"} ! in taxon Eumetazoa relationship: RO:0002202 UBERON:0007383 ! develops from enveloping layer of ectoderm property_value: IAO:0000116 "this grouping class exists primarily to align with GO - see GO:0008544." xsd:string @@ -233441,7 +236254,7 @@ is_a: UBERON:0007389 ! paired limb/fin cartilage intersection_of: UBERON:0002418 ! cartilage tissue intersection_of: part_of UBERON:0004710 ! pectoral appendage relationship: part_of UBERON:0007272 ! pectoral appendage skeleton -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata [Term] id: UBERON:0007391 @@ -233456,7 +236269,7 @@ is_a: UBERON:0007389 ! paired limb/fin cartilage intersection_of: UBERON:0002418 ! cartilage tissue intersection_of: part_of UBERON:0004709 ! pelvic appendage relationship: part_of UBERON:0007273 ! pelvic appendage skeleton -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata [Term] id: UBERON:0007414 @@ -234262,7 +237075,7 @@ intersection_of: filtered_through UBERON:0001982 ! capillary intersection_of: RO:0000086 PATO:0001548 ! has quality quality of a liquid intersection_of: RO:0002494 UBERON:0001969 ! transformation of blood plasma relationship: filtered_through UBERON:0001982 ! capillary -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002494 UBERON:0001969 ! transformation of blood plasma [Term] @@ -234395,7 +237208,7 @@ intersection_of: UBERON:0002415 ! tail intersection_of: part_of UBERON:0006071 ! caudal region relationship: capable_of_part_of GO:0007626 ! locomotory behavior relationship: part_of UBERON:0006071 ! caudal region -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002494 UBERON:0007144 ! transformation of embryonic post-anal tail property_value: RO:0002161 NCBITaxon:314295 @@ -234418,7 +237231,7 @@ is_a: UBERON:0000475 ! organism subdivision intersection_of: UBERON:0000475 ! organism subdivision intersection_of: RO:0002551 UBERON:0010719 ! has skeleton girdle skeleton relationship: part_of UBERON:0010707 ! appendage girdle complex -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002551 UBERON:0010719 ! has skeleton girdle skeleton [Term] @@ -234636,6 +237449,7 @@ namespace: uberon def: "Connective tissue, which consists of fibroblasts, the intercellular matrix of which contains a regular network of collagen and elastic fiber bundles. Examples: bone (tissue), cartilage (tissue), dense regular connective tissue." [FMA:20103] xref: FMA:20103 is_a: BFO:0000002 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002384 {source="FMA"} ! connective tissue disjoint_from: UBERON:0011821 ! irregular connective tissue relationship: has_part CL:0000057 ! fibroblast @@ -234734,7 +237548,7 @@ is_a: UBERON:0000982 {source="MA"} ! skeletal joint intersection_of: UBERON:0000982 ! skeletal joint intersection_of: part_of UBERON:0007823 ! appendage girdle region relationship: part_of UBERON:0007823 ! appendage girdle region -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002176 UBERON:0007828 ! connects girdle bone/zone [Term] @@ -234977,7 +237791,7 @@ xref: BTO:0005090 xref: Wikipedia:The_Free_Encyclopedia is_a: UBERON:0002384 ! connective tissue relationship: part_of UBERON:0002222 {source="BTO"} ! perichondrium -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata [Term] id: UBERON:0008305 @@ -235023,7 +237837,7 @@ def: "With numerous vascular spaces that may become engorged with blood." [Wikip comment: Examples: corpus cavernosum or penis or clitoris xref: Wikipedia:Erectile_tissue is_a: UBERON:0000479 ! tissue -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria [Term] id: UBERON:0008331 @@ -235503,7 +238317,7 @@ intersection_of: adjacent_to UBERON:0001828 ! gingiva relationship: adjacent_to UBERON:0001091 ! calcareous tooth relationship: adjacent_to UBERON:0001828 ! gingiva relationship: part_of UBERON:0000165 ! mouth -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/5/5e/Gingival_sulcus.PNG" xsd:anyURI [Term] @@ -235524,7 +238338,7 @@ xref: TGMA:0000585 xref: Wikipedia:Intromittent_organ is_a: UBERON:0003135 ! male reproductive organ relationship: capable_of_part_of GO:0007620 ! copulation -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0008814 @@ -235545,7 +238359,7 @@ xref: UMLS:C1519038 {source="ncithesaurus:Pharyngeal_Apparatus"} is_a: UBERON:0034921 ! multi organ part structure relationship: part_of UBERON:0000922 ! embryo relationship: part_of UBERON:0009145 ! pharyngeal region of foregut -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata property_value: IAO:0000116 "Currently defined in a vertebrate specific manner. The arch system has origins in basal deuterostomes, consider generalizing" xsd:string [Term] @@ -235706,6 +238520,7 @@ xref: SCTID:410744003 xref: VSAO:0000072 xref: Wikipedia:Ligament#Articular_ligaments is_a: BFO:0000002 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000211 ! ligament intersection_of: UBERON:0000211 ! ligament intersection_of: part_of UBERON:0001434 ! skeletal system @@ -235973,6 +238788,7 @@ synonym: "pulmonary system" EXACT [ISBN:0073040584] xref: FMA:45621 xref: Wikipedia:Pulmonary_circulation is_a: BFO:0000002 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0007798 {source="Obol"} ! vascular system relationship: has_part UBERON:0002012 ! pulmonary artery relationship: has_part UBERON:0002016 ! pulmonary vein @@ -236647,7 +239463,7 @@ intersection_of: UBERON:0007023 ! adult organism intersection_of: has_part UBERON:0000922 ! embryo relationship: has_part UBERON:0000922 ! embryo relationship: participates_in GO:0007565 ! female pregnancy -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0009098 @@ -236783,7 +239599,7 @@ xref: XAO:0000440 is_a: UBERON:0003067 {source="ISBN:0471888893"} ! dorsolateral placode intersection_of: UBERON:0005085 ! ectodermal placode intersection_of: RO:0002387 UBERON:0002540 ! has potential to develop into lateral line system -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002387 UBERON:0002540 ! has potential to develop into lateral line system property_value: IAO:0000116 "TODO - compare with protoneuromast" xsd:string property_value: RO:0002161 NCBITaxon:32524 {source="http://tolweb.org/Amniota"} @@ -237670,6 +240486,16 @@ intersection_of: UBERON:0005478 ! sulcus limitans of neural tube intersection_of: part_of UBERON:0006241 ! future spinal cord relationship: part_of UBERON:0006241 ! future spinal cord +[Term] +id: UBERON:0009571 +name: ventral midline +namespace: uberon +def: "In protostomes (such as insects, snails and worms) as well as deuterostomes (vertebrates), the midline is an embryonic region that functions in patterning of the adjacent nervous tissue. The ventral midline in insects is a cell population extending along the ventral surface of the embryo and is the region from which cells detach to form the ventrally located nerve cords. In vertebrates, the midline is originally located dorsally. During development, it folds inwards and becomes the ventral part of the dorsally located neural tube and is then called the ventral midline, or floor plate." [GOC:bf, GOC:go_curators, PMID:12075342] +xref: FBbt:00000093 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} +is_a: UBERON:0002050 {source="FMA"} ! embryonic structure +relationship: part_of UBERON:0001016 ! nervous system +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria + [Term] id: UBERON:0009572 name: lumen of central canal of spinal cord @@ -238703,7 +241529,7 @@ synonym: "renal tubule (generic)" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "tubule of excretory system" EXACT [https://orcid.org/0000-0002-6601-2165, OBOL:automatic] is_a: UBERON:0003914 ! epithelial tube is_a: UBERON:0006555 ! excretory tube -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria [Term] id: UBERON:0009778 @@ -239170,7 +241996,7 @@ is_a: UBERON:0007688 ! anlage relationship: BSPO:0000096 UBERON:0004140 {source="PMID:17276708"} ! primary heart field relationship: BSPO:0000098 UBERON:0004140 {source="PMID:17276708"} ! primary heart field relationship: part_of UBERON:0003081 {source="GO:0003129"} ! lateral plate mesoderm -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata [Term] id: UBERON:0009891 @@ -239381,7 +242207,7 @@ def: "A vertebrate nasal chemosensory system that is responsible for detecting i is_a: UBERON:0001032 ! sensory system relationship: capable_of GO:0043695 {source="Wikipedia"} ! detection of pheromone relationship: part_of UBERON:0005725 ! olfactory system -relationship: RO:0002160 NCBITaxon:8287 ! only in taxon Sarcopterygii +relationship: RO:0002162 NCBITaxon:8287 ! in taxon Sarcopterygii property_value: IAO:0000116 "check relationship to olfactory system. Evolution: The morphological components of the VNS are found only in tetrapods, but the genetic components of the system have been found in teleost fish, in addition to tetrapods. In tetrapods, the VNS was thought to be the olfactory system for detecting pheromones, while the main olfactory system detected general odorants (Scalia and Winans 1975). However, experimental evidence suggests that there is not such a clear functional distinction (Restrepo et al. 2004; Baxi, Dorries, and Eisthen 2006; Spehr et al. 2006; Kelliher 2007). Sea lampreys produce unique bile acids which act as pheromones both in migration and mate finding (Li, Sorensen, and Gallaher 1995; Li et al. 2002; Siefkes and Li 2004). However, bile acids in teleost fish are known to require components of the main olfactory signal transduction pathway (Hansen et al. 2003), and interruption of the VNS signal transduction pathway had no effect on bile acid olfactory response (Hansen et al. 2003)[Grus - EVOLUTION OF THE VOMERONASAL SYSTEM VIEWED THROUGH SYSTEM-SPECIFIC GENES]" xsd:string [Term] @@ -240540,7 +243366,7 @@ namespace: uberon xref: EHDAA2:0004512 is_a: UBERON:0011216 ! organ system subdivision relationship: part_of UBERON:0004571 {source="Wikipedia"} ! systemic arterial system -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata [Term] id: UBERON:0010192 @@ -240621,6 +243447,7 @@ xref: BTO:0000102 xref: galen:BloodClot xref: Wikipedia:Thrombus is_a: BFO:0000002 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000463 ! organism substance intersection_of: UBERON:0000463 ! organism substance intersection_of: output_of GO:0007596 ! blood coagulation @@ -241055,7 +243882,7 @@ xref: BTO:0004800 xref: EFO:0000250 xref: FBbt:00000095 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0010303 {source="DOI:10.1073/pnas.0709145105"} ! extraembryonic epithelium -relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda +relationship: RO:0002162 NCBITaxon:6656 ! in taxon Arthropoda property_value: IAO:0000116 "May be obsoleted once added to insect ontology. Coordinate with cell type in CL" xsd:string [Term] @@ -241182,7 +244009,7 @@ xref: XAO:0003075 xref: ZFA:0000737 is_a: UBERON:0000075 ! subdivision of skeletal system relationship: part_of UBERON:0011137 ! axial skeletal system -relationship: RO:0002160 NCBITaxon:89593 ! only in taxon Craniata +relationship: RO:0002162 NCBITaxon:89593 ! in taxon Craniata property_value: IAO:0000116 "we use 'cranial skeletal system', so that we can include the skull, which has joints/sutures as parts (recall, we follow FMA in distinguishing between the skeleton and skeletal system - only the latter includes joints)" xsd:string [Term] @@ -241503,7 +244330,7 @@ xref: VSAO:0000037 xref: Wikipedia:Endoskeleton xref: XAO:0004026 is_a: UBERON:0010912 {source="VSAO"} ! subdivision of skeleton -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002473 UBERON:0010522 ! composed primarily of replacement element [Term] @@ -241531,7 +244358,7 @@ synonym: "exoskeleton" BROAD INCONSISTENT [VSAO:curator] xref: VSAO:0000035 xref: XAO:0004025 is_a: UBERON:0010912 {source="VSAO"} ! subdivision of skeleton -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata [Term] id: UBERON:0010365 @@ -241812,7 +244639,7 @@ is_a: UBERON:0010001 ! cell cluster organ intersection_of: UBERON:0010001 ! cell cluster organ intersection_of: RO:0002473 CL:0000542 ! composed primarily of lymphocyte relationship: part_of UBERON:0002465 ! lymphoid system -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002473 CL:0000542 ! composed primarily of lymphocyte property_value: IAO:0000116 "TODO - check" xsd:string property_value: seeAlso "https://github.com/obophenotype/uberon/issues/513" xsd:anyURI @@ -242053,6 +244880,7 @@ synonym: "primary follicle" RELATED [] synonym: "primary lymphoid follicle" EXACT [] synonym: "primary lymphoid nodule" EXACT [FMA:55223] xref: FMA:55223 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000444 {source="FMA"} ! lymphoid follicle relationship: has_part CL:0000788 {source="CL:tm"} ! naive B cell @@ -242086,7 +244914,7 @@ is_a: UBERON:0000003 ! naris intersection_of: UBERON:0000003 ! naris intersection_of: RO:0002176 UBERON:0001707 ! connects nasal cavity intersection_of: RO:0002176 UBERON:0006562 ! connects pharynx -relationship: RO:0002160 NCBITaxon:8287 ! only in taxon Sarcopterygii +relationship: RO:0002162 NCBITaxon:8287 ! in taxon Sarcopterygii relationship: RO:0002176 UBERON:0006562 ! connects pharynx [Term] @@ -242323,7 +245151,7 @@ intersection_of: UBERON:0010758 ! subdivision of organism along appendicular axi intersection_of: part_of UBERON:0004708 ! paired limb/fin disjoint_from: UBERON:0010912 ! subdivision of skeleton relationship: part_of UBERON:0004708 ! paired limb/fin -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata [Term] id: UBERON:0010540 @@ -242754,7 +245582,7 @@ xref: VSAO:0000214 is_a: UBERON:0000475 ! organism subdivision is_a: UBERON:0015212 ! lateral structure relationship: BSPO:0000126 UBERON:0000468 ! multicellular organism -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002328 GO:0040011 ! functionally related to locomotion property_value: IAO:0000116 "It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO]" xsd:string property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 @@ -242958,6 +245786,7 @@ xref: UMLS:C0228116 xref: Wikipedia:Meninges is_a: BFO:0000002 is_a: BFO:0000004 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0034925 ! anatomical collection intersection_of: UBERON:0034925 ! anatomical collection intersection_of: bounding_layer_of UBERON:0001017 ! central nervous system @@ -243281,7 +246110,7 @@ synonym: "horny denticle" EXACT [http://tolweb.org/Hyperoartia] is_a: UBERON:0003913 ! tooth-like structure intersection_of: UBERON:0003913 ! tooth-like structure intersection_of: RO:0002473 GO:0045095 ! composed primarily of keratin filament -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002473 GO:0045095 ! composed primarily of keratin filament property_value: RO:0002175 NCBITaxon:117569 property_value: RO:0002175 NCBITaxon:7762 @@ -243646,7 +246475,6 @@ is_a: UBERON:0010913 ! vertebral element intersection_of: UBERON:0010913 ! vertebral element intersection_of: RO:0002473 UBERON:0002418 ! composed primarily of cartilage tissue relationship: RO:0002202 UBERON:0011095 ! develops from vertebra pre-cartilage condensation -relationship: RO:0002387 UBERON:0002412 ! has potential to develop into vertebra [Term] id: UBERON:0011095 @@ -243659,7 +246487,7 @@ xref: VHOG:0000582 is_a: UBERON:0010913 ! vertebral element intersection_of: UBERON:0010913 ! vertebral element intersection_of: RO:0002473 UBERON:0005866 ! composed primarily of pre-cartilage condensation -relationship: RO:0002387 UBERON:0002412 ! has potential to develop into vertebra +relationship: RO:0002387 UBERON:0011094 ! has potential to develop into vertebra cartilage element relationship: RO:0002473 UBERON:0005866 ! composed primarily of pre-cartilage condensation [Term] @@ -244291,6 +247119,7 @@ id: UBERON:0011234 name: fibrous membrane of synovial tendon sheath namespace: uberon xref: FMA:40877 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004923 ! organ component layer intersection_of: UBERON:0004923 ! organ component layer intersection_of: bounding_layer_of UBERON:0000304 ! tendon sheath @@ -244448,6 +247277,7 @@ def: "An acellular strand that runs from subcommissural organ caudally through t synonym: "Reissner's fibre" EXACT [] xref: NLX:151878 xref: Wikipedia:Reissner's_fiber +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000476 ! acellular anatomical structure is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0001017 ! central nervous system @@ -244743,7 +247573,7 @@ is_a: UBERON:0010314 ! structure with developmental contribution from neural cre intersection_of: UBERON:0000475 ! organism subdivision intersection_of: RO:0002551 UBERON:0001708 ! has skeleton jaw skeleton relationship: part_of UBERON:0000165 {source="EMAPA", source="FMA-abduced", source="ZFA-abduced"} ! mouth -relationship: RO:0002160 NCBITaxon:7776 ! only in taxon Gnathostomata +relationship: RO:0002162 NCBITaxon:7776 ! in taxon Gnathostomata relationship: RO:0002551 UBERON:0001708 ! has skeleton jaw skeleton property_value: seeAlso "http://eol.org/collections/11578" xsd:anyURI @@ -245165,6 +247995,7 @@ xref: AAO:0000121 xref: NCIT:C32450 xref: UMLS:C1511770 {source="ncithesaurus:Dense_Connective_Tissue"} xref: Wikipedia:Dense_connective_tissue +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002384 ! connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: RO:0002473 UBERON:0011860 ! composed primarily of collection of collagen fibrils @@ -245277,6 +248108,7 @@ xref: FMA:63212 xref: MESH:D024022 xref: NCIT:C32339 xref: NIF_Subcellular:sao7547390221 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000476 {source="ZFA"} ! acellular anatomical structure relationship: RO:0002473 GO:0005581 ! composed primarily of collagen trimer relationship: RO:0002473 GO:0098643 ! composed primarily of banded collagen fibril @@ -245556,6 +248388,7 @@ xref: EMAPA:36582 xref: FMA:70661 xref: Wikipedia:Pilosebaceous_unit is_a: BFO:0000002 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000063 ! organ subunit relationship: has_part UBERON:0001821 ! sebaceous gland relationship: has_part UBERON:0002033 ! arrector muscle of hair @@ -245566,8 +248399,10 @@ relationship: part_of UBERON:0006003 {source="ISBN:0123813611"} ! integumentary id: UBERON:0011945 name: luminal layer of epithelium namespace: uberon +subset: human_reference_atlas is_a: UBERON:0005162 ! multi cell part structure relationship: part_of UBERON:0000483 ! epithelium +property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0011947 @@ -245636,6 +248471,7 @@ xref: MA:0001613 xref: NCIT:C77661 xref: SCTID:27633001 xref: UMLS:C0227197 {source="ncithesaurus:Glandular_Stomach"} +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0009870 ! zone of stomach intersection_of: UBERON:0009870 ! zone of stomach intersection_of: has_part UBERON:0006924 ! stomach glandular epithelium @@ -245843,7 +248679,7 @@ synonym: "schizocoelom" NARROW [] xref: EHDAA2:0004731 xref: Wikipedia:Coelom is_a: UBERON:0000481 {source="EHDAA2"} ! multi-tissue structure -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria property_value: IAO:0000116 "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." xsd:string property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} @@ -246158,6 +248994,17 @@ intersection_of: UBERON:0000014 ! zone of skin intersection_of: part_of UBERON:0007811 ! craniocervical region relationship: part_of UBERON:0007811 ! craniocervical region +[Term] +id: UBERON:0012186 +name: ovary growing follicle +namespace: uberon +def: "An ovarian follicle undergoing maturation." [ncithesaurus:Growing_Follicle] +xref: EMAPA:35628 +xref: MA:0001708 +xref: NCIT:C32702 +xref: UMLS:C1512279 {source="ncithesaurus:Growing_Follicle"} +is_a: UBERON:0001305 {source="MA"} ! ovarian follicle + [Term] id: UBERON:0012193 name: phrenic vein @@ -246321,6 +249168,7 @@ xref: NCIT:C12310 xref: SCTID:264459002 xref: UMLS:C0227829 {source="ncithesaurus:Ectocervix"} xref: Wikipedia:Vaginal_portion_of_cervix +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000064 ! organ part is_a: UBERON:0005156 ! reproductive structure intersection_of: UBERON:0000064 ! organ part @@ -246564,7 +249412,7 @@ xref: FMA:293103 xref: SCTID:89066004 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0000033 ! head -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata [Term] id: UBERON:0012317 @@ -246908,7 +249756,7 @@ intersection_of: UBERON:0004923 ! organ component layer intersection_of: adjacent_to UBERON:0000042 ! serous membrane intersection_of: RO:0002473 UBERON:0006815 ! composed primarily of areolar connective tissue relationship: adjacent_to UBERON:0000042 ! serous membrane -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002473 UBERON:0006815 ! composed primarily of areolar connective tissue property_value: RO:0002175 NCBITaxon:9606 @@ -247142,6 +249990,7 @@ synonym: "tunica fibrosa" BROAD [] xref: FMA:58102 xref: SCTID:361318005 xref: Wikipedia:Fibrous_tunic_of_eyeball +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004923 {source="FMA"} ! organ component layer is_a: UBERON:0010314 ! structure with developmental contribution from neural crest @@ -247243,7 +250092,7 @@ is_a: UBERON:0003913 ! tooth-like structure intersection_of: UBERON:0003913 ! tooth-like structure intersection_of: part_of UBERON:0001353 ! anal region relationship: part_of UBERON:0001353 ! anal region -relationship: RO:0002160 NCBITaxon:7586 ! only in taxon Echinodermata +relationship: RO:0002162 NCBITaxon:7586 ! in taxon Echinodermata [Term] id: UBERON:0012469 @@ -247616,7 +250465,7 @@ is_a: UBERON:0000093 ! sulcus intersection_of: UBERON:0000093 ! sulcus intersection_of: part_of UBERON:0000955 ! brain relationship: part_of UBERON:0000955 ! brain -relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia +relationship: RO:0002162 NCBITaxon:40674 ! in taxon Mammalia relationship: RO:0002221 UBERON:0000200 ! surrounds gyrus property_value: IAO:0000116 "sulci are considered absent from lissencephalic mammals such as mice, but they may possess fissures. For example, the Allen mouse brain Atlas includes hippocampal, rhinal and choroid fissure. For this reason we do not place a taxon constraint on this class" xsd:string @@ -247957,6 +250806,20 @@ intersection_of: part_of UBERON:0000409 ! serous gland relationship: part_of UBERON:0000409 ! serous gland relationship: RO:0002473 CL:0000313 ! composed primarily of serous secreting cell +[Term] +id: UBERON:0013235 +name: ventrum +namespace: uberon +def: "A major organism subdivisionthat is the entire part of an anatomical structure ventral to a horizontal plane and bounded on one side by the same horizontal plane." [BSPO:0000068, UBERONREF:0000006] +synonym: "front" BROAD [] +synonym: "front of body proper" EXACT [FMA:259204] +synonym: "ventral part of organism" EXACT [] +synonym: "ventral region" BROAD [] +synonym: "ventral region of organism" EXACT [] +xref: FMA:259204 +is_a: UBERON:0000475 ! organism subdivision +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria + [Term] id: UBERON:0013238 name: future glans @@ -248100,7 +250963,7 @@ is_a: UBERON:0001962 ! gut-associated lymphoid tissue intersection_of: UBERON:0001961 ! mucosa-associated lymphoid tissue intersection_of: part_of UBERON:0001153 ! caecum relationship: part_of UBERON:0000314 ! cecum mucosa -relationship: RO:0002160 NCBITaxon:8782 ! only in taxon Aves +relationship: RO:0002162 NCBITaxon:8782 ! in taxon Aves [Term] id: UBERON:0013479 @@ -248466,7 +251329,7 @@ synonym: "sesamoid" EXACT [VSAO:0000137] xref: VSAO:0000137 is_a: BFO:0000002 is_a: UBERON:0010911 {source="VSAO"} ! ossicle -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002226 UBERON:0007846 {source="VSAO"} ! develops in dense regular connective tissue [Term] @@ -248714,7 +251577,7 @@ namespace: uberon def: "A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages." [https://orcid.org/0000-0002-6601-2165] subset: non_informative is_a: UBERON:0000475 ! organism subdivision -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0013702 @@ -248771,6 +251634,74 @@ intersection_of: RO:0001025 UBERON:0013704 ! located in notochordal canal relationship: part_of UBERON:0036242 ! post-embryonic notochord relationship: RO:0001025 UBERON:0013704 ! located in notochordal canal +[Term] +id: UBERON:0013739 +name: base of crypt of Lieberkuhn +namespace: uberon +def: "The basal portion (further from lumen) of an intestinal crypt. Contains multipotent stem cells. Stem cells in the crypts divide to form daughter cells. One daughter cell from each stem cell division is retained as a stem cell. The other becomes committed to differentiate along one of four pathways to become an enterocyte, enteroendocrine cell, goblet cell or Paneth cell." [http://orcid.org/0000-0002-6601-2165, UBERON:md] +synonym: "basal portion of intestinal gland" EXACT [] +synonym: "base of intestinal gland" EXACT [] +synonym: "base part of epithelium of intestinal gland" EXACT [] +is_a: UBERON:0011184 ! epithelium of crypt of Lieberkuhn +intersection_of: UBERON:0000483 ! epithelium +intersection_of: part_of UBERON:0001983 ! crypt of Lieberkuhn +intersection_of: RO:0002150 UBERON:0013740 ! continuous with wall of crypt of Lieberkuhn +relationship: RO:0002150 UBERON:0013740 ! continuous with wall of crypt of Lieberkuhn + +[Term] +id: UBERON:0013740 +name: wall of crypt of Lieberkuhn +namespace: uberon +def: "The lateral parts of an intestinal crypt, continuous distally with the base and proximally with the intestinal villus epithelium." [http://orcid.org/0000-0002-6601-2165, UBERON:md] +synonym: "wall of intestinal gland" EXACT [] +synonym: "wall part of epithelium of intestinal gland" EXACT [] +is_a: UBERON:0011184 ! epithelium of crypt of Lieberkuhn +intersection_of: UBERON:0000483 ! epithelium +intersection_of: part_of UBERON:0001983 ! crypt of Lieberkuhn +intersection_of: RO:0002150 UBERON:0013739 ! continuous with base of crypt of Lieberkuhn +relationship: RO:0002150 UBERON:0013636 ! continuous with epithelium of intestinal villus +relationship: RO:0002150 UBERON:0013739 ! continuous with base of crypt of Lieberkuhn + +[Term] +id: UBERON:0013741 +name: base of crypt of Lieberkuhn of large intestine +namespace: uberon +def: "A base of crypt of Lieberkuhn that is part of a large intestine." [OBOL:automatic] +is_a: UBERON:0001278 ! epithelium of large intestine +is_a: UBERON:0013739 ! base of crypt of Lieberkuhn +intersection_of: UBERON:0013739 ! base of crypt of Lieberkuhn +intersection_of: part_of UBERON:0000059 ! large intestine + +[Term] +id: UBERON:0013742 +name: wall of crypt of Lieberkuhn of large intestine +namespace: uberon +def: "A wall of crypt of Lieberkuhn that is part of a large intestine." [OBOL:automatic] +is_a: UBERON:0001278 ! epithelium of large intestine +is_a: UBERON:0013740 ! wall of crypt of Lieberkuhn +intersection_of: UBERON:0013740 ! wall of crypt of Lieberkuhn +intersection_of: part_of UBERON:0000059 ! large intestine + +[Term] +id: UBERON:0013743 +name: base of crypt of Lieberkuhn of small intestine +namespace: uberon +def: "The basal portion (further from lumen) of a intestinal crypt that is located in the small intestine." [http://orcid.org/0000-0002-6601-2165] +is_a: UBERON:0001902 ! epithelium of small intestine +is_a: UBERON:0013739 ! base of crypt of Lieberkuhn +intersection_of: UBERON:0013739 ! base of crypt of Lieberkuhn +intersection_of: part_of UBERON:0002108 ! small intestine + +[Term] +id: UBERON:0013744 +name: wall of crypt of Lieberkuhn of small intestine +namespace: uberon +def: "The lateral parts of an intestinal crypt that is located in the small intestine, continuous distally with the base and proximally with the intestinal villus epithelium." [http://orcid.org/0000-0002-6601-2165] +is_a: UBERON:0001902 ! epithelium of small intestine +is_a: UBERON:0013740 ! wall of crypt of Lieberkuhn +intersection_of: UBERON:0013740 ! wall of crypt of Lieberkuhn +intersection_of: part_of UBERON:0002108 ! small intestine + [Term] id: UBERON:0013749 name: metaphysis of humerus @@ -249982,6 +252913,61 @@ intersection_of: RO:0002176 UBERON:0009912 ! connects anatomical lobe relationship: part_of UBERON:0002384 ! connective tissue relationship: RO:0002176 UBERON:0009912 ! connects anatomical lobe +[Term] +id: UBERON:0014725 +name: intercalated duct +namespace: uberon +def: "A small duct which drains individual secretory units. These are usually inconspicuous, lined by a simple epithelium consisting of low cuboidal cells." [http://www.siumed.edu/~dking2/intro/glands.htm] +synonym: "secretory duct" RELATED [] +xref: NCIT:C32820 +xref: UMLS:C1512817 +is_a: UBERON:0014719 ! intralobular duct + +[Term] +id: UBERON:0014726 +name: intercalated duct of pancreas +namespace: uberon +def: "An intercalated duct that is part of a pancreas." [OBOL:automatic] +subset: human_reference_atlas +synonym: "ductus intercalatus (pancreas)" EXACT [FMA:16013] +synonym: "pancreatic ductule" EXACT [FMA:16013] +xref: FMA:16013 +xref: NCIT:C49267 +xref: SCTID:247520007 +is_a: UBERON:0014725 ! intercalated duct +intersection_of: UBERON:0014725 ! intercalated duct +intersection_of: part_of UBERON:0001264 ! pancreas +relationship: part_of UBERON:0001264 ! pancreas +property_value: RO:0002175 NCBITaxon:9606 + +[Term] +id: UBERON:0014727 +name: intercalated duct of salivary gland +namespace: uberon +def: "The tiny tubules with a very thin epithelial layer in the salivary glands running from the salivary acini into the striated duct." [ncithesaurus:Intercalated_Duct_of_the_Salivary_Gland_System] +xref: FMA:60050 +xref: NCIT:C49266 +is_a: UBERON:0001837 ! duct of salivary gland +is_a: UBERON:0014725 ! intercalated duct +intersection_of: UBERON:0014725 ! intercalated duct +intersection_of: part_of UBERON:0001044 ! saliva-secreting gland + +[Term] +id: UBERON:0014729 +name: striated duct of salivary gland +namespace: uberon +def: "Gland duct which connects an intercalated duct to an interlobular duct in a salivary gland." [http://orcid.org/0000-0002-6601-2165, Wikipedia:Striated_duct] +xref: FMA:60051 +xref: NCIT:C33635 +xref: UMLS:C1514993 +is_a: UBERON:0001837 ! duct of salivary gland +is_a: UBERON:0014719 ! intralobular duct +intersection_of: UBERON:0001837 ! duct of salivary gland +intersection_of: RO:0002176 UBERON:0014720 ! connects interlobar duct +intersection_of: RO:0002176 UBERON:0014727 ! connects intercalated duct of salivary gland +relationship: RO:0002176 UBERON:0014720 ! connects interlobar duct +relationship: RO:0002176 UBERON:0014727 ! connects intercalated duct of salivary gland + [Term] id: UBERON:0014769 name: palpebral vein @@ -250210,7 +253196,7 @@ intersection_of: RO:0002219 UBERON:0011899 ! surrounded by epimysium intersection_of: RO:0002473 UBERON:0001134 ! composed primarily of skeletal muscle tissue relationship: part_of UBERON:0018254 ! skeletal musculature relationship: RO:0002103 CL:0000100 ! synapsed by motor neuron -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002202 UBERON:0003082 ! develops from myotome relationship: RO:0002219 UBERON:0011899 ! surrounded by epimysium relationship: RO:0002473 UBERON:0001134 ! composed primarily of skeletal muscle tissue @@ -250825,6 +253811,17 @@ intersection_of: UBERON:0001037 ! strand of hair intersection_of: part_of UBERON:0002415 ! tail relationship: part_of UBERON:0002415 ! tail +[Term] +id: UBERON:0015149 +name: ventral hair +namespace: uberon +def: "A strand of hair that is part of a ventrum." [OBOL:automatic] +synonym: "ventral coat hair" RELATED [] +is_a: UBERON:0001037 ! strand of hair +intersection_of: UBERON:0001037 ! strand of hair +intersection_of: part_of UBERON:0013235 ! ventrum +relationship: part_of UBERON:0013235 ! ventrum + [Term] id: UBERON:0015150 name: dorsal hair @@ -250990,7 +253987,7 @@ is_a: UBERON:0000061 ! anatomical structure intersection_of: UBERON:0000061 ! anatomical structure intersection_of: BSPO:0000126 UBERON:0000465 ! material anatomical entity relationship: BSPO:0000126 UBERON:0000465 ! material anatomical entity -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria [Term] id: UBERON:0015214 @@ -251153,6 +254150,7 @@ name: axilla skin namespace: uberon def: "A zone of skin that is part of a axilla." [OBOL:automatic] synonym: "axillary skin" EXACT [FMA:37322] +synonym: "skin of armpit" EXACT [PMID:38565739] synonym: "skin of axilla" EXACT [FMA:37322] xref: EMAPA:37349 {source="MA:th"} xref: FMA:37322 @@ -251766,6 +254764,7 @@ synonym: "tunica fibrosa hepatis" EXACT OMO:0003011 [FMA:15813, FMA:TA] xref: FMA:15813 xref: SCTID:362185005 xref: Wikipedia:Fibrous_capsule_of_Glisson +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0003893 ! capsule is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0003893 ! capsule @@ -252348,6 +255347,21 @@ intersection_of: BSPO:0015101 UBERON:0003072 ! optic cup relationship: BSPO:0015101 UBERON:0003072 ! optic cup relationship: part_of UBERON:0003072 ! optic cup +[Term] +id: UBERON:0016855 +name: ventral part of optic cup +namespace: uberon +def: "The ventral region of the optic cup that gives rise to the ventral part of the retina." [http://orcid.org/0000-0002-6601-2165] +comment: optic fissure, hyaloid artery, pecten +synonym: "ventral optic cup" EXACT [http://orcid.org/0000-0002-6601-2165] +synonym: "ventral region of optic cup" EXACT [http://orcid.org/0000-0002-6601-2165] +is_a: UBERON:0000481 ! multi-tissue structure +is_a: UBERON:0004121 ! ectoderm-derived structure +intersection_of: UBERON:0000481 ! multi-tissue structure +intersection_of: BSPO:0015102 UBERON:0003072 ! optic cup +relationship: BSPO:0015102 UBERON:0003072 ! optic cup +relationship: part_of UBERON:0003072 ! optic cup + [Term] id: UBERON:0016879 name: future central nervous system @@ -252521,6 +255535,19 @@ intersection_of: UBERON:0005486 ! venous dural sinus intersection_of: BSPO:0000126 UBERON:0000033 ! head relationship: BSPO:0000126 UBERON:0000033 ! head +[Term] +id: UBERON:0017648 +name: ventral body wall +namespace: uberon +def: "The ventral part of the body wall." [http://orcid.org/0000-0002-6601-2165] +synonym: "anterior body wall" RELATED [FMA:86934] +xref: EMAPA:37984 {source="MA:th"} +xref: FMA:86934 +is_a: UBERON:0000309 ! body wall +intersection_of: UBERON:0000309 ! body wall +intersection_of: part_of UBERON:0013235 ! ventrum +relationship: part_of UBERON:0013235 ! ventrum + [Term] id: UBERON:0017649 name: dorsal body wall @@ -252553,6 +255580,19 @@ intersection_of: UBERON:0001048 ! primordium intersection_of: RO:0002387 UBERON:0001044 ! has potential to develop into saliva-secreting gland relationship: RO:0002387 UBERON:0001044 ! has potential to develop into saliva-secreting gland +[Term] +id: UBERON:0017659 +name: ventral surface of penis +namespace: uberon +subset: pheno_slim +synonym: "urethral surface of penis" EXACT [FMA:19624] +xref: FMA:19624 +is_a: UBERON:0036215 ! anatomical surface region +intersection_of: UBERON:0036215 ! anatomical surface region +intersection_of: BSPO:0015102 UBERON:0000989 ! penis +relationship: BSPO:0015102 UBERON:0000989 ! penis +relationship: part_of UBERON:0000989 ! penis + [Term] id: UBERON:0017672 name: abdominal viscera @@ -252825,6 +255865,7 @@ subset: pheno_slim synonym: "pulmonary lymphatic chain" EXACT [FMA:67999] synonym: "pulmonary lymphatic vasculature" RELATED [] xref: FMA:67999 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0011216 ! organ system subdivision intersection_of: UBERON:0011216 ! organ system subdivision @@ -252843,6 +255884,7 @@ subset: human_reference_atlas synonym: "lymphatic vessel of lung" EXACT [] xref: FMA:234006 xref: SCTID:321862009 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0003456 ! respiratory system lymphatic vessel is_a: UBERON:0004119 ! endoderm-derived structure intersection_of: UBERON:0001473 ! lymphatic vessel @@ -253260,7 +256302,18 @@ is_a: BFO:0000003 is_a: UBERON:0000105 ! life cycle stage relationship: has_part UBERON:0007221 ! neonate stage relationship: part_of UBERON:0000092 ! post-embryonic stage -relationship: RO:0002160 NCBITaxon:40674 ! only in taxon Mammalia +relationship: RO:0002162 NCBITaxon:40674 ! in taxon Mammalia + +[Term] +id: UBERON:0018691 +name: ventral side of post-anal tail +namespace: uberon +is_a: UBERON:0034929 ! external soft tissue zone +intersection_of: UBERON:0034929 ! external soft tissue zone +intersection_of: BSPO:0015102 UBERON:0007812 ! post-anal tail +relationship: BSPO:0015102 UBERON:0007812 ! post-anal tail +relationship: part_of UBERON:0007812 ! post-anal tail +relationship: part_of UBERON:0013235 ! ventrum [Term] id: UBERON:0018692 @@ -254156,7 +257209,7 @@ is_a: UBERON:0000122 ! neuron projection bundle is_a: UBERON:0015212 ! lateral structure relationship: BSPO:0000126 UBERON:0000033 ! head relationship: extends_fibers_into UBERON:0000955 ! brain -relationship: RO:0002160 NCBITaxon:89593 ! only in taxon Craniata +relationship: RO:0002162 NCBITaxon:89593 ! in taxon Craniata property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -254561,6 +257614,7 @@ name: external soft tissue zone namespace: uberon def: "A region or zone on the surface of an organism that encompasses skin and any adnexa, down through muscles and bounded by underlying skeletal support structures." [http://orcid.org/0000-0002-6601-2165] is_a: BFO:0000002 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0010000 ! multicellular anatomical structure relationship: has_part UBERON:0000014 ! zone of skin relationship: has_part UBERON:0001015 ! musculature @@ -256543,6 +259597,16 @@ intersection_of: UBERON:0000060 ! anatomical wall intersection_of: part_of UBERON:0002285 ! telencephalic ventricle relationship: part_of UBERON:0002285 {source="FMA"} ! telencephalic ventricle +[Term] +id: UBERON:0036656 +name: wall of third ventricle +namespace: uberon +xref: FMA:242776 +is_a: UBERON:0036661 ! wall of ventricular system of brain +intersection_of: UBERON:0000060 ! anatomical wall +intersection_of: part_of UBERON:0002286 ! third ventricle +relationship: part_of UBERON:0002286 {source="FMA"} ! third ventricle + [Term] id: UBERON:0036657 name: wall of fourth ventricle @@ -257459,7 +260523,7 @@ def: "One of the main divisions of the whole organism of arthropods formed from comment: Strictly speaking the term "tagma" cam be used for any metameric organism, however we follow the common usage which is to restrict the term to arthropods. xref: FBbt:00000002 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} is_a: UBERON:0011676 ! subdivision of organism along main body axis -relationship: RO:0002160 NCBITaxon:6656 ! only in taxon Arthropoda +relationship: RO:0002162 NCBITaxon:6656 ! in taxon Arthropoda property_value: RO:0002161 NCBITaxon:7742 [Term] @@ -257503,9 +260567,9 @@ xref: FBbt:00001730 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ is_a: UBERON:0000033 ! head intersection_of: UBERON:0000033 ! head intersection_of: part_of UBERON:0002548 ! larva -intersection_of: RO:0002160 NCBITaxon:50557 ! only in taxon Insecta +intersection_of: RO:0002162 NCBITaxon:50557 ! in taxon Insecta relationship: part_of UBERON:0002548 ! larva -relationship: RO:0002160 NCBITaxon:50557 ! only in taxon Insecta +relationship: RO:0002162 NCBITaxon:50557 ! in taxon Insecta [Term] id: UBERON:6002639 @@ -257517,9 +260581,9 @@ xref: FBbt:00002639 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ is_a: UBERON:0000020 ! sense organ intersection_of: UBERON:0000020 ! sense organ intersection_of: part_of UBERON:0002548 ! larva -intersection_of: RO:0002160 NCBITaxon:50557 ! only in taxon Insecta +intersection_of: RO:0002162 NCBITaxon:50557 ! in taxon Insecta relationship: part_of UBERON:0002548 ! larva -relationship: RO:0002160 NCBITaxon:50557 ! only in taxon Insecta +relationship: RO:0002162 NCBITaxon:50557 ! in taxon Insecta [Term] id: UBERON:6003005 @@ -257915,6 +260979,7 @@ name: ductal plate namespace: uberon def: "In human, ductal plate is a double-layered cylindrical structure of bile duct epithelium that surrounds the portal ramifications by the eighth gestational week. After approximately the 12th gestational week, remodelling of ductal plate begins, and maturity is attained by the end of gestation or early postnatal period." [http://orcid.org/0000-0002-7073-9172, PMID:28515578] subset: added_for_HCA +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004119 ! endoderm-derived structure is_a: UBERON:0010000 ! multicellular anatomical structure relationship: has_part UBERON:0004820 ! bile duct epithelium @@ -260633,9 +263698,7 @@ inverse_of: output_of ! output of [Typedef] id: has_part name: has part -name: has_part namespace: external -namespace: quality def: "a core relation that holds between a whole and its part" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology @@ -260846,9 +263909,7 @@ expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://p [Typedef] id: part_of name: part of -name: part_of namespace: external -namespace: quality def: "a core relation that holds between a part and its whole" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term diff --git a/patterns/definitions.owl b/patterns/definitions.owl index 16ea5f6ce..5455e8867 100644 --- a/patterns/definitions.owl +++ b/patterns/definitions.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2024-08-16") + +Annotation(owl:versionInfo "2024-09-25") Declaration(Class()) Declaration(Class()) @@ -57,6 +57,7 @@ Declaration(ObjectProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -66,6 +67,44 @@ Declaration(AnnotationProperty( () + +AnnotationAssertion(Annotation( "DOI:10.1016/j.coi.2005.11.008") Annotation( "DOI:10.1038/nri3087") Annotation( "DOI:10.3389/fimmu.2019.01893") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Mononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. +In addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses. +Mononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000113") + +# Class: () + +AnnotationAssertion(Annotation( "DOI:10.1002/glia.24343") Annotation( "DOI:10.1038/nn1988") Annotation( "DOI:10.1101/cshperspect.a020602") Annotation( "DOI:10.1126/science.aat0473") Annotation( "DOI:10.3389/fncel.2017.00024") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Glial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons. +These different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning. +Oligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. +Microglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response. +Despite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000125") + +# Class: () + +AnnotationAssertion(Annotation( "DOI:10.1016/0166-4328(96)00075-7") Annotation( "DOI:10.1016/j.cell.2017.05.034") Annotation( "DOI:10.1038/s41574-019-0168-8") Annotation( "DOI:10.1073/pnas.1804938115") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Type EC enteroendocrine cells, also known as enterochromaffin cells, are a vital hormone-secreting cell type found in the gastrointestinal tract. These cells are named after their location in the intestines (“entero”) and because they are stainable by chromium salts (“chromaffin”). +The primary function of type EC enteroendocrine cells is to act as chemosensors and lies in their capacity to produce and secrete serotonin, also known as 5-hydroxytryptamine (5-HT). Serotonin is a neurotransmitter that plays a significant role in modulating motility, secretion, vasodilation, perception of pain, and appetite in the gastrointestinal system. However, its function is not limited to the gastrointestinal tract; once secreted, serotonin is distributed via the bloodstream and contributes to regulating mood, appetite, and sleep in the brain. +Via specific chemosensory receptors type EC enteroendocrine cells are able to respond to various environmental, metabolic, and homeostatic stimuli and transduce information from the gut to the nervous system: Food intake, particularly the ingestion of fats and carbohydrates, prompts these cells to produce and release serotonin; the mechanical stimulus of food in the lumen can also trigger release. The distribution, function, and responsiveness of type EC cells reveal them as a crucial link between the intestinal environment, the nervous system, and the regulation of numerous bodily functions.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000577") + +# Class: () + +AnnotationAssertion(Annotation( "DOI:10.1007/s00424-017-1965-3") Annotation( "DOI:10.1016/j.cellimm.2018.01.005") Annotation( "DOI:10.1038/nri3600") Annotation( "DOI:10.14348/molcells.2021.0058") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Alveolar macrophages are unique tissue-resident macrophages found in the lungs, specifically in the air sacs or alveoli where gas exchange occurs. They are characterized by specific surface markers including: F4/80-positive, CD11b-/low, CD11c-positive, CD68-positive, sialoadhesin-positive, dectin-1-positive, MR-positive, CX3CR1-negative. These specialized immune cells form a crucial part of the body's defense mechanism, playing important roles in pulmonary health and homeostasis. They are the first line of defense in the pulmonary immune response, acting as scavengers that patrol the alveoli and engulf foreign particles like bacteria, dust, and other debris that enter the lungs through inhalation. +The primary function of these alveolar macrophages is phagocytosis, whereby they consume and digest foreign substances, dead cells, and other particulates. In the lung, alveolar macrophages are also responsible for clearing surfactant. Additionally, alveolar macrophages also play an integral role in initiating the immune response, as they secrete several pro-inflammatory cytokines and chemokines that recruit other immune cells to the site of infection or inflammation. +Beyond their role in host defense, alveolar macrophages contribute to tissue remodeling and wound repair in the lungs, aiding in maintaining lung integrity. They also regulate local inflammation and control the immune response to prevent excessive inflammation that may be harmful. However, an imbalance in the function of alveolar macrophages can contribute to various lung diseases. Abnormal alveolar macrophage activation has been implicated in chronic inflammatory diseases such as emphysema, asthma, and fibrosis.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000583") + # Class: (cycling B cell) AnnotationAssertion(Annotation( "PMID:31348891") "A(n) B cell that is cycling.") @@ -247,4 +286,422 @@ AnnotationAssertion(rdfs:label "cycl EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ) ObjectSomeValuesFrom( ))) +AnnotationAssertion(Annotation( "DOI:10.1002/cphy.c120026") Annotation( "DOI:10.1007/978-1-4939-1311-4_10") Annotation( "DOI:10.1016/j.immuni.2022.08.002") Annotation( "DOI:10.1038/nri.2017.11") Annotation( "DOI:10.1111/j.1478-3231.2006.01342.x") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Kupffer cells are tissue-resident macrophages located in the liver. They are an integral part of the mononuclear phagocyte system and are responsible for the phagocytosis of dead or dying cells, microbes, and other foreign substances. Kupffer cells account for approximately 80-90% of tissue-resident macrophages in the body. They are found within the lumen of liver sinusoids and interface with microbial populations and products. +The primary role of Kupffer cells is to maintain homeostasis in the liver. They continuously filter and cleanse the blood that flows through the liver, removing pathogens, endotoxins, particulate matter, aged and dysfunctional red blood cells, and miscellaneous waste products. These cells also play an important role in maintaining iron homeostasis. During the process of phagocytosis, Kupffer cells recycle iron from degraded red blood cells, which is then utilized in the formation of new erythrocytes. +Kupffer cells also play key roles in various immune responses and inflammatory processes. They secrete various types of cytokines and chemokines, which contribute to the activation and mobilization of other immune cells. They can also produce reactive oxygen species and nitric oxide, which have microbicidal actions. Although their activity is essential for host defense, excessive or prolonged activation of Kupffer cells may contribute to hepatic injury, inflammation, and fibrosis.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000091") +AnnotationAssertion(Annotation( "DOI:10.1007/s12311-018-0985-7") Annotation( "DOI:10.1038/nrn3886") Annotation( "DOI:10.7554/eLife.63668") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK545154/") Annotation( "https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/purkinje-cell") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Purkinje cells, named after the Czech anatomist Jan Evangelista Purkyně who discovered them, are unique inhibitory neurons in the cerebellar cortex. They are a critical part of the vertebrate nervous system as they provide the only signal output from the cortex to the cerebellar nuclei. They are one of the few types of neurons that are large enough to be seen with the naked eye. The most distinct hallmark of Purkinje cells is their elaborate dendritic arbor, which forms a broad and intricately branching structure resembling a tree. These numerous branches each receive excitatory synaptic inputs from more than 100,000 parallel fibers; in addition, a single climbing fiber makes hundreds of synapses to the soma and proximal dendrites. A single long axon forms an inhibitory projection to the cerebellar nuclei. +Purkinje cells play key roles in the coordination of fine, voluntary motor movements and balance. As the sole output of all motor coordination in the cerebellar cortex, they serve as a central relay in the cerebro-cerebellar loop. Each Purkinje cell receives two types of synaptic input: one from parallel fibers (which are axons of granule cells), and the other from climbing fibers (originating from the inferior olivary nucleus). The Purkinje cells process and integrate these diverse kinds of input signals to generate output that controls timing and coordination of movements. +Purkinje neurons show considerable synaptic plasticity. Throughout life, these cells continue to undergo long-term potentiation and depression at parallel fiber synapses, which cause long-lasting increase or decrease, respectively, of synaptic transmission and have been proposed as mechanisms for motor learning. +Purkinje cells are also known to be implicated in a variety of diseases. Their progressive loss is a prime feature in certain types of ataxia, a collective term used to describe conditions characterized by loss of muscular control and coordination. Furthermore, a significant reduction in the density of Purkinje cells has been reported in conditions such as autism and Huntington’s disease.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000121") +AnnotationAssertion(Annotation( "DOI:10.1016/S1357-2725(02)00083-3") Annotation( "DOI:10.1038/s41575-022-00675-x") Annotation( "DOI:10.1165/ajrcmb.25.5.f218") Annotation( "DOI:10.1242/bio.20121701") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK553208/") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Goblet cells are specialized, simple columnar, secretory epithelial cells that are mostly found in the respiratory and intestinal tracts. The term \"goblet\" refers to their shape, which resembles a flask or goblet, specially at their apical end which is swollen due to the accumulation of secretory granules. +The primary function of goblet cells is to to protect and lubricate the underlying tissues by secreting large quantities of mucin, a complex glycoprotein, which forms mucus when hydrated. In the respiratory tract, the mucus secreted by these cells traps dust, bacteria, viruses, and other potentially harmful particles in the inhaled air, preventing them from reaching the delicate tissues of the lungs. In the intestines, the goblet cells secrete mucus that acts as a protective barrier shielding the intestinal epithelium from dietary antigens, pathogens and prevents the intestinal epithelium from being eroded by the actions of the digestive enzymes and the abrasive action of passing food material. +Goblet cells are capable of rapidly altering their secretory output in response to stimuli. For example, irritants like smoke or dust can trigger an increased rate of mucus production, as the body attempts to flush out the harmful particles. Conversely, in conditions such as chronic bronchitis and cystic fibrosis, overactive goblet cells can create a thick accumulation of mucus that obstructs the airways and fosters bacterial growth. Lastly, goblet cells are not static, rather, they undergo a dynamic process known as goblet cell metaplasia-differentiation, wherein non-goblet cells in response to chronic injury or inflammation, can differentiate into goblet cells leading to an accumulation of these cells in the tissue, known as goblet cell hyperplasia.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000160") +AnnotationAssertion(Annotation( "DOI:10.1038/s41574-019-0168-8") Annotation( "DOI:10.1111/j.1463-1326.2011.01438.x") Annotation( "DOI:10.1196/annals.1294.001") Annotation( "DOI:10.1210/endrev/bnaa018") Annotation( "DOI:10.7554/elife.78512") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Enteroendocrine cells are a specialized subset of cells located within the epithelial lining of both the small and large intestines, as well as the stomach and pancreas. Constituting less than 1% of the total population of intestinal cells, they are differentiated from a common intestinal cell progenitor, thus sharing lineage with absorptive and goblet cells of the intestines. +The distinct characteristic feature of an enteroendocrine cell is its inherent capacity to synthesize and secrete a plethora of gut hormones such as serotonin, somatostatin, neurotensin, cholecystokinin, secretin, gastric inhibitory peptide, motilin, and glucagon-like peptide-1. Integrated within this complex network of signaling agents, these substances control various aspects of the digestive system. Each enteroendocrine cell has its unique combination of hormones to release, determined by its position along the intestinal tract. Intriguingly, these hormones not only modulate local gut function, including motility, absorption and secretion, but also potentiate distant actions on other systems such as endocrine, nervous and immune and play a role in the feeling of satiety. +The release of these hormones from enteroendocrine cells is a highly regulated and dynamic process. The cells are equipped with sensory receptors localized on its luminal side that respond to various stimuli, including changes in nutrient composition, chemical or mechanical changes in the gut lumen, or even signals arising from commensal microbiota. This sensory input stimulates a signaling cascade within the cell, culminating in the release of specific hormones into the interstitial fluid. These hormones then make their way into the bloodstream, acting on their respective target receptors to mediate their duties. The multifunctional characteristics of enteroendocrine cells make them crucial for maintaining gut homeostasis and the overall physiological well being of the body.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000164") +AnnotationAssertion(Annotation( "DOI:10.1002/cphy.c190003") Annotation( "DOI:10.1016/j.biocel.2016.02.003") Annotation( "DOI:10.3389/fendo.2018.00711") Annotation( "DOI:10.3389/fimmu.2022.977175") Annotation( "DOI:10.3389/fimmu.2022.977175/full") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Chromaffin cells, also known as pheochromocytes, are neuroendocrine cells that are typically located in the adrenal medulla, the innermost part of the adrenal gland, which is situated on top of each kidney. Chromaffin cells are also found in small clusters, known as paraganglia, in various locations throughout the body, including the sympathetic nervous system. They derive their name from their ability to stain a brownish-black color upon exposure to chromic salts, a feature made possible due to their high content of granules rich in catecholamines and catecholamine-related neurotransmitters. +The primary function of chromaffin cells is the synthesis and release of catecholamines, specifically epinephrine (adrenaline) and norepinephrine (noradrenaline). These neurotransmitters are vital stress hormones that, when released by the adrenal chromaffing cells into the bloodstream, prepare the body for the 'fight or flight' response. This response can enhance the body's performance in a dangerous situation by increasing heart rate, elevating blood sugar, and increasing blood flow to the muscles. The chromaffin cells in paraganglia are responsible for the local release of catecholamines and play a role in regulating blood pressure and other autonomic functions. +In addition to their role in stress response, chromaffin cells also contribute to the body's immune response. They secrete several peptides including antimicrobial peptides, and the discovery of LPS and cytokine receptors on chromaffin cells suggests that the adrenal medulla may participate in some aspects of the immune response.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000166") +AnnotationAssertion(Annotation( "DOI:10.1016/j.coemr.2019.03.001") Annotation( "DOI:10.1093/biolre/ioy059") Annotation( "DOI:10.1210/clinem/dgaa603") Annotation( "DOI:10.3389/fendo.2014.00006") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK556007/#:~:text=Leydig%20cells%20are%20the%20primary,secondary%20sexual%20characteristics%20and%20behaviors.") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Leydig cells are a testosterone-secreting cell in the interstitial area in the testes of males. They are named after Franz Leydig, a German anatomist who discovered these cells in 1850. Uniquely situated within the soft connective tissue surrounding the seminiferous tubules, Leydig cells form an integral part of the male reproductive system. They are usually polygonal cells characterized by well developed smooth endoplasmic reticulum, high lipid content and a large round nucleus. They are found across mammalian species, including humans. +The primary function of Leydig cells is the production of androgens, the male sex hormones, the most notable of which is testosterone. Leydig cells synthesize testosterone from cholesterol through a series of enzymatic reactions. The production and release of testosterone are mainly regulated by the luteinizing hormone (LH) released by the anterior pituitary gland. In response to LH, Leydig cells convert cholesterol into testosterone, which then plays a crucial role in the development and maintenance of primary and secondary male sexual characteristics. These include the formation and maturation of male reproductive organs, onset of spermatogenesis, and the presentation of male secondary sexual traits such as the deepening of the voice, growth of facial hair, development of muscles, and a broadening of shoulders. +Apart from testosterone production, Leydig cells also secrete insulin-like factor 3 (INSL3) that is essential for testicular descent during embryonic development in males. Dysregulation or loss of Leydig cells can lead to numerous conditions like testosterone deficiency, infertility, and certain forms of testicular cancer. Although not typical, Leydig cells can regenerate if they are damaged, ensuring the continuous production of testosterone and maintaining male reproductive health. They provide an excellent model to study cell differentiation and hormone regulation, thereby enhancing our understanding of reproductive biology and associated disorders.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000178") +AnnotationAssertion(Annotation( "DOI:10.1016/j.biocel.2011.11.011") Annotation( "DOI:10.1055/s-2007-1007096") Annotation( "DOI:10.1083/jcb.201903090") Annotation( "DOI:10.1111/j.1439-0396.2007.00752.x") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Hepatocytes are the major cell type constituting 70-80% of the liver's cytoplasmic mass, playing crucial roles in maintaining the body's metabolic homeostasis. Dimensions of mature hepatocytes typically range from 20 to 30 μm in humans, but size may vary depending on their location within the liver lobule. Hepatocytes are characterized by high biosynthetic, enzymatic, and endocytic activity. They contain abundant mitochondria, smooth and rough endoplasmic reticulum, peroxisomes, lysosomes, and a large nucleus that is often binucleate. +The liver consists of three zones - the periportal Zone 1, midzone 2, and pericentral Zone 3 - which have differential nutrient and oxygen status, and damage susceptibility; hepatocytes in the different zones show signifcant functional heterogeneity ('hepatocyte functional zonation'). Hepatocytes are involved in a multitude of critical functions including the metabolism of lipids, carbohydrates, and proteins, the synthesis of serum proteins (e.g., albumin, transferrin, and lipoproteins), the detoxification and excretion of endogenous and exogenous substances, the storage of vitamins and minerals, and the production and secretion of bile. +Heterocytes demonstrate a remarkable regenerative capacity, which enables the liver to recover from injury and loss of tissue mass. Notably, hepatocytes perform biotransformation with both phase I and phase II enzymes, which modify drugs, xenobiotics, and various substances for elimination from the body. Phase I enzymes, such as cytochrome P450, catalyze both oxidative and reductive reactions of many xenobiotics; many of the products of phase I enzymes are substrates for the phase II enzymes, which catalyze conjugation reactions. +Alterations in hepatocyte function have significant implications for overall human health and disease. Certain conditions, such as hepatitis, cirrhosis, and liver cancer, can profoundly affect hepatocyte structure and function, thereby disrupting the liver's ability to perform its vital roles within the body. As the primary site for drug metabolism, changes in hepatocyte function can also impact the effectiveness and toxicity of pharmaceuticals. The regenerative ability of hepatocytes makes them valuable cells for liver regenerative medicine and bioartificial liver support systems, and their study has provided significant insights into liver biology and disease.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000182") +AnnotationAssertion(Annotation( "DOI:10.1016/j.ejogrb.2004.01.010") Annotation( "DOI:10.1093/humrep/del408") Annotation( "DOI:10.1093/humupd/6.3.279") Annotation( "DOI:10.1210/jcem-28-3-355") Annotation( "DOI:10.3389/fendo.2019.00832/full") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Granulosa cells are a type of somatic cell most commonly known for their crucial role within the ovarian follicles of female mammalian species. Named for their grainy appearance, they are situated in the follicular epithelium, lining the inner part of the follicle and directly surrounding the oocyte. These cells stand as an integral part of the ovarian structure and function. +One of the primary roles of granulosa cells is to aid in the production and secretion of sex hormones, particularly estrogen. They achieve this by working in tandem with theca cells, which stay attached to the external layer of the follicle. Theca cells produce androstenedione (a type of androgen) which granulosa cells then convert into estradiol, a form of estrogen, with the help of the enzyme aromatase. Moreover, granulosa cells participate in luteinization, transforming into luteal granulosa cells as a response to the luteinizing hormone during ovulation. This allows the formation of the corpus luteum, responsible for the secretion of progesterone necessary to maintain pregnancy. +Granulosa cells also play a significant role in follicular development and oocyte maturation, involving close communication with the contained oocyte. They support the oocyte through the provision of nutrients and growth factors, control its meiotic cycle and ensure it is appropriately oriented and instructed for impending ovulation. Furthermore, granulosa cells contribute to the formation of the zona pellucida and the follicular fluid, providing an optimal environment for the oocyte's growth and maturation. These cells, thus, perform multiple vital roles, underscoring their importance in fertility and reproductive health.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000501") +AnnotationAssertion(Annotation( "DOI:10.1016/j.pharmthera.2015.05.007") Annotation( "DOI:10.1038/s41574-018-0020-6") Annotation( "DOI:10.1093/annonc/mdh216") Annotation( "https://www.sciencedirect.com/topics/neuroscience/somatostatin-cell") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Type D enteroendocrine cells, also known as D or delta cells, are specialized hormone-releasing cells found in the pancreas and also scattered throughout the lining of the gastrointestinal tract in mammals, notably within the stomach and the upper part of the small intestine known as the duodenum. The primary role of D cells is to produce and secrete somatostatin, a potent paracrine inhibitor. +In the gastrointestinal tract, somatostatin slows down digestion. It reduces gastric acid secretion and slows down the rate of gastric emptying, thereby prolonging and controling the digestive p. Functionally, these effects are aimed at sustaining nutrient absorption to optimize energy extraction from consumed food. +In the pancreas, D cells maintain a vital role in endocrine regulation. D cells in the pancreatic islands secrete somatostatin to inhibit the release of both insulin and glucagon from type A cells and B cells, glucoregulatory hormones that control blood sugar levels. Hence, D cells contribute considerably to the homeostasis of the body's metabolic processes. It is also noteworthy that dysfunctional D cells or irregular somatostatin signaling has been associated with certain pathologies such as neuroendocrine tumors and gastric ulcers.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000502") +AnnotationAssertion(Annotation( "DOI:10.1007/s00018-002-8412-z") Annotation( "DOI:10.1038/nature09637") Annotation( "DOI:10.1038/nrmicro2546") Annotation( "DOI:10.1146/annurev-physiol-030212-183744") Annotation( "DOI:10.3389/fimmu.2020.00587") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Paneth cells are specialized epithelial cells that are primarily located at the bottom of the crypts of Lieberkühn in the small intestine, where they play a pivotal role in maintaining gut homeostasis. They have also been found in smaller numbers in the colonic crypts and other parts of the gastrointestinal tract. Paneth cells are characterized by large acidophilic granules, which take up most of the cytoplasmic volume, causing the nucleus to be pushed toward the base of the cell. +Paneth cells function as a part of the innate immune system. The large granules inside the cells are filled with antimicrobial peptides, such as defensins and lysozymes. Upon bacterial intrusion or cellular signaling indicating a potential infection, Paneth cells release the granules containing the antimicrobial substances into the crypt lumen, effectively serving as the first line of defense against bacterial invasion within the gastrointestinal tract. In essence, Paneth cells serve as guardians, protecting the intestinal stem cells from harmful pathogens that may disturb the gut ecosystem. +In addition to their primary role in immunity, Paneth cells are also crucial for supporting the stem cell niche in the intestinal crypts. They are located adjacent to Lgr5+ stem cells and secrete various growth factors such as EGF, TGF-alpha, Wnt3, and Notch ligand Dll4. These factors regulate the self-renewal and differentiation of these stem cells, which continuously replenish the intestinal epithelium. Consequently, any abnormality or dysfunction in Paneth cells could lead to a disturbance in gut homeostasis, possibly resulting in various illnesses such as inflammatory bowel disease.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000510") +AnnotationAssertion(Annotation( "DOI:10.1007/BF00710764") Annotation( "DOI:10.1038/nrgastro.2013.36") Annotation( "DOI:10.1097/MOG.0b013e32832ebfac") Annotation( "DOI:10.1111/prd.12116") Annotation( "DOI:10.1152/physrev.00011.2011") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Acinar cells are specialized exocrine gland cells that secrete specific enzymes and fluids to aid in digestion. Found primarily in the pancreas and salivary glands, the term acinar is derived from the Latin word 'acinus' which means 'grape'; this is because acinar cells are arranged in a grape-like cluster around small ducts, formulating an acinus structure. +In the salivary glands, acinar cells secrete digestive enzymes as well as other substances such as mucus and water. These secretions service the initial stages of the digestive process, preparing the consumed food for onward digestion in the stomach and intestines by lubricating and partially breaking it down. +In the pancreas, acinar cells are responsible for synthesizing and secreting a significant amount of digestive enzymes, such as trypsin, chymotrypsin, and amylase. These enzymes are stored in zymogen granules inside the acinar cells until they are dispatched into the small intestine. Once within the small intestine, they break down proteins, carbohydrates, and fats into substances that can be absorbed. This is vital to the effective and efficient digestion and absorption of nutrients from the food we consume. +Acinar cells have high protein synthesis rates and are susceptible to accumulation of misfolded proteins; the subsequential induction of ER stress is thought to be involved in the development of pancreatitis, a serious inflammatory disease of the exocrine pancreas.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000622") +AnnotationAssertion(Annotation( "DOI:10.1038/s41467-022-33748-1") Annotation( "DOI:10.1038/s41572-020-0196-7") Annotation( "DOI:10.1146/annurev-physiol-020911-153238") Annotation( "DOI:10.1159/000481633") Annotation( "DOI:10.3389/fcell.2021.771931") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Podocytes are highly specialized, terminally differentiated glomerular visceral epithelial cells that wrap around the capillaries in the kidneys. They play an essential role in kidney function, particularly in the filtration selectivity of the glomerulus. Each podocyte is characterized by a unique architecture with a large cell body, ‘major processes’ extending outwardly from the cell body and ‘foot processes’, also known as pedicels, which surround. the glomerular capillary loops +Podocytes represent the last barrier of the glomerular filtration membrane in the kidney. This barrier prevents the leakage of plasma proteins from the blood into the urine, hence maintaining protein homeostasis in the body. The foot processes of the podocytes interdigitate with those from neighboring cells. The cell-cell junctions between the foot processes, the slit-diaphragms, are thought to create a molecular sensor of renal filtration that prevents the passage of macromolecules while allowing water and small solutes to pass. +Podocytes also contribute to the glomerular basement membrane by secreting collagen and maintain glomerular endothelial cell fenestration by secreting VEGFA. They have been shown to play a role in inducing cytoskeletal regulation, cell adhesion, and inflammatory response, consistent with their essential function in the kidney. +The importance of podocytes is further emphasized by the effects of their damage or loss. Abnormalities in podocytes often result in severe kidney diseases (podocytopathies), including focal segmental glomerulosclerosis (FSGS) and minimal change disease (MCD). Injury to the podocytes can result in \"effacement\" or flattening of foot processes, leading to increased permeability of the filtration barrier and proteinuria (an excess of serum protein in urine) which is a common symptom of kidney diseases.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000653") +AnnotationAssertion(Annotation( "DOI:10.1002/ar.1092200109") Annotation( "DOI:10.1016/0306-4522(86)90162-4") Annotation( "DOI:10.1016/j.devcel.2012.11.003") Annotation( "DOI:10.1038/s41467-022-31571-2") Annotation( "DOI:10.1152/ajprenal.90601.2008") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Fenestrated cells are specialized epithelial cells that are characterized by a distinctive structural feature, fenestrations or tiny pores, which allow an exchange of substances such as fluids, nutrients, and waste between blood vessels and the surrounding tissue environments. These cells are present in various types of epithelial tissues in the human body, including the intestinal tract, endocrine glands, and certain parts of the renal system. +There are multiple types of endothelial cell fenestrations. The most common type is found in systemic capillaries of the endocrine tissue (e.g., pancreatic islets), gastrointestinal mucosa, and renal peritubular capillaries. Here, the fenestrated cells have fenestrations in their peripheral cytoplasm with a unique thin and permeable diaphragm that provides a high degree of selectivity, blocking the passage of larger molecules while allowing the free movement of smaller ones. In contrast, other types of fenestrations, such as the discontinuous epithelium of the liver sinusoidal endothelial cells, do not have diaphragms. +Characteristically, fenestrated cells play a vital role in the filtering process of body systems. They are a key part of the glomeruli in the kidneys where blood is filtered under high pressure. The fenestrations present in the endothelial cells lining the capillaries of the glomerulus allow the free passage of water and small solute molecules towards the Bowman's capsule, leaving behind larger proteins and cells in the blood, thereby aiding in the filtration and waste removal process. +In the endocrine system, fenestrated cells in glandular capillaries allow the prompt release of hormones into the bloodstream. These cells have tightly clustered fenestrations which increase the surface area available for passive diffusion, improving the efficiency of hormone secretion. In villi of the small intestine, these cells increase absorption efficiency, permitting the exchange of water, electrolytes, and nutrients. +Overall, fenestrated cells contribute immensely to important physiological processes of filtration, absorption, and secretion, primarily connecting our body's circulation system with the surrounding tissues and organs.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000666") +AnnotationAssertion(Annotation( "DOI:10.1038/nature08529") Annotation( "DOI:10.1093/jb/mvv121") Annotation( "DOI:10.1136/gut.47.5.735") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK534232/") Annotation( "https://www.sciencedirect.com/topics/medicine-and-dentistry/microfold-cell") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +M cells, or microfold cells, of the gut are specialized epithelial cells found in the lining of the gut, specifically in the follicle-associated epithelium of mucosa-associated lymphoid tissue, where they function as sentries against toxins and pathogens. M cells are characterized by apical microfolds (hence their alternate name) which express unique adhesion molecules that enable them to sample the luminal macromolecules. +Other morphological features that distinguish M cells from other intestinal mucosal cells include sparse microvilli and a reduced thickness of the glycocalyx, which permits adhesion while not hindering the transport of molecules. They also have unique intraepithelial invaginations on the basolateral side which are filled with macrophages and other immune cells that can process the engulfed macromolecules quickly. +These morphological characteristics enable M cells to serve a dual role in immune responses. They initiate the immune response by transporting antigens (such as toxic or pathogenic substances) across the epithelial layer to lymphocytes and antigen-presenting cells in the underlying lymphoid tissue. This specialized transport process is called 'transcytosis.' They also have specialized molecules like glycoprotein-2 for bacterial uptake. Simultaneously, M cells help maintain immune tolerance to food antigens and commensal bacteria, preventing unnecessary reactions to non-pathogenic substances and hypersensitivity conditions. While these functions are crucial for well-being, M cell dysfunction can lead to serious conditions like Crohn's disease and other inflammatory bowel diseases.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000682") +AnnotationAssertion(Annotation( "DOI:10.1016/j.febslet.2014.07.005") Annotation( "DOI:10.1016/j.mce.2015.06.028") Annotation( "DOI:10.1038/s41580-020-00317-7") Annotation( "DOI:10.1210/jc.2003-030630") Annotation( "DOI:10.1369/00221554155835") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +PP cells, also known as pancreatic polypeptide cells (and previously called F cells or gamma cells), are enteroendocrine cells predominantly found in the islets of Langerhans in the head of the pancreas. They are one of the four main endocrine cell types present in the pancreatic islets, along with type A, B and D cells. PP cells are notable for their production of pancreatic polypeptide, an anorexigenic hormone that modulates food intake and energy homeostasis. +By secreting pancreatic polypeptide, PP cells play a significant role in the management of both digestive and appetite regulation. Upon ingestion of food, there is a significant increase in the secretion of pancreatic polypeptide, which then reduces biliary secretion and helps slow down the movement of food through the digestive tract. This allows more time for digestion to take place and nutrients to be absorbed, promoting the efficient use of dietary intake. The pancreatic polypeptide further reduces appetite by interacting with the hypothalamus, the area of the brain responsible for control of hunger. +Given their important role in digestion, malfunction or damage to PP cells can lead to a disturbance in the digestive process and contribute to some disease conditions. For example, an overproduction of pancreatic polypeptide can result in conditions such as pancreatic tumors and diabetes. Conversely, an under secretion might contribute to obesity due to impaired dietary control. Furthermore, PP cells may also play a role in the body's energy balance, suggesting their implication in conditions related to energy metabolism.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000696") +AnnotationAssertion(Annotation( "DOI:10.1002/nau.22195") Annotation( "DOI:10.1038/ki.2009.73") Annotation( "DOI:10.1038/ncpuro0672") Annotation( "DOI:10.1038/s41579-020-0324-0") Annotation( "DOI:10.1152/physrev.00041.2019") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Urothelial cells are a unique type of epithelial cell found lining the urinary tract system. They form the urothelium, a specialized, multi-layered epithelium that lines major portions of the urinary tract, including the renal pelvis, ureters, bladder, and the proximal part of the urethra. The distinct characteristic of urothelial cells is their ability to stretch and contract depending on the volume of liquid they contain - a feature that facilitates the essential role they play in maintaining the functionality and integrity of the urinary system. +The primary function of urothelial cells is to provide an impermeable barrier to urine, preventing the toxic components present in the urine from seeping back into the body's bloodstream. The urothelium consists of a superficial umbrella cell layer, 1–2 layers of intermediate cells, and a basal cell layer. The umbrella layer is composed of large, mostly binucleated cells that are covered in an asymmetrical unit membrane, the uroplakin plaques. These plaques function to seal the apical membrane of the bladder from the toxic and highly variable contents of urine. The lipid bilayer structure of uroplakin plaques has an exceptionally high concentration of uroplakins that contribute to the barrier function of the urothelium. +Beyond their mechanical function, urothelial cells also play a role in sensing and signaling changes in the urinary system. They express a number of sensor molecules or respond to thermal, mechanical and chemical stimuli and can release chemical mediators. This allows them to act as sensory transducers because they detect changes in the filling state of the bladder and transmit this information to the nervous system. Moreover, these versatile cells contribute to the defense mechanism against urinary tract pathogens. They respond to bacterial infections by releasing chemical messengers, cytokines and chemokines, to attract immune cells, and also can engulf pathogens via endocytosis.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000731") +AnnotationAssertion(Annotation( "DOI:10.1038/nri.2017.28") Annotation( "DOI:10.1111/sji.12883") Annotation( "DOI:10.1182/blood-2009-07-235028") Annotation( "DOI:10.3389/fimmu.2015.00423/full") Annotation( "DOI:10.3389/fimmu.2019.02035") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Classical monocytes are a subtype of monocytes that are characterized by high CD14 but no CD16 expression. Emerging from the bone marrow and entering the bloodstream, these cells play central roles in immune responses and regulation of inflammation. CD14-positive CD16-negative monocytes form the majority of circulating monocytes in the body, typically contributing to around 80-90% of the total monocyte pool. +The primary function of the classical monocytes is to serve in the frontline of host defense against infections. They are primed to migrate to sites of infection, and they express pattern recognition receptors that help them identify and phagocytose pathogens, leading to their destruction. Classical monocytes also contribute to inflammation by producing several pro-inflammatory cytokines including interleukins and tumor necrosis factors. +In response to specific signals from tissues under pathological conditions, such as infection or injury, classical monocytes can leave the bloodstream and migrate towards the affected sites. Following their arrival, these cells differentiate into diverse cell types including macrophages and dendritic cells to combat specific pathogens or injury. Dysregulated monocyte activity can lead to the development of many human diseases including inflammation, infection, tissue injury, and various autoimmune diseases.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000860") +AnnotationAssertion(Annotation( "DOI:10.1038/s41392-023-01452-1") Annotation( "DOI:10.1186/s12935-021-02089-2") Annotation( "DOI:10.3389/fimmu.2015.00263") Annotation( "DOI:10.3389/fimmu.2020.583084") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Inflammatory macrophages, also sometimes referred to as M1 or classically activated macrophages, play an important role in the inflammatory response. The M1/M2 classification is based upon macrophage polarization rather than macrophage location and refers to macrophage activation towards either a more inflammatory or more resolving phenotype, respectively, although the functional diversity of macrophages is more nuanced than such a dichotomy suggests. +Inflammatory macrophages are derived from monocytes recruited to a site of infection or injury. M1 macrophages are classically activated, typically by IFN-γ or lipopolysaccharide (LPS). Upon sensing signs of inflammation, they quickly respond by increasing their pro-inflammatory activity. They achieve this by producing a range of signaling molecules, such as nitric oxide, reactive oxygen species, and numerous cytokines such as tumor necrosis factor-alpha (TNF-alpha) and interleukin-1, -6 and -12. The release of these potent molecules helps to recruit other immune cells to the site, killing off pathogenic organisms and facilitation inflammation. At the same time, M1 macrophages can also present antigens to T cells, thereby helping to induce an adaptive immune response. Over time, these macrophages may transition in phenotype and function to help resolve the inflammation and promote tissue repair. +Despite the beneficial role of inflammatory macrophages in dealing with pathogens, chronic activation of these cells can lead to harmful effects. Over time, continuous production of pro-inflammatory molecules can cause damage to tissues and organs. This is seen in certain chronic inflammatory diseases, such as atherosclerosis, diabetes, obesity, asthma, and various autoimmune disorders. In such situations, the normally protective function of inflammatory macrophages is not properly controlled, which can contribute to disease pathology.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000863") +AnnotationAssertion(Annotation( "DOI:10.1038/s41392-023-01452-1") Annotation( "DOI:10.1186/s12935-021-02089-2") Annotation( "DOI:10.3389/fimmu.2015.00263") Annotation( "DOI:10.3389/fimmu.2020.583084") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Alternatively activated macrophages, also referred to as M2 macrophages, are immune cells originating from monocytes. The M1/M2 classification is based upon macrophage polarization rather than macrophage location and refers to macrophage activation towards either a more inflammatory or more resolving phenotype, respectively, although the functional diversity of macrophages is more nuanced than such a dichotomy suggests. +M2 macrophages cells are differentiated from their precursors generally in response to Th2 cytokines, such as interleukin-4 (IL-4), interleukin-10 (IL-10), and interleukin-13 (IL-13). Tissue-resident macrophages are also sometimes said to have an “M2-like” phenotype. M2 macrophages play key roles in immunoregulation and disease resolution. +Functionally, alternatively activated macrophages are essential in wound healing and tissue repair and remodeling, largely due to their potent anti-inflammatory actions and their ability to promote angiogenesis. They achieve these functions by the production of specific growth factors and signaling proteins including Arg1, Ym1/2, Fizz1, and TGF-β. Additionally, they provide defense against specific categories of pathogens, particularly parasites, through specific communication with Th2 cells. +However, dysfunction of M2 macrophages can be harmful. Alternatively activated macrophages have been associated with several pathological conditions such as asthma, fibrosis, and tumor progression. This is due to their capacity to inhibit inflammatory responses, promote unneeded wound healing processes, and support tumour growth and spreading. Furthermore, complex roles have been observed in metabolic disorders, cardiovascular diseases, and neurodegenerative diseases, showing the diverse functional spectrum of these cells.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0000890") +AnnotationAssertion(Annotation( "DOI:10.1016/0165-6147(89)90192-2") Annotation( "DOI:10.1038/nrgastro.2013.36") Annotation( "DOI:10.1097/01.mog.0000239863.96833.c0") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK54134/") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Pancreatic acinar cells are the functional units of the exocrine pancreas. These cells are structurally arranged in small clusters - or acini - with a small central lumen, and their primary function is to produce and secrete enzymes that facilitate digestion of proteins, carbohydrates, and fats within the small intestine. +Some of the most important digestive enzymes synthesized by the pancreatic acinar cells include amylase, which digests carbohydrates, lipase, which breaks down fats, and several proteases such as trypsin and chymotrypsin which are vital for the digestion of proteins. Importantly, these enzymes are produced as proenzymes or zymogens to avoid autolysis, or the breakdown of the pancreas itself. +The release of these enzymes by the pancreatic acinar cells is strictly regulated by hormones and neurochemicals. Cholecystokinin (CCK) released from the enteroendocrine cells in the duodenum cause the release of these enzymes. Moreover, acinar cells also respond to another hormone, secretin, by releasing bicarbonate-rich fluid which helps to neutralize the gastric acid in the duodenum. +Dysregulation in the function of pancreatic acinar cells can lead to severe health issues, including pancreatitis, which is characterized by inflammatory damage to the organ due to the premature activation of digestive enzymes.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002064") +AnnotationAssertion(Annotation( "DOI:10.1016/j.diabres.2018.06.013") Annotation( "DOI:10.1210/en.2016-1748") Annotation( "DOI:10.2337/db15-1541") Annotation( "DOI:10.2337/dbi19-0002") Annotation( "DOI:10.3389/fphys.2012.00349/full") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Type A enteroendocrine cells, also known as alpha cells or A cells, are a species of endocrine cells primarily located in the pancreatic islets of Langerhans; they have also been identified within the lining of the stomach. Functionally, these cells are pivotal in glucose metabolism and homeostasis, accounting for about 20% of the total population of cells in the pancreatic islets. +The primary role of type A enteroendocrine cells involves the synthesis, storage, and secretion of the peptide hormone glucagon, which is critical in energy regulation throughout the body. In response to a decrease in blood glucose levels, the pancreatic A cells are stimulated to secrete glucagon into the bloodstream. Glucagon acts on its target cells, mainly in the liver, to stimulate glycogenolysis and gluconeogenesis processes, thereby increasing blood glucose levels back to normal. In this way, pancreatic A cells play an integral role in maintaining glucose homeostasis and preventing hypoglycemia. +Pancreatic A cells also participate in the local regulation of islet activities as glucagon acts through glucagon receptors on A, B and D type cells within the islets. Recent studies have also shown that Pancreatic A cells play a role in the generation and regeneration of B type cells. Following beta cell injuries pancreatic A cells increase in numbers and produce Glucagon-like peptide-1 (GLP-1), which increases the proliferation and cytoprotection of beta cells. In response to extreme injury of B type cells pancreatic A cells can transform (transdifferentiate) into functioning B type cells. +Until recently, glucagon has been considered a pancreas-specific hormone; however, extrapancreatic glucagon has been reported in patients who had undergone complete, and glucagon-positive cells been identified in the human stomach, indicating that Type A enteroendocrine cells are not restricted to the pancreas.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002067") +AnnotationAssertion(Annotation( "DOI:10.1101/cshperspect.a028241") Annotation( "DOI:10.1146/annurev-physiol-021014-071931") Annotation( "DOI:10.1152/ajplung.00329.2019") Annotation( "DOI:10.1159/000196486") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Ciliated columnar cells of the tracheobronchial tree compose the inner lining of the tracheobronchial tree, the system of airways consisting of trachea, bronchi and bronchioles that allow passage of air into the lungs, where gas exchange occurs. A defining feature of these endo-epithelial cells are the tiny hair-like structures covering their surface, known as cilia. The nucleus is located at the base of the cell, and the area above it is rich in mitochondria and well-developed endoplasmic reticulum, both crucial for the energy-intensive process of cilia operation. +The primary function of these ciliated cells is to keep the respiratory tract clean via mucociliary clearance or the respiratory escalator. These cells create a two-layered 'coat': The lower \"sol\" layer is watery where the cilia can beat in coordinated waves, and the upper \"gel\" layer is thick and sticky, trapping inhaled particles, such as dust, bacteria, viruses, and other potentially harmful substances. This rhythmical beating of the cilia then moves the mucus and trapped particles upwards and out of the respiratory tract, which is then either coughed out or swallowed. +Damage or dysfunction of these ciliated cells, as seen in diseases such as primary ciliary dyskinesia, cystic fibrosis, or chronic bronchitis, may lead to reduced or ineffective mucociliary clearance and an increased susceptibility to respiratory infections.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002145") +AnnotationAssertion(Annotation( "DOI:10.1007/978-3-211-99390-3_83") Annotation( "DOI:10.1038/nature16161") Annotation( "DOI:10.1111/j.1469-7580.2005.00403.x") Annotation( "DOI:10.3389/fphys.2015.00087") Annotation( "DOI:10.5114/ceji.2022.124416") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Brush cells, also referred to as tuft cells or multivesicular cells, are a specialized type of epithelial cell mainly noted for their characteristic 'brush border' composed of microvilli. These cells reside in the epithelial lining of tissue organs such as the respiratory tract, gastrointestinal tract, and the bile ducts. The name derives from their distinct appearance under the microscope, which resembles a brush due to the dense layer of microvilli protruding into the lumen. +A key function of brush cells is chemosensation: They express a variety of signaling molecules and receptors that enable them to detect specific chemical stimuli in the environment and act as sensory transducers. Many of these receptors are responsive to luminal content, which makes brush cells vital for regulating and coordinating appropriate physiological responses to changes in these substances. +Recent research has also elucidated an important role for these cells in immunity. Intestinal brush cells have been found to be the source of a cytokine called interleukin-25, which can initiate type 2 immune responses during parasitic infections. This immune function, along with the chemosensing abilities, signifies that brush cells could serve crucial roles in health and disease, although much research is still required to fully elucidate their myriad roles in physiology and pathology. Overall, brush cells are a versatile cell type, whose distinct morphology and functional capabilities allow them to perform a unique set of functions within the body.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002204") +AnnotationAssertion(Annotation( "DOI:10.1016/B978-1-4377-1926-0.10005-0") Annotation( "DOI:10.1016/j.biocel.2007.10.034") Annotation( "DOI:10.1098/rstb.2010.0324") Annotation( "DOI:10.1136/bmjophth-2020-000459") Annotation( "https://www.sciencedirect.com/topics/immunology-and-microbiology/lens-fiber") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Secondary lens fibers are a specialized type of elongated cells located within the structure of the eye's lens. They play an essential role in vision by enabling light transmission and focus on the retina, which allows for clear, distinct vision. These cells are characterized by their lack of nuclei and organelles, their orderly alignment, and their high protein content, particularly crystallins. +Lens fibers are differentiated from equatorial epithelial cells of the lens in a process that involves cell elongation, denucleation and tight packing, which serve to reduce light scattering occurrences in the eye. This differentiation accelerates substantially after birth in comparison to during embryogenesis and continues throughout life, contributing to the growth of the eye lens. Secondary lens fibers are specifically those cells that are newly differentiated and cover the old lens fiber core. This process also leads to the removal of light-obstructing cellular components, mainly nuclei and organelles, making these fibers transparent and ideal for their function. +The fibers carry out their primary function of light refraction via a high concentration of specialized proteins known as crystallins, which form a gradient of refractive index together with the cytoplasm. This index manipulation facilitates precise light focus onto the retina. Secondary lens fibers also contribute to the lens's shape and biomechanical properties through intercellular interactions, particularly at the sutures where the ends of the fibers meet. Any disruption to secondary lens fibers can lead to vision problems, including cataracts, which is the clouding of the lens resulting from the aggregation of crystallin proteins.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002225") +AnnotationAssertion(Annotation( "DOI:10.1016/j.cell.2013.07.004") Annotation( "DOI:10.1038/s41575-018-0081-y") Annotation( "DOI:10.1038/s41580-020-0278-0") Annotation( "DOI:10.1101/gad.1674008") Annotation( "DOI:10.1111/j.1365-2184.2009.00642.x") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Intestinal crypt stem cells, also known as crypt base columnar cells, are a unique type of cell, characterized by the highly specific marker LGR5, found in the intestinal epithelium. Situated at the bottom of the minute pockets known as crypts of Lieberkühn, these are undifferentiated cells that have the ability to perpetually self-renew, as well as differentiate into various other cell types that constitute the epithelial lining of the intestine. +The fundamental role of intestinal crypt stem cells is to provide a constant supply of new cells to maintain the cellular turnover of the intestinal epithelium, a tissue known for rapid self-renewal. These stem cells are nurtured and protected by specialized epithelial and mesenchymal cells, and together constitute the intestinal stem cell niche. +An important function of intestinal crypt stem cells is to sustain the balance between cell division and programmed cell death, called apoptosis, to ensure the integrity of the intestinal lining. Given their active proliferation rate, these stem cells initiate the creation of diverse differentiated cell types, including enterocytes (the primary absorptive cells in the intestinal lumen), goblet cells (that produce mucus to protect the epithelial layer), enteroendocrine cells (involved in producing gastrointestinal hormones), and Paneth cells (involved in secreting antimicrobial peptides). This diversity in output regulates the physiological activities of the gut ranging from nutrient absorption, hormone secretion, bacterial balance, to immunity. +Research studies suggest that dysregulation in intestinal crypt stem cell proliferation and differentiation is associated with several intestinal disorders including intestinal cancer, and various enteropathies.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002250") +AnnotationAssertion(Annotation( "DOI:10.1016/B978-0-12-819402-7.00001-2") Annotation( "DOI:10.1016/B978-012369442-3/50154-9") Annotation( "DOI:10.1016/j.mce.2015.06.028") Annotation( "DOI:10.1038/s42255-019-0148-2") Annotation( "DOI:10.3389/fendo.2023.1192311") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Pancreatic polypeptide (PP) cells (also called F or gamma cells) are unique endocrine cells located within the Islets of Langerhans in the pancreas. PP cells are one of the rarer pancreatic cell types and are more prevalent in the head and neck of the pancreas. They are critical in normal pancreatic physiological functions and are involved in the development of pancreatic endocrine disorders. +The primary function of PP cells is the production and secretion of the pancreatic polypeptide hormone (PP). This hormone plays a crucial role in several gastrointestinal functions and metabolic responses. The release of the PP hormone is stimulated after eating, especially in protein-rich meals, leading to it being present in large amounts during digestion. The fundamental role of PP is to self-regulate pancreatic secretion activities ensuring its exocrine and endocrine functions are under control. +The pancreatic polypeptide hormone from PP cells also aids in adapting to low physical activity and fasting by reducing the production of insulin and glucagon and inhibiting the hepatic glucose production. Additionally, this hormone influences gut motility by slowing down the gastric emptying and reducing small intestinal transit, thereby controlling the pace at which nutritional substances are absorbed. Because of these functions, any malfunction or irregularity in PP cells can result in various disorders such as diabetes and pancreatic diseases.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002275") +AnnotationAssertion(Annotation( "DOI:10.1016/S1569-2590(05)10005-6") Annotation( "DOI:10.1111/j.1444-0938.2002.tb02384.x") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Pigmented ciliary epithelial cells, which are a type of pigment cell, have a crucial function within the eye's ciliary body. The ciliary body, located behind the iris, is one of the eye’s most vital structures and consists of two types of epithelial cells: the pigmented and the non-pigmented ciliary epithelial cells. The pigmented ciliary epithelial cells form the outer layer of the ciliary body and exhibit a black or brown pigmentation due to the melanin they contain. +One key function of pigmented ciliary epithelial cells is to aid in the formation of aqueous humor, an intraocular fluid that nourishes the cornea and lens, and maintains intraocular pressure which is essential for the eye’s shape and light refraction. These cells facilitate this function in conjunction with the non-pigmented ciliary epithelial cells. Together, the pigmented and non-pigmented ciliary epithelial cells form a bilayer epithelium that allows the secretion of aqueous humor through a bi-directional fluid transport mechanism. +Pigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, a physiological frontier that controls the entry and exit of various substances from the blood to the aqueous humor and vice versa. The pigmentation in these cells, intensified by melanin, helps to absorb scattered light coming into the eye, reducing any potential damage and glare.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002303") +AnnotationAssertion(Annotation( "DOI:10.1165/rcmb.2013-0049OC") Annotation( "DOI:10.1186/s12931-014-0160-8") Annotation( "DOI:10.2353/ajpath.2010.090870") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +The basal epithelial cells of the tracheobronchial tree are critical components found in the lining of the airway passages, including the trachea and bronchi. They are keratin-5-positive, nonciliated, cuboidal cells and typically tightly attached to the basement membrane. In humans, the proportion of basal cells in the respiratory epithelium gradually decreases going down the tracheobronchial tree: they represent approximately 34% of the cells in the trachea, 27% in the large airways, and 10% in the small airways, although it is worth noting that there are differences in the compositions of the tracheobronchial epithelia between different species. +Basal epithelial cells serve as the basal layer of the tracheobronchial epithelium, providing both structural and regenerative support for the epithelial tissue that lines the upper regions of the respiratory tract. They serve as progenitor or stem cells that are capable of differentiating into multiple cell types, such as ciliated and secretory cells. This gives them a central role in homeostatic maintenance of the epithelium, and in repairing damaged epithelium after an injury or during disease. This regenerative capacity is crucial in maintaining the integrity of the tracheobronchial surface, especially given its continual exposure to inhaled irritants and microorganisms. +In addition to their primary restorative function, basal epithelial cells are also involved in the initial immune response within the tracheobronchial tree. Equipped with pattern recognition receptors, these cells can identify and respond to pathogenic organisms, triggering an immune response and producing a range of inflammatory mediators, such as cytokines and chemokines, to help combat infections.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002329") +AnnotationAssertion(Annotation( "DOI:10.1016/S1357-2725(02)00083-3") Annotation( "DOI:10.1111/febs.15731") Annotation( "DOI:10.1165/ajrcmb.25.5.f218") Annotation( "DOI:10.2147/COPD.S38938") Annotation( "DOI:10.3109/01902148.2013.791733") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +The respiratory goblet cell is a highly specialized cell type found primarily within the respiratory tract, including the nose, trachea, and lungs. Named because their shape resembles a goblet - a drinking vessel with a wide body and narrow neck - these cells form a vital part of the respiratory system's protective mechanisms. They are found within the columnar epithelium lining these organs, which forms a barrier between the internal body and the exterior environment. +A principal function of the respiratory goblet cell is the production and secretion of mucus, a carbohydrate-rich, viscous and gel-like substance that plays a critical role in trapping dust, bacteria, viruses, and other airborne particles that are inhaled. The mucus secreted by the goblet cells covers the lining of the respiratory tract, effectively catching these particles and preventing them from reaching the lungs and causing infection. Mucus also provides hydration and lubrication to the respiratory tract surfaces, which is important in maintaining the tissue's health and functioning. +In addition to their mucus-secreting capabilities, respiratory goblet cells also play a significant role in the body's inflammatory responses. When the respiratory system is exposed to irritants or pathogens, the number and activity of goblet cells often increase, leading to a higher production of mucus. This is a protective response designed to trap and neutralize the harmful substances more effectively. However, in conditions like chronic obstructive pulmonary disease (COPD) and asthma, an overproliferation of goblet cells, also known as goblet cell hyperplasia, can lead to excessive mucus production and airway obstruction.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002370") +AnnotationAssertion(Annotation( "DOI:10.1002/hep.31252") Annotation( "DOI:10.1016/j.ajpath.2023.02.012") Annotation( "DOI:10.1016/j.biocel.2010.06.020") Annotation( "DOI:10.1016/j.gastha.2022.07.015") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Intrahepatic cholangiocytes represent a subset of the biliary epithelial cells that form a network of tubes in the liver called the biliary tree The intrahepatic cholangiocytes reside specifically in the intrahepatic bile ducts and play a crucial role in liver physiology and bile production and secretion, thereby aiding in the digestion and absorption of fats in the small intestine. These specific cholangiocytes arise from bipotent hepatoblasts, whereas extrahepatic cholangiocytes share an embryologic origin with the ventral pancreas. +Recent research suggests that there is also heterogeneity within populations of intrahepatic cholangiocytes with different transcriptional profiles, proliferative capacity, and biological function; for example, subpopulations differ in calcium-mobilizing receptors. +The primary function of intrahepatic cholangiocytes is related to bile formation and maintenance of its flow. In addition to their secretory and absorptive activities, they are involved in the regulation of bile composition, volume, and alkalinization, contributing to the neutralization of the acidic chyme (partly digested food) that enters the intestine from the stomach. Intrahepatic cholangiocytes are also recognized for their role in liver regeneration and repair, often proliferating in response to injury. +Intrahepatic cholangiocytes take part in certain pathological conditions, like primary biliary cirrhosis and cholangiocarcinoma. Changes in these cells often lead to abnormalities in bile formation and transport, causing cholestatic liver diseases. Overall, the primary and secondary functional activities of intrahepatic cholangiocytes are vital in maintaining liver function, digestive processes, and contributing to the body's response to liver injury.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002538") +AnnotationAssertion(Annotation( "DOI:10.1007/s00441-008-0706-5") Annotation( "DOI:10.1038/s41569-022-00770-1") Annotation( "DOI:10.1038/s41598-021-01360-w") Annotation( "DOI:10.3390/ijms20184411") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Vein endothelial cells form a thin layer of squamous cells, the endothelium, lining the interior surface of veins throughout the body. They shape the inner cellular lining of the entire vascular system, including the heart, playing a crucial role in blood circulation. The unique characteristic compact arrangement of these cells enables veins to act as a barrier between the blood (that can contain foreign substances) and the surrounding venous tissue and maintain the integrity of the vascular system. +The primary function of vein endothelial cells is to control the exchange of substances between the bloodstream and the surrounding tissues. They facilitate selective transportation of molecules depending on their size and solubility, including gases, nutrients, hormones, and waste products. Vein endothelial cells also play a protective role by inhibiting the translocation of toxins or pathogens from blood to tissues. Additionally, these cells are involved in blood coagulation and inflammation response, primarily by producing substances that inhibit blood clot formation under normal conditions and initiating clotting when necessary. +Another significant function of vein endothelial cells is the regulation of blood flow and blood pressure. They produce and release several substances, including nitric oxide and prostacyclin, which help in controlling vasodilation and vasoconstriction, thereby regulating blood pressure. These cells are also responsible for angiogenesis, the formation of new blood vessels, which is crucial during wound healing and in the formation of granulation tissue. Consequently, any dysfunction in vein endothelial cells can lead to severe health problems like atherosclerosis, hypertension, and thrombosis.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002543") +AnnotationAssertion(Annotation( "DOI:10.1016/j.biopha.2019.108765") Annotation( "DOI:10.1016/j.tibtech.2006.01.010") Annotation( "DOI:10.1038/s41536-019-0083-6") Annotation( "DOI:10.1096/fj.202100332R") Annotation( "DOI:10.1111/dgd.12049") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Mesenchymal stem cells of adipose tissue, also known commonly as adipose-derived stem cells (ADSCs), are a population of adult stem cells that can be obtained easily from adipose tissues. They have many of the same regenerative properties as other mesenchymal stem cells, but are more easily accessible than bone marrow-derived stem cells. +Adipose-derived stem cells show immense promise in the field of regenerative medicine due to their ability to differentiate into adipocytes, chondrocytes, myocytes, osteoblasts, and other cell types. ADSCs also possess immunomodulatory and homeostatic functions: they have the ability to suppress immune responses and provide a therapeutic environment for tissue repair and regeneration, as well as supporting the proliferation of adipocytes and the overall expansion of adipose tissue and contributing to the tissue's ability to react to demands of energy storage and mobilization. Dysfunction of these cells may contribute to metabolic complications observed in obesity and diabetes. +ADSCs have been used for therapeutic applications such as pathological wound healing, severe refractory acute graft-versus-host disease, and idiopathic thrombocytopenic purpura.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002570") +AnnotationAssertion(Annotation( "DOI:10.1002/glia.23892") Annotation( "DOI:10.1016/B978-0-444-52902-2.00005-9") Annotation( "DOI:10.1016/j.biocel.2006.05.007") Annotation( "DOI:10.1186/1742-2094-8-110") Annotation( "DOI:10.1186/s13064-020-00140-y") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Schwann cells, also known as neurolemmocytes, are a type of glial cell located in the peripheral nervous system. These cells play a significant role in the healthy functioning of nerves by producing myelin, a fatty substance that forms a coating around nerve fibers. Myelin serves as an insulator and enhances the speed and efficiency of electrical nerve impulses; a single Schwann cell can myelinate a single axon. Myelination starts by the elongation and envelopment of the Schwann cell around the axon, followed by the synthesis and deposition of myelin layers. Some studies suggest that Schwann cells may regulate neuronal action potential, muscular contraction, and the sensitive response. +While Schwann cells are most commonly known for the formation of the myelin sheath, some Schwann cells do not form myelin: Remak Schwann cells, a class of nonmyelinating Schwann cells, ensheath axons with smaller diameter, such as C fiber nociceptors in sciatic nerves and form Remak bundles. +Schwann cells are found along both motor and sensory neurons and are crucial for the advancement and recovery of peripheral nerve injuries, due to their capacity to support nerve regeneration. In cases of nerve injury, Schwann cells play a vital role in recovery by initiating Wallerian degeneration, a process in which the part of the axon distal to the injury site degrades and is then cleared away. Following this, Schwann cells can guide the regrowth of the nerve, providing a conducive environment for axon regeneration. They remodel themselves into a regenerative phenotype, proliferate, and organize themselves into bands of Büngner that provide physical and chemical guidance for the regrowths of axons. This function of Schwann cells in the repair and regeneration of nervous system highlights their therapeutic potential in peripheral nerve injury treatments.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002573") +AnnotationAssertion(Annotation( "DOI:0.1016/j.preteyeres.2015.08.001") Annotation( "DOI:10.1016/j.preteyeres.2012.08.004") Annotation( "DOI:10.1038/nature04482") Annotation( "DOI:10.5301/EJO.2010.6049") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Retinal blood vessel endothelial cells constitute the innermost lining of the blood vessels found in the retina, the light-sensitive layer of tissue at the back of the eye. The primary role of these cells revolves around their location within the retinal vascular system, forming the structure of the blood-retinal barrier, a subset of the larger blood-ocular barrier system. +The endothelial cells are particularly involved in the growth of new retinal blood vessels from pre-existing ones (angiogenesis); this is critical in managing the amount of oxygen and essential nutrients delivered to the ocular tissues. They are crucial for maintaining homeostasis in the retinal environment by controlling the exchange of molecules between the blood and the retina. Furthermore, they mediate immune cell trafficking, supporting the immune privilege of the eye by preventing the unrestricted infiltration of inflammatory cells into the retina, thus maintaining ocular health and normal vision. +The malfunction or dysfunction of retinal blood vessel endothelial cells is implicated in numerous ocular pathologies, particularly diabetic retinopathy, which is one of the leading causes of blindness worldwide. In such conditions, the compromise in the integrity of the blood-retinal barrier and excess angiogenesis can lead to retinal edema and pathological neovascularization, resulting in vision loss.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002585") +AnnotationAssertion(Annotation( "DOI:10.1111/febs.16018") Annotation( "DOI:10.1152/physrev.00021.2004") Annotation( "DOI:10.3389/fphar.2021.727870/full") Annotation( "https://www.sciencedirect.com/topics/chemistry/retinal-pigment") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Retinal pigment epithelial (RPE) cells form a single layer of cells at the back of the eye sandwiched between the neurosensory retina and the choroid, playing a significant role in maintaining vision health. These pigment-laden cells are highly specialized and perform an array of metabolic and transport functions essential for the maintenance of the photoreceptor cells (rods and cones) in the retina. The pigmentation of RPE cells actively aids in the absorption of excess light and the prevention of light scattering, thus enhancing the eye's optical properties. +The retinal pigment epithelium forms a key part of the blood/retina barrier. The cells have long sheet-like microvilli on their apical membrane that project into the light-sensitive outer segments of the photoreceptors, forming a close structural interaction. The basolateral membrane of the RPE interacts with the underlying Bruch’s membrane, which separates the RPE cells from fenestrated endothelium of the choriocapillaris. +RPE cells support the photoreceptor by providing them with oxygen and nutrients (such as glucose, retinol and fatty acids) and removing waste products. They also recycle the visual pigment, in a process called the \"visual cycle\", where the RPE cells play a vital role in the regeneration of visual pigment (11-cis retinol) following the absorption of light. This is essential for the maintenance of photoreceptor excitability. +Beyond this, RPE cells take part in the phagocytosis process, where they digest the shed ends of photoreceptor outer segments, thus, preventing the build-up of waste residue that could otherwise harm retinal health. They also secrete various factors, including growth factors required to maintain the structural integrity of choriocapillaris endothelium and photoreceptors, as well as immunosuppressive factors that play an important role in establishing the immune privilege of the eye.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002586") +AnnotationAssertion(Annotation( "DOI:10.1002/cyto.a.20952") Annotation( "DOI:10.1007/s12015-006-0015-x") Annotation( "DOI:10.1172/JCI107470") Annotation( "DOI:10.3390/app10030938") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK53254/") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Endothelial cells of the umbilical vein form the inner lining of the veins found in the umbilical cord. They are involved in tube formation and migration which are essential for angiogenesis, the process of generating new blood vessels; this is critical during the fetal stage for the development of the circulatory system. Endothelial cells of the umbilical vein also play a role in controlling the passage of white blood cells into tissues during inflammatory responses. +Because human umbilical vein endothelial cells (HUVECs) can easily be derived from the umbilical cord, and because they express common endothelial cell markers, they have been used as an epithelial cell model for studies on cell proliferation, migration, angiogenesis, and inflammation. They have been used as models for vascular diseases like atherosclerosis, for investigating how tumor cells infiltrate blood vessels and form metastases. +Thus, while endothelial cells of the umbilical vein play a critical role in vascular biology, they also represent a powerful tool in disease studies and potential treatment strategies.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002618") +AnnotationAssertion(Annotation( "DOI:10.1186/s12931-022-02042-5") Annotation( "DOI:10.3389/falgy.2021.787128") Annotation( "DOI:110.1038/s41385-020-00370-7") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Respiratory basal cells are highly specialized cells that serve a crucial role in the human airway epithelium, predominantly found lining the surfaces of the trachea and bronchi. These cells exhibit a distinctive columnar shape and are attached directly to the basal lamina. They are characterized by the presence of high amounts of cytoplasmic keratins, predominantly keratin 5 and 14, and transcription factor tumor protein (tp63), which set them apart from other types of lung epithelial cells such as ciliated cells and secretory cells. +Basal cells are essential for maintaining airway integrity. They make up one third of all respiratory epithelial cells and serve as stem cells as they can transform into different cell types, like goblet cells, ciliated cells, and club cells, when needed for homeostatic maintenance of the epithelial barrier or to repair and restore a healthy cellular environment after injury. +Their position at the interface between the internal environment and the external atmosphere makes these cells a first line of defense against air-borne irritants, allergens, and pathogens. Their robust, intrinsic reparative properties facilitate effective recovery from such adversities. However, damage to respiratory basal cells or abnormalities in their function are associated with several respiratory pathologies such as asthma, chronic obstructive pulmonary disease, and lung cancer. Therefore, understanding these cells' function, and their role in disease, is crucial for the development of new therapeutic strategies for respiratory disorders.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002633") +AnnotationAssertion(Annotation( "DOI:10.1007/s12079-019-00511-z") Annotation( "DOI:10.1016/j.cmet.2013.08.001") Annotation( "DOI:10.1101/cshperspect.a006569") Annotation( "DOI:10.3389/fcell.2021.642352") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Endothelial stalk cells are specialized vascular cells vital in angiogenesis, a process through which new blood vessels are formed from pre-existing ones; specifically, endothelial stalk cells are involved in sprouting angiogenesis, where they help form the body of new blood vessels. +Vascular sprouting relies on the coordinated activity of migrating endothelial tip cells at the forefront and proliferating stalk cells that elongate the sprout. The process is tightly controlled by different growths factors: Vascular Endothelial Growth Factor acts on endothelial cells, inducing them to become endothelial tip cells that initiate sprouting. After sprouting initiation, activation of Notch signaling suppresses differentiation toward a tip cell phenotype and some of the endothelial cells differentiate into stalk cells, which follow tip cells, multiply, and elongate to provide a structural backbone to the growing vessel sprout. +In contrast to endothelial tip cells, which migrate and lead the angiogenic sprout, endothelial stalk cells behind the sprouts continue forming the tube or lumen for blood flow and facilitate maturation and stability of the new vessel. The delicate balance between the activities of stalk and tip cells during angiogenesis is crucial to build a functional vascular network. Dysfunctions in endothelial stalk cells can lead to pathological conditions such as impaired wound healing, unregulated tumor growth, and metastasis due to abnormal angiogenesis.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0002671") +AnnotationAssertion(Annotation( "DOI:10.1016/j.jcf.2019.09.010") Annotation( "DOI:10.1038/s41586-018-0393-7") Annotation( "DOI:10.1038/s41598-023-30603-1") Annotation( "DOI:10.1146/annurev-pathol-042420-094031") Annotation( "DOI:10.3389/fmars.2020.00709") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Ionocytes are specialized cells predominantly found in the mammalian respiratory and renal systems as well as in the gills, skin, and intestinal tract of fish. These cells play crucial roles in maintaining ion and acid-base homeostasis. Ionocytes demonstrate remarkable plasticity and are able to adapt themselves in response to changes in environmental conditions such as pH, salinity, ion concentration, and temperature. +These cells work by selectively absorbing specific ions from the environment, thus maintaining the body's internal ionic balance. The most commonly absorbed ions include sodium (Na+), chloride (Cl-), calcium (Ca2+), and hydrogen (H+). Moreover, ionocytes contribute to acid-base regulation. In response to acidosis or alkalosis, ionocytes can either excrete or retain hydrogen (H+) and bicarbonate (HCO3-) ions to readjust the blood pH. Further, experimental evidence suggests a functional complexity of ionocytes, implying diverse roles beyond ion regulation. Recent research highlights ionocytes' involvement in ammonia excretion and the regulation of extracellular fluid volume, highlighting their contribution to the overall homeostatic process. +Malfunctioning ionocytes have been implicated in various diseases, including cystic fibrosis which is caused by mutations in the chloride channel CFTR, an ionocyte marker.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0005006") +AnnotationAssertion(Annotation( "DOI:10.1016/j.krcp.2013.07.005") Annotation( "DOI:10.2215/CJN.05760513") Annotation( "DOI:10.2215/CJN.08580813") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Renal principal cells are the major cell type in the initial collecting tubule and the cortical and outer medullary collecting ducts, as well as the connecting tubule, in the nephrons of the kidneys. +A key function of renal principal cells is the regulation of water balance in the body. These cells express aquaporin-2 (AQP2) water channels, which facilitate the reabsorption of water from the fluid within the renal tubule lumen back into the blood. The translocation of AQP2 to the cell membrane is controlled by the hormone vasopressin: In response to high vasopressin levels, AQP2 moves to the cell membrane, allowing water to pass through effectively and be reabsorbed, therefore concentrating the urine. Conversely, in low vasopressin conditions, AQP2 is removed from the membrane, reducing water reabsorption and diluting the urine. +Renal principal cells are also involved in the regulation of sodium and potassium levels in the body. They have sodium channels (ENaC) in their luminal membranes which permit the reabsorption of sodium ions from the tubule fluid back into the blood, resulting in a net reabsorption of sodium ions into the systemic circulation. This process is controlled, in part, by the hormone aldosterone. Additionally, renal principal cells contain potassium channels that facilitate the secretion of potassium ions into the urine. The activities of these channels, in coordination with other cell types in the nephron, are critical for maintaining electrolyte balance and overall body homeostasis.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0005009") +AnnotationAssertion(Annotation( "DOI:10.1152/ajprenal.2000.279.1.F195") Annotation( "DOI:10.1161/HYPERTENSIONAHA.121.16492") Annotation( "DOI:10.1681/ASN.V1011") Annotation( "DOI:10.2215/CJN.08880914") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Renal intercalated cells are specialized cells located in the collecting duct system of the kidneys. The primary role of intercalated cells is to reabsorb bicarbonate ions and secrete hydrogen ions, thereby maintaining the acid-base homeostasis in the blood. They comprise two main subtypes primarily distinguished by their functional and morphological attributes: alpha and beta intercalated cells. +Alpha intercalated cells are more predominant when the body is in a state of acidosis, a condition characterized by an increased acidity of the blood. These cells are specialized in secreting excessive hydrogen ions into the urine through a mechanism involving vacuolar H+-ATPase and H+/K+-ATPase pumps on their apical membranes. They simultaneously reabsorb bicarbonate ions from the tubular fluid and return them to the bloodstream via mechanisms involving carbonic anhydrase II and bicarbonate/chloride exchangers on the basolateral membrane. This dual process helps to increase blood pH towards normal levels. +When the body is in a state of alkalosis, a condition characterized by lowered levels of hydrogen ions in the blood, beta intercalated cells are more predominant. They primarily reabsorb hydrogen ions from the tubular fluid through vacuolar H+-ATPase and H+/K+-ATPase pumps on their basolateral membranes, while secreting bicarbonate ions into the urine via pendrin, a bicarbonate/chloride exchanger in the apical membrane. These mechanisms work together to decrease blood pH towards normal levels. +In summary, renal intercalated cells play a critical role in the delicate balance of the body’s pH, safeguarding the body from potential harm caused by acidemia or alkalemia.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0005010") +AnnotationAssertion(Annotation( "DOI:10.1016/j.semnephrol.2019.04.005") Annotation( "DOI:10.1152/physiol.00008.2011") Annotation( "DOI:10.1172/JCI63492") Annotation( "DOI:10.3390/diseases2020071") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Renal alpha-intercalated cells are located within the connecting tubules and collecting ducts of the kidneys, which are components of the kidney's complex nephron system. Along with beta-intercalated cells, they play a critical role in the body’s acid-base balance. +Renal alpha-intercalated cells contain an abundance of proton pumps and enzymes like carbonic anhydrase, which aid in the transport of hydrogen ions for secretion in the urine. The bicarbonate/chloride transporters on their apical membrane meanwhile take up bicarbonate ions from the urine and supply them back into the blood. Through this mechanism, these cells contribute significantly to the neutrality of blood pH, and dysfunction of renal alpha-intercalated cells often leads to distal renal tubular acidosis, a condition resulting in acidic blood and alkaline urine.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0005011") +AnnotationAssertion(Annotation( "DOI:10.1016/j.cub.2014.08.047") Annotation( "DOI:10.1038/nrm.2017.21") Annotation( "DOI:10.1101/cshperspect.a028233") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +The multi-ciliated epithelial cell are terminally differentiated epithelia that line brain ventricles, the respiratory tract and parts of the female and male reproductive organs in animals, playing critical roles in the maintenance of homeostasis through ciliary motion. They are characterized by the presence of hundreds of motile cilia, hair-like microtubule-based organelles that beat in a coordinated fashion to direct fluid flow over the cell surface. +Multi-ciliated epithelial cells have fundamental roles in the proper functioning of many organ systems. In the respiratory system, they line the airways and orchestrate the coordinated movement of mucus, effectively clearing the airways of inhaled particles and pathogens. These cells are also vital in the ventricular system of the brain where they facilitate cerebrospinal fluid circulation, thus contributing to the maintenance of the brain's microenvironment. In the fallopian tube, multi-ciliated epithelial cells aid in the transport of oocytes from the ovary to the uterus, a process crucial to reproduction. +The formation and function of multi-ciliated epithelial cells is a highly regulated process that involves several stages of development including cell specification, centriole multiplication, and ciliogenesis. Any disruption in these processes can result in dysfunctional or decreased numbers of cilia, which can lead to a myriad of health issues, ranging from chronic respiratory infections to infertility.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0005012") +AnnotationAssertion(Annotation( "DOI:10.1007/s00125-008-1238-y") Annotation( "DOI:10.1152/physrev.00012.2004") Annotation( "DOI:10.1210/en.2018-00833") Annotation( "DOI:10.3389/fendo.2022.904004") Annotation( "DOI:10.3390/ijms20081867") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Pancreatic epsilon cells are a specialized type of endocrine cell found in the islets of Langerhans, a region of the pancreas responsible for hormone production. These clusters of cells constitute only about 1% of the pancreatic islet cell population, making them a relatively small yet significant component of the pancreas. Pancreatic epsilon cells have a round or ovoid shape with occasional cytoplasmic extensions and are characterized by small and spherical granules. +The principal function of pancreatic epsilon cells involves the synthesis and release of the hormone ghrelin, a peptide hormone predominantly produced in the stomach; pancreatic epsilon cells are one of the few sites outside the gastrointestinal tract known to produce this hormone. Ghrelin has multiple vital roles, playing a significant part in generating hunger sensations, promoting fat storage, and influencing various metabolic processes. It also stimulates the release of Growth Hormone (GH) from the anterior pituitary gland. +During fetal development, when they form a layer around the islet, epsilon cells are an important source of ghrelin, likely secreting the hormone into the circulation; their numbers decrease in adults. While research on pancreatic epsilon cells is still ongoing, these cells have been implicated in several disease states, most notably Type 2 diabetes and metabolic syndrome. The dysfunction or reduction in the number of pancreatic epsilon cells can lead to anomalies in ghrelin production, impacting overall metabolic homeostasis and glucose regulation.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0005019") +AnnotationAssertion(Annotation( "DOI:10.1016/j.stem.2014.04.010") Annotation( "DOI:10.1093/jb/mvr001") Annotation( "DOI:10.1242/dev.031369") Annotation( "DOI:10.1242/dev.114215") Annotation( "DOI:10.5966/sctm.2015-0051") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Hepatoblasts are immature precursor cells that predominate during the early stages of liver development, specifically in the embryonic phase of life. They first arise from the endoderm, one of the three primary germ layers in the very early embryo, and then differentiate into two distinct mature liver cell types - the hepatocytes and cholangiocytes. +During liver organogenesis hepatoblasts proliferate and migrate into the septum transversum to form the liver bud. Proliferation and differentiation of these cells are regulated by several soluble factors, such as hepatocyte growth factor, which is a mitogen of both hepatoblasts and mature hepatocytes. As they start to differentiate into hepatocytes and cholangiocytes, the cells begin to express hepatic markers like albumin and alpha-fetoprotein. +Although hepatoblasts are specified embryonic liver cells that are bipotential for hepatocytes and cholangiocytes, a subset of liver cells (called oval cells) has been identified in adults that express stem cell markers, such as CD133 and cKIT, and has been suggested to have the same potential as hepatoblasts to differentiate into hepatocytes and cholangiocytes.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0005026") +AnnotationAssertion(Annotation( "DOI:10.1016/j.celrep.2020.107952") Annotation( "DOI:10.1038/s41575-018-0081-y") Annotation( "DOI:10.1073/pnas.1607327113") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Intestinal crypt stem cells of the small intestine are a type of adult stem cell intimately involved in the continuous replenishment of the intestinal epithelium, the innermost layer of the intestine responsible for nutrient absorption. These cells, located within the crypts of Lieberkühn, are the origin of various cell lineages that make up the functional units of the small intestine. They possess self-renewal ability, an essential feature of stem cells, which allows them to maintain a steady population in the small intestine. +One of the critical roles of intestinal crypt stem cells is to drive the continual renewal process taking place in the small intestine every 3-5 days. By proliferating intensively, these cells produce transient amplifying (TA) cells that are characterized by quick division and progressive differentiation. These cells eventually differentiate into specialized cell types, encompassing absorptive enterocytes, mucin-secreting goblet cells, hormone-secreting enteroendocrine cells, and Paneth cells, all of which have essential roles in digestion and nutrient absorption in the small intestine. +Intestinal crypt stem cells of the small intestine are also play a significant part in injury recovery. Under regular conditions, these cells primarily exist in an active state, facilitating the constant renovation of the gut lining. However, upon injury or loss of regular intestinal crypt stem cells reserve intestinal stem cells, a slow-cycling and radio-resistant population, can be stimulated to take over the duties of active crypt stem cells. Such plasticity provides a powerful regenerative mechanism that ensures the intestinal epithelium's function and structural integrity amidst diverse conditions.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0009017") +AnnotationAssertion(Annotation( "DOI:10.1016/j.cell.2013.07.004") Annotation( "DOI:10.1038/s41575-018-0081-y") Annotation( "DOI:10.1073/pnas.1607327113") Annotation( "DOI:10.1111/j.1365-2184.2009.00642.x") Annotation( "DOI:10.1186/s12943-019-0962-x") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Intestinal crypt stem cells of the colon, also known as colon crypt base columnar (CBC) cells, are highly specialized cells primarily responsible for the constant self-renewal of the colonic epithelium. These cells are found in the crypts of Lieberkühn - deeply invaginated sections of the colon's mucosal layer. +The prime function of intestinal crypt stem cells of the colon is to serve as the source of constant cell regeneration in the colon. Every few days, these stem cells divide and differentiate into the various other types of intestinal cells, such as enterocytes, goblet cells, and enteroendocrine cells. +A constant renewal cycle is necessary due to the harsh environment of the colon where cells continuously encounter abrasive food matter and potential pathogens, leading to a high turnover rate. When the colon's mucosal layer suffers damage, a rapid response is triggered whereby colon crypt stem cells divide faster and are directed to injured sites to repair the epithelial layer. Dysregulation of these cells' function or proliferation can contribute to disorders such as colorectal cancer.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0009043") +AnnotationAssertion(Annotation( "DOI:10.1002/dvg.23276") Annotation( "DOI:10.1242/dev.193193") Annotation( "DOI:10.3389/fcell.2020.00635/full") Annotation( "https://doi.org/10.1016/j.ydbio.2011.12.042") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. +After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. +Disorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0011012") +AnnotationAssertion(Annotation( "DOI:10.1038/s41586-018-0393-7") Annotation( "DOI:10.1146/annurev-pathol-042420-094031") Annotation( "DOI:10.1172/JCI171268") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +The pulmonary ionocyte is a relatively newly identified, specific epithelial cell type found primarily in the pulmonary or respiratory system. Discovered through novel mapping techniques in 2018, these cells are surprisingly rare, making up less than 2% of the cells in the lung's airway, yet they play an essential role in the airway surface liquid and mucus regulation, a crucial factor in lung health. +The main responsibility of the pulmonary ionocyte pertains to the regulation and mobilization of chloride ions. They express a high level of CFTR (Cystic Fibrosis Transmembrane Conductance Regulator) gene, which encodes a protein channel across the membrane of cells that produce mucus, sweat, saliva, tears, and digestive enzymes. The activity of CFTR regulates the movement of chloride ions and fluids in and out of cells, which helps maintain a balance of fluid in the organs they are expressed in. If CFTR is dysfunctional, it can cause conditions such as cystic fibrosis, characterized by thick, sticky mucus that can clog the lungs and obstruct the pancreas, leading to respiratory and digestive issues. +The discovery of this cell type offers new doors to the treatment and further understanding of diseases like cystic fibrosis. Increased understanding of pulmonary ionocytes could contribute to the development of novel therapeutic approaches to manipulate the function of CFTR in the lungs and other organs affected by dysfunctional CFTR.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_0017000") +AnnotationAssertion(Annotation( "DOI:10.1038/s41385-018-0039-y") Annotation( "DOI:10.1038/s41385-020-00370-7") Annotation( "DOI:10.1159/000512268") Annotation( "DOI:10.1513/AnnalsATS.201802-128AW") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK553208/") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Lung goblet cells are critical components of the respiratory tract, specifically found in the bronchial segments. They are secretory epithelial cells known for their signature \"goblet\" or cup-like shape. Their primary function is to produce and secrete mucus that aids in trapping airborne particles and pathogens, preventing them from reaching the delicate environment of the lung. As part of the lung's epithelial lining, they act as frontline defenders, maintaining lung health and function. +The lung goblet cells are densely packed with granules containing mucin glycoproteins, the primary component of mucus. As mucus is produced and secreted, it moves towards the lumen of the lungs where the cilia, hair-like structures of the neighboring ciliated epithelial cells, help to navigate it upwards and out of the respiratory tract. This coordinated action ensures the expulsion of unwanted particles and pathogens, effectively cleaning the respiratory tract. +Dysfunction or abnormal proliferation of lung goblet cells can result in pathological conditions such as chronic obstructive pulmonary disorder (COPD) and asthma, where excessive mucus production leads to airway obstruction. Furthermore, lung goblet cells respond to a variety of stimuli, including toxins, allergens, irritants, and infections, adjusting their mucus production accordingly.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000143") +AnnotationAssertion(Annotation( "DOI:10.1016/bs.ctdb.2018.12.002") Annotation( "DOI:10.1016/j.devcel.2020.09.024") Annotation( "DOI:10.1242/dmm.046920") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Lung neuroendocrine cells, also commonly known as pulmonary neuroendocrine cells (PNECs), are predominantly located in the respiratory epithelium of the bronchial and bronchiolar airways in the lungs. These cells, characterised by their small size and granular appearance, have a distinctive morphology that sets them apart from other lung cells. They are considered part of the diffuse neuroendocrine system due to their scattered distribution through the epithelium and have been classified into solitary cells and clustered forms known as neuroepithelial bodies. +The primary function of PNECs is linked to regulation and maintenance of the lung environment. They are sensory in nature and can secrete various bioactive substances such as serotonin, calcitonin, calcitonin gene-related peptides, and bombesin-like peptides which modulate airway smooth muscle tone and influence gut motility. For example, they act as oxygen sensors in response to hypoxia and are responsible for releasing neuropeptides that can induce responses. Moreover, PNECs provide an afferent function as they are equipped with long microvilli that project into the lumen of the bronchus and react to changes in the chemical composition of the luminal content.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000223") +AnnotationAssertion(Annotation( "DOI:10.1038/nrgastro.2013.35") Annotation( "DOI:10.1038/nri3738") Annotation( "DOI:10.1084/jem.20191130") Annotation( "DOI:10.3389/fphys.2021.699152/full") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Enterocytes of the epithelium of the small intestine are specialized cells that reside in the lining of the small intestine, and are primarily responsible for the essential process of nutrient absorption. These cells are columnar epithelial cells with an apical surface lined with microvilli, a feature referred to as the 'brush border', to maximize the surface area available for absorption. +Enterocytes play a critical role in both the digestion and absorption of nutrients from food. Their extensive brush border contains enzymes that further assist in nutrient breakdown and transport proteins that transfer nutrients, such as glucose, amino acids, lipids, and vitamins, across the cell membrane. +The enterocytes of the small intestine also participate in the barrier function of the gut lining. Enterocytes are connected by tight junctions, which act as a primary defense line against pathogenic invasion by maintaining intestinal barrier integrity. Additionally, their cell surface is coated in glycocalyx and mucus which forms a defensive barrier preventing the penetration of harmful bacteria into the systemic circulation.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000334") +AnnotationAssertion(Annotation( "DOI:10.1038/nri3738") Annotation( "DOI:10.1084/jem.20191130") Annotation( "DOI:10.1111/j.1365-2249.2011.04523.x") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Enterocytes of the epithelium proper of the ileum, commonly known as ileal enterocytes, are specialized epithelial cells found lining the inner surface of the ileum, the final section of the small intestine in the human body. They play a pivotal role in nutrient absorption, digestive metabolic functions, and the maintenance of the host’s immune response. +Like enterocytes in other parts of the intestine, ileal enterocytes exhibit distinct characteristics specific to their function and role. They have microvilli on their apical surfaces to increase absorption and are important in the absorption of vitamins and the reabsorption of bile salts. These cells also produce enzymes that metabolize lipids and xenobiotics.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000342") +AnnotationAssertion(Annotation( "DOI:10.1007/s11894-010-0130-3") Annotation( "DOI:10.1038/nrgastro.2013.35") Annotation( "DOI:10.1038/nri3738") Annotation( "DOI:10.1084/jem.20191130") Annotation( "DOI:10.3389/fimmu.2019.00277") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Enterocytes of the colon are specialized epithelial cells located in the lining of the colon, the largest part of the large intestine. These cells play a critical role in absorbing water, electrolytes, and certain vitamins from the food material passed on from the small intestine. With a unique structure of finger-like protrusions referred to as microvilli, the enterocytes increase their surface area for effective absorption. The colon is the last part of the digestive system, and as such, it is responsible for compacting undigested food materials and forming fecal matter. Enterocytes of the colon facilitate this process effectively through absorption of water. +Enterocytes are known for their high regeneration potential, replenishing every 4-5 days, enabling the healthy functioning of the colon. They originate from stem cells located in the crypt of the colon and differentiate into mature enterocytes as they migrate upwards towards the luminal surface. This constant turnover aids in maintaining the intestinal barrier, preventing the entry of detrimental substances into the systemic circulation. Their tight junctions with other epithelial cells provide a robust barrier against invasive pathogens. +Enterocytes of the colon are involved in the communication with the gut microbiota. These cells harbor enzymes necessary for the metabolism of short-chain fatty acids, which are the byproducts of the fermentation process by gut bacteria. Short-chain fatty acids serve as a major energy source for colonocytes and are important for maintaining colonic health. The dysfunction of enterocytes, therefore, could lead to disorders such as inflammatory bowel disease or colorectal cancer.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000347") +AnnotationAssertion(Annotation( "DOI:10.1007/s00441-008-0706-5") Annotation( "DOI:10.1007/s10456-021-09785-7") Annotation( "DOI:10.1016/j.ccm.2021.08.005") Annotation( "DOI:10.1016/j.jvs.2004.03.043") Annotation( "DOI:10.1177/153857440303700107") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Endothelial cells of the artery, also referred to as arterial endothelial cells, form an integral part of the arterial system. They form a single layer, known as the endothelium, lining the interior surface of arteries, and are able to respond to the high-pressure and flow conditions present in arteries. The primary role of these cells is to provide a barrier between the vessel wall and the blood, exhibiting selective permeability to regulate the movement of liquids, gases, and blood-borne substances across the vascular wall. +Arterial endothelial cells significantly contribute to maintaining vascular homeostasis. They are at the forefront of sensations and responses to mechanical stimuli, like shear stress and blood pressure changes. An additional key function pertains to the production of nitric oxide, which helps to regulate vascular tone and blood pressure, prevents platelet aggregation, limits leukocyte adhesion to the endothelium, and inhibits smooth muscle cell proliferation. These varied but connected functions help to preclude the development of atherosclerosis, ensuring normal circulation and arterial health. +Moreover, these cells play a pivotal role in inflammation and coagulation processes. During inflammatory events, they express various adhesion molecules, aiding in leukocyte recruitment and rolling onto the vessel walls for immune response. They also produce anticoagulant and procoagulant substances, involved in blood clotting and clot dissolution, respectively. Dysregulation of the usual functions of arterial endothelial cells can result in serious pathophysiological conditions, such as atherosclerosis, hypertension, and other cardiovascular diseases.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000413") +AnnotationAssertion(Annotation( "DOI:10.1007/s004290050160") Annotation( "DOI:10.1111/j.1442-9071.2012.02818.x") Annotation( "DOI:10.1167/tvst.8.4.32") Annotation( "DOI:10.2147/OPTH.S26048") Annotation( "DOI:10.3389/fimmu.2022.918619") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Epithelial cells of the lacrimal sac play a significant role in the physiology of tear drainage, acting as an integral part of the lacrimal drainage system. The lacrimal sac is part of the nasolacrimal duct system, a conduit which connects the eye to the nasal cavity, and is lined by multilayered, non-keratinizing, squamous epithelial cells. +The epithelial cells of the lacrimal sac are specialized for the purpose of maintaining a moist environment and protecting the surface of the eye. They form a barrier that traps and removes potential contaminants from the tear film during the drainage process. These cells also actively contribute to tear turnover by expediting the drainage of excess tears. Dysfunctional epithelial cells of the lacrimal sac can lead to dacryocystitis, a condition characterized by inflammation of the lacrimal sac. +Epithelial cells of the lacrimal sac also perform various other tasks which ensure the overall health of the eye. They are involved in the regulation of immune responses within the lacrimal apparatus and may have a possible role in host-microbiome interactions. Thus, epithelial cells of the lacrimal sac play a multifaceted role in tear drainage and ocular surface defence, directly translating to eye health and vision quality.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000436") +AnnotationAssertion(Annotation( "DOI:10.1016/j.ajpath.2014.01.014") Annotation( "DOI:10.1016/j.semnephrol.2019.04.005") Annotation( "DOI:10.2215/CJN.05760513") Annotation( "DOI:10.2215/CJN.08880914") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Kidney collecting duct epithelial cells are a specialized type of cells that form an integral part of the renal system. Located in the collecting duct system of the kidneys, these cells are responsible for one of the final steps in the process of urine formation, and they are instrumental in the fine tuning of the volume and composition of urine by reabsorbing water and certain solutes back into the bloodstream. +These cells express specific channels and carriers that actively and passively transport ions and water. They also have channels on their membranes, such as sodium channels and potassium channels, involved in reabsorbing or secreting these electrolytes depending upon the body's needs. The function of renal collecting duct epithelial cells can be regulated by a variety of hormones, including vasopressin (antidiuretic hormone), which can modulate the ion channels and carriers and hence indirectly influence body fluid homeostasis. +Aside from their function in ion and water balance, kidney collecting duct epithelial cells also aid in maintaining the body's acid-base balance. They have specialized functionality to secret hydrogen ions into the tubular lumen, which contributes to acid excretion. Any dysfunction may have serious implications and lead to various renal or systemic diseases, exemplifying the importance of these cells in maintaining overall body homeostasis.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000454") +AnnotationAssertion(Annotation( "DOI:10.1016/j.jcmgh.2015.05.005") Annotation( "DOI:10.1016/j.jhep.2012.10.011") Annotation( "DOI:10.1038/s41575-019-0125-y") Annotation( "DOI:10.1152/ajpgi.00227.2012") Annotation( "DOI:10.5009/gnl16033") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Cholangiocytes, also known as biliary epithelial cells, are specialized epithelial cells that line the biliary tract, which constitutes the gall bladder and bile ducts inside the liver. Crucial to the maintenance of the liver's health and function, cholangiocytes have a key role in the modification and secretion of bile, a fluid produced by hepatocytes that is essential to digestion and the absorption of fats and vitamins. +Cholangiocytes accomplish their primary function through the expression of a variety of transport proteins located on their apical and basolateral membranes, which propel bile acids and other contents of the bile into the biliary lumen. The hepatic bile, once secreted by the hepatocytes, is further modified by cholangiocytes via secretion and absorption processes. These processes help in the regulation of bile volume and composition, which is fundamental in ensuring the efficient digestion of dietary fats and fat-soluble vitamins and the excretion of cholesterol. +In addition to their role in bile modification, cholangiocytes also perform several other integral functions. For instance, these cells express Toll-like receptors (TLRs) which allow cholangiocytes to initiate an immune response against pathogens in the biliary lumen. When functioning normally, these cells contribute to biliary integrity, hepatic architecture, and overall hepatic physiology. However, when they become pathological, they are involved in the progression of liver diseases, such as primary biliary cirrhosis and cholangiocarcinoma – the malignancy of the biliary tract.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000488") +AnnotationAssertion(Annotation( "DOI:10.1016/j.ccm.2021.08.005") Annotation( "DOI:10.1016/j.coi.2020.04.005") Annotation( "DOI:10.1152/ajplung.90587.2008") Annotation( "DOI:10.3389/fphys.2014.00284") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Mesothelial cells of the pleura form a significant part of the pleural membrane, a thin, double-layered serous membrane that lines the thoracic cavity and encompasses the lungs. These specialized cells contribute to the pleura's key function of producing a lubricating serous fluid, which reduces friction between the lung's outer surface (visceral pleura) and the inner lining of the thoracic cavity (parietal pleura) during respiration. +The cellular structure of mesothelial cells, characterized by microvilli on their surface, aids in the secretion and absorption of the pleural fluid, effectively supporting the smooth expansion and contraction of the lungs. Dysregulation in mesothelial cells can lead to pathologies, including pleural effusion and malignant mesothelioma. +Mesothelial cells of the pleura display unique immunologic properties. They act as a first line of defense against infection because they are able to recognize pathogens and respond by secreting various cytokines and chemokines. Additionally, these cells are directly involved in the translocation of immune cells into the pleural cavity during inflammatory response, thereby playing an active role in the immune response within the pleural environment. +In the event of pleural injury, these cells are also involved in the mesothelial-mesenchymal transition, a process that allows mesothelial cells to transdifferentiate into myofibroblasts and promote tissue repair.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000491") +AnnotationAssertion(Annotation( "DOI:10.1016/S1357-2725(03)00242-5") Annotation( "DOI:10.1152/physrev.00026.2003") Annotation( "DOI:10.1371/journal.pone.0276978") Annotation( "DOI:10.3389/fphys.2014.00221") Annotation( "DOI:10.3390/jdb7020007") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Mesothelial cells of visceral pleura are specialized epithelial cells that line the inner layer of the pleura, the membrane that envelops the lungs. Positioned adjacent to the lung tissue, these cells form a protective barrier and contribute to the structure of the visceral pleura. They are characterized by their cuboidal to squamous epithelial shape and the presence of microvilli on their surface, a feature aiding in fluid and solute exchange between the pleura and the lungs. +The primary function of mesothelial cells of visceral pleura is to secrete a lubricating serous fluid to facilitate smooth, frictionless lung movement within the thoracic cavity during respiration. This helps in the prevention of trauma or damage stemming from the constant rubbing of the lung tissue against the chest wall, hence playing a pivotal role in maintaining respiratory function. Besides fluid secretion, these cells have an essential role in the transportation of fluids and particles across the pleura, as well as in inflammation, wound healing, and tissue repair processes within the pleura. +Mesothelial cells of visceral pleura are notably implicated in the development of pleural diseases such as pleural effusion and pleural mesothelioma, a rare and aggressive form of cancer primarily linked with exposure to asbestos. Alterations, such as hyperplasia or metaplasia, may occur in these mesothelial cells under pathological conditions.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1000493") +AnnotationAssertion(Annotation( "DOI:10.1016/j.biocel.2010.05.015") Annotation( "DOI:10.1016/j.yexcr.2012.02.032") Annotation( "DOI:10.1111/j.1523-1755.2005.00260.x") Annotation( "DOI:10.2337/diacare.28.1.164") Annotation( "DOI:10.3389/fphys.2021.689083") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +The glomerular capillary endothelial cell comprises an intrinsic component of the glomerulus in the kidney. Glomeruli contain a network of capillaries where the first step of blood filtration takes place, with glomerular capillary endothelial cells acting as an integral part of this process. Unlike regular endothelial cells that line the vasculature, unique fenestrations (openings) characterize these cells, allowing for enhanced permeability and filtration efficacy. +Together with the glomerular basement membrane and podocytes, the glomerular endothelial cells form the glomerular filtration barrier, which is responsible for blood filtration and therefore critical for removal of waste products, such as urea and creatinine, and excess substances, such as glucose and ions, from the bloodstream. The glomerular capillary endothelial cells' fenestrations permit the free flow of a variety of particles, barring larger, negatively charged proteins like serum albumin, enabling the formation of an ultrafiltrate. This ultrafiltrate is the primitive form of urine, which then passes through the proximal tubule for further processing and ultimately helps maintain systemic fluid and electrolyte balance. +Moreover, the glomerular capillary endothelial cells are also believed to play a crucial role in renal pathologies. Any compromise to their structural integrity or functional performance can lead to kidney diseases, including but not limited to, diabetic nephropathy and glomerulonephritis. For instance, in diabetes, persistent hyperglycemia can injure these cells, leading to a compromised glomerular filtration barrier and proteinuria, indicating the loss of proteins in the urine.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1001005") +AnnotationAssertion(Annotation( "DOI:10.1046/j.0001-6772.2003.01205.x") Annotation( "DOI:10.1093/ndt/gfl308") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Kidney afferent arteriole endothelial cells are a specialized type of cell located within the kidneys, forming the inner lining of the afferent arterioles, which are responsible for delivering blood to the glomeruli - capillary networks responsible for filtration - from where the process of urine formation begins in the nephrons. +The endothelial cells in the kidney afferent arterioles have a key function in regulating the blood flow and filtration. They have autocrine and paracrine signaling capabilities, meaning they can signal to themselves and other nearby cells. They produce nitric oxide, prostacyclin, and endothelin, which are powerful vasodilators and vasoconstrictors that regulate renal blood flow. These cells also engage in the mitigation of kidney injury and inflammation by promoting repair and regeneration, demonstrating the multifaceted roles these cells play in maintaining renal health.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1001096") +AnnotationAssertion(Annotation( "DOI:10.1016/j.semcdb.2014.08.002") Annotation( "DOI:10.1016/j.semnephrol.2015.01.010") Annotation( "DOI:10.1038/s41581-021-00411-9") Annotation( "DOI:10.1681/ASN.2019111179") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Kidney efferent arteriole endothelial cells constitute a vital component of the kidney's microvascular system. They are unique endothelial cells found lining the walls of efferent arterioles, which transport blood away from the glomeruli in the kidney. +The primary responsibilities of the kidney efferent arteriole endothelial cells involve controling renal blood flow, regulating glomerular filtration rate (GFR), and managing perfusion pressure. They do this by contracting and relaxing, effectively narrowing and widening the arteriole's lumen thereby controling the volume and rate of blood flow to the peritubular capillaries and creating the pressure gradient necessary for filtration in the glomerulus. +Furthermore, kidney efferent arteriole endothelial cells show a high degree of plasticity in response to pathophysiological stimuli and can undergo structural and functional changes based on local needs. In conditions like hypertension and diabetes, these cells can experience hypertrophy and endothelial dysfunction, contributing to the progression of renal disease.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1001099") +AnnotationAssertion(Annotation( "DOI:10.1016/B978-0-323-35515-5.00009-9") Annotation( "DOI:10.1053/j.ajkd.2005.01.008") Annotation( "DOI:10.1081/jdi-100101958") Annotation( "DOI:10.1111/apha.12026") Annotation( "DOI:10.1152/ajpregu.00657.2002") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +The vasa recta ascending limb cells are specialized epithelial cells that are part of the vasa recta in the kidney, a crucial component of the renal medulla that functions as a counter-current exchanger to maintain the concentration gradient required for water reabsorption. These particular cells are located in the ascending limb of the vasa recta, which takes blood flow from the medulla back to the cortex. +The primary function of vasa recta ascending limb cells is to preserve the renal medulla's hypertonicity, necessary for the kidney's urine concentration mechanism. Unlike the vasa recta descending limb cells, the venous-like epithelial cells of the ascending vasa recta are highly fenestrated and lack pericyte coverage, which facilitates water reuptake. +As the blood flows through the ascending limb, it loses solutes and gains water, which is driven by the high solute concentration in the surrounding interstitium. This process acts in concert with cellular action in the descending limb and contributions from the so-called Loop of Henle, which helps with water and sodium chloride retrieval from the urine. +In the context of normal physiological processes, the function of the vasa recta ascending limb cells is essential in maintaining the body's overall fluid balance, electrolyte concentration, and systemic blood pressure. Any dysfunction in these cells may lead to impaired urine concentration or dilution capability of the kidney, potentially resulting in conditions like diabetes insipidus or hyponatremia.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1001131") +AnnotationAssertion(Annotation( "DOI:10.1053/j.ajkd.2005.01.008") Annotation( "DOI:10.1081/jdi-100101958") Annotation( "DOI:10.1111/apha.12026#apha12026-bib-0039") Annotation( "DOI:10.1152/ajpregu.00657.2002") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Vasa recta descending limb cells are specialized epithelial cells found in the vasa recta, a network of blood vessels in the renal medulla. These cells line the interior surface of the descending limb of the vasa recta and play a crucial role in the filtering and regulation of substances within the blood. +In contrast to vasa recta ascending limb cells, the arterial-like epithelial cells of the descending vasa recta are non-fenestrated and covered by a pericyte layer that regulates the medullary blood flow. They help keeping the body’s fluid and electrolyte balance in check through a process known as countercurrent exchange system, in which the cells of the descending limb are permeable to water but relatively impermeable to solutes, such as sodium and urea. As the blood descends into the medulla along its descending limb, water passively diffuses out of the vasa recta, concentrating the blood in solutes. +In addition to their central role in water and solute exchange, these cells contribute to maintaining the medullary osmotic gradient, a critical function to concentrate urine. The osmotic gradient is created by the counterflow of water and solutes between the descending and ascending limbs of the vasa recta and the adjacent Loop of Henle. The selective permeability of the descending limb cells allows them to maintain this gradient, which in turn helps to conserve water, a vital role in the overall function of the renal system. Thus, vasa recta descending limb cells have a significant function in renal physiology, particularly in osmoregulation and fluid balance.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1001285") +AnnotationAssertion(Annotation( "DOI:10.1007/s11906-015-0538-0") Annotation( "DOI:10.1016/B978-0-12-386456-7.05402-2") Annotation( "DOI:10.1016/j.biocel.2022.106261") Annotation( "DOI:10.1073/pnas.1710964114") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +The kidney collecting duct principal cell is a highly specialized type of cell found in the late distal convoluted tubule and collecting duct of the kidney's nephron. Principal cells are located at the final segments of the renal tubules, where they play a pivotal role in key homeostatic processes. +One of their fundamental functions of kidney collecting duct principal cells is the regulation of water reabsorption, which is mediated by aquaporins (water channel proteins). Antidiuretic hormones, such as vasopressin, can stimulate the redistribution of these water channels from an intracellular pools to the apical plasma membrane of the principal cell; translocation of aquaporin (specifically, AQP2) is associated with an increase of osmotic water permeability. The water reabsorption affects the concentration of the final urine; these cells are therefore directly involved in the maintenance of the body's fluid balance. +Kidney collecting duct principal cells also participate in sodium and potassium ions regulation. They reabsorb sodium ions from the tubular fluid back into the bloodstream, a process facilitated by the action of aldosterone, a hormone released by the adrenal glands. Similarly, the principal cells secrete potassium ions into the tubular fluid in response to aldosterone, contributing to the regulation of potassium levels in the body. Impaired function of cells can lead to various renal diseases and disorders, highlighting the vital role of kidney collecting duct principal cells in the body's homeostatic processes.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1001431") +AnnotationAssertion(Annotation( "DOI:10.1007/978-3-030-32300-4_26") Annotation( "DOI:10.1007/s00265-006-0178-0") Annotation( "DOI:10.1111/j.1439-0272.1992.tb02636.x") Annotation( "https://www.ncbi.nlm.nih.gov/books/NBK499854/") Annotation( "https://www.sciencedirect.com/topics/veterinary-science-and-veterinary-medicine/seminal-vesicle") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Seminal vesicle glandular cells belong to a specialized group of epithelial cells that form the internal lining of the seminal vesicles, a pair of male reproductive organs. These cells are located within the complex tubuloalveolar glands that make up the seminal vesicles and are known for their unique pseudostratified columnar epithelium structure. +The primary function of these cells is the secretion of a variety of substances that ultimately constitute around 70% of the fluid volume of semen. Seminal cells produce a high-fructose fluid that serves as an energy source for the spermatozoa and promotes their motility. They also secrete other essential substances like proteins, enzymes, vitamin C, prostaglandins, and various other compounds. Collectively, these substances help in the nourishment, protection, and transportation of the spermatozoa throughout the male reproductive system and during the ejaculation process. +Secondary to the production of seminal fluid, the seminal vesicle glandular cells also play a role in the contraction of the seminal vesicles during ejaculation. The contraction of these glands, induced by sympathetic nerves, ensures the efficient propulsion of the seminal fluid mixed with spermatozoa into the ejaculatory ducts and subsequently to the urethra. Notably, any malfunction or pathological condition affecting these cells can impact male fertility, emphasizing the importance of understanding the intricate functions of seminal vesicle glandular cells in maintaining the healthy physiological function of male reproduction.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_1001597") +AnnotationAssertion(Annotation( "DOI:10.1002/(SICI)1097-0029(19980415)41:2<98::AID-JEMT2>3.0.CO;2-M") Annotation( "DOI:10.1111/joa.13709") Annotation( "DOI:10.3389/fncel.2015.00480") "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Hypendymal cells are secretory cells located between the ependymal layer and the posterior commissure, forming the hypendmal layer of the subcommissural organ (SCO), a highly conserved gland that is part of the circumventricular system within the brain. +Hypendymal cells are bipolar cells with a thin apical pole and basal process. Most of the ultrastructural characteristics of these cells are similar to those described for the ependymal cells (which are arranged into another layer – the ependyma). However, ependymal cells release their secretion into the ventricular cerebrospinal fluid whereas hypendymal cells project processes to the local blood vessels and to the subarachnoidal space.") +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/CL_4023181") ) \ No newline at end of file diff --git a/patterns/pattern.owl b/patterns/pattern.owl index 873e3e4d6..f84d0c449 100644 --- a/patterns/pattern.owl +++ b/patterns/pattern.owl @@ -32,6 +32,7 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) +Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) Declaration(AnnotationProperty()) @@ -89,4 +90,9 @@ AnnotationAssertion(rdfs:label EquivalentClasses( ObjectIntersectionOf( ObjectSomeValuesFrom( ))) +AnnotationAssertion(Annotation( "xsd:string"^^xsd:string) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +xsd:string"^^xsd:string) +AnnotationAssertion( "ExtendedDescription"^^xsd:string) +AnnotationAssertion( "https://cellxgene.cziscience.com/cellguide/xsd:string"^^xsd:string) ) \ No newline at end of file diff --git a/src/ontology/reports/cl-base-diff.md b/src/ontology/reports/cl-base-diff.md index 13108928b..5d76b1e39 100644 --- a/src/ontology/reports/cl-base-diff.md +++ b/src/ontology/reports/cl-base-diff.md @@ -2,12 +2,12 @@ ## Left - Ontology IRI: `http://purl.obolibrary.org/obo/cl/cl-base.owl` -- Version IRI: `http://purl.obolibrary.org/obo/cl/cl-base/cl/releases/2024-05-15/cl-base.owl/cl/cl-base.owl` +- Version IRI: `http://purl.obolibrary.org/obo/cl/cl-base/cl/releases/2024-08-16/cl-base.owl/cl/cl-base.owl` - Loaded from: `file:/work/src/ontology/tmp/current-base-release.obo` ## Right - Ontology IRI: `http://purl.obolibrary.org/obo/cl/cl-base.owl` -- Version IRI: `http://purl.obolibrary.org/obo/cl/cl-base/cl/releases/2024-08-16/cl-base.owl/cl/cl-base.owl` +- Version IRI: `http://purl.obolibrary.org/obo/cl/cl-base/cl/releases/2024-09-26/cl-base.owl/cl/cl-base.owl` - Loaded from: `file:/work/src/ontology/../../cl-base.obo` ### Ontology imports @@ -16,8688 +16,5643 @@ ### Ontology annotations #### Removed -- [versionInfo](http://www.w3.org/2002/07/owl#versionInfo) "2024-05-15"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [comment](http://www.w3.org/2000/01/rdf-schema#comment) "See PMID:15693950, PMID:12799354, PMID:20123131, PMID:21208450; Contact Alexander Diehl, addiehl@buffalo.edu, University at Buffalo."^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added - [versionInfo](http://www.w3.org/2002/07/owl#versionInfo) "2024-08-16"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [comment](http://www.w3.org/2000/01/rdf-schema#comment) "See PMID:15693950, PMID:12799354, PMID:20123131, PMID:21208450; Contact Alexander Diehl, addiehl@buffalo.edu, university at buffalo."^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [versionInfo](http://www.w3.org/2002/07/owl#versionInfo) "2024-09-26"^^[string](http://www.w3.org/2001/XMLSchema#string) -### Ammon's horn basket cell `http://purl.obolibrary.org/obo/CL_2000088` +### B cell, CD19-positive `http://purl.obolibrary.org/obo/CL_0001201` #### Removed -- [Ammon's horn basket cell](http://purl.obolibrary.org/obo/CL_2000088) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +- [B cell, CD19-positive](http://purl.obolibrary.org/obo/CL_0001201) EquivalentTo [lymphocyte of B lineage, CD19-positive](http://purl.obolibrary.org/obo/CL_0001200) and ([RO_0002104](http://purl.obolibrary.org/obo/RO_0002104) some [PR_000001002](http://purl.obolibrary.org/obo/PR_000001002)) and ([RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_40674](http://purl.obolibrary.org/obo/NCBITaxon_40674)) and ([RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0019724](http://purl.obolibrary.org/obo/GO_0019724)) #### Added -- [Ammon's horn basket cell](http://purl.obolibrary.org/obo/CL_2000088) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [B cell, CD19-positive](http://purl.obolibrary.org/obo/CL_0001201) EquivalentTo [lymphocyte of B lineage, CD19-positive](http://purl.obolibrary.org/obo/CL_0001200) and ([RO_0002104](http://purl.obolibrary.org/obo/RO_0002104) some [PR_000001002](http://purl.obolibrary.org/obo/PR_000001002)) and ([RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0019724](http://purl.obolibrary.org/obo/GO_0019724)) -### B cell `http://purl.obolibrary.org/obo/CL_0000236` -#### Removed -- [B cell](http://purl.obolibrary.org/obo/CL_0000236) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009142"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### BEST4+ colonocyte `http://purl.obolibrary.org/obo/CL_4047052` #### Added -- [B cell](http://purl.obolibrary.org/obo/CL_0000236) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009142"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - +- [BEST4+ colonocyte](http://purl.obolibrary.org/obo/CL_4047052) [label](http://www.w3.org/2000/01/rdf-schema#label) "BEST4+ colonocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) -### BDS_subset `http://purl.obolibrary.org/obo/cl/cl-base#BDS_subset` +- [BEST4+ colonocyte](http://purl.obolibrary.org/obo/CL_4047052) [contributor](http://purl.org/dc/terms/contributor) [0009-0005-7919-4905](https://orcid.org/0009-0005-7919-4905) -#### Added -- [BDS_subset](http://purl.obolibrary.org/obo/cl/cl-base#BDS_subset) [comment](http://www.w3.org/2000/01/rdf-schema#comment) ""^^[string](http://www.w3.org/2001/XMLSchema#string) +- [BEST4+ colonocyte](http://purl.obolibrary.org/obo/CL_4047052) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An enterocyte of the human colon expressing bestrophin-4 (BEST4) calcium-activated ion channels. These cells have a distinct transcriptomic profile compared to other enterocytes and are scattered through the colon epithelium."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34497389"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [BDS_subset](http://purl.obolibrary.org/obo/cl/cl-base#BDS_subset) SubPropertyOf: [subset_property](http://www.geneontology.org/formats/oboInOwl#SubsetProperty) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:24223998"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [BEST4+ colonocyte](http://purl.obolibrary.org/obo/CL_4047052) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4047052"^^[string](http://www.w3.org/2001/XMLSchema#string) -### Bergmann glial cell `http://purl.obolibrary.org/obo/CL_0000644` -#### Removed -- [Bergmann glial cell](http://purl.obolibrary.org/obo/CL_0000644) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009282"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [BEST4+ colonocyte](http://purl.obolibrary.org/obo/CL_4047052) [date](http://purl.org/dc/terms/date) "2024-07-25T13:21:19Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -#### Added -- [Bergmann glial cell](http://purl.obolibrary.org/obo/CL_0000644) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009282"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [BEST4+ colonocyte](http://purl.obolibrary.org/obo/CL_4047052) +- [BEST4+ colonocyte](http://purl.obolibrary.org/obo/CL_4047052) EquivalentTo [enterocyte of colon](http://purl.obolibrary.org/obo/CL_1000347) and ([RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_Q8NFU0](http://purl.obolibrary.org/obo/PR_Q8NFU0)) -### CAP motoneuron `http://purl.obolibrary.org/obo/CL_0000532` -#### Removed -- [CAP motoneuron](http://purl.obolibrary.org/obo/CL_0000532) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009243"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [BEST4+ colonocyte](http://purl.obolibrary.org/obo/CL_4047052) SubClassOf [BEST4+ intestinal epithelial cell, human](http://purl.obolibrary.org/obo/CL_4030026) -#### Added -- [CAP motoneuron](http://purl.obolibrary.org/obo/CL_0000532) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009243"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [BEST4+ colonocyte](http://purl.obolibrary.org/obo/CL_4047052) SubClassOf [enterocyte of colon](http://purl.obolibrary.org/obo/CL_1000347) -### CNS interneuron `http://purl.obolibrary.org/obo/CL_0000402` +### BEST4+ intestinal epithelial cell, human `http://purl.obolibrary.org/obo/CL_4030026` #### Removed -- [CNS interneuron](http://purl.obolibrary.org/obo/CL_0000402) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009191"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [BEST4+ intestinal epithelial cell, human](http://purl.obolibrary.org/obo/CL_4030026) [label](http://www.w3.org/2000/01/rdf-schema#label) "BEST4+ intestinal epithelial cell, human"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [CNS interneuron](http://purl.obolibrary.org/obo/CL_0000402) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009191"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [BEST4+ intestinal epithelial cell, human](http://purl.obolibrary.org/obo/CL_4030026) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An absorptive epithelial cell of the human intestine expressing bestrophin-4 (BEST4) calcium-activated ion channels."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35176508"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:24223998"^^[string](http://www.w3.org/2001/XMLSchema#string) -### CNS long range interneuron `http://purl.obolibrary.org/obo/CL_0000410` -#### Removed -- [CNS long range interneuron](http://purl.obolibrary.org/obo/CL_0000410) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009195"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://orcid.org/0000-0002-7431-4139"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [CNS long range interneuron](http://purl.obolibrary.org/obo/CL_0000410) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009195"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [BEST4+ intestinal epithelial cell, human](http://purl.obolibrary.org/obo/CL_4030026) SubClassOf [gut absorptive cell](http://purl.obolibrary.org/obo/CL_0000677) +- [BEST4+ intestinal epithelial cell, human](http://purl.obolibrary.org/obo/CL_4030026) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### CNS neuron (sensu Vertebrata) `http://purl.obolibrary.org/obo/CL_0000117` -#### Removed -- [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009067"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [BEST4+ intestinal epithelial cell, human](http://purl.obolibrary.org/obo/CL_4030026) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) + +- [BEST4+ intestinal epithelial cell, human](http://purl.obolibrary.org/obo/CL_4030026) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) #### Added -- [CNS neuron (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000117) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009067"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [BEST4+ intestinal epithelial cell, human](http://purl.obolibrary.org/obo/CL_4030026) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An enterocyte of the human intestine expressing bestrophin-4 (BEST4) calcium-activated ion channels."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35176508"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:24223998"^^[string](http://www.w3.org/2001/XMLSchema#string) -### CNS short range interneuron `http://purl.obolibrary.org/obo/CL_0000406` -#### Removed -- [CNS short range interneuron](http://purl.obolibrary.org/obo/CL_0000406) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009194"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://orcid.org/0000-0002-7431-4139"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [CNS short range interneuron](http://purl.obolibrary.org/obo/CL_0000406) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009194"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [BEST4+ intestinal epithelial cell, human](http://purl.obolibrary.org/obo/CL_4030026) [label](http://www.w3.org/2000/01/rdf-schema#label) "BEST4+ enteroycte"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [BEST4+ intestinal epithelial cell, human](http://purl.obolibrary.org/obo/CL_4030026) EquivalentTo [enterocyte](http://purl.obolibrary.org/obo/CL_0000584) and ([RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_Q8NFU0](http://purl.obolibrary.org/obo/PR_Q8NFU0)) -### Caenorhabditis hypodermal cell `http://purl.obolibrary.org/obo/CL_0000411` -#### Removed -- [Caenorhabditis hypodermal cell](http://purl.obolibrary.org/obo/CL_0000411) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009196"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [BEST4+ intestinal epithelial cell, human](http://purl.obolibrary.org/obo/CL_4030026) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) -#### Added -- [Caenorhabditis hypodermal cell](http://purl.obolibrary.org/obo/CL_0000411) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009196"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [BEST4+ intestinal epithelial cell, human](http://purl.obolibrary.org/obo/CL_4030026) SubClassOf [enterocyte](http://purl.obolibrary.org/obo/CL_0000584) -### Cajal-Retzius cell `http://purl.obolibrary.org/obo/CL_0000695` -#### Removed -- [Cajal-Retzius cell](http://purl.obolibrary.org/obo/CL_0000695) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009300"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### CD115-positive monocyte `http://purl.obolibrary.org/obo/CL_0001022` #### Added -- [Cajal-Retzius cell](http://purl.obolibrary.org/obo/CL_0000695) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009300"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [CD115-positive monocyte](http://purl.obolibrary.org/obo/CL_0001022) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### GABAergic neuron `http://purl.obolibrary.org/obo/CL_0000617` -#### Removed -- [GABAergic neuron](http://purl.obolibrary.org/obo/CL_0000617) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007228"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [GABAergic neuron](http://purl.obolibrary.org/obo/CL_0000617) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009276"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### CD14-positive monocyte `http://purl.obolibrary.org/obo/CL_0001054` #### Added -- [GABAergic neuron](http://purl.obolibrary.org/obo/CL_0000617) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007228"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [CD14-positive monocyte](http://purl.obolibrary.org/obo/CL_0001054) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -- [GABAergic neuron](http://purl.obolibrary.org/obo/CL_0000617) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009276"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -### GO_0005903 `http://purl.obolibrary.org/obo/GO_0005903` +### CD16-negative, CD56-bright natural killer cell, human `http://purl.obolibrary.org/obo/CL_0000938` #### Added -- Class: [GO_0005903](http://purl.obolibrary.org/obo/GO_0005903) +- [CD16-negative, CD56-bright natural killer cell, human](http://purl.obolibrary.org/obo/CL_0000938) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### GO_0022402 `http://purl.obolibrary.org/obo/GO_0022402` +### CD16-positive, CD56-dim natural killer cell, human `http://purl.obolibrary.org/obo/CL_0000939` #### Added -- Class: [GO_0022402](http://purl.obolibrary.org/obo/GO_0022402) +- [CD16-positive, CD56-dim natural killer cell, human](http://purl.obolibrary.org/obo/CL_0000939) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### GO_0031514 `http://purl.obolibrary.org/obo/GO_0031514` +### CD1c-positive myeloid dendritic cell `http://purl.obolibrary.org/obo/CL_0002399` +#### Removed +- [CD1c-positive myeloid dendritic cell](http://purl.obolibrary.org/obo/CL_0002399) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A myeloid dendritic cell found in the blood that is CD1c-positive."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20628149"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- Class: [GO_0031514](http://purl.obolibrary.org/obo/GO_0031514) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:dsd"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20204387"^^[string](http://www.w3.org/2001/XMLSchema#string) -### GO_0036053 `http://purl.obolibrary.org/obo/GO_0036053` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- Class: [GO_0036053](http://purl.obolibrary.org/obo/GO_0036053) +- [CD1c-positive myeloid dendritic cell](http://purl.obolibrary.org/obo/CL_0002399) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A myeloid dendritic cell that is CD1c-positive."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20628149"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:dsd"^^[string](http://www.w3.org/2001/XMLSchema#string) -### GO_0097729 `http://purl.obolibrary.org/obo/GO_0097729` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20204387"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- Class: [GO_0097729](http://purl.obolibrary.org/obo/GO_0097729) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) -### GO_0098594 `http://purl.obolibrary.org/obo/GO_0098594` +### CD25+ mast cell `http://purl.obolibrary.org/obo/CL_0011023` #### Added -- Class: [GO_0098594](http://purl.obolibrary.org/obo/GO_0098594) +- [CD25+ mast cell](http://purl.obolibrary.org/obo/CL_0011023) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### Hofbauer cell `http://purl.obolibrary.org/obo/CL_3000001` -#### Removed -- [Hofbauer cell](http://purl.obolibrary.org/obo/CL_3000001) [contributor](http://purl.org/dc/terms/contributor) [Q97529981](https://www.wikidata.org/entity/Q97529981) +### CD27-high, CD11b-high natural killer cell, mouse `http://purl.obolibrary.org/obo/CL_0002347` #### Added -- [Hofbauer cell](http://purl.obolibrary.org/obo/CL_3000001) [contributor](http://purl.org/dc/terms/contributor) [Q97529981](http://www.wikidata.org/entity/Q97529981) +- [CD27-high, CD11b-high natural killer cell, mouse](http://purl.obolibrary.org/obo/CL_0002347) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### Kenyon cell `http://purl.obolibrary.org/obo/CL_0000673` -#### Removed -- [Kenyon cell](http://purl.obolibrary.org/obo/CL_0000673) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00003686"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +### CD27-high, CD11b-low natural killer cell, mouse `http://purl.obolibrary.org/obo/CL_0002349` #### Added -- [Kenyon cell](http://purl.obolibrary.org/obo/CL_0000673) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00003686"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [CD27-high, CD11b-low natural killer cell, mouse](http://purl.obolibrary.org/obo/CL_0002349) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### Kolmer-Agduhr neuron `http://purl.obolibrary.org/obo/CL_0005007` -#### Removed -- [Kolmer-Agduhr neuron](http://purl.obolibrary.org/obo/CL_0005007) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005240"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### CD27-low, CD11b-high natural killer cell, mouse `http://purl.obolibrary.org/obo/CL_0002348` #### Added -- [Kolmer-Agduhr neuron](http://purl.obolibrary.org/obo/CL_0005007) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005240"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [CD27-low, CD11b-high natural killer cell, mouse](http://purl.obolibrary.org/obo/CL_0002348) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### L2 marginal neuron `http://purl.obolibrary.org/obo/CL_4042012` +### CD27-low, CD11b-low immature natural killer cell, mouse `http://purl.obolibrary.org/obo/CL_0002345` #### Added -- [L2 marginal neuron](http://purl.obolibrary.org/obo/CL_4042012) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "layer 2 marginal neuron"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32108571"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [L2 marginal neuron](http://purl.obolibrary.org/obo/CL_4042012) [label](http://www.w3.org/2000/01/rdf-schema#label) "L2 marginal neuron"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [CD27-low, CD11b-low immature natural killer cell, mouse](http://purl.obolibrary.org/obo/CL_0002345) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -- [L2 marginal neuron](http://purl.obolibrary.org/obo/CL_4042012) [date](http://purl.org/dc/terms/date) "2024-04-23T09:31:39Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -- [L2 marginal neuron](http://purl.obolibrary.org/obo/CL_4042012) [IAO_0000028](http://purl.obolibrary.org/obo/IAO_0000028) "L2MN"^^[string](http://www.w3.org/2001/XMLSchema#string) +### CD34-negative, CD117-positive innate lymphoid cell, human `http://purl.obolibrary.org/obo/CL_0001072` -- [L2 marginal neuron](http://purl.obolibrary.org/obo/CL_4042012) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042012"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [L2 marginal neuron](http://purl.obolibrary.org/obo/CL_4042012) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "L2MN"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) +#### Added +- [CD34-negative, CD117-positive innate lymphoid cell, human](http://purl.obolibrary.org/obo/CL_0001072) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29311847"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32108571"^^[string](http://www.w3.org/2001/XMLSchema#string) +### CD34-negative, CD41-positive, CD42-positive megakaryocyte cell `http://purl.obolibrary.org/obo/CL_0002026` -- [L2 marginal neuron](http://purl.obolibrary.org/obo/CL_4042012) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) +#### Added +- [CD34-negative, CD41-positive, CD42-positive megakaryocyte cell](http://purl.obolibrary.org/obo/CL_0002026) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -- [L2 marginal neuron](http://purl.obolibrary.org/obo/CL_4042012) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An L2 intratelencephalic projecting glutamatergic neuron with a soma on the L1-L2 border. This neuron type has small apical dendrites projecting to L1."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29311847"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32108571"^^[string](http://www.w3.org/2001/XMLSchema#string) +### CD34-positive, CD38-negative hematopoietic stem cell `http://purl.obolibrary.org/obo/CL_0001024` -- Class: [L2 marginal neuron](http://purl.obolibrary.org/obo/CL_4042012) +#### Added +- [CD34-positive, CD38-negative hematopoietic stem cell](http://purl.obolibrary.org/obo/CL_0001024) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -- [L2 marginal neuron](http://purl.obolibrary.org/obo/CL_4042012) SubClassOf [L2 intratelencephalic projecting glutamatergic neuron](http://purl.obolibrary.org/obo/CL_4030060) +### CD34-positive, CD38-positive common lymphoid progenitor `http://purl.obolibrary.org/obo/CL_0001021` -### L2/3 bipolar VIP GABAergic interneuron (Mmus) `http://purl.obolibrary.org/obo/CL_4023007` -#### Removed -- [L2/3 bipolar VIP GABAergic interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023007) [label](http://www.w3.org/2000/01/rdf-schema#label) "L2/3 bipolar vip GABAergic interneuron (Mmus)"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [CD34-positive, CD38-positive common lymphoid progenitor](http://purl.obolibrary.org/obo/CL_0001021) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -- [L2/3 bipolar VIP GABAergic interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023007) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A vip GABAergic cortical interneuron with bipolar morphology, with a soma found in L2/3. L2/3 bipolar vip cells have extending axons across all layers (with preferences for layers II/III and Va) and a dendritic tree that is vertically more restricted than deeper layer vip cells and extend fewer dendrites into the layers outside their home layer (location of soma). L2/3 bipolar vip cells have great variability in firing patterns, though most are continuous adapting. L2/3 bipolar vip cells are more depolarized in their resting state, had less fast rectification, and had smaller after hyperpolarization than deeper vip cells."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:26420784"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [L2/3 bipolar VIP GABAergic interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023007) [IAO_0000028](http://purl.obolibrary.org/obo/IAO_0000028) "L2/3 bipolar vip interneuron (Mus)"^^[string](http://www.w3.org/2001/XMLSchema#string) +### CD34-positive, CD38-positive megakaryocyte erythroid progenitor cell `http://purl.obolibrary.org/obo/CL_0002005` #### Added -- [L2/3 bipolar VIP GABAergic interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023007) [IAO_0000028](http://purl.obolibrary.org/obo/IAO_0000028) "L2/3 bipolar VIP interneuron (Mus)"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [CD34-positive, CD38-positive megakaryocyte erythroid progenitor cell](http://purl.obolibrary.org/obo/CL_0002005) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -- [L2/3 bipolar VIP GABAergic interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023007) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A VIP GABAergic cortical interneuron with bipolar morphology, with a soma found in L2/3. L2/3 bipolar VIP cells have extending axons across all layers (with preferences for layers II/III and Va) and a dendritic tree that is vertically more restricted than deeper layer VIP cells and extend fewer dendrites into the layers outside their home layer (location of soma). L2/3 bipolar VIP cells have great variability in firing patterns, though most are continuous adapting. L2/3 bipolar VIP cells are more depolarized in their resting state, had less fast rectification, and had smaller after hyperpolarization than deeper VIP cells."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:26420784"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [L2/3 bipolar VIP GABAergic interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023007) [label](http://www.w3.org/2000/01/rdf-schema#label) "L2/3 bipolar VIP GABAergic interneuron (Mmus)"^^[string](http://www.w3.org/2001/XMLSchema#string) +### CD34-positive, CD41-positive, CD42-negative megakaryocyte progenitor cell `http://purl.obolibrary.org/obo/CL_0002025` -### L5 VIP GABAergic interneuron (Mmus) `http://purl.obolibrary.org/obo/CL_4023014` -#### Removed -- [L5 VIP GABAergic interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023014) [IAO_0000028](http://purl.obolibrary.org/obo/IAO_0000028) "L5 vip interneuron (Mus)"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [L5 VIP GABAergic interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023014) [label](http://www.w3.org/2000/01/rdf-schema#label) "L5 vip GABAergic interneuron (Mmus)"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [CD34-positive, CD41-positive, CD42-negative megakaryocyte progenitor cell](http://purl.obolibrary.org/obo/CL_0002025) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -- [L5 VIP GABAergic interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023014) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A vip GABAergic cortical interneuron with a soma found in L5. L5 vip cells have mostly local morphology with some deep-projecting axons. They show only moderate resistance, comparable to that of sst subclass and unlike typical Vip subclass cells that tend to show high input resistance. L5 vip cells show particularly low resting membrane potential."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:26420784"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:26612957"^^[string](http://www.w3.org/2001/XMLSchema#string) +### CD34-positive, CD41-positive, CD42-positive megakaryocyte progenitor cell `http://purl.obolibrary.org/obo/CL_0002023` #### Added -- [L5 VIP GABAergic interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023014) [IAO_0000028](http://purl.obolibrary.org/obo/IAO_0000028) "L5 VIP interneuron (Mus)"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [CD34-positive, CD41-positive, CD42-positive megakaryocyte progenitor cell](http://purl.obolibrary.org/obo/CL_0002023) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -- [L5 VIP GABAergic interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023014) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A VIP GABAergic cortical interneuron with a soma found in L5. L5 VIP cells have mostly local morphology with some deep-projecting axons. They show only moderate resistance, comparable to that of sst subclass and unlike typical VIP subclass cells that tend to show high input resistance. L5 VIP cells show particularly low resting membrane potential."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:26420784"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:26612957"^^[string](http://www.w3.org/2001/XMLSchema#string) +### CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human `http://purl.obolibrary.org/obo/CL_0001074` -- [L5 VIP GABAergic interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023014) [label](http://www.w3.org/2000/01/rdf-schema#label) "L5 VIP GABAergic interneuron (Mmus)"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [CD34-positive, CD56-positive, CD117-positive common innate lymphoid precursor, human](http://purl.obolibrary.org/obo/CL_0001074) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### L5/6 cck, VIP GABAergic interneuron (Mmus) `http://purl.obolibrary.org/obo/CL_4023019` +### CD4-positive, alpha-beta memory T cell, CD45RO-positive `http://purl.obolibrary.org/obo/CL_0001204` #### Removed -- [L5/6 cck, VIP GABAergic interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023019) [label](http://www.w3.org/2000/01/rdf-schema#label) "L5/6 cck, vip GABAergic interneuron (Mmus)"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [CD4-positive, alpha-beta memory T cell, CD45RO-positive](http://purl.obolibrary.org/obo/CL_0001204) EquivalentTo [CD4-positive, alpha-beta memory T cell](http://purl.obolibrary.org/obo/CL_0000897) and ([lacks_plasma_membrane_part](http://purl.obolibrary.org/obo/CL_4030046) some [PR_000001380](http://purl.obolibrary.org/obo/PR_000001380)) and ([RO_0002104](http://purl.obolibrary.org/obo/RO_0002104) some [PR_000001017](http://purl.obolibrary.org/obo/PR_000001017)) and ([RO_0002104](http://purl.obolibrary.org/obo/RO_0002104) some [PR_000001869](http://purl.obolibrary.org/obo/PR_000001869)) and ([RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606)) and ([RO_0002353](http://purl.obolibrary.org/obo/RO_0002353) some [GO_0043379](http://purl.obolibrary.org/obo/GO_0043379)) and ([RO_0015015](http://purl.obolibrary.org/obo/RO_0015015) some [PR_000001307](http://purl.obolibrary.org/obo/PR_000001307)) and ([RO_0015015](http://purl.obolibrary.org/obo/RO_0015015) some [PR_000001381](http://purl.obolibrary.org/obo/PR_000001381)) -- [L5/6 cck, VIP GABAergic interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023019) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A vip GABAergic cortical interneuron that expresses cck. L5/6 cck cells have soma found mainly in L5 and L6 and have large axonal arborization."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33184512"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [CD4-positive, alpha-beta memory T cell, CD45RO-positive](http://purl.obolibrary.org/obo/CL_0001204) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) #### Added -- [L5/6 cck, VIP GABAergic interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023019) [label](http://www.w3.org/2000/01/rdf-schema#label) "L5/6 cck, VIP GABAergic interneuron (Mmus)"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [CD4-positive, alpha-beta memory T cell, CD45RO-positive](http://purl.obolibrary.org/obo/CL_0001204) EquivalentTo [CD4-positive, alpha-beta memory T cell](http://purl.obolibrary.org/obo/CL_0000897) and ([lacks_plasma_membrane_part](http://purl.obolibrary.org/obo/CL_4030046) some [PR_000001380](http://purl.obolibrary.org/obo/PR_000001380)) and ([RO_0002104](http://purl.obolibrary.org/obo/RO_0002104) some [PR_000001017](http://purl.obolibrary.org/obo/PR_000001017)) and ([RO_0002104](http://purl.obolibrary.org/obo/RO_0002104) some [PR_000001869](http://purl.obolibrary.org/obo/PR_000001869)) and ([RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606)) and ([RO_0002353](http://purl.obolibrary.org/obo/RO_0002353) some [GO_0043379](http://purl.obolibrary.org/obo/GO_0043379)) and ([RO_0015015](http://purl.obolibrary.org/obo/RO_0015015) some [PR_000001307](http://purl.obolibrary.org/obo/PR_000001307)) and ([RO_0015015](http://purl.obolibrary.org/obo/RO_0015015) some [PR_000001381](http://purl.obolibrary.org/obo/PR_000001381)) -- [L5/6 cck, VIP GABAergic interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023019) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A VIP GABAergic cortical interneuron that expresses cck. L5/6 cck cells have soma found mainly in L5 and L6 and have large axonal arborization."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33184512"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [CD4-positive, alpha-beta memory T cell, CD45RO-positive](http://purl.obolibrary.org/obo/CL_0001204) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) -### Lamp5 Lhx6 neuron `http://purl.obolibrary.org/obo/CL_4042013` +### CD56-negative, CD161-positive immature natural killer cell, human `http://purl.obolibrary.org/obo/CL_0002344` #### Added -- [Lamp5 Lhx6 neuron](http://purl.obolibrary.org/obo/CL_4042013) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "Ivy cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36007006"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [CD56-negative, CD161-positive immature natural killer cell, human](http://purl.obolibrary.org/obo/CL_0002344) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -- [Lamp5 Lhx6 neuron](http://purl.obolibrary.org/obo/CL_4042013) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042013"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [Lamp5 Lhx6 neuron](http://purl.obolibrary.org/obo/CL_4042013) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "Lamp5-Lhx6 type"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30382198"^^[string](http://www.w3.org/2001/XMLSchema#string) +### CD56-positive, CD161-positive immature natural killer cell, human `http://purl.obolibrary.org/obo/CL_0002338` -- [Lamp5 Lhx6 neuron](http://purl.obolibrary.org/obo/CL_4042013) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A transcriptomically distinct lamp5 GABAergic cortical interneuron located in the cerebral cortex that expresses Lamp5 and Lhx6. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_subclass', Lamp5 Lhx6."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824669"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [CD56-positive, CD161-positive immature natural killer cell, human](http://purl.obolibrary.org/obo/CL_0002338) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/e/e4ddac12-f48f-4455-8e8d-c2a48a683437.cxg/"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36007006"^^[string](http://www.w3.org/2001/XMLSchema#string) +### CD7-negative lymphoid progenitor cell `http://purl.obolibrary.org/obo/CL_0001027` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34004146"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [CD7-negative lymphoid progenitor cell](http://purl.obolibrary.org/obo/CL_0001027) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [Lamp5 Lhx6 neuron](http://purl.obolibrary.org/obo/CL_4042013) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) +### CD7-positive lymphoid progenitor cell `http://purl.obolibrary.org/obo/CL_0001028` -- [Lamp5 Lhx6 neuron](http://purl.obolibrary.org/obo/CL_4042013) [date](http://purl.org/dc/terms/date) "2024-04-23T09:37:55Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) +#### Added +- [CD7-positive lymphoid progenitor cell](http://purl.obolibrary.org/obo/CL_0001028) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -- [Lamp5 Lhx6 neuron](http://purl.obolibrary.org/obo/CL_4042013) [label](http://www.w3.org/2000/01/rdf-schema#label) "Lamp5 Lhx6 neuron"^^[string](http://www.w3.org/2001/XMLSchema#string) -- Class: [Lamp5 Lhx6 neuron](http://purl.obolibrary.org/obo/CL_4042013) +### CD71-negative, GlyA-positive orthochromatic erythroblast `http://purl.obolibrary.org/obo/CL_0002018` -- [Lamp5 Lhx6 neuron](http://purl.obolibrary.org/obo/CL_4042013) SubClassOf [lamp5 GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023011) +#### Added +- [CD71-negative, GlyA-positive orthochromatic erythroblast](http://purl.obolibrary.org/obo/CL_0002018) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### Leydig cell `http://purl.obolibrary.org/obo/CL_0000178` +### CD8-positive, alpha-beta memory T cell, CD45RO-positive `http://purl.obolibrary.org/obo/CL_0001203` #### Removed -- [Leydig cell](http://purl.obolibrary.org/obo/CL_0000178) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009108"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [CD8-positive, alpha-beta memory T cell, CD45RO-positive](http://purl.obolibrary.org/obo/CL_0001203) EquivalentTo [CD8-positive, alpha-beta memory T cell](http://purl.obolibrary.org/obo/CL_0000909) and ([lacks_plasma_membrane_part](http://purl.obolibrary.org/obo/CL_4030046) some [PR_000001380](http://purl.obolibrary.org/obo/PR_000001380)) and ([RO_0002104](http://purl.obolibrary.org/obo/RO_0002104) some [PR_000001017](http://purl.obolibrary.org/obo/PR_000001017)) and ([RO_0002104](http://purl.obolibrary.org/obo/RO_0002104) some [PR_000001869](http://purl.obolibrary.org/obo/PR_000001869)) and ([RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606)) and ([RO_0002353](http://purl.obolibrary.org/obo/RO_0002353) some [GO_0043379](http://purl.obolibrary.org/obo/GO_0043379)) and ([RO_0015015](http://purl.obolibrary.org/obo/RO_0015015) some [PR_000001307](http://purl.obolibrary.org/obo/PR_000001307)) and ([RO_0015015](http://purl.obolibrary.org/obo/RO_0015015) some [PR_000001381](http://purl.obolibrary.org/obo/PR_000001381)) + +- [CD8-positive, alpha-beta memory T cell, CD45RO-positive](http://purl.obolibrary.org/obo/CL_0001203) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) #### Added -- [Leydig cell](http://purl.obolibrary.org/obo/CL_0000178) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009108"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [CD8-positive, alpha-beta memory T cell, CD45RO-positive](http://purl.obolibrary.org/obo/CL_0001203) EquivalentTo [CD8-positive, alpha-beta memory T cell](http://purl.obolibrary.org/obo/CL_0000909) and ([lacks_plasma_membrane_part](http://purl.obolibrary.org/obo/CL_4030046) some [PR_000001380](http://purl.obolibrary.org/obo/PR_000001380)) and ([RO_0002104](http://purl.obolibrary.org/obo/RO_0002104) some [PR_000001017](http://purl.obolibrary.org/obo/PR_000001017)) and ([RO_0002104](http://purl.obolibrary.org/obo/RO_0002104) some [PR_000001869](http://purl.obolibrary.org/obo/PR_000001869)) and ([RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606)) and ([RO_0002353](http://purl.obolibrary.org/obo/RO_0002353) some [GO_0043379](http://purl.obolibrary.org/obo/GO_0043379)) and ([RO_0015015](http://purl.obolibrary.org/obo/RO_0015015) some [PR_000001307](http://purl.obolibrary.org/obo/PR_000001307)) and ([RO_0015015](http://purl.obolibrary.org/obo/RO_0015015) some [PR_000001381](http://purl.obolibrary.org/obo/PR_000001381)) +- [CD8-positive, alpha-beta memory T cell, CD45RO-positive](http://purl.obolibrary.org/obo/CL_0001203) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) -### M cell of gut `http://purl.obolibrary.org/obo/CL_0000682` -#### Removed -- [M cell of gut](http://purl.obolibrary.org/obo/CL_0000682) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009293"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +### CD9-positive, CD41-positive megakaryocyte cell `http://purl.obolibrary.org/obo/CL_0002027` #### Added -- [M cell of gut](http://purl.obolibrary.org/obo/CL_0000682) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009293"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [CD9-positive, CD41-positive megakaryocyte cell](http://purl.obolibrary.org/obo/CL_0002027) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### Malpighian tubule stellate cell `http://purl.obolibrary.org/obo/CL_1000155` -#### Removed -- [Malpighian tubule stellate cell](http://purl.obolibrary.org/obo/CL_1000155) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005797"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +### DN1 thymic pro-T cell `http://purl.obolibrary.org/obo/CL_0000894` #### Added -- [Malpighian tubule stellate cell](http://purl.obolibrary.org/obo/CL_1000155) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005797"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [DN1 thymic pro-T cell](http://purl.obolibrary.org/obo/CL_0000894) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### Mauthner neuron `http://purl.obolibrary.org/obo/CL_0000246` -#### Removed -- [Mauthner neuron](http://purl.obolibrary.org/obo/CL_0000246) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009149"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### DN2 thymocyte `http://purl.obolibrary.org/obo/CL_0000806` #### Added -- [Mauthner neuron](http://purl.obolibrary.org/obo/CL_0000246) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009149"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [DN2 thymocyte](http://purl.obolibrary.org/obo/CL_0000806) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### Merkel cell `http://purl.obolibrary.org/obo/CL_0000242` -#### Removed -- [Merkel cell](http://purl.obolibrary.org/obo/CL_0000242) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009146"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### DN3 thymocyte `http://purl.obolibrary.org/obo/CL_0000807` #### Added -- [Merkel cell](http://purl.obolibrary.org/obo/CL_0000242) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009146"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [DN3 thymocyte](http://purl.obolibrary.org/obo/CL_0000807) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### Meynert cell `http://purl.obolibrary.org/obo/CL_2000056` -#### Removed -- [Meynert cell](http://purl.obolibrary.org/obo/CL_2000056) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +### DN4 thymocyte `http://purl.obolibrary.org/obo/CL_0000808` #### Added -- [Meynert cell](http://purl.obolibrary.org/obo/CL_2000056) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [DN4 thymocyte](http://purl.obolibrary.org/obo/CL_0000808) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### Mueller cell `http://purl.obolibrary.org/obo/CL_0000636` -#### Removed -- [Mueller cell](http://purl.obolibrary.org/obo/CL_0000636) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009280"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### Dx5-negative, NK1.1-positive immature natural killer cell, mouse `http://purl.obolibrary.org/obo/CL_0002346` #### Added -- [Mueller cell](http://purl.obolibrary.org/obo/CL_0000636) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009280"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [Dx5-negative, NK1.1-positive immature natural killer cell, mouse](http://purl.obolibrary.org/obo/CL_0002346) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### OFF-bipolar cell `http://purl.obolibrary.org/obo/CL_0000750` +### Eumycetozoan cell `http://purl.obolibrary.org/obo/CL_0000257` #### Removed -- [OFF-bipolar cell](http://purl.obolibrary.org/obo/CL_0000750) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009320"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [Eumycetozoan cell](http://purl.obolibrary.org/obo/CL_0000257) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any cell that only exists in Eumycetozoa."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [Eumycetozoan cell](http://purl.obolibrary.org/obo/CL_0000257) EquivalentTo [cell](http://purl.obolibrary.org/obo/CL_0000000) and ([RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_142796](http://purl.obolibrary.org/obo/NCBITaxon_142796)) + +- [Eumycetozoan cell](http://purl.obolibrary.org/obo/CL_0000257) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_142796](http://purl.obolibrary.org/obo/NCBITaxon_142796) #### Added -- [OFF-bipolar cell](http://purl.obolibrary.org/obo/CL_0000750) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009320"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [Eumycetozoan cell](http://purl.obolibrary.org/obo/CL_0000257) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any cell that in taxon some Eumycetozoa."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [Eumycetozoan cell](http://purl.obolibrary.org/obo/CL_0000257) EquivalentTo [cell](http://purl.obolibrary.org/obo/CL_0000000) and ([RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_142796](http://purl.obolibrary.org/obo/NCBITaxon_142796)) + +- [Eumycetozoan cell](http://purl.obolibrary.org/obo/CL_0000257) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_142796](http://purl.obolibrary.org/obo/NCBITaxon_142796) -### ON-bipolar cell `http://purl.obolibrary.org/obo/CL_0000749` -#### Removed -- [ON-bipolar cell](http://purl.obolibrary.org/obo/CL_0000749) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009319"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +### GABAergic interneuron of the anterior substantia nigra pars reticulata `http://purl.obolibrary.org/obo/CL_4042026` #### Added -- [ON-bipolar cell](http://purl.obolibrary.org/obo/CL_0000749) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009319"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [GABAergic interneuron of the anterior substantia nigra pars reticulata](http://purl.obolibrary.org/obo/CL_4042026) [date](http://purl.org/dc/terms/date) "2024-09-23T13:56:01Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) +- [GABAergic interneuron of the anterior substantia nigra pars reticulata](http://purl.obolibrary.org/obo/CL_4042026) [label](http://www.w3.org/2000/01/rdf-schema#label) "GABAergic interneuron of the anterior substantia nigra pars reticulata"^^[string](http://www.w3.org/2001/XMLSchema#string) -### PATO_0002064 `http://purl.obolibrary.org/obo/PATO_0002064` +- [GABAergic interneuron of the anterior substantia nigra pars reticulata](http://purl.obolibrary.org/obo/CL_4042026) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "aSNpr"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) -#### Added -- Class: [PATO_0002064](http://purl.obolibrary.org/obo/PATO_0002064) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36148148"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [GABAergic interneuron of the anterior substantia nigra pars reticulata](http://purl.obolibrary.org/obo/CL_4042026) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042026"^^[string](http://www.w3.org/2001/XMLSchema#string) -### PATO_0002354 `http://purl.obolibrary.org/obo/PATO_0002354` +- [GABAergic interneuron of the anterior substantia nigra pars reticulata](http://purl.obolibrary.org/obo/CL_4042026) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A GABAergic interneuron that has its soma in the anterior section of the substantia nigra pars reticulata. This GABAergic interneuron is characterized by the expression of Six3 and Foxp1 and it develops from Nkx6-2 expressing neuronal progenitors in the ventrolateral midbrain-diencephalon region."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36148148"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- Class: [PATO_0002354](http://purl.obolibrary.org/obo/PATO_0002354) +- [GABAergic interneuron of the anterior substantia nigra pars reticulata](http://purl.obolibrary.org/obo/CL_4042026) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) +- Class: [GABAergic interneuron of the anterior substantia nigra pars reticulata](http://purl.obolibrary.org/obo/CL_4042026) -### Purkinje cell `http://purl.obolibrary.org/obo/CL_0000121` -#### Removed -- [Purkinje cell](http://purl.obolibrary.org/obo/CL_0000121) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009071"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [GABAergic interneuron of the anterior substantia nigra pars reticulata](http://purl.obolibrary.org/obo/CL_4042026) SubClassOf [RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000014898](http://purl.obolibrary.org/obo/PR_000014898) -- [Purkinje cell](http://purl.obolibrary.org/obo/CL_0000121) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cerebellum Purkinje cell"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [GABAergic interneuron of the anterior substantia nigra pars reticulata](http://purl.obolibrary.org/obo/CL_4042026) SubClassOf [RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000007643](http://purl.obolibrary.org/obo/PR_000007643) -- [Purkinje cell](http://purl.obolibrary.org/obo/CL_0000121) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "Purkinje's cell"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [GABAergic interneuron of the anterior substantia nigra pars reticulata](http://purl.obolibrary.org/obo/CL_4042026) SubClassOf [RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000013047](http://purl.obolibrary.org/obo/PR_000013047) -- [Purkinje cell](http://purl.obolibrary.org/obo/CL_0000121) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "The output neuron of the cerebellar cortex."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D011689"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [GABAergic interneuron of the anterior substantia nigra pars reticulata](http://purl.obolibrary.org/obo/CL_4042026) SubClassOf [neuron of the substantia nigra](http://purl.obolibrary.org/obo/CL_0002614) -- [Purkinje cell](http://purl.obolibrary.org/obo/CL_0000121) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cerebellar Purkinje cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [Purkinje cell](http://purl.obolibrary.org/obo/CL_0000121) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "Purkinje neuron"^^[string](http://www.w3.org/2001/XMLSchema#string) +### GABAergic interneuron of the posterior substantia nigra pars reticulata `http://purl.obolibrary.org/obo/CL_4042027` #### Added -- [Purkinje cell](http://purl.obolibrary.org/obo/CL_0000121) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cerebellar Purkinje cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.1016/j.proghi.2004.07.002"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [GABAergic interneuron of the posterior substantia nigra pars reticulata](http://purl.obolibrary.org/obo/CL_4042027) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042027"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [Purkinje cell](http://purl.obolibrary.org/obo/CL_0000121) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An inhibitory neuron and the sole output neuron of the cerebellar cortex, the Purkinje cell's soma is located between the granular and molecular layers of the cerebellum. It is one of the largest neural cells in the mammalian brain, ranging from 50 to 80 micrometres in diameter. Purkinje cells have planar, fan-shaped dendrites that branch extensively with little overlap. This cell type receives synaptic input from parallel fibres, which modulate high-frequency spike activity known as "simple spikes," and climbing fibres, which modulate infrequent calcium spike activity known as "complex spikes". Purkinje cells are involved in motor coordination, particularly in correcting movements in progress."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:12907269"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [GABAergic interneuron of the posterior substantia nigra pars reticulata](http://purl.obolibrary.org/obo/CL_4042027) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A GABAergic interneuron that has its soma in the posterior section of the substantia nigra pars reticulata. This GABAergic interneuron is characterised by the expression of the transcription factors Pax5, Ctip2 and Pou6f2 and it develops from the ventrolateral r1 neuroepithelium expresing NKX61."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36148148"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33288911"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [GABAergic interneuron of the posterior substantia nigra pars reticulata](http://purl.obolibrary.org/obo/CL_4042027) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:14568361"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [GABAergic interneuron of the posterior substantia nigra pars reticulata](http://purl.obolibrary.org/obo/CL_4042027) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pSNpr"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36148148"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31424738"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [GABAergic interneuron of the posterior substantia nigra pars reticulata](http://purl.obolibrary.org/obo/CL_4042027) [date](http://purl.org/dc/terms/date) "2024-09-23T14:49:11Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D011689"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [GABAergic interneuron of the posterior substantia nigra pars reticulata](http://purl.obolibrary.org/obo/CL_4042027) [label](http://www.w3.org/2000/01/rdf-schema#label) "GABAergic interneuron of the posterior substantia nigra pars reticulata"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:38168772"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [GABAergic interneuron of the posterior substantia nigra pars reticulata](http://purl.obolibrary.org/obo/CL_4042027) -- [Purkinje cell](http://purl.obolibrary.org/obo/CL_0000121) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Neurodegenerative disorders affecting Purkinje cells disrupt motor functions. Some of the neurodegenerative disorders that causes loss and degeration of Purkinje cells are Spinocerebellar ataxias (SCAs) (Josef P Kapfhammer and Etsuko Shimobayashi 2023), Friedreich's ataxia (FRDA) (Kevin C Kemp et al., 2016), Fetal alcohol syndrome (Laurent Servais et al., 2016), Dandy-Walker malformation (Alexander Atamian et al., 2024)."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:17535929"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [GABAergic interneuron of the posterior substantia nigra pars reticulata](http://purl.obolibrary.org/obo/CL_4042027) SubClassOf [neuron of the substantia nigra](http://purl.obolibrary.org/obo/CL_0002614) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27215193"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [GABAergic interneuron of the posterior substantia nigra pars reticulata](http://purl.obolibrary.org/obo/CL_4042027) SubClassOf [RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000001903](http://purl.obolibrary.org/obo/PR_000001903) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.1016/j.stem.2023.11.013"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37426070"^^[string](http://www.w3.org/2001/XMLSchema#string) +### GO_0000768 `http://purl.obolibrary.org/obo/GO_0000768` -- [Purkinje cell](http://purl.obolibrary.org/obo/CL_0000121) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009071"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- Class: [GO_0000768](http://purl.obolibrary.org/obo/GO_0000768) -- [Purkinje cell](http://purl.obolibrary.org/obo/CL_0000121) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "Purkinje neuron"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:28821816"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [Purkinje cell](http://purl.obolibrary.org/obo/CL_0000121) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "PC"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) +### GO_0036376 `http://purl.obolibrary.org/obo/GO_0036376` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:38168772"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- Class: [GO_0036376](http://purl.obolibrary.org/obo/GO_0036376) -- [Purkinje cell](http://purl.obolibrary.org/obo/CL_0000121) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "PN"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:28821816"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) +### GO_0050962 `http://purl.obolibrary.org/obo/GO_0050962` +#### Removed +- Class: [GO_0050962](http://purl.obolibrary.org/obo/GO_0050962) -### R1 photoreceptor cell `http://purl.obolibrary.org/obo/CL_0000687` -#### Removed -- [R1 photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000687) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004213"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +### GO_1990573 `http://purl.obolibrary.org/obo/GO_1990573` #### Added -- [R1 photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000687) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004213"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [GO_1990573](http://purl.obolibrary.org/obo/GO_1990573) -### R2 photoreceptor cell `http://purl.obolibrary.org/obo/CL_0000690` -#### Removed -- [R2 photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000690) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004215"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +### GlyA-positive erythrocyte `http://purl.obolibrary.org/obo/CL_0002021` #### Added -- [R2 photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000690) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004215"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [GlyA-positive erythrocyte](http://purl.obolibrary.org/obo/CL_0002021) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### R3 photoreceptor cell `http://purl.obolibrary.org/obo/CL_0000694` -#### Removed -- [R3 photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000694) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004217"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +### ILC1, human `http://purl.obolibrary.org/obo/CL_0001077` #### Added -- [R3 photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000694) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004217"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [ILC1, human](http://purl.obolibrary.org/obo/CL_0001077) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### R4 photoreceptor cell `http://purl.obolibrary.org/obo/CL_0000697` -#### Removed -- [R4 photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000697) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004219"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +### Kit and Sca1-positive hematopoietic stem cell `http://purl.obolibrary.org/obo/CL_0001008` #### Added -- [R4 photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000697) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004219"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [Kit and Sca1-positive hematopoietic stem cell](http://purl.obolibrary.org/obo/CL_0001008) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### R5 photoreceptor cell `http://purl.obolibrary.org/obo/CL_0000702` -#### Removed -- [R5 photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000702) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004221"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +### Kit-negative, Ly-76 high orthochromatophilic erythroblasts `http://purl.obolibrary.org/obo/CL_0002017` #### Added -- [R5 photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000702) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004221"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [Kit-negative, Ly-76 high orthochromatophilic erythroblasts](http://purl.obolibrary.org/obo/CL_0002017) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### R6 photoreceptor cell `http://purl.obolibrary.org/obo/CL_0000705` -#### Removed -- [R6 photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000705) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004223"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +### Kit-positive macrophage dendritic cell progenitor `http://purl.obolibrary.org/obo/CL_0002011` #### Added -- [R6 photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000705) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004223"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [Kit-positive macrophage dendritic cell progenitor](http://purl.obolibrary.org/obo/CL_0002011) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### R7 photoreceptor cell `http://purl.obolibrary.org/obo/CL_0000707` -#### Removed -- [R7 photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000707) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004225"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +### Kit-positive megakaryocyte progenitor cell `http://purl.obolibrary.org/obo/CL_0002024` #### Added -- [R7 photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000707) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004225"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [Kit-positive megakaryocyte progenitor cell](http://purl.obolibrary.org/obo/CL_0002024) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### R8 photoreceptor cell `http://purl.obolibrary.org/obo/CL_0000709` -#### Removed -- [R8 photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000709) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004227"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +### Kit-positive, CD34-negative megakaryocyte erythroid progenitor cell `http://purl.obolibrary.org/obo/CL_0002006` #### Added -- [R8 photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000709) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004227"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [Kit-positive, CD34-negative megakaryocyte erythroid progenitor cell](http://purl.obolibrary.org/obo/CL_0002006) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### Rohon-Beard neuron `http://purl.obolibrary.org/obo/CL_0000247` -#### Removed -- [Rohon-Beard neuron](http://purl.obolibrary.org/obo/CL_0000247) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009150"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### Kit-positive, Sca1-positive common lymphoid progenitor `http://purl.obolibrary.org/obo/CL_0001025` #### Added -- [Rohon-Beard neuron](http://purl.obolibrary.org/obo/CL_0000247) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009150"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [Kit-positive, Sca1-positive common lymphoid progenitor](http://purl.obolibrary.org/obo/CL_0001025) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### Schwann cell `http://purl.obolibrary.org/obo/CL_0002573` +### Kupffer cell `http://purl.obolibrary.org/obo/CL_0000091` #### Added -- [Schwann cell](http://purl.obolibrary.org/obo/CL_0002573) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "neurolemmocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32119275"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [Kupffer cell](http://purl.obolibrary.org/obo/CL_0000091) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000091"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:38638689"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [Kupffer cell](http://purl.obolibrary.org/obo/CL_0000091) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +Kupffer cells are tissue-resident macrophages located in the liver. They are an integral part of the mononuclear phagocyte system and are responsible for the phagocytosis of dead or dying cells, microbes, and other foreign substances. Kupffer cells account for approximately 80-90% of tissue-resident macrophages in the body. They are found within the lumen of liver sinusoids and interface with microbial populations and products. +The primary role of Kupffer cells is to maintain homeostasis in the liver. They continuously filter and cleanse the blood that flows through the liver, removing pathogens, endotoxins, particulate matter, aged and dysfunctional red blood cells, and miscellaneous waste products. These cells also play an important role in maintaining iron homeostasis. During the process of phagocytosis, Kupffer cells recycle iron from degraded red blood cells, which is then utilized in the formation of new erythrocytes. +Kupffer cells also play key roles in various immune responses and inflammatory processes. They secrete various types of cytokines and chemokines, which contribute to the activation and mobilization of other immune cells. They can also produce reactive oxygen species and nitric oxide, which have microbicidal actions. Although their activity is essential for host defense, excessive or prolonged activation of Kupffer cells may contribute to hepatic injury, inflammation, and fibrosis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nri.2017.11"^^[string](http://www.w3.org/2001/XMLSchema#string) -### Schwann cell precursor `http://purl.obolibrary.org/obo/CL_0002375` -#### Removed -- [Schwann cell precursor](http://purl.obolibrary.org/obo/CL_0002375) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A giioblast cell that develops from a migratory neural crest cell. The SCP is embedded among neurons (axons) with minimal extracellular spaces separating them from nerve cell membranes and has no basal lamina. In rodents SCPs are the only cells in the Schwann cell linage that expresses Cdh19."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/978-1-4939-1311-4_10"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [Schwann cell precursor](http://purl.obolibrary.org/obo/CL_0002375) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A glioblast cell that develops from a migratory neural crest cell. The SCP is embedded among neurons (axons) with minimal extracellular spaces separating them from nerve cell membranes and has no basal lamina. In rodents SCPs are the only cells in the Schwann cell linage that expresses Cdh19."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1478-3231.2006.01342.x"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/cphy.c120026"^^[string](http://www.w3.org/2001/XMLSchema#string) -### Sertoli cell `http://purl.obolibrary.org/obo/CL_0000216` -#### Removed -- [Sertoli cell](http://purl.obolibrary.org/obo/CL_0000216) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009133"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.immuni.2022.08.002"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [Kupffer cell](http://purl.obolibrary.org/obo/CL_0000091) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + + +### L cone cell `http://purl.obolibrary.org/obo/CL_0003048` #### Added -- [Sertoli cell](http://purl.obolibrary.org/obo/CL_0000216) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009133"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [L cone cell](http://purl.obolibrary.org/obo/CL_0003048) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### T cell `http://purl.obolibrary.org/obo/CL_0000084` +### L2/3/5 fan Martinotti sst GABAergic interneuron (Mmus) `http://purl.obolibrary.org/obo/CL_4023030` #### Removed -- [T cell](http://purl.obolibrary.org/obo/CL_0000084) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009046"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [L2/3/5 fan Martinotti sst GABAergic interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023030) SubClassOf [sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023017) #### Added -- [T cell](http://purl.obolibrary.org/obo/CL_0000084) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009046"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [L2/3/5 fan Martinotti sst GABAergic interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023030) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) +- [L2/3/5 fan Martinotti sst GABAergic interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023030) SubClassOf [cerebral cortex GABAergic interneuron](http://purl.obolibrary.org/obo/CL_0010011) -### UBERON_0000065 `http://purl.obolibrary.org/obo/UBERON_0000065` + +### L4 sst Martinotti interneuron (Mmus) `http://purl.obolibrary.org/obo/CL_4023031` #### Removed -- Class: [UBERON_0000065](http://purl.obolibrary.org/obo/UBERON_0000065) +- [L4 sst Martinotti interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023031) SubClassOf [sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023017) + +#### Added +- [L4 sst Martinotti interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023031) SubClassOf [cerebral cortex GABAergic interneuron](http://purl.obolibrary.org/obo/CL_0010011) +- [L4 sst Martinotti interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023031) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) -### UBERON_0000358 `http://purl.obolibrary.org/obo/UBERON_0000358` +### L5 extratelencephalic projecting glutamatergic cortical neuron `http://purl.obolibrary.org/obo/CL_4023041` #### Removed -- Class: [UBERON_0000358](http://purl.obolibrary.org/obo/UBERON_0000358) +- [L5 extratelencephalic projecting glutamatergic cortical neuron](http://purl.obolibrary.org/obo/CL_4023041) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A glutamatergic neuron, with a soma found in the deeper portion of L5, that has long-range axonal projections including deep subcortical targets outside of the telencephalon and, in some cases, the spinal cord. While the L5 ET neuron projections are not limited to ET targets, they are clearly differentiated from the neuron subclasses whose projections are constrained to intratelencephalic (IT) targets. L5 ET neurons are generally the largest excitatory cortical neurons, typically having a thick apical dendrite with a prominent dendritic tuft in layer 1 and displaying burst-firing physiological characteristics."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34616075"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [L5 extratelencephalic projecting glutamatergic cortical neuron](http://purl.obolibrary.org/obo/CL_4023041) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A transcriptomically distinct glutamatergic neuron, with a soma found in the deeper portion of L5, that has long-range axonal projections including deep subcortical targets outside of the telencephalon and, in some cases, the spinal cord. While the L5 ET neuron projections are not limited to ET targets, they are clearly differentiated from the neuron subclasses whose projections are constrained to intratelencephalic (IT) targets. L5 ET neurons are generally the largest excitatory cortical neurons, typically having a thick apical dendrite with a prominent dendritic tuft in layer 1 and displaying burst-firing physiological characteristics. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: Deep layer (non-IT) excitatory neurons ', Author Categories: 'CrossArea_subclass', clusters L5 ET."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34616075"^^[string](http://www.w3.org/2001/XMLSchema#string) -### UBERON_0000458 `http://purl.obolibrary.org/obo/UBERON_0000458` -#### Removed -- Class: [UBERON_0000458](http://purl.obolibrary.org/obo/UBERON_0000458) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/e/d01c9dff-abd1-4825-bf30-2eb2ba74597e.cxg/"^^[string](http://www.w3.org/2001/XMLSchema#string) -### UBERON_0001199 `http://purl.obolibrary.org/obo/UBERON_0001199` +### L5 non-Martinotti sst GABAergic interneuron (Mmus) `http://purl.obolibrary.org/obo/CL_4023028` #### Removed -- Class: [UBERON_0001199](http://purl.obolibrary.org/obo/UBERON_0001199) +- [L5 non-Martinotti sst GABAergic interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023028) SubClassOf [sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023017) + +#### Added +- [L5 non-Martinotti sst GABAergic interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023028) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) +- [L5 non-Martinotti sst GABAergic interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023028) SubClassOf [cerebral cortex GABAergic interneuron](http://purl.obolibrary.org/obo/CL_0010011) -### UBERON_0001557 `http://purl.obolibrary.org/obo/UBERON_0001557` +### L5 sst T-Martinotti interneuron (Mmus) `http://purl.obolibrary.org/obo/CL_4023027` #### Removed -- Class: [UBERON_0001557](http://purl.obolibrary.org/obo/UBERON_0001557) +- [L5 sst T-Martinotti interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023027) SubClassOf [sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023017) + +#### Added +- [L5 sst T-Martinotti interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023027) SubClassOf [cerebral cortex GABAergic interneuron](http://purl.obolibrary.org/obo/CL_0010011) +- [L5 sst T-Martinotti interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023027) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) -### UBERON_0001558 `http://purl.obolibrary.org/obo/UBERON_0001558` +### L5/6 near-projecting glutamatergic neuron of the primary motor cortex `http://purl.obolibrary.org/obo/CL_4023043` #### Removed -- Class: [UBERON_0001558](http://purl.obolibrary.org/obo/UBERON_0001558) +- [L5/6 near-projecting glutamatergic neuron of the primary motor cortex](http://purl.obolibrary.org/obo/CL_4023043) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A near-projecting glutamatergic neuron with a soma found in layer 5/6 of the primary motor cortex."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31209381"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34616075"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [L5/6 near-projecting glutamatergic neuron of the primary motor cortex](http://purl.obolibrary.org/obo/CL_4023043) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A transcriptomically distinct near-projecting glutamatergic neuron with a soma found in layer 5/6 of the primary motor cortex. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: Deep layer (non-IT) excitatory neurons', Author Categories: 'CrossArea_subclass', cluster L5/6 NP."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31209381"^^[string](http://www.w3.org/2001/XMLSchema#string) -### UBERON_0002051 `http://purl.obolibrary.org/obo/UBERON_0002051` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34616075"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- Class: [UBERON_0002051](http://purl.obolibrary.org/obo/UBERON_0002051) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/e/d01c9dff-abd1-4825-bf30-2eb2ba74597e.cxg/"^^[string](http://www.w3.org/2001/XMLSchema#string) -### UBERON_0003889 `http://purl.obolibrary.org/obo/UBERON_0003889` +### L5/6 non-Martinotti sst GABAergic interneuron (Mmus) `http://purl.obolibrary.org/obo/CL_4023118` +#### Removed +- [L5/6 non-Martinotti sst GABAergic interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023118) SubClassOf [sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023017) #### Added -- Class: [UBERON_0003889](http://purl.obolibrary.org/obo/UBERON_0003889) +- [L5/6 non-Martinotti sst GABAergic interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023118) SubClassOf [cerebral cortex GABAergic interneuron](http://purl.obolibrary.org/obo/CL_0010011) +- [L5/6 non-Martinotti sst GABAergic interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023118) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) -### UBERON_0004196 `http://purl.obolibrary.org/obo/UBERON_0004196` - -#### Added -- Class: [UBERON_0004196](http://purl.obolibrary.org/obo/UBERON_0004196) +### L6 corticothalamic-projecting glutamatergic cortical neuron `http://purl.obolibrary.org/obo/CL_4023042` +#### Removed +- [L6 corticothalamic-projecting glutamatergic cortical neuron](http://purl.obolibrary.org/obo/CL_4023042) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A corticothalamic-projecting neuron with a soma found in cortical layer 6."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34616075"^^[string](http://www.w3.org/2001/XMLSchema#string) -### UBERON_0004197 `http://purl.obolibrary.org/obo/UBERON_0004197` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- Class: [UBERON_0004197](http://purl.obolibrary.org/obo/UBERON_0004197) +- [L6 corticothalamic-projecting glutamatergic cortical neuron](http://purl.obolibrary.org/obo/CL_4023042) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A transcriptomically distinct corticothalamic-projecting neuron with a soma found in cortical layer 6. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: Deep layer (non-IT) excitatory neurons', Author Categories: 'CrossArea_subclass', clusters L6 CT."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34616075"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/e/d01c9dff-abd1-4825-bf30-2eb2ba74597e.cxg/"^^[string](http://www.w3.org/2001/XMLSchema#string) -### UBERON_0004814 `http://purl.obolibrary.org/obo/UBERON_0004814` + +### L6 th sst GABAergic interneuron (Mmus) `http://purl.obolibrary.org/obo/CL_4023075` +#### Removed +- [L6 th sst GABAergic interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023075) SubClassOf [sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023017) #### Added -- Class: [UBERON_0004814](http://purl.obolibrary.org/obo/UBERON_0004814) +- [L6 th sst GABAergic interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023075) SubClassOf [cerebral cortex GABAergic interneuron](http://purl.obolibrary.org/obo/CL_0010011) +- [L6 th sst GABAergic interneuron (Mmus)](http://purl.obolibrary.org/obo/CL_4023075) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) -### UBERON_0004815 `http://purl.obolibrary.org/obo/UBERON_0004815` -#### Added -- Class: [UBERON_0004815](http://purl.obolibrary.org/obo/UBERON_0004815) +### L6b glutamatergic cortical neuron `http://purl.obolibrary.org/obo/CL_4023038` +#### Removed +- [L6b glutamatergic cortical neuron](http://purl.obolibrary.org/obo/CL_4023038) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A glutamatergic neuron with a soma found in cortical layer 6b. They are transcriptomically related to corticothalamic-projecting neurons but have differential projections to the thalamus or anterior cingulate."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30382198"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) -### UBERON_0004903 `http://purl.obolibrary.org/obo/UBERON_0004903` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1101/2020.10.19.34312"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- Class: [UBERON_0004903](http://purl.obolibrary.org/obo/UBERON_0004903) +- [L6b glutamatergic cortical neuron](http://purl.obolibrary.org/obo/CL_4023038) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/cl/cl-base#human_reference_atlas) +- [L6b glutamatergic cortical neuron](http://purl.obolibrary.org/obo/CL_4023038) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A glutamatergic neuron with a soma found in cortical layer 6b. They are transcriptomically related to corticothalamic-projecting neurons but have differential projections to the thalamus or anterior cingulate. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: Deep layer (non-IT) excitatory neuron', Author Categories: 'CrossArea_subclass', cluster L6b."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30382198"^^[string](http://www.w3.org/2001/XMLSchema#string) -### UBERON_0005272 `http://purl.obolibrary.org/obo/UBERON_0005272` -#### Removed -- Class: [UBERON_0005272](http://purl.obolibrary.org/obo/UBERON_0005272) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1101/2020.10.19.34312"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/e/d01c9dff-abd1-4825-bf30-2eb2ba74597e.cxg/"^^[string](http://www.w3.org/2001/XMLSchema#string) -### UBERON_0006955 `http://purl.obolibrary.org/obo/UBERON_0006955` +- [L6b glutamatergic cortical neuron](http://purl.obolibrary.org/obo/CL_4023038) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) -#### Added -- Class: [UBERON_0006955](http://purl.obolibrary.org/obo/UBERON_0006955) + +### Lamp5 Lhx6 neuron `http://purl.obolibrary.org/obo/CL_4042013` +#### Removed +- [Lamp5 Lhx6 neuron](http://purl.obolibrary.org/obo/CL_4042013) SubClassOf [lamp5 GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023011) -### UBERON_0008397 `http://purl.obolibrary.org/obo/UBERON_0008397` + +### Leydig cell `http://purl.obolibrary.org/obo/CL_0000178` #### Added -- Class: [UBERON_0008397](http://purl.obolibrary.org/obo/UBERON_0008397) +- [Leydig cell](http://purl.obolibrary.org/obo/CL_0000178) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +Leydig cells are a testosterone-secreting cell in the interstitial area in the testes of males. They are named after Franz Leydig, a German anatomist who discovered these cells in 1850. Uniquely situated within the soft connective tissue surrounding the seminiferous tubules, Leydig cells form an integral part of the male reproductive system. They are usually polygonal cells characterized by well developed smooth endoplasmic reticulum, high lipid content and a large round nucleus. They are found across mammalian species, including humans. +The primary function of Leydig cells is the production of androgens, the male sex hormones, the most notable of which is testosterone. Leydig cells synthesize testosterone from cholesterol through a series of enzymatic reactions. The production and release of testosterone are mainly regulated by the luteinizing hormone (LH) released by the anterior pituitary gland. In response to LH, Leydig cells convert cholesterol into testosterone, which then plays a crucial role in the development and maintenance of primary and secondary male sexual characteristics. These include the formation and maturation of male reproductive organs, onset of spermatogenesis, and the presentation of male secondary sexual traits such as the deepening of the voice, growth of facial hair, development of muscles, and a broadening of shoulders. +Apart from testosterone production, Leydig cells also secrete insulin-like factor 3 (INSL3) that is essential for testicular descent during embryonic development in males. Dysregulation or loss of Leydig cells can lead to numerous conditions like testosterone deficiency, infertility, and certain forms of testicular cancer. Although not typical, Leydig cells can regenerate if they are damaged, ensuring the continuous production of testosterone and maintaining male reproductive health. They provide an excellent model to study cell differentiation and hormone regulation, thereby enhancing our understanding of reproductive biology and associated disorders."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1093/biolre/ioy059"^^[string](http://www.w3.org/2001/XMLSchema#string) -### UBERON_0011148 `http://purl.obolibrary.org/obo/UBERON_0011148` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1210/clinem/dgaa603"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- Class: [UBERON_0011148](http://purl.obolibrary.org/obo/UBERON_0011148) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK556007/#:~:text=Leydig%20cells%20are%20the%20primary,secondary%20sexual%20characteristics%20and%20behaviors."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.coemr.2019.03.001"^^[string](http://www.w3.org/2001/XMLSchema#string) -### UBERON_0012251 `http://purl.obolibrary.org/obo/UBERON_0012251` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fendo.2014.00006"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- Class: [UBERON_0012251](http://purl.obolibrary.org/obo/UBERON_0012251) +- [Leydig cell](http://purl.obolibrary.org/obo/CL_0000178) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000178"^^[string](http://www.w3.org/2001/XMLSchema#string) -### UBERON_0012252 `http://purl.obolibrary.org/obo/UBERON_0012252` +### Ly-76 high positive erythrocyte `http://purl.obolibrary.org/obo/CL_0002022` #### Added -- Class: [UBERON_0012252](http://purl.obolibrary.org/obo/UBERON_0012252) +- [Ly-76 high positive erythrocyte](http://purl.obolibrary.org/obo/CL_0002022) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### UBERON_8850000 `http://purl.obolibrary.org/obo/UBERON_8850000` +### M cell of gut `http://purl.obolibrary.org/obo/CL_0000682` #### Added -- Class: [UBERON_8850000](http://purl.obolibrary.org/obo/UBERON_8850000) +- [M cell of gut](http://purl.obolibrary.org/obo/CL_0000682) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000682"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [M cell of gut](http://purl.obolibrary.org/obo/CL_0000682) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -### UV sensitive photoreceptor cell `http://purl.obolibrary.org/obo/CL_0000494` -#### Removed -- [UV sensitive photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000494) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009221"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +M cells, or microfold cells, of the gut are specialized epithelial cells found in the lining of the gut, specifically in the follicle-associated epithelium of mucosa-associated lymphoid tissue, where they function as sentries against toxins and pathogens. M cells are characterized by apical microfolds (hence their alternate name) which express unique adhesion molecules that enable them to sample the luminal macromolecules. +Other morphological features that distinguish M cells from other intestinal mucosal cells include sparse microvilli and a reduced thickness of the glycocalyx, which permits adhesion while not hindering the transport of molecules. They also have unique intraepithelial invaginations on the basolateral side which are filled with macrophages and other immune cells that can process the engulfed macromolecules quickly. +These morphological characteristics enable M cells to serve a dual role in immune responses. They initiate the immune response by transporting antigens (such as toxic or pathogenic substances) across the epithelial layer to lymphocytes and antigen-presenting cells in the underlying lymphoid tissue. This specialized transport process is called 'transcytosis.' They also have specialized molecules like glycoprotein-2 for bacterial uptake. Simultaneously, M cells help maintain immune tolerance to food antigens and commensal bacteria, preventing unnecessary reactions to non-pathogenic substances and hypersensitivity conditions. While these functions are crucial for well-being, M cell dysfunction can lead to serious conditions like Crohn's disease and other inflammatory bowel diseases."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nature08529"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [UV sensitive photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000494) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009221"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1093/jb/mvv121"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1136/gut.47.5.735"^^[string](http://www.w3.org/2001/XMLSchema#string) -### VIP GABAergic cortical interneuron `http://purl.obolibrary.org/obo/CL_4023016` -#### Removed -- [VIP GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023016) [label](http://www.w3.org/2000/01/rdf-schema#label) "vip GABAergic cortical interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK534232/"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [VIP GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023016) [IAO_0000028](http://purl.obolibrary.org/obo/IAO_0000028) "vip cortical interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/medicine-and-dentistry/microfold-cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [VIP GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023016) SubClassOf [cerebral cortex GABAergic interneuron](http://purl.obolibrary.org/obo/CL_0010011) -- [VIP GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023016) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) +### M cone cell `http://purl.obolibrary.org/obo/CL_0003049` #### Added -- [VIP GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023016) [IAO_0000028](http://purl.obolibrary.org/obo/IAO_0000028) "VIP cortical interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [M cone cell](http://purl.obolibrary.org/obo/CL_0003049) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) + -- [VIP GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023016) [label](http://www.w3.org/2000/01/rdf-schema#label) "VIP GABAergic cortical interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) +### Malpighian tubule stellate cell `http://purl.obolibrary.org/obo/CL_1000155` -- [VIP GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023016) SubClassOf [caudal ganglionic eminence derived interneuron](http://purl.obolibrary.org/obo/CL_4023064) +#### Added +- [Malpighian tubule stellate cell](http://purl.obolibrary.org/obo/CL_1000155) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### VIP-ChAT interneuron `http://purl.obolibrary.org/obo/CL_4042015` +### NK1.1-positive natural killer cell, mouse `http://purl.obolibrary.org/obo/CL_0002438` #### Added -- [VIP-ChAT interneuron](http://purl.obolibrary.org/obo/CL_4042015) [date](http://purl.org/dc/terms/date) "2024-07-11T12:22:48Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) +- [NK1.1-positive natural killer cell, mouse](http://purl.obolibrary.org/obo/CL_0002438) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -- [VIP-ChAT interneuron](http://purl.obolibrary.org/obo/CL_4042015) [label](http://www.w3.org/2000/01/rdf-schema#label) "VIP-ChAT interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [VIP-ChAT interneuron](http://purl.obolibrary.org/obo/CL_4042015) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "VIP+/ChAT+ interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33301603"^^[string](http://www.w3.org/2001/XMLSchema#string) +### PATO_0010007 `http://purl.obolibrary.org/obo/PATO_0010007` -- [VIP-ChAT interneuron](http://purl.obolibrary.org/obo/CL_4042015) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Work in the mouse barrel cortex and somatosensory cortex shows that a VIP-ChAT interneuron is predominantely located in L2/3 and more rarely in the deeper layers of the cortex (Dudai et al., 2021; Dudai et al., 2020). This neuronal type could be transcriptomically distinct as transcriptomic studies have identified VIP neurons expressing ChAT in a whole brain mouse transcriptomic study (Tasic et al., 2018)."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33301603"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- Class: [PATO_0010007](http://purl.obolibrary.org/obo/PATO_0010007) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30382198"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32027647"^^[string](http://www.w3.org/2001/XMLSchema#string) +### PP cell `http://purl.obolibrary.org/obo/CL_0000696` -- [VIP-ChAT interneuron](http://purl.obolibrary.org/obo/CL_4042015) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042015"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [PP cell](http://purl.obolibrary.org/obo/CL_0000696) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -- [VIP-ChAT interneuron](http://purl.obolibrary.org/obo/CL_4042015) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "VChI"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) +PP cells, also known as pancreatic polypeptide cells (and previously called F cells or gamma cells), are enteroendocrine cells predominantly found in the islets of Langerhans in the head of the pancreas. They are one of the four main endocrine cell types present in the pancreatic islets, along with type A, B and D cells. PP cells are notable for their production of pancreatic polypeptide, an anorexigenic hormone that modulates food intake and energy homeostasis. +By secreting pancreatic polypeptide, PP cells play a significant role in the management of both digestive and appetite regulation. Upon ingestion of food, there is a significant increase in the secretion of pancreatic polypeptide, which then reduces biliary secretion and helps slow down the movement of food through the digestive tract. This allows more time for digestion to take place and nutrients to be absorbed, promoting the efficient use of dietary intake. The pancreatic polypeptide further reduces appetite by interacting with the hypothalamus, the area of the brain responsible for control of hunger. +Given their important role in digestion, malfunction or damage to PP cells can lead to a disturbance in the digestive process and contribute to some disease conditions. For example, an overproduction of pancreatic polypeptide can result in conditions such as pancreatic tumors and diabetes. Conversely, an under secretion might contribute to obesity due to impaired dietary control. Furthermore, PP cells may also play a role in the body's energy balance, suggesting their implication in conditions related to energy metabolism."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1210/jc.2003-030630"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32027647"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.mce.2015.06.028"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [VIP-ChAT interneuron](http://purl.obolibrary.org/obo/CL_4042015) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.febslet.2014.07.005"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [VIP-ChAT interneuron](http://purl.obolibrary.org/obo/CL_4042015) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A VIP GABAergic cortical interneuron expressing vasoactive intestinal polypeptide and choline acetyltransferase in the Mmus neocortex. This interneuron releases both γ-aminobutyric acid and acetylcholine."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33301603"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1369/00221554155835"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30382198"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41580-020-00317-7"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32027647"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [PP cell](http://purl.obolibrary.org/obo/CL_0000696) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000696"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31754098"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [VIP-ChAT interneuron](http://purl.obolibrary.org/obo/CL_4042015) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "VIP/ChAT interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32027647"^^[string](http://www.w3.org/2001/XMLSchema#string) +### PR_000007479 `http://purl.obolibrary.org/obo/PR_000007479` -- [VIP-ChAT interneuron](http://purl.obolibrary.org/obo/CL_4042015) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "VIP+/ChAT+ cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33301603"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- Class: [PR_000007479](http://purl.obolibrary.org/obo/PR_000007479) -- Class: [VIP-ChAT interneuron](http://purl.obolibrary.org/obo/CL_4042015) -- [VIP-ChAT interneuron](http://purl.obolibrary.org/obo/CL_4042015) SubClassOf [cholinergic neuron](http://purl.obolibrary.org/obo/CL_0000108) +### PR_000007489 `http://purl.obolibrary.org/obo/PR_000007489` +#### Added +- Class: [PR_000007489](http://purl.obolibrary.org/obo/PR_000007489) -### absorptive cell `http://purl.obolibrary.org/obo/CL_0000212` -#### Removed -- [absorptive cell](http://purl.obolibrary.org/obo/CL_0000212) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009129"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +### PR_000007643 `http://purl.obolibrary.org/obo/PR_000007643` #### Added -- [absorptive cell](http://purl.obolibrary.org/obo/CL_0000212) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009129"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [PR_000007643](http://purl.obolibrary.org/obo/PR_000007643) -### acinar cell `http://purl.obolibrary.org/obo/CL_0000622` -#### Removed -- [acinar cell](http://purl.obolibrary.org/obo/CL_0000622) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009277"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### PR_000010529 `http://purl.obolibrary.org/obo/PR_000010529` #### Added -- [acinar cell](http://purl.obolibrary.org/obo/CL_0000622) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009277"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [PR_000010529](http://purl.obolibrary.org/obo/PR_000010529) -### adaxial cell `http://purl.obolibrary.org/obo/CL_0007016` -#### Removed -- [adaxial cell](http://purl.obolibrary.org/obo/CL_0007016) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0000003"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### PR_000013047 `http://purl.obolibrary.org/obo/PR_000013047` #### Added -- [adaxial cell](http://purl.obolibrary.org/obo/CL_0007016) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0000003"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [PR_000013047](http://purl.obolibrary.org/obo/PR_000013047) -### added_for_HCA `http://purl.obolibrary.org/obo/cl/cl-base#added_for_HCA` +### PR_000013433 `http://purl.obolibrary.org/obo/PR_000013433` #### Added -- [added_for_HCA](http://purl.obolibrary.org/obo/cl/cl-base#added_for_HCA) [comment](http://www.w3.org/2000/01/rdf-schema#comment) ""^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [PR_000013433](http://purl.obolibrary.org/obo/PR_000013433) -- [added_for_HCA](http://purl.obolibrary.org/obo/cl/cl-base#added_for_HCA) SubPropertyOf: [subset_property](http://www.geneontology.org/formats/oboInOwl#SubsetProperty) - -### adepithelial cell `http://purl.obolibrary.org/obo/CL_0000462` -#### Removed -- [adepithelial cell](http://purl.obolibrary.org/obo/CL_0000462) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00003219"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +### PR_000014419 `http://purl.obolibrary.org/obo/PR_000014419` #### Added -- [adepithelial cell](http://purl.obolibrary.org/obo/CL_0000462) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00003219"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [PR_000014419](http://purl.obolibrary.org/obo/PR_000014419) -### adipocyte `http://purl.obolibrary.org/obo/CL_0000136` -#### Removed -- [adipocyte](http://purl.obolibrary.org/obo/CL_0000136) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009082"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### PR_000014898 `http://purl.obolibrary.org/obo/PR_000014898` #### Added -- [adipocyte](http://purl.obolibrary.org/obo/CL_0000136) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009082"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [PR_000014898](http://purl.obolibrary.org/obo/PR_000014898) -### adipose microvascular endothelial cell `http://purl.obolibrary.org/obo/CL_2000072` -#### Removed -- [adipose microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000072) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +### Peyer's patch follicular dendritic cell `http://purl.obolibrary.org/obo/CL_0009015` #### Added -- [adipose microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000072) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [Peyer's patch follicular dendritic cell](http://purl.obolibrary.org/obo/CL_0009015) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### adrenal medulla chromaffin cell `http://purl.obolibrary.org/obo/CL_0000336` -#### Removed -- [adrenal medulla chromaffin cell](http://purl.obolibrary.org/obo/CL_0000336) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009167"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### Purkinje cell `http://purl.obolibrary.org/obo/CL_0000121` #### Added -- [adrenal medulla chromaffin cell](http://purl.obolibrary.org/obo/CL_0000336) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009167"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [Purkinje cell](http://purl.obolibrary.org/obo/CL_0000121) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000121"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [Purkinje cell](http://purl.obolibrary.org/obo/CL_0000121) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -### adrenergic neuron `http://purl.obolibrary.org/obo/CL_0000109` -#### Removed -- [adrenergic neuron](http://purl.obolibrary.org/obo/CL_0000109) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009061"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +Purkinje cells, named after the Czech anatomist Jan Evangelista Purkyně who discovered them, are unique inhibitory neurons in the cerebellar cortex. They are a critical part of the vertebrate nervous system as they provide the only signal output from the cortex to the cerebellar nuclei. They are one of the few types of neurons that are large enough to be seen with the naked eye. The most distinct hallmark of Purkinje cells is their elaborate dendritic arbor, which forms a broad and intricately branching structure resembling a tree. These numerous branches each receive excitatory synaptic inputs from more than 100,000 parallel fibers; in addition, a single climbing fiber makes hundreds of synapses to the soma and proximal dendrites. A single long axon forms an inhibitory projection to the cerebellar nuclei. +Purkinje cells play key roles in the coordination of fine, voluntary motor movements and balance. As the sole output of all motor coordination in the cerebellar cortex, they serve as a central relay in the cerebro-cerebellar loop. Each Purkinje cell receives two types of synaptic input: one from parallel fibers (which are axons of granule cells), and the other from climbing fibers (originating from the inferior olivary nucleus). The Purkinje cells process and integrate these diverse kinds of input signals to generate output that controls timing and coordination of movements. +Purkinje neurons show considerable synaptic plasticity. Throughout life, these cells continue to undergo long-term potentiation and depression at parallel fiber synapses, which cause long-lasting increase or decrease, respectively, of synaptic transmission and have been proposed as mechanisms for motor learning. +Purkinje cells are also known to be implicated in a variety of diseases. Their progressive loss is a prime feature in certain types of ataxia, a collective term used to describe conditions characterized by loss of muscular control and coordination. Furthermore, a significant reduction in the density of Purkinje cells has been reported in conditions such as autism and Huntington’s disease."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.7554/eLife.63668"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [adrenergic neuron](http://purl.obolibrary.org/obo/CL_0000109) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009061"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/purkinje-cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nrn3886"^^[string](http://www.w3.org/2001/XMLSchema#string) -### adrenocorticotropic hormone secreting cell `http://purl.obolibrary.org/obo/CL_0000467` -#### Removed -- [adrenocorticotropic hormone secreting cell](http://purl.obolibrary.org/obo/CL_0000467) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009216"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK545154/"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [adrenocorticotropic hormone secreting cell](http://purl.obolibrary.org/obo/CL_0000467) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009216"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s12311-018-0985-7"^^[string](http://www.w3.org/2001/XMLSchema#string) -### afferent neuron `http://purl.obolibrary.org/obo/CL_0000526` -#### Removed -- [afferent neuron](http://purl.obolibrary.org/obo/CL_0000526) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009238"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### Schwann cell `http://purl.obolibrary.org/obo/CL_0002573` #### Added -- [afferent neuron](http://purl.obolibrary.org/obo/CL_0000526) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009238"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [Schwann cell](http://purl.obolibrary.org/obo/CL_0002573) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002573"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [Schwann cell](http://purl.obolibrary.org/obo/CL_0002573) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -### alkali secreting cell `http://purl.obolibrary.org/obo/CL_0000435` -#### Removed -- [alkali secreting cell](http://purl.obolibrary.org/obo/CL_0000435) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009201"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +Schwann cells, also known as neurolemmocytes, are a type of glial cell located in the peripheral nervous system. These cells play a significant role in the healthy functioning of nerves by producing myelin, a fatty substance that forms a coating around nerve fibers. Myelin serves as an insulator and enhances the speed and efficiency of electrical nerve impulses; a single Schwann cell can myelinate a single axon. Myelination starts by the elongation and envelopment of the Schwann cell around the axon, followed by the synthesis and deposition of myelin layers. Some studies suggest that Schwann cells may regulate neuronal action potential, muscular contraction, and the sensitive response. +While Schwann cells are most commonly known for the formation of the myelin sheath, some Schwann cells do not form myelin: Remak Schwann cells, a class of nonmyelinating Schwann cells, ensheath axons with smaller diameter, such as C fiber nociceptors in sciatic nerves and form Remak bundles. +Schwann cells are found along both motor and sensory neurons and are crucial for the advancement and recovery of peripheral nerve injuries, due to their capacity to support nerve regeneration. In cases of nerve injury, Schwann cells play a vital role in recovery by initiating Wallerian degeneration, a process in which the part of the axon distal to the injury site degrades and is then cleared away. Following this, Schwann cells can guide the regrowth of the nerve, providing a conducive environment for axon regeneration. They remodel themselves into a regenerative phenotype, proliferate, and organize themselves into bands of Büngner that provide physical and chemical guidance for the regrowths of axons. This function of Schwann cells in the repair and regeneration of nervous system highlights their therapeutic potential in peripheral nerve injury treatments."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.biocel.2006.05.007"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [alkali secreting cell](http://purl.obolibrary.org/obo/CL_0000435) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009201"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/B978-0-444-52902-2.00005-9"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/glia.23892"^^[string](http://www.w3.org/2001/XMLSchema#string) -### alpha-beta T cell `http://purl.obolibrary.org/obo/CL_0000789` -#### Removed -- [alpha-beta T cell](http://purl.obolibrary.org/obo/CL_0000789) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009335"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1186/s13064-020-00140-y"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [alpha-beta T cell](http://purl.obolibrary.org/obo/CL_0000789) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009335"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1186/1742-2094-8-110"^^[string](http://www.w3.org/2001/XMLSchema#string) -### alveolar adventitial fibroblast `http://purl.obolibrary.org/obo/CL_4028006` +### Schwann cell precursor `http://purl.obolibrary.org/obo/CL_0002375` #### Removed -- [alveolar adventitial fibroblast](http://purl.obolibrary.org/obo/CL_4028006) [label](http://www.w3.org/2000/01/rdf-schema#label) "alveolar type 2 fibroblast cell"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [Schwann cell precursor](http://purl.obolibrary.org/obo/CL_0002375) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A glioblast cell that develops from a migratory neural crest cell. The SCP is embedded among neurons (axons) with minimal extracellular spaces separating them from nerve cell membranes and has no basal lamina. In rodents SCPs are the only cells in the Schwann cell linage that expresses Cdh19."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [Schwann cell precursor](http://purl.obolibrary.org/obo/CL_0002375) SubClassOf [glioblast](http://purl.obolibrary.org/obo/CL_0000030) #### Added -- [alveolar adventitial fibroblast](http://purl.obolibrary.org/obo/CL_4028006) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "AdvF"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [Schwann cell precursor](http://purl.obolibrary.org/obo/CL_0002375) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Schwann cell precursor are capable of differentiating into Schwann cells and other cell types such as melanocytes, neurons, and mesenchymal cells."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35815410"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [Schwann cell precursor](http://purl.obolibrary.org/obo/CL_0002375) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "SCP"^^[string](http://www.w3.org/2001/XMLSchema#string) - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33208946"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35815410"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [Schwann cell precursor](http://purl.obolibrary.org/obo/CL_0002375) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A multipotent progenitor cell that develops from a migratory neural crest cell. The schwann cell precursor is embedded among axons, with minimal extracellular space separating them from nerve cell membranes. This cell lacks a basal lamina, which distinguishes it from more mature Schwann cells. In rodents, cadherin-19 (Cdh19) serves as a specific marker for this developmental stage."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30971890"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [alveolar adventitial fibroblast](http://purl.obolibrary.org/obo/CL_4028006) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "alveolar type 2 fibroblast cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [alveolar adventitial fibroblast](http://purl.obolibrary.org/obo/CL_4028006) [label](http://www.w3.org/2000/01/rdf-schema#label) "alveolar adventitial fibroblast"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:15580626"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35815410"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [Schwann cell precursor](http://purl.obolibrary.org/obo/CL_0002375) SubClassOf [RO_0002387](http://purl.obolibrary.org/obo/RO_0002387) some [Schwann cell](http://purl.obolibrary.org/obo/CL_0002573) + +- [Schwann cell precursor](http://purl.obolibrary.org/obo/CL_0002375) SubClassOf [RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0001402](http://purl.obolibrary.org/obo/PATO_0001402) -### alveolar capillary type 1 endothelial cell `http://purl.obolibrary.org/obo/CL_4028002` -#### Removed -- [alveolar capillary type 1 endothelial cell](http://purl.obolibrary.org/obo/CL_4028002) SubClassOf [epithelial cell of alveolus of lung](http://purl.obolibrary.org/obo/CL_0010003) + +### TAC3-positive medium spiny neuron `http://purl.obolibrary.org/obo/CL_4042002` #### Added -- [alveolar capillary type 1 endothelial cell](http://purl.obolibrary.org/obo/CL_4028002) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002299](http://purl.obolibrary.org/obo/UBERON_0002299) +- [TAC3-positive medium spiny neuron](http://purl.obolibrary.org/obo/CL_4042002) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### alveolar capillary type 2 endothelial cell `http://purl.obolibrary.org/obo/CL_4028003` +### TAC3-positive striatal interneuron `http://purl.obolibrary.org/obo/CL_4042001` #### Removed -- [alveolar capillary type 2 endothelial cell](http://purl.obolibrary.org/obo/CL_4028003) SubClassOf [epithelial cell of alveolus of lung](http://purl.obolibrary.org/obo/CL_0010003) +- [TAC3-positive striatal interneuron](http://purl.obolibrary.org/obo/CL_4042001) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A GABAergic interneuron that has its soma located in the striatum and that has an enriched expression of the gene TAC3."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32999462"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34727523"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [alveolar capillary type 2 endothelial cell](http://purl.obolibrary.org/obo/CL_4028003) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002299](http://purl.obolibrary.org/obo/UBERON_0002299) +- [TAC3-positive striatal interneuron](http://purl.obolibrary.org/obo/CL_4042001) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A GABAergic interneuron that has its soma located in the striatum and that has an enriched expression of the genes TAC3 and LHX6."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32999462"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34727523"^^[string](http://www.w3.org/2001/XMLSchema#string) -### alveolar macrophage `http://purl.obolibrary.org/obo/CL_0000583` -#### Removed -- [alveolar macrophage](http://purl.obolibrary.org/obo/CL_0000583) EquivalentTo [tissue-resident macrophage](http://purl.obolibrary.org/obo/CL_0000864) and ([lacks_plasma_membrane_part](http://purl.obolibrary.org/obo/CL_4030046) some [PR_000001206](http://purl.obolibrary.org/obo/PR_000001206)) and ([RO_0001025](http://purl.obolibrary.org/obo/RO_0001025) some [UBERON_0002299](http://purl.obolibrary.org/obo/UBERON_0002299)) and ([RO_0002104](http://purl.obolibrary.org/obo/RO_0002104) some [PR_000001013](http://purl.obolibrary.org/obo/PR_000001013)) and ([RO_0002104](http://purl.obolibrary.org/obo/RO_0002104) some [PR_000001807](http://purl.obolibrary.org/obo/PR_000001807)) and ([RO_0002104](http://purl.obolibrary.org/obo/RO_0002104) some [PR_000001813](http://purl.obolibrary.org/obo/PR_000001813)) and ([RO_0002104](http://purl.obolibrary.org/obo/RO_0002104) some [PR_000001931](http://purl.obolibrary.org/obo/PR_000001931)) and ([RO_0002104](http://purl.obolibrary.org/obo/RO_0002104) some [PR_000002064](http://purl.obolibrary.org/obo/PR_000002064)) and ([RO_0002104](http://purl.obolibrary.org/obo/RO_0002104) some [PR_000002972](http://purl.obolibrary.org/obo/PR_000002972)) and ([RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0019882](http://purl.obolibrary.org/obo/GO_0019882)) and ([RO_0015016](http://purl.obolibrary.org/obo/RO_0015016) some [PR_000001012](http://purl.obolibrary.org/obo/PR_000001012)) +- [TAC3-positive striatal interneuron](http://purl.obolibrary.org/obo/CL_4042001) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -- [alveolar macrophage](http://purl.obolibrary.org/obo/CL_0000583) SubClassOf [RO_0001025](http://purl.obolibrary.org/obo/RO_0001025) some [UBERON_0002299](http://purl.obolibrary.org/obo/UBERON_0002299) + +### TCR-positive macrophage `http://purl.obolibrary.org/obo/CL_4030058` #### Added -- [alveolar macrophage](http://purl.obolibrary.org/obo/CL_0000583) EquivalentTo [tissue-resident macrophage](http://purl.obolibrary.org/obo/CL_0000864) and ([lacks_plasma_membrane_part](http://purl.obolibrary.org/obo/CL_4030046) some [PR_000001206](http://purl.obolibrary.org/obo/PR_000001206)) and ([RO_0001025](http://purl.obolibrary.org/obo/RO_0001025) some [UBERON_8850000](http://purl.obolibrary.org/obo/UBERON_8850000)) and ([RO_0002104](http://purl.obolibrary.org/obo/RO_0002104) some [PR_000001013](http://purl.obolibrary.org/obo/PR_000001013)) and ([RO_0002104](http://purl.obolibrary.org/obo/RO_0002104) some [PR_000001807](http://purl.obolibrary.org/obo/PR_000001807)) and ([RO_0002104](http://purl.obolibrary.org/obo/RO_0002104) some [PR_000001813](http://purl.obolibrary.org/obo/PR_000001813)) and ([RO_0002104](http://purl.obolibrary.org/obo/RO_0002104) some [PR_000001931](http://purl.obolibrary.org/obo/PR_000001931)) and ([RO_0002104](http://purl.obolibrary.org/obo/RO_0002104) some [PR_000002064](http://purl.obolibrary.org/obo/PR_000002064)) and ([RO_0002104](http://purl.obolibrary.org/obo/RO_0002104) some [PR_000002972](http://purl.obolibrary.org/obo/PR_000002972)) and ([RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0019882](http://purl.obolibrary.org/obo/GO_0019882)) and ([RO_0015016](http://purl.obolibrary.org/obo/RO_0015016) some [PR_000001012](http://purl.obolibrary.org/obo/PR_000001012)) +- [TCR-positive macrophage](http://purl.obolibrary.org/obo/CL_4030058) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -- [alveolar macrophage](http://purl.obolibrary.org/obo/CL_0000583) SubClassOf [RO_0001025](http://purl.obolibrary.org/obo/RO_0001025) some [UBERON_8850000](http://purl.obolibrary.org/obo/UBERON_8850000) +### UBERON_0001136 `http://purl.obolibrary.org/obo/UBERON_0001136` + +#### Added +- Class: [UBERON_0001136](http://purl.obolibrary.org/obo/UBERON_0001136) -### amacrine cell `http://purl.obolibrary.org/obo/CL_0000561` -#### Removed -- [amacrine cell](http://purl.obolibrary.org/obo/CL_0000561) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009255"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +### UBERON_0001243 `http://purl.obolibrary.org/obo/UBERON_0001243` #### Added -- [amacrine cell](http://purl.obolibrary.org/obo/CL_0000561) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009255"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [UBERON_0001243](http://purl.obolibrary.org/obo/UBERON_0001243) -### androgen secreting cell `http://purl.obolibrary.org/obo/CL_0000593` -#### Removed -- [androgen secreting cell](http://purl.obolibrary.org/obo/CL_0000593) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009271"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### UBERON_0002197 `http://purl.obolibrary.org/obo/UBERON_0002197` #### Added -- [androgen secreting cell](http://purl.obolibrary.org/obo/CL_0000593) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009271"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [UBERON_0002197](http://purl.obolibrary.org/obo/UBERON_0002197) -### angioblastic mesenchymal cell `http://purl.obolibrary.org/obo/CL_0000566` -#### Removed -- [angioblastic mesenchymal cell](http://purl.obolibrary.org/obo/CL_0000566) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009258"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### UBERON_0003981 `http://purl.obolibrary.org/obo/UBERON_0003981` #### Added -- [angioblastic mesenchymal cell](http://purl.obolibrary.org/obo/CL_0000566) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009258"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [UBERON_0003981](http://purl.obolibrary.org/obo/UBERON_0003981) -### anterior horn motor neuron `http://purl.obolibrary.org/obo/CL_2000048` -#### Removed -- [anterior horn motor neuron](http://purl.obolibrary.org/obo/CL_2000048) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +### UBERON_0004642 `http://purl.obolibrary.org/obo/UBERON_0004642` #### Added -- [anterior horn motor neuron](http://purl.obolibrary.org/obo/CL_2000048) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- Class: [UBERON_0004642](http://purl.obolibrary.org/obo/UBERON_0004642) -### anterior lateral line neuromast hair cell `http://purl.obolibrary.org/obo/CL_2000034` -#### Removed -- [anterior lateral line neuromast hair cell](http://purl.obolibrary.org/obo/CL_2000034) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +### UBERON_0004670 `http://purl.obolibrary.org/obo/UBERON_0004670` #### Added -- [anterior lateral line neuromast hair cell](http://purl.obolibrary.org/obo/CL_2000034) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- Class: [UBERON_0004670](http://purl.obolibrary.org/obo/UBERON_0004670) -### anterior lateral line neuromast mantle cell `http://purl.obolibrary.org/obo/CL_2000035` -#### Removed -- [anterior lateral line neuromast mantle cell](http://purl.obolibrary.org/obo/CL_2000035) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +### UBERON_0005357 `http://purl.obolibrary.org/obo/UBERON_0005357` #### Added -- [anterior lateral line neuromast mantle cell](http://purl.obolibrary.org/obo/CL_2000035) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- Class: [UBERON_0005357](http://purl.obolibrary.org/obo/UBERON_0005357) -### anterior lateral line neuromast supporting cell `http://purl.obolibrary.org/obo/CL_2000036` -#### Removed -- [anterior lateral line neuromast supporting cell](http://purl.obolibrary.org/obo/CL_2000036) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +### UBERON_0006250 `http://purl.obolibrary.org/obo/UBERON_0006250` #### Added -- [anterior lateral line neuromast supporting cell](http://purl.obolibrary.org/obo/CL_2000036) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- Class: [UBERON_0006250](http://purl.obolibrary.org/obo/UBERON_0006250) -### anterior visceral endoderm cell `http://purl.obolibrary.org/obo/CL_2000075` -#### Removed -- [anterior visceral endoderm cell](http://purl.obolibrary.org/obo/CL_2000075) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +### UBERON_0006914 `http://purl.obolibrary.org/obo/UBERON_0006914` #### Added -- [anterior visceral endoderm cell](http://purl.obolibrary.org/obo/CL_2000075) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- Class: [UBERON_0006914](http://purl.obolibrary.org/obo/UBERON_0006914) -### appendix goblet cell `http://purl.obolibrary.org/obo/CL_1000327` -#### Removed -- [appendix goblet cell](http://purl.obolibrary.org/obo/CL_1000327) SubClassOf [appendix glandular cell](http://purl.obolibrary.org/obo/CL_1001585) +### UBERON_0006915 `http://purl.obolibrary.org/obo/UBERON_0006915` #### Added -- [appendix goblet cell](http://purl.obolibrary.org/obo/CL_1000327) SubClassOf [epithelial cell of appendix](http://purl.obolibrary.org/obo/CL_1000405) +- Class: [UBERON_0006915](http://purl.obolibrary.org/obo/UBERON_0006915) -### arcuate artery endothelial cell `http://purl.obolibrary.org/obo/CL_1001213` -#### Removed -- [arcuate artery endothelial cell](http://purl.obolibrary.org/obo/CL_1001213) SubClassOf [endothelial cell of artery](http://purl.obolibrary.org/obo/CL_1000413) - - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) +### UBERON_0010077 `http://purl.obolibrary.org/obo/UBERON_0010077` #### Added -- [arcuate artery endothelial cell](http://purl.obolibrary.org/obo/CL_1001213) SubClassOf [endothelial cell of artery](http://purl.obolibrary.org/obo/CL_1000413) +- Class: [UBERON_0010077](http://purl.obolibrary.org/obo/UBERON_0010077) -### articular chondrocyte of knee joint `http://purl.obolibrary.org/obo/CL_2000007` -#### Removed -- [articular chondrocyte of knee joint](http://purl.obolibrary.org/obo/CL_2000007) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +### UBERON_0012186 `http://purl.obolibrary.org/obo/UBERON_0012186` #### Added -- [articular chondrocyte of knee joint](http://purl.obolibrary.org/obo/CL_2000007) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- Class: [UBERON_0012186](http://purl.obolibrary.org/obo/UBERON_0012186) -### astrocyte `http://purl.obolibrary.org/obo/CL_0000127` -#### Removed -- [astrocyte](http://purl.obolibrary.org/obo/CL_0000127) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009075"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### UBERON_0012375 `http://purl.obolibrary.org/obo/UBERON_0012375` #### Added -- [astrocyte](http://purl.obolibrary.org/obo/CL_0000127) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009075"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [UBERON_0012375](http://purl.obolibrary.org/obo/UBERON_0012375) -### auditory epithelial supporting cell `http://purl.obolibrary.org/obo/CL_0005014` -#### Removed -- [auditory epithelial supporting cell](http://purl.obolibrary.org/obo/CL_0005014) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005244"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### UBERON_0013739 `http://purl.obolibrary.org/obo/UBERON_0013739` #### Added -- [auditory epithelial supporting cell](http://purl.obolibrary.org/obo/CL_0005014) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005244"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [UBERON_0013739](http://purl.obolibrary.org/obo/UBERON_0013739) -### auditory hair cell `http://purl.obolibrary.org/obo/CL_0000202` -#### Removed -- [auditory hair cell](http://purl.obolibrary.org/obo/CL_0000202) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009121"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### UBERON_0013740 `http://purl.obolibrary.org/obo/UBERON_0013740` #### Added -- [auditory hair cell](http://purl.obolibrary.org/obo/CL_0000202) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009121"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [UBERON_0013740](http://purl.obolibrary.org/obo/UBERON_0013740) -### autonomic neuron `http://purl.obolibrary.org/obo/CL_0000107` -#### Removed -- [autonomic neuron](http://purl.obolibrary.org/obo/CL_0000107) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009059"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### UBERON_0014727 `http://purl.obolibrary.org/obo/UBERON_0014727` #### Added -- [autonomic neuron](http://purl.obolibrary.org/obo/CL_0000107) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009059"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [UBERON_0014727](http://purl.obolibrary.org/obo/UBERON_0014727) -### band form neutrophil `http://purl.obolibrary.org/obo/CL_0000560` -#### Removed -- [band form neutrophil](http://purl.obolibrary.org/obo/CL_0000560) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009254"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### UBERON_0014729 `http://purl.obolibrary.org/obo/UBERON_0014729` #### Added -- [band form neutrophil](http://purl.obolibrary.org/obo/CL_0000560) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009254"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [UBERON_0014729](http://purl.obolibrary.org/obo/UBERON_0014729) -### barrier cell `http://purl.obolibrary.org/obo/CL_0000215` -#### Removed -- [barrier cell](http://purl.obolibrary.org/obo/CL_0000215) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009132"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### UBERON_0015766 `http://purl.obolibrary.org/obo/UBERON_0015766` #### Added -- [barrier cell](http://purl.obolibrary.org/obo/CL_0000215) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009132"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [UBERON_0015766](http://purl.obolibrary.org/obo/UBERON_0015766) -### basal cell of epithelium of lobular bronchiole `http://purl.obolibrary.org/obo/CL_1000352` +### VIP GABAergic cortical interneuron `http://purl.obolibrary.org/obo/CL_4023016` #### Removed -- [basal cell of epithelium of lobular bronchiole](http://purl.obolibrary.org/obo/CL_1000352) SubClassOf [epithelial cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002202) +- [VIP GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023016) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A GABAergic neuron located in the cerebral cortex that expresses vasoactive intestinal polypeptide"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33186530"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [basal cell of epithelium of lobular bronchiole](http://purl.obolibrary.org/obo/CL_1000352) SubClassOf [epithelial cell of lung](http://purl.obolibrary.org/obo/CL_0000082) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [VIP GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023016) [description](http://purl.org/dc/terms/description) "This neuronal type is distinguished by its heterogeneous morphology and electrophysiological characteristics (Pronneke et al., 2015,2020; Apicella and Marchionni, 2022). Variations in morphology and firing patterns are observed in human cortical VIP interneurons. In a study by Lee et al., 2023, four distinct subtypes of VIP neurons were identified, each exhibiting unique morphologies, soma locations, and electrophysiological properties. These subtypes are defined according to their transcriptomic markers: LBH-VIP and CCD184-VIP, both of which display a bipolar morphology with axons and dendrites extending across cortical layers; and SY16-VIP and ADAMTSL1-VIP, characterized by a dendritic arbor that spreads horizontally within the same layer as the soma (Lee et al., 2023). Disruption or malfunction of VIP cortical interneuron is implicated in neurodevelopmental disorders such as Rett Syndrome and Dravet Syndrome (Goff and Goldberg 2021)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:26420784"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31210267"^^[string](http://www.w3.org/2001/XMLSchema#string) -### basal cell of epithelium of respiratory bronchiole `http://purl.obolibrary.org/obo/CL_1000351` -#### Removed -- [basal cell of epithelium of respiratory bronchiole](http://purl.obolibrary.org/obo/CL_1000351) SubClassOf [epithelial cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002202) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35221922"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [basal cell of epithelium of respiratory bronchiole](http://purl.obolibrary.org/obo/CL_1000351) SubClassOf [epithelial cell of lung](http://purl.obolibrary.org/obo/CL_0000082) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33794534"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [VIP GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023016) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A transcriptomically distinct cortical GABAergic neuron that expresses the vasocactive intestinal polypeptide and that has its soma located in the cerebral cortex. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_subclass', cluster Vip."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/e/e4ddac12-f48f-4455-8e8d-c2a48a683437.cxg/"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33186530"^^[string](http://www.w3.org/2001/XMLSchema#string) -### basal cell of epithelium of terminal bronchiole `http://purl.obolibrary.org/obo/CL_1000350` -#### Removed -- [basal cell of epithelium of terminal bronchiole](http://purl.obolibrary.org/obo/CL_1000350) SubClassOf [epithelial cell of lung](http://purl.obolibrary.org/obo/CL_0000082) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [basal cell of epithelium of terminal bronchiole](http://purl.obolibrary.org/obo/CL_1000350) SubClassOf [epithelial cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002202) +- [VIP GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023016) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "VIP-IN"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33794534"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [VIP GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023016) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cortical VIP neuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36384143"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [VIP GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023016) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "VIP-Expressing GABAergic Neuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35221922"^^[string](http://www.w3.org/2001/XMLSchema#string) -### basal cell of epithelium of trachea `http://purl.obolibrary.org/obo/CL_1000348` -#### Removed -- [basal cell of epithelium of trachea](http://purl.obolibrary.org/obo/CL_1000348) SubClassOf [tracheal epithelial cell](http://purl.obolibrary.org/obo/CL_0000307) +- [VIP GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023016) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "VIP neuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33108272"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [VIP GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023016) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "Vip GABAergic neuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ILX:0770151"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [VIP GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023016) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "VIP type"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) -### basal cell of olfactory epithelium `http://purl.obolibrary.org/obo/CL_0002169` +- [VIP GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023016) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "VIP interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33108272"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [basal cell of olfactory epithelium](http://purl.obolibrary.org/obo/CL_0002169) SubClassOf [epithelial cell of upper respiratory tract](http://purl.obolibrary.org/obo/CL_0002631) +- [VIP GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023016) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "Vip"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ILX:0770151"^^[string](http://www.w3.org/2001/XMLSchema#string) -### basket cell `http://purl.obolibrary.org/obo/CL_0000118` -#### Removed -- [basket cell](http://purl.obolibrary.org/obo/CL_0000118) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009068"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### acinar cell `http://purl.obolibrary.org/obo/CL_0000622` #### Added -- [basket cell](http://purl.obolibrary.org/obo/CL_0000118) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009068"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [acinar cell](http://purl.obolibrary.org/obo/CL_0000622) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000622"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [acinar cell](http://purl.obolibrary.org/obo/CL_0000622) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -### basophilic erythroblast `http://purl.obolibrary.org/obo/CL_0000549` -#### Removed -- [basophilic erythroblast](http://purl.obolibrary.org/obo/CL_0000549) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005236"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +Acinar cells are specialized exocrine gland cells that secrete specific enzymes and fluids to aid in digestion. Found primarily in the pancreas and salivary glands, the term acinar is derived from the Latin word 'acinus' which means 'grape'; this is because acinar cells are arranged in a grape-like cluster around small ducts, formulating an acinus structure. +In the salivary glands, acinar cells secrete digestive enzymes as well as other substances such as mucus and water. These secretions service the initial stages of the digestive process, preparing the consumed food for onward digestion in the stomach and intestines by lubricating and partially breaking it down. +In the pancreas, acinar cells are responsible for synthesizing and secreting a significant amount of digestive enzymes, such as trypsin, chymotrypsin, and amylase. These enzymes are stored in zymogen granules inside the acinar cells until they are dispatched into the small intestine. Once within the small intestine, they break down proteins, carbohydrates, and fats into substances that can be absorbed. This is vital to the effective and efficient digestion and absorption of nutrients from the food we consume. +Acinar cells have high protein synthesis rates and are susceptible to accumulation of misfolded proteins; the subsequential induction of ER stress is thought to be involved in the development of pancreatitis, a serious inflammatory disease of the exocrine pancreas."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/prd.12116"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [basophilic erythroblast](http://purl.obolibrary.org/obo/CL_0000549) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005236"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/physrev.00011.2011"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/BF00710764"^^[string](http://www.w3.org/2001/XMLSchema#string) -### biogenic amine secreting cell `http://purl.obolibrary.org/obo/CL_0000457` -#### Removed -- [biogenic amine secreting cell](http://purl.obolibrary.org/obo/CL_0000457) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009212"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1097/MOG.0b013e32832ebfac"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [biogenic amine secreting cell](http://purl.obolibrary.org/obo/CL_0000457) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009212"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nrgastro.2013.36"^^[string](http://www.w3.org/2001/XMLSchema#string) -### bipolar neuron `http://purl.obolibrary.org/obo/CL_0000103` +### adepithelial cell `http://purl.obolibrary.org/obo/CL_0000462` #### Removed -- [bipolar neuron](http://purl.obolibrary.org/obo/CL_0000103) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009055"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [adepithelial cell](http://purl.obolibrary.org/obo/CL_0000462) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) + +- [adepithelial cell](http://purl.obolibrary.org/obo/CL_0000462) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_50557](http://purl.obolibrary.org/obo/NCBITaxon_50557) #### Added -- [bipolar neuron](http://purl.obolibrary.org/obo/CL_0000103) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009055"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [adepithelial cell](http://purl.obolibrary.org/obo/CL_0000462) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_50557](http://purl.obolibrary.org/obo/NCBITaxon_50557) -### bladder microvascular endothelial cell `http://purl.obolibrary.org/obo/CL_2000040` -#### Removed -- [bladder microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000040) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +### adipose macrophage `http://purl.obolibrary.org/obo/CL_0002477` #### Added -- [bladder microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000040) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [adipose macrophage](http://purl.obolibrary.org/obo/CL_0002477) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### blastemal cell `http://purl.obolibrary.org/obo/CL_0000354` -#### Removed -- [blastemal cell](http://purl.obolibrary.org/obo/CL_0000354) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009178"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### alarm substance cell `http://purl.obolibrary.org/obo/CL_0007021` #### Added -- [blastemal cell](http://purl.obolibrary.org/obo/CL_0000354) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009178"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [alarm substance cell](http://purl.obolibrary.org/obo/CL_0007021) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### blastoderm cell `http://purl.obolibrary.org/obo/CL_0000353` -#### Removed -- [blastoderm cell](http://purl.obolibrary.org/obo/CL_0000353) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009177"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### alpha-beta T cell `http://purl.obolibrary.org/obo/CL_0000789` #### Added -- [blastoderm cell](http://purl.obolibrary.org/obo/CL_0000353) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009177"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [alpha-beta T cell](http://purl.obolibrary.org/obo/CL_0000789) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### blood cell `http://purl.obolibrary.org/obo/CL_0000081` -#### Removed -- [blood cell](http://purl.obolibrary.org/obo/CL_0000081) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009044"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### alpha1-tanycyte `http://purl.obolibrary.org/obo/CL_4042017` #### Added -- [blood cell](http://purl.obolibrary.org/obo/CL_0000081) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009044"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [alpha1-tanycyte](http://purl.obolibrary.org/obo/CL_4042017) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042017"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [alpha1-tanycyte](http://purl.obolibrary.org/obo/CL_4042017) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A tanycyte cell found in the ventromedial and dorsomedial nuclei of the hypothalamus. This type of tanycyte extends its protrusions close to parenchymal neurons without contacting blood vessels. It expresses the glial marker S-100β."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:16344112"^^[string](http://www.w3.org/2001/XMLSchema#string) -### blood vessel endothelial cell `http://purl.obolibrary.org/obo/CL_0000071` -#### Removed -- [blood vessel endothelial cell](http://purl.obolibrary.org/obo/CL_0000071) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cuboidal endothelial cell of vascular tree"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "wikipedia:Tanycyte"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [blood vessel endothelial cell](http://purl.obolibrary.org/obo/CL_0000071) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009036"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:26578855"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [blood vessel endothelial cell](http://purl.obolibrary.org/obo/CL_0000071) EquivalentTo [squamous epithelial cell](http://purl.obolibrary.org/obo/CL_0000076) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004638](http://purl.obolibrary.org/obo/UBERON_0004638)) +- [alpha1-tanycyte](http://purl.obolibrary.org/obo/CL_4042017) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "In rodents, a1 tanycytes are known to express DARPP-32, GPR50, NA Vimentin, Connexin 43, GLT-1, GLUT1(+) (Goodman and Hajihosseini 2015; Prevot et al., 2018)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:26578855"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [blood vessel endothelial cell](http://purl.obolibrary.org/obo/CL_0000071) SubClassOf [squamous epithelial cell](http://purl.obolibrary.org/obo/CL_0000076) - - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [alpha1-tanycyte](http://purl.obolibrary.org/obo/CL_4042017) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) -#### Added -- [blood vessel endothelial cell](http://purl.obolibrary.org/obo/CL_0000071) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009036"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [alpha1-tanycyte](http://purl.obolibrary.org/obo/CL_4042017) [label](http://www.w3.org/2000/01/rdf-schema#label) "alpha1-tanycyte"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [blood vessel endothelial cell](http://purl.obolibrary.org/obo/CL_0000071) EquivalentTo [endothelial cell](http://purl.obolibrary.org/obo/CL_0000115) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001981](http://purl.obolibrary.org/obo/UBERON_0001981)) +- [alpha1-tanycyte](http://purl.obolibrary.org/obo/CL_4042017) [date](http://purl.org/dc/terms/date) "2024-08-19T13:06:16Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) +- [alpha1-tanycyte](http://purl.obolibrary.org/obo/CL_4042017) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "DMH tanycyte"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29351662"^^[string](http://www.w3.org/2001/XMLSchema#string) -### blood_and_immune_upper_slim `http://purl.obolibrary.org/obo/cl/cl-base#blood_and_immune_upper_slim` +- [alpha1-tanycyte](http://purl.obolibrary.org/obo/CL_4042017) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "VMH tanycyte"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29351662"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [blood_and_immune_upper_slim](http://purl.obolibrary.org/obo/cl/cl-base#blood_and_immune_upper_slim) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "a subset of general classes related to blood and the immune system, primarily of hematopoietic origin"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [alpha1-tanycyte](http://purl.obolibrary.org/obo/CL_4042017) -- [blood_and_immune_upper_slim](http://purl.obolibrary.org/obo/cl/cl-base#blood_and_immune_upper_slim) SubPropertyOf: [subset_property](http://www.geneontology.org/formats/oboInOwl#SubsetProperty) +- [alpha1-tanycyte](http://purl.obolibrary.org/obo/CL_4042017) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004642](http://purl.obolibrary.org/obo/UBERON_0004642) +- [alpha1-tanycyte](http://purl.obolibrary.org/obo/CL_4042017) SubClassOf [tanycyte](http://purl.obolibrary.org/obo/CL_0002085) -### blue sensitive photoreceptor cell `http://purl.obolibrary.org/obo/CL_0000495` -#### Removed -- [blue sensitive photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000495) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009222"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [alpha1-tanycyte](http://purl.obolibrary.org/obo/CL_4042017) SubClassOf [RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000014419](http://purl.obolibrary.org/obo/PR_000014419) -#### Added -- [blue sensitive photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000495) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009222"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [alpha1-tanycyte](http://purl.obolibrary.org/obo/CL_4042017) SubClassOf [astrocyte of the forebrain](http://purl.obolibrary.org/obo/CL_0012000) -### border follicle cell `http://purl.obolibrary.org/obo/CL_0000579` -#### Removed -- [border follicle cell](http://purl.obolibrary.org/obo/CL_0000579) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004905"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +### alpha2-tanycyte `http://purl.obolibrary.org/obo/CL_4042018` #### Added -- [border follicle cell](http://purl.obolibrary.org/obo/CL_0000579) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004905"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [alpha2-tanycyte](http://purl.obolibrary.org/obo/CL_4042018) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "In rodents, this type of tanycyte is more developmentally advanced than alpha1 tanycytes, shows a high neurogenic competence and expresses the following markers DARPP-32, Vimentin, GPR50, Connexin-43, GLT-1, GLUT1(+) (Goodman and Hajihosseini 2015; Prevot et al., 2018)"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:26578855"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [alpha2-tanycyte](http://purl.obolibrary.org/obo/CL_4042018) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042018"^^[string](http://www.w3.org/2001/XMLSchema#string) -### brain macroglial cell `http://purl.obolibrary.org/obo/CL_2000005` -#### Removed -- [brain macroglial cell](http://purl.obolibrary.org/obo/CL_2000005) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) - -#### Added -- [brain macroglial cell](http://purl.obolibrary.org/obo/CL_2000005) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [alpha2-tanycyte](http://purl.obolibrary.org/obo/CL_4042018) [label](http://www.w3.org/2000/01/rdf-schema#label) "alpha2-tanycyte"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [alpha2-tanycyte](http://purl.obolibrary.org/obo/CL_4042018) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "dmARH tanycyte"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29351662"^^[string](http://www.w3.org/2001/XMLSchema#string) -### brain microvascular endothelial cell `http://purl.obolibrary.org/obo/CL_2000044` -#### Removed -- [brain microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000044) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +- [alpha2-tanycyte](http://purl.obolibrary.org/obo/CL_4042018) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) -#### Added -- [brain microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000044) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [alpha2-tanycyte](http://purl.obolibrary.org/obo/CL_4042018) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A type of tanycyte found in the dorsomedial arcuate nucleus of the hypothalamus. This mono-ciliated tanycyte extends its protrusion to the arcuate nucleus and expresses the glial marker S-100β."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:16344112"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "wikipedia:Tanycyte"^^[string](http://www.w3.org/2001/XMLSchema#string) -### brain pericyte `http://purl.obolibrary.org/obo/CL_2000043` -#### Removed -- [brain pericyte](http://purl.obolibrary.org/obo/CL_2000043) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29351662"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [brain pericyte](http://purl.obolibrary.org/obo/CL_2000043) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:26578855"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [alpha2-tanycyte](http://purl.obolibrary.org/obo/CL_4042018) [date](http://purl.org/dc/terms/date) "2024-08-19T13:13:20Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -### brainstem motor neuron `http://purl.obolibrary.org/obo/CL_2000047` -#### Removed -- [brainstem motor neuron](http://purl.obolibrary.org/obo/CL_2000047) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +- Class: [alpha2-tanycyte](http://purl.obolibrary.org/obo/CL_4042018) -#### Added -- [brainstem motor neuron](http://purl.obolibrary.org/obo/CL_2000047) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [alpha2-tanycyte](http://purl.obolibrary.org/obo/CL_4042018) SubClassOf [RO_0002131](http://purl.obolibrary.org/obo/RO_0002131) some [UBERON_0001932](http://purl.obolibrary.org/obo/UBERON_0001932) +- [alpha2-tanycyte](http://purl.obolibrary.org/obo/CL_4042018) SubClassOf [RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000014419](http://purl.obolibrary.org/obo/PR_000014419) -### branchiomotor neuron `http://purl.obolibrary.org/obo/CL_0005023` -#### Removed -- [branchiomotor neuron](http://purl.obolibrary.org/obo/CL_0005023) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005731"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [alpha2-tanycyte](http://purl.obolibrary.org/obo/CL_4042018) SubClassOf [tanycyte](http://purl.obolibrary.org/obo/CL_0002085) -#### Added -- [branchiomotor neuron](http://purl.obolibrary.org/obo/CL_0005023) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005731"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### alternatively activated macrophage `http://purl.obolibrary.org/obo/CL_0000890` -### bronchioalveolar stem cell `http://purl.obolibrary.org/obo/CL_0002638` -#### Removed -- [bronchioalveolar stem cell](http://purl.obolibrary.org/obo/CL_0002638) EquivalentTo [respiratory basal cell](http://purl.obolibrary.org/obo/CL_0002633) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001955](http://purl.obolibrary.org/obo/UBERON_0001955)) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001958](http://purl.obolibrary.org/obo/UBERON_0001958)) +#### Added +- [alternatively activated macrophage](http://purl.obolibrary.org/obo/CL_0000890) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000890"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [bronchioalveolar stem cell](http://purl.obolibrary.org/obo/CL_0002638) SubClassOf [basal cell of epithelium of terminal bronchiole](http://purl.obolibrary.org/obo/CL_1000350) +- [alternatively activated macrophage](http://purl.obolibrary.org/obo/CL_0000890) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -- [bronchioalveolar stem cell](http://purl.obolibrary.org/obo/CL_0002638) SubClassOf [basal cell of epithelium of respiratory bronchiole](http://purl.obolibrary.org/obo/CL_1000351) +Alternatively activated macrophages, also referred to as M2 macrophages, are immune cells originating from monocytes. The M1/M2 classification is based upon macrophage polarization rather than macrophage location and refers to macrophage activation towards either a more inflammatory or more resolving phenotype, respectively, although the functional diversity of macrophages is more nuanced than such a dichotomy suggests. +M2 macrophages cells are differentiated from their precursors generally in response to Th2 cytokines, such as interleukin-4 (IL-4), interleukin-10 (IL-10), and interleukin-13 (IL-13). Tissue-resident macrophages are also sometimes said to have an “M2-like” phenotype. M2 macrophages play key roles in immunoregulation and disease resolution. +Functionally, alternatively activated macrophages are essential in wound healing and tissue repair and remodeling, largely due to their potent anti-inflammatory actions and their ability to promote angiogenesis. They achieve these functions by the production of specific growth factors and signaling proteins including Arg1, Ym1/2, Fizz1, and TGF-β. Additionally, they provide defense against specific categories of pathogens, particularly parasites, through specific communication with Th2 cells. +However, dysfunction of M2 macrophages can be harmful. Alternatively activated macrophages have been associated with several pathological conditions such as asthma, fibrosis, and tumor progression. This is due to their capacity to inhibit inflammatory responses, promote unneeded wound healing processes, and support tumour growth and spreading. Furthermore, complex roles have been observed in metabolic disorders, cardiovascular diseases, and neurodegenerative diseases, showing the diverse functional spectrum of these cells."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1186/s12935-021-02089-2"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [bronchioalveolar stem cell](http://purl.obolibrary.org/obo/CL_0002638) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002051](http://purl.obolibrary.org/obo/UBERON_0002051) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2020.583084"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [bronchioalveolar stem cell](http://purl.obolibrary.org/obo/CL_0002638) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004903](http://purl.obolibrary.org/obo/UBERON_0004903) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2015.00263"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [bronchioalveolar stem cell](http://purl.obolibrary.org/obo/CL_0002638) SubClassOf [respiratory basal cell](http://purl.obolibrary.org/obo/CL_0002633) - - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41392-023-01452-1"^^[string](http://www.w3.org/2001/XMLSchema#string) -### bronchus fibroblast of lung `http://purl.obolibrary.org/obo/CL_2000093` -#### Removed -- [bronchus fibroblast of lung](http://purl.obolibrary.org/obo/CL_2000093) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +### alveolar macrophage `http://purl.obolibrary.org/obo/CL_0000583` #### Added -- [bronchus fibroblast of lung](http://purl.obolibrary.org/obo/CL_2000093) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) - +- [alveolar macrophage](http://purl.obolibrary.org/obo/CL_0000583) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -### brush border cell of the proximal tubule `http://purl.obolibrary.org/obo/CL_0002307` -#### Removed -- [brush border cell of the proximal tubule](http://purl.obolibrary.org/obo/CL_0002307) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A brush border epithelial cell located in the proximal tubule of the kidney that detects fluid flow."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:1-4160-2328-3"^^[string](http://www.w3.org/2001/XMLSchema#string) +Alveolar macrophages are unique tissue-resident macrophages found in the lungs, specifically in the air sacs or alveoli where gas exchange occurs. They are characterized by specific surface markers including: F4/80-positive, CD11b-/low, CD11c-positive, CD68-positive, sialoadhesin-positive, dectin-1-positive, MR-positive, CX3CR1-negative. These specialized immune cells form a crucial part of the body's defense mechanism, playing important roles in pulmonary health and homeostasis. They are the first line of defense in the pulmonary immune response, acting as scavengers that patrol the alveoli and engulf foreign particles like bacteria, dust, and other debris that enter the lungs through inhalation. +The primary function of these alveolar macrophages is phagocytosis, whereby they consume and digest foreign substances, dead cells, and other particulates. In the lung, alveolar macrophages are also responsible for clearing surfactant. Additionally, alveolar macrophages also play an integral role in initiating the immune response, as they secrete several pro-inflammatory cytokines and chemokines that recruit other immune cells to the site of infection or inflammation. +Beyond their role in host defense, alveolar macrophages contribute to tissue remodeling and wound repair in the lungs, aiding in maintaining lung integrity. They also regulate local inflammation and control the immune response to prevent excessive inflammation that may be harmful. However, an imbalance in the function of alveolar macrophages can contribute to various lung diseases. Abnormal alveolar macrophage activation has been implicated in chronic inflammatory diseases such as emphysema, asthma, and fibrosis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.cellimm.2018.01.005"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s00424-017-1965-3"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [brush border cell of the proximal tubule](http://purl.obolibrary.org/obo/CL_0002307) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The vast majority of proximal tubule epithelial cells have a brush border, but there are rare exceptions."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.14348/molcells.2021.0058"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [brush border cell of the proximal tubule](http://purl.obolibrary.org/obo/CL_0002307) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A brush border epithelial cell located in the proximal tubule of the kidney, essential for reabsorbing substances like glucose and amino acids from the glomerular filtrate. These cells also secrete organic ions, playing a crucial role in maintaining kidney homeostasis, including electrolyte and acid-base balance, and excreting metabolic waste."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:1-4160-2328-3"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nri3600"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [alveolar macrophage](http://purl.obolibrary.org/obo/CL_0000583) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000583"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:23799132"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [alveolar macrophage](http://purl.obolibrary.org/obo/CL_0000583) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -- [brush border cell of the proximal tubule](http://purl.obolibrary.org/obo/CL_0002307) EquivalentTo [epithelial cell of proximal tubule](http://purl.obolibrary.org/obo/CL_0002306) and ([BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0005903](http://purl.obolibrary.org/obo/GO_0005903)) -- [brush border cell of the proximal tubule](http://purl.obolibrary.org/obo/CL_0002307) SubClassOf [brush border epithelial cell](http://purl.obolibrary.org/obo/CL_0000239) +### angioblastic mesenchymal cell `http://purl.obolibrary.org/obo/CL_0000566` +#### Added +- [angioblastic mesenchymal cell](http://purl.obolibrary.org/obo/CL_0000566) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### brush border epithelial cell `http://purl.obolibrary.org/obo/CL_0000239` -#### Removed -- [brush border epithelial cell](http://purl.obolibrary.org/obo/CL_0000239) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009143"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [brush border epithelial cell](http://purl.obolibrary.org/obo/CL_0000239) SubClassOf [ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0000067) +### angiogenic pericyte `http://purl.obolibrary.org/obo/CL_4047012` #### Added -- [brush border epithelial cell](http://purl.obolibrary.org/obo/CL_0000239) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:25422372"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [angiogenic pericyte](http://purl.obolibrary.org/obo/CL_4047012) [contributor](http://purl.org/dc/terms/contributor) [0009-0005-7919-4905](https://orcid.org/0009-0005-7919-4905) + +- [angiogenic pericyte](http://purl.obolibrary.org/obo/CL_4047012) [date](http://purl.org/dc/terms/date) "2024-09-06T08:41:39Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -- [brush border epithelial cell](http://purl.obolibrary.org/obo/CL_0000239) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell characterized by the presence of a brush border on its apical surface, which increases the surface area for absorption."^^[string](http://www.w3.org/2001/XMLSchema#string) +- [angiogenic pericyte](http://purl.obolibrary.org/obo/CL_4047012) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4047012"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [brush border epithelial cell](http://purl.obolibrary.org/obo/CL_0000239) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "All brush border cells are columnar-cuboidal. The formal logical definition of this term asserts this. Brush border epithelial cells are predominantly found lining the small intestine and the proximal tubules of the kidneys."^^[string](http://www.w3.org/2001/XMLSchema#string) +- [angiogenic pericyte](http://purl.obolibrary.org/obo/CL_4047012) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A specialized pericyte that actively participates in the formation of new blood vessels during angiogenesis by undergoing phenotypic changes, increasing proliferation, and interacting closely with endothelial cells."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34497389"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [brush border epithelial cell](http://purl.obolibrary.org/obo/CL_0000239) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.1152/ajpgi.00005.2011"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:24853910"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [brush border epithelial cell](http://purl.obolibrary.org/obo/CL_0000239) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009143"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [angiogenic pericyte](http://purl.obolibrary.org/obo/CL_4047012) [label](http://www.w3.org/2000/01/rdf-schema#label) "angiogenic pericyte"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [brush border epithelial cell](http://purl.obolibrary.org/obo/CL_0000239) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0005903](http://purl.obolibrary.org/obo/GO_0005903)) +- Class: [angiogenic pericyte](http://purl.obolibrary.org/obo/CL_4047012) -- [brush border epithelial cell](http://purl.obolibrary.org/obo/CL_0000239) SubClassOf [BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0005903](http://purl.obolibrary.org/obo/GO_0005903) +- [angiogenic pericyte](http://purl.obolibrary.org/obo/CL_4047012) SubClassOf [pericyte](http://purl.obolibrary.org/obo/CL_0000669) -### brush cell of tracheobronchial tree `http://purl.obolibrary.org/obo/CL_0002075` +### animal zygote `http://purl.obolibrary.org/obo/CL_0000365` #### Removed -- [brush cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002075) EquivalentTo [brush cell](http://purl.obolibrary.org/obo/CL_0002204) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0007196](http://purl.obolibrary.org/obo/UBERON_0007196)) +- [animal zygote](http://purl.obolibrary.org/obo/CL_0000365) EquivalentTo [zygote](http://purl.obolibrary.org/obo/CL_0010017) and ([RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_33208](http://purl.obolibrary.org/obo/NCBITaxon_33208)) + +- [animal zygote](http://purl.obolibrary.org/obo/CL_0000365) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_33208](http://purl.obolibrary.org/obo/NCBITaxon_33208) #### Added -- [brush cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002075) EquivalentTo [brush cell](http://purl.obolibrary.org/obo/CL_0002204) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0008397](http://purl.obolibrary.org/obo/UBERON_0008397)) +- [animal zygote](http://purl.obolibrary.org/obo/CL_0000365) EquivalentTo [zygote](http://purl.obolibrary.org/obo/CL_0010017) and ([RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_33208](http://purl.obolibrary.org/obo/NCBITaxon_33208)) +- [animal zygote](http://purl.obolibrary.org/obo/CL_0000365) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_33208](http://purl.obolibrary.org/obo/NCBITaxon_33208) -### calcitonin secreting cell `http://purl.obolibrary.org/obo/CL_0000443` + +### astrocyte of the cerebral cortex `http://purl.obolibrary.org/obo/CL_0002605` #### Removed -- [calcitonin secreting cell](http://purl.obolibrary.org/obo/CL_0000443) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009206"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [astrocyte of the cerebral cortex](http://purl.obolibrary.org/obo/CL_0002605) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An astrocyte of the cerebral cortex."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [calcitonin secreting cell](http://purl.obolibrary.org/obo/CL_0000443) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009206"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [astrocyte of the cerebral cortex](http://purl.obolibrary.org/obo/CL_0002605) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A transcriptomically distinct astrocyte that is found in the cerebral cortex."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) -### calvarial osteoblast `http://purl.obolibrary.org/obo/CL_2000058` -#### Removed -- [calvarial osteoblast](http://purl.obolibrary.org/obo/CL_2000058) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +### astrocyte-restricted precursor `http://purl.obolibrary.org/obo/CL_4042022` #### Added -- [calvarial osteoblast](http://purl.obolibrary.org/obo/CL_2000058) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [astrocyte-restricted precursor](http://purl.obolibrary.org/obo/CL_4042022) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042022"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [astrocyte-restricted precursor](http://purl.obolibrary.org/obo/CL_4042022) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "astrocyte precursor cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33052610"^^[string](http://www.w3.org/2001/XMLSchema#string) -### capillary endothelial cell `http://purl.obolibrary.org/obo/CL_0002144` +- [astrocyte-restricted precursor](http://purl.obolibrary.org/obo/CL_4042022) [date](http://purl.org/dc/terms/date) "2024-09-02T11:44:45Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -#### Added -- [capillary endothelial cell](http://purl.obolibrary.org/obo/CL_0002144) SubClassOf [squamous endothelial cell](http://purl.obolibrary.org/obo/CL_0002653) +- [astrocyte-restricted precursor](http://purl.obolibrary.org/obo/CL_4042022) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ARP"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [synonym_type_property](http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty) "OMO:0003000"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33052610"^^[string](http://www.w3.org/2001/XMLSchema#string) -### cardiac atrium fibroblast `http://purl.obolibrary.org/obo/CL_2000067` -#### Removed -- [cardiac atrium fibroblast](http://purl.obolibrary.org/obo/CL_2000067) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +- [astrocyte-restricted precursor](http://purl.obolibrary.org/obo/CL_4042022) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "In vitro, this progenitor cell can differentiate from glial-restricted precursor cells."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33052610"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [cardiac atrium fibroblast](http://purl.obolibrary.org/obo/CL_2000067) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [astrocyte-restricted precursor](http://purl.obolibrary.org/obo/CL_4042022) [label](http://www.w3.org/2000/01/rdf-schema#label) "astrocyte-restricted precursor"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [astrocyte-restricted precursor](http://purl.obolibrary.org/obo/CL_4042022) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A progenitor cell of the central nervous system that differentiates exclusively onto astrocytes. This progenitor cell expresses CD44 and S100 calcium-binding protein B."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:15531362"^^[string](http://www.w3.org/2001/XMLSchema#string) -### cardiac mesenchymal cell `http://purl.obolibrary.org/obo/CL_0000569` -#### Removed -- [cardiac mesenchymal cell](http://purl.obolibrary.org/obo/CL_0000569) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009259"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33052610"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [cardiac mesenchymal cell](http://purl.obolibrary.org/obo/CL_0000569) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009259"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [astrocyte-restricted precursor](http://purl.obolibrary.org/obo/CL_4042022) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) +- Class: [astrocyte-restricted precursor](http://purl.obolibrary.org/obo/CL_4042022) -### cardiac muscle cell `http://purl.obolibrary.org/obo/CL_0000746` -#### Removed -- [cardiac muscle cell](http://purl.obolibrary.org/obo/CL_0000746) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009316"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [astrocyte-restricted precursor](http://purl.obolibrary.org/obo/CL_4042022) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001017](http://purl.obolibrary.org/obo/UBERON_0001017) -#### Added -- [cardiac muscle cell](http://purl.obolibrary.org/obo/CL_0000746) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009316"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [astrocyte-restricted precursor](http://purl.obolibrary.org/obo/CL_4042022) SubClassOf [RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000001307](http://purl.obolibrary.org/obo/PR_000001307) +- [astrocyte-restricted precursor](http://purl.obolibrary.org/obo/CL_4042022) SubClassOf [progenitor cell](http://purl.obolibrary.org/obo/CL_0011026) -### cardiac muscle myoblast `http://purl.obolibrary.org/obo/CL_0000513` -#### Removed -- [cardiac muscle myoblast](http://purl.obolibrary.org/obo/CL_0000513) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009234"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [astrocyte-restricted precursor](http://purl.obolibrary.org/obo/CL_4042022) SubClassOf [neuron associated cell (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000123) -#### Added -- [cardiac muscle myoblast](http://purl.obolibrary.org/obo/CL_0000513) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009234"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [astrocyte-restricted precursor](http://purl.obolibrary.org/obo/CL_4042022) SubClassOf [RO_0002203](http://purl.obolibrary.org/obo/RO_0002203) some [astrocyte](http://purl.obolibrary.org/obo/CL_0000127) -### cardiac septum cell `http://purl.obolibrary.org/obo/CL_2000022` -#### Removed -- [cardiac septum cell](http://purl.obolibrary.org/obo/CL_2000022) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +### basal epithelial cell of tracheobronchial tree `http://purl.obolibrary.org/obo/CL_0002329` #### Added -- [cardiac septum cell](http://purl.obolibrary.org/obo/CL_2000022) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [basal epithelial cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002329) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002329"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [basal epithelial cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002329) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -### cardiac valve cell `http://purl.obolibrary.org/obo/CL_1000147` -#### Removed -- [cardiac valve cell](http://purl.obolibrary.org/obo/CL_1000147) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009402"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +The basal epithelial cells of the tracheobronchial tree are critical components found in the lining of the airway passages, including the trachea and bronchi. They are keratin-5-positive, nonciliated, cuboidal cells and typically tightly attached to the basement membrane. In humans, the proportion of basal cells in the respiratory epithelium gradually decreases going down the tracheobronchial tree: they represent approximately 34% of the cells in the trachea, 27% in the large airways, and 10% in the small airways, although it is worth noting that there are differences in the compositions of the tracheobronchial epithelia between different species. +Basal epithelial cells serve as the basal layer of the tracheobronchial epithelium, providing both structural and regenerative support for the epithelial tissue that lines the upper regions of the respiratory tract. They serve as progenitor or stem cells that are capable of differentiating into multiple cell types, such as ciliated and secretory cells. This gives them a central role in homeostatic maintenance of the epithelium, and in repairing damaged epithelium after an injury or during disease. This regenerative capacity is crucial in maintaining the integrity of the tracheobronchial surface, especially given its continual exposure to inhaled irritants and microorganisms. +In addition to their primary restorative function, basal epithelial cells are also involved in the initial immune response within the tracheobronchial tree. Equipped with pattern recognition receptors, these cells can identify and respond to pathogenic organisms, triggering an immune response and producing a range of inflammatory mediators, such as cytokines and chemokines, to help combat infections."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2353/ajpath.2010.090870"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [cardiac valve cell](http://purl.obolibrary.org/obo/CL_1000147) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009402"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1186/s12931-014-0160-8"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1165/rcmb.2013-0049OC"^^[string](http://www.w3.org/2001/XMLSchema#string) -### cardiac ventricle fibroblast `http://purl.obolibrary.org/obo/CL_2000066` -#### Removed -- [cardiac ventricle fibroblast](http://purl.obolibrary.org/obo/CL_2000066) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +### basophil mast progenitor cell `http://purl.obolibrary.org/obo/CL_0002028` #### Added -- [cardiac ventricle fibroblast](http://purl.obolibrary.org/obo/CL_2000066) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [basophil mast progenitor cell](http://purl.obolibrary.org/obo/CL_0002028) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### cardioblast (sensu Arthropoda) `http://purl.obolibrary.org/obo/CL_0000465` -#### Removed -- [cardioblast (sensu Arthropoda)](http://purl.obolibrary.org/obo/CL_0000465) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00001666"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +### basophil progenitor cell `http://purl.obolibrary.org/obo/CL_0000613` #### Added -- [cardioblast (sensu Arthropoda)](http://purl.obolibrary.org/obo/CL_0000465) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00001666"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [basophil progenitor cell](http://purl.obolibrary.org/obo/CL_0000613) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### caudal ganglionic eminence derived interneuron `http://purl.obolibrary.org/obo/CL_4023064` -#### Removed -- [caudal ganglionic eminence derived interneuron](http://purl.obolibrary.org/obo/CL_4023064) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "CGE interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [caudal ganglionic eminence derived interneuron](http://purl.obolibrary.org/obo/CL_4023064) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An interneuron that is derived from the caudal ganglionic eminence."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1101/2022.10.12.511898"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [caudal ganglionic eminence derived interneuron](http://purl.obolibrary.org/obo/CL_4023064) SubClassOf [interneuron](http://purl.obolibrary.org/obo/CL_0000099) +### basophilic erythroblast `http://purl.obolibrary.org/obo/CL_0000549` #### Added -- [caudal ganglionic eminence derived interneuron](http://purl.obolibrary.org/obo/CL_4023064) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "CGE-derived interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20130169"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [basophilic erythroblast](http://purl.obolibrary.org/obo/CL_0000549) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [caudal ganglionic eminence derived interneuron](http://purl.obolibrary.org/obo/CL_4023064) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "CGE cortical interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20130169"^^[string](http://www.w3.org/2001/XMLSchema#string) +### beta1-tanycyte `http://purl.obolibrary.org/obo/CL_4042019` -- [caudal ganglionic eminence derived interneuron](http://purl.obolibrary.org/obo/CL_4023064) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "CGE interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) +#### Added +- [beta1-tanycyte](http://purl.obolibrary.org/obo/CL_4042019) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042019"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824663"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [beta1-tanycyte](http://purl.obolibrary.org/obo/CL_4042019) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A type of tanycyte found in the lateral infundibular recess of the brain. This tanycyte has an elongated morphology with multiple microvilli extending to the third ventricle in the lateral zones of the median eminence. This type of tanycyte expresses FGF receptors 1 and 2, is in contact with GnRH neurons, and is involved in the release of gonadotropin-releasing hormone (GnRH)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:16344112"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [caudal ganglionic eminence derived interneuron](http://purl.obolibrary.org/obo/CL_4023064) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "caudal ganglionic eminence derived GABAergic cortical interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20130169"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29351662"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [caudal ganglionic eminence derived interneuron](http://purl.obolibrary.org/obo/CL_4023064) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "CGE-derived cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Tanycyte"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27034423"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:26578855"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [caudal ganglionic eminence derived interneuron](http://purl.obolibrary.org/obo/CL_4023064) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "CGE interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) +- [beta1-tanycyte](http://purl.obolibrary.org/obo/CL_4042019) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "vmARH tanycyte"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29351662"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824663"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [beta1-tanycyte](http://purl.obolibrary.org/obo/CL_4042019) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) -- [caudal ganglionic eminence derived interneuron](http://purl.obolibrary.org/obo/CL_4023064) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "CGE-derived GABAergic IN"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) +- [beta1-tanycyte](http://purl.obolibrary.org/obo/CL_4042019) [date](http://purl.org/dc/terms/date) "2024-08-19T13:17:32Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27034423"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [beta1-tanycyte](http://purl.obolibrary.org/obo/CL_4042019) [label](http://www.w3.org/2000/01/rdf-schema#label) "beta1-tanycyte"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [caudal ganglionic eminence derived interneuron](http://purl.obolibrary.org/obo/CL_4023064) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An interneuron that is derived from the caudal ganglionic eminence."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20130169"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [beta1-tanycyte](http://purl.obolibrary.org/obo/CL_4042019) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [beta1-tanycyte](http://purl.obolibrary.org/obo/CL_4042019) SubClassOf [astrocyte of the forebrain](http://purl.obolibrary.org/obo/CL_0012000) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824663"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [beta1-tanycyte](http://purl.obolibrary.org/obo/CL_4042019) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0006250](http://purl.obolibrary.org/obo/UBERON_0006250) -- [caudal ganglionic eminence derived interneuron](http://purl.obolibrary.org/obo/CL_4023064) SubClassOf [cerebral cortex GABAergic interneuron](http://purl.obolibrary.org/obo/CL_0010011) +- [beta1-tanycyte](http://purl.obolibrary.org/obo/CL_4042019) SubClassOf [RO_0002131](http://purl.obolibrary.org/obo/RO_0002131) some [UBERON_0002197](http://purl.obolibrary.org/obo/UBERON_0002197) +- [beta1-tanycyte](http://purl.obolibrary.org/obo/CL_4042019) SubClassOf [tanycyte](http://purl.obolibrary.org/obo/CL_0002085) -### cell `http://purl.obolibrary.org/obo/CL_0000000` -#### Removed -- [cell](http://purl.obolibrary.org/obo/CL_0000000) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007002"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [beta1-tanycyte](http://purl.obolibrary.org/obo/CL_4042019) SubClassOf [RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000007489](http://purl.obolibrary.org/obo/PR_000007489) -- [cell](http://purl.obolibrary.org/obo/CL_0000000) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009000"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [beta1-tanycyte](http://purl.obolibrary.org/obo/CL_4042019) SubClassOf [RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000007479](http://purl.obolibrary.org/obo/PR_000007479) -#### Added -- [cell](http://purl.obolibrary.org/obo/CL_0000000) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007002"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [beta1-tanycyte](http://purl.obolibrary.org/obo/CL_4042019) SubClassOf [secretory cell](http://purl.obolibrary.org/obo/CL_0000151) -- [cell](http://purl.obolibrary.org/obo/CL_0000000) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009000"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [beta1-tanycyte](http://purl.obolibrary.org/obo/CL_4042019) SubClassOf [RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0032274](http://purl.obolibrary.org/obo/GO_0032274) -### cell of skeletal muscle `http://purl.obolibrary.org/obo/CL_0000188` -#### Removed -- [cell of skeletal muscle](http://purl.obolibrary.org/obo/CL_0000188) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009115"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### beta2-tanycyte `http://purl.obolibrary.org/obo/CL_4042020` #### Added -- [cell of skeletal muscle](http://purl.obolibrary.org/obo/CL_0000188) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009115"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [beta2-tanycyte](http://purl.obolibrary.org/obo/CL_4042020) [label](http://www.w3.org/2000/01/rdf-schema#label) "beta2-tanycyte"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [beta2-tanycyte](http://purl.obolibrary.org/obo/CL_4042020) [date](http://purl.org/dc/terms/date) "2024-08-19T13:21:39Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -### cementoblast `http://purl.obolibrary.org/obo/CL_0000061` -#### Removed -- [cementoblast](http://purl.obolibrary.org/obo/CL_0000061) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009030"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [beta2-tanycyte](http://purl.obolibrary.org/obo/CL_4042020) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042020"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [cementoblast](http://purl.obolibrary.org/obo/CL_0000061) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009030"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [beta2-tanycyte](http://purl.obolibrary.org/obo/CL_4042020) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) +- [beta2-tanycyte](http://purl.obolibrary.org/obo/CL_4042020) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A type of tanycyte found in the floor of the infundibular recess in the brain. This tanycyte has an elongated morphology with multiple microvilli extending medially and ventrally to the median eminence, contacting the pial surface and blood vessels. This type of tanycyte expresses FGF receptors 1 and 2, is in contact with GnRH neurons, and is involved in the release of gonadotropin-releasing hormone (GnRH)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:16344112"^^[string](http://www.w3.org/2001/XMLSchema#string) -### cementocyte `http://purl.obolibrary.org/obo/CL_0000141` -#### Removed -- [cementocyte](http://purl.obolibrary.org/obo/CL_0000141) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009087"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "wikipedia:Tanycyte"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [cementocyte](http://purl.obolibrary.org/obo/CL_0000141) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009087"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29351662"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:26578855"^^[string](http://www.w3.org/2001/XMLSchema#string) -### central nervous system neuron `http://purl.obolibrary.org/obo/CL_2000029` -#### Removed -- [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +- [beta2-tanycyte](http://purl.obolibrary.org/obo/CL_4042020) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ME tanycyte"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29351662"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [central nervous system neuron](http://purl.obolibrary.org/obo/CL_2000029) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- Class: [beta2-tanycyte](http://purl.obolibrary.org/obo/CL_4042020) +- [beta2-tanycyte](http://purl.obolibrary.org/obo/CL_4042020) SubClassOf [RO_0002131](http://purl.obolibrary.org/obo/RO_0002131) some [UBERON_0002197](http://purl.obolibrary.org/obo/UBERON_0002197) -### centripetally migrating follicle cell `http://purl.obolibrary.org/obo/CL_0000671` -#### Removed -- [centripetally migrating follicle cell](http://purl.obolibrary.org/obo/CL_0000671) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004906"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [beta2-tanycyte](http://purl.obolibrary.org/obo/CL_4042020) SubClassOf [RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000007479](http://purl.obolibrary.org/obo/PR_000007479) -#### Added -- [centripetally migrating follicle cell](http://purl.obolibrary.org/obo/CL_0000671) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004906"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [beta2-tanycyte](http://purl.obolibrary.org/obo/CL_4042020) SubClassOf [RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000007489](http://purl.obolibrary.org/obo/PR_000007489) +- [beta2-tanycyte](http://purl.obolibrary.org/obo/CL_4042020) SubClassOf [tanycyte](http://purl.obolibrary.org/obo/CL_0002085) -### cerebellar Golgi cell `http://purl.obolibrary.org/obo/CL_0000119` -#### Removed -- [cerebellar Golgi cell](http://purl.obolibrary.org/obo/CL_0000119) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009069"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [beta2-tanycyte](http://purl.obolibrary.org/obo/CL_4042020) SubClassOf [astrocyte of the forebrain](http://purl.obolibrary.org/obo/CL_0012000) -#### Added -- [cerebellar Golgi cell](http://purl.obolibrary.org/obo/CL_0000119) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009069"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [beta2-tanycyte](http://purl.obolibrary.org/obo/CL_4042020) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0006250](http://purl.obolibrary.org/obo/UBERON_0006250) -### cerebellar granule cell `http://purl.obolibrary.org/obo/CL_0001031` +### blood vessel endothelial cell `http://purl.obolibrary.org/obo/CL_0000071` #### Removed -- [cerebellar granule cell](http://purl.obolibrary.org/obo/CL_0001031) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0001691"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [blood vessel endothelial cell](http://purl.obolibrary.org/obo/CL_0000071) SubClassOf [RO_0002202](http://purl.obolibrary.org/obo/RO_0002202) some [embryonic blood vessel endothelial progenitor cell](http://purl.obolibrary.org/obo/CL_0002546) -#### Added -- [cerebellar granule cell](http://purl.obolibrary.org/obo/CL_0001031) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0001691"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) -### cerebellum basket cell `http://purl.obolibrary.org/obo/CL_2000027` +### bone cell `http://purl.obolibrary.org/obo/CL_0001035` #### Removed -- [cerebellum basket cell](http://purl.obolibrary.org/obo/CL_2000027) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +- [bone cell](http://purl.obolibrary.org/obo/CL_0001035) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) #### Added -- [cerebellum basket cell](http://purl.obolibrary.org/obo/CL_2000027) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [bone cell](http://purl.obolibrary.org/obo/CL_0001035) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### cerebellum glutamatergic neuron `http://purl.obolibrary.org/obo/CL_2000028` -#### Removed -- [cerebellum glutamatergic neuron](http://purl.obolibrary.org/obo/CL_2000028) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +### bone marrow macrophage `http://purl.obolibrary.org/obo/CL_0002476` #### Added -- [cerebellum glutamatergic neuron](http://purl.obolibrary.org/obo/CL_2000028) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [bone marrow macrophage](http://purl.obolibrary.org/obo/CL_0002476) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### cerebrospinal fluid secreting cell `http://purl.obolibrary.org/obo/CL_0000686` -#### Removed -- [cerebrospinal fluid secreting cell](http://purl.obolibrary.org/obo/CL_0000686) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009295"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### brush cell `http://purl.obolibrary.org/obo/CL_0002204` #### Added -- [cerebrospinal fluid secreting cell](http://purl.obolibrary.org/obo/CL_0000686) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009295"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [brush cell](http://purl.obolibrary.org/obo/CL_0002204) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002204"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [brush cell](http://purl.obolibrary.org/obo/CL_0002204) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -### chemoreceptor cell `http://purl.obolibrary.org/obo/CL_0000206` -#### Removed -- [chemoreceptor cell](http://purl.obolibrary.org/obo/CL_0000206) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009124"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +Brush cells, also referred to as tuft cells or multivesicular cells, are a specialized type of epithelial cell mainly noted for their characteristic 'brush border' composed of microvilli. These cells reside in the epithelial lining of tissue organs such as the respiratory tract, gastrointestinal tract, and the bile ducts. The name derives from their distinct appearance under the microscope, which resembles a brush due to the dense layer of microvilli protruding into the lumen. +A key function of brush cells is chemosensation: They express a variety of signaling molecules and receptors that enable them to detect specific chemical stimuli in the environment and act as sensory transducers. Many of these receptors are responsive to luminal content, which makes brush cells vital for regulating and coordinating appropriate physiological responses to changes in these substances. +Recent research has also elucidated an important role for these cells in immunity. Intestinal brush cells have been found to be the source of a cytokine called interleukin-25, which can initiate type 2 immune responses during parasitic infections. This immune function, along with the chemosensing abilities, signifies that brush cells could serve crucial roles in health and disease, although much research is still required to fully elucidate their myriad roles in physiology and pathology. Overall, brush cells are a versatile cell type, whose distinct morphology and functional capabilities allow them to perform a unique set of functions within the body."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fphys.2015.00087"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [chemoreceptor cell](http://purl.obolibrary.org/obo/CL_0000206) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009124"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/978-3-211-99390-3_83"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.5114/ceji.2022.124416"^^[string](http://www.w3.org/2001/XMLSchema#string) -### cholangiocyte `http://purl.obolibrary.org/obo/CL_1000488` -#### Removed -- [cholangiocyte](http://purl.obolibrary.org/obo/CL_1000488) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009397"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nature16161"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [cholangiocyte](http://purl.obolibrary.org/obo/CL_1000488) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009397"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1469-7580.2005.00403.x"^^[string](http://www.w3.org/2001/XMLSchema#string) -### cholinergic neuron `http://purl.obolibrary.org/obo/CL_0000108` +### cardioblast (sensu Arthropoda) `http://purl.obolibrary.org/obo/CL_0000465` #### Removed -- [cholinergic neuron](http://purl.obolibrary.org/obo/CL_0000108) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007173"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [cardioblast (sensu Arthropoda)](http://purl.obolibrary.org/obo/CL_0000465) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_6656](http://purl.obolibrary.org/obo/NCBITaxon_6656) -- [cholinergic neuron](http://purl.obolibrary.org/obo/CL_0000108) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009060"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [cardioblast (sensu Arthropoda)](http://purl.obolibrary.org/obo/CL_0000465) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) #### Added -- [cholinergic neuron](http://purl.obolibrary.org/obo/CL_0000108) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009060"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [cardioblast (sensu Arthropoda)](http://purl.obolibrary.org/obo/CL_0000465) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_6656](http://purl.obolibrary.org/obo/NCBITaxon_6656) -- [cholinergic neuron](http://purl.obolibrary.org/obo/CL_0000108) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007173"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - -### chondroblast `http://purl.obolibrary.org/obo/CL_0000058` +### cardiocyte `http://purl.obolibrary.org/obo/CL_0002494` #### Removed -- [chondroblast](http://purl.obolibrary.org/obo/CL_0000058) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009027"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [cardiocyte](http://purl.obolibrary.org/obo/CL_0002494) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) #### Added -- [chondroblast](http://purl.obolibrary.org/obo/CL_0000058) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009027"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [cardiocyte](http://purl.obolibrary.org/obo/CL_0002494) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### chondrocyte `http://purl.obolibrary.org/obo/CL_0000138` +### caudal ganglionic eminence derived interneuron `http://purl.obolibrary.org/obo/CL_4023064` #### Removed -- [chondrocyte](http://purl.obolibrary.org/obo/CL_0000138) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009084"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [chondrocyte](http://purl.obolibrary.org/obo/CL_0000138) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009084"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [caudal ganglionic eminence derived interneuron](http://purl.obolibrary.org/obo/CL_4023064) [label](http://www.w3.org/2000/01/rdf-schema#label) "caudal ganglionic eminence derived interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [caudal ganglionic eminence derived interneuron](http://purl.obolibrary.org/obo/CL_4023064) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "CGE interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) -### chorionic girdle cell `http://purl.obolibrary.org/obo/CL_4040001` -#### Removed -- [chorionic girdle cell](http://purl.obolibrary.org/obo/CL_4040001) [note](http://purl.obolibrary.org/obo/cl/cl-base#note) "Humans, mice and rats have a highly invasive (hemochorial) placentation. Horses have a non-invasive epitheliochorial placenta, except for the transient endometrial cup."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27280409"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824663"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [chorionic girdle cell](http://purl.obolibrary.org/obo/CL_4040001) [note](http://www.geneontology.org/formats/oboInOwl#note) "Humans, mice and rats have a highly invasive (hemochorial) placentation. Horses have a non-invasive epitheliochorial placenta, except for the transient endometrial cup."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27280409"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [caudal ganglionic eminence derived interneuron](http://purl.obolibrary.org/obo/CL_4023064) [label](http://www.w3.org/2000/01/rdf-schema#label) "caudal ganglionic eminence derived cortical interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) -### choroid plexus epithelial cell `http://purl.obolibrary.org/obo/CL_0000706` +### cell `http://purl.obolibrary.org/obo/CL_0000000` #### Removed -- [choroid plexus epithelial cell](http://purl.obolibrary.org/obo/CL_0000706) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009304"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [cell](http://purl.obolibrary.org/obo/CL_0000000) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_131567](http://purl.obolibrary.org/obo/NCBITaxon_131567) #### Added -- [choroid plexus epithelial cell](http://purl.obolibrary.org/obo/CL_0000706) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009304"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [cell](http://purl.obolibrary.org/obo/CL_0000000) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_131567](http://purl.obolibrary.org/obo/NCBITaxon_131567) -### choroidal cell of the eye `http://purl.obolibrary.org/obo/CL_0000348` +### cell of skeletal muscle `http://purl.obolibrary.org/obo/CL_0000188` #### Removed -- [choroidal cell of the eye](http://purl.obolibrary.org/obo/CL_0000348) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009175"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [cell of skeletal muscle](http://purl.obolibrary.org/obo/CL_0000188) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) #### Added -- [choroidal cell of the eye](http://purl.obolibrary.org/obo/CL_0000348) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009175"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [cell of skeletal muscle](http://purl.obolibrary.org/obo/CL_0000188) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### chromaffin cell `http://purl.obolibrary.org/obo/CL_0000166` +### cerebral cortex endothelial cell `http://purl.obolibrary.org/obo/CL_1001602` #### Removed -- [chromaffin cell](http://purl.obolibrary.org/obo/CL_0000166) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009099"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [cerebral cortex endothelial cell](http://purl.obolibrary.org/obo/CL_1001602) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Endothelial cells forming the walls of the capillaries within the cerebral cortex."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NPX:PDR"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [chromaffin cell](http://purl.obolibrary.org/obo/CL_0000166) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009099"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [cerebral cortex endothelial cell](http://purl.obolibrary.org/obo/CL_1001602) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A distinct endothelial cell forming the walls of the capillaries within the cerebral cortex."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NPX:PDR"^^[string](http://www.w3.org/2001/XMLSchema#string) -### ciliated cell `http://purl.obolibrary.org/obo/CL_0000064` +### chandelier pvalb GABAergic cortical interneuron `http://purl.obolibrary.org/obo/CL_4023036` #### Removed -- [ciliated cell](http://purl.obolibrary.org/obo/CL_0000064) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009032"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [chandelier pvalb GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023036) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A pvalb GABAergic cortical interneuron that is recognizable by the straight terminal axonal 'cartridges' of vertically oriented strings of synaptic boutons. Chandelier PV cells' boutons target exclusively the axon initial segment (AIS) of pyramidal cells, with a single cell innervating hundreds of pyramidal cells in a clustered manner."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27477017"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [ciliated cell](http://purl.obolibrary.org/obo/CL_0000064) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009032"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [chandelier pvalb GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023036) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A transcriptomically distinct pvalb GABAergic cortical interneuron that is recognizable by the straight terminal axonal 'cartridges' of vertically oriented strings of synaptic boutons. Chandelier PV cells' boutons target exclusively the axon initial segment (AIS) of pyramidal cells, with a single cell innervating hundreds of pyramidal cells in a clustered manner. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_subclass', clusters Chandelier."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27477017"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/e/9c63201d-bfd9-41a8-bbbc-18d947556f3d.cxg/"^^[string](http://www.w3.org/2001/XMLSchema#string) -### ciliated columnar cell of tracheobronchial tree `http://purl.obolibrary.org/obo/CL_0002145` -#### Removed -- [ciliated columnar cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002145) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A ciliated columnar cell found in the trachea and bronchus. Vary from low to tall columnar; possesses up to 300 cilia at its surface, interspersed with long irregular microvilli with the cilia varying in length from about 6um in the trachea to about 4um in the terminal bronchioles; driving force of the ciliary current in the bronchial tree."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0517223651"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) +### cholangiocyte `http://purl.obolibrary.org/obo/CL_1000488` #### Added -- [ciliated columnar cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002145) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "These cells possess numerous cilia on their surface, typically ranging from 200 to 300 per cell. The cilia vary in length, measuring between 6 to 7 μm in the upper airways (trachea) and becoming shorter, around 4 μm, in the smaller airways (terminal bronchioles). These cells form a two-layered 'coat' in the airway: the lower 'sol' layer is watery, allowing the cilia to beat in coordinated waves, while the upper 'gel' layer is thick and sticky, trapping inhaled particles."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.1016/B978-032304048-8.50071-2"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:25386990"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [cholangiocyte](http://purl.obolibrary.org/obo/CL_1000488) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000488"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [ciliated columnar cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002145) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A multi-ciliated epithelial cell located in the trachea and bronchi, characterized by a columnar shape and motile cilia on its apical surface. These cilia facilitate mucociliary clearance by moving mucus and trapped particles toward the pharynx."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [cholangiocyte](http://purl.obolibrary.org/obo/CL_1000488) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:28400610"^^[string](http://www.w3.org/2001/XMLSchema#string) +Cholangiocytes, also known as biliary epithelial cells, are specialized epithelial cells that line the biliary tract, which constitutes the gall bladder and bile ducts inside the liver. Crucial to the maintenance of the liver's health and function, cholangiocytes have a key role in the modification and secretion of bile, a fluid produced by hepatocytes that is essential to digestion and the absorption of fats and vitamins. +Cholangiocytes accomplish their primary function through the expression of a variety of transport proteins located on their apical and basolateral membranes, which propel bile acids and other contents of the bile into the biliary lumen. The hepatic bile, once secreted by the hepatocytes, is further modified by cholangiocytes via secretion and absorption processes. These processes help in the regulation of bile volume and composition, which is fundamental in ensuring the efficient digestion of dietary fats and fat-soluble vitamins and the excretion of cholesterol. +In addition to their role in bile modification, cholangiocytes also perform several other integral functions. For instance, these cells express Toll-like receptors (TLRs) which allow cholangiocytes to initiate an immune response against pathogens in the biliary lumen. When functioning normally, these cells contribute to biliary integrity, hepatic architecture, and overall hepatic physiology. However, when they become pathological, they are involved in the progression of liver diseases, such as primary biliary cirrhosis and cholangiocarcinoma – the malignancy of the biliary tract."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.jhep.2012.10.011"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [ciliated columnar cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002145) SubClassOf [BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0031514](http://purl.obolibrary.org/obo/GO_0031514) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/ajpgi.00227.2012"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41575-019-0125-y"^^[string](http://www.w3.org/2001/XMLSchema#string) -### ciliated epithelial cell `http://purl.obolibrary.org/obo/CL_0000067` -#### Removed -- [ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0000067) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009035"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.5009/gnl16033"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0000067) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009035"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.jcmgh.2015.05.005"^^[string](http://www.w3.org/2001/XMLSchema#string) -### ciliated epithelial cell of esophagus `http://purl.obolibrary.org/obo/CL_3000000` +### choroid plexus epithelial cell `http://purl.obolibrary.org/obo/CL_0000706` #### Removed -- [ciliated epithelial cell of esophagus](http://purl.obolibrary.org/obo/CL_3000000) [contributor](http://purl.org/dc/terms/contributor) [Q97529981](https://www.wikidata.org/entity/Q97529981) +- [choroid plexus epithelial cell](http://purl.obolibrary.org/obo/CL_0000706) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Specialized ependymal cell that produces the cerebrospinal fluid from the blood and secretes it into the lumen of the brain and spinal chord."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:add"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [ciliated epithelial cell of esophagus](http://purl.obolibrary.org/obo/CL_3000000) [contributor](http://purl.org/dc/terms/contributor) [Q97529981](http://www.wikidata.org/entity/Q97529981) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "JB:jb"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) -### ciliated olfactory receptor neuron `http://purl.obolibrary.org/obo/CL_0000847` -#### Removed -- [ciliated olfactory receptor neuron](http://purl.obolibrary.org/obo/CL_0000847) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009358"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:9550134"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [ciliated olfactory receptor neuron](http://purl.obolibrary.org/obo/CL_0000847) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009358"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [choroid plexus epithelial cell](http://purl.obolibrary.org/obo/CL_0000706) EquivalentTo [ependymal cell](http://purl.obolibrary.org/obo/CL_0000065) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001886](http://purl.obolibrary.org/obo/UBERON_0001886)) +- [choroid plexus epithelial cell](http://purl.obolibrary.org/obo/CL_0000706) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001886](http://purl.obolibrary.org/obo/UBERON_0001886) -### circulating cell `http://purl.obolibrary.org/obo/CL_0000080` -#### Removed -- [circulating cell](http://purl.obolibrary.org/obo/CL_0000080) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009043"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [choroid plexus epithelial cell](http://purl.obolibrary.org/obo/CL_0000706) SubClassOf [neural cell](http://purl.obolibrary.org/obo/CL_0002319) #### Added -- [circulating cell](http://purl.obolibrary.org/obo/CL_0000080) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009043"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [choroid plexus epithelial cell](http://purl.obolibrary.org/obo/CL_0000706) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A specialized ependymal cell that is part of the choroid plexus epithelium, responsible for producing cerebrospinal fluid (CSF) by selectively filtering and modifying blood plasma components before secreting it into the brain and spinal cord. This cell is characterized by a brush border on its apical surface, which enhances the secretion of CSF."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:add"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "JB:jb"^^[string](http://www.w3.org/2001/XMLSchema#string) -### club-like cell of the urethral epithelium `http://purl.obolibrary.org/obo/CL_4032000` -#### Removed -- [club-like cell of the urethral epithelium](http://purl.obolibrary.org/obo/CL_4032000) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) - -- [club-like cell of the urethral epithelium](http://purl.obolibrary.org/obo/CL_4032000) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/cl/cl-base#human_reference_atlas) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:15561411"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:9550134"^^[string](http://www.w3.org/2001/XMLSchema#string) -### collagen secreting cell `http://purl.obolibrary.org/obo/CL_0000667` -#### Removed -- [collagen secreting cell](http://purl.obolibrary.org/obo/CL_0000667) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009287"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [choroid plexus epithelial cell](http://purl.obolibrary.org/obo/CL_0000706) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "A choroid plexus epithelial cell possesses non-motile 9+0 cilia. While these cilia can exhibit transient motility during development, they generally do not contribute significantly to the directional flow of cerebrospinal fluid (CSF). Instead, they are primarily involved in sensory functions."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:25729351"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [collagen secreting cell](http://purl.obolibrary.org/obo/CL_0000667) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009287"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [choroid plexus epithelial cell](http://purl.obolibrary.org/obo/CL_0000706) EquivalentTo [ependymal cell](http://purl.obolibrary.org/obo/CL_0000065) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0003911](http://purl.obolibrary.org/obo/UBERON_0003911)) +- [choroid plexus epithelial cell](http://purl.obolibrary.org/obo/CL_0000706) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0003911](http://purl.obolibrary.org/obo/UBERON_0003911) -### colon endothelial cell `http://purl.obolibrary.org/obo/CL_1001572` -#### Removed -- [colon endothelial cell](http://purl.obolibrary.org/obo/CL_1001572) SubClassOf [colon epithelial cell](http://purl.obolibrary.org/obo/CL_0011108) +- [choroid plexus epithelial cell](http://purl.obolibrary.org/obo/CL_0000706) SubClassOf [RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0033326](http://purl.obolibrary.org/obo/GO_0033326) +- [choroid plexus epithelial cell](http://purl.obolibrary.org/obo/CL_0000706) SubClassOf [brush border epithelial cell](http://purl.obolibrary.org/obo/CL_0000239) -### colon goblet cell `http://purl.obolibrary.org/obo/CL_0009039` -#### Removed -- [colon goblet cell](http://purl.obolibrary.org/obo/CL_0009039) SubClassOf [colon glandular cell](http://purl.obolibrary.org/obo/CL_1001588) +### choroidal cell of the eye `http://purl.obolibrary.org/obo/CL_0000348` #### Added -- [colon goblet cell](http://purl.obolibrary.org/obo/CL_0009039) SubClassOf [colon epithelial cell](http://purl.obolibrary.org/obo/CL_0011108) - - -### columnar cell of endocervix `http://purl.obolibrary.org/obo/CL_0002152` -#### Removed -- [columnar cell of endocervix](http://purl.obolibrary.org/obo/CL_0002152) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A columnar cell of the cervix uteri."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0721662544"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [choroidal cell of the eye](http://purl.obolibrary.org/obo/CL_0000348) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -- [columnar cell of endocervix](http://purl.obolibrary.org/obo/CL_0002152) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000458](http://purl.obolibrary.org/obo/UBERON_0000458) -- [columnar cell of endocervix](http://purl.obolibrary.org/obo/CL_0002152) SubClassOf [epithelial cell of uterus](http://purl.obolibrary.org/obo/CL_0002149) +### chromaffin cell `http://purl.obolibrary.org/obo/CL_0000166` #### Added -- [columnar cell of endocervix](http://purl.obolibrary.org/obo/CL_0002152) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A simple columnar epithelial cell located in the endocervix."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [chromaffin cell](http://purl.obolibrary.org/obo/CL_0000166) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000166"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:/10.1016/j.autneu.2015.04.008"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [chromaffin cell](http://purl.obolibrary.org/obo/CL_0000166) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0721662544"^^[string](http://www.w3.org/2001/XMLSchema#string) +Chromaffin cells, also known as pheochromocytes, are neuroendocrine cells that are typically located in the adrenal medulla, the innermost part of the adrenal gland, which is situated on top of each kidney. Chromaffin cells are also found in small clusters, known as paraganglia, in various locations throughout the body, including the sympathetic nervous system. They derive their name from their ability to stain a brownish-black color upon exposure to chromic salts, a feature made possible due to their high content of granules rich in catecholamines and catecholamine-related neurotransmitters. +The primary function of chromaffin cells is the synthesis and release of catecholamines, specifically epinephrine (adrenaline) and norepinephrine (noradrenaline). These neurotransmitters are vital stress hormones that, when released by the adrenal chromaffing cells into the bloodstream, prepare the body for the 'fight or flight' response. This response can enhance the body's performance in a dangerous situation by increasing heart rate, elevating blood sugar, and increasing blood flow to the muscles. The chromaffin cells in paraganglia are responsible for the local release of catecholamines and play a role in regulating blood pressure and other autonomic functions. +In addition to their role in stress response, chromaffin cells also contribute to the body's immune response. They secrete several peptides including antimicrobial peptides, and the discovery of LPS and cytokine receptors on chromaffin cells suggests that the adrenal medulla may participate in some aspects of the immune response."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fendo.2018.00711"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [columnar cell of endocervix](http://purl.obolibrary.org/obo/CL_0002152) EquivalentTo [simple columnar epithelial cell](http://purl.obolibrary.org/obo/CL_0000146) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0012252](http://purl.obolibrary.org/obo/UBERON_0012252)) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2022.977175/full"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [columnar cell of endocervix](http://purl.obolibrary.org/obo/CL_0002152) SubClassOf [simple columnar epithelial cell](http://purl.obolibrary.org/obo/CL_0000146) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/cphy.c190003"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [columnar cell of endocervix](http://purl.obolibrary.org/obo/CL_0002152) SubClassOf [epithelial cell of cervix](http://purl.obolibrary.org/obo/CL_0002535) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2022.977175"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [columnar cell of endocervix](http://purl.obolibrary.org/obo/CL_0002152) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0012252](http://purl.obolibrary.org/obo/UBERON_0012252) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.biocel.2016.02.003"^^[string](http://www.w3.org/2001/XMLSchema#string) -### columnar chondrocyte `http://purl.obolibrary.org/obo/CL_0000744` +### ciliated cell `http://purl.obolibrary.org/obo/CL_0000064` #### Removed -- [columnar chondrocyte](http://purl.obolibrary.org/obo/CL_0000744) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009314"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [ciliated cell](http://purl.obolibrary.org/obo/CL_0000064) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) #### Added -- [columnar chondrocyte](http://purl.obolibrary.org/obo/CL_0000744) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009314"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [ciliated cell](http://purl.obolibrary.org/obo/CL_0000064) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [ciliated cell](http://purl.obolibrary.org/obo/CL_0000064) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### columnar/cuboidal epithelial cell `http://purl.obolibrary.org/obo/CL_0000075` + +### ciliated cell of the bronchus `http://purl.obolibrary.org/obo/CL_0002332` #### Removed -- [columnar/cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000075) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009038"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [ciliated cell of the bronchus](http://purl.obolibrary.org/obo/CL_0002332) EquivalentTo [ciliated cell](http://purl.obolibrary.org/obo/CL_0000064) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002185](http://purl.obolibrary.org/obo/UBERON_0002185)) #### Added -- [columnar/cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000075) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009038"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [ciliated cell of the bronchus](http://purl.obolibrary.org/obo/CL_0002332) EquivalentTo [ciliated cell](http://purl.obolibrary.org/obo/CL_0000064) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002031](http://purl.obolibrary.org/obo/UBERON_0002031)) -### committed double negative thymocyte (Homo sapiens) `http://purl.obolibrary.org/obo/CL_0009082` +### ciliated columnar cell of tracheobronchial tree `http://purl.obolibrary.org/obo/CL_0002145` +#### Removed +- [ciliated columnar cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002145) SubClassOf [BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0031514](http://purl.obolibrary.org/obo/GO_0031514) #### Added -- [committed double negative thymocyte (Homo sapiens)](http://purl.obolibrary.org/obo/CL_0009082) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/cl/cl-base#human_reference_atlas) +- [ciliated columnar cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002145) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002145"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [ciliated columnar cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002145) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -### common lymphoid progenitor `http://purl.obolibrary.org/obo/CL_0000051` -#### Removed -- [common lymphoid progenitor](http://purl.obolibrary.org/obo/CL_0000051) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009023"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [common lymphoid progenitor](http://purl.obolibrary.org/obo/CL_0000051) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009023"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +Ciliated columnar cells of the tracheobronchial tree compose the inner lining of the tracheobronchial tree, the system of airways consisting of trachea, bronchi and bronchioles that allow passage of air into the lungs, where gas exchange occurs. A defining feature of these endo-epithelial cells are the tiny hair-like structures covering their surface, known as cilia. The nucleus is located at the base of the cell, and the area above it is rich in mitochondria and well-developed endoplasmic reticulum, both crucial for the energy-intensive process of cilia operation. +The primary function of these ciliated cells is to keep the respiratory tract clean via mucociliary clearance or the respiratory escalator. These cells create a two-layered 'coat': The lower "sol" layer is watery where the cilia can beat in coordinated waves, and the upper "gel" layer is thick and sticky, trapping inhaled particles, such as dust, bacteria, viruses, and other potentially harmful substances. This rhythmical beating of the cilia then moves the mucus and trapped particles upwards and out of the respiratory tract, which is then either coughed out or swallowed. +Damage or dysfunction of these ciliated cells, as seen in diseases such as primary ciliary dyskinesia, cystic fibrosis, or chronic bronchitis, may lead to reduced or ineffective mucociliary clearance and an increased susceptibility to respiratory infections."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1146/annurev-physiol-021014-071931"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1159/000196486"^^[string](http://www.w3.org/2001/XMLSchema#string) -### common myeloid progenitor `http://purl.obolibrary.org/obo/CL_0000049` -#### Removed -- [common myeloid progenitor](http://purl.obolibrary.org/obo/CL_0000049) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009021"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/ajplung.00329.2019"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [common myeloid progenitor](http://purl.obolibrary.org/obo/CL_0000049) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009021"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1101/cshperspect.a028241"^^[string](http://www.w3.org/2001/XMLSchema#string) -### compound eye cone cell `http://purl.obolibrary.org/obo/CL_0000718` +### circulating cell `http://purl.obolibrary.org/obo/CL_0000080` #### Removed -- [compound eye cone cell](http://purl.obolibrary.org/obo/CL_0000718) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004193"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [circulating cell](http://purl.obolibrary.org/obo/CL_0000080) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) #### Added -- [compound eye cone cell](http://purl.obolibrary.org/obo/CL_0000718) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004193"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [circulating cell](http://purl.obolibrary.org/obo/CL_0000080) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### compound eye photoreceptor cell `http://purl.obolibrary.org/obo/CL_2000019` -#### Removed -- [compound eye photoreceptor cell](http://purl.obolibrary.org/obo/CL_2000019) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00006009"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [compound eye photoreceptor cell](http://purl.obolibrary.org/obo/CL_2000019) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +### classical monocyte `http://purl.obolibrary.org/obo/CL_0000860` #### Added -- [compound eye photoreceptor cell](http://purl.obolibrary.org/obo/CL_2000019) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00006009"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [classical monocyte](http://purl.obolibrary.org/obo/CL_0000860) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000860"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [compound eye photoreceptor cell](http://purl.obolibrary.org/obo/CL_2000019) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [classical monocyte](http://purl.obolibrary.org/obo/CL_0000860) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +Classical monocytes are a subtype of monocytes that are characterized by high CD14 but no CD16 expression. Emerging from the bone marrow and entering the bloodstream, these cells play central roles in immune responses and regulation of inflammation. CD14-positive CD16-negative monocytes form the majority of circulating monocytes in the body, typically contributing to around 80-90% of the total monocyte pool. +The primary function of the classical monocytes is to serve in the frontline of host defense against infections. They are primed to migrate to sites of infection, and they express pattern recognition receptors that help them identify and phagocytose pathogens, leading to their destruction. Classical monocytes also contribute to inflammation by producing several pro-inflammatory cytokines including interleukins and tumor necrosis factors. +In response to specific signals from tissues under pathological conditions, such as infection or injury, classical monocytes can leave the bloodstream and migrate towards the affected sites. Following their arrival, these cells differentiate into diverse cell types including macrophages and dendritic cells to combat specific pathogens or injury. Dysregulated monocyte activity can lead to the development of many human diseases including inflammation, infection, tissue injury, and various autoimmune diseases."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nri.2017.28"^^[string](http://www.w3.org/2001/XMLSchema#string) -### cone retinal bipolar cell `http://purl.obolibrary.org/obo/CL_0000752` -#### Removed -- [cone retinal bipolar cell](http://purl.obolibrary.org/obo/CL_0000752) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009322"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1182/blood-2009-07-235028"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [cone retinal bipolar cell](http://purl.obolibrary.org/obo/CL_0000752) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009322"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/sji.12883"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2015.00423/full"^^[string](http://www.w3.org/2001/XMLSchema#string) -### conjunctiva goblet cell `http://purl.obolibrary.org/obo/CL_2000084` -#### Removed -- [conjunctiva goblet cell](http://purl.obolibrary.org/obo/CL_2000084) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2019.02035"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [conjunctiva goblet cell](http://purl.obolibrary.org/obo/CL_2000084) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [classical monocyte](http://purl.obolibrary.org/obo/CL_0000860) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### connective tissue cell `http://purl.obolibrary.org/obo/CL_0002320` -#### Removed -- [connective tissue cell](http://purl.obolibrary.org/obo/CL_0002320) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009392"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### cnidocyte `http://purl.obolibrary.org/obo/CL_0011029` #### Added -- [connective tissue cell](http://purl.obolibrary.org/obo/CL_0002320) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009392"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [cnidocyte](http://purl.obolibrary.org/obo/CL_0011029) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### cord blood hematopoietic stem cell `http://purl.obolibrary.org/obo/CL_2000095` -#### Removed -- [cord blood hematopoietic stem cell](http://purl.obolibrary.org/obo/CL_2000095) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +### common dendritic progenitor `http://purl.obolibrary.org/obo/CL_0001029` #### Added -- [cord blood hematopoietic stem cell](http://purl.obolibrary.org/obo/CL_2000095) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) - +- [common dendritic progenitor](http://purl.obolibrary.org/obo/CL_0001029) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### corneal endothelial cell `http://purl.obolibrary.org/obo/CL_0000132` -#### Removed -- [corneal endothelial cell](http://purl.obolibrary.org/obo/CL_0000132) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009079"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [corneal endothelial cell](http://purl.obolibrary.org/obo/CL_0000132) SubClassOf [neurecto-epithelial cell](http://purl.obolibrary.org/obo/CL_0000710) +### common myeloid progenitor, CD34-positive `http://purl.obolibrary.org/obo/CL_0001059` #### Added -- [corneal endothelial cell](http://purl.obolibrary.org/obo/CL_0000132) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009079"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [common myeloid progenitor, CD34-positive](http://purl.obolibrary.org/obo/CL_0001059) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### corneal epithelial cell `http://purl.obolibrary.org/obo/CL_0000575` +### connective tissue cell `http://purl.obolibrary.org/obo/CL_0002320` #### Removed -- [corneal epithelial cell](http://purl.obolibrary.org/obo/CL_0000575) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009264"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [connective tissue cell](http://purl.obolibrary.org/obo/CL_0002320) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) #### Added -- [corneal epithelial cell](http://purl.obolibrary.org/obo/CL_0000575) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009264"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [connective tissue cell](http://purl.obolibrary.org/obo/CL_0002320) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### cranial motor neuron `http://purl.obolibrary.org/obo/CL_0015000` -#### Removed -- [cranial motor neuron](http://purl.obolibrary.org/obo/CL_0015000) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005730"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### corneocyte `http://purl.obolibrary.org/obo/CL_0002153` #### Added -- [cranial motor neuron](http://purl.obolibrary.org/obo/CL_0015000) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005730"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [corneocyte](http://purl.obolibrary.org/obo/CL_0002153) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### crypt olfactory receptor neuron `http://purl.obolibrary.org/obo/CL_0000849` -#### Removed -- [crypt olfactory receptor neuron](http://purl.obolibrary.org/obo/CL_0000849) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009360"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### crypt-bottom fibroblast `http://purl.obolibrary.org/obo/CL_4052008` #### Added -- [crypt olfactory receptor neuron](http://purl.obolibrary.org/obo/CL_0000849) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009360"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [crypt-bottom fibroblast](http://purl.obolibrary.org/obo/CL_4052008) [label](http://www.w3.org/2000/01/rdf-schema#label) "crypt-bottom fibroblast"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [crypt-bottom fibroblast](http://purl.obolibrary.org/obo/CL_4052008) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "bottom pericryptic-associated fibroblasts"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33916891"^^[string](http://www.w3.org/2001/XMLSchema#string) -### cyanoblast `http://purl.obolibrary.org/obo/CL_0005005` -#### Removed -- [cyanoblast](http://purl.obolibrary.org/obo/CL_0005005) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005332"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [crypt-bottom fibroblast](http://purl.obolibrary.org/obo/CL_4052008) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "CBFs"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) -#### Added -- [cyanoblast](http://purl.obolibrary.org/obo/CL_0005005) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005332"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:/10.1371/journal.pbio.3001032"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [crypt-bottom fibroblast](http://purl.obolibrary.org/obo/CL_4052008) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A subepithelial intestinal fibroblast that is located adjacent to the base of the crypt of Lieberkühn, near the intestinal stem cells. Characterized by low PDGFRα expression, this cell is crucial for maintaining the intestinal stem cell niche. Crypt-bottom fibroblast secretes key signaling molecules including canonical Wnt ligands (Wnt2, Wnt2b), Wnt potentiators (Rspo3), and BMP inhibitors (Grem1), which collectively regulate intestinal stem cell function and epithelial homeostasis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:/10.1371/journal.pbio.3001032"^^[string](http://www.w3.org/2001/XMLSchema#string) -### cyanophore `http://purl.obolibrary.org/obo/CL_0000747` -#### Removed -- [cyanophore](http://purl.obolibrary.org/obo/CL_0000747) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009317"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33916891"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [cyanophore](http://purl.obolibrary.org/obo/CL_0000747) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009317"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [crypt-bottom fibroblast](http://purl.obolibrary.org/obo/CL_4052008) [date](http://purl.org/dc/terms/date) "2024-09-23T10:23:18Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) +- [crypt-bottom fibroblast](http://purl.obolibrary.org/obo/CL_4052008) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052008"^^[string](http://www.w3.org/2001/XMLSchema#string) -### cycling B cell `http://purl.obolibrary.org/obo/CL_4033068` +- [crypt-bottom fibroblast](http://purl.obolibrary.org/obo/CL_4052008) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) -#### Added -- [cycling B cell](http://purl.obolibrary.org/obo/CL_4033068) [date](http://purl.org/dc/terms/date) "2024-07-02T09:14:23Z"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [crypt-bottom fibroblast](http://purl.obolibrary.org/obo/CL_4052008) + +- [crypt-bottom fibroblast](http://purl.obolibrary.org/obo/CL_4052008) SubClassOf [subepithelial intestinal fibroblast](http://purl.obolibrary.org/obo/CL_4052007) -- [cycling B cell](http://purl.obolibrary.org/obo/CL_4033068) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) +- [crypt-bottom fibroblast](http://purl.obolibrary.org/obo/CL_4052008) SubClassOf [RO_0002220](http://purl.obolibrary.org/obo/RO_0002220) some [UBERON_0013739](http://purl.obolibrary.org/obo/UBERON_0013739) -- [cycling B cell](http://purl.obolibrary.org/obo/CL_4033068) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "proliferating B cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31348891"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [crypt-bottom fibroblast](http://purl.obolibrary.org/obo/CL_4052008) SubClassOf [RO_0002220](http://purl.obolibrary.org/obo/RO_0002220) some [intestinal crypt stem cell](http://purl.obolibrary.org/obo/CL_0002250) -- [cycling B cell](http://purl.obolibrary.org/obo/CL_4033068) [label](http://www.w3.org/2000/01/rdf-schema#label) "cycling B cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling B cell](http://purl.obolibrary.org/obo/CL_4033068) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4033068"^^[string](http://www.w3.org/2001/XMLSchema#string) +### crypt-top fibroblast `http://purl.obolibrary.org/obo/CL_4052009` -- [cycling B cell](http://purl.obolibrary.org/obo/CL_4033068) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A(n) B cell that is cycling."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31348891"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [crypt-top fibroblast](http://purl.obolibrary.org/obo/CL_4052009) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052009"^^[string](http://www.w3.org/2001/XMLSchema#string) -- Class: [cycling B cell](http://purl.obolibrary.org/obo/CL_4033068) +- [crypt-top fibroblast](http://purl.obolibrary.org/obo/CL_4052009) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) -- [cycling B cell](http://purl.obolibrary.org/obo/CL_4033068) EquivalentTo [B cell](http://purl.obolibrary.org/obo/CL_0000236) and ([RO_0000056](http://purl.obolibrary.org/obo/RO_0000056) some [GO_0022402](http://purl.obolibrary.org/obo/GO_0022402)) and ([RO_0000086](http://purl.obolibrary.org/obo/RO_0000086) some [PATO_0002354](http://purl.obolibrary.org/obo/PATO_0002354)) +- [crypt-top fibroblast](http://purl.obolibrary.org/obo/CL_4052009) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "S2b fibroblast"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37495570"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling B cell](http://purl.obolibrary.org/obo/CL_4033068) SubClassOf [RO_0000056](http://purl.obolibrary.org/obo/RO_0000056) some [GO_0022402](http://purl.obolibrary.org/obo/GO_0022402) +- [crypt-top fibroblast](http://purl.obolibrary.org/obo/CL_4052009) [date](http://purl.org/dc/terms/date) "2024-09-23T11:14:04Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -- [cycling B cell](http://purl.obolibrary.org/obo/CL_4033068) SubClassOf [RO_0000086](http://purl.obolibrary.org/obo/RO_0000086) some [PATO_0002354](http://purl.obolibrary.org/obo/PATO_0002354) +- [crypt-top fibroblast](http://purl.obolibrary.org/obo/CL_4052009) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "CTFs"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) -- [cycling B cell](http://purl.obolibrary.org/obo/CL_4033068) SubClassOf [B cell](http://purl.obolibrary.org/obo/CL_0000236) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:/10.1371/journal.pbio.3001032"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [crypt-top fibroblast](http://purl.obolibrary.org/obo/CL_4052009) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "S2b fibroblasts are located at the top of the crypt and express NRG1 and NPY."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37495570"^^[string](http://www.w3.org/2001/XMLSchema#string) -### cycling CD4-positive, alpha-beta T cell `http://purl.obolibrary.org/obo/CL_4033075` +- [crypt-top fibroblast](http://purl.obolibrary.org/obo/CL_4052009) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "top pericryptic fibroblast"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33916891"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [cycling CD4-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_4033075) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A(n) CD4-positive, alpha-beta T cell that is cycling."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34062119"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [crypt-top fibroblast](http://purl.obolibrary.org/obo/CL_4052009) [label](http://www.w3.org/2000/01/rdf-schema#label) "crypt-top fibroblast"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling CD4-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_4033075) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) +- [crypt-top fibroblast](http://purl.obolibrary.org/obo/CL_4052009) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A subepithelial intestinal fibroblast that is located adjacent to the top of the crypt of Lieberkuhn. Characterized by high experession of PDGFRα, this cell secretes a range of signaling factors, including WNTs and BMPs, that drive epithelial differentiation, creating a gradient that regulates the balance between stem cell maintenance and differentiation."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:/10.1371/journal.pbio.3001032"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling CD4-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_4033075) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "proliferating CD4-positive, alpha-beta T cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34062119"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33916891"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling CD4-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_4033075) [label](http://www.w3.org/2000/01/rdf-schema#label) "cycling CD4-positive, alpha-beta T cell"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [crypt-top fibroblast](http://purl.obolibrary.org/obo/CL_4052009) -- [cycling CD4-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_4033075) [date](http://purl.org/dc/terms/date) "2024-07-02T09:14:23Z"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [crypt-top fibroblast](http://purl.obolibrary.org/obo/CL_4052009) SubClassOf [subepithelial intestinal fibroblast](http://purl.obolibrary.org/obo/CL_4052007) -- [cycling CD4-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_4033075) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4033075"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [crypt-top fibroblast](http://purl.obolibrary.org/obo/CL_4052009) SubClassOf [RO_0002220](http://purl.obolibrary.org/obo/RO_0002220) some [UBERON_0013740](http://purl.obolibrary.org/obo/UBERON_0013740) -- Class: [cycling CD4-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_4033075) -- [cycling CD4-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_4033075) EquivalentTo [CD4-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_0000624) and ([RO_0000056](http://purl.obolibrary.org/obo/RO_0000056) some [GO_0022402](http://purl.obolibrary.org/obo/GO_0022402)) and ([RO_0000086](http://purl.obolibrary.org/obo/RO_0000086) some [PATO_0002354](http://purl.obolibrary.org/obo/PATO_0002354)) +### cuboidal granulosa cell `http://purl.obolibrary.org/obo/CL_4033084` -- [cycling CD4-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_4033075) SubClassOf [CD4-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_0000624) +#### Added +- [cuboidal granulosa cell](http://purl.obolibrary.org/obo/CL_4033084) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "cuboidal GC"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) -- [cycling CD4-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_4033075) SubClassOf [cycling T cell](http://purl.obolibrary.org/obo/CL_4033069) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33914868"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [cuboidal granulosa cell](http://purl.obolibrary.org/obo/CL_4033084) [label](http://www.w3.org/2000/01/rdf-schema#label) "cuboidal granulosa cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -### cycling CD8-positive, alpha-beta T cell `http://purl.obolibrary.org/obo/CL_4033074` +- [cuboidal granulosa cell](http://purl.obolibrary.org/obo/CL_4033084) [date](http://purl.org/dc/terms/date) "2024-09-24T13:14:57Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -#### Added -- [cycling CD8-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_4033074) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A(n) CD8-positive, alpha-beta T cell that is cycling."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34062119"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [cuboidal granulosa cell](http://purl.obolibrary.org/obo/CL_4033084) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "cuboidal epithelial granulosa cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31849844"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling CD8-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_4033074) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4033074"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [cuboidal granulosa cell](http://purl.obolibrary.org/obo/CL_4033084) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) -- [cycling CD8-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_4033074) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "proliferating CD8-positive, alpha-beta T cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34062119"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [cuboidal granulosa cell](http://purl.obolibrary.org/obo/CL_4033084) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4033084"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling CD8-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_4033074) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) +- [cuboidal granulosa cell](http://purl.obolibrary.org/obo/CL_4033084) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A granulosa cell that has a cuboidal morphology and develops from squamous granulosa cell during the transition between primordial follicle to primary follicle. Cuboidal granulosa cells proliferate to form a second layer within secondary follicles."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:28892263"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling CD8-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_4033074) [date](http://purl.org/dc/terms/date) "2024-07-02T09:14:23Z"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [cuboidal granulosa cell](http://purl.obolibrary.org/obo/CL_4033084) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "columnar granulosa cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:19001500"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling CD8-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_4033074) [label](http://www.w3.org/2000/01/rdf-schema#label) "cycling CD8-positive, alpha-beta T cell"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [cuboidal granulosa cell](http://purl.obolibrary.org/obo/CL_4033084) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "columnar GC"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) -- Class: [cycling CD8-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_4033074) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:19001500"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling CD8-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_4033074) EquivalentTo [CD8-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_0000625) and ([RO_0000056](http://purl.obolibrary.org/obo/RO_0000056) some [GO_0022402](http://purl.obolibrary.org/obo/GO_0022402)) and ([RO_0000086](http://purl.obolibrary.org/obo/RO_0000086) some [PATO_0002354](http://purl.obolibrary.org/obo/PATO_0002354)) +- Class: [cuboidal granulosa cell](http://purl.obolibrary.org/obo/CL_4033084) -- [cycling CD8-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_4033074) SubClassOf [CD8-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_0000625) +- [cuboidal granulosa cell](http://purl.obolibrary.org/obo/CL_4033084) SubClassOf [granulosa cell](http://purl.obolibrary.org/obo/CL_0000501) -- [cycling CD8-positive, alpha-beta T cell](http://purl.obolibrary.org/obo/CL_4033074) SubClassOf [cycling T cell](http://purl.obolibrary.org/obo/CL_4033069) +- [cuboidal granulosa cell](http://purl.obolibrary.org/obo/CL_4033084) SubClassOf [UBERON_0004120](http://purl.obolibrary.org/obo/UBERON_0004120) +- [cuboidal granulosa cell](http://purl.obolibrary.org/obo/CL_4033084) SubClassOf [RO_0002207](http://purl.obolibrary.org/obo/RO_0002207) some [squamous granulosa cell](http://purl.obolibrary.org/obo/CL_4033083) -### cycling T cell `http://purl.obolibrary.org/obo/CL_4033069` -#### Added -- [cycling T cell](http://purl.obolibrary.org/obo/CL_4033069) [date](http://purl.org/dc/terms/date) "2024-07-02T09:14:23Z"^^[string](http://www.w3.org/2001/XMLSchema#string) +### cumulus cell `http://purl.obolibrary.org/obo/CL_0000711` +#### Removed +- [cumulus cell](http://purl.obolibrary.org/obo/CL_0000711) SubClassOf [RO_0002202](http://purl.obolibrary.org/obo/RO_0002202) some [granulosa cell](http://purl.obolibrary.org/obo/CL_0000501) -- [cycling T cell](http://purl.obolibrary.org/obo/CL_4033069) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "proliferating T cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37291214"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [cumulus cell](http://purl.obolibrary.org/obo/CL_0000711) SubClassOf [follicular cell of ovary](http://purl.obolibrary.org/obo/CL_0002174) -- [cycling T cell](http://purl.obolibrary.org/obo/CL_4033069) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) +#### Added +- [cumulus cell](http://purl.obolibrary.org/obo/CL_0000711) SubClassOf [UBERON_0004120](http://purl.obolibrary.org/obo/UBERON_0004120) -- [cycling T cell](http://purl.obolibrary.org/obo/CL_4033069) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4033069"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [cumulus cell](http://purl.obolibrary.org/obo/CL_0000711) SubClassOf [RO_0002202](http://purl.obolibrary.org/obo/RO_0002202) some [cuboidal granulosa cell](http://purl.obolibrary.org/obo/CL_4033084) -- [cycling T cell](http://purl.obolibrary.org/obo/CL_4033069) [label](http://www.w3.org/2000/01/rdf-schema#label) "cycling T cell"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [cumulus cell](http://purl.obolibrary.org/obo/CL_0000711) SubClassOf [granulosa cell](http://purl.obolibrary.org/obo/CL_0000501) -- [cycling T cell](http://purl.obolibrary.org/obo/CL_4033069) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A(n) T cell that is cycling."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37291214"^^[string](http://www.w3.org/2001/XMLSchema#string) -- Class: [cycling T cell](http://purl.obolibrary.org/obo/CL_4033069) +### cyanophore `http://purl.obolibrary.org/obo/CL_0000747` -- [cycling T cell](http://purl.obolibrary.org/obo/CL_4033069) EquivalentTo [T cell](http://purl.obolibrary.org/obo/CL_0000084) and ([RO_0000056](http://purl.obolibrary.org/obo/RO_0000056) some [GO_0022402](http://purl.obolibrary.org/obo/GO_0022402)) and ([RO_0000086](http://purl.obolibrary.org/obo/RO_0000086) some [PATO_0002354](http://purl.obolibrary.org/obo/PATO_0002354)) +#### Added +- [cyanophore](http://purl.obolibrary.org/obo/CL_0000747) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -- [cycling T cell](http://purl.obolibrary.org/obo/CL_4033069) SubClassOf [RO_0000086](http://purl.obolibrary.org/obo/RO_0000086) some [PATO_0002354](http://purl.obolibrary.org/obo/PATO_0002354) -- [cycling T cell](http://purl.obolibrary.org/obo/CL_4033069) SubClassOf [RO_0000056](http://purl.obolibrary.org/obo/RO_0000056) some [GO_0022402](http://purl.obolibrary.org/obo/GO_0022402) +### cystoblast `http://purl.obolibrary.org/obo/CL_0000722` +#### Removed +- [cystoblast](http://purl.obolibrary.org/obo/CL_0000722) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_6656](http://purl.obolibrary.org/obo/NCBITaxon_6656) -- [cycling T cell](http://purl.obolibrary.org/obo/CL_4033069) SubClassOf [T cell](http://purl.obolibrary.org/obo/CL_0000084) +#### Added +- [cystoblast](http://purl.obolibrary.org/obo/CL_0000722) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_6656](http://purl.obolibrary.org/obo/NCBITaxon_6656) -### cycling alveolar macrophage `http://purl.obolibrary.org/obo/CL_4033077` +### decidual natural killer cell, human `http://purl.obolibrary.org/obo/CL_0002343` #### Added -- [cycling alveolar macrophage](http://purl.obolibrary.org/obo/CL_4033077) [label](http://www.w3.org/2000/01/rdf-schema#label) "cycling alveolar macrophage"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [decidual natural killer cell, human](http://purl.obolibrary.org/obo/CL_0002343) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -- [cycling alveolar macrophage](http://purl.obolibrary.org/obo/CL_4033077) [date](http://purl.org/dc/terms/date) "2024-07-02T09:14:23Z"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling alveolar macrophage](http://purl.obolibrary.org/obo/CL_4033077) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4033077"^^[string](http://www.w3.org/2001/XMLSchema#string) +### dendritic cell `http://purl.obolibrary.org/obo/CL_0000451` -- [cycling alveolar macrophage](http://purl.obolibrary.org/obo/CL_4033077) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "proliferating alveolar macrophage"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37291214"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [dendritic cell](http://purl.obolibrary.org/obo/CL_0000451) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -- [cycling alveolar macrophage](http://purl.obolibrary.org/obo/CL_4033077) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A(n) alveolar macrophage that is cycling."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37291214"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling alveolar macrophage](http://purl.obolibrary.org/obo/CL_4033077) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) +### dermal chromatophore `http://purl.obolibrary.org/obo/CL_4040006` -- Class: [cycling alveolar macrophage](http://purl.obolibrary.org/obo/CL_4033077) +#### Added +- [dermal chromatophore](http://purl.obolibrary.org/obo/CL_4040006) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -- [cycling alveolar macrophage](http://purl.obolibrary.org/obo/CL_4033077) EquivalentTo [alveolar macrophage](http://purl.obolibrary.org/obo/CL_0000583) and ([RO_0000056](http://purl.obolibrary.org/obo/RO_0000056) some [GO_0022402](http://purl.obolibrary.org/obo/GO_0022402)) and ([RO_0000086](http://purl.obolibrary.org/obo/RO_0000086) some [PATO_0002354](http://purl.obolibrary.org/obo/PATO_0002354)) -- [cycling alveolar macrophage](http://purl.obolibrary.org/obo/CL_4033077) SubClassOf [alveolar macrophage](http://purl.obolibrary.org/obo/CL_0000583) +### early T lineage precursor `http://purl.obolibrary.org/obo/CL_0002425` -- [cycling alveolar macrophage](http://purl.obolibrary.org/obo/CL_4033077) SubClassOf [cycling macrophage](http://purl.obolibrary.org/obo/CL_4033076) +#### Added +- [early T lineage precursor](http://purl.obolibrary.org/obo/CL_0002425) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### cycling basal cell `http://purl.obolibrary.org/obo/CL_4033082` +### early colonocyte `http://purl.obolibrary.org/obo/CL_4047018` #### Added -- [cycling basal cell](http://purl.obolibrary.org/obo/CL_4033082) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) +- [early colonocyte](http://purl.obolibrary.org/obo/CL_4047018) [contributor](http://purl.org/dc/terms/contributor) [0009-0005-7919-4905](https://orcid.org/0009-0005-7919-4905) -- [cycling basal cell](http://purl.obolibrary.org/obo/CL_4033082) [label](http://www.w3.org/2000/01/rdf-schema#label) "cycling basal cell"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [early colonocyte](http://purl.obolibrary.org/obo/CL_4047018) [label](http://www.w3.org/2000/01/rdf-schema#label) "early colonocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling basal cell](http://purl.obolibrary.org/obo/CL_4033082) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A(n) basal cell that is cycling."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33208946"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [early colonocyte](http://purl.obolibrary.org/obo/CL_4047018) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4047018"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling basal cell](http://purl.obolibrary.org/obo/CL_4033082) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4033082"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [early colonocyte](http://purl.obolibrary.org/obo/CL_4047018) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An enterocyte that is part of the colon, in the early stages of differentiation, located in the intestinal crypt-villus axis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36060223"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling basal cell](http://purl.obolibrary.org/obo/CL_4033082) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "proliferating basal cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33208946"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:28049136"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling basal cell](http://purl.obolibrary.org/obo/CL_4033082) [date](http://purl.org/dc/terms/date) "2024-07-02T09:14:23Z"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [early colonocyte](http://purl.obolibrary.org/obo/CL_4047018) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "early enterocyte of colon"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.1101/2021.01.13.426602"^^[string](http://www.w3.org/2001/XMLSchema#string) -- Class: [cycling basal cell](http://purl.obolibrary.org/obo/CL_4033082) +- [early colonocyte](http://purl.obolibrary.org/obo/CL_4047018) [date](http://purl.org/dc/terms/date) "2024-09-24T11:50:13Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -- [cycling basal cell](http://purl.obolibrary.org/obo/CL_4033082) EquivalentTo [basal cell](http://purl.obolibrary.org/obo/CL_0000646) and ([RO_0000056](http://purl.obolibrary.org/obo/RO_0000056) some [GO_0022402](http://purl.obolibrary.org/obo/GO_0022402)) and ([RO_0000086](http://purl.obolibrary.org/obo/RO_0000086) some [PATO_0002354](http://purl.obolibrary.org/obo/PATO_0002354)) +- Class: [early colonocyte](http://purl.obolibrary.org/obo/CL_4047018) -- [cycling basal cell](http://purl.obolibrary.org/obo/CL_4033082) SubClassOf [basal cell](http://purl.obolibrary.org/obo/CL_0000646) +- [early colonocyte](http://purl.obolibrary.org/obo/CL_4047018) EquivalentTo [early enterocyte](http://purl.obolibrary.org/obo/CL_4047019) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001155](http://purl.obolibrary.org/obo/UBERON_0001155)) -- [cycling basal cell](http://purl.obolibrary.org/obo/CL_4033082) SubClassOf [RO_0000086](http://purl.obolibrary.org/obo/RO_0000086) some [PATO_0002354](http://purl.obolibrary.org/obo/PATO_0002354) +- [early colonocyte](http://purl.obolibrary.org/obo/CL_4047018) SubClassOf [early enterocyte](http://purl.obolibrary.org/obo/CL_4047019) -- [cycling basal cell](http://purl.obolibrary.org/obo/CL_4033082) SubClassOf [RO_0000056](http://purl.obolibrary.org/obo/RO_0000056) some [GO_0022402](http://purl.obolibrary.org/obo/GO_0022402) +- [early colonocyte](http://purl.obolibrary.org/obo/CL_4047018) SubClassOf [enterocyte of colon](http://purl.obolibrary.org/obo/CL_1000347) -- [cycling basal cell](http://purl.obolibrary.org/obo/CL_4033082) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) - -### cycling dendritic cell `http://purl.obolibrary.org/obo/CL_4033070` +### early enterocyte `http://purl.obolibrary.org/obo/CL_4047019` #### Added -- [cycling dendritic cell](http://purl.obolibrary.org/obo/CL_4033070) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A(n) dendritic cell that is cycling."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32066951"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [early enterocyte](http://purl.obolibrary.org/obo/CL_4047019) [label](http://www.w3.org/2000/01/rdf-schema#label) "early enterocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling dendritic cell](http://purl.obolibrary.org/obo/CL_4033070) [date](http://purl.org/dc/terms/date) "2024-07-02T09:14:23Z"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [early enterocyte](http://purl.obolibrary.org/obo/CL_4047019) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An enterocyte in the early stages of development, located above the transit-amplifying cell zone in the intestinal crypt-villus axis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35235783"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling dendritic cell](http://purl.obolibrary.org/obo/CL_4033070) [label](http://www.w3.org/2000/01/rdf-schema#label) "cycling dendritic cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20683682"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling dendritic cell](http://purl.obolibrary.org/obo/CL_4033070) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4033070"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [early enterocyte](http://purl.obolibrary.org/obo/CL_4047019) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4047019"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling dendritic cell](http://purl.obolibrary.org/obo/CL_4033070) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) +- [early enterocyte](http://purl.obolibrary.org/obo/CL_4047019) [date](http://purl.org/dc/terms/date) "2024-09-24T12:11:09Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -- [cycling dendritic cell](http://purl.obolibrary.org/obo/CL_4033070) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "proliferating dendritic cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32066951"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [early enterocyte](http://purl.obolibrary.org/obo/CL_4047019) [contributor](http://purl.org/dc/terms/contributor) [0009-0005-7919-4905](https://orcid.org/0009-0005-7919-4905) -- Class: [cycling dendritic cell](http://purl.obolibrary.org/obo/CL_4033070) +- Class: [early enterocyte](http://purl.obolibrary.org/obo/CL_4047019) -- [cycling dendritic cell](http://purl.obolibrary.org/obo/CL_4033070) EquivalentTo [dendritic cell](http://purl.obolibrary.org/obo/CL_0000451) and ([RO_0000056](http://purl.obolibrary.org/obo/RO_0000056) some [GO_0022402](http://purl.obolibrary.org/obo/GO_0022402)) and ([RO_0000086](http://purl.obolibrary.org/obo/RO_0000086) some [PATO_0002354](http://purl.obolibrary.org/obo/PATO_0002354)) +- [early enterocyte](http://purl.obolibrary.org/obo/CL_4047019) EquivalentTo [enterocyte](http://purl.obolibrary.org/obo/CL_0000584) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0013740](http://purl.obolibrary.org/obo/UBERON_0013740)) -- [cycling dendritic cell](http://purl.obolibrary.org/obo/CL_4033070) SubClassOf [cycling mononuclear phagocyte](http://purl.obolibrary.org/obo/CL_4033078) +- [early enterocyte](http://purl.obolibrary.org/obo/CL_4047019) SubClassOf [enterocyte](http://purl.obolibrary.org/obo/CL_0000584) -- [cycling dendritic cell](http://purl.obolibrary.org/obo/CL_4033070) SubClassOf [dendritic cell](http://purl.obolibrary.org/obo/CL_0000451) +- [early enterocyte](http://purl.obolibrary.org/obo/CL_4047019) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0013740](http://purl.obolibrary.org/obo/UBERON_0013740) -### cycling endothelial cell of lymphatic vessel `http://purl.obolibrary.org/obo/CL_4033079` +### ectodermal cell `http://purl.obolibrary.org/obo/CL_0000221` #### Added -- [cycling endothelial cell of lymphatic vessel](http://purl.obolibrary.org/obo/CL_4033079) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A(n) endothelial cell of lymphatic vessel that is cycling."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37291214"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [ectodermal cell](http://purl.obolibrary.org/obo/CL_0000221) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -- [cycling endothelial cell of lymphatic vessel](http://purl.obolibrary.org/obo/CL_4033079) [date](http://purl.org/dc/terms/date) "2024-07-02T09:14:23Z"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling endothelial cell of lymphatic vessel](http://purl.obolibrary.org/obo/CL_4033079) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "proliferating endothelial cell of lymphatic vessel"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37291214"^^[string](http://www.w3.org/2001/XMLSchema#string) +### elicited macrophage `http://purl.obolibrary.org/obo/CL_0000861` -- [cycling endothelial cell of lymphatic vessel](http://purl.obolibrary.org/obo/CL_4033079) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4033079"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [cycling endothelial cell of lymphatic vessel](http://purl.obolibrary.org/obo/CL_4033079) [label](http://www.w3.org/2000/01/rdf-schema#label) "cycling endothelial cell of lymphatic vessel"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [elicited macrophage](http://purl.obolibrary.org/obo/CL_0000861) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -- [cycling endothelial cell of lymphatic vessel](http://purl.obolibrary.org/obo/CL_4033079) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) -- Class: [cycling endothelial cell of lymphatic vessel](http://purl.obolibrary.org/obo/CL_4033079) +### endocrine cell `http://purl.obolibrary.org/obo/CL_0000163` -- [cycling endothelial cell of lymphatic vessel](http://purl.obolibrary.org/obo/CL_4033079) EquivalentTo [endothelial cell of lymphatic vessel](http://purl.obolibrary.org/obo/CL_0002138) and ([RO_0000056](http://purl.obolibrary.org/obo/RO_0000056) some [GO_0022402](http://purl.obolibrary.org/obo/GO_0022402)) and ([RO_0000086](http://purl.obolibrary.org/obo/RO_0000086) some [PATO_0002354](http://purl.obolibrary.org/obo/PATO_0002354)) +#### Added +- [endocrine cell](http://purl.obolibrary.org/obo/CL_0000163) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -- [cycling endothelial cell of lymphatic vessel](http://purl.obolibrary.org/obo/CL_4033079) SubClassOf [RO_0000086](http://purl.obolibrary.org/obo/RO_0000086) some [PATO_0002354](http://purl.obolibrary.org/obo/PATO_0002354) -- [cycling endothelial cell of lymphatic vessel](http://purl.obolibrary.org/obo/CL_4033079) SubClassOf [RO_0000056](http://purl.obolibrary.org/obo/RO_0000056) some [GO_0022402](http://purl.obolibrary.org/obo/GO_0022402) +### endodermal cell `http://purl.obolibrary.org/obo/CL_0000223` -- [cycling endothelial cell of lymphatic vessel](http://purl.obolibrary.org/obo/CL_4033079) SubClassOf [endothelial cell of lymphatic vessel](http://purl.obolibrary.org/obo/CL_0002138) +#### Added +- [endodermal cell](http://purl.obolibrary.org/obo/CL_0000223) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### cycling gamma-delta T cell `http://purl.obolibrary.org/obo/CL_4033072` +### endothelial cell `http://purl.obolibrary.org/obo/CL_0000115` #### Added -- [cycling gamma-delta T cell](http://purl.obolibrary.org/obo/CL_4033072) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4033072"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [endothelial cell](http://purl.obolibrary.org/obo/CL_0000115) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -- [cycling gamma-delta T cell](http://purl.obolibrary.org/obo/CL_4033072) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A(n) gamma-delta T cell that is cycling."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32066951"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling gamma-delta T cell](http://purl.obolibrary.org/obo/CL_4033072) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) +### endothelial cell of artery `http://purl.obolibrary.org/obo/CL_1000413` -- [cycling gamma-delta T cell](http://purl.obolibrary.org/obo/CL_4033072) [label](http://www.w3.org/2000/01/rdf-schema#label) "cycling gamma-delta T cell"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [endothelial cell of artery](http://purl.obolibrary.org/obo/CL_1000413) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -- [cycling gamma-delta T cell](http://purl.obolibrary.org/obo/CL_4033072) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "proliferating gamma-delta T cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32066951"^^[string](http://www.w3.org/2001/XMLSchema#string) +Endothelial cells of the artery, also referred to as arterial endothelial cells, form an integral part of the arterial system. They form a single layer, known as the endothelium, lining the interior surface of arteries, and are able to respond to the high-pressure and flow conditions present in arteries. The primary role of these cells is to provide a barrier between the vessel wall and the blood, exhibiting selective permeability to regulate the movement of liquids, gases, and blood-borne substances across the vascular wall. +Arterial endothelial cells significantly contribute to maintaining vascular homeostasis. They are at the forefront of sensations and responses to mechanical stimuli, like shear stress and blood pressure changes. An additional key function pertains to the production of nitric oxide, which helps to regulate vascular tone and blood pressure, prevents platelet aggregation, limits leukocyte adhesion to the endothelium, and inhibits smooth muscle cell proliferation. These varied but connected functions help to preclude the development of atherosclerosis, ensuring normal circulation and arterial health. +Moreover, these cells play a pivotal role in inflammation and coagulation processes. During inflammatory events, they express various adhesion molecules, aiding in leukocyte recruitment and rolling onto the vessel walls for immune response. They also produce anticoagulant and procoagulant substances, involved in blood clotting and clot dissolution, respectively. Dysregulation of the usual functions of arterial endothelial cells can result in serious pathophysiological conditions, such as atherosclerosis, hypertension, and other cardiovascular diseases."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1177/153857440303700107"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling gamma-delta T cell](http://purl.obolibrary.org/obo/CL_4033072) [date](http://purl.org/dc/terms/date) "2024-07-02T09:14:23Z"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s00441-008-0706-5"^^[string](http://www.w3.org/2001/XMLSchema#string) -- Class: [cycling gamma-delta T cell](http://purl.obolibrary.org/obo/CL_4033072) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.jvs.2004.03.043"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling gamma-delta T cell](http://purl.obolibrary.org/obo/CL_4033072) EquivalentTo [gamma-delta T cell](http://purl.obolibrary.org/obo/CL_0000798) and ([RO_0000056](http://purl.obolibrary.org/obo/RO_0000056) some [GO_0022402](http://purl.obolibrary.org/obo/GO_0022402)) and ([RO_0000086](http://purl.obolibrary.org/obo/RO_0000086) some [PATO_0002354](http://purl.obolibrary.org/obo/PATO_0002354)) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.ccm.2021.08.005"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling gamma-delta T cell](http://purl.obolibrary.org/obo/CL_4033072) SubClassOf [gamma-delta T cell](http://purl.obolibrary.org/obo/CL_0000798) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s10456-021-09785-7"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling gamma-delta T cell](http://purl.obolibrary.org/obo/CL_4033072) SubClassOf [cycling T cell](http://purl.obolibrary.org/obo/CL_4033069) +- [endothelial cell of artery](http://purl.obolibrary.org/obo/CL_1000413) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000413"^^[string](http://www.w3.org/2001/XMLSchema#string) -### cycling glial cell `http://purl.obolibrary.org/obo/CL_4047002` +### endothelial cell of umbilical vein `http://purl.obolibrary.org/obo/CL_0002618` #### Added -- [cycling glial cell](http://purl.obolibrary.org/obo/CL_4047002) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "proliferating glial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34497389"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [endothelial cell of umbilical vein](http://purl.obolibrary.org/obo/CL_0002618) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002618"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling glial cell](http://purl.obolibrary.org/obo/CL_4047002) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4047002"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [endothelial cell of umbilical vein](http://purl.obolibrary.org/obo/CL_0002618) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -- [cycling glial cell](http://purl.obolibrary.org/obo/CL_4047002) [date](http://purl.org/dc/terms/date) "2024-07-19T09:14:23Z"^^[string](http://www.w3.org/2001/XMLSchema#string) +Endothelial cells of the umbilical vein form the inner lining of the veins found in the umbilical cord. They are involved in tube formation and migration which are essential for angiogenesis, the process of generating new blood vessels; this is critical during the fetal stage for the development of the circulatory system. Endothelial cells of the umbilical vein also play a role in controlling the passage of white blood cells into tissues during inflammatory responses. +Because human umbilical vein endothelial cells (HUVECs) can easily be derived from the umbilical cord, and because they express common endothelial cell markers, they have been used as an epithelial cell model for studies on cell proliferation, migration, angiogenesis, and inflammation. They have been used as models for vascular diseases like atherosclerosis, for investigating how tumor cells infiltrate blood vessels and form metastases. +Thus, while endothelial cells of the umbilical vein play a critical role in vascular biology, they also represent a powerful tool in disease studies and potential treatment strategies."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s12015-006-0015-x"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling glial cell](http://purl.obolibrary.org/obo/CL_4047002) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A(n) glial cell that is cycling."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34497389"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1172/JCI107470"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling glial cell](http://purl.obolibrary.org/obo/CL_4047002) [contributor](http://purl.org/dc/terms/contributor) [0009-0005-7919-4905](https://orcid.org/0009-0005-7919-4905) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK53254/"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling glial cell](http://purl.obolibrary.org/obo/CL_4047002) [label](http://www.w3.org/2000/01/rdf-schema#label) "cycling glial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3390/app10030938"^^[string](http://www.w3.org/2001/XMLSchema#string) -- Class: [cycling glial cell](http://purl.obolibrary.org/obo/CL_4047002) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/cyto.a.20952"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling glial cell](http://purl.obolibrary.org/obo/CL_4047002) EquivalentTo [glial cell](http://purl.obolibrary.org/obo/CL_0000125) and ([RO_0000056](http://purl.obolibrary.org/obo/RO_0000056) some [GO_0022402](http://purl.obolibrary.org/obo/GO_0022402)) and ([RO_0000086](http://purl.obolibrary.org/obo/RO_0000086) some [PATO_0002354](http://purl.obolibrary.org/obo/PATO_0002354)) -- [cycling glial cell](http://purl.obolibrary.org/obo/CL_4047002) SubClassOf [RO_0000056](http://purl.obolibrary.org/obo/RO_0000056) some [GO_0022402](http://purl.obolibrary.org/obo/GO_0022402) +### endothelial stalk cell `http://purl.obolibrary.org/obo/CL_0002671` -- [cycling glial cell](http://purl.obolibrary.org/obo/CL_4047002) SubClassOf [RO_0000086](http://purl.obolibrary.org/obo/RO_0000086) some [PATO_0002354](http://purl.obolibrary.org/obo/PATO_0002354) +#### Added +- [endothelial stalk cell](http://purl.obolibrary.org/obo/CL_0002671) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002671"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling glial cell](http://purl.obolibrary.org/obo/CL_4047002) SubClassOf [glial cell](http://purl.obolibrary.org/obo/CL_0000125) +- [endothelial stalk cell](http://purl.obolibrary.org/obo/CL_0002671) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +Endothelial stalk cells are specialized vascular cells vital in angiogenesis, a process through which new blood vessels are formed from pre-existing ones; specifically, endothelial stalk cells are involved in sprouting angiogenesis, where they help form the body of new blood vessels. +Vascular sprouting relies on the coordinated activity of migrating endothelial tip cells at the forefront and proliferating stalk cells that elongate the sprout. The process is tightly controlled by different growths factors: Vascular Endothelial Growth Factor acts on endothelial cells, inducing them to become endothelial tip cells that initiate sprouting. After sprouting initiation, activation of Notch signaling suppresses differentiation toward a tip cell phenotype and some of the endothelial cells differentiate into stalk cells, which follow tip cells, multiply, and elongate to provide a structural backbone to the growing vessel sprout. +In contrast to endothelial tip cells, which migrate and lead the angiogenic sprout, endothelial stalk cells behind the sprouts continue forming the tube or lumen for blood flow and facilitate maturation and stability of the new vessel. The delicate balance between the activities of stalk and tip cells during angiogenesis is crucial to build a functional vascular network. Dysfunctions in endothelial stalk cells can lead to pathological conditions such as impaired wound healing, unregulated tumor growth, and metastasis due to abnormal angiogenesis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.cmet.2013.08.001"^^[string](http://www.w3.org/2001/XMLSchema#string) -### cycling macrophage `http://purl.obolibrary.org/obo/CL_4033076` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fcell.2021.642352"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [cycling macrophage](http://purl.obolibrary.org/obo/CL_4033076) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4033076"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s12079-019-00511-z"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling macrophage](http://purl.obolibrary.org/obo/CL_4033076) [date](http://purl.org/dc/terms/date) "2024-07-02T09:14:23Z"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1101/cshperspect.a006569"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling macrophage](http://purl.obolibrary.org/obo/CL_4033076) [label](http://www.w3.org/2000/01/rdf-schema#label) "cycling macrophage"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling macrophage](http://purl.obolibrary.org/obo/CL_4033076) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "proliferating macrophage"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33208946"^^[string](http://www.w3.org/2001/XMLSchema#string) +### enterocyte of colon `http://purl.obolibrary.org/obo/CL_1000347` +#### Removed +- [enterocyte of colon](http://purl.obolibrary.org/obo/CL_1000347) [label](http://www.w3.org/2000/01/rdf-schema#label) "enterocyte of colon"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling macrophage](http://purl.obolibrary.org/obo/CL_4033076) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) +#### Added +- [enterocyte of colon](http://purl.obolibrary.org/obo/CL_1000347) [label](http://www.w3.org/2000/01/rdf-schema#label) "colonocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling macrophage](http://purl.obolibrary.org/obo/CL_4033076) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A(n) macrophage that is cycling."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33208946"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [enterocyte of colon](http://purl.obolibrary.org/obo/CL_1000347) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "enterocyte of colon"^^[string](http://www.w3.org/2001/XMLSchema#string) -- Class: [cycling macrophage](http://purl.obolibrary.org/obo/CL_4033076) +- [enterocyte of colon](http://purl.obolibrary.org/obo/CL_1000347) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -- [cycling macrophage](http://purl.obolibrary.org/obo/CL_4033076) EquivalentTo [macrophage](http://purl.obolibrary.org/obo/CL_0000235) and ([RO_0000056](http://purl.obolibrary.org/obo/RO_0000056) some [GO_0022402](http://purl.obolibrary.org/obo/GO_0022402)) and ([RO_0000086](http://purl.obolibrary.org/obo/RO_0000086) some [PATO_0002354](http://purl.obolibrary.org/obo/PATO_0002354)) +Enterocytes of the colon are specialized epithelial cells located in the lining of the colon, the largest part of the large intestine. These cells play a critical role in absorbing water, electrolytes, and certain vitamins from the food material passed on from the small intestine. With a unique structure of finger-like protrusions referred to as microvilli, the enterocytes increase their surface area for effective absorption. The colon is the last part of the digestive system, and as such, it is responsible for compacting undigested food materials and forming fecal matter. Enterocytes of the colon facilitate this process effectively through absorption of water. +Enterocytes are known for their high regeneration potential, replenishing every 4-5 days, enabling the healthy functioning of the colon. They originate from stem cells located in the crypt of the colon and differentiate into mature enterocytes as they migrate upwards towards the luminal surface. This constant turnover aids in maintaining the intestinal barrier, preventing the entry of detrimental substances into the systemic circulation. Their tight junctions with other epithelial cells provide a robust barrier against invasive pathogens. +Enterocytes of the colon are involved in the communication with the gut microbiota. These cells harbor enzymes necessary for the metabolism of short-chain fatty acids, which are the byproducts of the fermentation process by gut bacteria. Short-chain fatty acids serve as a major energy source for colonocytes and are important for maintaining colonic health. The dysfunction of enterocytes, therefore, could lead to disorders such as inflammatory bowel disease or colorectal cancer."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nrgastro.2013.35"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling macrophage](http://purl.obolibrary.org/obo/CL_4033076) SubClassOf [cycling mononuclear phagocyte](http://purl.obolibrary.org/obo/CL_4033078) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nri3738"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling macrophage](http://purl.obolibrary.org/obo/CL_4033076) SubClassOf [cycling myeloid cell](http://purl.obolibrary.org/obo/CL_4033081) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1084/jem.20191130"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling macrophage](http://purl.obolibrary.org/obo/CL_4033076) SubClassOf [macrophage](http://purl.obolibrary.org/obo/CL_0000235) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2019.00277"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s11894-010-0130-3"^^[string](http://www.w3.org/2001/XMLSchema#string) -### cycling monocyte `http://purl.obolibrary.org/obo/CL_4033073` +- [enterocyte of colon](http://purl.obolibrary.org/obo/CL_1000347) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000347"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [cycling monocyte](http://purl.obolibrary.org/obo/CL_4033073) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4033073"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling monocyte](http://purl.obolibrary.org/obo/CL_4033073) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) +### enterocyte of epithelium of small intestine `http://purl.obolibrary.org/obo/CL_1000334` -- [cycling monocyte](http://purl.obolibrary.org/obo/CL_4033073) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "proliferating monocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31348891"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [enterocyte of epithelium of small intestine](http://purl.obolibrary.org/obo/CL_1000334) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -- [cycling monocyte](http://purl.obolibrary.org/obo/CL_4033073) [label](http://www.w3.org/2000/01/rdf-schema#label) "cycling monocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) +Enterocytes of the epithelium of the small intestine are specialized cells that reside in the lining of the small intestine, and are primarily responsible for the essential process of nutrient absorption. These cells are columnar epithelial cells with an apical surface lined with microvilli, a feature referred to as the 'brush border', to maximize the surface area available for absorption. +Enterocytes play a critical role in both the digestion and absorption of nutrients from food. Their extensive brush border contains enzymes that further assist in nutrient breakdown and transport proteins that transfer nutrients, such as glucose, amino acids, lipids, and vitamins, across the cell membrane. +The enterocytes of the small intestine also participate in the barrier function of the gut lining. Enterocytes are connected by tight junctions, which act as a primary defense line against pathogenic invasion by maintaining intestinal barrier integrity. Additionally, their cell surface is coated in glycocalyx and mucus which forms a defensive barrier preventing the penetration of harmful bacteria into the systemic circulation."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nrgastro.2013.35"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling monocyte](http://purl.obolibrary.org/obo/CL_4033073) [date](http://purl.org/dc/terms/date) "2024-07-02T09:14:23Z"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fphys.2021.699152/full"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling monocyte](http://purl.obolibrary.org/obo/CL_4033073) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A(n) monocyte that is cycling."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31348891"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nri3738"^^[string](http://www.w3.org/2001/XMLSchema#string) -- Class: [cycling monocyte](http://purl.obolibrary.org/obo/CL_4033073) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1084/jem.20191130"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling monocyte](http://purl.obolibrary.org/obo/CL_4033073) EquivalentTo [monocyte](http://purl.obolibrary.org/obo/CL_0000576) and ([RO_0000056](http://purl.obolibrary.org/obo/RO_0000056) some [GO_0022402](http://purl.obolibrary.org/obo/GO_0022402)) and ([RO_0000086](http://purl.obolibrary.org/obo/RO_0000086) some [PATO_0002354](http://purl.obolibrary.org/obo/PATO_0002354)) +- [enterocyte of epithelium of small intestine](http://purl.obolibrary.org/obo/CL_1000334) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000334"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling monocyte](http://purl.obolibrary.org/obo/CL_4033073) SubClassOf [cycling myeloid cell](http://purl.obolibrary.org/obo/CL_4033081) -- [cycling monocyte](http://purl.obolibrary.org/obo/CL_4033073) SubClassOf [monocyte](http://purl.obolibrary.org/obo/CL_0000576) +### enterocyte of epithelium proper of ileum `http://purl.obolibrary.org/obo/CL_1000342` -- [cycling monocyte](http://purl.obolibrary.org/obo/CL_4033073) SubClassOf [cycling mononuclear phagocyte](http://purl.obolibrary.org/obo/CL_4033078) +#### Added +- [enterocyte of epithelium proper of ileum](http://purl.obolibrary.org/obo/CL_1000342) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000342"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [enterocyte of epithelium proper of ileum](http://purl.obolibrary.org/obo/CL_1000342) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -### cycling mononuclear phagocyte `http://purl.obolibrary.org/obo/CL_4033078` +Enterocytes of the epithelium proper of the ileum, commonly known as ileal enterocytes, are specialized epithelial cells found lining the inner surface of the ileum, the final section of the small intestine in the human body. They play a pivotal role in nutrient absorption, digestive metabolic functions, and the maintenance of the host’s immune response. +Like enterocytes in other parts of the intestine, ileal enterocytes exhibit distinct characteristics specific to their function and role. They have microvilli on their apical surfaces to increase absorption and are important in the absorption of vitamins and the reabsorption of bile salts. These cells also produce enzymes that metabolize lipids and xenobiotics."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nri3738"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [cycling mononuclear phagocyte](http://purl.obolibrary.org/obo/CL_4033078) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1084/jem.20191130"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling mononuclear phagocyte](http://purl.obolibrary.org/obo/CL_4033078) [label](http://www.w3.org/2000/01/rdf-schema#label) "cycling mononuclear phagocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1365-2249.2011.04523.x"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling mononuclear phagocyte](http://purl.obolibrary.org/obo/CL_4033078) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A(n) mononuclear phagocyte that is cycling."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37468583"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling mononuclear phagocyte](http://purl.obolibrary.org/obo/CL_4033078) [date](http://purl.org/dc/terms/date) "2024-07-02T09:14:23Z"^^[string](http://www.w3.org/2001/XMLSchema#string) +### enteroendocrine cell `http://purl.obolibrary.org/obo/CL_0000164` -- [cycling mononuclear phagocyte](http://purl.obolibrary.org/obo/CL_4033078) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "proliferating mononuclear phagocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37468583"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000164) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000164"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling mononuclear phagocyte](http://purl.obolibrary.org/obo/CL_4033078) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4033078"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000164) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -- Class: [cycling mononuclear phagocyte](http://purl.obolibrary.org/obo/CL_4033078) +Enteroendocrine cells are a specialized subset of cells located within the epithelial lining of both the small and large intestines, as well as the stomach and pancreas. Constituting less than 1% of the total population of intestinal cells, they are differentiated from a common intestinal cell progenitor, thus sharing lineage with absorptive and goblet cells of the intestines. +The distinct characteristic feature of an enteroendocrine cell is its inherent capacity to synthesize and secrete a plethora of gut hormones such as serotonin, somatostatin, neurotensin, cholecystokinin, secretin, gastric inhibitory peptide, motilin, and glucagon-like peptide-1. Integrated within this complex network of signaling agents, these substances control various aspects of the digestive system. Each enteroendocrine cell has its unique combination of hormones to release, determined by its position along the intestinal tract. Intriguingly, these hormones not only modulate local gut function, including motility, absorption and secretion, but also potentiate distant actions on other systems such as endocrine, nervous and immune and play a role in the feeling of satiety. +The release of these hormones from enteroendocrine cells is a highly regulated and dynamic process. The cells are equipped with sensory receptors localized on its luminal side that respond to various stimuli, including changes in nutrient composition, chemical or mechanical changes in the gut lumen, or even signals arising from commensal microbiota. This sensory input stimulates a signaling cascade within the cell, culminating in the release of specific hormones into the interstitial fluid. These hormones then make their way into the bloodstream, acting on their respective target receptors to mediate their duties. The multifunctional characteristics of enteroendocrine cells make them crucial for maintaining gut homeostasis and the overall physiological well being of the body."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.7554/elife.78512"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling mononuclear phagocyte](http://purl.obolibrary.org/obo/CL_4033078) EquivalentTo [mononuclear phagocyte](http://purl.obolibrary.org/obo/CL_0000113) and ([RO_0000056](http://purl.obolibrary.org/obo/RO_0000056) some [GO_0022402](http://purl.obolibrary.org/obo/GO_0022402)) and ([RO_0000086](http://purl.obolibrary.org/obo/RO_0000086) some [PATO_0002354](http://purl.obolibrary.org/obo/PATO_0002354)) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1463-1326.2011.01438.x"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling mononuclear phagocyte](http://purl.obolibrary.org/obo/CL_4033078) SubClassOf [RO_0000056](http://purl.obolibrary.org/obo/RO_0000056) some [GO_0022402](http://purl.obolibrary.org/obo/GO_0022402) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1196/annals.1294.001"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling mononuclear phagocyte](http://purl.obolibrary.org/obo/CL_4033078) SubClassOf [RO_0000086](http://purl.obolibrary.org/obo/RO_0000086) some [PATO_0002354](http://purl.obolibrary.org/obo/PATO_0002354) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1210/endrev/bnaa018"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling mononuclear phagocyte](http://purl.obolibrary.org/obo/CL_4033078) SubClassOf [mononuclear phagocyte](http://purl.obolibrary.org/obo/CL_0000113) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41574-019-0168-8"^^[string](http://www.w3.org/2001/XMLSchema#string) -### cycling myeloid cell `http://purl.obolibrary.org/obo/CL_4033081` +### eosinophil progenitor cell `http://purl.obolibrary.org/obo/CL_0000611` #### Added -- [cycling myeloid cell](http://purl.obolibrary.org/obo/CL_4033081) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4033081"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [eosinophil progenitor cell](http://purl.obolibrary.org/obo/CL_0000611) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -- [cycling myeloid cell](http://purl.obolibrary.org/obo/CL_4033081) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "proliferating myeloid cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:38301653"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling myeloid cell](http://purl.obolibrary.org/obo/CL_4033081) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) +### ependymal cell `http://purl.obolibrary.org/obo/CL_0000065` +#### Removed +- [ependymal cell](http://purl.obolibrary.org/obo/CL_0000065) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A neurectoderm derived cell that lines the neural lumen."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "JB:jb"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling myeloid cell](http://purl.obolibrary.org/obo/CL_4033081) [date](http://purl.org/dc/terms/date) "2024-07-02T09:14:23Z"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling myeloid cell](http://purl.obolibrary.org/obo/CL_4033081) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A(n) myeloid cell that is cycling."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:38301653"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:9550134"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling myeloid cell](http://purl.obolibrary.org/obo/CL_4033081) [label](http://www.w3.org/2000/01/rdf-schema#label) "cycling myeloid cell"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [ependymal cell](http://purl.obolibrary.org/obo/CL_0000065) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ependymocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) -- Class: [cycling myeloid cell](http://purl.obolibrary.org/obo/CL_4033081) +#### Added +- [ependymal cell](http://purl.obolibrary.org/obo/CL_0000065) [has_narrow_synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "ependymocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.53347/rID-51713"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling myeloid cell](http://purl.obolibrary.org/obo/CL_4033081) EquivalentTo [myeloid cell](http://purl.obolibrary.org/obo/CL_0000763) and ([RO_0000056](http://purl.obolibrary.org/obo/RO_0000056) some [GO_0022402](http://purl.obolibrary.org/obo/GO_0022402)) and ([RO_0000086](http://purl.obolibrary.org/obo/RO_0000086) some [PATO_0002354](http://purl.obolibrary.org/obo/PATO_0002354)) +- [ependymal cell](http://purl.obolibrary.org/obo/CL_0000065) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A neuroepithelial glial cell, derived from a radial glial cell originating from the neuroectoderm, lines the ventricles of the brain and the central canal of the spinal cord. This cell is characterized by the presence of cilia on its apical surface, which can be motile or non-motile."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34335193"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling myeloid cell](http://purl.obolibrary.org/obo/CL_4033081) SubClassOf [myeloid cell](http://purl.obolibrary.org/obo/CL_0000763) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "JB:jb"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling myeloid cell](http://purl.obolibrary.org/obo/CL_4033081) SubClassOf [RO_0000086](http://purl.obolibrary.org/obo/RO_0000086) some [PATO_0002354](http://purl.obolibrary.org/obo/PATO_0002354) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:/10.3389/fncel.2021.703951"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling myeloid cell](http://purl.obolibrary.org/obo/CL_4033081) SubClassOf [RO_0000056](http://purl.obolibrary.org/obo/RO_0000056) some [GO_0022402](http://purl.obolibrary.org/obo/GO_0022402) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37008045"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.britannica.com/science/ependymal-cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -### cycling natural killer cell `http://purl.obolibrary.org/obo/CL_4033071` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [cycling natural killer cell](http://purl.obolibrary.org/obo/CL_4033071) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4033071"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:9550134"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling natural killer cell](http://purl.obolibrary.org/obo/CL_4033071) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) +- [ependymal cell](http://purl.obolibrary.org/obo/CL_0000065) EquivalentTo [neurecto-epithelial cell](http://purl.obolibrary.org/obo/CL_0000710) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004670](http://purl.obolibrary.org/obo/UBERON_0004670)) -- [cycling natural killer cell](http://purl.obolibrary.org/obo/CL_4033071) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A(n) natural killer cell that is cycling."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34062119"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [ependymal cell](http://purl.obolibrary.org/obo/CL_0000065) SubClassOf [glial cell](http://purl.obolibrary.org/obo/CL_0000125) -- [cycling natural killer cell](http://purl.obolibrary.org/obo/CL_4033071) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "proliferating natural killer cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34062119"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [ependymal cell](http://purl.obolibrary.org/obo/CL_0000065) SubClassOf [RO_0002207](http://purl.obolibrary.org/obo/RO_0002207) some [radial glial cell](http://purl.obolibrary.org/obo/CL_0000681) -- [cycling natural killer cell](http://purl.obolibrary.org/obo/CL_4033071) [date](http://purl.org/dc/terms/date) "2024-07-02T09:14:23Z"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [ependymal cell](http://purl.obolibrary.org/obo/CL_0000065) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004670](http://purl.obolibrary.org/obo/UBERON_0004670) -- [cycling natural killer cell](http://purl.obolibrary.org/obo/CL_4033071) [label](http://www.w3.org/2000/01/rdf-schema#label) "cycling natural killer cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -- Class: [cycling natural killer cell](http://purl.obolibrary.org/obo/CL_4033071) +### epidermal cell (sensu Arthropoda) `http://purl.obolibrary.org/obo/CL_0000463` +#### Removed +- [epidermal cell (sensu Arthropoda)](http://purl.obolibrary.org/obo/CL_0000463) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -- [cycling natural killer cell](http://purl.obolibrary.org/obo/CL_4033071) EquivalentTo [natural killer cell](http://purl.obolibrary.org/obo/CL_0000623) and ([RO_0000056](http://purl.obolibrary.org/obo/RO_0000056) some [GO_0022402](http://purl.obolibrary.org/obo/GO_0022402)) and ([RO_0000086](http://purl.obolibrary.org/obo/RO_0000086) some [PATO_0002354](http://purl.obolibrary.org/obo/PATO_0002354)) +- [epidermal cell (sensu Arthropoda)](http://purl.obolibrary.org/obo/CL_0000463) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_6656](http://purl.obolibrary.org/obo/NCBITaxon_6656) -- [cycling natural killer cell](http://purl.obolibrary.org/obo/CL_4033071) SubClassOf [RO_0000056](http://purl.obolibrary.org/obo/RO_0000056) some [GO_0022402](http://purl.obolibrary.org/obo/GO_0022402) +#### Added +- [epidermal cell (sensu Arthropoda)](http://purl.obolibrary.org/obo/CL_0000463) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_6656](http://purl.obolibrary.org/obo/NCBITaxon_6656) -- [cycling natural killer cell](http://purl.obolibrary.org/obo/CL_4033071) SubClassOf [RO_0000086](http://purl.obolibrary.org/obo/RO_0000086) some [PATO_0002354](http://purl.obolibrary.org/obo/PATO_0002354) -- [cycling natural killer cell](http://purl.obolibrary.org/obo/CL_4033071) SubClassOf [natural killer cell](http://purl.obolibrary.org/obo/CL_0000623) +### epithelial cell `http://purl.obolibrary.org/obo/CL_0000066` +#### Removed +- [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) +#### Added +- [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### cycling neuroblast (sensu Vertebrata) `http://purl.obolibrary.org/obo/CL_4047005` -#### Added -- [cycling neuroblast (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_4047005) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4047005"^^[string](http://www.w3.org/2001/XMLSchema#string) +### epithelial cell of alveolus of lung `http://purl.obolibrary.org/obo/CL_0010003` +#### Removed +- [epithelial cell of alveolus of lung](http://purl.obolibrary.org/obo/CL_0010003) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell that is part_of a alveolus of lung."^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling neuroblast (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_4047005) [label](http://www.w3.org/2000/01/rdf-schema#label) "cycling neuroblast (sensu Vertebrata)"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [epithelial cell of alveolus of lung](http://purl.obolibrary.org/obo/CL_0010003) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "May be merged with pneumocyte in future"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling neuroblast (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_4047005) [contributor](http://purl.org/dc/terms/contributor) [0009-0005-7919-4905](https://orcid.org/0009-0005-7919-4905) +- [epithelial cell of alveolus of lung](http://purl.obolibrary.org/obo/CL_0010003) [label](http://www.w3.org/2000/01/rdf-schema#label) "epithelial cell of alveolus of lung"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling neuroblast (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_4047005) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A(n) neuroblast (sensu Vertebrata) that is cycling."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34497389"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [epithelial cell of alveolus of lung](http://purl.obolibrary.org/obo/CL_0010003) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002299](http://purl.obolibrary.org/obo/UBERON_0002299)) -- [cycling neuroblast (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_4047005) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "proliferating neuroblast (sensu Vertebrata)"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34497389"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [epithelial cell of alveolus of lung](http://purl.obolibrary.org/obo/CL_0010003) SubClassOf [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) -- [cycling neuroblast (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_4047005) [date](http://purl.org/dc/terms/date) "2024-07-19T09:14:23Z"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [epithelial cell of alveolus of lung](http://purl.obolibrary.org/obo/CL_0010003) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002299](http://purl.obolibrary.org/obo/UBERON_0002299) -- Class: [cycling neuroblast (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_4047005) +#### Added +- [epithelial cell of alveolus of lung](http://purl.obolibrary.org/obo/CL_0010003) [IAO_0000233](http://purl.obolibrary.org/obo/IAO_0000233) [2429](https://github.com/obophenotype/cell-ontology/issues/2429) -- [cycling neuroblast (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_4047005) EquivalentTo [neuroblast (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000031) and ([RO_0000056](http://purl.obolibrary.org/obo/RO_0000056) some [GO_0022402](http://purl.obolibrary.org/obo/GO_0022402)) and ([RO_0000086](http://purl.obolibrary.org/obo/RO_0000086) some [PATO_0002354](http://purl.obolibrary.org/obo/PATO_0002354)) +- [epithelial cell of alveolus of lung](http://purl.obolibrary.org/obo/CL_0010003) [label](http://www.w3.org/2000/01/rdf-schema#label) "obsolete epithelial cell of alveolus of lung"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling neuroblast (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_4047005) SubClassOf [neuroblast (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000031) +- [epithelial cell of alveolus of lung](http://purl.obolibrary.org/obo/CL_0010003) [deprecated](http://www.w3.org/2002/07/owl#deprecated) true -- [cycling neuroblast (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_4047005) SubClassOf [RO_0000056](http://purl.obolibrary.org/obo/RO_0000056) some [GO_0022402](http://purl.obolibrary.org/obo/GO_0022402) +- [epithelial cell of alveolus of lung](http://purl.obolibrary.org/obo/CL_0010003) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "This cell type is exactly the same as 'pulmonary alveolar epithelial cell'."^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling neuroblast (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_4047005) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) +- [epithelial cell of alveolus of lung](http://purl.obolibrary.org/obo/CL_0010003) [term replaced by](http://purl.obolibrary.org/obo/IAO_0100001) [pulmonary alveolar epithelial cell](http://purl.obolibrary.org/obo/CL_0000322) -- [cycling neuroblast (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_4047005) SubClassOf [RO_0000086](http://purl.obolibrary.org/obo/RO_0000086) some [PATO_0002354](http://purl.obolibrary.org/obo/PATO_0002354) +- [epithelial cell of alveolus of lung](http://purl.obolibrary.org/obo/CL_0010003) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "OBSOLETE. An epithelial cell that is part_of a alveolus of lung."^^[string](http://www.w3.org/2001/XMLSchema#string) -### cycling plasma cell `http://purl.obolibrary.org/obo/CL_4047003` +### epithelial cell of lacrimal sac `http://purl.obolibrary.org/obo/CL_1000436` #### Added -- [cycling plasma cell](http://purl.obolibrary.org/obo/CL_4047003) [date](http://purl.org/dc/terms/date) "2024-07-19T09:14:23Z"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [epithelial cell of lacrimal sac](http://purl.obolibrary.org/obo/CL_1000436) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -- [cycling plasma cell](http://purl.obolibrary.org/obo/CL_4047003) [label](http://www.w3.org/2000/01/rdf-schema#label) "cycling plasma cell"^^[string](http://www.w3.org/2001/XMLSchema#string) +Epithelial cells of the lacrimal sac play a significant role in the physiology of tear drainage, acting as an integral part of the lacrimal drainage system. The lacrimal sac is part of the nasolacrimal duct system, a conduit which connects the eye to the nasal cavity, and is lined by multilayered, non-keratinizing, squamous epithelial cells. +The epithelial cells of the lacrimal sac are specialized for the purpose of maintaining a moist environment and protecting the surface of the eye. They form a barrier that traps and removes potential contaminants from the tear film during the drainage process. These cells also actively contribute to tear turnover by expediting the drainage of excess tears. Dysfunctional epithelial cells of the lacrimal sac can lead to dacryocystitis, a condition characterized by inflammation of the lacrimal sac. +Epithelial cells of the lacrimal sac also perform various other tasks which ensure the overall health of the eye. They are involved in the regulation of immune responses within the lacrimal apparatus and may have a possible role in host-microbiome interactions. Thus, epithelial cells of the lacrimal sac play a multifaceted role in tear drainage and ocular surface defence, directly translating to eye health and vision quality."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2147/OPTH.S26048"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling plasma cell](http://purl.obolibrary.org/obo/CL_4047003) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4047003"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1167/tvst.8.4.32"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling plasma cell](http://purl.obolibrary.org/obo/CL_4047003) [contributor](http://purl.org/dc/terms/contributor) [0009-0005-7919-4905](https://orcid.org/0009-0005-7919-4905) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s004290050160"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling plasma cell](http://purl.obolibrary.org/obo/CL_4047003) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "proliferating plasma cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34497389"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [cycling plasma cell](http://purl.obolibrary.org/obo/CL_4047003) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A(n) plasma cell that is cycling."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34497389"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1442-9071.2012.02818.x"^^[string](http://www.w3.org/2001/XMLSchema#string) -- Class: [cycling plasma cell](http://purl.obolibrary.org/obo/CL_4047003) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2022.918619"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling plasma cell](http://purl.obolibrary.org/obo/CL_4047003) EquivalentTo [plasma cell](http://purl.obolibrary.org/obo/CL_0000786) and ([RO_0000056](http://purl.obolibrary.org/obo/RO_0000056) some [GO_0022402](http://purl.obolibrary.org/obo/GO_0022402)) and ([RO_0000086](http://purl.obolibrary.org/obo/RO_0000086) some [PATO_0002354](http://purl.obolibrary.org/obo/PATO_0002354)) +- [epithelial cell of lacrimal sac](http://purl.obolibrary.org/obo/CL_1000436) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000436"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling plasma cell](http://purl.obolibrary.org/obo/CL_4047003) SubClassOf [RO_0000056](http://purl.obolibrary.org/obo/RO_0000056) some [GO_0022402](http://purl.obolibrary.org/obo/GO_0022402) -- [cycling plasma cell](http://purl.obolibrary.org/obo/CL_4047003) SubClassOf [plasma cell](http://purl.obolibrary.org/obo/CL_0000786) +### erythroid progenitor cell, mammalian `http://purl.obolibrary.org/obo/CL_0001066` -- [cycling plasma cell](http://purl.obolibrary.org/obo/CL_4047003) SubClassOf [RO_0000086](http://purl.obolibrary.org/obo/RO_0000086) some [PATO_0002354](http://purl.obolibrary.org/obo/PATO_0002354) +#### Added +- [erythroid progenitor cell, mammalian](http://purl.obolibrary.org/obo/CL_0001066) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### cycling pulmonary alveolar type 2 cell `http://purl.obolibrary.org/obo/CL_4033080` +### erythrophore `http://purl.obolibrary.org/obo/CL_0000574` #### Added -- [cycling pulmonary alveolar type 2 cell](http://purl.obolibrary.org/obo/CL_4033080) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A(n) pulmonary alveolar type 2 cell that is cycling."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37291214"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [erythrophore](http://purl.obolibrary.org/obo/CL_0000574) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -- [cycling pulmonary alveolar type 2 cell](http://purl.obolibrary.org/obo/CL_4033080) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "proliferating pulmonary alveolar type 2 cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37291214"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling pulmonary alveolar type 2 cell](http://purl.obolibrary.org/obo/CL_4033080) [label](http://www.w3.org/2000/01/rdf-schema#label) "cycling pulmonary alveolar type 2 cell"^^[string](http://www.w3.org/2001/XMLSchema#string) +### eukaryotic cell `http://purl.obolibrary.org/obo/CL_0000255` +#### Removed +- [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any cell that only exists in Eukaryota."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling pulmonary alveolar type 2 cell](http://purl.obolibrary.org/obo/CL_4033080) [date](http://purl.org/dc/terms/date) "2024-07-02T09:14:23Z"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) EquivalentTo [cell](http://purl.obolibrary.org/obo/CL_0000000) and ([RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_2759](http://purl.obolibrary.org/obo/NCBITaxon_2759)) -- [cycling pulmonary alveolar type 2 cell](http://purl.obolibrary.org/obo/CL_4033080) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4033080"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_2759](http://purl.obolibrary.org/obo/NCBITaxon_2759) -- [cycling pulmonary alveolar type 2 cell](http://purl.obolibrary.org/obo/CL_4033080) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) +#### Added +- [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any cell that in taxon some Eukaryota."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) -- Class: [cycling pulmonary alveolar type 2 cell](http://purl.obolibrary.org/obo/CL_4033080) +- [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) EquivalentTo [cell](http://purl.obolibrary.org/obo/CL_0000000) and ([RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_2759](http://purl.obolibrary.org/obo/NCBITaxon_2759)) -- [cycling pulmonary alveolar type 2 cell](http://purl.obolibrary.org/obo/CL_4033080) EquivalentTo [pulmonary alveolar type 2 cell](http://purl.obolibrary.org/obo/CL_0002063) and ([RO_0000056](http://purl.obolibrary.org/obo/RO_0000056) some [GO_0022402](http://purl.obolibrary.org/obo/GO_0022402)) and ([RO_0000086](http://purl.obolibrary.org/obo/RO_0000086) some [PATO_0002354](http://purl.obolibrary.org/obo/PATO_0002354)) +- [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_2759](http://purl.obolibrary.org/obo/NCBITaxon_2759) -- [cycling pulmonary alveolar type 2 cell](http://purl.obolibrary.org/obo/CL_4033080) SubClassOf [RO_0000086](http://purl.obolibrary.org/obo/RO_0000086) some [PATO_0002354](http://purl.obolibrary.org/obo/PATO_0002354) -- [cycling pulmonary alveolar type 2 cell](http://purl.obolibrary.org/obo/CL_4033080) SubClassOf [RO_0000056](http://purl.obolibrary.org/obo/RO_0000056) some [GO_0022402](http://purl.obolibrary.org/obo/GO_0022402) +### exocrine cell `http://purl.obolibrary.org/obo/CL_0000152` -- [cycling pulmonary alveolar type 2 cell](http://purl.obolibrary.org/obo/CL_4033080) SubClassOf [pulmonary alveolar type 2 cell](http://purl.obolibrary.org/obo/CL_0002063) +#### Added +- [exocrine cell](http://purl.obolibrary.org/obo/CL_0000152) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### cycling stromal cell `http://purl.obolibrary.org/obo/CL_4047001` +### extraembryonic cell `http://purl.obolibrary.org/obo/CL_0000349` +#### Removed +- [extraembryonic cell](http://purl.obolibrary.org/obo/CL_0000349) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) #### Added -- [cycling stromal cell](http://purl.obolibrary.org/obo/CL_4047001) [date](http://purl.org/dc/terms/date) "2024-07-19T09:14:23Z"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [extraembryonic cell](http://purl.obolibrary.org/obo/CL_0000349) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -- [cycling stromal cell](http://purl.obolibrary.org/obo/CL_4047001) [label](http://www.w3.org/2000/01/rdf-schema#label) "cycling stromal cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling stromal cell](http://purl.obolibrary.org/obo/CL_4047001) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "proliferating stromal cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34497389"^^[string](http://www.w3.org/2001/XMLSchema#string) +### eye photoreceptor cell `http://purl.obolibrary.org/obo/CL_0000287` -- [cycling stromal cell](http://purl.obolibrary.org/obo/CL_4047001) [contributor](http://purl.org/dc/terms/contributor) [0009-0005-7919-4905](https://orcid.org/0009-0005-7919-4905) +#### Added +- [eye photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000287) SubClassOf [neuronal receptor cell](http://purl.obolibrary.org/obo/CL_0000006) -- [cycling stromal cell](http://purl.obolibrary.org/obo/CL_4047001) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4047001"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling stromal cell](http://purl.obolibrary.org/obo/CL_4047001) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A(n) stromal cell that is cycling."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34497389"^^[string](http://www.w3.org/2001/XMLSchema#string) +### fallopian tube ciliated cell `http://purl.obolibrary.org/obo/CL_4030007` +#### Removed +- [fallopian tube ciliated cell](http://purl.obolibrary.org/obo/CL_4030007) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial ciliated cell that is part of the fallopian tube. This cell type is found mainly on the apex of the mucosal folds and contributes, together with peristaltic contractions, to the self-propulsion of spermatozoa, the transport of ovum during ovulation and the transport of the fertilized ovum to the intramural fallopian tube. A fallopian tube ciliated cell has a columnar shape and contains an oval or round nucleus, often located perpendicular or parallel to the long axis of the cell."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:16565155"^^[string](http://www.w3.org/2001/XMLSchema#string) -- Class: [cycling stromal cell](http://purl.obolibrary.org/obo/CL_4047001) + - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0002-0819-0473"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling stromal cell](http://purl.obolibrary.org/obo/CL_4047001) EquivalentTo [stromal cell](http://purl.obolibrary.org/obo/CL_0000499) and ([RO_0000056](http://purl.obolibrary.org/obo/RO_0000056) some [GO_0022402](http://purl.obolibrary.org/obo/GO_0022402)) and ([RO_0000086](http://purl.obolibrary.org/obo/RO_0000086) some [PATO_0002354](http://purl.obolibrary.org/obo/PATO_0002354)) +#### Added +- [fallopian tube ciliated cell](http://purl.obolibrary.org/obo/CL_4030007) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial ciliated cell that is part of the fallopian tube. This cell type is found mainly on the apex of the mucosal folds and contributes, together with peristaltic contractions, to the self-propulsion of spermatozoa, the transport of ovum during ovulation and the transport of the fertilized ovum to the intramural fallopian tube. A fallopian tube ciliated cell has a columnar shape and contains an oval or round nucleus, often located perpendicular or parallel to the long axis of the cell."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:16565155"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling stromal cell](http://purl.obolibrary.org/obo/CL_4047001) SubClassOf [RO_0000056](http://purl.obolibrary.org/obo/RO_0000056) some [GO_0022402](http://purl.obolibrary.org/obo/GO_0022402) +- [fallopian tube ciliated cell](http://purl.obolibrary.org/obo/CL_4030007) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0819-0473](https://orcid.org/0000-0002-0819-0473) -- [cycling stromal cell](http://purl.obolibrary.org/obo/CL_4047001) SubClassOf [stromal cell](http://purl.obolibrary.org/obo/CL_0000499) -- [cycling stromal cell](http://purl.obolibrary.org/obo/CL_4047001) SubClassOf [RO_0000086](http://purl.obolibrary.org/obo/RO_0000086) some [PATO_0002354](http://purl.obolibrary.org/obo/PATO_0002354) +### fallopian tube secretory epithelial cell `http://purl.obolibrary.org/obo/CL_4030006` +#### Removed +- [fallopian tube secretory epithelial cell](http://purl.obolibrary.org/obo/CL_4030006) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell that is part of the fallopian tube epithelium that secretes mucous fluid and oviduct-specific products through the stimulation of estrogen and luteinizing hormone. The fallopian tube secretory cell has approximately the same height as the ciliated cell and is usually a more narrow columnar cell. The nucleus is ovoid and perpendicular to the long axis of the cell. The chromatin is more dense and the nucleolus smaller than that seen in the ciliated cell."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.3390/cells8080933"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.1186/1477-7827-7-129"^^[string](http://www.w3.org/2001/XMLSchema#string) -### cycling type EC enteroendocrine cell `http://purl.obolibrary.org/obo/CL_4047004` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.proteinatlas.org/learn/dictionary/normal/fallopian+tube"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0002-0819-0473"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [cycling type EC enteroendocrine cell](http://purl.obolibrary.org/obo/CL_4047004) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4047004"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [fallopian tube secretory epithelial cell](http://purl.obolibrary.org/obo/CL_4030006) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0819-0473](https://orcid.org/0000-0002-0819-0473) -- [cycling type EC enteroendocrine cell](http://purl.obolibrary.org/obo/CL_4047004) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "proliferating type EC enteroendocrine cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34497389"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [fallopian tube secretory epithelial cell](http://purl.obolibrary.org/obo/CL_4030006) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell that is part of the fallopian tube epithelium that secretes mucous fluid and oviduct-specific products through the stimulation of estrogen and luteinizing hormone. The fallopian tube secretory cell has approximately the same height as the ciliated cell and is usually a more narrow columnar cell. The nucleus is ovoid and perpendicular to the long axis of the cell. The chromatin is more dense and the nucleolus smaller than that seen in the ciliated cell."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.3390/cells8080933"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling type EC enteroendocrine cell](http://purl.obolibrary.org/obo/CL_4047004) [label](http://www.w3.org/2000/01/rdf-schema#label) "cycling type EC enteroendocrine cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.1186/1477-7827-7-129"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.proteinatlas.org/learn/dictionary/normal/fallopian+tube"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling type EC enteroendocrine cell](http://purl.obolibrary.org/obo/CL_4047004) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A(n) type EC enteroendocrine cell that is cycling."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34497389"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling type EC enteroendocrine cell](http://purl.obolibrary.org/obo/CL_4047004) [contributor](http://purl.org/dc/terms/contributor) [0009-0005-7919-4905](https://orcid.org/0009-0005-7919-4905) +### female germ cell `http://purl.obolibrary.org/obo/CL_0000021` + +#### Added +- [female germ cell](http://purl.obolibrary.org/obo/CL_0000021) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -- [cycling type EC enteroendocrine cell](http://purl.obolibrary.org/obo/CL_4047004) [date](http://purl.org/dc/terms/date) "2024-07-19T09:14:23Z"^^[string](http://www.w3.org/2001/XMLSchema#string) -- Class: [cycling type EC enteroendocrine cell](http://purl.obolibrary.org/obo/CL_4047004) +### fenestrated endothelial cell `http://purl.obolibrary.org/obo/CL_0000666` -- [cycling type EC enteroendocrine cell](http://purl.obolibrary.org/obo/CL_4047004) EquivalentTo [type EC enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000577) and ([RO_0000056](http://purl.obolibrary.org/obo/RO_0000056) some [GO_0022402](http://purl.obolibrary.org/obo/GO_0022402)) and ([RO_0000086](http://purl.obolibrary.org/obo/RO_0000086) some [PATO_0002354](http://purl.obolibrary.org/obo/PATO_0002354)) +#### Added +- [fenestrated endothelial cell](http://purl.obolibrary.org/obo/CL_0000666) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000666"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling type EC enteroendocrine cell](http://purl.obolibrary.org/obo/CL_4047004) SubClassOf [type EC enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000577) +- [fenestrated endothelial cell](http://purl.obolibrary.org/obo/CL_0000666) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -- [cycling type EC enteroendocrine cell](http://purl.obolibrary.org/obo/CL_4047004) SubClassOf [RO_0000056](http://purl.obolibrary.org/obo/RO_0000056) some [GO_0022402](http://purl.obolibrary.org/obo/GO_0022402) +Fenestrated cells are specialized epithelial cells that are characterized by a distinctive structural feature, fenestrations or tiny pores, which allow an exchange of substances such as fluids, nutrients, and waste between blood vessels and the surrounding tissue environments. These cells are present in various types of epithelial tissues in the human body, including the intestinal tract, endocrine glands, and certain parts of the renal system. +There are multiple types of endothelial cell fenestrations. The most common type is found in systemic capillaries of the endocrine tissue (e.g., pancreatic islets), gastrointestinal mucosa, and renal peritubular capillaries. Here, the fenestrated cells have fenestrations in their peripheral cytoplasm with a unique thin and permeable diaphragm that provides a high degree of selectivity, blocking the passage of larger molecules while allowing the free movement of smaller ones. In contrast, other types of fenestrations, such as the discontinuous epithelium of the liver sinusoidal endothelial cells, do not have diaphragms. +Characteristically, fenestrated cells play a vital role in the filtering process of body systems. They are a key part of the glomeruli in the kidneys where blood is filtered under high pressure. The fenestrations present in the endothelial cells lining the capillaries of the glomerulus allow the free passage of water and small solute molecules towards the Bowman's capsule, leaving behind larger proteins and cells in the blood, thereby aiding in the filtration and waste removal process. +In the endocrine system, fenestrated cells in glandular capillaries allow the prompt release of hormones into the bloodstream. These cells have tightly clustered fenestrations which increase the surface area available for passive diffusion, improving the efficiency of hormone secretion. In villi of the small intestine, these cells increase absorption efficiency, permitting the exchange of water, electrolytes, and nutrients. +Overall, fenestrated cells contribute immensely to important physiological processes of filtration, absorption, and secretion, primarily connecting our body's circulation system with the surrounding tissues and organs."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/ar.1092200109"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [cycling type EC enteroendocrine cell](http://purl.obolibrary.org/obo/CL_4047004) SubClassOf [RO_0000086](http://purl.obolibrary.org/obo/RO_0000086) some [PATO_0002354](http://purl.obolibrary.org/obo/PATO_0002354) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41467-022-31571-2"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.devcel.2012.11.003"^^[string](http://www.w3.org/2001/XMLSchema#string) -### dendritic cell `http://purl.obolibrary.org/obo/CL_0000451` -#### Removed -- [dendritic cell](http://purl.obolibrary.org/obo/CL_0000451) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009209"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/ajprenal.90601.2008"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [dendritic cell](http://purl.obolibrary.org/obo/CL_0000451) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009209"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/0306-4522(86)90162-4"^^[string](http://www.w3.org/2001/XMLSchema#string) -### dental papilla cell `http://purl.obolibrary.org/obo/CL_0000345` -#### Removed -- [dental papilla cell](http://purl.obolibrary.org/obo/CL_0000345) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009173"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### fetal artery endothelial cell `http://purl.obolibrary.org/obo/CL_4047006` #### Added -- [dental papilla cell](http://purl.obolibrary.org/obo/CL_0000345) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009173"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [fetal artery endothelial cell](http://purl.obolibrary.org/obo/CL_4047006) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "endothelial cell of fetal artery"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34497389"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [fetal artery endothelial cell](http://purl.obolibrary.org/obo/CL_4047006) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "fetal arterial EC"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34497389"^^[string](http://www.w3.org/2001/XMLSchema#string) -### dentate gyrus granule cell `http://purl.obolibrary.org/obo/CL_2000089` -#### Removed -- [dentate gyrus granule cell](http://purl.obolibrary.org/obo/CL_2000089) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +- [fetal artery endothelial cell](http://purl.obolibrary.org/obo/CL_4047006) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "fetal artery EC"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34497389"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [dentate gyrus granule cell](http://purl.obolibrary.org/obo/CL_2000089) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [fetal artery endothelial cell](http://purl.obolibrary.org/obo/CL_4047006) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An endothelial cell that lines an artery in the fetal circulatory system."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34497389"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [fetal artery endothelial cell](http://purl.obolibrary.org/obo/CL_4047006) [contributor](http://purl.org/dc/terms/contributor) [0009-0005-7919-4905](https://orcid.org/0009-0005-7919-4905) -### dentate gyrus of hippocampal formation basket cell `http://purl.obolibrary.org/obo/CL_2000087` -#### Removed -- [dentate gyrus of hippocampal formation basket cell](http://purl.obolibrary.org/obo/CL_2000087) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +- [fetal artery endothelial cell](http://purl.obolibrary.org/obo/CL_4047006) [label](http://www.w3.org/2000/01/rdf-schema#label) "fetal artery endothelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [dentate gyrus of hippocampal formation basket cell](http://purl.obolibrary.org/obo/CL_2000087) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [fetal artery endothelial cell](http://purl.obolibrary.org/obo/CL_4047006) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4047006"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [fetal artery endothelial cell](http://purl.obolibrary.org/obo/CL_4047006) [date](http://purl.org/dc/terms/date) "2024-08-16T13:52:25Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -### dentate gyrus of hippocampal formation stellate cell `http://purl.obolibrary.org/obo/CL_2000090` -#### Removed -- [dentate gyrus of hippocampal formation stellate cell](http://purl.obolibrary.org/obo/CL_2000090) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +- Class: [fetal artery endothelial cell](http://purl.obolibrary.org/obo/CL_4047006) -#### Added -- [dentate gyrus of hippocampal formation stellate cell](http://purl.obolibrary.org/obo/CL_2000090) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [fetal artery endothelial cell](http://purl.obolibrary.org/obo/CL_4047006) SubClassOf [endothelial cell of artery](http://purl.obolibrary.org/obo/CL_1000413) -### dermis blood vessel endothelial cell `http://purl.obolibrary.org/obo/CL_2000010` -#### Removed -- [dermis blood vessel endothelial cell](http://purl.obolibrary.org/obo/CL_2000010) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +### fetal derived definitive erythrocyte `http://purl.obolibrary.org/obo/CL_0002357` #### Added -- [dermis blood vessel endothelial cell](http://purl.obolibrary.org/obo/CL_2000010) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [fetal derived definitive erythrocyte](http://purl.obolibrary.org/obo/CL_0002357) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### dermis lymphatic vessel endothelial cell `http://purl.obolibrary.org/obo/CL_2000011` -#### Removed -- [dermis lymphatic vessel endothelial cell](http://purl.obolibrary.org/obo/CL_2000011) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +### fetal liver hematopoietic progenitor cell `http://purl.obolibrary.org/obo/CL_0002353` #### Added -- [dermis lymphatic vessel endothelial cell](http://purl.obolibrary.org/obo/CL_2000011) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [fetal liver hematopoietic progenitor cell](http://purl.obolibrary.org/obo/CL_0002353) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### dermis microvascular lymphatic vessel endothelial cell `http://purl.obolibrary.org/obo/CL_2000041` -#### Removed -- [dermis microvascular lymphatic vessel endothelial cell](http://purl.obolibrary.org/obo/CL_2000041) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) - -- [dermis microvascular lymphatic vessel endothelial cell](http://purl.obolibrary.org/obo/CL_2000041) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0008339](http://purl.obolibrary.org/obo/UBERON_0008339) +### fetal vein endothelial cell `http://purl.obolibrary.org/obo/CL_4047011` #### Added -- [dermis microvascular lymphatic vessel endothelial cell](http://purl.obolibrary.org/obo/CL_2000041) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [fetal vein endothelial cell](http://purl.obolibrary.org/obo/CL_4047011) [contributor](http://purl.org/dc/terms/contributor) [0009-0005-7919-4905](https://orcid.org/0009-0005-7919-4905) -- [dermis microvascular lymphatic vessel endothelial cell](http://purl.obolibrary.org/obo/CL_2000041) SubClassOf [dermal microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_0011030) +- [fetal vein endothelial cell](http://purl.obolibrary.org/obo/CL_4047011) [label](http://www.w3.org/2000/01/rdf-schema#label) "fetal vein endothelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [fetal vein endothelial cell](http://purl.obolibrary.org/obo/CL_4047011) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "fetal venous EC"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) -### deuterosomal cell `http://purl.obolibrary.org/obo/CL_4033044` -#### Removed -- [deuterosomal cell](http://purl.obolibrary.org/obo/CL_4033044) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004802](http://purl.obolibrary.org/obo/UBERON_0004802) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.1101/2021.04.07.438755"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [fetal vein endothelial cell](http://purl.obolibrary.org/obo/CL_4047011) [date](http://purl.org/dc/terms/date) "2024-09-05T15:45:32Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) +- [fetal vein endothelial cell](http://purl.obolibrary.org/obo/CL_4047011) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An endothelial cell that lines the veins in the fetal circulatory system."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.1101/2021.04.07.438755"^^[string](http://www.w3.org/2001/XMLSchema#string) -### digestive enzyme secreting cell `http://purl.obolibrary.org/obo/CL_0000470` -#### Removed -- [digestive enzyme secreting cell](http://purl.obolibrary.org/obo/CL_0000470) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009217"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [fetal vein endothelial cell](http://purl.obolibrary.org/obo/CL_4047011) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "fetal venous endothelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.1101/2021.04.07.438755"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [digestive enzyme secreting cell](http://purl.obolibrary.org/obo/CL_0000470) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009217"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [fetal vein endothelial cell](http://purl.obolibrary.org/obo/CL_4047011) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "fetal vein EC"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.1101/2021.04.07.438755"^^[string](http://www.w3.org/2001/XMLSchema#string) -### dopaminergic neuron `http://purl.obolibrary.org/obo/CL_0000700` -#### Removed -- [dopaminergic neuron](http://purl.obolibrary.org/obo/CL_0000700) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005131"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [fetal vein endothelial cell](http://purl.obolibrary.org/obo/CL_4047011) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4047011"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- Class: [fetal vein endothelial cell](http://purl.obolibrary.org/obo/CL_4047011) + +- [fetal vein endothelial cell](http://purl.obolibrary.org/obo/CL_4047011) SubClassOf [vein endothelial cell](http://purl.obolibrary.org/obo/CL_0002543) -- [dopaminergic neuron](http://purl.obolibrary.org/obo/CL_0000700) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009301"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +### fibroblastic reticular cell `http://purl.obolibrary.org/obo/CL_0009101` #### Added -- [dopaminergic neuron](http://purl.obolibrary.org/obo/CL_0000700) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009301"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_0009101) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "FRC"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) -- [dopaminergic neuron](http://purl.obolibrary.org/obo/CL_0000700) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005131"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35440118"^^[string](http://www.w3.org/2001/XMLSchema#string) -### duct epithelial cell `http://purl.obolibrary.org/obo/CL_0000068` +### flask cell `http://purl.obolibrary.org/obo/CL_0007023` #### Removed -- [duct epithelial cell](http://purl.obolibrary.org/obo/CL_0000068) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009372"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [flask cell](http://purl.obolibrary.org/obo/CL_0007023) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) #### Added -- [duct epithelial cell](http://purl.obolibrary.org/obo/CL_0000068) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009372"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [flask cell](http://purl.obolibrary.org/obo/CL_0007023) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### duodenal goblet cell `http://purl.obolibrary.org/obo/CL_1000324` -#### Removed -- [duodenal goblet cell](http://purl.obolibrary.org/obo/CL_1000324) SubClassOf [duodenum glandular cell](http://purl.obolibrary.org/obo/CL_1001589) +### follicle associated enterocyte `http://purl.obolibrary.org/obo/CL_4052011` #### Added -- [duodenal goblet cell](http://purl.obolibrary.org/obo/CL_1000324) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0008346](http://purl.obolibrary.org/obo/UBERON_0008346) +- [follicle associated enterocyte](http://purl.obolibrary.org/obo/CL_4052011) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "follicle-associated epithelium enterocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:7107724"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [follicle associated enterocyte](http://purl.obolibrary.org/obo/CL_4052011) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) -### early embryonic cell (metazoa) `http://purl.obolibrary.org/obo/CL_0000007` -#### Removed -- [early embryonic cell (metazoa)](http://purl.obolibrary.org/obo/CL_0000007) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009002"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [follicle associated enterocyte](http://purl.obolibrary.org/obo/CL_4052011) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "follicular enterocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:7107724"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [early embryonic cell (metazoa)](http://purl.obolibrary.org/obo/CL_0000007) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009002"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [follicle associated enterocyte](http://purl.obolibrary.org/obo/CL_4052011) [label](http://www.w3.org/2000/01/rdf-schema#label) "follicle associated enterocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [follicle associated enterocyte](http://purl.obolibrary.org/obo/CL_4052011) [date](http://purl.org/dc/terms/date) "2024-09-25T15:28:25Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + +- [follicle associated enterocyte](http://purl.obolibrary.org/obo/CL_4052011) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052011"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [follicle associated enterocyte](http://purl.obolibrary.org/obo/CL_4052011) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An enterocyte found in the follicle-associated epithelium (FAE) that covers Peyer's patches and other mucosa-associated lymphoid tissues. This cell has reduced absorptive capacity and expresses higher levels of chemokines CCL20 and CXCL16, compared to regular villus enterocytes. It contributes to antigen sampling and immune interactions, supporting the specialized function of the FAE in mucosal immunity."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:7107724"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29339448"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34634036"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [follicle associated enterocyte](http://purl.obolibrary.org/obo/CL_4052011) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "FAE enterocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:7107724"^^[string](http://www.w3.org/2001/XMLSchema#string) -### ecto-epithelial cell `http://purl.obolibrary.org/obo/CL_0002077` +- Class: [follicle associated enterocyte](http://purl.obolibrary.org/obo/CL_4052011) + +- [follicle associated enterocyte](http://purl.obolibrary.org/obo/CL_4052011) SubClassOf [enterocyte](http://purl.obolibrary.org/obo/CL_0000584) + + +### follicle cell of egg chamber `http://purl.obolibrary.org/obo/CL_0000477` #### Removed -- [ecto-epithelial cell](http://purl.obolibrary.org/obo/CL_0002077) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009385"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [follicle cell of egg chamber](http://purl.obolibrary.org/obo/CL_0000477) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) + +- [follicle cell of egg chamber](http://purl.obolibrary.org/obo/CL_0000477) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_50557](http://purl.obolibrary.org/obo/NCBITaxon_50557) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "https://github.com/obophenotype/cell-ontology/issues/589"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [ecto-epithelial cell](http://purl.obolibrary.org/obo/CL_0002077) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009385"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [follicle cell of egg chamber](http://purl.obolibrary.org/obo/CL_0000477) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_50557](http://purl.obolibrary.org/obo/NCBITaxon_50557) + - [source](http://www.geneontology.org/formats/oboInOwl#source) "https://github.com/obophenotype/cell-ontology/issues/589"^^[string](http://www.w3.org/2001/XMLSchema#string) -### ectodermal cell `http://purl.obolibrary.org/obo/CL_0000221` +### follicle stem cell (sensu Arthropoda) `http://purl.obolibrary.org/obo/CL_0000441` #### Removed -- [ectodermal cell](http://purl.obolibrary.org/obo/CL_0000221) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009137"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [follicle stem cell (sensu Arthropoda)](http://purl.obolibrary.org/obo/CL_0000441) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_6656](http://purl.obolibrary.org/obo/NCBITaxon_6656) + - [IAO_0000233](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/obophenotype/cell-ontology/issues/1943"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [follicle stem cell (sensu Arthropoda)](http://purl.obolibrary.org/obo/CL_0000441) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) #### Added -- [ectodermal cell](http://purl.obolibrary.org/obo/CL_0000221) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009137"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [follicle stem cell (sensu Arthropoda)](http://purl.obolibrary.org/obo/CL_0000441) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_6656](http://purl.obolibrary.org/obo/NCBITaxon_6656) + - [IAO_0000233](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/obophenotype/cell-ontology/issues/1943"^^[string](http://www.w3.org/2001/XMLSchema#string) -### efferent neuron `http://purl.obolibrary.org/obo/CL_0000527` -#### Removed -- [efferent neuron](http://purl.obolibrary.org/obo/CL_0000527) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009239"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### follicular cell of ovary `http://purl.obolibrary.org/obo/CL_0002174` #### Added -- [efferent neuron](http://purl.obolibrary.org/obo/CL_0000527) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009239"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [follicular cell of ovary](http://purl.obolibrary.org/obo/CL_0002174) SubClassOf [ovarian surface epithelial cell](http://purl.obolibrary.org/obo/CL_2000064) + +- [follicular cell of ovary](http://purl.obolibrary.org/obo/CL_0002174) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001305](http://purl.obolibrary.org/obo/UBERON_0001305) -### egg cell `http://purl.obolibrary.org/obo/CL_0000025` +### fungal cell `http://purl.obolibrary.org/obo/CL_0000521` #### Removed -- [egg cell](http://purl.obolibrary.org/obo/CL_0000025) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00057012"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [fungal cell](http://purl.obolibrary.org/obo/CL_0000521) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any cell that only exists in Fungi."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [fungal cell](http://purl.obolibrary.org/obo/CL_0000521) EquivalentTo [cell](http://purl.obolibrary.org/obo/CL_0000000) and ([RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_4751](http://purl.obolibrary.org/obo/NCBITaxon_4751)) -- [egg cell](http://purl.obolibrary.org/obo/CL_0000025) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0001570"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [fungal cell](http://purl.obolibrary.org/obo/CL_0000521) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_4751](http://purl.obolibrary.org/obo/NCBITaxon_4751) #### Added -- [egg cell](http://purl.obolibrary.org/obo/CL_0000025) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00057012"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [fungal cell](http://purl.obolibrary.org/obo/CL_0000521) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any cell that in taxon some Fungi."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [egg cell](http://purl.obolibrary.org/obo/CL_0000025) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0001570"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [fungal cell](http://purl.obolibrary.org/obo/CL_0000521) EquivalentTo [cell](http://purl.obolibrary.org/obo/CL_0000000) and ([RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_4751](http://purl.obolibrary.org/obo/NCBITaxon_4751)) +- [fungal cell](http://purl.obolibrary.org/obo/CL_0000521) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_4751](http://purl.obolibrary.org/obo/NCBITaxon_4751) -### electrically active cell `http://purl.obolibrary.org/obo/CL_0000211` -#### Removed -- [electrically active cell](http://purl.obolibrary.org/obo/CL_0000211) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009128"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +### gamma-delta T cell `http://purl.obolibrary.org/obo/CL_0000798` #### Added -- [electrically active cell](http://purl.obolibrary.org/obo/CL_0000211) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009128"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [gamma-delta T cell](http://purl.obolibrary.org/obo/CL_0000798) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### electrically responsive cell `http://purl.obolibrary.org/obo/CL_0000393` -#### Removed -- [electrically responsive cell](http://purl.obolibrary.org/obo/CL_0000393) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009190"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### ganglion mother cell `http://purl.obolibrary.org/obo/CL_0000469` #### Added -- [electrically responsive cell](http://purl.obolibrary.org/obo/CL_0000393) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009190"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [ganglion mother cell](http://purl.obolibrary.org/obo/CL_0000469) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### electrically signaling cell `http://purl.obolibrary.org/obo/CL_0000404` +### gingival epithelial cell `http://purl.obolibrary.org/obo/CL_0002621` #### Removed -- [electrically signaling cell](http://purl.obolibrary.org/obo/CL_0000404) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009193"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [gingival epithelial cell](http://purl.obolibrary.org/obo/CL_0002621) SubClassOf [epithelial cell of alimentary canal](http://purl.obolibrary.org/obo/CL_0002251) #### Added -- [electrically signaling cell](http://purl.obolibrary.org/obo/CL_0000404) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009193"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [gingival epithelial cell](http://purl.obolibrary.org/obo/CL_0002621) SubClassOf [oral mucosa squamous cell](http://purl.obolibrary.org/obo/CL_1001576) -### embryonic blood vessel endothelial progenitor cell `http://purl.obolibrary.org/obo/CL_0002546` -#### Removed -- [embryonic blood vessel endothelial progenitor cell](http://purl.obolibrary.org/obo/CL_0002546) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005773"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### glial cell `http://purl.obolibrary.org/obo/CL_0000125` #### Added -- [embryonic blood vessel endothelial progenitor cell](http://purl.obolibrary.org/obo/CL_0002546) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005773"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [glial cell](http://purl.obolibrary.org/obo/CL_0000125) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000125"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [glial cell](http://purl.obolibrary.org/obo/CL_0000125) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -### embryonic cell (metazoa) `http://purl.obolibrary.org/obo/CL_0002321` -#### Removed -- [embryonic cell (metazoa)](http://purl.obolibrary.org/obo/CL_0002321) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0007089"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +Glial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons. +These different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning. +Oligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. +Microglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response. +Despite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1101/cshperspect.a020602"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [embryonic cell (metazoa)](http://purl.obolibrary.org/obo/CL_0002321) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0007089"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1126/science.aat0473"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nn1988"^^[string](http://www.w3.org/2001/XMLSchema#string) -### embryonic crystal cell `http://purl.obolibrary.org/obo/CL_0000715` -#### Removed -- [embryonic crystal cell](http://purl.obolibrary.org/obo/CL_0000715) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00001690"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/glia.24343"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [embryonic crystal cell](http://purl.obolibrary.org/obo/CL_0000715) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00001690"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fncel.2017.00024"^^[string](http://www.w3.org/2001/XMLSchema#string) -### embryonic fibroblast `http://purl.obolibrary.org/obo/CL_2000042` -#### Removed -- [embryonic fibroblast](http://purl.obolibrary.org/obo/CL_2000042) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +### glioblast `http://purl.obolibrary.org/obo/CL_0000030` #### Added -- [embryonic fibroblast](http://purl.obolibrary.org/obo/CL_2000042) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [glioblast](http://purl.obolibrary.org/obo/CL_0000030) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### endo-epithelial cell `http://purl.obolibrary.org/obo/CL_0002076` -#### Removed -- [endo-epithelial cell](http://purl.obolibrary.org/obo/CL_0002076) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009383"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### glomerular capillary endothelial cell `http://purl.obolibrary.org/obo/CL_1001005` #### Added -- [endo-epithelial cell](http://purl.obolibrary.org/obo/CL_0002076) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009383"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [glomerular capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1001005) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1001005"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [endo-epithelial cell](http://purl.obolibrary.org/obo/CL_0002076) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([RO_0002202](http://purl.obolibrary.org/obo/RO_0002202) some [endodermal cell](http://purl.obolibrary.org/obo/CL_0000223)) +- [glomerular capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1001005) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +The glomerular capillary endothelial cell comprises an intrinsic component of the glomerulus in the kidney. Glomeruli contain a network of capillaries where the first step of blood filtration takes place, with glomerular capillary endothelial cells acting as an integral part of this process. Unlike regular endothelial cells that line the vasculature, unique fenestrations (openings) characterize these cells, allowing for enhanced permeability and filtration efficacy. +Together with the glomerular basement membrane and podocytes, the glomerular endothelial cells form the glomerular filtration barrier, which is responsible for blood filtration and therefore critical for removal of waste products, such as urea and creatinine, and excess substances, such as glucose and ions, from the bloodstream. The glomerular capillary endothelial cells' fenestrations permit the free flow of a variety of particles, barring larger, negatively charged proteins like serum albumin, enabling the formation of an ultrafiltrate. This ultrafiltrate is the primitive form of urine, which then passes through the proximal tubule for further processing and ultimately helps maintain systemic fluid and electrolyte balance. +Moreover, the glomerular capillary endothelial cells are also believed to play a crucial role in renal pathologies. Any compromise to their structural integrity or functional performance can lead to kidney diseases, including but not limited to, diabetic nephropathy and glomerulonephritis. For instance, in diabetes, persistent hyperglycemia can injure these cells, leading to a compromised glomerular filtration barrier and proteinuria, indicating the loss of proteins in the urine."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.biocel.2010.05.015"^^[string](http://www.w3.org/2001/XMLSchema#string) -### endocrine cell `http://purl.obolibrary.org/obo/CL_0000163` -#### Removed -- [endocrine cell](http://purl.obolibrary.org/obo/CL_0000163) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009096"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2337/diacare.28.1.164"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [endocrine cell](http://purl.obolibrary.org/obo/CL_0000163) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009096"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1523-1755.2005.00260.x"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fphys.2021.689083"^^[string](http://www.w3.org/2001/XMLSchema#string) -### endodermal cell `http://purl.obolibrary.org/obo/CL_0000223` -#### Removed -- [endodermal cell](http://purl.obolibrary.org/obo/CL_0000223) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009139"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.yexcr.2012.02.032"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### glomerular endothelial cell `http://purl.obolibrary.org/obo/CL_0002188` #### Added -- [endodermal cell](http://purl.obolibrary.org/obo/CL_0000223) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009139"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [glomerular endothelial cell](http://purl.obolibrary.org/obo/CL_0002188) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### endometrial ciliated epithelial cell `http://purl.obolibrary.org/obo/CL_4030040` +### glycinergic amacrine cell `http://purl.obolibrary.org/obo/CL_4030028` #### Removed -- [endometrial ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_4030040) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A ciliated cell of the endometrial epithelium. The cilia of this cell type help move mucus from glandular tissue of the endometrium."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.proteinatlas.org/humanproteome/single+cell+type/Glandular+epithelial+cells#endometrialciliatedcells"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [glycinergic amacrine cell](http://purl.obolibrary.org/obo/CL_4030028) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An amacrine cell that uses glycine as a neurotransmitter."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [definition](http://purl.obolibrary.org/obo/IAO_0000115) "https://doi.org/10.1016/j.cell.2020.08.013"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.1038/s41591-020-1040-z"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [glycinergic amacrine cell](http://purl.obolibrary.org/obo/CL_4030028) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An amacrine cell that uses glycine as a neurotransmitter."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.1016/j.cell.2020.08.013"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [endometrial ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_4030040) EquivalentTo [ciliated cell](http://purl.obolibrary.org/obo/CL_0000064) and [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004811](http://purl.obolibrary.org/obo/UBERON_0004811)) -- [endometrial ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_4030040) SubClassOf [ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0000067) +### goblet cell `http://purl.obolibrary.org/obo/CL_0000160` #### Added -- [endometrial ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_4030040) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A multi-ciliated cell of the endometrial epithelium. This cell is characterized by the presence of 9+2 motile cilia on its apical surface, which facilitates the movement of mucus across the endometrial surface."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.proteinatlas.org/humanproteome/single+cell+type/Glandular+epithelial+cells#endometrialciliatedcells"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31290979"^^[string](http://www.w3.org/2001/XMLSchema#string) +Goblet cells are specialized, simple columnar, secretory epithelial cells that are mostly found in the respiratory and intestinal tracts. The term "goblet" refers to their shape, which resembles a flask or goblet, specially at their apical end which is swollen due to the accumulation of secretory granules. +The primary function of goblet cells is to to protect and lubricate the underlying tissues by secreting large quantities of mucin, a complex glycoprotein, which forms mucus when hydrated. In the respiratory tract, the mucus secreted by these cells traps dust, bacteria, viruses, and other potentially harmful particles in the inhaled air, preventing them from reaching the delicate tissues of the lungs. In the intestines, the goblet cells secrete mucus that acts as a protective barrier shielding the intestinal epithelium from dietary antigens, pathogens and prevents the intestinal epithelium from being eroded by the actions of the digestive enzymes and the abrasive action of passing food material. +Goblet cells are capable of rapidly altering their secretory output in response to stimuli. For example, irritants like smoke or dust can trigger an increased rate of mucus production, as the body attempts to flush out the harmful particles. Conversely, in conditions such as chronic bronchitis and cystic fibrosis, overactive goblet cells can create a thick accumulation of mucus that obstructs the airways and fosters bacterial growth. Lastly, goblet cells are not static, rather, they undergo a dynamic process known as goblet cell metaplasia-differentiation, wherein non-goblet cells in response to chronic injury or inflammation, can differentiate into goblet cells leading to an accumulation of these cells in the tissue, known as goblet cell hyperplasia."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41575-022-00675-x"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.1016/j.coemr.2024.100503"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1242/bio.20121701"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37999981"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/S1357-2725(02)00083-3"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.1038/s41591-020-1040-z"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1165/ajrcmb.25.5.f218"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [endometrial ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_4030040) EquivalentTo [multi-ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005012) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004811](http://purl.obolibrary.org/obo/UBERON_0004811)) and ([BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0097729](http://purl.obolibrary.org/obo/GO_0097729)) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK553208/"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [endometrial ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_4030040) SubClassOf [multi-ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005012) +- [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000160"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [endometrial ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_4030040) SubClassOf [epithelial cell of uterus](http://purl.obolibrary.org/obo/CL_0002149) -- [endometrial ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_4030040) SubClassOf [BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0097729](http://purl.obolibrary.org/obo/GO_0097729) +### granulocyte `http://purl.obolibrary.org/obo/CL_0000094` + +#### Added +- [granulocyte](http://purl.obolibrary.org/obo/CL_0000094) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### endometrial microvascular endothelial cell `http://purl.obolibrary.org/obo/CL_2000091` -#### Removed -- [endometrial microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000091) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +### granulocyte monocyte progenitor cell `http://purl.obolibrary.org/obo/CL_0000557` #### Added -- [endometrial microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000091) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [granulocyte monocyte progenitor cell](http://purl.obolibrary.org/obo/CL_0000557) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### endorphin secreting cell `http://purl.obolibrary.org/obo/CL_0000507` +### granulosa cell `http://purl.obolibrary.org/obo/CL_0000501` #### Removed -- [endorphin secreting cell](http://purl.obolibrary.org/obo/CL_0000507) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009232"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [granulosa cell](http://purl.obolibrary.org/obo/CL_0000501) SubClassOf [RO_0002207](http://purl.obolibrary.org/obo/RO_0002207) some [pre-granulosa cell](http://purl.obolibrary.org/obo/CL_4033066) #### Added -- [endorphin secreting cell](http://purl.obolibrary.org/obo/CL_0000507) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009232"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [granulosa cell](http://purl.obolibrary.org/obo/CL_0000501) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +Granulosa cells are a type of somatic cell most commonly known for their crucial role within the ovarian follicles of female mammalian species. Named for their grainy appearance, they are situated in the follicular epithelium, lining the inner part of the follicle and directly surrounding the oocyte. These cells stand as an integral part of the ovarian structure and function. +One of the primary roles of granulosa cells is to aid in the production and secretion of sex hormones, particularly estrogen. They achieve this by working in tandem with theca cells, which stay attached to the external layer of the follicle. Theca cells produce androstenedione (a type of androgen) which granulosa cells then convert into estradiol, a form of estrogen, with the help of the enzyme aromatase. Moreover, granulosa cells participate in luteinization, transforming into luteal granulosa cells as a response to the luteinizing hormone during ovulation. This allows the formation of the corpus luteum, responsible for the secretion of progesterone necessary to maintain pregnancy. +Granulosa cells also play a significant role in follicular development and oocyte maturation, involving close communication with the contained oocyte. They support the oocyte through the provision of nutrients and growth factors, control its meiotic cycle and ensure it is appropriately oriented and instructed for impending ovulation. Furthermore, granulosa cells contribute to the formation of the zona pellucida and the follicular fluid, providing an optimal environment for the oocyte's growth and maturation. These cells, thus, perform multiple vital roles, underscoring their importance in fertility and reproductive health."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1093/humupd/6.3.279"^^[string](http://www.w3.org/2001/XMLSchema#string) -### endothelial cell `http://purl.obolibrary.org/obo/CL_0000115` -#### Removed -- [endothelial cell](http://purl.obolibrary.org/obo/CL_0000115) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009065"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fendo.2019.00832/full"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [endothelial cell](http://purl.obolibrary.org/obo/CL_0000115) SubClassOf [meso-epithelial cell](http://purl.obolibrary.org/obo/CL_0002078) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.ejogrb.2004.01.010"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [endothelial cell](http://purl.obolibrary.org/obo/CL_0000115) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009065"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1093/humrep/del408"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [endothelial cell](http://purl.obolibrary.org/obo/CL_0000115) SubClassOf [RO_0002202](http://purl.obolibrary.org/obo/RO_0002202) some [mesodermal cell](http://purl.obolibrary.org/obo/CL_0000222) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1210/jcem-28-3-355"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [endothelial cell](http://purl.obolibrary.org/obo/CL_0000115) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) +- [granulosa cell](http://purl.obolibrary.org/obo/CL_0000501) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000501"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [granulosa cell](http://purl.obolibrary.org/obo/CL_0000501) SubClassOf [RO_0002202](http://purl.obolibrary.org/obo/RO_0002202) some [pre-granulosa cell](http://purl.obolibrary.org/obo/CL_4033066) -### endothelial cell of Peyer's patch `http://purl.obolibrary.org/obo/CL_1000411` -#### Removed -- [endothelial cell of Peyer's patch](http://purl.obolibrary.org/obo/CL_1000411) SubClassOf [epithelial cell of small intestine](http://purl.obolibrary.org/obo/CL_0002254) +### group 2 innate lymphoid cell, human `http://purl.obolibrary.org/obo/CL_0001081` + +#### Added +- [group 2 innate lymphoid cell, human](http://purl.obolibrary.org/obo/CL_0001081) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### endothelial cell of central vein of liver `http://purl.obolibrary.org/obo/CL_4033061` -#### Removed -- [endothelial cell of central vein of liver](http://purl.obolibrary.org/obo/CL_4033061) SubClassOf [endothelial cell](http://purl.obolibrary.org/obo/CL_0000115) +### group 2 innate lymphoid cell, mouse `http://purl.obolibrary.org/obo/CL_0002089` #### Added -- [endothelial cell of central vein of liver](http://purl.obolibrary.org/obo/CL_4033061) SubClassOf [vein endothelial cell](http://purl.obolibrary.org/obo/CL_0002543) +- [group 2 innate lymphoid cell, mouse](http://purl.obolibrary.org/obo/CL_0002089) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### endothelial cell of coronary artery `http://purl.obolibrary.org/obo/CL_2000018` -#### Removed -- [endothelial cell of coronary artery](http://purl.obolibrary.org/obo/CL_2000018) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +### group 3 innate lymphoid cell `http://purl.obolibrary.org/obo/CL_0001071` #### Added -- [endothelial cell of coronary artery](http://purl.obolibrary.org/obo/CL_2000018) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [group 3 innate lymphoid cell](http://purl.obolibrary.org/obo/CL_0001071) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### endothelial cell of efferent lymphatic vessel `http://purl.obolibrary.org/obo/CL_4033006` +### gut absorptive cell `http://purl.obolibrary.org/obo/CL_0000677` #### Removed -- [endothelial cell of efferent lymphatic vessel](http://purl.obolibrary.org/obo/CL_4033006) SubClassOf [endothelial cell](http://purl.obolibrary.org/obo/CL_0000115) +- [gut absorptive cell](http://purl.obolibrary.org/obo/CL_0000677) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) #### Added -- [endothelial cell of efferent lymphatic vessel](http://purl.obolibrary.org/obo/CL_4033006) SubClassOf [endothelial cell of lymphatic vessel](http://purl.obolibrary.org/obo/CL_0002138) +- [gut absorptive cell](http://purl.obolibrary.org/obo/CL_0000677) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### endothelial cell of hepatic portal vein `http://purl.obolibrary.org/obo/CL_0009094` +### hair follicle cell `http://purl.obolibrary.org/obo/CL_0002559` #### Removed -- [endothelial cell of hepatic portal vein](http://purl.obolibrary.org/obo/CL_0009094) SubClassOf [endothelial cell](http://purl.obolibrary.org/obo/CL_0000115) +- [hair follicle cell](http://purl.obolibrary.org/obo/CL_0002559) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) #### Added -- [endothelial cell of hepatic portal vein](http://purl.obolibrary.org/obo/CL_0009094) SubClassOf [vein endothelial cell](http://purl.obolibrary.org/obo/CL_0002543) +- [hair follicle cell](http://purl.obolibrary.org/obo/CL_0002559) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### endothelial cell of hepatic sinusoid `http://purl.obolibrary.org/obo/CL_1000398` +### hematopoietic lineage restricted progenitor cell `http://purl.obolibrary.org/obo/CL_0002031` #### Added -- [endothelial cell of hepatic sinusoid](http://purl.obolibrary.org/obo/CL_1000398) SubClassOf [fenestrated endothelial cell](http://purl.obolibrary.org/obo/CL_0000666) +- [hematopoietic lineage restricted progenitor cell](http://purl.obolibrary.org/obo/CL_0002031) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### endothelial cell of high endothelial venule `http://purl.obolibrary.org/obo/CL_0002652` -#### Removed -- [endothelial cell of high endothelial venule](http://purl.obolibrary.org/obo/CL_0002652) EquivalentTo [endothelial cell](http://purl.obolibrary.org/obo/CL_0000115) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_8410037](http://purl.obolibrary.org/obo/UBERON_8410037)) - -- [endothelial cell of high endothelial venule](http://purl.obolibrary.org/obo/CL_0002652) SubClassOf [columnar/cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000075) +### hematopoietic multipotent progenitor cell `http://purl.obolibrary.org/obo/CL_0000837` #### Added -- [endothelial cell of high endothelial venule](http://purl.obolibrary.org/obo/CL_0002652) EquivalentTo [endothelial cell of vascular tree](http://purl.obolibrary.org/obo/CL_0002139) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_8410037](http://purl.obolibrary.org/obo/UBERON_8410037)) +- [hematopoietic multipotent progenitor cell](http://purl.obolibrary.org/obo/CL_0000837) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) +- [hematopoietic multipotent progenitor cell](http://purl.obolibrary.org/obo/CL_0000837) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### endothelial cell of lymphatic vessel `http://purl.obolibrary.org/obo/CL_0002138` -#### Removed -- [endothelial cell of lymphatic vessel](http://purl.obolibrary.org/obo/CL_0002138) EquivalentTo [endothelial cell of vascular tree](http://purl.obolibrary.org/obo/CL_0002139) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001473](http://purl.obolibrary.org/obo/UBERON_0001473)) and ([RO_0002202](http://purl.obolibrary.org/obo/RO_0002202) some [vascular lymphangioblast](http://purl.obolibrary.org/obo/CL_0005022)) + +### hematopoietic oligopotent progenitor cell `http://purl.obolibrary.org/obo/CL_0002032` #### Added -- [endothelial cell of lymphatic vessel](http://purl.obolibrary.org/obo/CL_0002138) EquivalentTo [endothelial cell](http://purl.obolibrary.org/obo/CL_0000115) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001473](http://purl.obolibrary.org/obo/UBERON_0001473)) +- [hematopoietic oligopotent progenitor cell](http://purl.obolibrary.org/obo/CL_0002032) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### endothelial cell of placenta `http://purl.obolibrary.org/obo/CL_0009092` +### hemocyte (sensu Arthropoda) `http://purl.obolibrary.org/obo/CL_0000387` #### Removed -- [endothelial cell of placenta](http://purl.obolibrary.org/obo/CL_0009092) SubClassOf [placental epithelial cell](http://purl.obolibrary.org/obo/CL_0002577) +- [hemocyte (sensu Arthropoda)](http://purl.obolibrary.org/obo/CL_0000387) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_6656](http://purl.obolibrary.org/obo/NCBITaxon_6656) #### Added -- [endothelial cell of placenta](http://purl.obolibrary.org/obo/CL_0009092) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001987](http://purl.obolibrary.org/obo/UBERON_0001987) +- [hemocyte (sensu Arthropoda)](http://purl.obolibrary.org/obo/CL_0000387) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_6656](http://purl.obolibrary.org/obo/NCBITaxon_6656) -### endothelial cell of respiratory system lymphatic vessel `http://purl.obolibrary.org/obo/CL_0009086` -#### Removed -- [endothelial cell of respiratory system lymphatic vessel](http://purl.obolibrary.org/obo/CL_0009086) SubClassOf [endothelial cell](http://purl.obolibrary.org/obo/CL_0000115) +### hepatic stellate cell `http://purl.obolibrary.org/obo/CL_0000632` #### Added -- [endothelial cell of respiratory system lymphatic vessel](http://purl.obolibrary.org/obo/CL_0009086) SubClassOf [endothelial cell of lymphatic vessel](http://purl.obolibrary.org/obo/CL_0002138) +- [hepatic stellate cell](http://purl.obolibrary.org/obo/CL_0000632) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### endothelial cell of sinusoid `http://purl.obolibrary.org/obo/CL_0002262` -#### Removed -- [endothelial cell of sinusoid](http://purl.obolibrary.org/obo/CL_0002262) SubClassOf [endothelial cell](http://purl.obolibrary.org/obo/CL_0000115) +### hepatoblast `http://purl.obolibrary.org/obo/CL_0005026` #### Added -- [endothelial cell of sinusoid](http://purl.obolibrary.org/obo/CL_0002262) SubClassOf [blood vessel endothelial cell](http://purl.obolibrary.org/obo/CL_0000071) +- [hepatoblast](http://purl.obolibrary.org/obo/CL_0005026) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +Hepatoblasts are immature precursor cells that predominate during the early stages of liver development, specifically in the embryonic phase of life. They first arise from the endoderm, one of the three primary germ layers in the very early embryo, and then differentiate into two distinct mature liver cell types - the hepatocytes and cholangiocytes. +During liver organogenesis hepatoblasts proliferate and migrate into the septum transversum to form the liver bud. Proliferation and differentiation of these cells are regulated by several soluble factors, such as hepatocyte growth factor, which is a mitogen of both hepatoblasts and mature hepatocytes. As they start to differentiate into hepatocytes and cholangiocytes, the cells begin to express hepatic markers like albumin and alpha-fetoprotein. +Although hepatoblasts are specified embryonic liver cells that are bipotential for hepatocytes and cholangiocytes, a subset of liver cells (called oval cells) has been identified in adults that express stem cell markers, such as CD133 and cKIT, and has been suggested to have the same potential as hepatoblasts to differentiate into hepatocytes and cholangiocytes."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1242/dev.031369"^^[string](http://www.w3.org/2001/XMLSchema#string) -### endothelial cell of venule `http://purl.obolibrary.org/obo/CL_1000414` -#### Removed -- [endothelial cell of venule](http://purl.obolibrary.org/obo/CL_1000414) SubClassOf [endothelial cell of vascular tree](http://purl.obolibrary.org/obo/CL_0002139) - - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1242/dev.114215"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [endothelial cell of venule](http://purl.obolibrary.org/obo/CL_1000414) SubClassOf [blood vessel endothelial cell](http://purl.obolibrary.org/obo/CL_0000071) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.5966/sctm.2015-0051"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1093/jb/mvr001"^^[string](http://www.w3.org/2001/XMLSchema#string) -### endothelial cell of venule of lymph node `http://purl.obolibrary.org/obo/CL_4033000` -#### Removed -- [endothelial cell of venule of lymph node](http://purl.obolibrary.org/obo/CL_4033000) SubClassOf [endothelial cell](http://purl.obolibrary.org/obo/CL_0000115) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.stem.2014.04.010"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [endothelial cell of venule of lymph node](http://purl.obolibrary.org/obo/CL_4033000) SubClassOf [endothelial cell of venule](http://purl.obolibrary.org/obo/CL_1000414) +- [hepatoblast](http://purl.obolibrary.org/obo/CL_0005026) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0005026"^^[string](http://www.w3.org/2001/XMLSchema#string) -### endothelial tip cell `http://purl.obolibrary.org/obo/CL_0000704` -#### Removed -- [endothelial tip cell](http://purl.obolibrary.org/obo/CL_0000704) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009303"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### hepatocyte `http://purl.obolibrary.org/obo/CL_0000182` #### Added -- [endothelial tip cell](http://purl.obolibrary.org/obo/CL_0000704) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009303"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [hepatocyte](http://purl.obolibrary.org/obo/CL_0000182) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +Hepatocytes are the major cell type constituting 70-80% of the liver's cytoplasmic mass, playing crucial roles in maintaining the body's metabolic homeostasis. Dimensions of mature hepatocytes typically range from 20 to 30 μm in humans, but size may vary depending on their location within the liver lobule. Hepatocytes are characterized by high biosynthetic, enzymatic, and endocytic activity. They contain abundant mitochondria, smooth and rough endoplasmic reticulum, peroxisomes, lysosomes, and a large nucleus that is often binucleate. +The liver consists of three zones - the periportal Zone 1, midzone 2, and pericentral Zone 3 - which have differential nutrient and oxygen status, and damage susceptibility; hepatocytes in the different zones show signifcant functional heterogeneity ('hepatocyte functional zonation'). Hepatocytes are involved in a multitude of critical functions including the metabolism of lipids, carbohydrates, and proteins, the synthesis of serum proteins (e.g., albumin, transferrin, and lipoproteins), the detoxification and excretion of endogenous and exogenous substances, the storage of vitamins and minerals, and the production and secretion of bile. +Heterocytes demonstrate a remarkable regenerative capacity, which enables the liver to recover from injury and loss of tissue mass. Notably, hepatocytes perform biotransformation with both phase I and phase II enzymes, which modify drugs, xenobiotics, and various substances for elimination from the body. Phase I enzymes, such as cytochrome P450, catalyze both oxidative and reductive reactions of many xenobiotics; many of the products of phase I enzymes are substrates for the phase II enzymes, which catalyze conjugation reactions. +Alterations in hepatocyte function have significant implications for overall human health and disease. Certain conditions, such as hepatitis, cirrhosis, and liver cancer, can profoundly affect hepatocyte structure and function, thereby disrupting the liver's ability to perform its vital roles within the body. As the primary site for drug metabolism, changes in hepatocyte function can also impact the effectiveness and toxicity of pharmaceuticals. The regenerative ability of hepatocytes makes them valuable cells for liver regenerative medicine and bioartificial liver support systems, and their study has provided significant insights into liver biology and disease."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1083/jcb.201903090"^^[string](http://www.w3.org/2001/XMLSchema#string) -### endovascular extravillous trophoblast cell `http://purl.obolibrary.org/obo/CL_4033063` -#### Removed -- [endovascular extravillous trophoblast cell](http://purl.obolibrary.org/obo/CL_4033063) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) - + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.biocel.2011.11.011"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1439-0396.2007.00752.x"^^[string](http://www.w3.org/2001/XMLSchema#string) -### enkephalin secreting cell `http://purl.obolibrary.org/obo/CL_0000506` -#### Removed -- [enkephalin secreting cell](http://purl.obolibrary.org/obo/CL_0000506) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009231"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1055/s-2007-1007096"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [enkephalin secreting cell](http://purl.obolibrary.org/obo/CL_0000506) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009231"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [hepatocyte](http://purl.obolibrary.org/obo/CL_0000182) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000182"^^[string](http://www.w3.org/2001/XMLSchema#string) -### enteric neuron `http://purl.obolibrary.org/obo/CL_0007011` +### histoblast `http://purl.obolibrary.org/obo/CL_0000373` #### Removed -- [enteric neuron](http://purl.obolibrary.org/obo/CL_0007011) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005775"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [histoblast](http://purl.obolibrary.org/obo/CL_0000373) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) + +- [histoblast](http://purl.obolibrary.org/obo/CL_0000373) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_50557](http://purl.obolibrary.org/obo/NCBITaxon_50557) #### Added -- [enteric neuron](http://purl.obolibrary.org/obo/CL_0007011) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005775"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [histoblast](http://purl.obolibrary.org/obo/CL_0000373) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_50557](http://purl.obolibrary.org/obo/NCBITaxon_50557) -### enterocyte `http://purl.obolibrary.org/obo/CL_0000584` -#### Removed -- [enterocyte](http://purl.obolibrary.org/obo/CL_0000584) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009269"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### hypendymal cell `http://purl.obolibrary.org/obo/CL_4023181` #### Added -- [enterocyte](http://purl.obolibrary.org/obo/CL_0000584) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009269"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [hypendymal cell](http://purl.obolibrary.org/obo/CL_4023181) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +Hypendymal cells are secretory cells located between the ependymal layer and the posterior commissure, forming the hypendmal layer of the subcommissural organ (SCO), a highly conserved gland that is part of the circumventricular system within the brain. +Hypendymal cells are bipolar cells with a thin apical pole and basal process. Most of the ultrastructural characteristics of these cells are similar to those described for the ependymal cells (which are arranged into another layer – the ependyma). However, ependymal cells release their secretion into the ventricular cerebrospinal fluid whereas hypendymal cells project processes to the local blood vessels and to the subarachnoidal space."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fncel.2015.00480"^^[string](http://www.w3.org/2001/XMLSchema#string) -### enterocyte of colon `http://purl.obolibrary.org/obo/CL_1000347` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/(SICI)1097-0029(19980415)41:2<98::AID-JEMT2>3.0.CO;2-M"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [enterocyte of colon](http://purl.obolibrary.org/obo/CL_1000347) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "colonocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34497389"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/joa.13709"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [hypendymal cell](http://purl.obolibrary.org/obo/CL_4023181) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_4023181"^^[string](http://www.w3.org/2001/XMLSchema#string) -### enteroendocrine cell `http://purl.obolibrary.org/obo/CL_0000164` + +### imaginal disc cell `http://purl.obolibrary.org/obo/CL_0000429` #### Removed -- [enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000164) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009097"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [imaginal disc cell](http://purl.obolibrary.org/obo/CL_0000429) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) + +- [imaginal disc cell](http://purl.obolibrary.org/obo/CL_0000429) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_50557](http://purl.obolibrary.org/obo/NCBITaxon_50557) #### Added -- [enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000164) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009097"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [imaginal disc cell](http://purl.obolibrary.org/obo/CL_0000429) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_50557](http://purl.obolibrary.org/obo/NCBITaxon_50557) -### ependymal cell `http://purl.obolibrary.org/obo/CL_0000065` -#### Removed -- [ependymal cell](http://purl.obolibrary.org/obo/CL_0000065) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009033"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### immature pericyte `http://purl.obolibrary.org/obo/CL_4047007` #### Added -- [ependymal cell](http://purl.obolibrary.org/obo/CL_0000065) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009033"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [immature pericyte](http://purl.obolibrary.org/obo/CL_4047007) [contributor](http://purl.org/dc/terms/contributor) [0009-0005-7919-4905](https://orcid.org/0009-0005-7919-4905) +- [immature pericyte](http://purl.obolibrary.org/obo/CL_4047007) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A pericyte that is in an early stage of development, found in newly forming or remodeling blood vessels. An immature pericyte is characterized by it's mesenchymal stem cell-like properties and high proliferative capacity, which allows it to differentiate into various types of pericytes and contribute to the structural and functional maturation of the vasculature. Immature pericytes are stellate in new vessels and elongated with less protrusions in remodeling vessels."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32466671"^^[string](http://www.w3.org/2001/XMLSchema#string) -### ependymoglial cell `http://purl.obolibrary.org/obo/CL_0000683` -#### Removed -- [ependymoglial cell](http://purl.obolibrary.org/obo/CL_0000683) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009294"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34497389"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [ependymoglial cell](http://purl.obolibrary.org/obo/CL_0000683) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009294"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36685855"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:21839917"^^[string](http://www.w3.org/2001/XMLSchema#string) -### epidermal cell `http://purl.obolibrary.org/obo/CL_0000362` -#### Removed -- [epidermal cell](http://purl.obolibrary.org/obo/CL_0000362) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009183"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:28564607"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [epidermal cell](http://purl.obolibrary.org/obo/CL_0000362) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009183"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [immature pericyte](http://purl.obolibrary.org/obo/CL_4047007) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "imPCs"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:28564607"^^[string](http://www.w3.org/2001/XMLSchema#string) -### epidermal cell (sensu Arthropoda) `http://purl.obolibrary.org/obo/CL_0000463` -#### Removed -- [epidermal cell (sensu Arthropoda)](http://purl.obolibrary.org/obo/CL_0000463) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007325"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [immature pericyte](http://purl.obolibrary.org/obo/CL_4047007) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4047007"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [epidermal cell (sensu Arthropoda)](http://purl.obolibrary.org/obo/CL_0000463) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007325"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [immature pericyte](http://purl.obolibrary.org/obo/CL_4047007) [date](http://purl.org/dc/terms/date) "2024-08-19T11:32:32Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) +- [immature pericyte](http://purl.obolibrary.org/obo/CL_4047007) [label](http://www.w3.org/2000/01/rdf-schema#label) "immature pericyte"^^[string](http://www.w3.org/2001/XMLSchema#string) -### epidermal melanocyte `http://purl.obolibrary.org/obo/CL_2000000` -#### Removed -- [epidermal melanocyte](http://purl.obolibrary.org/obo/CL_2000000) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +- [immature pericyte](http://purl.obolibrary.org/obo/CL_4047007) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "immature PCs"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) -#### Added -- [epidermal melanocyte](http://purl.obolibrary.org/obo/CL_2000000) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:28564607"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [immature pericyte](http://purl.obolibrary.org/obo/CL_4047007) + +- [immature pericyte](http://purl.obolibrary.org/obo/CL_4047007) SubClassOf [pericyte](http://purl.obolibrary.org/obo/CL_0000669) -### epidermoblast `http://purl.obolibrary.org/obo/CL_0000464` -#### Removed -- [epidermoblast](http://purl.obolibrary.org/obo/CL_0000464) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004994"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + +### immature single positive thymocyte `http://purl.obolibrary.org/obo/CL_0000805` #### Added -- [epidermoblast](http://purl.obolibrary.org/obo/CL_0000464) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004994"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [immature single positive thymocyte](http://purl.obolibrary.org/obo/CL_0000805) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### epinephrine secreting cell `http://purl.obolibrary.org/obo/CL_0000454` -#### Removed -- [epinephrine secreting cell](http://purl.obolibrary.org/obo/CL_0000454) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009211"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### inflammatory macrophage `http://purl.obolibrary.org/obo/CL_0000863` #### Added -- [epinephrine secreting cell](http://purl.obolibrary.org/obo/CL_0000454) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009211"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [inflammatory macrophage](http://purl.obolibrary.org/obo/CL_0000863) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +Inflammatory macrophages, also sometimes referred to as M1 or classically activated macrophages, play an important role in the inflammatory response. The M1/M2 classification is based upon macrophage polarization rather than macrophage location and refers to macrophage activation towards either a more inflammatory or more resolving phenotype, respectively, although the functional diversity of macrophages is more nuanced than such a dichotomy suggests. +Inflammatory macrophages are derived from monocytes recruited to a site of infection or injury. M1 macrophages are classically activated, typically by IFN-γ or lipopolysaccharide (LPS). Upon sensing signs of inflammation, they quickly respond by increasing their pro-inflammatory activity. They achieve this by producing a range of signaling molecules, such as nitric oxide, reactive oxygen species, and numerous cytokines such as tumor necrosis factor-alpha (TNF-alpha) and interleukin-1, -6 and -12. The release of these potent molecules helps to recruit other immune cells to the site, killing off pathogenic organisms and facilitation inflammation. At the same time, M1 macrophages can also present antigens to T cells, thereby helping to induce an adaptive immune response. Over time, these macrophages may transition in phenotype and function to help resolve the inflammation and promote tissue repair. +Despite the beneficial role of inflammatory macrophages in dealing with pathogens, chronic activation of these cells can lead to harmful effects. Over time, continuous production of pro-inflammatory molecules can cause damage to tissues and organs. This is seen in certain chronic inflammatory diseases, such as atherosclerosis, diabetes, obesity, asthma, and various autoimmune disorders. In such situations, the normally protective function of inflammatory macrophages is not properly controlled, which can contribute to disease pathology."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1186/s12935-021-02089-2"^^[string](http://www.w3.org/2001/XMLSchema#string) -### epithelial cell `http://purl.obolibrary.org/obo/CL_0000066` -#### Removed -- [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000124"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2020.583084"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009034"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2015.00263"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000124"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41392-023-01452-1"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009034"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [inflammatory macrophage](http://purl.obolibrary.org/obo/CL_0000863) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000863"^^[string](http://www.w3.org/2001/XMLSchema#string) -### epithelial cell of alveolus of lung `http://purl.obolibrary.org/obo/CL_0010003` +### inner cell mass cell `http://purl.obolibrary.org/obo/CL_2000020` #### Removed -- [epithelial cell of alveolus of lung](http://purl.obolibrary.org/obo/CL_0010003) SubClassOf [epithelial cell of lung](http://purl.obolibrary.org/obo/CL_0000082) +- [inner cell mass cell](http://purl.obolibrary.org/obo/CL_2000020) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) #### Added -- [epithelial cell of alveolus of lung](http://purl.obolibrary.org/obo/CL_0010003) SubClassOf [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) +- [inner cell mass cell](http://purl.obolibrary.org/obo/CL_2000020) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### epithelial cell of cervix `http://purl.obolibrary.org/obo/CL_0002535` -#### Removed -- [epithelial cell of cervix](http://purl.obolibrary.org/obo/CL_0002535) SubClassOf [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) +### insulin secreting cell `http://purl.obolibrary.org/obo/CL_0000168` #### Added -- [epithelial cell of cervix](http://purl.obolibrary.org/obo/CL_0002535) SubClassOf [epithelial cell of uterus](http://purl.obolibrary.org/obo/CL_0002149) +- [insulin secreting cell](http://purl.obolibrary.org/obo/CL_0000168) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### epithelial cell of endometrial gland `http://purl.obolibrary.org/obo/CL_0009084` -#### Removed -- [epithelial cell of endometrial gland](http://purl.obolibrary.org/obo/CL_0009084) SubClassOf [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) +### intercalated cell of salivary gland `http://purl.obolibrary.org/obo/CL_4052048` #### Added -- [epithelial cell of endometrial gland](http://purl.obolibrary.org/obo/CL_0009084) SubClassOf [epithelial cell of uterus](http://purl.obolibrary.org/obo/CL_0002149) - +- [intercalated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052048) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052048"^^[string](http://www.w3.org/2001/XMLSchema#string) -### epithelial cell of esophagus `http://purl.obolibrary.org/obo/CL_0002252` -#### Removed -- [epithelial cell of esophagus](http://purl.obolibrary.org/obo/CL_0002252) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009400"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [intercalated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052048) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cuboidal epithelial cell that is part of the intercalated duct of salivary gland. This cell expresses proteins commonly associated with acinar cells and displays calcium signaling characteristics similar to secretory cells, indicating an active role in the secretory process rather than ion reabsorption."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37724716"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [epithelial cell of esophagus](http://purl.obolibrary.org/obo/CL_0002252) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009400"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30855909"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35799078"^^[string](http://www.w3.org/2001/XMLSchema#string) -### epithelial cell of lower respiratory tract `http://purl.obolibrary.org/obo/CL_0002632` -#### Removed -- [epithelial cell of lower respiratory tract](http://purl.obolibrary.org/obo/CL_0002632) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any respiratory epithelial cell that is part of some lower respiratory tract."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36726292"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [epithelial cell of lower respiratory tract](http://purl.obolibrary.org/obo/CL_0002632) EquivalentTo [respiratory epithelial cell](http://purl.obolibrary.org/obo/CL_0002368) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001558](http://purl.obolibrary.org/obo/UBERON_0001558)) +- [intercalated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052048) [label](http://www.w3.org/2000/01/rdf-schema#label) "intercalated cell of salivary gland"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [epithelial cell of lower respiratory tract](http://purl.obolibrary.org/obo/CL_0002632) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001558](http://purl.obolibrary.org/obo/UBERON_0001558) +- [intercalated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052048) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) -- [epithelial cell of lower respiratory tract](http://purl.obolibrary.org/obo/CL_0002632) SubClassOf [respiratory epithelial cell](http://purl.obolibrary.org/obo/CL_0002368) - - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [intercalated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052048) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "Id cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35799078"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [epithelial cell of lower respiratory tract](http://purl.obolibrary.org/obo/CL_0002632) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any epithelial cell that is part of some lower respiratory tract epithelium."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [intercalated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052048) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "salivary intercalated duct cells"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37724716"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [epithelial cell of lower respiratory tract](http://purl.obolibrary.org/obo/CL_0002632) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004815](http://purl.obolibrary.org/obo/UBERON_0004815)) +- [intercalated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052048) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "intercalated duct cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37724716"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [epithelial cell of lower respiratory tract](http://purl.obolibrary.org/obo/CL_0002632) SubClassOf [respiratory epithelial cell](http://purl.obolibrary.org/obo/CL_0002368) +- [intercalated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052048) [date](http://purl.org/dc/terms/date) "2024-09-11T09:55:55Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -- [epithelial cell of lower respiratory tract](http://purl.obolibrary.org/obo/CL_0002632) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004815](http://purl.obolibrary.org/obo/UBERON_0004815) +- [intercalated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052048) [contributor](http://purl.org/dc/terms/contributor) [0000-0003-4389-9821](https://orcid.org/0000-0003-4389-9821) +- Class: [intercalated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052048) -### epithelial cell of lung `http://purl.obolibrary.org/obo/CL_0000082` -#### Removed -- [epithelial cell of lung](http://purl.obolibrary.org/obo/CL_0000082) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002048](http://purl.obolibrary.org/obo/UBERON_0002048)) +- [intercalated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052048) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0015766](http://purl.obolibrary.org/obo/UBERON_0015766) -- [epithelial cell of lung](http://purl.obolibrary.org/obo/CL_0000082) SubClassOf [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) +- [intercalated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052048) SubClassOf [duct epithelial cell](http://purl.obolibrary.org/obo/CL_0000068) -#### Added -- [epithelial cell of lung](http://purl.obolibrary.org/obo/CL_0000082) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000115](http://purl.obolibrary.org/obo/UBERON_0000115)) +- [intercalated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052048) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0014727](http://purl.obolibrary.org/obo/UBERON_0014727) -- [epithelial cell of lung](http://purl.obolibrary.org/obo/CL_0000082) SubClassOf [epithelial cell of lower respiratory tract](http://purl.obolibrary.org/obo/CL_0002632) +- [intercalated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052048) SubClassOf [salivary gland glandular cell](http://purl.obolibrary.org/obo/CL_1001596) -### epithelial cell of pancreas `http://purl.obolibrary.org/obo/CL_0000083` +### interstitial cell `http://purl.obolibrary.org/obo/CL_4030031` #### Removed -- [epithelial cell of pancreas](http://purl.obolibrary.org/obo/CL_0000083) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009045"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [interstitial cell](http://purl.obolibrary.org/obo/CL_4030031) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) -- [epithelial cell of pancreas](http://purl.obolibrary.org/obo/CL_0000083) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) +#### Added +- [interstitial cell](http://purl.obolibrary.org/obo/CL_4030031) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -- [epithelial cell of pancreas](http://purl.obolibrary.org/obo/CL_0000083) SubClassOf [RO_0002202](http://purl.obolibrary.org/obo/RO_0002202) some [endodermal cell](http://purl.obolibrary.org/obo/CL_0000223) -- [epithelial cell of pancreas](http://purl.obolibrary.org/obo/CL_0000083) SubClassOf [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) +### intestinal crypt stem cell `http://purl.obolibrary.org/obo/CL_0002250` #### Added -- [epithelial cell of pancreas](http://purl.obolibrary.org/obo/CL_0000083) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009045"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [intestinal crypt stem cell](http://purl.obolibrary.org/obo/CL_0002250) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -- [epithelial cell of pancreas](http://purl.obolibrary.org/obo/CL_0000083) SubClassOf [endo-epithelial cell](http://purl.obolibrary.org/obo/CL_0002076) +Intestinal crypt stem cells, also known as crypt base columnar cells, are a unique type of cell, characterized by the highly specific marker LGR5, found in the intestinal epithelium. Situated at the bottom of the minute pockets known as crypts of Lieberkühn, these are undifferentiated cells that have the ability to perpetually self-renew, as well as differentiate into various other cell types that constitute the epithelial lining of the intestine. +The fundamental role of intestinal crypt stem cells is to provide a constant supply of new cells to maintain the cellular turnover of the intestinal epithelium, a tissue known for rapid self-renewal. These stem cells are nurtured and protected by specialized epithelial and mesenchymal cells, and together constitute the intestinal stem cell niche. +An important function of intestinal crypt stem cells is to sustain the balance between cell division and programmed cell death, called apoptosis, to ensure the integrity of the intestinal lining. Given their active proliferation rate, these stem cells initiate the creation of diverse differentiated cell types, including enterocytes (the primary absorptive cells in the intestinal lumen), goblet cells (that produce mucus to protect the epithelial layer), enteroendocrine cells (involved in producing gastrointestinal hormones), and Paneth cells (involved in secreting antimicrobial peptides). This diversity in output regulates the physiological activities of the gut ranging from nutrient absorption, hormone secretion, bacterial balance, to immunity. +Research studies suggest that dysregulation in intestinal crypt stem cell proliferation and differentiation is associated with several intestinal disorders including intestinal cancer, and various enteropathies."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1101/gad.1674008"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41575-018-0081-y"^^[string](http://www.w3.org/2001/XMLSchema#string) -### epithelial cell of proximal tubule `http://purl.obolibrary.org/obo/CL_0002306` -#### Removed -- [epithelial cell of proximal tubule](http://purl.obolibrary.org/obo/CL_0002306) SubClassOf [brush border epithelial cell](http://purl.obolibrary.org/obo/CL_0000239) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.cell.2013.07.004"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [epithelial cell of proximal tubule](http://purl.obolibrary.org/obo/CL_0002306) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The vast majority of proximal tubule epithelial cells have a brush border, but there are rare exceptions."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41580-020-0278-0"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1365-2184.2009.00642.x"^^[string](http://www.w3.org/2001/XMLSchema#string) -### epithelial cell of proximal tubule segment 1 `http://purl.obolibrary.org/obo/CL_4030009` -#### Removed -- [epithelial cell of proximal tubule segment 1](http://purl.obolibrary.org/obo/CL_4030009) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Epithelial cell that is part of segment 1 (S1) of the proximal tubule epithelium."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31249312"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [intestinal crypt stem cell](http://purl.obolibrary.org/obo/CL_0002250) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002250"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [epithelial cell of proximal tubule segment 1](http://purl.obolibrary.org/obo/CL_4030009) SubClassOf [epithelial cell of proximal tubule](http://purl.obolibrary.org/obo/CL_0002306) + +### intestinal crypt stem cell of colon `http://purl.obolibrary.org/obo/CL_0009043` #### Added -- [epithelial cell of proximal tubule segment 1](http://purl.obolibrary.org/obo/CL_4030009) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A brush border cell that is part of segment 1 (S1) of the proximal tubule epithelium, located in the renal cortex."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31249312"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [intestinal crypt stem cell of colon](http://purl.obolibrary.org/obo/CL_0009043) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:23897681"^^[string](http://www.w3.org/2001/XMLSchema#string) +Intestinal crypt stem cells of the colon, also known as colon crypt base columnar (CBC) cells, are highly specialized cells primarily responsible for the constant self-renewal of the colonic epithelium. These cells are found in the crypts of Lieberkühn - deeply invaginated sections of the colon's mucosal layer. +The prime function of intestinal crypt stem cells of the colon is to serve as the source of constant cell regeneration in the colon. Every few days, these stem cells divide and differentiate into the various other types of intestinal cells, such as enterocytes, goblet cells, and enteroendocrine cells. +A constant renewal cycle is necessary due to the harsh environment of the colon where cells continuously encounter abrasive food matter and potential pathogens, leading to a high turnover rate. When the colon's mucosal layer suffers damage, a rapid response is triggered whereby colon crypt stem cells divide faster and are directed to injured sites to repair the epithelial layer. Dysregulation of these cells' function or proliferation can contribute to disorders such as colorectal cancer."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1186/s12943-019-0962-x"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:23799132"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41575-018-0081-y"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [epithelial cell of proximal tubule segment 1](http://purl.obolibrary.org/obo/CL_4030009) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004196](http://purl.obolibrary.org/obo/UBERON_0004196)) and ([BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0005903](http://purl.obolibrary.org/obo/GO_0005903)) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.cell.2013.07.004"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [epithelial cell of proximal tubule segment 1](http://purl.obolibrary.org/obo/CL_4030009) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004196](http://purl.obolibrary.org/obo/UBERON_0004196) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1073/pnas.1607327113"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [epithelial cell of proximal tubule segment 1](http://purl.obolibrary.org/obo/CL_4030009) SubClassOf [kidney proximal convoluted tubule epithelial cell](http://purl.obolibrary.org/obo/CL_1000838) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1365-2184.2009.00642.x"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [intestinal crypt stem cell of colon](http://purl.obolibrary.org/obo/CL_0009043) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0009043"^^[string](http://www.w3.org/2001/XMLSchema#string) -### epithelial cell of proximal tubule segment 2 `http://purl.obolibrary.org/obo/CL_4030010` -#### Removed -- [epithelial cell of proximal tubule segment 2](http://purl.obolibrary.org/obo/CL_4030010) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Epithelial cell that is part of segment 2 (S2) of the proximal tubule epithelium."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31249312"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [epithelial cell of proximal tubule segment 2](http://purl.obolibrary.org/obo/CL_4030010) SubClassOf [epithelial cell of proximal tubule](http://purl.obolibrary.org/obo/CL_0002306) +### intestinal crypt stem cell of small intestine `http://purl.obolibrary.org/obo/CL_0009017` #### Added -- [epithelial cell of proximal tubule segment 2](http://purl.obolibrary.org/obo/CL_4030010) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A brush border cell that is part of segment 2 (S2) of the proximal tubule epithelium, located in the renal cortex. In addition to its reabsorptive functions, it is also specialized in the secretion of organic anions and cations, including para-aminohippurate."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31249312"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [intestinal crypt stem cell of small intestine](http://purl.obolibrary.org/obo/CL_0009017) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:23897681"^^[string](http://www.w3.org/2001/XMLSchema#string) +Intestinal crypt stem cells of the small intestine are a type of adult stem cell intimately involved in the continuous replenishment of the intestinal epithelium, the innermost layer of the intestine responsible for nutrient absorption. These cells, located within the crypts of Lieberkühn, are the origin of various cell lineages that make up the functional units of the small intestine. They possess self-renewal ability, an essential feature of stem cells, which allows them to maintain a steady population in the small intestine. +One of the critical roles of intestinal crypt stem cells is to drive the continual renewal process taking place in the small intestine every 3-5 days. By proliferating intensively, these cells produce transient amplifying (TA) cells that are characterized by quick division and progressive differentiation. These cells eventually differentiate into specialized cell types, encompassing absorptive enterocytes, mucin-secreting goblet cells, hormone-secreting enteroendocrine cells, and Paneth cells, all of which have essential roles in digestion and nutrient absorption in the small intestine. +Intestinal crypt stem cells of the small intestine are also play a significant part in injury recovery. Under regular conditions, these cells primarily exist in an active state, facilitating the constant renovation of the gut lining. However, upon injury or loss of regular intestinal crypt stem cells reserve intestinal stem cells, a slow-cycling and radio-resistant population, can be stimulated to take over the duties of active crypt stem cells. Such plasticity provides a powerful regenerative mechanism that ensures the intestinal epithelium's function and structural integrity amidst diverse conditions."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.celrep.2020.107952"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31253652"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41575-018-0081-y"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:23799132"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1073/pnas.1607327113"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [epithelial cell of proximal tubule segment 2](http://purl.obolibrary.org/obo/CL_4030010) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004197](http://purl.obolibrary.org/obo/UBERON_0004197)) and ([BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0005903](http://purl.obolibrary.org/obo/GO_0005903)) +- [intestinal crypt stem cell of small intestine](http://purl.obolibrary.org/obo/CL_0009017) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0009017"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [epithelial cell of proximal tubule segment 2](http://purl.obolibrary.org/obo/CL_4030010) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004197](http://purl.obolibrary.org/obo/UBERON_0004197) -- [epithelial cell of proximal tubule segment 2](http://purl.obolibrary.org/obo/CL_4030010) SubClassOf [kidney proximal convoluted tubule epithelial cell](http://purl.obolibrary.org/obo/CL_1000838) +### intestinal enteroendocrine progenitor `http://purl.obolibrary.org/obo/CL_4052006` +#### Added +- [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The EEC progenitor is also present in other organisms; for example, flies have EEC progenitors but lack intestinal crypts and do not express the same markers. Instead, they are Dl+ and Pros+."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:25670791"^^[string](http://www.w3.org/2001/XMLSchema#string) -### epithelial cell of proximal tubule segment 3 `http://purl.obolibrary.org/obo/CL_4030011` -#### Removed -- [epithelial cell of proximal tubule segment 3](http://purl.obolibrary.org/obo/CL_4030011) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Epithelial cell that is part of segment 3 (S3) of the proximal tubule epithelium."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31249312"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) -- [epithelial cell of proximal tubule segment 3](http://purl.obolibrary.org/obo/CL_4030011) SubClassOf [epithelial cell of proximal tubule](http://purl.obolibrary.org/obo/CL_0002306) +- [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052006"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [epithelial cell of proximal tubule segment 3](http://purl.obolibrary.org/obo/CL_4030011) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A brush border cell that is part of segment 3 (S3) of the proximal tubule epithelium, which extends from the medullary rays of the renal cortex into the outer medulla."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31249312"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) [label](http://www.w3.org/2000/01/rdf-schema#label) "intestinal enteroendocrine progenitor"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:23799132"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "EEC Progenitor"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) -- [epithelial cell of proximal tubule segment 3](http://purl.obolibrary.org/obo/CL_4030011) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The epithelial cell of proximal tubule segment 3 operates under relatively hypoxic conditions and is particularly susceptible to ischemic injury."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31249312"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31756561"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [epithelial cell of proximal tubule segment 3](http://purl.obolibrary.org/obo/CL_4030011) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001290](http://purl.obolibrary.org/obo/UBERON_0001290)) and ([BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0005903](http://purl.obolibrary.org/obo/GO_0005903)) +- [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) [date](http://purl.org/dc/terms/date) "2024-09-20T12:13:26Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -- [epithelial cell of proximal tubule segment 3](http://purl.obolibrary.org/obo/CL_4030011) SubClassOf [kidney proximal straight tubule epithelial cell](http://purl.obolibrary.org/obo/CL_1000839) +- [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell that is part of the crypt of Lieberkuhn, originating from intestinal stem cells and giving rise to enteroendocrine cells (EECs). In mouse and human, this cell can be characterized by the expression of Neurog3, and has the ability to proliferate and differentiate into multiple EEC subtypes. Its proliferative potential contributes to crypt growth, distinguishing it from fully differentiated EECs."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32531023"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [epithelial cell of proximal tubule segment 3](http://purl.obolibrary.org/obo/CL_4030011) SubClassOf [brush border cell of the proximal tubule](http://purl.obolibrary.org/obo/CL_0002307) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:38260422"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:/10.1038/s41467-021-27901-5"^^[string](http://www.w3.org/2001/XMLSchema#string) -### epithelial cell of tracheobronchial tree `http://purl.obolibrary.org/obo/CL_0002202` -#### Removed -- [epithelial cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002202) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0007196](http://purl.obolibrary.org/obo/UBERON_0007196)) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35913117"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [epithelial cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002202) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0007196](http://purl.obolibrary.org/obo/UBERON_0007196) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31756561"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [epithelial cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002202) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0008397](http://purl.obolibrary.org/obo/UBERON_0008397)) +- Class: [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) -- [epithelial cell of tracheobronchial tree](http://purl.obolibrary.org/obo/CL_0002202) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0008397](http://purl.obolibrary.org/obo/UBERON_0008397) +- [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) SubClassOf [RO_0002202](http://purl.obolibrary.org/obo/RO_0002202) some [intestinal crypt stem cell](http://purl.obolibrary.org/obo/CL_0002250) +- [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0011184](http://purl.obolibrary.org/obo/UBERON_0011184) -### epithelial cell of upper respiratory tract `http://purl.obolibrary.org/obo/CL_0002631` -#### Removed -- [epithelial cell of upper respiratory tract](http://purl.obolibrary.org/obo/CL_0002631) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any respiratory epithelial cell that is part of some upper respiratory tract."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) SubClassOf [intestinal epithelial cell](http://purl.obolibrary.org/obo/CL_0002563) -- [epithelial cell of upper respiratory tract](http://purl.obolibrary.org/obo/CL_0002631) EquivalentTo [respiratory epithelial cell](http://purl.obolibrary.org/obo/CL_0002368) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001557](http://purl.obolibrary.org/obo/UBERON_0001557)) +- [intestinal enteroendocrine progenitor](http://purl.obolibrary.org/obo/CL_4052006) SubClassOf [progenitor cell](http://purl.obolibrary.org/obo/CL_0011026) -- [epithelial cell of upper respiratory tract](http://purl.obolibrary.org/obo/CL_0002631) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001557](http://purl.obolibrary.org/obo/UBERON_0001557) -- [epithelial cell of upper respiratory tract](http://purl.obolibrary.org/obo/CL_0002631) SubClassOf [respiratory epithelial cell](http://purl.obolibrary.org/obo/CL_0002368) - - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) +### intestinal fibroblastic reticular cell `http://purl.obolibrary.org/obo/CL_4052004` #### Added -- [epithelial cell of upper respiratory tract](http://purl.obolibrary.org/obo/CL_0002631) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any epithelial cell that is part of some upper respiratory tract epithelium."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) [label](http://www.w3.org/2000/01/rdf-schema#label) "intestinal fibroblastic reticular cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [epithelial cell of upper respiratory tract](http://purl.obolibrary.org/obo/CL_0002631) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004814](http://purl.obolibrary.org/obo/UBERON_0004814)) +- [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "gut-associated secondary lymphoid organs fibroblastic reticular cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35440118"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [epithelial cell of upper respiratory tract](http://purl.obolibrary.org/obo/CL_0002631) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004814](http://purl.obolibrary.org/obo/UBERON_0004814) +- [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) [date](http://purl.org/dc/terms/date) "2024-09-19T11:22:18Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -- [epithelial cell of upper respiratory tract](http://purl.obolibrary.org/obo/CL_0002631) SubClassOf [respiratory epithelial cell](http://purl.obolibrary.org/obo/CL_0002368) +- [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) [has_narrow_synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "Ccl19-expressing fibroblastic reticular cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35440118"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A specialized fibroblastic reticular cell that is part of gut-associated lymphoid tissue (GALT), responsible for forming a structural network that facilitates immune cell interactions. This cell is found in Peyer's patches, cryptopatches, and isolated lymphoid follicles. It plays crucial roles in maintaining intestinal immunity by controlling innate lymphoid cell homeostasis and function, organizing lymphoid structures, and contributing to intestinal microbiome balance."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35440118"^^[string](http://www.w3.org/2001/XMLSchema#string) -### epithelial cell of uterus `http://purl.obolibrary.org/obo/CL_0002149` -#### Removed -- [epithelial cell of uterus](http://purl.obolibrary.org/obo/CL_0002149) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell of the uterus."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [epithelial cell of uterus](http://purl.obolibrary.org/obo/CL_0002149) EquivalentTo [endo-epithelial cell](http://purl.obolibrary.org/obo/CL_0002076) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000995](http://purl.obolibrary.org/obo/UBERON_0000995)) - -- [epithelial cell of uterus](http://purl.obolibrary.org/obo/CL_0002149) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000995](http://purl.obolibrary.org/obo/UBERON_0000995) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33707780"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [epithelial cell of uterus](http://purl.obolibrary.org/obo/CL_0002149) SubClassOf [endo-epithelial cell](http://purl.obolibrary.org/obo/CL_0002076) - - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) -#### Added -- [epithelial cell of uterus](http://purl.obolibrary.org/obo/CL_0002149) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell of the uterus. This cell has a mesodermal origin."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:16960017"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052004"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:11331626"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) [has_narrow_synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "solitary intestinal lymphoid tissue fibroblastic reticular cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35440118"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) [description](http://purl.org/dc/terms/description) "Intestinal fibroblastic reticular cells develop from both perivascular and subepithelial progenitors during Peyer's patch formation. Intestinal fibroblastic reticular cells express key markers such as CCL19, CCL21, CXCL13, TNFSF13B (also known as BAFF), and produce IL-7, which are important for their immune regulatory functions and the organization of lymphoid structures."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35440118"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:21698266"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33707780"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [epithelial cell of uterus](http://purl.obolibrary.org/obo/CL_0002149) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0006955](http://purl.obolibrary.org/obo/UBERON_0006955)) +- Class: [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) -- [epithelial cell of uterus](http://purl.obolibrary.org/obo/CL_0002149) SubClassOf [meso-epithelial cell](http://purl.obolibrary.org/obo/CL_0002078) +- [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) SubClassOf [fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_0009101) -- [epithelial cell of uterus](http://purl.obolibrary.org/obo/CL_0002149) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0006955](http://purl.obolibrary.org/obo/UBERON_0006955) +- [intestinal fibroblastic reticular cell](http://purl.obolibrary.org/obo/CL_4052004) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001962](http://purl.obolibrary.org/obo/UBERON_0001962) -### erythroblast `http://purl.obolibrary.org/obo/CL_0000765` -#### Removed -- [erythroblast](http://purl.obolibrary.org/obo/CL_0000765) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005237"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### intestinal subserosal fibroblast `http://purl.obolibrary.org/obo/CL_4052005` #### Added -- [erythroblast](http://purl.obolibrary.org/obo/CL_0000765) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005237"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [intestinal subserosal fibroblast](http://purl.obolibrary.org/obo/CL_4052005) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A fibroblast that is part of the subserosa of intestine. This cell interacts with immune cells and play roles in inflammation and fibrosis. In certain conditions, such as Crohn's disease, subserosal fibroblast may differentiate into myofibroblasts."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:23143399"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:26694715"^^[string](http://www.w3.org/2001/XMLSchema#string) -### erythroid lineage cell `http://purl.obolibrary.org/obo/CL_0000764` -#### Removed -- [erythroid lineage cell](http://purl.obolibrary.org/obo/CL_0000764) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009325"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:38877292"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [erythroid lineage cell](http://purl.obolibrary.org/obo/CL_0000764) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009325"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [intestinal subserosal fibroblast](http://purl.obolibrary.org/obo/CL_4052005) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052005"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [intestinal subserosal fibroblast](http://purl.obolibrary.org/obo/CL_4052005) [label](http://www.w3.org/2000/01/rdf-schema#label) "intestinal subserosal fibroblast"^^[string](http://www.w3.org/2001/XMLSchema#string) -### erythroid progenitor cell `http://purl.obolibrary.org/obo/CL_0000038` -#### Removed -- [erythroid progenitor cell](http://purl.obolibrary.org/obo/CL_0000038) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009015"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [intestinal subserosal fibroblast](http://purl.obolibrary.org/obo/CL_4052005) [date](http://purl.org/dc/terms/date) "2024-09-19T12:58:29Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -#### Added -- [erythroid progenitor cell](http://purl.obolibrary.org/obo/CL_0000038) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009015"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [intestinal subserosal fibroblast](http://purl.obolibrary.org/obo/CL_4052005) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) +- Class: [intestinal subserosal fibroblast](http://purl.obolibrary.org/obo/CL_4052005) -### erythrophore `http://purl.obolibrary.org/obo/CL_0000574` -#### Removed -- [erythrophore](http://purl.obolibrary.org/obo/CL_0000574) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009263"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [intestinal subserosal fibroblast](http://purl.obolibrary.org/obo/CL_4052005) SubClassOf [fibroblast](http://purl.obolibrary.org/obo/CL_0000057) -#### Added -- [erythrophore](http://purl.obolibrary.org/obo/CL_0000574) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009263"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [intestinal subserosal fibroblast](http://purl.obolibrary.org/obo/CL_4052005) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001243](http://purl.obolibrary.org/obo/UBERON_0001243) +- [intestinal subserosal fibroblast](http://purl.obolibrary.org/obo/CL_4052005) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0012375](http://purl.obolibrary.org/obo/UBERON_0012375) -### estradiol secreting cell `http://purl.obolibrary.org/obo/CL_0000180` -#### Removed -- [estradiol secreting cell](http://purl.obolibrary.org/obo/CL_0000180) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009110"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +### intestinal villus capillary endothelial cell `http://purl.obolibrary.org/obo/CL_4052003` #### Added -- [estradiol secreting cell](http://purl.obolibrary.org/obo/CL_0000180) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009110"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [intestinal villus capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052003) [date](http://purl.org/dc/terms/date) "2024-09-17T10:03:25Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) +- [intestinal villus capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052003) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052003"^^[string](http://www.w3.org/2001/XMLSchema#string) -### eurydendroid cell `http://purl.obolibrary.org/obo/CL_0000253` -#### Removed -- [eurydendroid cell](http://purl.obolibrary.org/obo/CL_0000253) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009153"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [intestinal villus capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052003) [label](http://www.w3.org/2000/01/rdf-schema#label) "intestinal villus capillary endothelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [eurydendroid cell](http://purl.obolibrary.org/obo/CL_0000253) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009153"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [intestinal villus capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052003) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "villus tip endothelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:38051275"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [intestinal villus capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052003) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) -### exhausted T cell `http://purl.obolibrary.org/obo/CL_0011025` -#### Removed -- [exhausted T cell](http://purl.obolibrary.org/obo/CL_0011025) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "An effector T cell that displays impaired effector functions (e.g., rapid production of effector cytokines, cytotoxicity) and has limited proliferative potential."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:26544946"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [intestinal villus capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052003) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A capillary endothelial cell that is part of the intestinal villus. This cell is highly fenestrated, with fenestrations most numerous at the villus tips, and plays a vital role in nutrient absorption and maintaining the selective permeability of the intestinal barrier."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:18480313"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [exhausted T cell](http://purl.obolibrary.org/obo/CL_0011025) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An effector T cell that displays impaired effector functions (e.g., rapid production of effector cytokines, cytotoxicity) and has limited proliferative potential."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:26544946"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35810168"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:38051275"^^[string](http://www.w3.org/2001/XMLSchema#string) -### exocrine cell `http://purl.obolibrary.org/obo/CL_0000152` -#### Removed -- [exocrine cell](http://purl.obolibrary.org/obo/CL_0000152) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009092"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [intestinal villus capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052003) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "villus blood capillary endothelial cells"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35810168"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [exocrine cell](http://purl.obolibrary.org/obo/CL_0000152) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009092"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [intestinal villus capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052003) +- [intestinal villus capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052003) EquivalentTo [capillary endothelial cell](http://purl.obolibrary.org/obo/CL_0002144) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001213](http://purl.obolibrary.org/obo/UBERON_0001213)) -### extracellular matrix secreting cell `http://purl.obolibrary.org/obo/CL_0000327` -#### Removed -- [extracellular matrix secreting cell](http://purl.obolibrary.org/obo/CL_0000327) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009162"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [intestinal villus capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052003) SubClassOf [fenestrated endothelial cell](http://purl.obolibrary.org/obo/CL_0000666) -#### Added -- [extracellular matrix secreting cell](http://purl.obolibrary.org/obo/CL_0000327) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009162"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [intestinal villus capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052003) SubClassOf [capillary endothelial cell](http://purl.obolibrary.org/obo/CL_0002144) +- [intestinal villus capillary endothelial cell](http://purl.obolibrary.org/obo/CL_4052003) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001213](http://purl.obolibrary.org/obo/UBERON_0001213) -### extraembryonic cell `http://purl.obolibrary.org/obo/CL_0000349` -#### Removed -- [extraembryonic cell](http://purl.obolibrary.org/obo/CL_0000349) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009176"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +### intrahepatic cholangiocyte `http://purl.obolibrary.org/obo/CL_0002538` #### Added -- [extraembryonic cell](http://purl.obolibrary.org/obo/CL_0000349) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009176"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [intrahepatic cholangiocyte](http://purl.obolibrary.org/obo/CL_0002538) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +Intrahepatic cholangiocytes represent a subset of the biliary epithelial cells that form a network of tubes in the liver called the biliary tree The intrahepatic cholangiocytes reside specifically in the intrahepatic bile ducts and play a crucial role in liver physiology and bile production and secretion, thereby aiding in the digestion and absorption of fats in the small intestine. These specific cholangiocytes arise from bipotent hepatoblasts, whereas extrahepatic cholangiocytes share an embryologic origin with the ventral pancreas. +Recent research suggests that there is also heterogeneity within populations of intrahepatic cholangiocytes with different transcriptional profiles, proliferative capacity, and biological function; for example, subpopulations differ in calcium-mobilizing receptors. +The primary function of intrahepatic cholangiocytes is related to bile formation and maintenance of its flow. In addition to their secretory and absorptive activities, they are involved in the regulation of bile composition, volume, and alkalinization, contributing to the neutralization of the acidic chyme (partly digested food) that enters the intestine from the stomach. Intrahepatic cholangiocytes are also recognized for their role in liver regeneration and repair, often proliferating in response to injury. +Intrahepatic cholangiocytes take part in certain pathological conditions, like primary biliary cirrhosis and cholangiocarcinoma. Changes in these cells often lead to abnormalities in bile formation and transport, causing cholestatic liver diseases. Overall, the primary and secondary functional activities of intrahepatic cholangiocytes are vital in maintaining liver function, digestive processes, and contributing to the body's response to liver injury."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.ajpath.2023.02.012"^^[string](http://www.w3.org/2001/XMLSchema#string) -### extramedullary cell `http://purl.obolibrary.org/obo/CL_0000251` -#### Removed -- [extramedullary cell](http://purl.obolibrary.org/obo/CL_0000251) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009152"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/hep.31252"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [extramedullary cell](http://purl.obolibrary.org/obo/CL_0000251) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009152"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.gastha.2022.07.015"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.biocel.2010.06.020"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [intrahepatic cholangiocyte](http://purl.obolibrary.org/obo/CL_0002538) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002538"^^[string](http://www.w3.org/2001/XMLSchema#string) -### eye photoreceptor cell `http://purl.obolibrary.org/obo/CL_0000287` -#### Removed -- [eye photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000287) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009154"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +### invertebrate nurse cell `http://purl.obolibrary.org/obo/CL_0000026` #### Added -- [eye photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000287) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009154"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [invertebrate nurse cell](http://purl.obolibrary.org/obo/CL_0000026) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### eye_upper_slim `http://purl.obolibrary.org/obo/cl/cl-base#eye_upper_slim` +### ionocyte `http://purl.obolibrary.org/obo/CL_0005006` #### Added -- [eye_upper_slim](http://purl.obolibrary.org/obo/cl/cl-base#eye_upper_slim) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "a subset of general classes related to specific cell types in the eye."^^[string](http://www.w3.org/2001/XMLSchema#string) +- [ionocyte](http://purl.obolibrary.org/obo/CL_0005006) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -- [eye_upper_slim](http://purl.obolibrary.org/obo/cl/cl-base#eye_upper_slim) SubPropertyOf: [subset_property](http://www.geneontology.org/formats/oboInOwl#SubsetProperty) +Ionocytes are specialized cells predominantly found in the mammalian respiratory and renal systems as well as in the gills, skin, and intestinal tract of fish. These cells play crucial roles in maintaining ion and acid-base homeostasis. Ionocytes demonstrate remarkable plasticity and are able to adapt themselves in response to changes in environmental conditions such as pH, salinity, ion concentration, and temperature. +These cells work by selectively absorbing specific ions from the environment, thus maintaining the body's internal ionic balance. The most commonly absorbed ions include sodium (Na+), chloride (Cl-), calcium (Ca2+), and hydrogen (H+). Moreover, ionocytes contribute to acid-base regulation. In response to acidosis or alkalosis, ionocytes can either excrete or retain hydrogen (H+) and bicarbonate (HCO3-) ions to readjust the blood pH. Further, experimental evidence suggests a functional complexity of ionocytes, implying diverse roles beyond ion regulation. Recent research highlights ionocytes' involvement in ammonia excretion and the regulation of extracellular fluid volume, highlighting their contribution to the overall homeostatic process. +Malfunctioning ionocytes have been implicated in various diseases, including cystic fibrosis which is caused by mutations in the chloride channel CFTR, an ionocyte marker."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1146/annurev-pathol-042420-094031"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.jcf.2019.09.010"^^[string](http://www.w3.org/2001/XMLSchema#string) -### fallopian tube ciliated cell `http://purl.obolibrary.org/obo/CL_4030007` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41586-018-0393-7"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [fallopian tube ciliated cell](http://purl.obolibrary.org/obo/CL_4030007) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0003889](http://purl.obolibrary.org/obo/UBERON_0003889) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41598-023-30603-1"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fmars.2020.00709"^^[string](http://www.w3.org/2001/XMLSchema#string) -### fallopian tube secretory epithelial cell `http://purl.obolibrary.org/obo/CL_4030006` +- [ionocyte](http://purl.obolibrary.org/obo/CL_0005006) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0005006"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### iridophore `http://purl.obolibrary.org/obo/CL_0000431` #### Added -- [fallopian tube secretory epithelial cell](http://purl.obolibrary.org/obo/CL_4030006) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0003889](http://purl.obolibrary.org/obo/UBERON_0003889) +- [iridophore](http://purl.obolibrary.org/obo/CL_0000431) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### fast muscle cell `http://purl.obolibrary.org/obo/CL_0000190` -#### Removed -- [fast muscle cell](http://purl.obolibrary.org/obo/CL_0000190) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009117"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### kidney afferent arteriole endothelial cell `http://purl.obolibrary.org/obo/CL_1001096` #### Added -- [fast muscle cell](http://purl.obolibrary.org/obo/CL_0000190) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009117"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [kidney afferent arteriole endothelial cell](http://purl.obolibrary.org/obo/CL_1001096) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +Kidney afferent arteriole endothelial cells are a specialized type of cell located within the kidneys, forming the inner lining of the afferent arterioles, which are responsible for delivering blood to the glomeruli - capillary networks responsible for filtration - from where the process of urine formation begins in the nephrons. +The endothelial cells in the kidney afferent arterioles have a key function in regulating the blood flow and filtration. They have autocrine and paracrine signaling capabilities, meaning they can signal to themselves and other nearby cells. They produce nitric oxide, prostacyclin, and endothelin, which are powerful vasodilators and vasoconstrictors that regulate renal blood flow. These cells also engage in the mitigation of kidney injury and inflammation by promoting repair and regeneration, demonstrating the multifaceted roles these cells play in maintaining renal health."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1046/j.0001-6772.2003.01205.x"^^[string](http://www.w3.org/2001/XMLSchema#string) -### fast muscle myoblast `http://purl.obolibrary.org/obo/CL_0000858` -#### Removed -- [fast muscle myoblast](http://purl.obolibrary.org/obo/CL_0000858) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009369"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1093/ndt/gfl308"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [fast muscle myoblast](http://purl.obolibrary.org/obo/CL_0000858) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009369"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [kidney afferent arteriole endothelial cell](http://purl.obolibrary.org/obo/CL_1001096) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1001096"^^[string](http://www.w3.org/2001/XMLSchema#string) -### female germ line stem cell `http://purl.obolibrary.org/obo/CL_0000022` +### kidney cell `http://purl.obolibrary.org/obo/CL_1000497` #### Removed -- [female germ line stem cell](http://purl.obolibrary.org/obo/CL_0000022) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004873"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [kidney cell](http://purl.obolibrary.org/obo/CL_1000497) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) #### Added -- [female germ line stem cell](http://purl.obolibrary.org/obo/CL_0000022) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004873"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [kidney cell](http://purl.obolibrary.org/obo/CL_1000497) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### femural osteoblast `http://purl.obolibrary.org/obo/CL_2000057` +### kidney collecting duct alpha-intercalated cell `http://purl.obolibrary.org/obo/CL_4030015` #### Removed -- [femural osteoblast](http://purl.obolibrary.org/obo/CL_2000057) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +- [kidney collecting duct alpha-intercalated cell](http://purl.obolibrary.org/obo/CL_4030015) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A renal alpha-intercalated cell that is part of the collecting duct of the renal tubule."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0003-2804-127X"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31249312"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:9890303"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [femural osteoblast](http://purl.obolibrary.org/obo/CL_2000057) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [kidney collecting duct alpha-intercalated cell](http://purl.obolibrary.org/obo/CL_4030015) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A renal alpha-intercalated cell that is part of the collecting duct of the renal tubule."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31249312"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:9890303"^^[string](http://www.w3.org/2001/XMLSchema#string) -### fenestrated endothelial cell `http://purl.obolibrary.org/obo/CL_0000666` -#### Removed -- [fenestrated endothelial cell](http://purl.obolibrary.org/obo/CL_0000666) [label](http://www.w3.org/2000/01/rdf-schema#label) "fenestrated cell"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [kidney collecting duct alpha-intercalated cell](http://purl.obolibrary.org/obo/CL_4030015) [contributor](http://purl.org/dc/terms/contributor) [X](https://orcid.org/0000-0003-2804-127X) -- [fenestrated endothelial cell](http://purl.obolibrary.org/obo/CL_0000666) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009286"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [fenestrated endothelial cell](http://purl.obolibrary.org/obo/CL_0000666) SubClassOf [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) +### kidney collecting duct epithelial cell `http://purl.obolibrary.org/obo/CL_1000454` #### Added -- [fenestrated endothelial cell](http://purl.obolibrary.org/obo/CL_0000666) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An endothelial cell that has small pores, or fenestrations, which allow for the efficient exchange of substances between the blood and surrounding tissues."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/978-3-211-99390-3_133"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [kidney collecting duct epithelial cell](http://purl.obolibrary.org/obo/CL_1000454) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -- [fenestrated endothelial cell](http://purl.obolibrary.org/obo/CL_0000666) [label](http://www.w3.org/2000/01/rdf-schema#label) "fenestrated endothelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) +Kidney collecting duct epithelial cells are a specialized type of cells that form an integral part of the renal system. Located in the collecting duct system of the kidneys, these cells are responsible for one of the final steps in the process of urine formation, and they are instrumental in the fine tuning of the volume and composition of urine by reabsorbing water and certain solutes back into the bloodstream. +These cells express specific channels and carriers that actively and passively transport ions and water. They also have channels on their membranes, such as sodium channels and potassium channels, involved in reabsorbing or secreting these electrolytes depending upon the body's needs. The function of renal collecting duct epithelial cells can be regulated by a variety of hormones, including vasopressin (antidiuretic hormone), which can modulate the ion channels and carriers and hence indirectly influence body fluid homeostasis. +Aside from their function in ion and water balance, kidney collecting duct epithelial cells also aid in maintaining the body's acid-base balance. They have specialized functionality to secret hydrogen ions into the tubular lumen, which contributes to acid excretion. Any dysfunction may have serious implications and lead to various renal or systemic diseases, exemplifying the importance of these cells in maintaining overall body homeostasis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2215/CJN.05760513"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [fenestrated endothelial cell](http://purl.obolibrary.org/obo/CL_0000666) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009286"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.semnephrol.2019.04.005"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [fenestrated endothelial cell](http://purl.obolibrary.org/obo/CL_0000666) EquivalentTo [endothelial cell](http://purl.obolibrary.org/obo/CL_0000115) and ([RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0002064](http://purl.obolibrary.org/obo/PATO_0002064)) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.ajpath.2014.01.014"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [fenestrated endothelial cell](http://purl.obolibrary.org/obo/CL_0000666) SubClassOf [RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0002064](http://purl.obolibrary.org/obo/PATO_0002064) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2215/CJN.08880914"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [fenestrated endothelial cell](http://purl.obolibrary.org/obo/CL_0000666) SubClassOf [endothelial cell](http://purl.obolibrary.org/obo/CL_0000115) +- [kidney collecting duct epithelial cell](http://purl.obolibrary.org/obo/CL_1000454) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000454"^^[string](http://www.w3.org/2001/XMLSchema#string) -### fetal pre-type II pulmonary alveolar epithelial cell `http://purl.obolibrary.org/obo/CL_4040003` -#### Removed -- [fetal pre-type II pulmonary alveolar epithelial cell](http://purl.obolibrary.org/obo/CL_4040003) [label](http://www.w3.org/2000/01/rdf-schema#label) "fetal pre-type II pneumocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [fetal pre-type II pulmonary alveolar epithelial cell](http://purl.obolibrary.org/obo/CL_4040003) [note](http://purl.obolibrary.org/obo/cl/cl-base#note) "According to PMID:1316350 this cell type does not yet produce surfactant. According to PMID:9109447 and PMID:12114192 this cell type produces low levels of surfactant that can be increased by administration of very low-density lipoproteins. This cell type is of medical relevance, as a central feature of the fetal respiratory distress syndrome seems to be the presence in the lung of abundant pre-type II alveolar epithelial cells (PMID:1316350)."^^[string](http://www.w3.org/2001/XMLSchema#string) +### kidney collecting duct principal cell `http://purl.obolibrary.org/obo/CL_1001431` #### Added -- [fetal pre-type II pulmonary alveolar epithelial cell](http://purl.obolibrary.org/obo/CL_4040003) [note](http://www.geneontology.org/formats/oboInOwl#note) "According to PMID:1316350 this cell type does not yet produce surfactant. According to PMID:9109447 and PMID:12114192 this cell type produces low levels of surfactant that can be increased by administration of very low-density lipoproteins. This cell type is of medical relevance, as a central feature of the fetal respiratory distress syndrome seems to be the presence in the lung of abundant pre-type II alveolar epithelial cells (PMID:1316350)."^^[string](http://www.w3.org/2001/XMLSchema#string) +- [kidney collecting duct principal cell](http://purl.obolibrary.org/obo/CL_1001431) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1001431"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [fetal pre-type II pulmonary alveolar epithelial cell](http://purl.obolibrary.org/obo/CL_4040003) [label](http://www.w3.org/2000/01/rdf-schema#label) "fetal pre-type II pulmonary alveolar epithelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [kidney collecting duct principal cell](http://purl.obolibrary.org/obo/CL_1001431) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -- [fetal pre-type II pulmonary alveolar epithelial cell](http://purl.obolibrary.org/obo/CL_4040003) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "fetal pre-type II pneumocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) +The kidney collecting duct principal cell is a highly specialized type of cell found in the late distal convoluted tubule and collecting duct of the kidney's nephron. Principal cells are located at the final segments of the renal tubules, where they play a pivotal role in key homeostatic processes. +One of their fundamental functions of kidney collecting duct principal cells is the regulation of water reabsorption, which is mediated by aquaporins (water channel proteins). Antidiuretic hormones, such as vasopressin, can stimulate the redistribution of these water channels from an intracellular pools to the apical plasma membrane of the principal cell; translocation of aquaporin (specifically, AQP2) is associated with an increase of osmotic water permeability. The water reabsorption affects the concentration of the final urine; these cells are therefore directly involved in the maintenance of the body's fluid balance. +Kidney collecting duct principal cells also participate in sodium and potassium ions regulation. They reabsorb sodium ions from the tubular fluid back into the bloodstream, a process facilitated by the action of aldosterone, a hormone released by the adrenal glands. Similarly, the principal cells secrete potassium ions into the tubular fluid in response to aldosterone, contributing to the regulation of potassium levels in the body. Impaired function of cells can lead to various renal diseases and disorders, highlighting the vital role of kidney collecting duct principal cells in the body's homeostatic processes."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s11906-015-0538-0"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1073/pnas.1710964114"^^[string](http://www.w3.org/2001/XMLSchema#string) -### fibroblast `http://purl.obolibrary.org/obo/CL_0000057` -#### Removed -- [fibroblast](http://purl.obolibrary.org/obo/CL_0000057) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009026"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/B978-0-12-386456-7.05402-2"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [fibroblast](http://purl.obolibrary.org/obo/CL_0000057) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009026"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.biocel.2022.106261"^^[string](http://www.w3.org/2001/XMLSchema#string) -### fibroblast of arm `http://purl.obolibrary.org/obo/CL_2000015` -#### Removed -- [fibroblast of arm](http://purl.obolibrary.org/obo/CL_2000015) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +### kidney efferent arteriole endothelial cell `http://purl.obolibrary.org/obo/CL_1001099` #### Added -- [fibroblast of arm](http://purl.obolibrary.org/obo/CL_2000015) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [kidney efferent arteriole endothelial cell](http://purl.obolibrary.org/obo/CL_1001099) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1001099"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [kidney efferent arteriole endothelial cell](http://purl.obolibrary.org/obo/CL_1001099) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -### fibroblast of pedal digit skin `http://purl.obolibrary.org/obo/CL_2000012` -#### Removed -- [fibroblast of pedal digit skin](http://purl.obolibrary.org/obo/CL_2000012) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +Kidney efferent arteriole endothelial cells constitute a vital component of the kidney's microvascular system. They are unique endothelial cells found lining the walls of efferent arterioles, which transport blood away from the glomeruli in the kidney. +The primary responsibilities of the kidney efferent arteriole endothelial cells involve controling renal blood flow, regulating glomerular filtration rate (GFR), and managing perfusion pressure. They do this by contracting and relaxing, effectively narrowing and widening the arteriole's lumen thereby controling the volume and rate of blood flow to the peritubular capillaries and creating the pressure gradient necessary for filtration in the glomerulus. +Furthermore, kidney efferent arteriole endothelial cells show a high degree of plasticity in response to pathophysiological stimuli and can undergo structural and functional changes based on local needs. In conditions like hypertension and diabetes, these cells can experience hypertrophy and endothelial dysfunction, contributing to the progression of renal disease."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.semcdb.2014.08.002"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [fibroblast of pedal digit skin](http://purl.obolibrary.org/obo/CL_2000012) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41581-021-00411-9"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1681/ASN.2019111179"^^[string](http://www.w3.org/2001/XMLSchema#string) -### fibroblast of peridontal ligament `http://purl.obolibrary.org/obo/CL_2000017` -#### Removed -- [fibroblast of peridontal ligament](http://purl.obolibrary.org/obo/CL_2000017) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) - -#### Added -- [fibroblast of peridontal ligament](http://purl.obolibrary.org/obo/CL_2000017) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.semnephrol.2015.01.010"^^[string](http://www.w3.org/2001/XMLSchema#string) -### fibroblast of skin of abdomen `http://purl.obolibrary.org/obo/CL_2000013` +### kidney loop of Henle short descending thin limb epithelial cell `http://purl.obolibrary.org/obo/CL_4030012` #### Removed -- [fibroblast of skin of abdomen](http://purl.obolibrary.org/obo/CL_2000013) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +- [kidney loop of Henle short descending thin limb epithelial cell](http://purl.obolibrary.org/obo/CL_4030012) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Epithelial cell of the descending thin limb of the short loop (cortical) nephron limited to the outer medulla (mainly inner strip). It is known in some mammalian species that the short descending limb of the loop of Henle selectively expresses the serine protease Corin, the homeobox TF Uncx, and the urea channel Slc14a2."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0003-2804-127X"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [fibroblast of skin of abdomen](http://purl.obolibrary.org/obo/CL_2000013) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33769951"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [kidney loop of Henle short descending thin limb epithelial cell](http://purl.obolibrary.org/obo/CL_4030012) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Epithelial cell of the descending thin limb of the short loop (cortical) nephron limited to the outer medulla (mainly inner strip). It is known in some mammalian species that the short descending limb of the loop of Henle selectively expresses the serine protease Corin, the homeobox TF Uncx, and the urea channel Slc14a2."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33769951"^^[string](http://www.w3.org/2001/XMLSchema#string) -### fibroblast of the reticular layer of dermis `http://purl.obolibrary.org/obo/CL_2000096` -#### Removed -- [fibroblast of the reticular layer of dermis](http://purl.obolibrary.org/obo/CL_2000096) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +- [kidney loop of Henle short descending thin limb epithelial cell](http://purl.obolibrary.org/obo/CL_4030012) [contributor](http://purl.org/dc/terms/contributor) [X](https://orcid.org/0000-0003-2804-127X) -#### Added -- [fibroblast of the reticular layer of dermis](http://purl.obolibrary.org/obo/CL_2000096) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [kidney loop of Henle short descending thin limb epithelial cell](http://purl.obolibrary.org/obo/CL_4030012) SubClassOf [squamous epithelial cell](http://purl.obolibrary.org/obo/CL_0000076) -### fibroblast of upper leg skin `http://purl.obolibrary.org/obo/CL_2000014` +### lamp5 GABAergic cortical interneuron `http://purl.obolibrary.org/obo/CL_4023011` #### Removed -- [fibroblast of upper leg skin](http://purl.obolibrary.org/obo/CL_2000014) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +- [lamp5 GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023011) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A GABAergic neuron located in the cerebral cortex that expresses Lamp5"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30382198"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [fibroblast of upper leg skin](http://purl.obolibrary.org/obo/CL_2000014) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [lamp5 GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023011) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A transcriptomically distinct GABAergic neuron located in the cerebral cortex that expresses Lamp5. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_subclass', clusters Lamp5."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/e/e4ddac12-f48f-4455-8e8d-c2a48a683437.cxg/"^^[string](http://www.w3.org/2001/XMLSchema#string) -### follicle cell of egg chamber `http://purl.obolibrary.org/obo/CL_0000477` -#### Removed -- [follicle cell of egg chamber](http://purl.obolibrary.org/obo/CL_0000477) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004904"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30382198"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [follicle cell of egg chamber](http://purl.obolibrary.org/obo/CL_0000477) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004904"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) -### follicle stem cell (sensu Arthropoda) `http://purl.obolibrary.org/obo/CL_0000441` +### larval midgut cell `http://purl.obolibrary.org/obo/CL_0009003` #### Removed -- [follicle stem cell (sensu Arthropoda)](http://purl.obolibrary.org/obo/CL_0000441) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004903"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [larval midgut cell](http://purl.obolibrary.org/obo/CL_0009003) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) #### Added -- [follicle stem cell (sensu Arthropoda)](http://purl.obolibrary.org/obo/CL_0000441) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004903"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - +- [larval midgut cell](http://purl.obolibrary.org/obo/CL_0009003) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### folliculostellate cell `http://purl.obolibrary.org/obo/CL_0000642` -#### Removed -- [folliculostellate cell](http://purl.obolibrary.org/obo/CL_0000642) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009281"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [folliculostellate cell](http://purl.obolibrary.org/obo/CL_0000642) SubClassOf [obsolete paracrine cell](http://purl.obolibrary.org/obo/CL_0000512) +### leucophore `http://purl.obolibrary.org/obo/CL_0000571` #### Added -- [folliculostellate cell](http://purl.obolibrary.org/obo/CL_0000642) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009281"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [leucophore](http://purl.obolibrary.org/obo/CL_0000571) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### foreskin melanocyte `http://purl.obolibrary.org/obo/CL_2000045` +### leukocyte `http://purl.obolibrary.org/obo/CL_0000738` #### Removed -- [foreskin melanocyte](http://purl.obolibrary.org/obo/CL_2000045) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +- [leukocyte](http://purl.obolibrary.org/obo/CL_0000738) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_7742](http://purl.obolibrary.org/obo/NCBITaxon_7742) #### Added -- [foreskin melanocyte](http://purl.obolibrary.org/obo/CL_2000045) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [leukocyte](http://purl.obolibrary.org/obo/CL_0000738) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_7742](http://purl.obolibrary.org/obo/NCBITaxon_7742) -### gallbladder fibroblast `http://purl.obolibrary.org/obo/CL_2000069` +### lower urinary tract cell `http://purl.obolibrary.org/obo/CL_1000600` #### Removed -- [gallbladder fibroblast](http://purl.obolibrary.org/obo/CL_2000069) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +- [lower urinary tract cell](http://purl.obolibrary.org/obo/CL_1000600) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) #### Added -- [gallbladder fibroblast](http://purl.obolibrary.org/obo/CL_2000069) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) - +- [lower urinary tract cell](http://purl.obolibrary.org/obo/CL_1000600) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### gamete `http://purl.obolibrary.org/obo/CL_0000300` -#### Removed -- [gamete](http://purl.obolibrary.org/obo/CL_0000300) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009156"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [gamete](http://purl.obolibrary.org/obo/CL_0000300) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005412"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +### luminal hormone-sensing cell of mammary gland `http://purl.obolibrary.org/obo/CL_4033058` #### Added -- [gamete](http://purl.obolibrary.org/obo/CL_0000300) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005412"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [luminal hormone-sensing cell of mammary gland](http://purl.obolibrary.org/obo/CL_4033058) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -- [gamete](http://purl.obolibrary.org/obo/CL_0000300) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009156"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -### gamma-delta T cell `http://purl.obolibrary.org/obo/CL_0000798` +### lung ciliated cell `http://purl.obolibrary.org/obo/CL_1000271` #### Removed -- [gamma-delta T cell](http://purl.obolibrary.org/obo/CL_0000798) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009336"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [gamma-delta T cell](http://purl.obolibrary.org/obo/CL_0000798) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009336"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [lung ciliated cell](http://purl.obolibrary.org/obo/CL_1000271) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any ciliated cell that is part of some lung."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [lung ciliated cell](http://purl.obolibrary.org/obo/CL_1000271) EquivalentTo [ciliated cell](http://purl.obolibrary.org/obo/CL_0000064) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002048](http://purl.obolibrary.org/obo/UBERON_0002048)) -### gamma-delta intraepithelial T cell `http://purl.obolibrary.org/obo/CL_0000801` -#### Removed -- [gamma-delta intraepithelial T cell](http://purl.obolibrary.org/obo/CL_0000801) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009339"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [lung ciliated cell](http://purl.obolibrary.org/obo/CL_1000271) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002048](http://purl.obolibrary.org/obo/UBERON_0002048) #### Added -- [gamma-delta intraepithelial T cell](http://purl.obolibrary.org/obo/CL_0000801) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009339"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [lung ciliated cell](http://purl.obolibrary.org/obo/CL_1000271) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell that is part of the lung epithelium. This cell is characterised by the presence of cilia on its apical surface."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27864314"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [lung ciliated cell](http://purl.obolibrary.org/obo/CL_1000271) EquivalentTo [ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0000067) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000115](http://purl.obolibrary.org/obo/UBERON_0000115)) -### ganglion mother cell `http://purl.obolibrary.org/obo/CL_0000469` -#### Removed -- [ganglion mother cell](http://purl.obolibrary.org/obo/CL_0000469) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005149"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [lung ciliated cell](http://purl.obolibrary.org/obo/CL_1000271) SubClassOf [epithelial cell of lung](http://purl.obolibrary.org/obo/CL_0000082) -#### Added -- [ganglion mother cell](http://purl.obolibrary.org/obo/CL_0000469) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005149"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [lung ciliated cell](http://purl.obolibrary.org/obo/CL_1000271) SubClassOf [ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0000067) -### garland cell `http://purl.obolibrary.org/obo/CL_0000486` -#### Removed -- [garland cell](http://purl.obolibrary.org/obo/CL_0000486) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005059"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +### lung goblet cell `http://purl.obolibrary.org/obo/CL_1000143` #### Added -- [garland cell](http://purl.obolibrary.org/obo/CL_0000486) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005059"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - +- [lung goblet cell](http://purl.obolibrary.org/obo/CL_1000143) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -### gastrula cell `http://purl.obolibrary.org/obo/CL_0000361` -#### Removed -- [gastrula cell](http://purl.obolibrary.org/obo/CL_0000361) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009182"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +Lung goblet cells are critical components of the respiratory tract, specifically found in the bronchial segments. They are secretory epithelial cells known for their signature "goblet" or cup-like shape. Their primary function is to produce and secrete mucus that aids in trapping airborne particles and pathogens, preventing them from reaching the delicate environment of the lung. As part of the lung's epithelial lining, they act as frontline defenders, maintaining lung health and function. +The lung goblet cells are densely packed with granules containing mucin glycoproteins, the primary component of mucus. As mucus is produced and secreted, it moves towards the lumen of the lungs where the cilia, hair-like structures of the neighboring ciliated epithelial cells, help to navigate it upwards and out of the respiratory tract. This coordinated action ensures the expulsion of unwanted particles and pathogens, effectively cleaning the respiratory tract. +Dysfunction or abnormal proliferation of lung goblet cells can result in pathological conditions such as chronic obstructive pulmonary disorder (COPD) and asthma, where excessive mucus production leads to airway obstruction. Furthermore, lung goblet cells respond to a variety of stimuli, including toxins, allergens, irritants, and infections, adjusting their mucus production accordingly."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1159/000512268"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [gastrula cell](http://purl.obolibrary.org/obo/CL_0000361) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009182"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41385-018-0039-y"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1513/AnnalsATS.201802-128AW"^^[string](http://www.w3.org/2001/XMLSchema#string) -### general_cell_types_upper_slim `http://purl.obolibrary.org/obo/cl/cl-base#general_cell_types_upper_slim` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41385-020-00370-7"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [general_cell_types_upper_slim](http://purl.obolibrary.org/obo/cl/cl-base#general_cell_types_upper_slim) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "a subset of general classes of cell types in the cell ontology."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK553208/"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [general_cell_types_upper_slim](http://purl.obolibrary.org/obo/cl/cl-base#general_cell_types_upper_slim) SubPropertyOf: [subset_property](http://www.geneontology.org/formats/oboInOwl#SubsetProperty) +- [lung goblet cell](http://purl.obolibrary.org/obo/CL_1000143) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000143"^^[string](http://www.w3.org/2001/XMLSchema#string) -### germ line cell `http://purl.obolibrary.org/obo/CL_0000039` -#### Removed -- [germ line cell](http://purl.obolibrary.org/obo/CL_0000039) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009016"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### lung neuroendocrine cell `http://purl.obolibrary.org/obo/CL_1000223` #### Added -- [germ line cell](http://purl.obolibrary.org/obo/CL_0000039) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009016"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - +- [lung neuroendocrine cell](http://purl.obolibrary.org/obo/CL_1000223) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000223"^^[string](http://www.w3.org/2001/XMLSchema#string) -### germ line stem cell `http://purl.obolibrary.org/obo/CL_0000014` -#### Removed -- [germ line stem cell](http://purl.obolibrary.org/obo/CL_0000014) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004861"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [lung neuroendocrine cell](http://purl.obolibrary.org/obo/CL_1000223) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -- [germ line stem cell](http://purl.obolibrary.org/obo/CL_0000014) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005956"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +Lung neuroendocrine cells, also commonly known as pulmonary neuroendocrine cells (PNECs), are predominantly located in the respiratory epithelium of the bronchial and bronchiolar airways in the lungs. These cells, characterised by their small size and granular appearance, have a distinctive morphology that sets them apart from other lung cells. They are considered part of the diffuse neuroendocrine system due to their scattered distribution through the epithelium and have been classified into solitary cells and clustered forms known as neuroepithelial bodies. +The primary function of PNECs is linked to regulation and maintenance of the lung environment. They are sensory in nature and can secrete various bioactive substances such as serotonin, calcitonin, calcitonin gene-related peptides, and bombesin-like peptides which modulate airway smooth muscle tone and influence gut motility. For example, they act as oxygen sensors in response to hypoxia and are responsible for releasing neuropeptides that can induce responses. Moreover, PNECs provide an afferent function as they are equipped with long microvilli that project into the lumen of the bronchus and react to changes in the chemical composition of the luminal content."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/bs.ctdb.2018.12.002"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [germ line stem cell](http://purl.obolibrary.org/obo/CL_0000014) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005956"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.devcel.2020.09.024"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [germ line stem cell](http://purl.obolibrary.org/obo/CL_0000014) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004861"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1242/dmm.046920"^^[string](http://www.w3.org/2001/XMLSchema#string) -### ghrelin secreting cell `http://purl.obolibrary.org/obo/CL_0005018` -#### Removed -- [ghrelin secreting cell](http://purl.obolibrary.org/obo/CL_0005018) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005599"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### lung secretory cell `http://purl.obolibrary.org/obo/CL_1000272` #### Added -- [ghrelin secreting cell](http://purl.obolibrary.org/obo/CL_0005018) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005599"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - +- [lung secretory cell](http://purl.obolibrary.org/obo/CL_1000272) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### glandular cell of endometrium `http://purl.obolibrary.org/obo/CL_0002656` -#### Removed -- [glandular cell of endometrium](http://purl.obolibrary.org/obo/CL_0002656) EquivalentTo [glandular epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001295](http://purl.obolibrary.org/obo/UBERON_0001295)) -- [glandular cell of endometrium](http://purl.obolibrary.org/obo/CL_0002656) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001295](http://purl.obolibrary.org/obo/UBERON_0001295) +### lymph node macrophage `http://purl.obolibrary.org/obo/CL_0000868` #### Added -- [glandular cell of endometrium](http://purl.obolibrary.org/obo/CL_0002656) EquivalentTo [glandular epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004811](http://purl.obolibrary.org/obo/UBERON_0004811)) - -- [glandular cell of endometrium](http://purl.obolibrary.org/obo/CL_0002656) SubClassOf [epithelial cell of uterus](http://purl.obolibrary.org/obo/CL_0002149) +- [lymph node macrophage](http://purl.obolibrary.org/obo/CL_0000868) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -- [glandular cell of endometrium](http://purl.obolibrary.org/obo/CL_0002656) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004811](http://purl.obolibrary.org/obo/UBERON_0004811) - -### glandular endometrial ciliated epithelial cell `http://purl.obolibrary.org/obo/CL_4030042` -#### Removed -- [glandular endometrial ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_4030042) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A ciliated cell of the endometrial glandular epithelium."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.1038/s41591-020-1040-z"^^[string](http://www.w3.org/2001/XMLSchema#string) +### lymphocyte of B lineage, CD19-positive `http://purl.obolibrary.org/obo/CL_0001200` #### Added -- [glandular endometrial ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_4030042) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A ciliated cell of the endometrial glandular epithelium. This cell is characterized by the presence of motile cilia on its apical surface."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.1038/s41591-020-1040-z"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [lymphocyte of B lineage, CD19-positive](http://purl.obolibrary.org/obo/CL_0001200) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### glandular epithelial cell of stomach `http://purl.obolibrary.org/obo/CL_0002659` -#### Removed -- [glandular epithelial cell of stomach](http://purl.obolibrary.org/obo/CL_0002659) [label](http://www.w3.org/2000/01/rdf-schema#label) "glandular cell of stomach"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [glandular epithelial cell of stomach](http://purl.obolibrary.org/obo/CL_0002659) SubClassOf [glandular epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) - - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) +### macrophage derived foam cell `http://purl.obolibrary.org/obo/CL_0000517` #### Added -- [glandular epithelial cell of stomach](http://purl.obolibrary.org/obo/CL_0002659) [label](http://www.w3.org/2000/01/rdf-schema#label) "glandular epithelial cell of stomach"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [macrophage derived foam cell](http://purl.obolibrary.org/obo/CL_0000517) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -- [glandular epithelial cell of stomach](http://purl.obolibrary.org/obo/CL_0002659) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "glandular cell of stomach"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [glandular epithelial cell of stomach](http://purl.obolibrary.org/obo/CL_0002659) SubClassOf [glandular epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) +### malpighian tubule tip cell `http://purl.obolibrary.org/obo/CL_1000182` +#### Added +- [malpighian tubule tip cell](http://purl.obolibrary.org/obo/CL_1000182) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### glial cell `http://purl.obolibrary.org/obo/CL_0000125` -#### Removed -- [glial cell](http://purl.obolibrary.org/obo/CL_0000125) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005144"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [glial cell](http://purl.obolibrary.org/obo/CL_0000125) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009073"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### mast cell `http://purl.obolibrary.org/obo/CL_0000097` #### Added -- [glial cell](http://purl.obolibrary.org/obo/CL_0000125) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005144"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [mast cell](http://purl.obolibrary.org/obo/CL_0000097) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -- [glial cell](http://purl.obolibrary.org/obo/CL_0000125) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009073"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -### glioblast `http://purl.obolibrary.org/obo/CL_0000030` -#### Removed -- [glioblast](http://purl.obolibrary.org/obo/CL_0000030) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009010"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### mast cell progenitor `http://purl.obolibrary.org/obo/CL_0000831` #### Added -- [glioblast](http://purl.obolibrary.org/obo/CL_0000030) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009010"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [mast cell progenitor](http://purl.obolibrary.org/obo/CL_0000831) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### glioblast (sensu Nematoda and Protostomia) `http://purl.obolibrary.org/obo/CL_0000340` -#### Removed -- [glioblast (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000340) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005145"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +### mature T cell `http://purl.obolibrary.org/obo/CL_0002419` #### Added -- [glioblast (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000340) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005145"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [mature T cell](http://purl.obolibrary.org/obo/CL_0002419) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### glioblast (sensu Vertebrata) `http://purl.obolibrary.org/obo/CL_0000339` -#### Removed -- [glioblast (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000339) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009169"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### melanocyte `http://purl.obolibrary.org/obo/CL_0000148` #### Added -- [glioblast (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000339) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009169"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [melanocyte](http://purl.obolibrary.org/obo/CL_0000148) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### glomerular capillary endothelial cell `http://purl.obolibrary.org/obo/CL_1001005` +### memory CCR4-positive regulatory T cell `http://purl.obolibrary.org/obo/CL_0001046` #### Removed -- [glomerular capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1001005) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any kidney capillary endothelial cell that is part of some glomerular capillary endothelium."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [glomerular capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1001005) SubClassOf [kidney capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1000892) - - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [memory CCR4-positive regulatory T cell](http://purl.obolibrary.org/obo/CL_0001046) EquivalentTo [memory regulatory T cell](http://purl.obolibrary.org/obo/CL_0002678) and ([RO_0002104](http://purl.obolibrary.org/obo/RO_0002104) some [PR_000001017](http://purl.obolibrary.org/obo/PR_000001017)) and ([RO_0002104](http://purl.obolibrary.org/obo/RO_0002104) some [PR_000001200](http://purl.obolibrary.org/obo/PR_000001200)) and ([RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606)) -- [glomerular capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1001005) SubClassOf [capillary endothelial cell](http://purl.obolibrary.org/obo/CL_0002144) - -- [glomerular capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1001005) SubClassOf [kidney glomerular epithelial cell](http://purl.obolibrary.org/obo/CL_1000510) +- [memory CCR4-positive regulatory T cell](http://purl.obolibrary.org/obo/CL_0001046) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) #### Added -- [glomerular capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1001005) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An endothelial cell that is part of the glomerular capillary of the kidney."^^[string](http://www.w3.org/2001/XMLSchema#string) +- [memory CCR4-positive regulatory T cell](http://purl.obolibrary.org/obo/CL_0001046) EquivalentTo [memory regulatory T cell](http://purl.obolibrary.org/obo/CL_0002678) and ([RO_0002104](http://purl.obolibrary.org/obo/RO_0002104) some [PR_000001017](http://purl.obolibrary.org/obo/PR_000001017)) and ([RO_0002104](http://purl.obolibrary.org/obo/RO_0002104) some [PR_000001200](http://purl.obolibrary.org/obo/PR_000001200)) and ([RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606)) -- [glomerular capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1001005) SubClassOf [kidney capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1000892) +- [memory CCR4-positive regulatory T cell](http://purl.obolibrary.org/obo/CL_0001046) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) -### glomerular cell `http://purl.obolibrary.org/obo/CL_1000746` -#### Removed -- [glomerular cell](http://purl.obolibrary.org/obo/CL_1000746) SubClassOf [kidney corpuscule cell](http://purl.obolibrary.org/obo/CL_1000612) - - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) +### mesenchymal cell `http://purl.obolibrary.org/obo/CL_0008019` #### Added -- [glomerular cell](http://purl.obolibrary.org/obo/CL_1000746) SubClassOf [kidney corpuscule cell](http://purl.obolibrary.org/obo/CL_1000612) - +- [mesenchymal cell](http://purl.obolibrary.org/obo/CL_0008019) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### glomerular endothelial cell `http://purl.obolibrary.org/obo/CL_0002188` -#### Removed -- [glomerular endothelial cell](http://purl.obolibrary.org/obo/CL_0002188) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An endothelial cell found in the glomerulus of the kidney. This cell is flattened, highly fenestrated, and plays a vital role in the formation of glomerular ultrafiltrate."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:15840009"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [glomerular endothelial cell](http://purl.obolibrary.org/obo/CL_0002188) SubClassOf [endothelial cell](http://purl.obolibrary.org/obo/CL_0000115) - - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [glomerular endothelial cell](http://purl.obolibrary.org/obo/CL_0002188) SubClassOf [glomerular cell](http://purl.obolibrary.org/obo/CL_1000746) +### mesenchymal stem cell of adipose tissue `http://purl.obolibrary.org/obo/CL_0002570` #### Added -- [glomerular endothelial cell](http://purl.obolibrary.org/obo/CL_0002188) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An endothelial cell that is part of the glomerulus of the kidney. This cell is flattened, highly fenestrated, and plays a vital role in the formation of glomerular ultrafiltrate."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:15840009"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [mesenchymal stem cell of adipose tissue](http://purl.obolibrary.org/obo/CL_0002570) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -- [glomerular endothelial cell](http://purl.obolibrary.org/obo/CL_0002188) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Glomerular endothelial cells have 60-80 nm fenestrations typically lacking diaphragms in adults but present during embryonic development. Some studies found diaphragms in 2-6% of mature rat glomerular capillaries. Their presence may depend on fixation techniques, developmental stage, or dynamic cell changes. Additionally, these cells help maintain the structural integrity of glomerular capillaries through interactions with the basement membrane and podocytes."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:18480313"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:19129259"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33123011"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [glomerular endothelial cell](http://purl.obolibrary.org/obo/CL_0002188) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000074](http://purl.obolibrary.org/obo/UBERON_0000074) +Mesenchymal stem cells of adipose tissue, also known commonly as adipose-derived stem cells (ADSCs), are a population of adult stem cells that can be obtained easily from adipose tissues. They have many of the same regenerative properties as other mesenchymal stem cells, but are more easily accessible than bone marrow-derived stem cells. +Adipose-derived stem cells show immense promise in the field of regenerative medicine due to their ability to differentiate into adipocytes, chondrocytes, myocytes, osteoblasts, and other cell types. ADSCs also possess immunomodulatory and homeostatic functions: they have the ability to suppress immune responses and provide a therapeutic environment for tissue repair and regeneration, as well as supporting the proliferation of adipocytes and the overall expansion of adipose tissue and contributing to the tissue's ability to react to demands of energy storage and mobilization. Dysfunction of these cells may contribute to metabolic complications observed in obesity and diabetes. +ADSCs have been used for therapeutic applications such as pathological wound healing, severe refractory acute graft-versus-host disease, and idiopathic thrombocytopenic purpura."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/dgd.12049"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [glomerular endothelial cell](http://purl.obolibrary.org/obo/CL_0002188) SubClassOf [BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0036053](http://purl.obolibrary.org/obo/GO_0036053) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.tibtech.2006.01.010"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [glomerular endothelial cell](http://purl.obolibrary.org/obo/CL_0002188) SubClassOf [kidney cortical cell](http://purl.obolibrary.org/obo/CL_0002681) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1096/fj.202100332R"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.biopha.2019.108765"^^[string](http://www.w3.org/2001/XMLSchema#string) -### glucagon secreting cell `http://purl.obolibrary.org/obo/CL_0000170` -#### Removed -- [glucagon secreting cell](http://purl.obolibrary.org/obo/CL_0000170) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009103"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41536-019-0083-6"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [glucagon secreting cell](http://purl.obolibrary.org/obo/CL_0000170) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009103"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [mesenchymal stem cell of adipose tissue](http://purl.obolibrary.org/obo/CL_0002570) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002570"^^[string](http://www.w3.org/2001/XMLSchema#string) -### glucocorticoid secreting cell `http://purl.obolibrary.org/obo/CL_0000460` -#### Removed -- [glucocorticoid secreting cell](http://purl.obolibrary.org/obo/CL_0000460) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009215"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### mesodermal cell `http://purl.obolibrary.org/obo/CL_0000222` #### Added -- [glucocorticoid secreting cell](http://purl.obolibrary.org/obo/CL_0000460) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009215"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [mesodermal cell](http://purl.obolibrary.org/obo/CL_0000222) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### glutamatergic neuron `http://purl.obolibrary.org/obo/CL_0000679` +### mesonephric podocyte `http://purl.obolibrary.org/obo/CL_0002523` #### Removed -- [glutamatergic neuron](http://purl.obolibrary.org/obo/CL_0000679) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00100291"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [mesonephric podocyte](http://purl.obolibrary.org/obo/CL_0002523) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A specialized epithelial cell that contains "feet" that interdigitate with the "feet" of other glomerular epithelial cells in the mesonephros."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0002-2244-7917"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [glutamatergic neuron](http://purl.obolibrary.org/obo/CL_0000679) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009290"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [glutamatergic neuron](http://purl.obolibrary.org/obo/CL_0000679) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00100291"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [mesonephric podocyte](http://purl.obolibrary.org/obo/CL_0002523) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A specialized epithelial cell that contains "feet" that interdigitate with the "feet" of other glomerular epithelial cells in the mesonephros."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [glutamatergic neuron](http://purl.obolibrary.org/obo/CL_0000679) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009290"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [mesonephric podocyte](http://purl.obolibrary.org/obo/CL_0002523) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-2244-7917](https://orcid.org/0000-0002-2244-7917) -### glycinergic neuron `http://purl.obolibrary.org/obo/CL_1001509` +### mesothelial cell `http://purl.obolibrary.org/obo/CL_0000077` #### Removed -- [glycinergic neuron](http://purl.obolibrary.org/obo/CL_1001509) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00048032"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [mesothelial cell](http://purl.obolibrary.org/obo/CL_0000077) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A flattened epithelial cell of mesenchymal origin that lines the serous cavity."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [glycinergic neuron](http://purl.obolibrary.org/obo/CL_1001509) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009396"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0721662544"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [glycinergic neuron](http://purl.obolibrary.org/obo/CL_1001509) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009396"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [glycinergic neuron](http://purl.obolibrary.org/obo/CL_1001509) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00048032"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### glycosaminoglycan secreting cell `http://purl.obolibrary.org/obo/CL_0000153` -#### Removed -- [glycosaminoglycan secreting cell](http://purl.obolibrary.org/obo/CL_0000153) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009093"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [mesothelial cell](http://purl.obolibrary.org/obo/CL_0000077) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A flat, squamous-like epithelial cell of mesodermal origin. It forms the mesothelium, which lines the body's serous cavities including the pleural, peritoneal, and pericardial spaces. This cell plays a crucial role in synthesizing and secreting lubricants, such as glycosaminoglycans and surfactants, which minimize friction between adjacent tissues during movement."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:26106328"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [glycosaminoglycan secreting cell](http://purl.obolibrary.org/obo/CL_0000153) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009093"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0721662544"^^[string](http://www.w3.org/2001/XMLSchema#string) -### goblet cell `http://purl.obolibrary.org/obo/CL_0000160` -#### Removed -- [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009094"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [mesothelial cell](http://purl.obolibrary.org/obo/CL_0000077) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Mesothelial cells, which morphologically resemble squamous epithelial cells, express both epithelial markers (cytokeratins) and mesenchymal markers (vimentin), reflecting their mesodermal origin. They feature surface microvilli and apical-basal polarity. Under certain conditions, they can undergo mesothelial-to-mesenchymal transition. These cells also produce extracellular matrix proteins, maintain serosal homeostasis, and facilitate fluid transport."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:26106328"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cell of the epithelial lining that produce and secrete mucins."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D020397"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [mesothelial cell](http://purl.obolibrary.org/obo/CL_0000077) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001136](http://purl.obolibrary.org/obo/UBERON_0001136) -- [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) SubClassOf [mucus secreting cell](http://purl.obolibrary.org/obo/CL_0000319) -- [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) SubClassOf [glandular epithelial cell](http://purl.obolibrary.org/obo/CL_0000150) +### mesothelial cell of pleura `http://purl.obolibrary.org/obo/CL_1000491` #### Added -- [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009094"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) [depiction](http://xmlns.com/foaf/0.1/depiction) "https://upload.wikimedia.org/wikipedia/commons/thumb/c/c4/404_Goblet_Cell_new.jpg/800px-404_Goblet_Cell_new.jpg"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://cnx.org/content/col11496/1.6/"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://commons.wikimedia.org/w/index.php?curid=30131227"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [mesothelial cell of pleura](http://purl.obolibrary.org/obo/CL_1000491) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -- [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A specialized, columnar, mucus secreting epithelial cell shaped like a flask or goblet. A narrow basal end contains the nucleus while the apical end is swollen by the accumulation of mucus laden secretory granules. Short microvilli project from the apical plasma membrane."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://en.wikipedia.org/wiki/Goblet_cell"^^[string](http://www.w3.org/2001/XMLSchema#string) +Mesothelial cells of the pleura form a significant part of the pleural membrane, a thin, double-layered serous membrane that lines the thoracic cavity and encompasses the lungs. These specialized cells contribute to the pleura's key function of producing a lubricating serous fluid, which reduces friction between the lung's outer surface (visceral pleura) and the inner lining of the thoracic cavity (parietal pleura) during respiration. +The cellular structure of mesothelial cells, characterized by microvilli on their surface, aids in the secretion and absorption of the pleural fluid, effectively supporting the smooth expansion and contraction of the lungs. Dysregulation in mesothelial cells can lead to pathologies, including pleural effusion and malignant mesothelioma. +Mesothelial cells of the pleura display unique immunologic properties. They act as a first line of defense against infection because they are able to recognize pathogens and respond by secreting various cytokines and chemokines. Additionally, these cells are directly involved in the translocation of immune cells into the pleural cavity during inflammatory response, thereby playing an active role in the immune response within the pleural environment. +In the event of pleural injury, these cells are also involved in the mesothelial-mesenchymal transition, a process that allows mesothelial cells to transdifferentiate into myofibroblasts and promote tissue repair."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/ajplung.90587.2008"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D020397"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.coi.2020.04.005"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) SubClassOf [BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0098594](http://purl.obolibrary.org/obo/GO_0098594) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fphys.2014.00284"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) SubClassOf [RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0070254](http://purl.obolibrary.org/obo/GO_0070254) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.ccm.2021.08.005"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) SubClassOf [BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0005902](http://purl.obolibrary.org/obo/GO_0005902) +- [mesothelial cell of pleura](http://purl.obolibrary.org/obo/CL_1000491) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000491"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) SubClassOf [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) - -### gonadtroph `http://purl.obolibrary.org/obo/CL_0000437` -#### Removed -- [gonadtroph](http://purl.obolibrary.org/obo/CL_0000437) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009202"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### mesothelial cell of visceral pleura `http://purl.obolibrary.org/obo/CL_1000493` #### Added -- [gonadtroph](http://purl.obolibrary.org/obo/CL_0000437) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009202"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [mesothelial cell of visceral pleura](http://purl.obolibrary.org/obo/CL_1000493) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +Mesothelial cells of visceral pleura are specialized epithelial cells that line the inner layer of the pleura, the membrane that envelops the lungs. Positioned adjacent to the lung tissue, these cells form a protective barrier and contribute to the structure of the visceral pleura. They are characterized by their cuboidal to squamous epithelial shape and the presence of microvilli on their surface, a feature aiding in fluid and solute exchange between the pleura and the lungs. +The primary function of mesothelial cells of visceral pleura is to secrete a lubricating serous fluid to facilitate smooth, frictionless lung movement within the thoracic cavity during respiration. This helps in the prevention of trauma or damage stemming from the constant rubbing of the lung tissue against the chest wall, hence playing a pivotal role in maintaining respiratory function. Besides fluid secretion, these cells have an essential role in the transportation of fluids and particles across the pleura, as well as in inflammation, wound healing, and tissue repair processes within the pleura. +Mesothelial cells of visceral pleura are notably implicated in the development of pleural diseases such as pleural effusion and pleural mesothelioma, a rare and aggressive form of cancer primarily linked with exposure to asbestos. Alterations, such as hyperplasia or metaplasia, may occur in these mesothelial cells under pathological conditions."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/physrev.00026.2003"^^[string](http://www.w3.org/2001/XMLSchema#string) -### granule cell `http://purl.obolibrary.org/obo/CL_0000120` -#### Removed -- [granule cell](http://purl.obolibrary.org/obo/CL_0000120) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009070"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1371/journal.pone.0276978"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [granule cell](http://purl.obolibrary.org/obo/CL_0000120) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009070"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fphys.2014.00221"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3390/jdb7020007"^^[string](http://www.w3.org/2001/XMLSchema#string) -### granulocyte `http://purl.obolibrary.org/obo/CL_0000094` -#### Removed -- [granulocyte](http://purl.obolibrary.org/obo/CL_0000094) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009048"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/S1357-2725(03)00242-5"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [granulocyte](http://purl.obolibrary.org/obo/CL_0000094) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009048"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [mesothelial cell of visceral pleura](http://purl.obolibrary.org/obo/CL_1000493) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1000493"^^[string](http://www.w3.org/2001/XMLSchema#string) -### granulocyte monocyte progenitor cell `http://purl.obolibrary.org/obo/CL_0000557` +### microglial cell `http://purl.obolibrary.org/obo/CL_0000129` #### Removed -- [granulocyte monocyte progenitor cell](http://purl.obolibrary.org/obo/CL_0000557) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009251"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [granulocyte monocyte progenitor cell](http://purl.obolibrary.org/obo/CL_0000557) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009251"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [microglial cell](http://purl.obolibrary.org/obo/CL_0000129) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A central nervous system macrophage found in the parenchyma of the central nervous system. Marker include CD11b-positive, F4/80-positive, and CD68-positive."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:add"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:14561199"^^[string](http://www.w3.org/2001/XMLSchema#string) -### granulosa cell `http://purl.obolibrary.org/obo/CL_0000501` -#### Removed -- [granulosa cell](http://purl.obolibrary.org/obo/CL_0000501) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009227"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://en.wikipedia.org/wiki/Microglia"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [granulosa cell](http://purl.obolibrary.org/obo/CL_0000501) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009227"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:2089275"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [granulosa cell](http://purl.obolibrary.org/obo/CL_0000501) SubClassOf [RO_0002207](http://purl.obolibrary.org/obo/RO_0002207) some [pre-granulosa cell](http://purl.obolibrary.org/obo/CL_4033066) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:14612429"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:dsd"^^[string](http://www.w3.org/2001/XMLSchema#string) -### green sensitive photoreceptor cell `http://purl.obolibrary.org/obo/CL_0000496` -#### Removed -- [green sensitive photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000496) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009223"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:12430718"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [green sensitive photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000496) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009223"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D017628"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:11517395"^^[string](http://www.w3.org/2001/XMLSchema#string) -### gut absorptive cell `http://purl.obolibrary.org/obo/CL_0000677` -#### Removed -- [gut absorptive cell](http://purl.obolibrary.org/obo/CL_0000677) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009289"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [gut absorptive cell](http://purl.obolibrary.org/obo/CL_0000677) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009289"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:16177057"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0721601464"^^[string](http://www.w3.org/2001/XMLSchema#string) -### gut endothelial cell `http://purl.obolibrary.org/obo/CL_0000131` -#### Removed -- [gut endothelial cell](http://purl.obolibrary.org/obo/CL_0000131) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009078"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:19461673"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [gut endothelial cell](http://purl.obolibrary.org/obo/CL_0000131) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009078"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - +- [microglial cell](http://purl.obolibrary.org/obo/CL_0000129) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A transcriptomically distinct central nervous system macrophage found in the parenchyma of the central nervous system. Marker include CD11b-positive, F4/80-positive, and CD68-positive."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:add"^^[string](http://www.w3.org/2001/XMLSchema#string) -### hair follicle dermal papilla cell of scalp `http://purl.obolibrary.org/obo/CL_2000083` -#### Removed -- [hair follicle dermal papilla cell of scalp](http://purl.obolibrary.org/obo/CL_2000083) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:14561199"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [hair follicle dermal papilla cell of scalp](http://purl.obolibrary.org/obo/CL_2000083) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://en.wikipedia.org/wiki/Microglia"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:2089275"^^[string](http://www.w3.org/2001/XMLSchema#string) -### hair follicle melanocyte `http://purl.obolibrary.org/obo/CL_0002483` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:14612429"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [hair follicle melanocyte](http://purl.obolibrary.org/obo/CL_0002483) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/cl/cl-base#human_reference_atlas) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:dsd"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [hair follicle melanocyte](http://purl.obolibrary.org/obo/CL_0002483) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:12430718"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D017628"^^[string](http://www.w3.org/2001/XMLSchema#string) -### hair follicular keratinocyte `http://purl.obolibrary.org/obo/CL_2000092` -#### Removed -- [hair follicular keratinocyte](http://purl.obolibrary.org/obo/CL_2000092) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:11517395"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [hair follicular keratinocyte](http://purl.obolibrary.org/obo/CL_2000092) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:16177057"^^[string](http://www.w3.org/2001/XMLSchema#string) -### hair germinal matrix cell `http://purl.obolibrary.org/obo/CL_0002562` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0721601464"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [hair germinal matrix cell](http://purl.obolibrary.org/obo/CL_0002562) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/cl/cl-base#human_reference_atlas) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:19461673"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [hair germinal matrix cell](http://purl.obolibrary.org/obo/CL_0002562) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) +- [microglial cell](http://purl.obolibrary.org/obo/CL_0000129) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### hatching gland cell `http://purl.obolibrary.org/obo/CL_0000249` +### micropylar cell `http://purl.obolibrary.org/obo/CL_0007022` #### Removed -- [hatching gland cell](http://purl.obolibrary.org/obo/CL_0000249) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009151"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [micropylar cell](http://purl.obolibrary.org/obo/CL_0007022) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) #### Added -- [hatching gland cell](http://purl.obolibrary.org/obo/CL_0000249) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009151"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [micropylar cell](http://purl.obolibrary.org/obo/CL_0007022) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### hematopoietic cell `http://purl.obolibrary.org/obo/CL_0000988` -#### Removed -- [hematopoietic cell](http://purl.obolibrary.org/obo/CL_0000988) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005830"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### monoblast `http://purl.obolibrary.org/obo/CL_0000040` #### Added -- [hematopoietic cell](http://purl.obolibrary.org/obo/CL_0000988) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005830"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [monoblast](http://purl.obolibrary.org/obo/CL_0000040) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### hematopoietic multipotent progenitor cell `http://purl.obolibrary.org/obo/CL_0000837` -#### Removed -- [hematopoietic multipotent progenitor cell](http://purl.obolibrary.org/obo/CL_0000837) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009354"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### mononuclear phagocyte `http://purl.obolibrary.org/obo/CL_0000113` #### Added -- [hematopoietic multipotent progenitor cell](http://purl.obolibrary.org/obo/CL_0000837) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009354"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### hematopoietic stem cell `http://purl.obolibrary.org/obo/CL_0000037` -#### Removed -- [hematopoietic stem cell](http://purl.obolibrary.org/obo/CL_0000037) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009014"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [mononuclear phagocyte](http://purl.obolibrary.org/obo/CL_0000113) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -#### Added -- [hematopoietic stem cell](http://purl.obolibrary.org/obo/CL_0000037) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009014"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +Mononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. +In addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses. +Mononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.coi.2005.11.008"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nri3087"^^[string](http://www.w3.org/2001/XMLSchema#string) -### hemocyte (sensu Arthropoda) `http://purl.obolibrary.org/obo/CL_0000387` -#### Removed -- [hemocyte (sensu Arthropoda)](http://purl.obolibrary.org/obo/CL_0000387) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005063"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2019.01893"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [hemocyte (sensu Arthropoda)](http://purl.obolibrary.org/obo/CL_0000387) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005063"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [mononuclear phagocyte](http://purl.obolibrary.org/obo/CL_0000113) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000113"^^[string](http://www.w3.org/2001/XMLSchema#string) -### hepatic stellate cell `http://purl.obolibrary.org/obo/CL_0000632` -#### Removed -- [hepatic stellate cell](http://purl.obolibrary.org/obo/CL_0000632) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009279"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### morula cell `http://purl.obolibrary.org/obo/CL_0000360` #### Added -- [hepatic stellate cell](http://purl.obolibrary.org/obo/CL_0000632) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009279"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [morula cell](http://purl.obolibrary.org/obo/CL_0000360) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### hepatocyte `http://purl.obolibrary.org/obo/CL_0000182` +### multi-ciliated epithelial cell `http://purl.obolibrary.org/obo/CL_0005012` #### Removed -- [hepatocyte](http://purl.obolibrary.org/obo/CL_0000182) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009111"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [multi-ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005012) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A ciliated epithelial cell with many cilia."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "CL:CVS"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [hepatocyte](http://purl.obolibrary.org/obo/CL_0000182) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009111"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [multi-ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005012) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A columnar/cuboidal epithelial cell with multiple motile cilia on its apical surface. These cells facilitate the movement of liquids such as mucus or cerebrospinal fluid across the epithelial surface."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30422572"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "CL:CVS"^^[string](http://www.w3.org/2001/XMLSchema#string) -### hillock cell of prostatic urethral epithelium `http://purl.obolibrary.org/obo/CL_0017011` -#### Removed -- [hillock cell of prostatic urethral epithelium](http://purl.obolibrary.org/obo/CL_0017011) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:28400610"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [hillock cell of prostatic urethral epithelium](http://purl.obolibrary.org/obo/CL_0017011) [in_subset](http://www.geneontology.org/formats/oboInOwl#inSubset) [human_reference_atlas](http://purl.obolibrary.org/obo/cl/cl-base#human_reference_atlas) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:38032388"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [multi-ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005012) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "While the term 'multi-ciliated epithelial cell' refers to cells with multiple motile cilia, there are exceptions where epithelial cells may have multiple non-motile cilia. Examples include olfactory sensory neurons, which have non-motile cilia for sensory detection, and choroid plexus epithelial cells, which possess multiple non-motile cilia with transient motility during development. Multiciliated cells are essential for human health, and their dysfunction can lead to various diseases known as ciliopathies, such as primary ciliary dyskinesia. This condition affects the respiratory system, brain ventricles, and reproductive system, leading to chronic respiratory infections, hydrocephalus, and infertility"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:23959957"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:22118931"^^[string](http://www.w3.org/2001/XMLSchema#string) -### hindlimb stylopod vein endothelial cell `http://purl.obolibrary.org/obo/CL_2000076` -#### Removed -- [hindlimb stylopod vein endothelial cell](http://purl.obolibrary.org/obo/CL_2000076) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:26378583"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [hindlimb stylopod vein endothelial cell](http://purl.obolibrary.org/obo/CL_2000076) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:25729351"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [multi-ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005012) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0005012"^^[string](http://www.w3.org/2001/XMLSchema#string) -### histaminergic neuron `http://purl.obolibrary.org/obo/CL_0011110` -#### Removed -- [histaminergic neuron](http://purl.obolibrary.org/obo/CL_0011110) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007367"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [multi-ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005012) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -#### Added -- [histaminergic neuron](http://purl.obolibrary.org/obo/CL_0011110) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007367"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +The multi-ciliated epithelial cell are terminally differentiated epithelia that line brain ventricles, the respiratory tract and parts of the female and male reproductive organs in animals, playing critical roles in the maintenance of homeostasis through ciliary motion. They are characterized by the presence of hundreds of motile cilia, hair-like microtubule-based organelles that beat in a coordinated fashion to direct fluid flow over the cell surface. +Multi-ciliated epithelial cells have fundamental roles in the proper functioning of many organ systems. In the respiratory system, they line the airways and orchestrate the coordinated movement of mucus, effectively clearing the airways of inhaled particles and pathogens. These cells are also vital in the ventricular system of the brain where they facilitate cerebrospinal fluid circulation, thus contributing to the maintenance of the brain's microenvironment. In the fallopian tube, multi-ciliated epithelial cells aid in the transport of oocytes from the ovary to the uterus, a process crucial to reproduction. +The formation and function of multi-ciliated epithelial cells is a highly regulated process that involves several stages of development including cell specification, centriole multiplication, and ciliogenesis. Any disruption in these processes can result in dysfunctional or decreased numbers of cilia, which can lead to a myriad of health issues, ranging from chronic respiratory infections to infertility."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1101/cshperspect.a028233"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.cub.2014.08.047"^^[string](http://www.w3.org/2001/XMLSchema#string) -### histoblast `http://purl.obolibrary.org/obo/CL_0000373` -#### Removed -- [histoblast](http://purl.obolibrary.org/obo/CL_0000373) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00001789"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nrm.2017.21"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [histoblast](http://purl.obolibrary.org/obo/CL_0000373) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00001789"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [multi-ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005012) EquivalentTo [columnar/cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000075) and ([BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0031514](http://purl.obolibrary.org/obo/GO_0031514)) and ([RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0010007](http://purl.obolibrary.org/obo/PATO_0010007)) +- [multi-ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005012) SubClassOf [columnar/cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000075) -### hypertrophic chondrocyte `http://purl.obolibrary.org/obo/CL_0000743` -#### Removed -- [hypertrophic chondrocyte](http://purl.obolibrary.org/obo/CL_0000743) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009313"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [multi-ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005012) SubClassOf [RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0010007](http://purl.obolibrary.org/obo/PATO_0010007) -#### Added -- [hypertrophic chondrocyte](http://purl.obolibrary.org/obo/CL_0000743) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009313"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [multi-ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005012) SubClassOf [BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0031514](http://purl.obolibrary.org/obo/GO_0031514) -### hypocretin-secreting neuron `http://purl.obolibrary.org/obo/CL_0011109` -#### Removed -- [hypocretin-secreting neuron](http://purl.obolibrary.org/obo/CL_0011109) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005778"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### multiciliated ependymal cell `http://purl.obolibrary.org/obo/CL_4052001` #### Added -- [hypocretin-secreting neuron](http://purl.obolibrary.org/obo/CL_0011109) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005778"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [multiciliated ependymal cell](http://purl.obolibrary.org/obo/CL_4052001) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An ependymal cell that lines the lateral, third, and fourth ventricles of the brain. The cell is characterized by multiple motile cilia on its apical surface, which beats in a coordinated manner to facilitate the movement of cerebrospinal fluid (CSF), contributing to brain homeostasis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:28067220"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:25045600"^^[string](http://www.w3.org/2001/XMLSchema#string) -### hypothalamus cell `http://purl.obolibrary.org/obo/CL_2000030` -#### Removed -- [hypothalamus cell](http://purl.obolibrary.org/obo/CL_2000030) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) - -#### Added -- [hypothalamus cell](http://purl.obolibrary.org/obo/CL_2000030) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) - + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37008045"^^[string](http://www.w3.org/2001/XMLSchema#string) -### imaginal disc cell `http://purl.obolibrary.org/obo/CL_0000429` -#### Removed -- [imaginal disc cell](http://purl.obolibrary.org/obo/CL_0000429) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007108"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [multiciliated ependymal cell](http://purl.obolibrary.org/obo/CL_4052001) [date](http://purl.org/dc/terms/date) "2024-08-20T10:06:15Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -#### Added -- [imaginal disc cell](http://purl.obolibrary.org/obo/CL_0000429) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00007108"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [multiciliated ependymal cell](http://purl.obolibrary.org/obo/CL_4052001) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "E1"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:28067220"^^[string](http://www.w3.org/2001/XMLSchema#string) -### immature B cell `http://purl.obolibrary.org/obo/CL_0000816` -#### Removed -- [immature B cell](http://purl.obolibrary.org/obo/CL_0000816) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009343"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37008045"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [immature B cell](http://purl.obolibrary.org/obo/CL_0000816) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009343"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [multiciliated ependymal cell](http://purl.obolibrary.org/obo/CL_4052001) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "multiciliated ependymal cells"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:25045600"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [multiciliated ependymal cell](http://purl.obolibrary.org/obo/CL_4052001) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "multiciliated ependymal cell, with an average of 16 motile cilia per cell, exhibits two types of planar cell polarity (PCP): rotational polarity, with unidirectional cilia orientation, and translational polarity, with asymmetric cilia positioning in the apical area. This location-specific PCP varies across the ventricular wall, aligning with the direction of CSF flow. These cells are interconnected by adherens and gap junctions, which support intercellular communication and maintain the structural integrity of the ependymal layer. Unlike some other cell types, these cells lack tight junctions."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27311928"^^[string](http://www.w3.org/2001/XMLSchema#string) -### immature Schwann cell `http://purl.obolibrary.org/obo/CL_0002377` -#### Removed -- [immature Schwann cell](http://purl.obolibrary.org/obo/CL_0002377) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0001725"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:25045600"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [immature Schwann cell](http://purl.obolibrary.org/obo/CL_0002377) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0001725"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [multiciliated ependymal cell](http://purl.obolibrary.org/obo/CL_4052001) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) +- [multiciliated ependymal cell](http://purl.obolibrary.org/obo/CL_4052001) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052001"^^[string](http://www.w3.org/2001/XMLSchema#string) -### immature gamma-delta T cell `http://purl.obolibrary.org/obo/CL_0000799` -#### Removed -- [immature gamma-delta T cell](http://purl.obolibrary.org/obo/CL_0000799) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009337"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [multiciliated ependymal cell](http://purl.obolibrary.org/obo/CL_4052001) [label](http://www.w3.org/2000/01/rdf-schema#label) "multiciliated ependymal cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [immature gamma-delta T cell](http://purl.obolibrary.org/obo/CL_0000799) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009337"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [multiciliated ependymal cell](http://purl.obolibrary.org/obo/CL_4052001) +- [multiciliated ependymal cell](http://purl.obolibrary.org/obo/CL_4052001) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0005357](http://purl.obolibrary.org/obo/UBERON_0005357) -### immature natural killer cell `http://purl.obolibrary.org/obo/CL_0000823` -#### Removed -- [immature natural killer cell](http://purl.obolibrary.org/obo/CL_0000823) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009346"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [multiciliated ependymal cell](http://purl.obolibrary.org/obo/CL_4052001) SubClassOf [multi-ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005012) -#### Added -- [immature natural killer cell](http://purl.obolibrary.org/obo/CL_0000823) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009346"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [multiciliated ependymal cell](http://purl.obolibrary.org/obo/CL_4052001) SubClassOf [ependymal cell](http://purl.obolibrary.org/obo/CL_0000065) -### immature neutrophil `http://purl.obolibrary.org/obo/CL_0000776` +### multinuclear osteoclast `http://purl.obolibrary.org/obo/CL_0000779` #### Removed -- [immature neutrophil](http://purl.obolibrary.org/obo/CL_0000776) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009328"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [immature neutrophil](http://purl.obolibrary.org/obo/CL_0000776) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009328"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [multinuclear osteoclast](http://purl.obolibrary.org/obo/CL_0000779) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A specialized multinuclear osteoclast associated with the absorption and removal of bone."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:12713016"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:add"^^[string](http://www.w3.org/2001/XMLSchema#string) -### inhibitory interneuron `http://purl.obolibrary.org/obo/CL_0000498` -#### Removed -- [inhibitory interneuron](http://purl.obolibrary.org/obo/CL_0000498) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009225"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:9415452"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [inhibitory interneuron](http://purl.obolibrary.org/obo/CL_0000498) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009225"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - +- [multinuclear osteoclast](http://purl.obolibrary.org/obo/CL_0000779) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A specialized multinuclear osteoclast, forming a syncytium through the fusion of mononuclear precursor cells, associated with the absorption and removal of bone."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:12713016"^^[string](http://www.w3.org/2001/XMLSchema#string) -### inner cell mass cell `http://purl.obolibrary.org/obo/CL_2000020` -#### Removed -- [inner cell mass cell](http://purl.obolibrary.org/obo/CL_2000020) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:add"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [inner cell mass cell](http://purl.obolibrary.org/obo/CL_2000020) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:38903088"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29379067"^^[string](http://www.w3.org/2001/XMLSchema#string) -### inner renal medulla vasa recta cell `http://purl.obolibrary.org/obo/CL_1001126` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:9415452"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [inner renal medulla vasa recta cell](http://purl.obolibrary.org/obo/CL_1001126) SubClassOf [kidney venous blood vessel cell](http://purl.obolibrary.org/obo/CL_1000893) +- [multinuclear osteoclast](http://purl.obolibrary.org/obo/CL_0000779) SubClassOf [syncytial cell](http://purl.obolibrary.org/obo/CL_4052002) -### insect flight muscle cell `http://purl.obolibrary.org/obo/CL_0000196` +### multinucleate cell `http://purl.obolibrary.org/obo/CL_0000228` #### Removed -- [insect flight muscle cell](http://purl.obolibrary.org/obo/CL_0000196) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00003360"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [insect flight muscle cell](http://purl.obolibrary.org/obo/CL_0000196) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00003360"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [multinucleate cell](http://purl.obolibrary.org/obo/CL_0000228) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "syncytial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [multinucleate cell](http://purl.obolibrary.org/obo/CL_0000228) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "syncytium"^^[string](http://www.w3.org/2001/XMLSchema#string) -### insulating cell `http://purl.obolibrary.org/obo/CL_0000217` -#### Removed -- [insulating cell](http://purl.obolibrary.org/obo/CL_0000217) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009134"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [multinucleate cell](http://purl.obolibrary.org/obo/CL_0000228) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "AEO:0000203"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [insulating cell](http://purl.obolibrary.org/obo/CL_0000217) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009134"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [multinucleate cell](http://purl.obolibrary.org/obo/CL_0000228) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cell with more than one nucleus."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FB:ma"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [multinucleate cell](http://purl.obolibrary.org/obo/CL_0000228) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "syncitium"^^[string](http://www.w3.org/2001/XMLSchema#string) -### insulin secreting cell `http://purl.obolibrary.org/obo/CL_0000168` -#### Removed -- [insulin secreting cell](http://purl.obolibrary.org/obo/CL_0000168) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009101"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [multinucleate cell](http://purl.obolibrary.org/obo/CL_0000228) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "WBbt:0008074"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [insulin secreting cell](http://purl.obolibrary.org/obo/CL_0000168) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009101"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### interfollicle cell `http://purl.obolibrary.org/obo/CL_0000674` -#### Removed -- [interfollicle cell](http://purl.obolibrary.org/obo/CL_0000674) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004910"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [multinucleate cell](http://purl.obolibrary.org/obo/CL_0000228) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "polynuclear cells"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Multinucleate"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [interfollicle cell](http://purl.obolibrary.org/obo/CL_0000674) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004910"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [multinucleate cell](http://purl.obolibrary.org/obo/CL_0000228) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cell with more than one nucleus."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FB:ma"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Multinucleate"^^[string](http://www.w3.org/2001/XMLSchema#string) -### interneuromast cell `http://purl.obolibrary.org/obo/CL_0000854` -#### Removed -- [interneuromast cell](http://purl.obolibrary.org/obo/CL_0000854) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009365"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [multinucleate cell](http://purl.obolibrary.org/obo/CL_0000228) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "multinucleated cells"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Multinucleate"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [interneuromast cell](http://purl.obolibrary.org/obo/CL_0000854) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009365"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [multinucleate cell](http://purl.obolibrary.org/obo/CL_0000228) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### interneuron `http://purl.obolibrary.org/obo/CL_0000099` +### multinucleated giant cell `http://purl.obolibrary.org/obo/CL_0000647` #### Removed -- [interneuron](http://purl.obolibrary.org/obo/CL_0000099) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005125"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [multinucleated giant cell](http://purl.obolibrary.org/obo/CL_0000647) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A phagocytic cell formed by the fusion of macrophages, occurs in chronic inflammatory responses to persistent microorganism such as M.tuberculosis, component of granulomas. Sometimes used to refer to megakaryocytes."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:add"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [interneuron](http://purl.obolibrary.org/obo/CL_0000099) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009051"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [interneuron](http://purl.obolibrary.org/obo/CL_0000099) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009051"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [interneuron](http://purl.obolibrary.org/obo/CL_0000099) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005125"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### interstitial extravillous trophoblast cell `http://purl.obolibrary.org/obo/CL_4033062` -#### Removed -- [interstitial extravillous trophoblast cell](http://purl.obolibrary.org/obo/CL_4033062) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0702022918"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0702024783"^^[string](http://www.w3.org/2001/XMLSchema#string) -### intestinal epithelial cell `http://purl.obolibrary.org/obo/CL_0002563` -#### Removed -- [intestinal epithelial cell](http://purl.obolibrary.org/obo/CL_0002563) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009399"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [multinucleated giant cell](http://purl.obolibrary.org/obo/CL_0000647) SubClassOf [multinucleate cell](http://purl.obolibrary.org/obo/CL_0000228) #### Added -- [intestinal epithelial cell](http://purl.obolibrary.org/obo/CL_0002563) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009399"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - +- [multinucleated giant cell](http://purl.obolibrary.org/obo/CL_0000647) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "MGC"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) -### intrahepatic cholangiocyte `http://purl.obolibrary.org/obo/CL_0002538` -#### Removed -- [intrahepatic cholangiocyte](http://purl.obolibrary.org/obo/CL_0002538) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009379"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33348900"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [intrahepatic cholangiocyte](http://purl.obolibrary.org/obo/CL_0002538) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009379"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [multinucleated giant cell](http://purl.obolibrary.org/obo/CL_0000647) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A phagocytic syncytial cell formed by the fusion of macrophages, occurs in chronic inflammatory responses to persistent microorganism such as M.tuberculosis, component of granulomas. Sometimes used to refer to megakaryocytes."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:add"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0702022918"^^[string](http://www.w3.org/2001/XMLSchema#string) -### invertebrate nurse cell `http://purl.obolibrary.org/obo/CL_0000026` -#### Removed -- [invertebrate nurse cell](http://purl.obolibrary.org/obo/CL_0000026) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004878"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [invertebrate nurse cell](http://purl.obolibrary.org/obo/CL_0000026) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004878"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33348900"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0702024783"^^[string](http://www.w3.org/2001/XMLSchema#string) -### ionocyte `http://purl.obolibrary.org/obo/CL_0005006` -#### Removed -- [ionocyte](http://purl.obolibrary.org/obo/CL_0005006) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005323"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Giant_cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [ionocyte](http://purl.obolibrary.org/obo/CL_0005006) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005323"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [multinucleated giant cell](http://purl.obolibrary.org/obo/CL_0000647) SubClassOf [syncytial cell](http://purl.obolibrary.org/obo/CL_4052002) -### iridoblast `http://purl.obolibrary.org/obo/CL_0005001` +### mural granulosa cell `http://purl.obolibrary.org/obo/CL_4033067` #### Removed -- [iridoblast](http://purl.obolibrary.org/obo/CL_0005001) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005328"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [iridoblast](http://purl.obolibrary.org/obo/CL_0005001) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005328"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [mural granulosa cell](http://purl.obolibrary.org/obo/CL_4033067) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A follicular cell of ovary that differentiates from a granulosa cell during the secondary follicle stage. Mural granulosa cells line the inner surface of the follicle wall, surrounding the fluid-filled antral cavity. These cells produce oestrogen during the follicular phase in response to follicle-stimulating hormone (FSH), and progesterone after ovulation in response to luteinizing hormone (LH)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33970370"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27815559"^^[string](http://www.w3.org/2001/XMLSchema#string) -### iridophore `http://purl.obolibrary.org/obo/CL_0000431` -#### Removed -- [iridophore](http://purl.obolibrary.org/obo/CL_0000431) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009199"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34198768"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [iridophore](http://purl.obolibrary.org/obo/CL_0000431) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009199"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [mural granulosa cell](http://purl.obolibrary.org/obo/CL_4033067) SubClassOf [RO_0002207](http://purl.obolibrary.org/obo/RO_0002207) some [granulosa cell](http://purl.obolibrary.org/obo/CL_0000501) +- [mural granulosa cell](http://purl.obolibrary.org/obo/CL_4033067) SubClassOf [ovarian surface epithelial cell](http://purl.obolibrary.org/obo/CL_2000064) -### juvenile hormone secreting cell `http://purl.obolibrary.org/obo/CL_0000482` -#### Removed -- [juvenile hormone secreting cell](http://purl.obolibrary.org/obo/CL_0000482) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00058020"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [mural granulosa cell](http://purl.obolibrary.org/obo/CL_4033067) SubClassOf [follicular cell of ovary](http://purl.obolibrary.org/obo/CL_0002174) #### Added -- [juvenile hormone secreting cell](http://purl.obolibrary.org/obo/CL_0000482) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00058020"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### keratin accumulating cell `http://purl.obolibrary.org/obo/CL_0000311` -#### Removed -- [keratin accumulating cell](http://purl.obolibrary.org/obo/CL_0000311) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009157"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [mural granulosa cell](http://purl.obolibrary.org/obo/CL_4033067) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A follicular cell of ovary that differentiates from a cuboidal granulosa cell during the secondary follicle stage. Mural granulosa cells line the inner surface of the follicle wall, surrounding the fluid-filled antral cavity. These cells produce oestrogen during the follicular phase in response to follicle-stimulating hormone (FSH), and progesterone after ovulation in response to luteinizing hormone (LH)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33970370"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [keratin accumulating cell](http://purl.obolibrary.org/obo/CL_0000311) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009157"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27815559"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34198768"^^[string](http://www.w3.org/2001/XMLSchema#string) -### keratinocyte `http://purl.obolibrary.org/obo/CL_0000312` -#### Removed -- [keratinocyte](http://purl.obolibrary.org/obo/CL_0000312) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009158"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [mural granulosa cell](http://purl.obolibrary.org/obo/CL_4033067) SubClassOf [RO_0002202](http://purl.obolibrary.org/obo/RO_0002202) some [cuboidal granulosa cell](http://purl.obolibrary.org/obo/CL_4033084) -#### Added -- [keratinocyte](http://purl.obolibrary.org/obo/CL_0000312) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009158"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [mural granulosa cell](http://purl.obolibrary.org/obo/CL_4033067) SubClassOf [UBERON_0004120](http://purl.obolibrary.org/obo/UBERON_0004120) +- [mural granulosa cell](http://purl.obolibrary.org/obo/CL_4033067) SubClassOf [granulosa cell](http://purl.obolibrary.org/obo/CL_0000501) -### kidney afferent arteriole cell `http://purl.obolibrary.org/obo/CL_1001006` -#### Removed -- [kidney afferent arteriole cell](http://purl.obolibrary.org/obo/CL_1001006) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any kidney arterial blood vessel cell that is part of some renal afferent arteriole."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [kidney afferent arteriole cell](http://purl.obolibrary.org/obo/CL_1001006) SubClassOf [kidney corpuscule cell](http://purl.obolibrary.org/obo/CL_1000612) +### muscle cell `http://purl.obolibrary.org/obo/CL_0000187` #### Added -- [kidney afferent arteriole cell](http://purl.obolibrary.org/obo/CL_1001006) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An endothelial cell which is part of the afferent arteriole in the kidney. This cell is responsible for maintaining renal blood flow and glomerular filtration rate."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:24066938"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:22733355"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:25834230"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [muscle cell](http://purl.obolibrary.org/obo/CL_0000187) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:16990493"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [kidney afferent arteriole cell](http://purl.obolibrary.org/obo/CL_1001006) SubClassOf [kidney cortical cell](http://purl.obolibrary.org/obo/CL_0002681) - - -### kidney afferent arteriole endothelial cell `http://purl.obolibrary.org/obo/CL_1001096` -#### Removed -- [kidney afferent arteriole endothelial cell](http://purl.obolibrary.org/obo/CL_1001096) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any endothelial cell that is part of some renal afferent arteriole."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [kidney afferent arteriole endothelial cell](http://purl.obolibrary.org/obo/CL_1001096) SubClassOf [endothelial cell of arteriole](http://purl.obolibrary.org/obo/CL_1000412) - - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [kidney afferent arteriole endothelial cell](http://purl.obolibrary.org/obo/CL_1001096) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An endothelial cell that lines the interior surface of the afferent arteriole and maintains vascular tone. This cell responds to changing ion concentrations and blood pressure by releasing vasoactive substances, in order to regulate blood flow into the glomeruli, which is essential for glomerular filtration."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:24066938"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:22733355"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:25834230"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:16990493"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [kidney afferent arteriole endothelial cell](http://purl.obolibrary.org/obo/CL_1001096) SubClassOf [endothelial cell of arteriole](http://purl.obolibrary.org/obo/CL_1000412) - - -### kidney afferent arteriole smooth muscle cell `http://purl.obolibrary.org/obo/CL_1001097` -#### Removed -- [kidney afferent arteriole smooth muscle cell](http://purl.obolibrary.org/obo/CL_1001097) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any smooth muscle cell that is part of some renal afferent arteriole."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [kidney afferent arteriole smooth muscle cell](http://purl.obolibrary.org/obo/CL_1001097) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A smooth muscle cell found in the wall of the afferent arteriole. This cell contracts and relaxes in response to changes in blood pressure, a process known as a myogenic response, to alter artery diameter and regulate blood flow into the glomeruli."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:24066938"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:22733355"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:25834230"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:16990493"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### kidney arteriole smooth muscle cell `http://purl.obolibrary.org/obo/CL_1001066` -#### Removed -- [kidney arteriole smooth muscle cell](http://purl.obolibrary.org/obo/CL_1001066) SubClassOf [meso-epithelial cell](http://purl.obolibrary.org/obo/CL_0002078) - - - -### kidney artery smooth muscle cell `http://purl.obolibrary.org/obo/CL_1001064` -#### Removed -- [kidney artery smooth muscle cell](http://purl.obolibrary.org/obo/CL_1001064) SubClassOf [meso-epithelial cell](http://purl.obolibrary.org/obo/CL_0002078) - - - -### kidney blood vessel cell `http://purl.obolibrary.org/obo/CL_1000854` -#### Removed -- [kidney blood vessel cell](http://purl.obolibrary.org/obo/CL_1000854) SubClassOf [renal cortical epithelial cell](http://purl.obolibrary.org/obo/CL_0002584) - - - -### kidney capillary endothelial cell `http://purl.obolibrary.org/obo/CL_1000892` -#### Removed -- [kidney capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1000892) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any kidney blood vessel cell that is part of some kidney capillary."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [kidney capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1000892) EquivalentTo [kidney blood vessel cell](http://purl.obolibrary.org/obo/CL_1000854) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0003527](http://purl.obolibrary.org/obo/UBERON_0003527)) - -- [kidney capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1000892) SubClassOf [blood vessel endothelial cell](http://purl.obolibrary.org/obo/CL_0000071) - -#### Added -- [kidney capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1000892) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An endothelial cell that is part of the capillary of the kidney."^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [kidney capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1000892) EquivalentTo [endothelial cell](http://purl.obolibrary.org/obo/CL_0000115) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0003527](http://purl.obolibrary.org/obo/UBERON_0003527)) - -- [kidney capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1000892) SubClassOf [capillary endothelial cell](http://purl.obolibrary.org/obo/CL_0002144) - - -### kidney cell `http://purl.obolibrary.org/obo/CL_1000497` -#### Removed -- [kidney cell](http://purl.obolibrary.org/obo/CL_1000497) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009389"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [kidney cell](http://purl.obolibrary.org/obo/CL_1000497) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009389"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### kidney corpuscule cell `http://purl.obolibrary.org/obo/CL_1000612` -#### Removed -- [kidney corpuscule cell](http://purl.obolibrary.org/obo/CL_1000612) SubClassOf [renal cortical epithelial cell](http://purl.obolibrary.org/obo/CL_0002584) - - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [kidney corpuscule cell](http://purl.obolibrary.org/obo/CL_1000612) SubClassOf [renal cortical epithelial cell](http://purl.obolibrary.org/obo/CL_0002584) - - -### kidney cortex artery cell `http://purl.obolibrary.org/obo/CL_1001045` -#### Removed -- [kidney cortex artery cell](http://purl.obolibrary.org/obo/CL_1001045) SubClassOf [kidney arterial blood vessel cell](http://purl.obolibrary.org/obo/CL_1000891) - - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [kidney cortex artery cell](http://purl.obolibrary.org/obo/CL_1001045) SubClassOf [kidney cortical cell](http://purl.obolibrary.org/obo/CL_0002681) - -- [kidney cortex artery cell](http://purl.obolibrary.org/obo/CL_1001045) SubClassOf [kidney arterial blood vessel cell](http://purl.obolibrary.org/obo/CL_1000891) - - -### kidney cortex peritubular capillary cell `http://purl.obolibrary.org/obo/CL_1001124` -#### Removed -- [kidney cortex peritubular capillary cell](http://purl.obolibrary.org/obo/CL_1001124) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any peritubular capillary endothelial cell that is part of some renal cortex peritubular capillary."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [kidney cortex peritubular capillary cell](http://purl.obolibrary.org/obo/CL_1001124) SubClassOf [peritubular capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1001033) - - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [kidney cortex peritubular capillary cell](http://purl.obolibrary.org/obo/CL_1001124) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An endothelial cell that is part of the peritubular capillary of the renal cortex."^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [kidney cortex peritubular capillary cell](http://purl.obolibrary.org/obo/CL_1001124) SubClassOf [kidney cortical cell](http://purl.obolibrary.org/obo/CL_0002681) - -- [kidney cortex peritubular capillary cell](http://purl.obolibrary.org/obo/CL_1001124) SubClassOf [peritubular capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1001033) - - -### kidney cortex vein cell `http://purl.obolibrary.org/obo/CL_1001052` - -#### Added -- [kidney cortex vein cell](http://purl.obolibrary.org/obo/CL_1001052) SubClassOf [kidney cortical cell](http://purl.obolibrary.org/obo/CL_0002681) - - -### kidney efferent arteriole cell `http://purl.obolibrary.org/obo/CL_1001009` -#### Removed -- [kidney efferent arteriole cell](http://purl.obolibrary.org/obo/CL_1001009) SubClassOf [kidney corpuscule cell](http://purl.obolibrary.org/obo/CL_1000612) - -- [kidney efferent arteriole cell](http://purl.obolibrary.org/obo/CL_1001009) SubClassOf [kidney arterial blood vessel cell](http://purl.obolibrary.org/obo/CL_1000891) - - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [kidney efferent arteriole cell](http://purl.obolibrary.org/obo/CL_1001009) SubClassOf [kidney cortical cell](http://purl.obolibrary.org/obo/CL_0002681) - -- [kidney efferent arteriole cell](http://purl.obolibrary.org/obo/CL_1001009) SubClassOf [kidney arterial blood vessel cell](http://purl.obolibrary.org/obo/CL_1000891) - - -### kidney efferent arteriole endothelial cell `http://purl.obolibrary.org/obo/CL_1001099` -#### Removed -- [kidney efferent arteriole endothelial cell](http://purl.obolibrary.org/obo/CL_1001099) SubClassOf [endothelial cell of arteriole](http://purl.obolibrary.org/obo/CL_1000412) - - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [kidney efferent arteriole endothelial cell](http://purl.obolibrary.org/obo/CL_1001099) SubClassOf [endothelial cell of arteriole](http://purl.obolibrary.org/obo/CL_1000412) - - -### kidney epithelial cell `http://purl.obolibrary.org/obo/CL_0002518` -#### Removed -- [kidney epithelial cell](http://purl.obolibrary.org/obo/CL_0002518) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009374"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [kidney epithelial cell](http://purl.obolibrary.org/obo/CL_0002518) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009374"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### kidney granular cell `http://purl.obolibrary.org/obo/CL_0000648` -#### Removed -- [kidney granular cell](http://purl.obolibrary.org/obo/CL_0000648) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005238"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [kidney granular cell](http://purl.obolibrary.org/obo/CL_0000648) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005238"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### kidney interstitial cell `http://purl.obolibrary.org/obo/CL_1000500` -#### Removed -- [kidney interstitial cell](http://purl.obolibrary.org/obo/CL_1000500) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009390"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [kidney interstitial cell](http://purl.obolibrary.org/obo/CL_1000500) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009390"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### kidney medulla cell `http://purl.obolibrary.org/obo/CL_1000504` -#### Removed -- [kidney medulla cell](http://purl.obolibrary.org/obo/CL_1000504) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009391"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [kidney medulla cell](http://purl.obolibrary.org/obo/CL_1000504) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009391"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### kidney outer medulla peritubular capillary cell `http://purl.obolibrary.org/obo/CL_1001123` -#### Removed -- [kidney outer medulla peritubular capillary cell](http://purl.obolibrary.org/obo/CL_1001123) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any peritubular capillary endothelial cell that is part of some outer renal medulla peritubular capillary."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [kidney outer medulla peritubular capillary cell](http://purl.obolibrary.org/obo/CL_1001123) SubClassOf [peritubular capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1001033) - - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [kidney outer medulla peritubular capillary cell](http://purl.obolibrary.org/obo/CL_1001123) SubClassOf [kidney outer medulla cell](http://purl.obolibrary.org/obo/CL_1000616) - - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [kidney outer medulla peritubular capillary cell](http://purl.obolibrary.org/obo/CL_1001123) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An endothelial cell that is part of the peritubular capillary of the outer renal medulla."^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [kidney outer medulla peritubular capillary cell](http://purl.obolibrary.org/obo/CL_1001123) SubClassOf [kidney outer medulla cell](http://purl.obolibrary.org/obo/CL_1000616) - -- [kidney outer medulla peritubular capillary cell](http://purl.obolibrary.org/obo/CL_1001123) SubClassOf [peritubular capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1001033) - - -### kidney proximal convoluted tubule epithelial cell `http://purl.obolibrary.org/obo/CL_1000838` -#### Removed -- [kidney proximal convoluted tubule epithelial cell](http://purl.obolibrary.org/obo/CL_1000838) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any epithelial cell of proximal tubule that is part of some proximal convoluted tubule."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [kidney proximal convoluted tubule epithelial cell](http://purl.obolibrary.org/obo/CL_1000838) EquivalentTo [epithelial cell of proximal tubule](http://purl.obolibrary.org/obo/CL_0002306) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001287](http://purl.obolibrary.org/obo/UBERON_0001287)) - -- [kidney proximal convoluted tubule epithelial cell](http://purl.obolibrary.org/obo/CL_1000838) SubClassOf [epithelial cell of proximal tubule](http://purl.obolibrary.org/obo/CL_0002306) - - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [kidney proximal convoluted tubule epithelial cell](http://purl.obolibrary.org/obo/CL_1000838) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any epithelial cell of proximal tubule that is part of some proximal convoluted tubule and has part some brush border."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [kidney proximal convoluted tubule epithelial cell](http://purl.obolibrary.org/obo/CL_1000838) EquivalentTo [epithelial cell of proximal tubule](http://purl.obolibrary.org/obo/CL_0002306) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001287](http://purl.obolibrary.org/obo/UBERON_0001287)) and ([BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0005903](http://purl.obolibrary.org/obo/GO_0005903)) - -- [kidney proximal convoluted tubule epithelial cell](http://purl.obolibrary.org/obo/CL_1000838) SubClassOf [brush border cell of the proximal tubule](http://purl.obolibrary.org/obo/CL_0002307) - - -### kidney venous system smooth muscle cell `http://purl.obolibrary.org/obo/CL_1001068` -#### Removed -- [kidney venous system smooth muscle cell](http://purl.obolibrary.org/obo/CL_1001068) SubClassOf [meso-epithelial cell](http://purl.obolibrary.org/obo/CL_0002078) - - - -### kidney_upper_slim `http://purl.obolibrary.org/obo/cl/cl-base#kidney_upper_slim` - -#### Added -- [kidney_upper_slim](http://purl.obolibrary.org/obo/cl/cl-base#kidney_upper_slim) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "a subset of general classes related to specific cell types in the kidney"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [kidney_upper_slim](http://purl.obolibrary.org/obo/cl/cl-base#kidney_upper_slim) SubPropertyOf: [subset_property](http://www.geneontology.org/formats/oboInOwl#SubsetProperty) - - -### lamellocyte `http://purl.obolibrary.org/obo/CL_0000396` -#### Removed -- [lamellocyte](http://purl.obolibrary.org/obo/CL_0000396) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00001687"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [lamellocyte](http://purl.obolibrary.org/obo/CL_0000396) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00001687"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### lamp5 GABAergic cortical interneuron `http://purl.obolibrary.org/obo/CL_4023011` -#### Removed -- [lamp5 GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023011) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) - -- [lamp5 GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023011) SubClassOf [cerebral cortex GABAergic interneuron](http://purl.obolibrary.org/obo/CL_0010011) - -#### Added -- [lamp5 GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023011) SubClassOf [caudal ganglionic eminence derived interneuron](http://purl.obolibrary.org/obo/CL_4023064) - - -### large intestine goblet cell `http://purl.obolibrary.org/obo/CL_1000320` -#### Removed -- [large intestine goblet cell](http://purl.obolibrary.org/obo/CL_1000320) SubClassOf [glandular cell of the large intestine](http://purl.obolibrary.org/obo/CL_0002658) - -#### Added -- [large intestine goblet cell](http://purl.obolibrary.org/obo/CL_1000320) SubClassOf [epithelial cell of large intestine](http://purl.obolibrary.org/obo/CL_0002253) - - -### lateral line ganglion neuron `http://purl.obolibrary.org/obo/CL_2000031` -#### Removed -- [lateral line ganglion neuron](http://purl.obolibrary.org/obo/CL_2000031) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) - -#### Added -- [lateral line ganglion neuron](http://purl.obolibrary.org/obo/CL_2000031) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) - - -### lens fiber cell `http://purl.obolibrary.org/obo/CL_0011004` -#### Removed -- [lens fiber cell](http://purl.obolibrary.org/obo/CL_0011004) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009401"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [lens fiber cell](http://purl.obolibrary.org/obo/CL_0011004) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009401"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### leptomeningeal cell `http://purl.obolibrary.org/obo/CL_0000708` -#### Removed -- [leptomeningeal cell](http://purl.obolibrary.org/obo/CL_0000708) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009305"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [leptomeningeal cell](http://purl.obolibrary.org/obo/CL_0000708) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009305"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### leucoblast `http://purl.obolibrary.org/obo/CL_0005003` -#### Removed -- [leucoblast](http://purl.obolibrary.org/obo/CL_0005003) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005329"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [leucoblast](http://purl.obolibrary.org/obo/CL_0005003) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005329"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### leucophore `http://purl.obolibrary.org/obo/CL_0000571` -#### Removed -- [leucophore](http://purl.obolibrary.org/obo/CL_0000571) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009261"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [leucophore](http://purl.obolibrary.org/obo/CL_0000571) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009261"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### leukocyte `http://purl.obolibrary.org/obo/CL_0000738` -#### Removed -- [leukocyte](http://purl.obolibrary.org/obo/CL_0000738) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009309"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [leukocyte](http://purl.obolibrary.org/obo/CL_0000738) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009309"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### ligament cell `http://purl.obolibrary.org/obo/CL_0000384` -#### Removed -- [ligament cell](http://purl.obolibrary.org/obo/CL_0000384) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009188"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [ligament cell](http://purl.obolibrary.org/obo/CL_0000384) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009188"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### limb basal cell of epidermis `http://purl.obolibrary.org/obo/CL_2000033` -#### Removed -- [limb basal cell of epidermis](http://purl.obolibrary.org/obo/CL_2000033) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) - -#### Added -- [limb basal cell of epidermis](http://purl.obolibrary.org/obo/CL_2000033) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) - - -### lining cell `http://purl.obolibrary.org/obo/CL_0000213` -#### Removed -- [lining cell](http://purl.obolibrary.org/obo/CL_0000213) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009130"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [lining cell](http://purl.obolibrary.org/obo/CL_0000213) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009130"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### liver dendritic cell `http://purl.obolibrary.org/obo/CL_2000055` -#### Removed -- [liver dendritic cell](http://purl.obolibrary.org/obo/CL_2000055) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) - -#### Added -- [liver dendritic cell](http://purl.obolibrary.org/obo/CL_2000055) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) - - -### luminal endometrial ciliated epithelial cell `http://purl.obolibrary.org/obo/CL_4030041` -#### Removed -- [luminal endometrial ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_4030041) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A ciliated cell of the endometrial luminal epithelium."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.1038/s41591-020-1040-z"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [luminal endometrial ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_4030041) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A ciliated cell of the endometrial luminal epithelium. This cell is characterized by the presence of motile cilia on its apical surface."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.1038/s41591-020-1040-z"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### luminal hormone-sensing cell of mammary gland `http://purl.obolibrary.org/obo/CL_4033058` -#### Removed -- [luminal hormone-sensing cell of mammary gland](http://purl.obolibrary.org/obo/CL_4033058) SubClassOf [obsolete paracrine cell](http://purl.obolibrary.org/obo/CL_0000512) - -- [luminal hormone-sensing cell of mammary gland](http://purl.obolibrary.org/obo/CL_4033058) SubClassOf [exocrine cell](http://purl.obolibrary.org/obo/CL_0000152) - - - -### lung endothelial cell `http://purl.obolibrary.org/obo/CL_1001567` -#### Removed -- [lung endothelial cell](http://purl.obolibrary.org/obo/CL_1001567) SubClassOf [epithelial cell of lung](http://purl.obolibrary.org/obo/CL_0000082) - - - -### lung goblet cell `http://purl.obolibrary.org/obo/CL_1000143` -#### Removed -- [lung goblet cell](http://purl.obolibrary.org/obo/CL_1000143) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any goblet cell that is part of some lung."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [lung goblet cell](http://purl.obolibrary.org/obo/CL_1000143) EquivalentTo [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0002048](http://purl.obolibrary.org/obo/UBERON_0002048)) - -- [lung goblet cell](http://purl.obolibrary.org/obo/CL_1000143) SubClassOf [lung secretory cell](http://purl.obolibrary.org/obo/CL_1000272) - -#### Added -- [lung goblet cell](http://purl.obolibrary.org/obo/CL_1000143) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any goblet cell that is part of some lung epithelium."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [lung goblet cell](http://purl.obolibrary.org/obo/CL_1000143) EquivalentTo [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000115](http://purl.obolibrary.org/obo/UBERON_0000115)) - - -### lung microvascular endothelial cell `http://purl.obolibrary.org/obo/CL_2000016` -#### Removed -- [lung microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000016) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) - -#### Added -- [lung microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000016) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) - - -### lung neuroendocrine cell `http://purl.obolibrary.org/obo/CL_1000223` -#### Removed -- [lung neuroendocrine cell](http://purl.obolibrary.org/obo/CL_1000223) SubClassOf [epithelial cell of lung](http://purl.obolibrary.org/obo/CL_0000082) - - - -### luteinizing hormone secreting cell `http://purl.obolibrary.org/obo/CL_0000438` -#### Removed -- [luteinizing hormone secreting cell](http://purl.obolibrary.org/obo/CL_0000438) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009203"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [luteinizing hormone secreting cell](http://purl.obolibrary.org/obo/CL_0000438) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009203"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### lymph gland hemocyte `http://purl.obolibrary.org/obo/CL_0000735` -#### Removed -- [lymph gland hemocyte](http://purl.obolibrary.org/obo/CL_0000735) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005917"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [lymph gland hemocyte](http://purl.obolibrary.org/obo/CL_0000735) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005917"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### lymph node lymphatic vessel endothelial cell `http://purl.obolibrary.org/obo/CL_0009115` -#### Removed -- [lymph node lymphatic vessel endothelial cell](http://purl.obolibrary.org/obo/CL_0009115) SubClassOf [endothelial cell](http://purl.obolibrary.org/obo/CL_0000115) - -- [lymph node lymphatic vessel endothelial cell](http://purl.obolibrary.org/obo/CL_0009115) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001473](http://purl.obolibrary.org/obo/UBERON_0001473) - -#### Added -- [lymph node lymphatic vessel endothelial cell](http://purl.obolibrary.org/obo/CL_0009115) SubClassOf [endothelial cell of lymphatic vessel](http://purl.obolibrary.org/obo/CL_0002138) - - -### lymphangioblast `http://purl.obolibrary.org/obo/CL_0005020` -#### Removed -- [lymphangioblast](http://purl.obolibrary.org/obo/CL_0005020) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009393"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [lymphangioblast](http://purl.obolibrary.org/obo/CL_0005020) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009393"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### lymphatic endothelial cell of medulla ceiling `http://purl.obolibrary.org/obo/CL_0009110` -#### Removed -- [lymphatic endothelial cell of medulla ceiling](http://purl.obolibrary.org/obo/CL_0009110) SubClassOf [endothelial cell of lymphatic vessel](http://purl.obolibrary.org/obo/CL_0002138) - - - -### lymphatic endothelial cell of subcapsular sinus ceiling `http://purl.obolibrary.org/obo/CL_0009107` -#### Removed -- [lymphatic endothelial cell of subcapsular sinus ceiling](http://purl.obolibrary.org/obo/CL_0009107) SubClassOf [endothelial cell of lymphatic vessel](http://purl.obolibrary.org/obo/CL_0002138) - - - -### lymphatic endothelial cell of subcapsular sinus floor `http://purl.obolibrary.org/obo/CL_0009108` -#### Removed -- [lymphatic endothelial cell of subcapsular sinus floor](http://purl.obolibrary.org/obo/CL_0009108) SubClassOf [endothelial cell of lymphatic vessel](http://purl.obolibrary.org/obo/CL_0002138) - - - -### lymphatic endothelial cell of trabecula `http://purl.obolibrary.org/obo/CL_0009109` -#### Removed -- [lymphatic endothelial cell of trabecula](http://purl.obolibrary.org/obo/CL_0009109) SubClassOf [endothelial cell of lymphatic vessel](http://purl.obolibrary.org/obo/CL_0002138) - - - -### lymphocyte `http://purl.obolibrary.org/obo/CL_0000542` -#### Removed -- [lymphocyte](http://purl.obolibrary.org/obo/CL_0000542) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009250"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [lymphocyte](http://purl.obolibrary.org/obo/CL_0000542) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009250"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### lymphoid lineage restricted progenitor cell `http://purl.obolibrary.org/obo/CL_0000838` -#### Removed -- [lymphoid lineage restricted progenitor cell](http://purl.obolibrary.org/obo/CL_0000838) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009355"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [lymphoid lineage restricted progenitor cell](http://purl.obolibrary.org/obo/CL_0000838) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009355"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### macroglial cell `http://purl.obolibrary.org/obo/CL_0000126` -#### Removed -- [macroglial cell](http://purl.obolibrary.org/obo/CL_0000126) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009074"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [macroglial cell](http://purl.obolibrary.org/obo/CL_0000126) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009074"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### macrophage `http://purl.obolibrary.org/obo/CL_0000235` -#### Removed -- [macrophage](http://purl.obolibrary.org/obo/CL_0000235) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009141"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [macrophage](http://purl.obolibrary.org/obo/CL_0000235) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009141"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### male germ line stem cell `http://purl.obolibrary.org/obo/CL_0000016` -#### Removed -- [male germ line stem cell](http://purl.obolibrary.org/obo/CL_0000016) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004929"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [male germ line stem cell](http://purl.obolibrary.org/obo/CL_0000016) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004929"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### mammary microvascular endothelial cell `http://purl.obolibrary.org/obo/CL_2000071` -#### Removed -- [mammary microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000071) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) - -#### Added -- [mammary microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000071) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) - - -### mapping_justification `https://w3id.org/sssom/mapping_justification` - -#### Added -- AnnotationProperty: [mapping_justification](https://w3id.org/sssom/mapping_justification) - - -### mapping_justification `http://purl.obolibrary.org/obo/mapping_justification` -#### Removed -- AnnotationProperty: [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) - - - -### mature B cell `http://purl.obolibrary.org/obo/CL_0000785` -#### Removed -- [mature B cell](http://purl.obolibrary.org/obo/CL_0000785) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009331"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [mature B cell](http://purl.obolibrary.org/obo/CL_0000785) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009331"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### mature gamma-delta T cell `http://purl.obolibrary.org/obo/CL_0000800` -#### Removed -- [mature gamma-delta T cell](http://purl.obolibrary.org/obo/CL_0000800) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009338"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [mature gamma-delta T cell](http://purl.obolibrary.org/obo/CL_0000800) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009338"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### mature natural killer cell `http://purl.obolibrary.org/obo/CL_0000824` -#### Removed -- [mature natural killer cell](http://purl.obolibrary.org/obo/CL_0000824) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009347"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [mature natural killer cell](http://purl.obolibrary.org/obo/CL_0000824) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009347"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### mature neutrophil `http://purl.obolibrary.org/obo/CL_0000096` -#### Removed -- [mature neutrophil](http://purl.obolibrary.org/obo/CL_0000096) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009049"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [mature neutrophil](http://purl.obolibrary.org/obo/CL_0000096) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009049"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### mechanoreceptor cell `http://purl.obolibrary.org/obo/CL_0000199` -#### Removed -- [mechanoreceptor cell](http://purl.obolibrary.org/obo/CL_0000199) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009120"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [mechanoreceptor cell](http://purl.obolibrary.org/obo/CL_0000199) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009120"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### megakaryocyte-erythroid progenitor cell `http://purl.obolibrary.org/obo/CL_0000050` -#### Removed -- [megakaryocyte-erythroid progenitor cell](http://purl.obolibrary.org/obo/CL_0000050) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009022"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [megakaryocyte-erythroid progenitor cell](http://purl.obolibrary.org/obo/CL_0000050) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009022"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### melanoblast `http://purl.obolibrary.org/obo/CL_0000541` -#### Removed -- [melanoblast](http://purl.obolibrary.org/obo/CL_0000541) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009249"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [melanoblast](http://purl.obolibrary.org/obo/CL_0000541) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009249"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### melanocyte `http://purl.obolibrary.org/obo/CL_0000148` -#### Removed -- [melanocyte](http://purl.obolibrary.org/obo/CL_0000148) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009091"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [melanocyte](http://purl.obolibrary.org/obo/CL_0000148) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009091"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### melanocyte of skin of face `http://purl.obolibrary.org/obo/CL_2000081` -#### Removed -- [melanocyte of skin of face](http://purl.obolibrary.org/obo/CL_2000081) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) - -#### Added -- [melanocyte of skin of face](http://purl.obolibrary.org/obo/CL_2000081) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) - - -### melanocyte stimulating hormone secreting cell `http://purl.obolibrary.org/obo/CL_0000440` -#### Removed -- [melanocyte stimulating hormone secreting cell](http://purl.obolibrary.org/obo/CL_0000440) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009205"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [melanocyte stimulating hormone secreting cell](http://purl.obolibrary.org/obo/CL_0000440) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009205"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### memory B cell `http://purl.obolibrary.org/obo/CL_0000787` -#### Removed -- [memory B cell](http://purl.obolibrary.org/obo/CL_0000787) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009333"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [memory B cell](http://purl.obolibrary.org/obo/CL_0000787) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009333"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### memory T cell `http://purl.obolibrary.org/obo/CL_0000813` -#### Removed -- [memory T cell](http://purl.obolibrary.org/obo/CL_0000813) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009342"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [memory T cell](http://purl.obolibrary.org/obo/CL_0000813) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009342"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### mesangial cell `http://purl.obolibrary.org/obo/CL_0000650` -#### Removed -- [mesangial cell](http://purl.obolibrary.org/obo/CL_0000650) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009283"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [mesangial cell](http://purl.obolibrary.org/obo/CL_0000650) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009283"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### mesenchymal lymphangioblast `http://purl.obolibrary.org/obo/CL_0005021` -#### Removed -- [mesenchymal lymphangioblast](http://purl.obolibrary.org/obo/CL_0005021) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009394"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [mesenchymal lymphangioblast](http://purl.obolibrary.org/obo/CL_0005021) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009394"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### mesenchymal stem cell `http://purl.obolibrary.org/obo/CL_0000134` -#### Removed -- [mesenchymal stem cell](http://purl.obolibrary.org/obo/CL_0000134) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009081"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [mesenchymal stem cell](http://purl.obolibrary.org/obo/CL_0000134) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009081"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### mesenchymal stem cell of abdominal adipose tissue `http://purl.obolibrary.org/obo/CL_2000080` -#### Removed -- [mesenchymal stem cell of abdominal adipose tissue](http://purl.obolibrary.org/obo/CL_2000080) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) - -#### Added -- [mesenchymal stem cell of abdominal adipose tissue](http://purl.obolibrary.org/obo/CL_2000080) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) - - -### mesenchymal stem cell of femoral bone marrow `http://purl.obolibrary.org/obo/CL_2000079` -#### Removed -- [mesenchymal stem cell of femoral bone marrow](http://purl.obolibrary.org/obo/CL_2000079) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) - -#### Added -- [mesenchymal stem cell of femoral bone marrow](http://purl.obolibrary.org/obo/CL_2000079) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) - - -### mesenchyme condensation cell `http://purl.obolibrary.org/obo/CL_0000335` -#### Removed -- [mesenchyme condensation cell](http://purl.obolibrary.org/obo/CL_0000335) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009166"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [mesenchyme condensation cell](http://purl.obolibrary.org/obo/CL_0000335) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009166"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### meso-epithelial cell `http://purl.obolibrary.org/obo/CL_0002078` -#### Removed -- [meso-epithelial cell](http://purl.obolibrary.org/obo/CL_0002078) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009388"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [meso-epithelial cell](http://purl.obolibrary.org/obo/CL_0002078) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009388"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### mesodermal cell `http://purl.obolibrary.org/obo/CL_0000222` -#### Removed -- [mesodermal cell](http://purl.obolibrary.org/obo/CL_0000222) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009138"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [mesodermal cell](http://purl.obolibrary.org/obo/CL_0000222) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009138"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### mesothelial cell `http://purl.obolibrary.org/obo/CL_0000077` -#### Removed -- [mesothelial cell](http://purl.obolibrary.org/obo/CL_0000077) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009040"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [mesothelial cell](http://purl.obolibrary.org/obo/CL_0000077) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009040"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### mesothelial cell of visceral pleura `http://purl.obolibrary.org/obo/CL_1000493` -#### Removed -- [mesothelial cell of visceral pleura](http://purl.obolibrary.org/obo/CL_1000493) SubClassOf [epithelial cell of lung](http://purl.obolibrary.org/obo/CL_0000082) - - - -### microglial cell `http://purl.obolibrary.org/obo/CL_0000129` -#### Removed -- [microglial cell](http://purl.obolibrary.org/obo/CL_0000129) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009077"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [microglial cell](http://purl.obolibrary.org/obo/CL_0000129) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009077"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### micropylar cell `http://purl.obolibrary.org/obo/CL_0007022` -#### Removed -- [micropylar cell](http://purl.obolibrary.org/obo/CL_0007022) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005239"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [micropylar cell](http://purl.obolibrary.org/obo/CL_0007022) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005239"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### microvascular endothelial cell `http://purl.obolibrary.org/obo/CL_2000008` -#### Removed -- [microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000008) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) - -#### Added -- [microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000008) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) - - -### microvillous olfactory receptor neuron `http://purl.obolibrary.org/obo/CL_0000848` -#### Removed -- [microvillous olfactory receptor neuron](http://purl.obolibrary.org/obo/CL_0000848) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009359"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [microvillous olfactory receptor neuron](http://purl.obolibrary.org/obo/CL_0000848) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009359"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### midbrain dopaminergic neuron `http://purl.obolibrary.org/obo/CL_2000097` -#### Removed -- [midbrain dopaminergic neuron](http://purl.obolibrary.org/obo/CL_2000097) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) - -#### Added -- [midbrain dopaminergic neuron](http://purl.obolibrary.org/obo/CL_2000097) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) - - -### migratory cardiac neural crest cell `http://purl.obolibrary.org/obo/CL_2000073` -#### Removed -- [migratory cardiac neural crest cell](http://purl.obolibrary.org/obo/CL_2000073) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) - -#### Added -- [migratory cardiac neural crest cell](http://purl.obolibrary.org/obo/CL_2000073) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) - - -### migratory cranial neural crest cell `http://purl.obolibrary.org/obo/CL_0000008` -#### Removed -- [migratory cranial neural crest cell](http://purl.obolibrary.org/obo/CL_0000008) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0007091"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [migratory cranial neural crest cell](http://purl.obolibrary.org/obo/CL_0000008) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0007091"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### migratory neural crest cell `http://purl.obolibrary.org/obo/CL_0000333` -#### Removed -- [migratory neural crest cell](http://purl.obolibrary.org/obo/CL_0000333) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0007086"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [migratory neural crest cell](http://purl.obolibrary.org/obo/CL_0000333) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0007086"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### migratory trunk neural crest cell `http://purl.obolibrary.org/obo/CL_0000011` -#### Removed -- [migratory trunk neural crest cell](http://purl.obolibrary.org/obo/CL_0000011) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0007095"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [migratory trunk neural crest cell](http://purl.obolibrary.org/obo/CL_0000011) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0007095"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### monoblast `http://purl.obolibrary.org/obo/CL_0000040` -#### Removed -- [monoblast](http://purl.obolibrary.org/obo/CL_0000040) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009017"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [monoblast](http://purl.obolibrary.org/obo/CL_0000040) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009017"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### monocyte `http://purl.obolibrary.org/obo/CL_0000576` -#### Removed -- [monocyte](http://purl.obolibrary.org/obo/CL_0000576) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009265"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [monocyte](http://purl.obolibrary.org/obo/CL_0000576) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009265"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### mononuclear cell `http://purl.obolibrary.org/obo/CL_0000842` -#### Removed -- [mononuclear cell](http://purl.obolibrary.org/obo/CL_0000842) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009357"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [mononuclear cell](http://purl.obolibrary.org/obo/CL_0000842) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009357"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### mononuclear cell of umbilical cord `http://purl.obolibrary.org/obo/CL_2000085` -#### Removed -- [mononuclear cell of umbilical cord](http://purl.obolibrary.org/obo/CL_2000085) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) - -#### Added -- [mononuclear cell of umbilical cord](http://purl.obolibrary.org/obo/CL_2000085) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) - - -### mononuclear odontoclast `http://purl.obolibrary.org/obo/CL_0000781` -#### Removed -- [mononuclear odontoclast](http://purl.obolibrary.org/obo/CL_0000781) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009330"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [mononuclear odontoclast](http://purl.obolibrary.org/obo/CL_0000781) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009330"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### mononuclear osteoclast `http://purl.obolibrary.org/obo/CL_0000778` -#### Removed -- [mononuclear osteoclast](http://purl.obolibrary.org/obo/CL_0000778) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009329"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [mononuclear osteoclast](http://purl.obolibrary.org/obo/CL_0000778) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009329"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### mononuclear phagocyte `http://purl.obolibrary.org/obo/CL_0000113` -#### Removed -- [mononuclear phagocyte](http://purl.obolibrary.org/obo/CL_0000113) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009064"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [mononuclear phagocyte](http://purl.obolibrary.org/obo/CL_0000113) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009064"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### motile cell `http://purl.obolibrary.org/obo/CL_0000219` -#### Removed -- [motile cell](http://purl.obolibrary.org/obo/CL_0000219) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009136"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [motile cell](http://purl.obolibrary.org/obo/CL_0000219) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009136"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### motor neuron `http://purl.obolibrary.org/obo/CL_0000100` -#### Removed -- [motor neuron](http://purl.obolibrary.org/obo/CL_0000100) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009052"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [motor neuron](http://purl.obolibrary.org/obo/CL_0000100) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005123"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [motor neuron](http://purl.obolibrary.org/obo/CL_0000100) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009052"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [motor neuron](http://purl.obolibrary.org/obo/CL_0000100) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005123"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### mucous cell of stomach `http://purl.obolibrary.org/obo/CL_0002180` -#### Removed -- [mucous cell of stomach](http://purl.obolibrary.org/obo/CL_0002180) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A mucous cell in the epithelium of the stomach."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [mucous cell of stomach](http://purl.obolibrary.org/obo/CL_0002180) EquivalentTo [epithelial cell of stomach](http://purl.obolibrary.org/obo/CL_0002178) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001199](http://purl.obolibrary.org/obo/UBERON_0001199)) - -- [mucous cell of stomach](http://purl.obolibrary.org/obo/CL_0002180) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001199](http://purl.obolibrary.org/obo/UBERON_0001199) - -#### Added -- [mucous cell of stomach](http://purl.obolibrary.org/obo/CL_0002180) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell of the stomach. This cell produces mucous."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [mucous cell of stomach](http://purl.obolibrary.org/obo/CL_0002180) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000945](http://purl.obolibrary.org/obo/UBERON_0000945)) and ([RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0070254](http://purl.obolibrary.org/obo/GO_0070254)) - -- [mucous cell of stomach](http://purl.obolibrary.org/obo/CL_0002180) SubClassOf [mucus secreting cell](http://purl.obolibrary.org/obo/CL_0000319) - - -### mucous neck cell of gastric gland `http://purl.obolibrary.org/obo/CL_0002181` -#### Removed -- [mucous neck cell of gastric gland](http://purl.obolibrary.org/obo/CL_0002181) SubClassOf [mucous cell of stomach](http://purl.obolibrary.org/obo/CL_0002180) - - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [mucous neck cell of gastric gland](http://purl.obolibrary.org/obo/CL_0002181) SubClassOf [mucous neck cell](http://purl.obolibrary.org/obo/CL_0000651) - - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [mucous neck cell of gastric gland](http://purl.obolibrary.org/obo/CL_0002181) SubClassOf [mucous neck cell](http://purl.obolibrary.org/obo/CL_0000651) - -- [mucous neck cell of gastric gland](http://purl.obolibrary.org/obo/CL_0002181) SubClassOf [mucous cell of stomach](http://purl.obolibrary.org/obo/CL_0002180) - - -### mucus secreting cell `http://purl.obolibrary.org/obo/CL_0000319` -#### Removed -- [mucus secreting cell](http://purl.obolibrary.org/obo/CL_0000319) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009159"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [mucus secreting cell](http://purl.obolibrary.org/obo/CL_0000319) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009159"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### multi fate stem cell `http://purl.obolibrary.org/obo/CL_0000048` -#### Removed -- [multi fate stem cell](http://purl.obolibrary.org/obo/CL_0000048) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009020"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [multi fate stem cell](http://purl.obolibrary.org/obo/CL_0000048) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009020"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### multi-ciliated epithelial cell `http://purl.obolibrary.org/obo/CL_0005012` -#### Removed -- [multi-ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005012) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005242"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [multi-ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005012) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005242"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### multi-potent skeletal muscle stem cell `http://purl.obolibrary.org/obo/CL_0000355` -#### Removed -- [multi-potent skeletal muscle stem cell](http://purl.obolibrary.org/obo/CL_0000355) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009179"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [multi-potent skeletal muscle stem cell](http://purl.obolibrary.org/obo/CL_0000355) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009179"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### multipolar neuron `http://purl.obolibrary.org/obo/CL_0000104` -#### Removed -- [multipolar neuron](http://purl.obolibrary.org/obo/CL_0000104) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009056"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [multipolar neuron](http://purl.obolibrary.org/obo/CL_0000104) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009056"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### mural cell `http://purl.obolibrary.org/obo/CL_0008034` -#### Removed -- [mural cell](http://purl.obolibrary.org/obo/CL_0008034) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005944"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [mural cell](http://purl.obolibrary.org/obo/CL_0008034) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005944"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### mural granulosa cell `http://purl.obolibrary.org/obo/CL_4033067` - -#### Added -- [mural granulosa cell](http://purl.obolibrary.org/obo/CL_4033067) [label](http://www.w3.org/2000/01/rdf-schema#label) "mural granulosa cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [mural granulosa cell](http://purl.obolibrary.org/obo/CL_4033067) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A follicular cell of ovary that differentiates from a granulosa cell during the secondary follicle stage. Mural granulosa cells line the inner surface of the follicle wall, surrounding the fluid-filled antral cavity. These cells produce oestrogen during the follicular phase in response to follicle-stimulating hormone (FSH), and progesterone after ovulation in response to luteinizing hormone (LH)."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33970370"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27815559"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34198768"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [mural granulosa cell](http://purl.obolibrary.org/obo/CL_4033067) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4033067"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [mural granulosa cell](http://purl.obolibrary.org/obo/CL_4033067) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "mural GC"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34198768"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [mural granulosa cell](http://purl.obolibrary.org/obo/CL_4033067) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "EFO:0005289"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [mural granulosa cell](http://purl.obolibrary.org/obo/CL_4033067) [date](http://purl.org/dc/terms/date) "2024-06-07T12:15:13Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - -- [mural granulosa cell](http://purl.obolibrary.org/obo/CL_4033067) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) - -- [mural granulosa cell](http://purl.obolibrary.org/obo/CL_4033067) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "MGC"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.1530/REP-16-0500"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [mural granulosa cell](http://purl.obolibrary.org/obo/CL_4033067) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-7655-4833](https://orcid.org/0000-0001-7655-4833) - -- Class: [mural granulosa cell](http://purl.obolibrary.org/obo/CL_4033067) - -- [mural granulosa cell](http://purl.obolibrary.org/obo/CL_4033067) SubClassOf [follicular cell of ovary](http://purl.obolibrary.org/obo/CL_0002174) - -- [mural granulosa cell](http://purl.obolibrary.org/obo/CL_4033067) SubClassOf [RO_0002207](http://purl.obolibrary.org/obo/RO_0002207) some [granulosa cell](http://purl.obolibrary.org/obo/CL_0000501) - -- [mural granulosa cell](http://purl.obolibrary.org/obo/CL_4033067) SubClassOf [ovarian surface epithelial cell](http://purl.obolibrary.org/obo/CL_2000064) - - -### muscle cell `http://purl.obolibrary.org/obo/CL_0000187` -#### Removed -- [muscle cell](http://purl.obolibrary.org/obo/CL_0000187) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005074"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [muscle cell](http://purl.obolibrary.org/obo/CL_0000187) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009114"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [muscle cell](http://purl.obolibrary.org/obo/CL_0000187) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005074"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [muscle cell](http://purl.obolibrary.org/obo/CL_0000187) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009114"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### muscle precursor cell `http://purl.obolibrary.org/obo/CL_0000680` -#### Removed -- [muscle precursor cell](http://purl.obolibrary.org/obo/CL_0000680) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009291"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [muscle precursor cell](http://purl.obolibrary.org/obo/CL_0000680) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009291"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### myelinating Schwann cell `http://purl.obolibrary.org/obo/CL_0000218` -#### Removed -- [myelinating Schwann cell](http://purl.obolibrary.org/obo/CL_0000218) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009135"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [myelinating Schwann cell](http://purl.obolibrary.org/obo/CL_0000218) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009135"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### myeloblast `http://purl.obolibrary.org/obo/CL_0000835` -#### Removed -- [myeloblast](http://purl.obolibrary.org/obo/CL_0000835) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009353"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [myeloblast](http://purl.obolibrary.org/obo/CL_0000835) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009353"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### myeloid cell `http://purl.obolibrary.org/obo/CL_0000763` -#### Removed -- [myeloid cell](http://purl.obolibrary.org/obo/CL_0000763) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009324"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [myeloid cell](http://purl.obolibrary.org/obo/CL_0000763) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009324"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### myeloid leukocyte `http://purl.obolibrary.org/obo/CL_0000766` -#### Removed -- [myeloid leukocyte](http://purl.obolibrary.org/obo/CL_0000766) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009326"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [myeloid leukocyte](http://purl.obolibrary.org/obo/CL_0000766) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009326"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### myeloid lineage restricted progenitor cell `http://purl.obolibrary.org/obo/CL_0000839` -#### Removed -- [myeloid lineage restricted progenitor cell](http://purl.obolibrary.org/obo/CL_0000839) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009356"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [myeloid lineage restricted progenitor cell](http://purl.obolibrary.org/obo/CL_0000839) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009356"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### myoblast `http://purl.obolibrary.org/obo/CL_0000056` -#### Removed -- [myoblast](http://purl.obolibrary.org/obo/CL_0000056) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005083"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [myoblast](http://purl.obolibrary.org/obo/CL_0000056) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009025"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [myoblast](http://purl.obolibrary.org/obo/CL_0000056) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005083"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [myoblast](http://purl.obolibrary.org/obo/CL_0000056) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009025"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### myoepithelial cell `http://purl.obolibrary.org/obo/CL_0000185` -#### Removed -- [myoepithelial cell](http://purl.obolibrary.org/obo/CL_0000185) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009113"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [myoepithelial cell](http://purl.obolibrary.org/obo/CL_0000185) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009113"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### myotube `http://purl.obolibrary.org/obo/CL_0002372` -#### Removed -- [myotube](http://purl.obolibrary.org/obo/CL_0002372) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005812"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [myotube](http://purl.obolibrary.org/obo/CL_0002372) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005812"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### naive B cell `http://purl.obolibrary.org/obo/CL_0000788` -#### Removed -- [naive B cell](http://purl.obolibrary.org/obo/CL_0000788) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009334"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [naive B cell](http://purl.obolibrary.org/obo/CL_0000788) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009334"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### nasal cavity respiratory epithelium epithelial cell of viscerocranial mucosa `http://purl.obolibrary.org/obo/CL_2000094` -#### Removed -- [nasal cavity respiratory epithelium epithelial cell of viscerocranial mucosa](http://purl.obolibrary.org/obo/CL_2000094) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) - -#### Added -- [nasal cavity respiratory epithelium epithelial cell of viscerocranial mucosa](http://purl.obolibrary.org/obo/CL_2000094) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) - -- [nasal cavity respiratory epithelium epithelial cell of viscerocranial mucosa](http://purl.obolibrary.org/obo/CL_2000094) SubClassOf [epithelial cell of upper respiratory tract](http://purl.obolibrary.org/obo/CL_0002631) - - -### nasal mucosa goblet cell `http://purl.obolibrary.org/obo/CL_0002480` - -#### Added -- [nasal mucosa goblet cell](http://purl.obolibrary.org/obo/CL_0002480) SubClassOf [epithelial cell of upper respiratory tract](http://purl.obolibrary.org/obo/CL_0002631) - - -### nasal serous secreting cell `http://purl.obolibrary.org/obo/CL_4042016` - -#### Added -- [nasal serous secreting cell](http://purl.obolibrary.org/obo/CL_4042016) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A serous secreting cell that is part of a submucosal gland in the nasal cavity respiratory epithelium."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37291214"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [nasal serous secreting cell](http://purl.obolibrary.org/obo/CL_4042016) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "nasal mucous secretory cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:11005715"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [nasal serous secreting cell](http://purl.obolibrary.org/obo/CL_4042016) [date](http://purl.org/dc/terms/date) "2024-07-12T10:58:06Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - -- [nasal serous secreting cell](http://purl.obolibrary.org/obo/CL_4042016) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/e/9f222629-9e39-47d0-b83f-e08d610c7479.cxg/"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [nasal serous secreting cell](http://purl.obolibrary.org/obo/CL_4042016) [label](http://www.w3.org/2000/01/rdf-schema#label) "nasal serous secreting cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [nasal serous secreting cell](http://purl.obolibrary.org/obo/CL_4042016) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) - -- [nasal serous secreting cell](http://purl.obolibrary.org/obo/CL_4042016) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042016"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- Class: [nasal serous secreting cell](http://purl.obolibrary.org/obo/CL_4042016) - -- [nasal serous secreting cell](http://purl.obolibrary.org/obo/CL_4042016) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0011148](http://purl.obolibrary.org/obo/UBERON_0011148) - -- [nasal serous secreting cell](http://purl.obolibrary.org/obo/CL_4042016) SubClassOf [serous secreting cell](http://purl.obolibrary.org/obo/CL_0000313) - -- [nasal serous secreting cell](http://purl.obolibrary.org/obo/CL_4042016) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0005385](http://purl.obolibrary.org/obo/UBERON_0005385) - -- [nasal serous secreting cell](http://purl.obolibrary.org/obo/CL_4042016) SubClassOf [exocrine cell](http://purl.obolibrary.org/obo/CL_0000152) - - -### natural killer cell `http://purl.obolibrary.org/obo/CL_0000623` -#### Removed -- [natural killer cell](http://purl.obolibrary.org/obo/CL_0000623) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009278"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [natural killer cell](http://purl.obolibrary.org/obo/CL_0000623) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009278"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### neocortex basket cell `http://purl.obolibrary.org/obo/CL_2000086` -#### Removed -- [neocortex basket cell](http://purl.obolibrary.org/obo/CL_2000086) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) - -#### Added -- [neocortex basket cell](http://purl.obolibrary.org/obo/CL_2000086) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) - - -### nephrogenic mesenchyme stem cell `http://purl.obolibrary.org/obo/CL_0000383` -#### Removed -- [nephrogenic mesenchyme stem cell](http://purl.obolibrary.org/obo/CL_0000383) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009187"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [nephrogenic mesenchyme stem cell](http://purl.obolibrary.org/obo/CL_0000383) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009187"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### neural crest derived neuron `http://purl.obolibrary.org/obo/CL_0000029` -#### Removed -- [neural crest derived neuron](http://purl.obolibrary.org/obo/CL_0000029) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009009"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [neural crest derived neuron](http://purl.obolibrary.org/obo/CL_0000029) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009009"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### neural stem cell `http://purl.obolibrary.org/obo/CL_0000047` -#### Removed -- [neural stem cell](http://purl.obolibrary.org/obo/CL_0000047) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009019"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [neural stem cell](http://purl.obolibrary.org/obo/CL_0000047) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009019"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### neurectodermal cell `http://purl.obolibrary.org/obo/CL_0000133` -#### Removed -- [neurectodermal cell](http://purl.obolibrary.org/obo/CL_0000133) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009080"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [neurectodermal cell](http://purl.obolibrary.org/obo/CL_0000133) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009080"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### neuroblast (sensu Nematoda and Protostomia) `http://purl.obolibrary.org/obo/CL_0000338` -#### Removed -- [neuroblast (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000338) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005146"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [neuroblast (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000338) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005146"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### neuroblast (sensu Vertebrata) `http://purl.obolibrary.org/obo/CL_0000031` -#### Removed -- [neuroblast (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000031) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009011"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [neuroblast (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000031) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009011"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### neuroendocrine cell `http://purl.obolibrary.org/obo/CL_0000165` -#### Removed -- [neuroendocrine cell](http://purl.obolibrary.org/obo/CL_0000165) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009098"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [neuroendocrine cell](http://purl.obolibrary.org/obo/CL_0000165) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005130"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [neuroendocrine cell](http://purl.obolibrary.org/obo/CL_0000165) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005130"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [neuroendocrine cell](http://purl.obolibrary.org/obo/CL_0000165) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009098"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### neuroendocrine cell of epithelium of lobar bronchus `http://purl.obolibrary.org/obo/CL_4033010` - -#### Added -- [neuroendocrine cell of epithelium of lobar bronchus](http://purl.obolibrary.org/obo/CL_4033010) SubClassOf [epithelial cell of lung](http://purl.obolibrary.org/obo/CL_0000082) - - -### neurogliaform cell `http://purl.obolibrary.org/obo/CL_0000693` -#### Removed -- [neurogliaform cell](http://purl.obolibrary.org/obo/CL_0000693) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009299"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [neurogliaform cell](http://purl.obolibrary.org/obo/CL_0000693) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009299"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### neuroglioblast (sensu Nematoda and Protostomia) `http://purl.obolibrary.org/obo/CL_0000468` -#### Removed -- [neuroglioblast (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000468) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005147"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [neuroglioblast (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000468) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005147"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### neuromast hair cell `http://purl.obolibrary.org/obo/CL_0000856` -#### Removed -- [neuromast hair cell](http://purl.obolibrary.org/obo/CL_0000856) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009367"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [neuromast hair cell](http://purl.obolibrary.org/obo/CL_0000856) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009367"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### neuromast mantle cell `http://purl.obolibrary.org/obo/CL_0000851` -#### Removed -- [neuromast mantle cell](http://purl.obolibrary.org/obo/CL_0000851) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009362"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [neuromast mantle cell](http://purl.obolibrary.org/obo/CL_0000851) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009362"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### neuromast supporting cell `http://purl.obolibrary.org/obo/CL_0000852` -#### Removed -- [neuromast supporting cell](http://purl.obolibrary.org/obo/CL_0000852) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009363"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [neuromast supporting cell](http://purl.obolibrary.org/obo/CL_0000852) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009363"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### neuron `http://purl.obolibrary.org/obo/CL_0000540` -#### Removed -- [neuron](http://purl.obolibrary.org/obo/CL_0000540) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009248"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [neuron](http://purl.obolibrary.org/obo/CL_0000540) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005106"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [neuron](http://purl.obolibrary.org/obo/CL_0000540) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005106"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [neuron](http://purl.obolibrary.org/obo/CL_0000540) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009248"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### neuronal receptor cell `http://purl.obolibrary.org/obo/CL_0000006` -#### Removed -- [neuronal receptor cell](http://purl.obolibrary.org/obo/CL_0000006) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009001"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [neuronal receptor cell](http://purl.obolibrary.org/obo/CL_0000006) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009001"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### neuroplacodal cell `http://purl.obolibrary.org/obo/CL_0000032` -#### Removed -- [neuroplacodal cell](http://purl.obolibrary.org/obo/CL_0000032) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009012"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [neuroplacodal cell](http://purl.obolibrary.org/obo/CL_0000032) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009012"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### neutrophil `http://purl.obolibrary.org/obo/CL_0000775` -#### Removed -- [neutrophil](http://purl.obolibrary.org/obo/CL_0000775) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009327"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [neutrophil](http://purl.obolibrary.org/obo/CL_0000775) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009327"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### neutrophil progenitor cell `http://purl.obolibrary.org/obo/CL_0000834` -#### Removed -- [neutrophil progenitor cell](http://purl.obolibrary.org/obo/CL_0000834) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009352"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [neutrophil progenitor cell](http://purl.obolibrary.org/obo/CL_0000834) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009352"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### neutrophilic metamyelocyte `http://purl.obolibrary.org/obo/CL_0000582` -#### Removed -- [neutrophilic metamyelocyte](http://purl.obolibrary.org/obo/CL_0000582) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009268"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [neutrophilic metamyelocyte](http://purl.obolibrary.org/obo/CL_0000582) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009268"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### neutrophilic myeloblast `http://purl.obolibrary.org/obo/CL_0000042` -#### Removed -- [neutrophilic myeloblast](http://purl.obolibrary.org/obo/CL_0000042) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009018"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [neutrophilic myeloblast](http://purl.obolibrary.org/obo/CL_0000042) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009018"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### neutrophilic myelocyte `http://purl.obolibrary.org/obo/CL_0000580` -#### Removed -- [neutrophilic myelocyte](http://purl.obolibrary.org/obo/CL_0000580) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009266"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [neutrophilic myelocyte](http://purl.obolibrary.org/obo/CL_0000580) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009266"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### neutrophilic promyelocyte `http://purl.obolibrary.org/obo/CL_0000564` -#### Removed -- [neutrophilic promyelocyte](http://purl.obolibrary.org/obo/CL_0000564) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009257"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [neutrophilic promyelocyte](http://purl.obolibrary.org/obo/CL_0000564) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009257"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### nitrergic neuron `http://purl.obolibrary.org/obo/CL_0000528` -#### Removed -- [nitrergic neuron](http://purl.obolibrary.org/obo/CL_0000528) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009240"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [nitrergic neuron](http://purl.obolibrary.org/obo/CL_0000528) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009240"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### noradrenergic cell `http://purl.obolibrary.org/obo/CL_0000459` -#### Removed -- [noradrenergic cell](http://purl.obolibrary.org/obo/CL_0000459) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009214"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [noradrenergic cell](http://purl.obolibrary.org/obo/CL_0000459) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009214"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### noradrenergic neuron `http://purl.obolibrary.org/obo/CL_0008025` -#### Removed -- [noradrenergic neuron](http://purl.obolibrary.org/obo/CL_0008025) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005873"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [noradrenergic neuron](http://purl.obolibrary.org/obo/CL_0008025) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005873"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### notochordal sheath cell `http://purl.obolibrary.org/obo/CL_0007007` -#### Removed -- [notochordal sheath cell](http://purl.obolibrary.org/obo/CL_0007007) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005744"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [notochordal sheath cell](http://purl.obolibrary.org/obo/CL_0007007) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005744"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### nucleate erythrocyte `http://purl.obolibrary.org/obo/CL_0000562` -#### Removed -- [nucleate erythrocyte](http://purl.obolibrary.org/obo/CL_0000562) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009256"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [nucleate erythrocyte](http://purl.obolibrary.org/obo/CL_0000562) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009256"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### nucleated thrombocyte `http://purl.obolibrary.org/obo/CL_0000762` -#### Removed -- [nucleated thrombocyte](http://purl.obolibrary.org/obo/CL_0000762) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009323"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [nucleated thrombocyte](http://purl.obolibrary.org/obo/CL_0000762) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009323"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### obsolete caudal ganglionic eminence derived GABAergic cortical interneuron `http://purl.obolibrary.org/obo/CL_4023070` -#### Removed -- [obsolete caudal ganglionic eminence derived GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023070) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A GABAergic cortical interneuron that develops from the caudal ganglionic eminence and has migrated to the cerebral cortex."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20130169"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [obsolete caudal ganglionic eminence derived GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023070) [label](http://www.w3.org/2000/01/rdf-schema#label) "caudal ganglionic eminence derived GABAergic cortical interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [obsolete caudal ganglionic eminence derived GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023070) EquivalentTo [interneuron](http://purl.obolibrary.org/obo/CL_0000099) and ([RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_0000956](http://purl.obolibrary.org/obo/UBERON_0000956)) and ([RO_0002202](http://purl.obolibrary.org/obo/RO_0002202) some [UBERON_0004026](http://purl.obolibrary.org/obo/UBERON_0004026)) and ([RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0061534](http://purl.obolibrary.org/obo/GO_0061534)) - -- [obsolete caudal ganglionic eminence derived GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023070) SubClassOf [cerebral cortex GABAergic interneuron](http://purl.obolibrary.org/obo/CL_0010011) - -- [obsolete caudal ganglionic eminence derived GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023070) SubClassOf [caudal ganglionic eminence derived interneuron](http://purl.obolibrary.org/obo/CL_4023064) - -#### Added -- [obsolete caudal ganglionic eminence derived GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023070) [deprecated](http://www.w3.org/2002/07/owl#deprecated) true - -- [obsolete caudal ganglionic eminence derived GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023070) [IAO_0000233](http://purl.obolibrary.org/obo/IAO_0000233) [2374](https://github.com/obophenotype/cell-ontology/pull/2374) - -- [obsolete caudal ganglionic eminence derived GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023070) [term replaced by](http://purl.obolibrary.org/obo/IAO_0100001) [caudal ganglionic eminence derived interneuron](http://purl.obolibrary.org/obo/CL_4023064) - -- [obsolete caudal ganglionic eminence derived GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023070) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "caudal ganglionic eminence derived GABAergic interneuron -and caudal ganglionic eminence derived interneuron are the same cell type. -The two must be merged and one needs to be defined as obsolete. -We decided to deprecate the entity with the more specific term and redundant qualities -in the label. See comments in issue 2357."^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [obsolete caudal ganglionic eminence derived GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023070) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "OBSOLETE. A GABAergic cortical interneuron that develops from the caudal ganglionic eminence and has migrated to the cerebral cortex."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20130169"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [obsolete caudal ganglionic eminence derived GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023070) [label](http://www.w3.org/2000/01/rdf-schema#label) "obsolete caudal ganglionic eminence derived GABAergic cortical interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### obsolete cerebellum Golgi cell `http://purl.obolibrary.org/obo/CL_2000026` -#### Removed -- [obsolete cerebellum Golgi cell](http://purl.obolibrary.org/obo/CL_2000026) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) - -#### Added -- [obsolete cerebellum Golgi cell](http://purl.obolibrary.org/obo/CL_2000026) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) - - -### obsolete embryonic gland hemocyte `http://purl.obolibrary.org/obo/CL_0000736` -#### Removed -- [obsolete embryonic gland hemocyte](http://purl.obolibrary.org/obo/CL_0000736) [label](http://www.w3.org/2000/01/rdf-schema#label) "embryonic gland hemocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [obsolete embryonic gland hemocyte](http://purl.obolibrary.org/obo/CL_0000736) [label](http://www.w3.org/2000/01/rdf-schema#label) "obsolete embryonic gland hemocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### obsolete melanocyte of foreskin `http://purl.obolibrary.org/obo/CL_2000082` -#### Removed -- [obsolete melanocyte of foreskin](http://purl.obolibrary.org/obo/CL_2000082) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) - -#### Added -- [obsolete melanocyte of foreskin](http://purl.obolibrary.org/obo/CL_2000082) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) - - -### obsolete microvascular endothelium blood vessel endothelial cell `http://purl.obolibrary.org/obo/CL_2000009` -#### Removed -- [obsolete microvascular endothelium blood vessel endothelial cell](http://purl.obolibrary.org/obo/CL_2000009) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) - -#### Added -- [obsolete microvascular endothelium blood vessel endothelial cell](http://purl.obolibrary.org/obo/CL_2000009) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) - - -### obsolete paracrine cell `http://purl.obolibrary.org/obo/CL_0000512` -#### Removed -- [obsolete paracrine cell](http://purl.obolibrary.org/obo/CL_0000512) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009233"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [obsolete paracrine cell](http://purl.obolibrary.org/obo/CL_0000512) [label](http://www.w3.org/2000/01/rdf-schema#label) "paracrine cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [obsolete paracrine cell](http://purl.obolibrary.org/obo/CL_0000512) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A paracrine cell is a secretory cell that secretes an agonist into intercellular spaces in which it diffuses to a target cell other than that which produced it."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0198529171"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [obsolete paracrine cell](http://purl.obolibrary.org/obo/CL_0000512) SubClassOf [secretory cell](http://purl.obolibrary.org/obo/CL_0000151) - -#### Added -- [obsolete paracrine cell](http://purl.obolibrary.org/obo/CL_0000512) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The term paracrine describes a role of a secreted hormone. There are a vast number of cell types that could fit this description, however it is difficult to know every case where a secreted hormone has paracrine effects."^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [obsolete paracrine cell](http://purl.obolibrary.org/obo/CL_0000512) [consider](http://www.geneontology.org/formats/oboInOwl#consider) [secretory cell](http://purl.obolibrary.org/obo/CL_0000151) - -- [obsolete paracrine cell](http://purl.obolibrary.org/obo/CL_0000512) [label](http://www.w3.org/2000/01/rdf-schema#label) "obsolete paracrine cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [obsolete paracrine cell](http://purl.obolibrary.org/obo/CL_0000512) [deprecated](http://www.w3.org/2002/07/owl#deprecated) true - - -### obsolete retina retinal ganglion cell `http://purl.obolibrary.org/obo/CL_2000050` -#### Removed -- [obsolete retina retinal ganglion cell](http://purl.obolibrary.org/obo/CL_2000050) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) - -#### Added -- [obsolete retina retinal ganglion cell](http://purl.obolibrary.org/obo/CL_2000050) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) - - -### odontoblast `http://purl.obolibrary.org/obo/CL_0000060` -#### Removed -- [odontoblast](http://purl.obolibrary.org/obo/CL_0000060) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009029"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [odontoblast](http://purl.obolibrary.org/obo/CL_0000060) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009029"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### odontoclast `http://purl.obolibrary.org/obo/CL_0000588` -#### Removed -- [odontoclast](http://purl.obolibrary.org/obo/CL_0000588) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009270"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [odontoclast](http://purl.obolibrary.org/obo/CL_0000588) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009270"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### odontocyte `http://purl.obolibrary.org/obo/CL_0000140` -#### Removed -- [odontocyte](http://purl.obolibrary.org/obo/CL_0000140) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009086"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [odontocyte](http://purl.obolibrary.org/obo/CL_0000140) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009086"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### oenocyte `http://purl.obolibrary.org/obo/CL_0000487` -#### Removed -- [oenocyte](http://purl.obolibrary.org/obo/CL_0000487) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004995"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [oenocyte](http://purl.obolibrary.org/obo/CL_0000487) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004995"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### olfactory ensheathing cell `http://purl.obolibrary.org/obo/CL_0011028` -#### Removed -- [olfactory ensheathing cell](http://purl.obolibrary.org/obo/CL_0011028) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "A neural-crest derived glial cell that supports the growth and survival of primary olfactory neuroons from the neuroepithelium in the nasal cavity to the brain by encasing large bundles of numerous unmyelinated axons."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:22456085"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [olfactory ensheathing cell](http://purl.obolibrary.org/obo/CL_0011028) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A neural-crest derived glial cell that supports the growth and survival of primary olfactory neuroons from the neuroepithelium in the nasal cavity to the brain by encasing large bundles of numerous unmyelinated axons."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:22456085"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### olfactory epithelial supporting cell `http://purl.obolibrary.org/obo/CL_0000853` -#### Removed -- [olfactory epithelial supporting cell](http://purl.obolibrary.org/obo/CL_0000853) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009364"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [olfactory epithelial supporting cell](http://purl.obolibrary.org/obo/CL_0000853) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009364"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### olfactory granule cell `http://purl.obolibrary.org/obo/CL_0000626` -#### Removed -- [olfactory granule cell](http://purl.obolibrary.org/obo/CL_0000626) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0001694"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [olfactory granule cell](http://purl.obolibrary.org/obo/CL_0000626) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0001694"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### olfactory receptor cell `http://purl.obolibrary.org/obo/CL_0000207` -#### Removed -- [olfactory receptor cell](http://purl.obolibrary.org/obo/CL_0000207) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009125"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [olfactory receptor cell](http://purl.obolibrary.org/obo/CL_0000207) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009125"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### oligodendrocyte `http://purl.obolibrary.org/obo/CL_0000128` -#### Removed -- [oligodendrocyte](http://purl.obolibrary.org/obo/CL_0000128) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009076"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [oligodendrocyte](http://purl.obolibrary.org/obo/CL_0000128) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009076"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### oocyte `http://purl.obolibrary.org/obo/CL_0000023` -#### Removed -- [oocyte](http://purl.obolibrary.org/obo/CL_0000023) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004886"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [oocyte](http://purl.obolibrary.org/obo/CL_0000023) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0001109"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [oocyte](http://purl.obolibrary.org/obo/CL_0000023) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0001109"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [oocyte](http://purl.obolibrary.org/obo/CL_0000023) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004886"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### oogonial cell `http://purl.obolibrary.org/obo/CL_0000024` -#### Removed -- [oogonial cell](http://purl.obolibrary.org/obo/CL_0000024) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005878"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [oogonial cell](http://purl.obolibrary.org/obo/CL_0000024) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005878"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### open tracheal system tracheocyte `http://purl.obolibrary.org/obo/CL_0008026` -#### Removed -- [open tracheal system tracheocyte](http://purl.obolibrary.org/obo/CL_0008026) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005038"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [open tracheal system tracheocyte](http://purl.obolibrary.org/obo/CL_0008026) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005038"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### optic choroid fibroblast `http://purl.obolibrary.org/obo/CL_2000070` -#### Removed -- [optic choroid fibroblast](http://purl.obolibrary.org/obo/CL_2000070) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +### muscle precursor cell `http://purl.obolibrary.org/obo/CL_0000680` #### Added -- [optic choroid fibroblast](http://purl.obolibrary.org/obo/CL_2000070) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [muscle precursor cell](http://purl.obolibrary.org/obo/CL_0000680) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### osteoblast `http://purl.obolibrary.org/obo/CL_0000062` -#### Removed -- [osteoblast](http://purl.obolibrary.org/obo/CL_0000062) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009031"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### myeloid cell `http://purl.obolibrary.org/obo/CL_0000763` #### Added -- [osteoblast](http://purl.obolibrary.org/obo/CL_0000062) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009031"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [myeloid cell](http://purl.obolibrary.org/obo/CL_0000763) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### osteoclast `http://purl.obolibrary.org/obo/CL_0000092` -#### Removed -- [osteoclast](http://purl.obolibrary.org/obo/CL_0000092) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009047"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### myeloid suppressor cell `http://purl.obolibrary.org/obo/CL_0000889` #### Added -- [osteoclast](http://purl.obolibrary.org/obo/CL_0000092) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009047"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [myeloid suppressor cell](http://purl.obolibrary.org/obo/CL_0000889) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### osteocyte `http://purl.obolibrary.org/obo/CL_0000137` +### myotube `http://purl.obolibrary.org/obo/CL_0002372` #### Removed -- [osteocyte](http://purl.obolibrary.org/obo/CL_0000137) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009083"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [myotube](http://purl.obolibrary.org/obo/CL_0002372) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A transversely striated, synctial muscle cell, formed by the fusion of myoblasts."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:dos"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [osteocyte](http://purl.obolibrary.org/obo/CL_0000137) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009083"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0323052908"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) -### outer renal medulla vasa recta cell `http://purl.obolibrary.org/obo/CL_1001127` + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:22274696"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [outer renal medulla vasa recta cell](http://purl.obolibrary.org/obo/CL_1001127) SubClassOf [kidney venous blood vessel cell](http://purl.obolibrary.org/obo/CL_1000893) +- [myotube](http://purl.obolibrary.org/obo/CL_0002372) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "single cell sarcomere"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [myotube](http://purl.obolibrary.org/obo/CL_0002372) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "myotubule"^^[string](http://www.w3.org/2001/XMLSchema#string) -### ovarian fibroblast `http://purl.obolibrary.org/obo/CL_2000063` -#### Removed -- [ovarian fibroblast](http://purl.obolibrary.org/obo/CL_2000063) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +- [myotube](http://purl.obolibrary.org/obo/CL_0002372) SubClassOf [multinucleate cell](http://purl.obolibrary.org/obo/CL_0000228) #### Added -- [ovarian fibroblast](http://purl.obolibrary.org/obo/CL_2000063) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [myotube](http://purl.obolibrary.org/obo/CL_0002372) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "myofibril"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005812"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [myotube](http://purl.obolibrary.org/obo/CL_0002372) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A transversely striated, multinucleated syncytial muscle cell, formed by the fusion of myoblasts during muscle development."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:dos"^^[string](http://www.w3.org/2001/XMLSchema#string) -### ovarian microvascular endothelial cell `http://purl.obolibrary.org/obo/CL_2000065` -#### Removed -- [ovarian microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000065) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0323052908"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [ovarian microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000065) SubClassOf [epithelial cell of urethra](http://purl.obolibrary.org/obo/CL_1000296) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [ovarian microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000065) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:22274696"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [ovarian microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000065) SubClassOf [urethra cell](http://purl.obolibrary.org/obo/CL_1001320) +- [myotube](http://purl.obolibrary.org/obo/CL_0002372) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "myofiber"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005812"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [myotube](http://purl.obolibrary.org/obo/CL_0002372) SubClassOf [syncytial cell](http://purl.obolibrary.org/obo/CL_4052002) -### ovarian surface epithelial cell `http://purl.obolibrary.org/obo/CL_2000064` -#### Removed -- [ovarian surface epithelial cell](http://purl.obolibrary.org/obo/CL_2000064) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +### natural helper lymphocyte `http://purl.obolibrary.org/obo/CL_0002679` #### Added -- [ovarian surface epithelial cell](http://purl.obolibrary.org/obo/CL_2000064) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [natural helper lymphocyte](http://purl.obolibrary.org/obo/CL_0002679) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### oxygen accumulating cell `http://purl.obolibrary.org/obo/CL_0000329` +### nephrocyte `http://purl.obolibrary.org/obo/CL_0002520` #### Removed -- [oxygen accumulating cell](http://purl.obolibrary.org/obo/CL_0000329) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009164"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [nephrocyte](http://purl.obolibrary.org/obo/CL_0002520) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) + +- [nephrocyte](http://purl.obolibrary.org/obo/CL_0002520) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_50557](http://purl.obolibrary.org/obo/NCBITaxon_50557) #### Added -- [oxygen accumulating cell](http://purl.obolibrary.org/obo/CL_0000329) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009164"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [nephrocyte](http://purl.obolibrary.org/obo/CL_0002520) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_50557](http://purl.obolibrary.org/obo/NCBITaxon_50557) -### pain receptor cell `http://purl.obolibrary.org/obo/CL_0000198` +### neural cell `http://purl.obolibrary.org/obo/CL_0002319` #### Removed -- [pain receptor cell](http://purl.obolibrary.org/obo/CL_0000198) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009119"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [neural cell](http://purl.obolibrary.org/obo/CL_0002319) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) #### Added -- [pain receptor cell](http://purl.obolibrary.org/obo/CL_0000198) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009119"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [neural cell](http://purl.obolibrary.org/obo/CL_0002319) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### pancreatic A cell `http://purl.obolibrary.org/obo/CL_0000171` -#### Removed -- [pancreatic A cell](http://purl.obolibrary.org/obo/CL_0000171) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009104"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### neural crest cell `http://purl.obolibrary.org/obo/CL_0011012` #### Added -- [pancreatic A cell](http://purl.obolibrary.org/obo/CL_0000171) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009104"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [neural crest cell](http://purl.obolibrary.org/obo/CL_0011012) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0011012"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [neural crest cell](http://purl.obolibrary.org/obo/CL_0011012) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -### pancreatic D cell `http://purl.obolibrary.org/obo/CL_0000173` -#### Removed -- [pancreatic D cell](http://purl.obolibrary.org/obo/CL_0000173) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005743"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [pancreatic D cell](http://purl.obolibrary.org/obo/CL_0000173) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005743"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. +After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. +Disorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fcell.2020.00635/full"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1242/dev.193193"^^[string](http://www.w3.org/2001/XMLSchema#string) -### pancreatic PP cell `http://purl.obolibrary.org/obo/CL_0002275` -#### Removed -- [pancreatic PP cell](http://purl.obolibrary.org/obo/CL_0002275) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005742"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/dvg.23276"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [pancreatic PP cell](http://purl.obolibrary.org/obo/CL_0002275) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005742"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://doi.org/10.1016/j.ydbio.2011.12.042"^^[string](http://www.w3.org/2001/XMLSchema#string) -### pancreatic acinar cell `http://purl.obolibrary.org/obo/CL_0002064` +### neuroblast (sensu Nematoda and Protostomia) `http://purl.obolibrary.org/obo/CL_0000338` #### Removed -- [pancreatic acinar cell](http://purl.obolibrary.org/obo/CL_0002064) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005739"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [neuroblast (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000338) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) + +- [neuroblast (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000338) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_33317](http://purl.obolibrary.org/obo/NCBITaxon_33317) #### Added -- [pancreatic acinar cell](http://purl.obolibrary.org/obo/CL_0002064) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005739"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [neuroblast (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000338) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_33317](http://purl.obolibrary.org/obo/NCBITaxon_33317) -### pancreatic centro-acinar cell `http://purl.obolibrary.org/obo/CL_0002080` +### neuroblast (sensu Vertebrata) `http://purl.obolibrary.org/obo/CL_0000031` #### Removed -- [pancreatic centro-acinar cell](http://purl.obolibrary.org/obo/CL_0002080) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005740"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [neuroblast (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000031) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_7742](http://purl.obolibrary.org/obo/NCBITaxon_7742) #### Added -- [pancreatic centro-acinar cell](http://purl.obolibrary.org/obo/CL_0002080) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005740"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [neuroblast (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000031) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_7742](http://purl.obolibrary.org/obo/NCBITaxon_7742) -### pancreatic ductal cell `http://purl.obolibrary.org/obo/CL_0002079` +### neuroglioblast (sensu Nematoda and Protostomia) `http://purl.obolibrary.org/obo/CL_0000468` #### Removed -- [pancreatic ductal cell](http://purl.obolibrary.org/obo/CL_0002079) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009380"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [neuroglioblast (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000468) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) + +- [neuroglioblast (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000468) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_33317](http://purl.obolibrary.org/obo/NCBITaxon_33317) #### Added -- [pancreatic ductal cell](http://purl.obolibrary.org/obo/CL_0002079) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009380"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [neuroglioblast (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000468) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_33317](http://purl.obolibrary.org/obo/NCBITaxon_33317) -### pancreatic epsilon cell `http://purl.obolibrary.org/obo/CL_0005019` -#### Removed -- [pancreatic epsilon cell](http://purl.obolibrary.org/obo/CL_0005019) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005598"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### neuromast mantle cell `http://purl.obolibrary.org/obo/CL_0000851` #### Added -- [pancreatic epsilon cell](http://purl.obolibrary.org/obo/CL_0005019) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005598"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [neuromast mantle cell](http://purl.obolibrary.org/obo/CL_0000851) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### pancreatic goblet cell `http://purl.obolibrary.org/obo/CL_1000322` -#### Removed -- [pancreatic goblet cell](http://purl.obolibrary.org/obo/CL_1000322) SubClassOf [pancreas exocrine glandular cell](http://purl.obolibrary.org/obo/CL_1001599) +### neuromast supporting cell `http://purl.obolibrary.org/obo/CL_0000852` #### Added -- [pancreatic goblet cell](http://purl.obolibrary.org/obo/CL_1000322) SubClassOf [epithelial cell of exocrine pancreas](http://purl.obolibrary.org/obo/CL_1001433) +- [neuromast supporting cell](http://purl.obolibrary.org/obo/CL_0000852) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### parafollicular cell `http://purl.obolibrary.org/obo/CL_0000570` +### neuron associated cell (sensu Nematoda and Protostomia) `http://purl.obolibrary.org/obo/CL_0000130` #### Removed -- [parafollicular cell](http://purl.obolibrary.org/obo/CL_0000570) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009260"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [neuron associated cell (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000130) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_33317](http://purl.obolibrary.org/obo/NCBITaxon_33317) + +- [neuron associated cell (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000130) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) #### Added -- [parafollicular cell](http://purl.obolibrary.org/obo/CL_0000570) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009260"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [neuron associated cell (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000130) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_33317](http://purl.obolibrary.org/obo/NCBITaxon_33317) -### parasympathetic neuron `http://purl.obolibrary.org/obo/CL_0011102` +### neuron associated cell (sensu Vertebrata) `http://purl.obolibrary.org/obo/CL_0000123` #### Removed -- [parasympathetic neuron](http://purl.obolibrary.org/obo/CL_0011102) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005776"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [neuron associated cell (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000123) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) + +- [neuron associated cell (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000123) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_7742](http://purl.obolibrary.org/obo/NCBITaxon_7742) #### Added -- [parasympathetic neuron](http://purl.obolibrary.org/obo/CL_0011102) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005776"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [neuron associated cell (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000123) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_7742](http://purl.obolibrary.org/obo/NCBITaxon_7742) -### peptide hormone secreting cell `http://purl.obolibrary.org/obo/CL_0000167` -#### Removed -- [peptide hormone secreting cell](http://purl.obolibrary.org/obo/CL_0000167) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009100"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### neuronal-restricted precursor `http://purl.obolibrary.org/obo/CL_4042021` #### Added -- [peptide hormone secreting cell](http://purl.obolibrary.org/obo/CL_0000167) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009100"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [neuronal-restricted precursor](http://purl.obolibrary.org/obo/CL_4042021) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "In vitro cultures of embryonic mouse neural tubes show that neuronal-restricted precursors (NRPs) are derived from multipotent neuroepithelial cells to give rise to neurons. This progression suggests a linear relationship between multipotent progenitors and neuronal-restricted differentiation. (Mayer-Proschel et al., 1997). In the spinal cord of rats, neural-restricted precursor cells give rise cholinergic, GABAergic, glutametergic neurons (Cao and Howard et al., 2002)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:9354325"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:12429182"^^[string](http://www.w3.org/2001/XMLSchema#string) -### peptidergic neuron `http://purl.obolibrary.org/obo/CL_0000110` -#### Removed -- [peptidergic neuron](http://purl.obolibrary.org/obo/CL_0000110) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009062"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [neuronal-restricted precursor](http://purl.obolibrary.org/obo/CL_4042021) [date](http://purl.org/dc/terms/date) "2024-09-02T11:42:12Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -- [peptidergic neuron](http://purl.obolibrary.org/obo/CL_0000110) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004101"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [neuronal-restricted precursor](http://purl.obolibrary.org/obo/CL_4042021) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042021"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [peptidergic neuron](http://purl.obolibrary.org/obo/CL_0000110) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009062"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [neuronal-restricted precursor](http://purl.obolibrary.org/obo/CL_4042021) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A progenitor cell of the central nervous system that differentiates exclusively onto neurons. This progenitor cell is found in a hippocampus subventricular zone, developing cortex and spinal cord of the central nervous system."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:10467245"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [peptidergic neuron](http://purl.obolibrary.org/obo/CL_0000110) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004101"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [neuronal-restricted precursor](http://purl.obolibrary.org/obo/CL_4042021) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) +- [neuronal-restricted precursor](http://purl.obolibrary.org/obo/CL_4042021) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "NRP"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [synonym_type_property](http://www.geneontology.org/formats/oboInOwl#SynonymTypeProperty) "OMO:0003000"^^[string](http://www.w3.org/2001/XMLSchema#string) -### periarticular chondrocyte `http://purl.obolibrary.org/obo/CL_0000742` -#### Removed -- [periarticular chondrocyte](http://purl.obolibrary.org/obo/CL_0000742) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009312"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:12429182"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [periarticular chondrocyte](http://purl.obolibrary.org/obo/CL_0000742) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009312"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [neuronal-restricted precursor](http://purl.obolibrary.org/obo/CL_4042021) [label](http://www.w3.org/2000/01/rdf-schema#label) "neuronal-restricted precursor"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [neuronal-restricted precursor](http://purl.obolibrary.org/obo/CL_4042021) -### pericardial nephrocyte `http://purl.obolibrary.org/obo/CL_0000474` -#### Removed -- [pericardial nephrocyte](http://purl.obolibrary.org/obo/CL_0000474) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005058"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [neuronal-restricted precursor](http://purl.obolibrary.org/obo/CL_4042021) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001017](http://purl.obolibrary.org/obo/UBERON_0001017) -#### Added -- [pericardial nephrocyte](http://purl.obolibrary.org/obo/CL_0000474) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005058"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [neuronal-restricted precursor](http://purl.obolibrary.org/obo/CL_4042021) SubClassOf [neuron associated cell (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000123) +- [neuronal-restricted precursor](http://purl.obolibrary.org/obo/CL_4042021) SubClassOf [progenitor cell](http://purl.obolibrary.org/obo/CL_0011026) -### pericardium fibroblast `http://purl.obolibrary.org/obo/CL_2000068` -#### Removed -- [pericardium fibroblast](http://purl.obolibrary.org/obo/CL_2000068) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +### neuroplacodal cell `http://purl.obolibrary.org/obo/CL_0000032` #### Added -- [pericardium fibroblast](http://purl.obolibrary.org/obo/CL_2000068) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [neuroplacodal cell](http://purl.obolibrary.org/obo/CL_0000032) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### pericyte `http://purl.obolibrary.org/obo/CL_0000669` -#### Removed -- [pericyte](http://purl.obolibrary.org/obo/CL_0000669) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009112"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### neutrophilic myeloblast `http://purl.obolibrary.org/obo/CL_0000042` #### Added -- [pericyte](http://purl.obolibrary.org/obo/CL_0000669) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009112"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [neutrophilic myeloblast](http://purl.obolibrary.org/obo/CL_0000042) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### peridermal cell `http://purl.obolibrary.org/obo/CL_0000078` -#### Removed -- [peridermal cell](http://purl.obolibrary.org/obo/CL_0000078) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009041"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### non-classical monocyte `http://purl.obolibrary.org/obo/CL_0000875` #### Added -- [peridermal cell](http://purl.obolibrary.org/obo/CL_0000078) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009041"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [non-classical monocyte](http://purl.obolibrary.org/obo/CL_0000875) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### perijunctional fibroblast `http://purl.obolibrary.org/obo/CL_0000688` +### notochordal cell `http://purl.obolibrary.org/obo/CL_0007005` #### Removed -- [perijunctional fibroblast](http://purl.obolibrary.org/obo/CL_0000688) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009296"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [notochordal cell](http://purl.obolibrary.org/obo/CL_0007005) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) #### Added -- [perijunctional fibroblast](http://purl.obolibrary.org/obo/CL_0000688) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009296"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [notochordal cell](http://purl.obolibrary.org/obo/CL_0007005) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### perineuronal satellite cell `http://purl.obolibrary.org/obo/CL_0000516` +### obliquely striated somatic muscle cell `http://purl.obolibrary.org/obo/CL_0008005` #### Removed -- [perineuronal satellite cell](http://purl.obolibrary.org/obo/CL_0000516) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009237"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [perineuronal satellite cell](http://purl.obolibrary.org/obo/CL_0000516) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009237"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [obliquely striated somatic muscle cell](http://purl.obolibrary.org/obo/CL_0008005) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A somatic muscle cell that is oblquely striated. Examples include the somatic muscles of nematodes."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:8720463"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [obliquely striated somatic muscle cell](http://purl.obolibrary.org/obo/CL_0008005) EquivalentTo [somatic muscle cell](http://purl.obolibrary.org/obo/CL_0008004) and ([BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0030017](http://purl.obolibrary.org/obo/GO_0030017)) and ([RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0001908](http://purl.obolibrary.org/obo/PATO_0001908)) and ([RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0002479](http://purl.obolibrary.org/obo/PATO_0002479)) -### peripheral blood mononuclear cell `http://purl.obolibrary.org/obo/CL_2000001` -#### Removed -- [peripheral blood mononuclear cell](http://purl.obolibrary.org/obo/CL_2000001) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +- [obliquely striated somatic muscle cell](http://purl.obolibrary.org/obo/CL_0008005) SubClassOf [multinucleate cell](http://purl.obolibrary.org/obo/CL_0000228) #### Added -- [peripheral blood mononuclear cell](http://purl.obolibrary.org/obo/CL_2000001) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [obliquely striated somatic muscle cell](http://purl.obolibrary.org/obo/CL_0008005) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A somatic muscle cell that is obliquely striated and mononucleated. Examples include the somatic muscles of nematodes."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.3908/wormatlas.1.7"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:8720463"^^[string](http://www.w3.org/2001/XMLSchema#string) -### peripheral nervous system neuron `http://purl.obolibrary.org/obo/CL_2000032` -#### Removed -- [peripheral nervous system neuron](http://purl.obolibrary.org/obo/CL_2000032) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +- [obliquely striated somatic muscle cell](http://purl.obolibrary.org/obo/CL_0008005) EquivalentTo [somatic muscle cell](http://purl.obolibrary.org/obo/CL_0008004) and ([BFO_0000051](http://purl.obolibrary.org/obo/BFO_0000051) some [GO_0030017](http://purl.obolibrary.org/obo/GO_0030017)) and ([RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0001407](http://purl.obolibrary.org/obo/PATO_0001407)) and ([RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0002479](http://purl.obolibrary.org/obo/PATO_0002479)) -#### Added -- [peripheral nervous system neuron](http://purl.obolibrary.org/obo/CL_2000032) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [obliquely striated somatic muscle cell](http://purl.obolibrary.org/obo/CL_0008005) SubClassOf [single nucleate cell](http://purl.obolibrary.org/obo/CL_0000226) -### peripheral sensory neuron `http://purl.obolibrary.org/obo/CL_3000004` +### oenocyte `http://purl.obolibrary.org/obo/CL_0000487` #### Removed -- [peripheral sensory neuron](http://purl.obolibrary.org/obo/CL_3000004) [contributor](http://purl.org/dc/terms/contributor) [Q97529981](https://www.wikidata.org/entity/Q97529981) +- [oenocyte](http://purl.obolibrary.org/obo/CL_0000487) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_6656](http://purl.obolibrary.org/obo/NCBITaxon_6656) #### Added -- [peripheral sensory neuron](http://purl.obolibrary.org/obo/CL_3000004) [contributor](http://purl.org/dc/terms/contributor) [Q97529981](http://www.wikidata.org/entity/Q97529981) +- [oenocyte](http://purl.obolibrary.org/obo/CL_0000487) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_6656](http://purl.obolibrary.org/obo/NCBITaxon_6656) -### peritoneal macrophage `http://purl.obolibrary.org/obo/CL_0000581` +### oligodendrocyte precursor cell `http://purl.obolibrary.org/obo/CL_0002453` #### Removed -- [peritoneal macrophage](http://purl.obolibrary.org/obo/CL_0000581) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009267"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [oligodendrocyte precursor cell](http://purl.obolibrary.org/obo/CL_0002453) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "This cell type can be purified from optic nerves and other regions of the embryonic, postnatal and adult rat CNS and can be differentiated in vitro to oligodendrocytes and type-2 astrocytes. Some references use the terms 'oligodendrocyte precursor cell' and 'oligodendrocyte type-2 astrocyte (O-2A) progenitor' to refer to the same entity (e.g., PMID:10704434), while others describe an oligodendrocyte type-2 astrocyte (O-2A) progenitor cell as the precurosr to oligodendrocyte- and type-2 astrocyte- progenitor cells (e.g, ISBN:9780702028991)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:2182078"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [peritoneal macrophage](http://purl.obolibrary.org/obo/CL_0000581) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009267"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:9780702028991"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:10704434"^^[string](http://www.w3.org/2001/XMLSchema#string) -### peritubular capillary endothelial cell `http://purl.obolibrary.org/obo/CL_1001033` -#### Removed -- [peritubular capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1001033) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An endothelial cell that is part of some peritubular capillary."^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [oligodendrocyte precursor cell](http://purl.obolibrary.org/obo/CL_0002453) [description](http://purl.org/dc/terms/description) "This cell type can be purified from optic nerves and other regions of the embryonic, postnatal and adult rat CNS and can be differentiated in vitro to oligodendrocytes and type-2 astrocytes. Some references use the terms 'oligodendrocyte precursor cell' and 'oligodendrocyte type-2 astrocyte (O-2A) progenitor' to refer to the same entity (e.g., PMID:10704434), while others describe an oligodendrocyte type-2 astrocyte (O-2A) progenitor cell as the precurosr to oligodendrocyte- and type-2 astrocyte- progenitor cells (e.g, ISBN:9780702028991)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:2182078"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [peritubular capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1001033) EquivalentTo [kidney capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1000892) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0005272](http://purl.obolibrary.org/obo/UBERON_0005272)) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:9780702028991"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [peritubular capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1001033) SubClassOf [kidney capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1000892) - - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:10704434"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [peritubular capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1001033) SubClassOf [capillary endothelial cell](http://purl.obolibrary.org/obo/CL_0002144) + +### ooblast `http://purl.obolibrary.org/obo/CL_0002239` #### Added -- [peritubular capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1001033) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Peritubular capillary endothelial cells feature fenestrations measuring 60-70 nm in diameter, each traversed by a thin diaphragm."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:19129259"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [ooblast](http://purl.obolibrary.org/obo/CL_0002239) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -- [peritubular capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1001033) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An endothelial cell that is part of the peritubular capillary of the kidney. This cell is highly fenestrated and plays a vital role in the kidney's filtration process, enabling the exchange of materials between the blood and the renal tubules."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:19129259"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [peritubular capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1001033) EquivalentTo [kidney capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1000892) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0012441](http://purl.obolibrary.org/obo/UBERON_0012441)) +### oocyte `http://purl.obolibrary.org/obo/CL_0000023` +#### Removed +- [oocyte](http://purl.obolibrary.org/obo/CL_0000023) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -- [peritubular capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1001033) SubClassOf [fenestrated endothelial cell](http://purl.obolibrary.org/obo/CL_0000666) +- [oocyte](http://purl.obolibrary.org/obo/CL_0000023) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_33208](http://purl.obolibrary.org/obo/NCBITaxon_33208) -- [peritubular capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1001033) SubClassOf [kidney capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1000892) +#### Added +- [oocyte](http://purl.obolibrary.org/obo/CL_0000023) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_33208](http://purl.obolibrary.org/obo/NCBITaxon_33208) -### phagocyte `http://purl.obolibrary.org/obo/CL_0000234` -#### Removed -- [phagocyte](http://purl.obolibrary.org/obo/CL_0000234) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009140"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### osteoclast `http://purl.obolibrary.org/obo/CL_0000092` #### Added -- [phagocyte](http://purl.obolibrary.org/obo/CL_0000234) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009140"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [osteoclast](http://purl.obolibrary.org/obo/CL_0000092) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### photopic photoreceptor cell `http://purl.obolibrary.org/obo/CL_0000490` +### oxytocin receptor sst GABAergic cortical interneuron `http://purl.obolibrary.org/obo/CL_4023122` #### Removed -- [photopic photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000490) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009220"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [oxytocin receptor sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023122) SubClassOf [sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023017) #### Added -- [photopic photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000490) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009220"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [oxytocin receptor sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023122) SubClassOf [RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000015665](http://purl.obolibrary.org/obo/PR_000015665) +- [oxytocin receptor sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023122) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) -### photoreceptor cell `http://purl.obolibrary.org/obo/CL_0000210` -#### Removed -- [photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000210) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004211"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [oxytocin receptor sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023122) SubClassOf [cerebral cortex GABAergic interneuron](http://purl.obolibrary.org/obo/CL_0010011) -- [photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000210) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009127"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000210) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004211"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +### pancreatic PP cell `http://purl.obolibrary.org/obo/CL_0002275` -- [photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000210) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009127"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [pancreatic PP cell](http://purl.obolibrary.org/obo/CL_0002275) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002275"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [pancreatic PP cell](http://purl.obolibrary.org/obo/CL_0002275) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -### pigment cell `http://purl.obolibrary.org/obo/CL_0000147` -#### Removed -- [pigment cell](http://purl.obolibrary.org/obo/CL_0000147) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009090"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +Pancreatic polypeptide (PP) cells (also called F or gamma cells) are unique endocrine cells located within the Islets of Langerhans in the pancreas. PP cells are one of the rarer pancreatic cell types and are more prevalent in the head and neck of the pancreas. They are critical in normal pancreatic physiological functions and are involved in the development of pancreatic endocrine disorders. +The primary function of PP cells is the production and secretion of the pancreatic polypeptide hormone (PP). This hormone plays a crucial role in several gastrointestinal functions and metabolic responses. The release of the PP hormone is stimulated after eating, especially in protein-rich meals, leading to it being present in large amounts during digestion. The fundamental role of PP is to self-regulate pancreatic secretion activities ensuring its exocrine and endocrine functions are under control. +The pancreatic polypeptide hormone from PP cells also aids in adapting to low physical activity and fasting by reducing the production of insulin and glucagon and inhibiting the hepatic glucose production. Additionally, this hormone influences gut motility by slowing down the gastric emptying and reducing small intestinal transit, thereby controlling the pace at which nutritional substances are absorbed. Because of these functions, any malfunction or irregularity in PP cells can result in various disorders such as diabetes and pancreatic diseases."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s42255-019-0148-2"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [pigment cell](http://purl.obolibrary.org/obo/CL_0000147) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009090"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.mce.2015.06.028"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/B978-0-12-819402-7.00001-2"^^[string](http://www.w3.org/2001/XMLSchema#string) -### pigment cell (sensu Vertebrata) `http://purl.obolibrary.org/obo/CL_0000342` -#### Removed -- [pigment cell (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000342) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009170"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fendo.2023.1192311"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [pigment cell (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000342) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009170"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/B978-012369442-3/50154-9"^^[string](http://www.w3.org/2001/XMLSchema#string) -### pigment erythroblast `http://purl.obolibrary.org/obo/CL_0005004` -#### Removed -- [pigment erythroblast](http://purl.obolibrary.org/obo/CL_0005004) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005331"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### pancreatic acinar cell `http://purl.obolibrary.org/obo/CL_0002064` #### Added -- [pigment erythroblast](http://purl.obolibrary.org/obo/CL_0005004) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005331"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [pancreatic acinar cell](http://purl.obolibrary.org/obo/CL_0002064) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002064"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [pancreatic acinar cell](http://purl.obolibrary.org/obo/CL_0002064) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -### pigmented epithelial cell `http://purl.obolibrary.org/obo/CL_0000529` -#### Removed -- [pigmented epithelial cell](http://purl.obolibrary.org/obo/CL_0000529) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009241"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +Pancreatic acinar cells are the functional units of the exocrine pancreas. These cells are structurally arranged in small clusters - or acini - with a small central lumen, and their primary function is to produce and secrete enzymes that facilitate digestion of proteins, carbohydrates, and fats within the small intestine. +Some of the most important digestive enzymes synthesized by the pancreatic acinar cells include amylase, which digests carbohydrates, lipase, which breaks down fats, and several proteases such as trypsin and chymotrypsin which are vital for the digestion of proteins. Importantly, these enzymes are produced as proenzymes or zymogens to avoid autolysis, or the breakdown of the pancreas itself. +The release of these enzymes by the pancreatic acinar cells is strictly regulated by hormones and neurochemicals. Cholecystokinin (CCK) released from the enteroendocrine cells in the duodenum cause the release of these enzymes. Moreover, acinar cells also respond to another hormone, secretin, by releasing bicarbonate-rich fluid which helps to neutralize the gastric acid in the duodenum. +Dysregulation in the function of pancreatic acinar cells can lead to severe health issues, including pancreatitis, which is characterized by inflammatory damage to the organ due to the premature activation of digestive enzymes."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1097/01.mog.0000239863.96833.c0"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [pigmented epithelial cell](http://purl.obolibrary.org/obo/CL_0000529) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009241"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK54134/"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/0165-6147(89)90192-2"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nrgastro.2013.36"^^[string](http://www.w3.org/2001/XMLSchema#string) -### pinealocyte `http://purl.obolibrary.org/obo/CL_0000652` -#### Removed -- [pinealocyte](http://purl.obolibrary.org/obo/CL_0000652) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009284"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +### pancreatic epsilon cell `http://purl.obolibrary.org/obo/CL_0005019` #### Added -- [pinealocyte](http://purl.obolibrary.org/obo/CL_0000652) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009284"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [pancreatic epsilon cell](http://purl.obolibrary.org/obo/CL_0005019) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0005019"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [pancreatic epsilon cell](http://purl.obolibrary.org/obo/CL_0005019) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -### pioneer neuron `http://purl.obolibrary.org/obo/CL_0000116` -#### Removed -- [pioneer neuron](http://purl.obolibrary.org/obo/CL_0000116) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009066"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +Pancreatic epsilon cells are a specialized type of endocrine cell found in the islets of Langerhans, a region of the pancreas responsible for hormone production. These clusters of cells constitute only about 1% of the pancreatic islet cell population, making them a relatively small yet significant component of the pancreas. Pancreatic epsilon cells have a round or ovoid shape with occasional cytoplasmic extensions and are characterized by small and spherical granules. +The principal function of pancreatic epsilon cells involves the synthesis and release of the hormone ghrelin, a peptide hormone predominantly produced in the stomach; pancreatic epsilon cells are one of the few sites outside the gastrointestinal tract known to produce this hormone. Ghrelin has multiple vital roles, playing a significant part in generating hunger sensations, promoting fat storage, and influencing various metabolic processes. It also stimulates the release of Growth Hormone (GH) from the anterior pituitary gland. +During fetal development, when they form a layer around the islet, epsilon cells are an important source of ghrelin, likely secreting the hormone into the circulation; their numbers decrease in adults. While research on pancreatic epsilon cells is still ongoing, these cells have been implicated in several disease states, most notably Type 2 diabetes and metabolic syndrome. The dysfunction or reduction in the number of pancreatic epsilon cells can lead to anomalies in ghrelin production, impacting overall metabolic homeostasis and glucose regulation."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fendo.2022.904004"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [pioneer neuron](http://purl.obolibrary.org/obo/CL_0000116) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005128"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3390/ijms20081867"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [pioneer neuron](http://purl.obolibrary.org/obo/CL_0000116) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005128"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s00125-008-1238-y"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [pioneer neuron](http://purl.obolibrary.org/obo/CL_0000116) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009066"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1210/en.2018-00833"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/physrev.00012.2004"^^[string](http://www.w3.org/2001/XMLSchema#string) -### pituitary gland cell `http://purl.obolibrary.org/obo/CL_2000004` -#### Removed -- [pituitary gland cell](http://purl.obolibrary.org/obo/CL_2000004) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + +### paneth cell `http://purl.obolibrary.org/obo/CL_0000510` #### Added -- [pituitary gland cell](http://purl.obolibrary.org/obo/CL_2000004) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [paneth cell](http://purl.obolibrary.org/obo/CL_0000510) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000510"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [paneth cell](http://purl.obolibrary.org/obo/CL_0000510) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -### placental amniotic mesenchymal stromal cell `http://purl.obolibrary.org/obo/CL_2000061` -#### Removed -- [placental amniotic mesenchymal stromal cell](http://purl.obolibrary.org/obo/CL_2000061) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +Paneth cells are specialized epithelial cells that are primarily located at the bottom of the crypts of Lieberkühn in the small intestine, where they play a pivotal role in maintaining gut homeostasis. They have also been found in smaller numbers in the colonic crypts and other parts of the gastrointestinal tract. Paneth cells are characterized by large acidophilic granules, which take up most of the cytoplasmic volume, causing the nucleus to be pushed toward the base of the cell. +Paneth cells function as a part of the innate immune system. The large granules inside the cells are filled with antimicrobial peptides, such as defensins and lysozymes. Upon bacterial intrusion or cellular signaling indicating a potential infection, Paneth cells release the granules containing the antimicrobial substances into the crypt lumen, effectively serving as the first line of defense against bacterial invasion within the gastrointestinal tract. In essence, Paneth cells serve as guardians, protecting the intestinal stem cells from harmful pathogens that may disturb the gut ecosystem. +In addition to their primary role in immunity, Paneth cells are also crucial for supporting the stem cell niche in the intestinal crypts. They are located adjacent to Lgr5+ stem cells and secrete various growth factors such as EGF, TGF-alpha, Wnt3, and Notch ligand Dll4. These factors regulate the self-renewal and differentiation of these stem cells, which continuously replenish the intestinal epithelium. Consequently, any abnormality or dysfunction in Paneth cells could lead to a disturbance in gut homeostasis, possibly resulting in various illnesses such as inflammatory bowel disease."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nature09637"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [placental amniotic mesenchymal stromal cell](http://purl.obolibrary.org/obo/CL_2000061) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fimmu.2020.00587"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1146/annurev-physiol-030212-183744"^^[string](http://www.w3.org/2001/XMLSchema#string) -### placental pericyte `http://purl.obolibrary.org/obo/CL_2000078` -#### Removed -- [placental pericyte](http://purl.obolibrary.org/obo/CL_2000078) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nrmicro2546"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s00018-002-8412-z"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### parafollicular cell `http://purl.obolibrary.org/obo/CL_0000570` #### Added -- [placental pericyte](http://purl.obolibrary.org/obo/CL_2000078) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [parafollicular cell](http://purl.obolibrary.org/obo/CL_0000570) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### placental villous trophoblast `http://purl.obolibrary.org/obo/CL_2000060` -#### Removed -- [placental villous trophoblast](http://purl.obolibrary.org/obo/CL_2000060) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +### parietal epithelial cell `http://purl.obolibrary.org/obo/CL_1000452` #### Added -- [placental villous trophoblast](http://purl.obolibrary.org/obo/CL_2000060) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [parietal epithelial cell](http://purl.obolibrary.org/obo/CL_1000452) SubClassOf [squamous epithelial cell](http://purl.obolibrary.org/obo/CL_0000076) -### placental villus capillary endothelial cell `http://purl.obolibrary.org/obo/CL_2000062` +### perineurial cell `http://purl.obolibrary.org/obo/CL_0002576` #### Removed -- [placental villus capillary endothelial cell](http://purl.obolibrary.org/obo/CL_2000062) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +- [perineurial cell](http://purl.obolibrary.org/obo/CL_0002576) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A glial cell that is part of the perineurium. This cell type has thin long bipolar cytoplasmic processes, pinocytotic vesicles, fragments of external lamina and/or external lamina-like material, attachment plaques, and desmosome-like junctions. Perineurial cells historically have been referred to as fibroblasts because of shape; however, unlike fibroblasts, a perineurial cell: does not have a compact nucleus and large endoplasmic reticulum; does have a double basement membrane opposed to a single basal lamina; is carefully joined to other perineurial cells by tight junctions into a single sheet as opposed to arranged in a large mass; and finally, can surround a small axon bundle at a nerve terminal whereas a fibroblast cannot."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:25818566"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NCIT:C41442"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [placental villus capillary endothelial cell](http://purl.obolibrary.org/obo/CL_2000062) EquivalentTo [capillary endothelial cell](http://purl.obolibrary.org/obo/CL_0002144) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0010005](http://purl.obolibrary.org/obo/UBERON_0010005)) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://en.wikipedia.org/wiki/Perineurium"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [placental villus capillary endothelial cell](http://purl.obolibrary.org/obo/CL_2000062) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0010005](http://purl.obolibrary.org/obo/UBERON_0010005) + - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "https://orcid.org/0000-0001-7655-4833"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [placental villus capillary endothelial cell](http://purl.obolibrary.org/obo/CL_2000062) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [perineurial cell](http://purl.obolibrary.org/obo/CL_0002576) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-7655-4833](https://orcid.org/0000-0001-7655-4833) -- [placental villus capillary endothelial cell](http://purl.obolibrary.org/obo/CL_2000062) EquivalentTo [capillary endothelial cell](http://purl.obolibrary.org/obo/CL_0002144) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001987](http://purl.obolibrary.org/obo/UBERON_0001987)) +- [perineurial cell](http://purl.obolibrary.org/obo/CL_0002576) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A glial cell that is part of the perineurium. This cell type has thin long bipolar cytoplasmic processes, pinocytotic vesicles, fragments of external lamina and/or external lamina-like material, attachment plaques, and desmosome-like junctions. Perineurial cells historically have been referred to as fibroblasts because of shape; however, unlike fibroblasts, a perineurial cell: does not have a compact nucleus and large endoplasmic reticulum; does have a double basement membrane opposed to a single basal lamina; is carefully joined to other perineurial cells by tight junctions into a single sheet as opposed to arranged in a large mass; and finally, can surround a small axon bundle at a nerve terminal whereas a fibroblast cannot."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:25818566"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GO:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) -### plasma cell `http://purl.obolibrary.org/obo/CL_0000786` -#### Removed -- [plasma cell](http://purl.obolibrary.org/obo/CL_0000786) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009332"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "NCIT:C41442"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [plasma cell](http://purl.obolibrary.org/obo/CL_0000786) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009332"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://en.wikipedia.org/wiki/Perineurium"^^[string](http://www.w3.org/2001/XMLSchema#string) -### plasmatocyte `http://purl.obolibrary.org/obo/CL_0000394` -#### Removed -- [plasmatocyte](http://purl.obolibrary.org/obo/CL_0000394) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00001685"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +### peripheral blood mesothelial cell `http://purl.obolibrary.org/obo/CL_0002318` #### Added -- [plasmatocyte](http://purl.obolibrary.org/obo/CL_0000394) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00001685"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [peripheral blood mesothelial cell](http://purl.obolibrary.org/obo/CL_0002318) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### podocyte `http://purl.obolibrary.org/obo/CL_0000653` -#### Removed -- [podocyte](http://purl.obolibrary.org/obo/CL_0000653) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009285"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### peritoneal macrophage `http://purl.obolibrary.org/obo/CL_0000581` #### Added -- [podocyte](http://purl.obolibrary.org/obo/CL_0000653) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009285"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [peritoneal macrophage](http://purl.obolibrary.org/obo/CL_0000581) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### pole cell `http://purl.obolibrary.org/obo/CL_0000301` -#### Removed -- [pole cell](http://purl.obolibrary.org/obo/CL_0000301) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000092"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +### perivascular macrophage `http://purl.obolibrary.org/obo/CL_0000881` #### Added -- [pole cell](http://purl.obolibrary.org/obo/CL_0000301) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00000092"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [perivascular macrophage](http://purl.obolibrary.org/obo/CL_0000881) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### polychromatophilic erythroblast `http://purl.obolibrary.org/obo/CL_0000550` +### phagocyte (sensu Vertebrata) `http://purl.obolibrary.org/obo/CL_0000518` #### Removed -- [polychromatophilic erythroblast](http://purl.obolibrary.org/obo/CL_0000550) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005241"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [phagocyte (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000518) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_7742](http://purl.obolibrary.org/obo/NCBITaxon_7742) #### Added -- [polychromatophilic erythroblast](http://purl.obolibrary.org/obo/CL_0000550) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005241"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [phagocyte (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000518) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_7742](http://purl.obolibrary.org/obo/NCBITaxon_7742) -### polymodal neuron `http://purl.obolibrary.org/obo/CL_0000102` +### photoreceptor cell `http://purl.obolibrary.org/obo/CL_0000210` #### Removed -- [polymodal neuron](http://purl.obolibrary.org/obo/CL_0000102) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009054"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000210) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cell specialized to detect and transduce light."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D010786"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [polymodal neuron](http://purl.obolibrary.org/obo/CL_0000102) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009054"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000210) EquivalentTo [neuron](http://purl.obolibrary.org/obo/CL_0000540) and ([RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0050962](http://purl.obolibrary.org/obo/GO_0050962)) +- [photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000210) SubClassOf [neuronal receptor cell](http://purl.obolibrary.org/obo/CL_0000006) + - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) -### posterior lateral line neuromast hair cell `http://purl.obolibrary.org/obo/CL_2000037` -#### Removed -- [posterior lateral line neuromast hair cell](http://purl.obolibrary.org/obo/CL_2000037) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +- [photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000210) SubClassOf [RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0050962](http://purl.obolibrary.org/obo/GO_0050962) #### Added -- [posterior lateral line neuromast hair cell](http://purl.obolibrary.org/obo/CL_2000037) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000210) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cell specialized in detecting light stimuli that are involved in visual perception."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D010786"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000210) EquivalentTo [neuron](http://purl.obolibrary.org/obo/CL_0000540) and ([RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0050908](http://purl.obolibrary.org/obo/GO_0050908)) -### posterior lateral line neuromast mantle cell `http://purl.obolibrary.org/obo/CL_2000038` -#### Removed -- [posterior lateral line neuromast mantle cell](http://purl.obolibrary.org/obo/CL_2000038) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +- [photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000210) SubClassOf [sensory neuron](http://purl.obolibrary.org/obo/CL_0000101) -#### Added -- [posterior lateral line neuromast mantle cell](http://purl.obolibrary.org/obo/CL_2000038) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000210) SubClassOf [visual system neuron](http://purl.obolibrary.org/obo/CL_0008028) + +- [photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000210) SubClassOf [RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0050908](http://purl.obolibrary.org/obo/GO_0050908) -### posterior lateral line neuromast supporting cell `http://purl.obolibrary.org/obo/CL_2000039` +### pigment cell (sensu Vertebrata) `http://purl.obolibrary.org/obo/CL_0000342` #### Removed -- [posterior lateral line neuromast supporting cell](http://purl.obolibrary.org/obo/CL_2000039) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +- [pigment cell (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000342) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_7742](http://purl.obolibrary.org/obo/NCBITaxon_7742) #### Added -- [posterior lateral line neuromast supporting cell](http://purl.obolibrary.org/obo/CL_2000039) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [pigment cell (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000342) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_7742](http://purl.obolibrary.org/obo/NCBITaxon_7742) -### pre-granulosa cell `http://purl.obolibrary.org/obo/CL_4033066` +### pigmented ciliary epithelial cell `http://purl.obolibrary.org/obo/CL_0002303` #### Added -- [pre-granulosa cell](http://purl.obolibrary.org/obo/CL_4033066) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4033066"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [pre-granulosa cell](http://purl.obolibrary.org/obo/CL_4033066) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-7655-4833](https://orcid.org/0000-0001-7655-4833) - -- [pre-granulosa cell](http://purl.obolibrary.org/obo/CL_4033066) [date](http://purl.org/dc/terms/date) "2024-06-07T12:04:57Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) +- [pigmented ciliary epithelial cell](http://purl.obolibrary.org/obo/CL_0002303) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002303"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [pre-granulosa cell](http://purl.obolibrary.org/obo/CL_4033066) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pregranulosa cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:17639032"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [pigmented ciliary epithelial cell](http://purl.obolibrary.org/obo/CL_0002303) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32759216"^^[string](http://www.w3.org/2001/XMLSchema#string) +Pigmented ciliary epithelial cells, which are a type of pigment cell, have a crucial function within the eye's ciliary body. The ciliary body, located behind the iris, is one of the eye’s most vital structures and consists of two types of epithelial cells: the pigmented and the non-pigmented ciliary epithelial cells. The pigmented ciliary epithelial cells form the outer layer of the ciliary body and exhibit a black or brown pigmentation due to the melanin they contain. +One key function of pigmented ciliary epithelial cells is to aid in the formation of aqueous humor, an intraocular fluid that nourishes the cornea and lens, and maintains intraocular pressure which is essential for the eye’s shape and light refraction. These cells facilitate this function in conjunction with the non-pigmented ciliary epithelial cells. Together, the pigmented and non-pigmented ciliary epithelial cells form a bilayer epithelium that allows the secretion of aqueous humor through a bi-directional fluid transport mechanism. +Pigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, a physiological frontier that controls the entry and exit of various substances from the blood to the aqueous humor and vice versa. The pigmentation in these cells, intensified by melanin, helps to absorb scattered light coming into the eye, reducing any potential damage and glare."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1444-0938.2002.tb02384.x"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [pre-granulosa cell](http://purl.obolibrary.org/obo/CL_4033066) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "PG cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/S1569-2590(05)10005-6"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32759216"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [pre-granulosa cell](http://purl.obolibrary.org/obo/CL_4033066) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ovarian pregranulosa cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32759216"^^[string](http://www.w3.org/2001/XMLSchema#string) +### plasma cell `http://purl.obolibrary.org/obo/CL_0000786` -- [pre-granulosa cell](http://purl.obolibrary.org/obo/CL_4033066) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) +#### Added +- [plasma cell](http://purl.obolibrary.org/obo/CL_0000786) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -- [pre-granulosa cell](http://purl.obolibrary.org/obo/CL_4033066) [label](http://www.w3.org/2000/01/rdf-schema#label) "pre-granulosa cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [pre-granulosa cell](http://purl.obolibrary.org/obo/CL_4033066) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A supporting cell that is part of the ovary and differentiates into a granulosa cell. A pre-granulosa cell develops from an early supporting gonadal cell by repressing testis determination, which can then proliferate to form primordial follicles."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33970370"^^[string](http://www.w3.org/2001/XMLSchema#string) +### podocyte `http://purl.obolibrary.org/obo/CL_0000653` - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:17639032"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [podocyte](http://purl.obolibrary.org/obo/CL_0000653) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32759216"^^[string](http://www.w3.org/2001/XMLSchema#string) +Podocytes are highly specialized, terminally differentiated glomerular visceral epithelial cells that wrap around the capillaries in the kidneys. They play an essential role in kidney function, particularly in the filtration selectivity of the glomerulus. Each podocyte is characterized by a unique architecture with a large cell body, ‘major processes’ extending outwardly from the cell body and ‘foot processes’, also known as pedicels, which surround. the glomerular capillary loops +Podocytes represent the last barrier of the glomerular filtration membrane in the kidney. This barrier prevents the leakage of plasma proteins from the blood into the urine, hence maintaining protein homeostasis in the body. The foot processes of the podocytes interdigitate with those from neighboring cells. The cell-cell junctions between the foot processes, the slit-diaphragms, are thought to create a molecular sensor of renal filtration that prevents the passage of macromolecules while allowing water and small solutes to pass. +Podocytes also contribute to the glomerular basement membrane by secreting collagen and maintain glomerular endothelial cell fenestration by secreting VEGFA. They have been shown to play a role in inducing cytoskeletal regulation, cell adhesion, and inflammatory response, consistent with their essential function in the kidney. +The importance of podocytes is further emphasized by the effects of their damage or loss. Abnormalities in podocytes often result in severe kidney diseases (podocytopathies), including focal segmental glomerulosclerosis (FSGS) and minimal change disease (MCD). Injury to the podocytes can result in "effacement" or flattening of foot processes, leading to increased permeability of the filtration barrier and proteinuria (an excess of serum protein in urine) which is a common symptom of kidney diseases."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41572-020-0196-7"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:38178246"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1146/annurev-physiol-020911-153238"^^[string](http://www.w3.org/2001/XMLSchema#string) -- Class: [pre-granulosa cell](http://purl.obolibrary.org/obo/CL_4033066) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41467-022-33748-1"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [pre-granulosa cell](http://purl.obolibrary.org/obo/CL_4033066) SubClassOf [supporting cell](http://purl.obolibrary.org/obo/CL_0000630) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1159/000481633"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [pre-granulosa cell](http://purl.obolibrary.org/obo/CL_4033066) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000992](http://purl.obolibrary.org/obo/UBERON_0000992) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fcell.2021.771931"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [pre-granulosa cell](http://purl.obolibrary.org/obo/CL_4033066) SubClassOf [RO_0002210](http://purl.obolibrary.org/obo/RO_0002210) some [granulosa cell](http://purl.obolibrary.org/obo/CL_0000501) +- [podocyte](http://purl.obolibrary.org/obo/CL_0000653) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000653"^^[string](http://www.w3.org/2001/XMLSchema#string) -### precursor B cell `http://purl.obolibrary.org/obo/CL_0000817` -#### Removed -- [precursor B cell](http://purl.obolibrary.org/obo/CL_0000817) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009344"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### polychromatophilic erythroblast `http://purl.obolibrary.org/obo/CL_0000550` #### Added -- [precursor B cell](http://purl.obolibrary.org/obo/CL_0000817) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009344"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [polychromatophilic erythroblast](http://purl.obolibrary.org/obo/CL_0000550) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### premigratory neural crest cell `http://purl.obolibrary.org/obo/CL_0007004` -#### Removed -- [premigratory neural crest cell](http://purl.obolibrary.org/obo/CL_0007004) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0007084"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### pre-conventional dendritic cell `http://purl.obolibrary.org/obo/CL_0002010` #### Added -- [premigratory neural crest cell](http://purl.obolibrary.org/obo/CL_0007004) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0007084"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [pre-conventional dendritic cell](http://purl.obolibrary.org/obo/CL_0002010) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### pressoreceptor cell `http://purl.obolibrary.org/obo/CL_0000602` +### pre-granulosa cell `http://purl.obolibrary.org/obo/CL_4033066` #### Removed -- [pressoreceptor cell](http://purl.obolibrary.org/obo/CL_0000602) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009274"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [pre-granulosa cell](http://purl.obolibrary.org/obo/CL_4033066) SubClassOf [RO_0002210](http://purl.obolibrary.org/obo/RO_0002210) some [granulosa cell](http://purl.obolibrary.org/obo/CL_0000501) #### Added -- [pressoreceptor cell](http://purl.obolibrary.org/obo/CL_0000602) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009274"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [pre-granulosa cell](http://purl.obolibrary.org/obo/CL_4033066) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) +- [pre-granulosa cell](http://purl.obolibrary.org/obo/CL_4033066) SubClassOf [RO_0002210](http://purl.obolibrary.org/obo/RO_0002210) some [squamous granulosa cell](http://purl.obolibrary.org/obo/CL_4033083) -### primary interneuron (sensu Teleostei) `http://purl.obolibrary.org/obo/CL_0000534` -#### Removed -- [primary interneuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000534) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009245"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +### pre-natural killer cell `http://purl.obolibrary.org/obo/CL_0000937` #### Added -- [primary interneuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000534) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009245"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [pre-natural killer cell](http://purl.obolibrary.org/obo/CL_0000937) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### primary motor cortex pyramidal cell `http://purl.obolibrary.org/obo/CL_2000049` -#### Removed -- [primary motor cortex pyramidal cell](http://purl.obolibrary.org/obo/CL_2000049) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +### pre-theca cell `http://purl.obolibrary.org/obo/CL_4052010` #### Added -- [primary motor cortex pyramidal cell](http://purl.obolibrary.org/obo/CL_2000049) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [pre-theca cell](http://purl.obolibrary.org/obo/CL_4052010) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "progenitor theca cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31320652"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [pre-theca cell](http://purl.obolibrary.org/obo/CL_4052010) [date](http://purl.org/dc/terms/date) "2024-09-25T11:15:57Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -### primary motor neuron (sensu Teleostei) `http://purl.obolibrary.org/obo/CL_0000533` -#### Removed -- [primary motor neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000533) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009244"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [pre-theca cell](http://purl.obolibrary.org/obo/CL_4052010) [label](http://www.w3.org/2000/01/rdf-schema#label) "pre-theca cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [primary motor neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000533) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009244"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [pre-theca cell](http://purl.obolibrary.org/obo/CL_4052010) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A stromal cell that serves as a precursor to the theca cell layers in the ovary growing follicles. This cell is present in the early stages of follicular growth, particularly in smaller follicles. Unlike mature theca cell, a pre-theca cell is initially non-steroidogenic and lacks luteinizing hormone receptors."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20628033"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31320652"^^[string](http://www.w3.org/2001/XMLSchema#string) -### primary neuron (sensu Teleostei) `http://purl.obolibrary.org/obo/CL_0000530` -#### Removed -- [primary neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000530) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009242"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36205477"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [primary neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000530) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009242"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [pre-theca cell](http://purl.obolibrary.org/obo/CL_4052010) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) +- [pre-theca cell](http://purl.obolibrary.org/obo/CL_4052010) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "early theca cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36205477"^^[string](http://www.w3.org/2001/XMLSchema#string) -### primordial germ cell `http://purl.obolibrary.org/obo/CL_0000670` -#### Removed -- [primordial germ cell](http://purl.obolibrary.org/obo/CL_0000670) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009288"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [pre-theca cell](http://purl.obolibrary.org/obo/CL_4052010) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052010"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [primordial germ cell](http://purl.obolibrary.org/obo/CL_0000670) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009288"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [pre-theca cell](http://purl.obolibrary.org/obo/CL_4052010) +- [pre-theca cell](http://purl.obolibrary.org/obo/CL_4052010) SubClassOf [RO_0002203](http://purl.obolibrary.org/obo/RO_0002203) some [theca cell](http://purl.obolibrary.org/obo/CL_0000503) -### pro-B cell `http://purl.obolibrary.org/obo/CL_0000826` -#### Removed -- [pro-B cell](http://purl.obolibrary.org/obo/CL_0000826) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009349"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [pre-theca cell](http://purl.obolibrary.org/obo/CL_4052010) SubClassOf [stromal cell of ovary](http://purl.obolibrary.org/obo/CL_0002132) -#### Added -- [pro-B cell](http://purl.obolibrary.org/obo/CL_0000826) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009349"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [pre-theca cell](http://purl.obolibrary.org/obo/CL_4052010) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0012186](http://purl.obolibrary.org/obo/UBERON_0012186) -### pro-NK cell `http://purl.obolibrary.org/obo/CL_0000825` -#### Removed -- [pro-NK cell](http://purl.obolibrary.org/obo/CL_0000825) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009348"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### preameloblast `http://purl.obolibrary.org/obo/CL_0007000` #### Added -- [pro-NK cell](http://purl.obolibrary.org/obo/CL_0000825) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009348"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [preameloblast](http://purl.obolibrary.org/obo/CL_0007000) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### pro-T cell `http://purl.obolibrary.org/obo/CL_0000827` -#### Removed -- [pro-T cell](http://purl.obolibrary.org/obo/CL_0000827) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009350"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### precementoblast `http://purl.obolibrary.org/obo/CL_0007002` #### Added -- [pro-T cell](http://purl.obolibrary.org/obo/CL_0000827) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009350"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [precementoblast](http://purl.obolibrary.org/obo/CL_0007002) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### procrystal cell `http://purl.obolibrary.org/obo/CL_0000395` +### primary neuron (sensu Teleostei) `http://purl.obolibrary.org/obo/CL_0000530` #### Removed -- [procrystal cell](http://purl.obolibrary.org/obo/CL_0000395) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00001689"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [primary neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000530) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) + +- [primary neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000530) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_32443](http://purl.obolibrary.org/obo/NCBITaxon_32443) + - [IAO_0000233](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/obophenotype/cell-ontology/pull/1950"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [procrystal cell](http://purl.obolibrary.org/obo/CL_0000395) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00001689"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [primary neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000530) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_32443](http://purl.obolibrary.org/obo/NCBITaxon_32443) + - [IAO_0000233](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/obophenotype/cell-ontology/pull/1950"^^[string](http://www.w3.org/2001/XMLSchema#string) -### professional antigen presenting cell `http://purl.obolibrary.org/obo/CL_0000145` -#### Removed -- [professional antigen presenting cell](http://purl.obolibrary.org/obo/CL_0000145) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009088"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### primary spermatocyte `http://purl.obolibrary.org/obo/CL_0000656` #### Added -- [professional antigen presenting cell](http://purl.obolibrary.org/obo/CL_0000145) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009088"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [primary spermatocyte](http://purl.obolibrary.org/obo/CL_0000656) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### progesterone secreting cell `http://purl.obolibrary.org/obo/CL_0000179` -#### Removed -- [progesterone secreting cell](http://purl.obolibrary.org/obo/CL_0000179) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009109"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### primitive erythroid progenitor `http://purl.obolibrary.org/obo/CL_0002361` #### Added -- [progesterone secreting cell](http://purl.obolibrary.org/obo/CL_0000179) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009109"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [primitive erythroid progenitor](http://purl.obolibrary.org/obo/CL_0002361) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### prohemocyte (sensu Nematoda and Protostomia) `http://purl.obolibrary.org/obo/CL_0000385` -#### Removed -- [prohemocyte (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000385) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005062"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +### primitive red blood cell `http://purl.obolibrary.org/obo/CL_0002355` #### Added -- [prohemocyte (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0000385) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005062"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [primitive red blood cell](http://purl.obolibrary.org/obo/CL_0002355) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### prolactin secreting cell `http://purl.obolibrary.org/obo/CL_0000439` -#### Removed -- [prolactin secreting cell](http://purl.obolibrary.org/obo/CL_0000439) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009204"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### pro-B cell `http://purl.obolibrary.org/obo/CL_0000826` #### Added -- [prolactin secreting cell](http://purl.obolibrary.org/obo/CL_0000439) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009204"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [pro-B cell](http://purl.obolibrary.org/obo/CL_0000826) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### promonocyte `http://purl.obolibrary.org/obo/CL_0000559` -#### Removed -- [promonocyte](http://purl.obolibrary.org/obo/CL_0000559) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009253"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### pro-NK cell `http://purl.obolibrary.org/obo/CL_0000825` #### Added -- [promonocyte](http://purl.obolibrary.org/obo/CL_0000559) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009253"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [pro-NK cell](http://purl.obolibrary.org/obo/CL_0000825) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### prostate gland microvascular endothelial cell `http://purl.obolibrary.org/obo/CL_2000059` -#### Removed -- [prostate gland microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000059) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +### proerythroblast `http://purl.obolibrary.org/obo/CL_0000547` #### Added -- [prostate gland microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000059) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [proerythroblast](http://purl.obolibrary.org/obo/CL_0000547) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### pseudounipolar neuron `http://purl.obolibrary.org/obo/CL_0000105` -#### Removed -- [pseudounipolar neuron](http://purl.obolibrary.org/obo/CL_0000105) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009057"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### progenitor cell `http://purl.obolibrary.org/obo/CL_0011026` #### Added -- [pseudounipolar neuron](http://purl.obolibrary.org/obo/CL_0000105) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009057"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### pulmonary alveolar epithelial cell `http://purl.obolibrary.org/obo/CL_0000322` -#### Removed -- [pulmonary alveolar epithelial cell](http://purl.obolibrary.org/obo/CL_0000322) [label](http://www.w3.org/2000/01/rdf-schema#label) "pneumocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [progenitor cell](http://purl.obolibrary.org/obo/CL_0011026) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -- [pulmonary alveolar epithelial cell](http://purl.obolibrary.org/obo/CL_0000322) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell that lines the peripheral gas exchange region of the lungs of air-breathing vertebrates."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20054144"^^[string](http://www.w3.org/2001/XMLSchema#string) +### progesterone secreting cell `http://purl.obolibrary.org/obo/CL_0000179` #### Added -- [pulmonary alveolar epithelial cell](http://purl.obolibrary.org/obo/CL_0000322) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell that lines the peripheral gas exchange region of the lungs of air-breathing vertebrates."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29463737"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [progesterone secreting cell](http://purl.obolibrary.org/obo/CL_0000179) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20054144"^^[string](http://www.w3.org/2001/XMLSchema#string) +### promonocyte `http://purl.obolibrary.org/obo/CL_0000559` -- [pulmonary alveolar epithelial cell](http://purl.obolibrary.org/obo/CL_0000322) [label](http://www.w3.org/2000/01/rdf-schema#label) "pulmonary alveolar epithelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [promonocyte](http://purl.obolibrary.org/obo/CL_0000559) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -- [pulmonary alveolar epithelial cell](http://purl.obolibrary.org/obo/CL_0000322) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "pneumocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32491474"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [pulmonary alveolar epithelial cell](http://purl.obolibrary.org/obo/CL_0000322) SubClassOf [epithelial cell of lung](http://purl.obolibrary.org/obo/CL_0000082) +### promyelocyte `http://purl.obolibrary.org/obo/CL_0000836` +#### Added +- [promyelocyte](http://purl.obolibrary.org/obo/CL_0000836) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### pulmonary alveolar type 1 cell `http://purl.obolibrary.org/obo/CL_0002062` -#### Removed -- [pulmonary alveolar type 1 cell](http://purl.obolibrary.org/obo/CL_0002062) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A type I pneumocyte is a flattened, branched pneumocyte that covers more than 98% of the alveolar surface. This large cell has thin (50-100 nm) cytoplasmic extensions to form the air-blood barrier essential for normal gas exchange."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://www.copewithcytokines.de"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) +### pronephric podocyte `http://purl.obolibrary.org/obo/CL_4030008` +#### Removed +- [pronephric podocyte](http://purl.obolibrary.org/obo/CL_4030008) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A specialized epithelial cell that contains "feet" that interdigitate with the "feet" of other glomerular epithelial cells in the pronephros."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0002-2244-7917"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20054144"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:10322630"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [pulmonary alveolar type 1 cell](http://purl.obolibrary.org/obo/CL_0002062) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "AT1"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [pronephric podocyte](http://purl.obolibrary.org/obo/CL_4030008) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A specialized epithelial cell that contains "feet" that interdigitate with the "feet" of other glomerular epithelial cells in the pronephros."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:10322630"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [pulmonary alveolar type 1 cell](http://purl.obolibrary.org/obo/CL_0002062) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ATI"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [pronephric podocyte](http://purl.obolibrary.org/obo/CL_4030008) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-2244-7917](https://orcid.org/0000-0002-2244-7917) -- [pulmonary alveolar type 1 cell](http://purl.obolibrary.org/obo/CL_0002062) [label](http://www.w3.org/2000/01/rdf-schema#label) "type I pneumocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [pulmonary alveolar type 1 cell](http://purl.obolibrary.org/obo/CL_0002062) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "type 1 pneumocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) +### pulmonary alveolar epithelial cell `http://purl.obolibrary.org/obo/CL_0000322` +#### Removed +- [pulmonary alveolar epithelial cell](http://purl.obolibrary.org/obo/CL_0000322) SubClassOf [epithelial cell of alveolus of lung](http://purl.obolibrary.org/obo/CL_0010003) #### Added -- [pulmonary alveolar type 1 cell](http://purl.obolibrary.org/obo/CL_0002062) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A squamous pulmonary alveolar epithelial cell that is flattened and branched. A pulmonary alveolar type 1 cell covers more than 98% of the alveolar surface. This large cell has thin (50-100 nm) cytoplasmic extensions to form the air-blood barrier essential for normal gas exchange."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29463737"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [pulmonary alveolar epithelial cell](http://purl.obolibrary.org/obo/CL_0000322) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "alveolus of lung epithelial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://www.copewithcytokines.de"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [pulmonary alveolar epithelial cell](http://purl.obolibrary.org/obo/CL_0000322) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "epithelial cell of alveolus of lung"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [pulmonary alveolar epithelial cell](http://purl.obolibrary.org/obo/CL_0000322) [date](http://purl.org/dc/terms/date) "2024-09-02T08:27:21Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20054144"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [pulmonary alveolar epithelial cell](http://purl.obolibrary.org/obo/CL_0000322) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D056809"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [pulmonary alveolar type 1 cell](http://purl.obolibrary.org/obo/CL_0002062) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "AT1"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29463737"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [pulmonary alveolar epithelial cell](http://purl.obolibrary.org/obo/CL_0000322) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) +- [pulmonary alveolar epithelial cell](http://purl.obolibrary.org/obo/CL_0000322) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004821](http://purl.obolibrary.org/obo/UBERON_0004821)) -- [pulmonary alveolar type 1 cell](http://purl.obolibrary.org/obo/CL_0002062) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ATI"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) +- [pulmonary alveolar epithelial cell](http://purl.obolibrary.org/obo/CL_0000322) SubClassOf [squamous epithelial cell](http://purl.obolibrary.org/obo/CL_0000076) -- [pulmonary alveolar type 1 cell](http://purl.obolibrary.org/obo/CL_0002062) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "type 1 pneumocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32491474"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [pulmonary alveolar type 1 cell](http://purl.obolibrary.org/obo/CL_0002062) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "type I pneumocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) +### pulmonary ionocyte `http://purl.obolibrary.org/obo/CL_0017000` -- [pulmonary alveolar type 1 cell](http://purl.obolibrary.org/obo/CL_0002062) [label](http://www.w3.org/2000/01/rdf-schema#label) "pulmonary alveolar type 1 cell"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [pulmonary ionocyte](http://purl.obolibrary.org/obo/CL_0017000) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +The pulmonary ionocyte is a relatively newly identified, specific epithelial cell type found primarily in the pulmonary or respiratory system. Discovered through novel mapping techniques in 2018, these cells are surprisingly rare, making up less than 2% of the cells in the lung's airway, yet they play an essential role in the airway surface liquid and mucus regulation, a crucial factor in lung health. +The main responsibility of the pulmonary ionocyte pertains to the regulation and mobilization of chloride ions. They express a high level of CFTR (Cystic Fibrosis Transmembrane Conductance Regulator) gene, which encodes a protein channel across the membrane of cells that produce mucus, sweat, saliva, tears, and digestive enzymes. The activity of CFTR regulates the movement of chloride ions and fluids in and out of cells, which helps maintain a balance of fluid in the organs they are expressed in. If CFTR is dysfunctional, it can cause conditions such as cystic fibrosis, characterized by thick, sticky mucus that can clog the lungs and obstruct the pancreas, leading to respiratory and digestive issues. +The discovery of this cell type offers new doors to the treatment and further understanding of diseases like cystic fibrosis. Increased understanding of pulmonary ionocytes could contribute to the development of novel therapeutic approaches to manipulate the function of CFTR in the lungs and other organs affected by dysfunctional CFTR."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1146/annurev-pathol-042420-094031"^^[string](http://www.w3.org/2001/XMLSchema#string) -### pulmonary alveolar type 2 cell `http://purl.obolibrary.org/obo/CL_0002063` -#### Removed -- [pulmonary alveolar type 2 cell](http://purl.obolibrary.org/obo/CL_0002063) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "TII"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41586-018-0393-7"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [pulmonary alveolar type 2 cell](http://purl.obolibrary.org/obo/CL_0002063) [label](http://www.w3.org/2000/01/rdf-schema#label) "type II pneumocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1172/JCI171268"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [pulmonary alveolar type 2 cell](http://purl.obolibrary.org/obo/CL_0002063) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "ATII"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [pulmonary ionocyte](http://purl.obolibrary.org/obo/CL_0017000) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0017000"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [pulmonary alveolar type 2 cell](http://purl.obolibrary.org/obo/CL_0002063) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A type II pneumocyte is a pneumocyte that modulates the fluid surrounding the alveolar epithelium by secreting and recycling surfactants. This cell type also contributes to tissue repair and can differentiate after injury into a type I pneumocyte. Thicker than squamous alveolar cells, have a rounded apical surface that projects above the level of surrounding epithelium. The free surface is covered by short microvilli."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:8540632"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://www.copewithcytokines.de"^^[string](http://www.w3.org/2001/XMLSchema#string) +### pvalb GABAergic cortical interneuron `http://purl.obolibrary.org/obo/CL_4023018` +#### Removed +- [pvalb GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023018) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A GABAergic interneuron located in the cerebral cortex that expresses Parvalbumin."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27477017"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0412046911"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [pvalb GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023018) EquivalentTo [interneuron](http://purl.obolibrary.org/obo/CL_0000099) and ([RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_0000956](http://purl.obolibrary.org/obo/UBERON_0000956)) and ([RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0061534](http://purl.obolibrary.org/obo/GO_0061534)) and ([RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000013502](http://purl.obolibrary.org/obo/PR_000013502)) -- [pulmonary alveolar type 2 cell](http://purl.obolibrary.org/obo/CL_0002063) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "AT2"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [pvalb GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023018) SubClassOf [cerebral cortex GABAergic interneuron](http://purl.obolibrary.org/obo/CL_0010011) -- [pulmonary alveolar type 2 cell](http://purl.obolibrary.org/obo/CL_0002063) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) +- [pvalb GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023018) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) #### Added -- [pulmonary alveolar type 2 cell](http://purl.obolibrary.org/obo/CL_0002063) [label](http://www.w3.org/2000/01/rdf-schema#label) "pulmonary alveolar type 2 cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [pulmonary alveolar type 2 cell](http://purl.obolibrary.org/obo/CL_0002063) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A pulmonary alveolar epithelial cell that modulates the fluid surrounding the alveolar epithelium by secreting and recycling surfactants. This cell type also contributes to tissue repair and can differentiate after injury into a pulmonary alveolar type 1 cell. This cuboidal cell is thicker than squamous alveolar cells, have a rounded apical surface that projects above the level of surrounding epithelium. The free surface is covered by short microvilli."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:8540632"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://www.copewithcytokines.de"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [pvalb GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023018) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A transcriptomically distinct GABAergic interneuron with a soma located in a cerebral cortex and it expresses Parvalbumin. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: MGE-derived interneurons', Author Categories: 'CrossArea_subclass', cluster Pvalb."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27477017"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0412046911"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) - - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36138472"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [pulmonary alveolar type 2 cell](http://purl.obolibrary.org/obo/CL_0002063) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "type II pneumocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32491474"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/e/9c63201d-bfd9-41a8-bbbc-18d947556f3d.cxg/"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [pulmonary alveolar type 2 cell](http://purl.obolibrary.org/obo/CL_0002063) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "AT2"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) +- [pvalb GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023018) EquivalentTo [medial ganglionic eminence derived GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023069) and ([RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_0000956](http://purl.obolibrary.org/obo/UBERON_0000956)) and ([RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0061534](http://purl.obolibrary.org/obo/GO_0061534)) and ([RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000013502](http://purl.obolibrary.org/obo/PR_000013502)) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36138472"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [pvalb GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023018) SubClassOf [medial ganglionic eminence derived GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023069) -- [pulmonary alveolar type 2 cell](http://purl.obolibrary.org/obo/CL_0002063) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "TII"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [pulmonary alveolar type 2 cell](http://purl.obolibrary.org/obo/CL_0002063) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "ATII"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) +### renal alpha-intercalated cell `http://purl.obolibrary.org/obo/CL_0005011` +#### Added +- [renal alpha-intercalated cell](http://purl.obolibrary.org/obo/CL_0005011) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0005011"^^[string](http://www.w3.org/2001/XMLSchema#string) -### pulmonary ionocyte `http://purl.obolibrary.org/obo/CL_0017000` +- [renal alpha-intercalated cell](http://purl.obolibrary.org/obo/CL_0005011) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -#### Added -- [pulmonary ionocyte](http://purl.obolibrary.org/obo/CL_0017000) EquivalentTo [ionocyte](http://purl.obolibrary.org/obo/CL_0005006) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000115](http://purl.obolibrary.org/obo/UBERON_0000115)) +Renal alpha-intercalated cells are located within the connecting tubules and collecting ducts of the kidneys, which are components of the kidney's complex nephron system. Along with beta-intercalated cells, they play a critical role in the body’s acid-base balance. +Renal alpha-intercalated cells contain an abundance of proton pumps and enzymes like carbonic anhydrase, which aid in the transport of hydrogen ions for secretion in the urine. The bicarbonate/chloride transporters on their apical membrane meanwhile take up bicarbonate ions from the urine and supply them back into the blood. Through this mechanism, these cells contribute significantly to the neutrality of blood pH, and dysfunction of renal alpha-intercalated cells often leads to distal renal tubular acidosis, a condition resulting in acidic blood and alkaline urine."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1172/JCI63492"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3390/diseases2020071"^^[string](http://www.w3.org/2001/XMLSchema#string) -### pyramidal neuron `http://purl.obolibrary.org/obo/CL_0000598` -#### Removed -- [pyramidal neuron](http://purl.obolibrary.org/obo/CL_0000598) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009273"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.semnephrol.2019.04.005"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [pyramidal neuron](http://purl.obolibrary.org/obo/CL_0000598) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009273"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/physiol.00008.2011"^^[string](http://www.w3.org/2001/XMLSchema#string) -### radial glial cell `http://purl.obolibrary.org/obo/CL_0000681` -#### Removed -- [radial glial cell](http://purl.obolibrary.org/obo/CL_0000681) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009292"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### renal filtration cell `http://purl.obolibrary.org/obo/CL_0002522` #### Added -- [radial glial cell](http://purl.obolibrary.org/obo/CL_0000681) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009292"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [renal filtration cell](http://purl.obolibrary.org/obo/CL_0002522) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### red sensitive photoreceptor cell `http://purl.obolibrary.org/obo/CL_0000497` -#### Removed -- [red sensitive photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000497) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009224"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### renal intercalated cell `http://purl.obolibrary.org/obo/CL_0005010` #### Added -- [red sensitive photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000497) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009224"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - +- [renal intercalated cell](http://purl.obolibrary.org/obo/CL_0005010) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0005010"^^[string](http://www.w3.org/2001/XMLSchema#string) -### renal alpha-intercalated cell `http://purl.obolibrary.org/obo/CL_0005011` -#### Removed -- [renal alpha-intercalated cell](http://purl.obolibrary.org/obo/CL_0005011) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009376"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [renal intercalated cell](http://purl.obolibrary.org/obo/CL_0005010) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -#### Added -- [renal alpha-intercalated cell](http://purl.obolibrary.org/obo/CL_0005011) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009376"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +Renal intercalated cells are specialized cells located in the collecting duct system of the kidneys. The primary role of intercalated cells is to reabsorb bicarbonate ions and secrete hydrogen ions, thereby maintaining the acid-base homeostasis in the blood. They comprise two main subtypes primarily distinguished by their functional and morphological attributes: alpha and beta intercalated cells. +Alpha intercalated cells are more predominant when the body is in a state of acidosis, a condition characterized by an increased acidity of the blood. These cells are specialized in secreting excessive hydrogen ions into the urine through a mechanism involving vacuolar H+-ATPase and H+/K+-ATPase pumps on their apical membranes. They simultaneously reabsorb bicarbonate ions from the tubular fluid and return them to the bloodstream via mechanisms involving carbonic anhydrase II and bicarbonate/chloride exchangers on the basolateral membrane. This dual process helps to increase blood pH towards normal levels. +When the body is in a state of alkalosis, a condition characterized by lowered levels of hydrogen ions in the blood, beta intercalated cells are more predominant. They primarily reabsorb hydrogen ions from the tubular fluid through vacuolar H+-ATPase and H+/K+-ATPase pumps on their basolateral membranes, while secreting bicarbonate ions into the urine via pendrin, a bicarbonate/chloride exchanger in the apical membrane. These mechanisms work together to decrease blood pH towards normal levels. +In summary, renal intercalated cells play a critical role in the delicate balance of the body’s pH, safeguarding the body from potential harm caused by acidemia or alkalemia."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1681/ASN.V1011"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1161/HYPERTENSIONAHA.121.16492"^^[string](http://www.w3.org/2001/XMLSchema#string) -### renal intercalated cell `http://purl.obolibrary.org/obo/CL_0005010` -#### Removed -- [renal intercalated cell](http://purl.obolibrary.org/obo/CL_0005010) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009375"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/ajprenal.2000.279.1.F195"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [renal intercalated cell](http://purl.obolibrary.org/obo/CL_0005010) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009375"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2215/CJN.08880914"^^[string](http://www.w3.org/2001/XMLSchema#string) ### renal principal cell `http://purl.obolibrary.org/obo/CL_0005009` -#### Removed -- [renal principal cell](http://purl.obolibrary.org/obo/CL_0005009) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005322"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [renal principal cell](http://purl.obolibrary.org/obo/CL_0005009) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005322"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - +- [renal principal cell](http://purl.obolibrary.org/obo/CL_0005009) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0005009"^^[string](http://www.w3.org/2001/XMLSchema#string) -### respiratory basal cell `http://purl.obolibrary.org/obo/CL_0002633` -#### Removed -- [respiratory basal cell](http://purl.obolibrary.org/obo/CL_0002633) SubClassOf [respiratory epithelial cell](http://purl.obolibrary.org/obo/CL_0002368) - -#### Added -- [respiratory basal cell](http://purl.obolibrary.org/obo/CL_0002633) EquivalentTo [basal cell](http://purl.obolibrary.org/obo/CL_0000646) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004802](http://purl.obolibrary.org/obo/UBERON_0004802)) +- [renal principal cell](http://purl.obolibrary.org/obo/CL_0005009) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -- [respiratory basal cell](http://purl.obolibrary.org/obo/CL_0002633) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004802](http://purl.obolibrary.org/obo/UBERON_0004802) +Renal principal cells are the major cell type in the initial collecting tubule and the cortical and outer medullary collecting ducts, as well as the connecting tubule, in the nephrons of the kidneys. +A key function of renal principal cells is the regulation of water balance in the body. These cells express aquaporin-2 (AQP2) water channels, which facilitate the reabsorption of water from the fluid within the renal tubule lumen back into the blood. The translocation of AQP2 to the cell membrane is controlled by the hormone vasopressin: In response to high vasopressin levels, AQP2 moves to the cell membrane, allowing water to pass through effectively and be reabsorbed, therefore concentrating the urine. Conversely, in low vasopressin conditions, AQP2 is removed from the membrane, reducing water reabsorption and diluting the urine. +Renal principal cells are also involved in the regulation of sodium and potassium levels in the body. They have sodium channels (ENaC) in their luminal membranes which permit the reabsorption of sodium ions from the tubule fluid back into the blood, resulting in a net reabsorption of sodium ions into the systemic circulation. This process is controlled, in part, by the hormone aldosterone. Additionally, renal principal cells contain potassium channels that facilitate the secretion of potassium ions into the urine. The activities of these channels, in coordination with other cell types in the nephron, are critical for maintaining electrolyte balance and overall body homeostasis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2215/CJN.05760513"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2215/CJN.08580813"^^[string](http://www.w3.org/2001/XMLSchema#string) -### respiratory epithelial cell `http://purl.obolibrary.org/obo/CL_0002368` -#### Removed -- [respiratory epithelial cell](http://purl.obolibrary.org/obo/CL_0002368) EquivalentTo [endo-epithelial cell](http://purl.obolibrary.org/obo/CL_0002076) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000065](http://purl.obolibrary.org/obo/UBERON_0000065)) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.krcp.2013.07.005"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [respiratory epithelial cell](http://purl.obolibrary.org/obo/CL_0002368) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000065](http://purl.obolibrary.org/obo/UBERON_0000065) -- [respiratory epithelial cell](http://purl.obolibrary.org/obo/CL_0002368) SubClassOf [endo-epithelial cell](http://purl.obolibrary.org/obo/CL_0002076) - - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) +### respiratory basal cell `http://purl.obolibrary.org/obo/CL_0002633` #### Added -- [respiratory epithelial cell](http://purl.obolibrary.org/obo/CL_0002368) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004802](http://purl.obolibrary.org/obo/UBERON_0004802)) - -- [respiratory epithelial cell](http://purl.obolibrary.org/obo/CL_0002368) SubClassOf [endo-epithelial cell](http://purl.obolibrary.org/obo/CL_0002076) +- [respiratory basal cell](http://purl.obolibrary.org/obo/CL_0002633) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -- [respiratory epithelial cell](http://purl.obolibrary.org/obo/CL_0002368) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004802](http://purl.obolibrary.org/obo/UBERON_0004802) - - -### respiratory goblet cell `http://purl.obolibrary.org/obo/CL_0002370` -#### Removed -- [respiratory goblet cell](http://purl.obolibrary.org/obo/CL_0002370) EquivalentTo [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000065](http://purl.obolibrary.org/obo/UBERON_0000065)) +Respiratory basal cells are highly specialized cells that serve a crucial role in the human airway epithelium, predominantly found lining the surfaces of the trachea and bronchi. These cells exhibit a distinctive columnar shape and are attached directly to the basal lamina. They are characterized by the presence of high amounts of cytoplasmic keratins, predominantly keratin 5 and 14, and transcription factor tumor protein (tp63), which set them apart from other types of lung epithelial cells such as ciliated cells and secretory cells. +Basal cells are essential for maintaining airway integrity. They make up one third of all respiratory epithelial cells and serve as stem cells as they can transform into different cell types, like goblet cells, ciliated cells, and club cells, when needed for homeostatic maintenance of the epithelial barrier or to repair and restore a healthy cellular environment after injury. +Their position at the interface between the internal environment and the external atmosphere makes these cells a first line of defense against air-borne irritants, allergens, and pathogens. Their robust, intrinsic reparative properties facilitate effective recovery from such adversities. However, damage to respiratory basal cells or abnormalities in their function are associated with several respiratory pathologies such as asthma, chronic obstructive pulmonary disease, and lung cancer. Therefore, understanding these cells' function, and their role in disease, is crucial for the development of new therapeutic strategies for respiratory disorders."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:110.1038/s41385-020-00370-7"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [respiratory goblet cell](http://purl.obolibrary.org/obo/CL_0002370) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004802](http://purl.obolibrary.org/obo/UBERON_0004802) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1186/s12931-022-02042-5"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [respiratory goblet cell](http://purl.obolibrary.org/obo/CL_0002370) EquivalentTo [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004802](http://purl.obolibrary.org/obo/UBERON_0004802)) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/falgy.2021.787128"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [respiratory goblet cell](http://purl.obolibrary.org/obo/CL_0002370) SubClassOf [respiratory epithelial cell](http://purl.obolibrary.org/obo/CL_0002368) +- [respiratory basal cell](http://purl.obolibrary.org/obo/CL_0002633) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002633"^^[string](http://www.w3.org/2001/XMLSchema#string) -### respiratory hillock cell `http://purl.obolibrary.org/obo/CL_4030023` -#### Removed -- [respiratory hillock cell](http://purl.obolibrary.org/obo/CL_4030023) EquivalentTo [hillock cell](http://purl.obolibrary.org/obo/CL_4030024) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000065](http://purl.obolibrary.org/obo/UBERON_0000065)) +### respiratory goblet cell `http://purl.obolibrary.org/obo/CL_0002370` #### Added -- [respiratory hillock cell](http://purl.obolibrary.org/obo/CL_4030023) EquivalentTo [hillock cell](http://purl.obolibrary.org/obo/CL_4030024) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004802](http://purl.obolibrary.org/obo/UBERON_0004802)) +- [respiratory goblet cell](http://purl.obolibrary.org/obo/CL_0002370) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002370"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [respiratory goblet cell](http://purl.obolibrary.org/obo/CL_0002370) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -### respiratory suprabasal cell `http://purl.obolibrary.org/obo/CL_4033048` -#### Removed -- [respiratory suprabasal cell](http://purl.obolibrary.org/obo/CL_4033048) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004802](http://purl.obolibrary.org/obo/UBERON_0004802) +The respiratory goblet cell is a highly specialized cell type found primarily within the respiratory tract, including the nose, trachea, and lungs. Named because their shape resembles a goblet - a drinking vessel with a wide body and narrow neck - these cells form a vital part of the respiratory system's protective mechanisms. They are found within the columnar epithelium lining these organs, which forms a barrier between the internal body and the exterior environment. +A principal function of the respiratory goblet cell is the production and secretion of mucus, a carbohydrate-rich, viscous and gel-like substance that plays a critical role in trapping dust, bacteria, viruses, and other airborne particles that are inhaled. The mucus secreted by the goblet cells covers the lining of the respiratory tract, effectively catching these particles and preventing them from reaching the lungs and causing infection. Mucus also provides hydration and lubrication to the respiratory tract surfaces, which is important in maintaining the tissue's health and functioning. +In addition to their mucus-secreting capabilities, respiratory goblet cells also play a significant role in the body's inflammatory responses. When the respiratory system is exposed to irritants or pathogens, the number and activity of goblet cells often increase, leading to a higher production of mucus. This is a protective response designed to trap and neutralize the harmful substances more effectively. However, in conditions like chronic obstructive pulmonary disease (COPD) and asthma, an overproliferation of goblet cells, also known as goblet cell hyperplasia, can lead to excessive mucus production and airway obstruction."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/febs.15731"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/S1357-2725(02)00083-3"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1165/ajrcmb.25.5.f218"^^[string](http://www.w3.org/2001/XMLSchema#string) -### reticular cell `http://purl.obolibrary.org/obo/CL_0000432` -#### Removed -- [reticular cell](http://purl.obolibrary.org/obo/CL_0000432) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009200"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3109/01902148.2013.791733"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [reticular cell](http://purl.obolibrary.org/obo/CL_0000432) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009200"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2147/COPD.S38938"^^[string](http://www.w3.org/2001/XMLSchema#string) ### reticulocyte `http://purl.obolibrary.org/obo/CL_0000558` -#### Removed -- [reticulocyte](http://purl.obolibrary.org/obo/CL_0000558) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009252"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [reticulocyte](http://purl.obolibrary.org/obo/CL_0000558) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009252"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - - -### retina horizontal cell `http://purl.obolibrary.org/obo/CL_0000745` -#### Removed -- [retina horizontal cell](http://purl.obolibrary.org/obo/CL_0000745) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009315"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [retina horizontal cell](http://purl.obolibrary.org/obo/CL_0000745) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009315"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [reticulocyte](http://purl.obolibrary.org/obo/CL_0000558) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### retinal bipolar neuron `http://purl.obolibrary.org/obo/CL_0000748` -#### Removed -- [retinal bipolar neuron](http://purl.obolibrary.org/obo/CL_0000748) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009318"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### retinal blood vessel endothelial cell `http://purl.obolibrary.org/obo/CL_0002585` #### Added -- [retinal bipolar neuron](http://purl.obolibrary.org/obo/CL_0000748) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009318"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - +- [retinal blood vessel endothelial cell](http://purl.obolibrary.org/obo/CL_0002585) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -### retinal cone cell `http://purl.obolibrary.org/obo/CL_0000573` -#### Removed -- [retinal cone cell](http://purl.obolibrary.org/obo/CL_0000573) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009262"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +Retinal blood vessel endothelial cells constitute the innermost lining of the blood vessels found in the retina, the light-sensitive layer of tissue at the back of the eye. The primary role of these cells revolves around their location within the retinal vascular system, forming the structure of the blood-retinal barrier, a subset of the larger blood-ocular barrier system. +The endothelial cells are particularly involved in the growth of new retinal blood vessels from pre-existing ones (angiogenesis); this is critical in managing the amount of oxygen and essential nutrients delivered to the ocular tissues. They are crucial for maintaining homeostasis in the retinal environment by controlling the exchange of molecules between the blood and the retina. Furthermore, they mediate immune cell trafficking, supporting the immune privilege of the eye by preventing the unrestricted infiltration of inflammatory cells into the retina, thus maintaining ocular health and normal vision. +The malfunction or dysfunction of retinal blood vessel endothelial cells is implicated in numerous ocular pathologies, particularly diabetic retinopathy, which is one of the leading causes of blindness worldwide. In such conditions, the compromise in the integrity of the blood-retinal barrier and excess angiogenesis can lead to retinal edema and pathological neovascularization, resulting in vision loss."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.5301/EJO.2010.6049"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [retinal cone cell](http://purl.obolibrary.org/obo/CL_0000573) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009262"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:0.1016/j.preteyeres.2015.08.001"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.preteyeres.2012.08.004"^^[string](http://www.w3.org/2001/XMLSchema#string) -### retinal ganglion cell `http://purl.obolibrary.org/obo/CL_0000740` -#### Removed -- [retinal ganglion cell](http://purl.obolibrary.org/obo/CL_0000740) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009310"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/nature04482"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [retinal ganglion cell](http://purl.obolibrary.org/obo/CL_0000740) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009310"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [retinal blood vessel endothelial cell](http://purl.obolibrary.org/obo/CL_0002585) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002585"^^[string](http://www.w3.org/2001/XMLSchema#string) -### retinal rod cell `http://purl.obolibrary.org/obo/CL_0000604` -#### Removed -- [retinal rod cell](http://purl.obolibrary.org/obo/CL_0000604) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009275"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### retinal pigment epithelial cell `http://purl.obolibrary.org/obo/CL_0002586` #### Added -- [retinal rod cell](http://purl.obolibrary.org/obo/CL_0000604) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009275"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - +- [retinal pigment epithelial cell](http://purl.obolibrary.org/obo/CL_0002586) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002586"^^[string](http://www.w3.org/2001/XMLSchema#string) -### rod bipolar cell `http://purl.obolibrary.org/obo/CL_0000751` -#### Removed -- [rod bipolar cell](http://purl.obolibrary.org/obo/CL_0000751) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009321"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [retinal pigment epithelial cell](http://purl.obolibrary.org/obo/CL_0002586) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -#### Added -- [rod bipolar cell](http://purl.obolibrary.org/obo/CL_0000751) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009321"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +Retinal pigment epithelial (RPE) cells form a single layer of cells at the back of the eye sandwiched between the neurosensory retina and the choroid, playing a significant role in maintaining vision health. These pigment-laden cells are highly specialized and perform an array of metabolic and transport functions essential for the maintenance of the photoreceptor cells (rods and cones) in the retina. The pigmentation of RPE cells actively aids in the absorption of excess light and the prevention of light scattering, thus enhancing the eye's optical properties. +The retinal pigment epithelium forms a key part of the blood/retina barrier. The cells have long sheet-like microvilli on their apical membrane that project into the light-sensitive outer segments of the photoreceptors, forming a close structural interaction. The basolateral membrane of the RPE interacts with the underlying Bruch’s membrane, which separates the RPE cells from fenestrated endothelium of the choriocapillaris. +RPE cells support the photoreceptor by providing them with oxygen and nutrients (such as glucose, retinol and fatty acids) and removing waste products. They also recycle the visual pigment, in a process called the "visual cycle", where the RPE cells play a vital role in the regeneration of visual pigment (11-cis retinol) following the absorption of light. This is essential for the maintenance of photoreceptor excitability. +Beyond this, RPE cells take part in the phagocytosis process, where they digest the shed ends of photoreceptor outer segments, thus, preventing the build-up of waste residue that could otherwise harm retinal health. They also secrete various factors, including growth factors required to maintain the structural integrity of choriocapillaris endothelium and photoreceptors, as well as immunosuppressive factors that play an important role in establishing the immune privilege of the eye."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/febs.16018"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/physrev.00021.2004"^^[string](http://www.w3.org/2001/XMLSchema#string) -### scleral cell `http://purl.obolibrary.org/obo/CL_0000347` -#### Removed -- [scleral cell](http://purl.obolibrary.org/obo/CL_0000347) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009174"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fphar.2021.727870/full"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [scleral cell](http://purl.obolibrary.org/obo/CL_0000347) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009174"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/chemistry/retinal-pigment"^^[string](http://www.w3.org/2001/XMLSchema#string) -### scolopale cell `http://purl.obolibrary.org/obo/CL_0000382` +### rod bipolar cell `http://purl.obolibrary.org/obo/CL_0000751` #### Removed -- [scolopale cell](http://purl.obolibrary.org/obo/CL_0000382) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005219"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [scolopale cell](http://purl.obolibrary.org/obo/CL_0000382) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005219"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [rod bipolar cell](http://purl.obolibrary.org/obo/CL_0000751) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) +- [rod bipolar cell](http://purl.obolibrary.org/obo/CL_0000751) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_40674](http://purl.obolibrary.org/obo/NCBITaxon_40674) -### scolopidial ligament cell `http://purl.obolibrary.org/obo/CL_0000407` -#### Removed -- [scolopidial ligament cell](http://purl.obolibrary.org/obo/CL_0000407) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005221"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [rod bipolar cell](http://purl.obolibrary.org/obo/CL_0000751) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) #### Added -- [scolopidial ligament cell](http://purl.obolibrary.org/obo/CL_0000407) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005221"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [rod bipolar cell](http://purl.obolibrary.org/obo/CL_0000751) [RO_0002175](http://purl.obolibrary.org/obo/RO_0002175) [NCBITaxon_32443](http://purl.obolibrary.org/obo/NCBITaxon_32443) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:38627529"^^[string](http://www.w3.org/2001/XMLSchema#string) -### sebaceous gland cell `http://purl.obolibrary.org/obo/CL_2000021` +### rosehip neuron `http://purl.obolibrary.org/obo/CL_0008032` #### Removed -- [sebaceous gland cell](http://purl.obolibrary.org/obo/CL_2000021) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +- [rosehip neuron](http://purl.obolibrary.org/obo/CL_0008032) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) + +- [rosehip neuron](http://purl.obolibrary.org/obo/CL_0008032) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) #### Added -- [sebaceous gland cell](http://purl.obolibrary.org/obo/CL_2000021) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [rosehip neuron](http://purl.obolibrary.org/obo/CL_0008032) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_9606](http://purl.obolibrary.org/obo/NCBITaxon_9606) -### secondary motor neuron (sensu Teleostei) `http://purl.obolibrary.org/obo/CL_0000536` +### salivary gland cell `http://purl.obolibrary.org/obo/CL_0009005` #### Removed -- [secondary motor neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000536) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009247"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [salivary gland cell](http://purl.obolibrary.org/obo/CL_0009005) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) #### Added -- [secondary motor neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000536) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009247"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [salivary gland cell](http://purl.obolibrary.org/obo/CL_0009005) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### secondary neuron (sensu Teleostei) `http://purl.obolibrary.org/obo/CL_0000535` -#### Removed -- [secondary neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000535) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009246"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### salivary gland glandular cell `http://purl.obolibrary.org/obo/CL_1001596` #### Added -- [secondary neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000535) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009246"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [salivary gland glandular cell](http://purl.obolibrary.org/obo/CL_1001596) SubClassOf [salivary gland cell](http://purl.obolibrary.org/obo/CL_0009005) -### secondary spermatocyte `http://purl.obolibrary.org/obo/CL_0000657` -#### Removed -- [secondary spermatocyte](http://purl.obolibrary.org/obo/CL_0000657) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004941"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +### scleral cell `http://purl.obolibrary.org/obo/CL_0000347` #### Added -- [secondary spermatocyte](http://purl.obolibrary.org/obo/CL_0000657) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004941"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [scleral cell](http://purl.obolibrary.org/obo/CL_0000347) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### sensory epithelial cell `http://purl.obolibrary.org/obo/CL_0000098` -#### Removed -- [sensory epithelial cell](http://purl.obolibrary.org/obo/CL_0000098) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009050"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### scolopale cell `http://purl.obolibrary.org/obo/CL_0000382` #### Added -- [sensory epithelial cell](http://purl.obolibrary.org/obo/CL_0000098) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009050"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [scolopale cell](http://purl.obolibrary.org/obo/CL_0000382) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### sensory hair cell `http://purl.obolibrary.org/obo/CL_0000855` -#### Removed -- [sensory hair cell](http://purl.obolibrary.org/obo/CL_0000855) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009366"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### scolopidial ligament cell `http://purl.obolibrary.org/obo/CL_0000407` #### Added -- [sensory hair cell](http://purl.obolibrary.org/obo/CL_0000855) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009366"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [scolopidial ligament cell](http://purl.obolibrary.org/obo/CL_0000407) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### sensory neuron `http://purl.obolibrary.org/obo/CL_0000101` +### sebaceous gland cell `http://purl.obolibrary.org/obo/CL_2000021` #### Removed -- [sensory neuron](http://purl.obolibrary.org/obo/CL_0000101) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005124"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [sensory neuron](http://purl.obolibrary.org/obo/CL_0000101) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009053"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [sebaceous gland cell](http://purl.obolibrary.org/obo/CL_2000021) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) #### Added -- [sensory neuron](http://purl.obolibrary.org/obo/CL_0000101) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005124"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [sensory neuron](http://purl.obolibrary.org/obo/CL_0000101) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009053"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [sebaceous gland cell](http://purl.obolibrary.org/obo/CL_2000021) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### sensory processing neuron `http://purl.obolibrary.org/obo/CL_0000379` -#### Removed -- [sensory processing neuron](http://purl.obolibrary.org/obo/CL_0000379) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009185"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### secondary lens fiber `http://purl.obolibrary.org/obo/CL_0002225` #### Added -- [sensory processing neuron](http://purl.obolibrary.org/obo/CL_0000379) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009185"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [secondary lens fiber](http://purl.obolibrary.org/obo/CL_0002225) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +Secondary lens fibers are a specialized type of elongated cells located within the structure of the eye's lens. They play an essential role in vision by enabling light transmission and focus on the retina, which allows for clear, distinct vision. These cells are characterized by their lack of nuclei and organelles, their orderly alignment, and their high protein content, particularly crystallins. +Lens fibers are differentiated from equatorial epithelial cells of the lens in a process that involves cell elongation, denucleation and tight packing, which serve to reduce light scattering occurrences in the eye. This differentiation accelerates substantially after birth in comparison to during embryogenesis and continues throughout life, contributing to the growth of the eye lens. Secondary lens fibers are specifically those cells that are newly differentiated and cover the old lens fiber core. This process also leads to the removal of light-obstructing cellular components, mainly nuclei and organelles, making these fibers transparent and ideal for their function. +The fibers carry out their primary function of light refraction via a high concentration of specialized proteins known as crystallins, which form a gradient of refractive index together with the cytoplasm. This index manipulation facilitates precise light focus onto the retina. Secondary lens fibers also contribute to the lens's shape and biomechanical properties through intercellular interactions, particularly at the sutures where the ends of the fibers meet. Any disruption to secondary lens fibers can lead to vision problems, including cataracts, which is the clouding of the lens resulting from the aggregation of crystallin proteins."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1136/bmjophth-2020-000459"^^[string](http://www.w3.org/2001/XMLSchema#string) -### serotonergic neuron `http://purl.obolibrary.org/obo/CL_0000850` -#### Removed -- [serotonergic neuron](http://purl.obolibrary.org/obo/CL_0000850) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009361"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/immunology-and-microbiology/lens-fiber"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [serotonergic neuron](http://purl.obolibrary.org/obo/CL_0000850) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005133"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.biocel.2007.10.034"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [serotonergic neuron](http://purl.obolibrary.org/obo/CL_0000850) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005133"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1098/rstb.2010.0324"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/B978-1-4377-1926-0.10005-0"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [serotonergic neuron](http://purl.obolibrary.org/obo/CL_0000850) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009361"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [secondary lens fiber](http://purl.obolibrary.org/obo/CL_0002225) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002225"^^[string](http://www.w3.org/2001/XMLSchema#string) -### serotonin secreting cell `http://purl.obolibrary.org/obo/CL_0000458` +### secondary neuron (sensu Teleostei) `http://purl.obolibrary.org/obo/CL_0000535` #### Removed -- [serotonin secreting cell](http://purl.obolibrary.org/obo/CL_0000458) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009213"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [secondary neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000535) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) + +- [secondary neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000535) SubClassOf [RO_0002160](http://purl.obolibrary.org/obo/RO_0002160) some [NCBITaxon_32443](http://purl.obolibrary.org/obo/NCBITaxon_32443) + - [IAO_0000233](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/obophenotype/cell-ontology/pull/1950"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [serotonin secreting cell](http://purl.obolibrary.org/obo/CL_0000458) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009213"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [secondary neuron (sensu Teleostei)](http://purl.obolibrary.org/obo/CL_0000535) SubClassOf [RO_0002162](http://purl.obolibrary.org/obo/RO_0002162) some [NCBITaxon_32443](http://purl.obolibrary.org/obo/NCBITaxon_32443) + - [IAO_0000233](http://purl.obolibrary.org/obo/IAO_0000233) "https://github.com/obophenotype/cell-ontology/pull/1950"^^[string](http://www.w3.org/2001/XMLSchema#string) -### simple columnar epithelial cell `http://purl.obolibrary.org/obo/CL_0000146` -#### Removed -- [simple columnar epithelial cell](http://purl.obolibrary.org/obo/CL_0000146) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009089"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### secondary spermatocyte `http://purl.obolibrary.org/obo/CL_0000657` #### Added -- [simple columnar epithelial cell](http://purl.obolibrary.org/obo/CL_0000146) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009089"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [secondary spermatocyte](http://purl.obolibrary.org/obo/CL_0000657) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### single ciliated epithelial cell `http://purl.obolibrary.org/obo/CL_0005013` -#### Removed -- [single ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005013) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005243"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### seminal vesicle glandular cell `http://purl.obolibrary.org/obo/CL_1001597` #### Added -- [single ciliated epithelial cell](http://purl.obolibrary.org/obo/CL_0005013) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005243"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [seminal vesicle glandular cell](http://purl.obolibrary.org/obo/CL_1001597) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +Seminal vesicle glandular cells belong to a specialized group of epithelial cells that form the internal lining of the seminal vesicles, a pair of male reproductive organs. These cells are located within the complex tubuloalveolar glands that make up the seminal vesicles and are known for their unique pseudostratified columnar epithelium structure. +The primary function of these cells is the secretion of a variety of substances that ultimately constitute around 70% of the fluid volume of semen. Seminal cells produce a high-fructose fluid that serves as an energy source for the spermatozoa and promotes their motility. They also secrete other essential substances like proteins, enzymes, vitamin C, prostaglandins, and various other compounds. Collectively, these substances help in the nourishment, protection, and transportation of the spermatozoa throughout the male reproductive system and during the ejaculation process. +Secondary to the production of seminal fluid, the seminal vesicle glandular cells also play a role in the contraction of the seminal vesicles during ejaculation. The contraction of these glands, induced by sympathetic nerves, ensures the efficient propulsion of the seminal fluid mixed with spermatozoa into the ejaculatory ducts and subsequently to the urethra. Notably, any malfunction or pathological condition affecting these cells can impact male fertility, emphasizing the importance of understanding the intricate functions of seminal vesicle glandular cells in maintaining the healthy physiological function of male reproduction."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/978-3-030-32300-4_26"^^[string](http://www.w3.org/2001/XMLSchema#string) -### single fate stem cell `http://purl.obolibrary.org/obo/CL_0000035` -#### Removed -- [single fate stem cell](http://purl.obolibrary.org/obo/CL_0000035) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009013"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.ncbi.nlm.nih.gov/books/NBK499854/"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [single fate stem cell](http://purl.obolibrary.org/obo/CL_0000035) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009013"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/veterinary-science-and-veterinary-medicine/seminal-vesicle"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/j.1439-0272.1992.tb02636.x"^^[string](http://www.w3.org/2001/XMLSchema#string) -### skeletal muscle myoblast `http://purl.obolibrary.org/obo/CL_0000515` -#### Removed -- [skeletal muscle myoblast](http://purl.obolibrary.org/obo/CL_0000515) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009236"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s00265-006-0178-0"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [skeletal muscle myoblast](http://purl.obolibrary.org/obo/CL_0000515) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009236"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [seminal vesicle glandular cell](http://purl.obolibrary.org/obo/CL_1001597) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1001597"^^[string](http://www.w3.org/2001/XMLSchema#string) -### skeletal muscle satellite cell `http://purl.obolibrary.org/obo/CL_0000594` +### sensory receptor cell `http://purl.obolibrary.org/obo/CL_0000197` #### Removed -- [skeletal muscle satellite cell](http://purl.obolibrary.org/obo/CL_0000594) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009272"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [sensory receptor cell](http://purl.obolibrary.org/obo/CL_0000197) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) #### Added -- [skeletal muscle satellite cell](http://purl.obolibrary.org/obo/CL_0000594) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009272"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [sensory receptor cell](http://purl.obolibrary.org/obo/CL_0000197) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### skeletal muscle tissue of pectoralis major striated muscle cell `http://purl.obolibrary.org/obo/CL_2000077` -#### Removed -- [skeletal muscle tissue of pectoralis major striated muscle cell](http://purl.obolibrary.org/obo/CL_2000077) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +### single nucleate cell `http://purl.obolibrary.org/obo/CL_0000226` #### Added -- [skeletal muscle tissue of pectoralis major striated muscle cell](http://purl.obolibrary.org/obo/CL_2000077) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [single nucleate cell](http://purl.obolibrary.org/obo/CL_0000226) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### slow muscle cell `http://purl.obolibrary.org/obo/CL_0000189` -#### Removed -- [slow muscle cell](http://purl.obolibrary.org/obo/CL_0000189) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009116"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### small intestine BEST4+ enterocyte `http://purl.obolibrary.org/obo/CL_4047051` #### Added -- [slow muscle cell](http://purl.obolibrary.org/obo/CL_0000189) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009116"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - +- [small intestine BEST4+ enterocyte](http://purl.obolibrary.org/obo/CL_4047051) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4047051"^^[string](http://www.w3.org/2001/XMLSchema#string) -### slow muscle myoblast `http://purl.obolibrary.org/obo/CL_0000857` -#### Removed -- [slow muscle myoblast](http://purl.obolibrary.org/obo/CL_0000857) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009368"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [small intestine BEST4+ enterocyte](http://purl.obolibrary.org/obo/CL_4047051) [date](http://purl.org/dc/terms/date) "2024-07-25T13:05:50Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -#### Added -- [slow muscle myoblast](http://purl.obolibrary.org/obo/CL_0000857) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009368"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [small intestine BEST4+ enterocyte](http://purl.obolibrary.org/obo/CL_4047051) [label](http://www.w3.org/2000/01/rdf-schema#label) "small intestine BEST4+ enterocyte"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [small intestine BEST4+ enterocyte](http://purl.obolibrary.org/obo/CL_4047051) [contributor](http://purl.org/dc/terms/contributor) [0009-0005-7919-4905](https://orcid.org/0009-0005-7919-4905) -### small intestine goblet cell `http://purl.obolibrary.org/obo/CL_1000495` -#### Removed -- [small intestine goblet cell](http://purl.obolibrary.org/obo/CL_1000495) SubClassOf [small intestine glandular cell](http://purl.obolibrary.org/obo/CL_1001598) +- [small intestine BEST4+ enterocyte](http://purl.obolibrary.org/obo/CL_4047051) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An enterocyte of the human small intestine expressing bestrophin-4 (BEST4) calcium-activated ion channels. These enterocytes have a disinctive transcriptomic profile and are scattered through the small intestine epithelium."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34497389"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [small intestine goblet cell](http://purl.obolibrary.org/obo/CL_1000495) SubClassOf [epithelial cell of small intestine](http://purl.obolibrary.org/obo/CL_0002254) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:24223998"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [small intestine goblet cell](http://purl.obolibrary.org/obo/CL_1000495) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001902](http://purl.obolibrary.org/obo/UBERON_0001902) +- Class: [small intestine BEST4+ enterocyte](http://purl.obolibrary.org/obo/CL_4047051) +- [small intestine BEST4+ enterocyte](http://purl.obolibrary.org/obo/CL_4047051) EquivalentTo [enterocyte](http://purl.obolibrary.org/obo/CL_0000584) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001902](http://purl.obolibrary.org/obo/UBERON_0001902)) and ([RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_Q8NFU0](http://purl.obolibrary.org/obo/PR_Q8NFU0)) -### smooth muscle cell `http://purl.obolibrary.org/obo/CL_0000192` -#### Removed -- [smooth muscle cell](http://purl.obolibrary.org/obo/CL_0000192) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009118"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [small intestine BEST4+ enterocyte](http://purl.obolibrary.org/obo/CL_4047051) SubClassOf [enterocyte of epithelium of small intestine](http://purl.obolibrary.org/obo/CL_1000334) -#### Added -- [smooth muscle cell](http://purl.obolibrary.org/obo/CL_0000192) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009118"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [small intestine BEST4+ enterocyte](http://purl.obolibrary.org/obo/CL_4047051) SubClassOf [BEST4+ intestinal epithelial cell, human](http://purl.obolibrary.org/obo/CL_4030026) -### smooth muscle myoblast `http://purl.obolibrary.org/obo/CL_0000514` -#### Removed -- [smooth muscle myoblast](http://purl.obolibrary.org/obo/CL_0000514) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009235"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### smooth muscle cell derived foam cell `http://purl.obolibrary.org/obo/CL_0000892` #### Added -- [smooth muscle myoblast](http://purl.obolibrary.org/obo/CL_0000514) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009235"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [smooth muscle cell derived foam cell](http://purl.obolibrary.org/obo/CL_0000892) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) ### sncg GABAergic cortical interneuron `http://purl.obolibrary.org/obo/CL_4023015` #### Removed -- [sncg GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023015) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) +- [sncg GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023015) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A GABAergic neuron located in the cerebral cortex that expresses Gamma-synuclein"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33186530"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [sncg GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023015) SubClassOf [cerebral cortex GABAergic interneuron](http://purl.obolibrary.org/obo/CL_0010011) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [sncg GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023015) SubClassOf [caudal ganglionic eminence derived interneuron](http://purl.obolibrary.org/obo/CL_4023064) +- [sncg GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023015) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A transcriptomically distinct GABAergic neuron located in the cerebral cortex that expresses Gamma-synuclein. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: CGE-derived interneurons', Author Categories: 'CrossArea_subclass', clusters Sncg."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/e/e4ddac12-f48f-4455-8e8d-c2a48a683437.cxg/"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33186530"^^[string](http://www.w3.org/2001/XMLSchema#string) -### somatic muscle cell `http://purl.obolibrary.org/obo/CL_0008004` -#### Removed -- [somatic muscle cell](http://purl.obolibrary.org/obo/CL_0008004) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005073"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) + + +### sperm `http://purl.obolibrary.org/obo/CL_0000019` #### Added -- [somatic muscle cell](http://purl.obolibrary.org/obo/CL_0008004) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005073"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [sperm](http://purl.obolibrary.org/obo/CL_0000019) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### somatic stem cell `http://purl.obolibrary.org/obo/CL_0000723` -#### Removed -- [somatic stem cell](http://purl.obolibrary.org/obo/CL_0000723) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009307"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### spermatid `http://purl.obolibrary.org/obo/CL_0000018` #### Added -- [somatic stem cell](http://purl.obolibrary.org/obo/CL_0000723) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009307"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [spermatid](http://purl.obolibrary.org/obo/CL_0000018) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### somatomotor neuron `http://purl.obolibrary.org/obo/CL_0005024` -#### Removed -- [somatomotor neuron](http://purl.obolibrary.org/obo/CL_0005024) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005733"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### splenic marginal zone macrophage `http://purl.obolibrary.org/obo/CL_0000872` #### Added -- [somatomotor neuron](http://purl.obolibrary.org/obo/CL_0005024) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005733"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [splenic marginal zone macrophage](http://purl.obolibrary.org/obo/CL_0000872) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### somatostatin secreting cell `http://purl.obolibrary.org/obo/CL_0000172` -#### Removed -- [somatostatin secreting cell](http://purl.obolibrary.org/obo/CL_0000172) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009105"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### splenic metallophillic macrophage `http://purl.obolibrary.org/obo/CL_0000873` #### Added -- [somatostatin secreting cell](http://purl.obolibrary.org/obo/CL_0000172) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009105"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [splenic metallophillic macrophage](http://purl.obolibrary.org/obo/CL_0000873) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### somatotropin secreting cell `http://purl.obolibrary.org/obo/CL_0000295` -#### Removed -- [somatotropin secreting cell](http://purl.obolibrary.org/obo/CL_0000295) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009155"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### splenic red pulp macrophage `http://purl.obolibrary.org/obo/CL_0000874` #### Added -- [somatotropin secreting cell](http://purl.obolibrary.org/obo/CL_0000295) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009155"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [splenic red pulp macrophage](http://purl.obolibrary.org/obo/CL_0000874) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### sperm `http://purl.obolibrary.org/obo/CL_0000019` -#### Removed -- [sperm](http://purl.obolibrary.org/obo/CL_0000019) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004954"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [sperm](http://purl.obolibrary.org/obo/CL_0000019) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009006"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### splenic white pulp macrophage `http://purl.obolibrary.org/obo/CL_0000876` #### Added -- [sperm](http://purl.obolibrary.org/obo/CL_0000019) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004954"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [sperm](http://purl.obolibrary.org/obo/CL_0000019) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009006"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [splenic white pulp macrophage](http://purl.obolibrary.org/obo/CL_0000876) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) -### spermatid `http://purl.obolibrary.org/obo/CL_0000018` +### squamous endothelial cell of venule `http://purl.obolibrary.org/obo/CL_0008040` #### Removed -- [spermatid](http://purl.obolibrary.org/obo/CL_0000018) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004942"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) - -- [spermatid](http://purl.obolibrary.org/obo/CL_0000018) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005769"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [squamous endothelial cell of venule](http://purl.obolibrary.org/obo/CL_0008040) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An endothelial cell of the venule that is squamous shaped. This is in contrast to the cubodial shape of high endothelial venule cells."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [spermatid](http://purl.obolibrary.org/obo/CL_0000018) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004942"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [squamous endothelial cell of venule](http://purl.obolibrary.org/obo/CL_0008040) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An endothelial cell of the venule that is squamous shaped. This is in contrast to the cubodial shape of high endothelial venule cells."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [spermatid](http://purl.obolibrary.org/obo/CL_0000018) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005769"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### squamous epithelial cell `http://purl.obolibrary.org/obo/CL_0000076` -### spermatocyte `http://purl.obolibrary.org/obo/CL_0000017` -#### Removed -- [spermatocyte](http://purl.obolibrary.org/obo/CL_0000017) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004936"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [squamous epithelial cell](http://purl.obolibrary.org/obo/CL_0000076) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Any epithelial cell that is part of some squamous epithelium."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBC:Autogenerated"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [spermatocyte](http://purl.obolibrary.org/obo/CL_0000017) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009005"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [squamous epithelial cell](http://purl.obolibrary.org/obo/CL_0000076) EquivalentTo [epithelial cell](http://purl.obolibrary.org/obo/CL_0000066) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0006914](http://purl.obolibrary.org/obo/UBERON_0006914)) -#### Added -- [spermatocyte](http://purl.obolibrary.org/obo/CL_0000017) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004936"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [squamous epithelial cell](http://purl.obolibrary.org/obo/CL_0000076) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0006914](http://purl.obolibrary.org/obo/UBERON_0006914) -- [spermatocyte](http://purl.obolibrary.org/obo/CL_0000017) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009005"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### squamous granulosa cell `http://purl.obolibrary.org/obo/CL_4033083` -### spermatogonium `http://purl.obolibrary.org/obo/CL_0000020` -#### Removed -- [spermatogonium](http://purl.obolibrary.org/obo/CL_0000020) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004934"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +#### Added +- [squamous granulosa cell](http://purl.obolibrary.org/obo/CL_4033083) [contributor](http://purl.org/dc/terms/contributor) [0000-0001-6677-8489](https://orcid.org/0000-0001-6677-8489) -- [spermatogonium](http://purl.obolibrary.org/obo/CL_0000020) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009007"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [squamous granulosa cell](http://purl.obolibrary.org/obo/CL_4033083) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "pre-granulosa cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33914868"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [spermatogonium](http://purl.obolibrary.org/obo/CL_0000020) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004935"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [squamous granulosa cell](http://purl.obolibrary.org/obo/CL_4033083) [date](http://purl.org/dc/terms/date) "2024-09-24T13:13:24Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -#### Added -- [spermatogonium](http://purl.obolibrary.org/obo/CL_0000020) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004935"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [squamous granulosa cell](http://purl.obolibrary.org/obo/CL_4033083) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "squamous GC"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) -- [spermatogonium](http://purl.obolibrary.org/obo/CL_0000020) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009007"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33914868"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [spermatogonium](http://purl.obolibrary.org/obo/CL_0000020) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004934"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [squamous granulosa cell](http://purl.obolibrary.org/obo/CL_4033083) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4033083"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [squamous granulosa cell](http://purl.obolibrary.org/obo/CL_4033083) [label](http://www.w3.org/2000/01/rdf-schema#label) "squamous granulosa cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -### spinal accessory motor neuron `http://purl.obolibrary.org/obo/CL_0000741` -#### Removed -- [spinal accessory motor neuron](http://purl.obolibrary.org/obo/CL_0000741) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009311"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [squamous granulosa cell](http://purl.obolibrary.org/obo/CL_4033083) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A granulosa cell that has a squamous morphology and form a single layer around the oocyte in primordial follicles. This cell develops directly into a cuboidal granulosa cell during the primordial-to-primary follicle transition."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:28892263"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [spinal accessory motor neuron](http://purl.obolibrary.org/obo/CL_0000741) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009311"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [squamous granulosa cell](http://purl.obolibrary.org/obo/CL_4033083) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "Often in literature squamous granulosa cell and pre-granulosa cell are used as synonyms. However, this term only makes reference to the quiescent granulosa cells that surround the primordial ovarian follicle, while a pre-granulosa cell proliferates to form the primordial follicle (and thus cells become the squamous granulosa cells)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://orcid.org/0000-0001-6677-8489"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [squamous granulosa cell](http://purl.obolibrary.org/obo/CL_4033083) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "flattened granulosa cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:22402964"^^[string](http://www.w3.org/2001/XMLSchema#string) -### spinal cord interneuron `http://purl.obolibrary.org/obo/CL_0005000` -#### Removed -- [spinal cord interneuron](http://purl.obolibrary.org/obo/CL_0005000) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0000778"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [squamous granulosa cell](http://purl.obolibrary.org/obo/CL_4033083) -#### Added -- [spinal cord interneuron](http://purl.obolibrary.org/obo/CL_0005000) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0000778"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [squamous granulosa cell](http://purl.obolibrary.org/obo/CL_4033083) SubClassOf [RO_0002210](http://purl.obolibrary.org/obo/RO_0002210) some [cuboidal granulosa cell](http://purl.obolibrary.org/obo/CL_4033084) +- [squamous granulosa cell](http://purl.obolibrary.org/obo/CL_4033083) SubClassOf [RO_0002207](http://purl.obolibrary.org/obo/RO_0002207) some [pre-granulosa cell](http://purl.obolibrary.org/obo/CL_4033066) -### spinal cord medial motor column neuron `http://purl.obolibrary.org/obo/CL_2000024` -#### Removed -- [spinal cord medial motor column neuron](http://purl.obolibrary.org/obo/CL_2000024) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +- [squamous granulosa cell](http://purl.obolibrary.org/obo/CL_4033083) SubClassOf [granulosa cell](http://purl.obolibrary.org/obo/CL_0000501) -#### Added -- [spinal cord medial motor column neuron](http://purl.obolibrary.org/obo/CL_2000024) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [squamous granulosa cell](http://purl.obolibrary.org/obo/CL_4033083) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0003981](http://purl.obolibrary.org/obo/UBERON_0003981) -### spinal cord oligodendrocyte `http://purl.obolibrary.org/obo/CL_2000025` +### sst GABAergic cortical interneuron `http://purl.obolibrary.org/obo/CL_4023017` #### Removed -- [spinal cord oligodendrocyte](http://purl.obolibrary.org/obo/CL_2000025) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +- [sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023017) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A GABAergic neuron located in the cerebral cortex that expresses somatostatin (sst)"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27477017"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [spinal cord oligodendrocyte](http://purl.obolibrary.org/obo/CL_2000025) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023017) EquivalentTo [interneuron](http://purl.obolibrary.org/obo/CL_0000099) and ([RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_0000956](http://purl.obolibrary.org/obo/UBERON_0000956)) and ([RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0061534](http://purl.obolibrary.org/obo/GO_0061534)) and ([RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000015665](http://purl.obolibrary.org/obo/PR_000015665)) -### spinal cord ventral column interneuron `http://purl.obolibrary.org/obo/CL_2000023` -#### Removed -- [spinal cord ventral column interneuron](http://purl.obolibrary.org/obo/CL_2000023) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +- [sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023017) SubClassOf [cerebral cortex GABAergic interneuron](http://purl.obolibrary.org/obo/CL_0010011) + +- [sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023017) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) #### Added -- [spinal cord ventral column interneuron](http://purl.obolibrary.org/obo/CL_2000023) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023017) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "SOM+ inhibitory interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30001424"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023017) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "SST+ IN"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33742131"^^[string](http://www.w3.org/2001/XMLSchema#string) -### spiny VIP neuron `http://purl.obolibrary.org/obo/CL_4042014` +- [sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023017) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "In the mouse cortex, sst GABAergic cortical interneurons show heterogeneous electrophysiological signatures varying between low-threshold spiking (LTS), regular-spiking and fast-spiking (Song, Y. H., Yoon, J., & Lee, S. H. 2021). Sst GABAergic cortical interneurons have multiple functional roles in the brain. In the mouse, they involved in the generation of slow-waves during the sleep phase of non-rapid eye-movement (NREM) (Funk, C. M. et al., 2017), they maintain synaptic plasticity during motor learning (Adler, A., Zhao, R., et al., 2021), they enhance visual perception in the V1 cortical area by suppressing the activity of pyramidal excitatory neurons (Song, YH. et al., 2020). In humans, malfunctioning of sst GABAergic cortical interneurons is associated with neurodegenerative and psychiatric disorders such as Parkinson's disease, Alzheimer's disease, major depressive disorder, bipolar disorder and schizophrenia as individuals affected by these pathologies show a decrease of expression of SST in the brain (Song YH., Yoon J. et al., 2021)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32494634"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [spiny VIP neuron](http://purl.obolibrary.org/obo/CL_4042014) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A VIP GABAergic cortical interneuron with a soma located in L1-3 of some neocortex in Mmus. This neuron has a multipolar morphology with spiny dendrites concentrating on L1 of the cortex, and has a burst firing electrophysiological signature with highly dynamic dendritic spines."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35418660"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30792151"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [spiny VIP neuron](http://purl.obolibrary.org/obo/CL_4042014) [date](http://purl.org/dc/terms/date) "2024-07-11T12:09:53Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33742131"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [spiny VIP neuron](http://purl.obolibrary.org/obo/CL_4042014) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "multipolar VIP neuron"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35418660"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:28821651"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [spiny VIP neuron](http://purl.obolibrary.org/obo/CL_4042014) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "superficial VIP-positive spiny neuron"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35418660"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023017) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "somatostatin-expressing inhibitory interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30001424"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [spiny VIP neuron](http://purl.obolibrary.org/obo/CL_4042014) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) +- [sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023017) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A transcriptomically distinct GABAergic neuron located in the cerebral cortex that expresses somatostatin (sst). The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: MGE-derived interneurons', Author Categories: 'CrossArea_subclass', cluster Sst."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27477017"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [spiny VIP neuron](http://purl.obolibrary.org/obo/CL_4042014) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042014"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [spiny VIP neuron](http://purl.obolibrary.org/obo/CL_4042014) [label](http://www.w3.org/2000/01/rdf-schema#label) "spiny VIP neuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33742131"^^[string](http://www.w3.org/2001/XMLSchema#string) -- Class: [spiny VIP neuron](http://purl.obolibrary.org/obo/CL_4042014) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/e/9c63201d-bfd9-41a8-bbbc-18d947556f3d.cxg/"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [spiny VIP neuron](http://purl.obolibrary.org/obo/CL_4042014) SubClassOf [VIP GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023016) +- [sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023017) EquivalentTo [medial ganglionic eminence derived GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023069) and ([RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_0000956](http://purl.obolibrary.org/obo/UBERON_0000956)) and ([RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0061534](http://purl.obolibrary.org/obo/GO_0061534)) and ([RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000015665](http://purl.obolibrary.org/obo/PR_000015665)) -- [spiny VIP neuron](http://purl.obolibrary.org/obo/CL_4042014) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001950](http://purl.obolibrary.org/obo/UBERON_0001950) +- [sst GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023017) SubClassOf [medial ganglionic eminence derived GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023069) -### splenic endothelial cell `http://purl.obolibrary.org/obo/CL_2000053` +### sst chodl GABAergic cortical interneuron `http://purl.obolibrary.org/obo/CL_4023121` #### Removed -- [splenic endothelial cell](http://purl.obolibrary.org/obo/CL_2000053) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +- [sst chodl GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023121) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A sst GABAergic cortical interneuron that also expresses Chodl. These neurons are rare and correspond to the only known cortical interneurons with long-range projection."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:15845086"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [splenic endothelial cell](http://purl.obolibrary.org/obo/CL_2000053) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31209381"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33372656"^^[string](http://www.w3.org/2001/XMLSchema#string) -### splenic fibroblast `http://purl.obolibrary.org/obo/CL_2000051` -#### Removed -- [splenic fibroblast](http://purl.obolibrary.org/obo/CL_2000051) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [splenic fibroblast](http://purl.obolibrary.org/obo/CL_2000051) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) +- [sst chodl GABAergic cortical interneuron](http://purl.obolibrary.org/obo/CL_4023121) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A transcriptomically distinct sst GABAergic cortical interneuron that also expresses Chodl. These neurons are rare and correspond to the only known cortical interneurons with long-range projection. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: MGE-derived interneurons', Author Categories: 'CrossArea_subclass', clusters Sst Chodl."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:15845086"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:31209381"^^[string](http://www.w3.org/2001/XMLSchema#string) -### splenocyte `http://purl.obolibrary.org/obo/CL_2000074` -#### Removed -- [splenocyte](http://purl.obolibrary.org/obo/CL_2000074) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33372656"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [splenocyte](http://purl.obolibrary.org/obo/CL_2000074) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/e/9c63201d-bfd9-41a8-bbbc-18d947556f3d.cxg/"^^[string](http://www.w3.org/2001/XMLSchema#string) -### squamous cell of ectocervix `http://purl.obolibrary.org/obo/CL_0002244` -#### Removed -- [squamous cell of ectocervix](http://purl.obolibrary.org/obo/CL_0002244) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A nonstratified squamous cell located in the ectocervix."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://www.bu.edu/histology/p/19404loa.htm"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) +### stem cell `http://purl.obolibrary.org/obo/CL_0000034` + +#### Added +- [stem cell](http://purl.obolibrary.org/obo/CL_0000034) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -- [squamous cell of ectocervix](http://purl.obolibrary.org/obo/CL_0002244) SubClassOf [epithelial cell of uterus](http://purl.obolibrary.org/obo/CL_0002149) -- [squamous cell of ectocervix](http://purl.obolibrary.org/obo/CL_0002244) SubClassOf [squamous epithelial cell](http://purl.obolibrary.org/obo/CL_0000076) +### stratified cuboidal epithelial cell `http://purl.obolibrary.org/obo/CL_0000241` #### Added -- [squamous cell of ectocervix](http://purl.obolibrary.org/obo/CL_0002244) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A stratified squamous epithelial cell located in the ectocervix."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32644501"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [stratified cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000241) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A stratified epithelial cell that is part of cuboidal epithelium, characterized by multiple layers of cuboidal cells forming the apical layer. This provides a protective lining for ducts in large glands, such as sweat glands."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30422572"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://www.bu.edu/histology/p/19404loa.htm"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Stratified_cuboidal_epithelium"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [stratified cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000241) EquivalentTo [stratified epithelial cell](http://purl.obolibrary.org/obo/CL_0000079) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0010077](http://purl.obolibrary.org/obo/UBERON_0010077)) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:/10.1016/j.autneu.2015.04.008"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [stratified cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000241) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0010077](http://purl.obolibrary.org/obo/UBERON_0010077) -- [squamous cell of ectocervix](http://purl.obolibrary.org/obo/CL_0002244) EquivalentTo [squamous epithelial cell](http://purl.obolibrary.org/obo/CL_0000076) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0012251](http://purl.obolibrary.org/obo/UBERON_0012251)) -- [squamous cell of ectocervix](http://purl.obolibrary.org/obo/CL_0002244) SubClassOf [uterine cervix squamous cell](http://purl.obolibrary.org/obo/CL_1001575) +### stratified epithelial cell `http://purl.obolibrary.org/obo/CL_0000079` -- [squamous cell of ectocervix](http://purl.obolibrary.org/obo/CL_0002244) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0012251](http://purl.obolibrary.org/obo/UBERON_0012251) +#### Added +- [stratified epithelial cell](http://purl.obolibrary.org/obo/CL_0000079) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell, organized into multiple layers, with only the basal layer being in contact with the basement membrane."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:/10.1016/B978-0-12-410424-2.00003-2"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Epithelium"^^[string](http://www.w3.org/2001/XMLSchema#string) -### squamous endothelial cell `http://purl.obolibrary.org/obo/CL_0002653` -#### Removed -- [squamous endothelial cell](http://purl.obolibrary.org/obo/CL_0002653) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A endothelial cell of the venule that is squamous shaped. This is in contrast to the cubodial shape of high endothelial venule cells."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.biologyonline.com/dictionary/stratified-epithelium"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [squamous endothelial cell](http://purl.obolibrary.org/obo/CL_0002653) SubClassOf [squamous epithelial cell](http://purl.obolibrary.org/obo/CL_0000076) -- [squamous endothelial cell](http://purl.obolibrary.org/obo/CL_0002653) SubClassOf [endothelial cell of venule](http://purl.obolibrary.org/obo/CL_1000414) +### stratified squamous epithelial cell `http://purl.obolibrary.org/obo/CL_0000240` #### Added -- [squamous endothelial cell](http://purl.obolibrary.org/obo/CL_0002653) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A squamous shaped endothelial cell."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:dos"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [stratified squamous epithelial cell](http://purl.obolibrary.org/obo/CL_0000240) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A stratified epithelial cell that is part of squamous epithelium, characterized by multiple layers of cells. The basal layer is directly attached to the basement membrane and the apical layer consists of flattened squamous cells. This provides a protective barrier, commonly found in areas subject to abrasion, such as the skin, oral cavity, and esophagus."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Epithelium"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [squamous endothelial cell](http://purl.obolibrary.org/obo/CL_0002653) SubClassOf [endothelial cell](http://purl.obolibrary.org/obo/CL_0000115) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30422572"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Stratified_squamous_epithelium"^^[string](http://www.w3.org/2001/XMLSchema#string) -### squamous endothelial cell of venule `http://purl.obolibrary.org/obo/CL_0008040` +- [stratified squamous epithelial cell](http://purl.obolibrary.org/obo/CL_0000240) EquivalentTo [stratified epithelial cell](http://purl.obolibrary.org/obo/CL_0000079) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0006915](http://purl.obolibrary.org/obo/UBERON_0006915)) -#### Added -- [squamous endothelial cell of venule](http://purl.obolibrary.org/obo/CL_0008040) [date](http://purl.org/dc/elements/1.1/date) "2024-07-03T19:52:47Z"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [stratified squamous epithelial cell](http://purl.obolibrary.org/obo/CL_0000240) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0006915](http://purl.obolibrary.org/obo/UBERON_0006915) -- [squamous endothelial cell of venule](http://purl.obolibrary.org/obo/CL_0008040) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:0008040"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [squamous endothelial cell of venule](http://purl.obolibrary.org/obo/CL_0008040) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An endothelial cell of the venule that is squamous shaped. This is in contrast to the cubodial shape of high endothelial venule cells."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) +### striatal PTHLH MOXD1 expressing interneuron `http://purl.obolibrary.org/obo/CL_4042024` -- [squamous endothelial cell of venule](http://purl.obolibrary.org/obo/CL_0008040) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-7073-9172](https://orcid.org/0000-0002-7073-9172) +#### Added +- [striatal PTHLH MOXD1 expressing interneuron](http://purl.obolibrary.org/obo/CL_4042024) [date](http://purl.org/dc/terms/date) "2024-09-17T10:26:57Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -- [squamous endothelial cell of venule](http://purl.obolibrary.org/obo/CL_0008040) [label](http://www.w3.org/2000/01/rdf-schema#label) "squamous endothelial cell of venule"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [striatal PTHLH MOXD1 expressing interneuron](http://purl.obolibrary.org/obo/CL_4042024) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042024"^^[string](http://www.w3.org/2001/XMLSchema#string) -- Class: [squamous endothelial cell of venule](http://purl.obolibrary.org/obo/CL_0008040) +- [striatal PTHLH MOXD1 expressing interneuron](http://purl.obolibrary.org/obo/CL_4042024) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) -- [squamous endothelial cell of venule](http://purl.obolibrary.org/obo/CL_0008040) SubClassOf [endothelial cell of venule](http://purl.obolibrary.org/obo/CL_1000414) +- [striatal PTHLH MOXD1 expressing interneuron](http://purl.obolibrary.org/obo/CL_4042024) [label](http://www.w3.org/2000/01/rdf-schema#label) "striatal PTHLH MOXD1 expressing interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [squamous endothelial cell of venule](http://purl.obolibrary.org/obo/CL_0008040) SubClassOf [squamous endothelial cell](http://purl.obolibrary.org/obo/CL_0002653) +- [striatal PTHLH MOXD1 expressing interneuron](http://purl.obolibrary.org/obo/CL_4042024) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A pthlh-expressing interneuron that expresses MOXD1 and has its soma in a striatum."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30134177"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [striatal PTHLH MOXD1 expressing interneuron](http://purl.obolibrary.org/obo/CL_4042024) -### squamous epithelial cell `http://purl.obolibrary.org/obo/CL_0000076` -#### Removed -- [squamous epithelial cell](http://purl.obolibrary.org/obo/CL_0000076) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009039"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [striatal PTHLH MOXD1 expressing interneuron](http://purl.obolibrary.org/obo/CL_4042024) SubClassOf [RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000010529](http://purl.obolibrary.org/obo/PR_000010529) -#### Added -- [squamous epithelial cell](http://purl.obolibrary.org/obo/CL_0000076) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009039"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [striatal PTHLH MOXD1 expressing interneuron](http://purl.obolibrary.org/obo/CL_4042024) SubClassOf [striatal pthlh-expressing interneuron](http://purl.obolibrary.org/obo/CL_4042023) -### stellate interneuron `http://purl.obolibrary.org/obo/CL_0000691` -#### Removed -- [stellate interneuron](http://purl.obolibrary.org/obo/CL_0000691) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009297"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### striatal pthlh-expressing interneuron `http://purl.obolibrary.org/obo/CL_4042023` #### Added -- [stellate interneuron](http://purl.obolibrary.org/obo/CL_0000691) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009297"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [striatal pthlh-expressing interneuron](http://purl.obolibrary.org/obo/CL_4042023) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "According to spatial transcriptomic data in the human striatum, pthlh-expressing interneurons are one of the most abundant population of interneurons in the striatum (Leonardo D. Garma, et al., 2024)."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37292997"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [striatal pthlh-expressing interneuron](http://purl.obolibrary.org/obo/CL_4042023) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "PTHLH/PVALB cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37292997"^^[string](http://www.w3.org/2001/XMLSchema#string) -### stellate neuron `http://purl.obolibrary.org/obo/CL_0000122` -#### Removed -- [stellate neuron](http://purl.obolibrary.org/obo/CL_0000122) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009072"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [stellate neuron](http://purl.obolibrary.org/obo/CL_0000122) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009072"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [striatal pthlh-expressing interneuron](http://purl.obolibrary.org/obo/CL_4042023) [date](http://purl.org/dc/terms/date) "2024-09-17T10:20:15Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) +- [striatal pthlh-expressing interneuron](http://purl.obolibrary.org/obo/CL_4042023) [label](http://www.w3.org/2000/01/rdf-schema#label) "striatal pthlh-expressing interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) -### stem cell `http://purl.obolibrary.org/obo/CL_0000034` -#### Removed -- [stem cell](http://purl.obolibrary.org/obo/CL_0000034) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005957"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [striatal pthlh-expressing interneuron](http://purl.obolibrary.org/obo/CL_4042023) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A GABAergic interneuron expressing PTHLH and PVALB that has its soma in a striatum. This GABAergic interneuron type presents a spatial expression gradient of PVALB in the mouse striatum."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30134177"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [stem cell](http://purl.obolibrary.org/obo/CL_0000034) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005957"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37292997"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [striatal pthlh-expressing interneuron](http://purl.obolibrary.org/obo/CL_4042023) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042023"^^[string](http://www.w3.org/2001/XMLSchema#string) -### stem cell of epidermis `http://purl.obolibrary.org/obo/CL_1000428` -#### Removed -- [stem cell of epidermis](http://purl.obolibrary.org/obo/CL_1000428) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0007122"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [striatal pthlh-expressing interneuron](http://purl.obolibrary.org/obo/CL_4042023) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "PTHLH +/PVALB+ interneuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37292997"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [stem cell of epidermis](http://purl.obolibrary.org/obo/CL_1000428) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0007122"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [striatal pthlh-expressing interneuron](http://purl.obolibrary.org/obo/CL_4042023) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) +- Class: [striatal pthlh-expressing interneuron](http://purl.obolibrary.org/obo/CL_4042023) -### stem cell of gastric gland `http://purl.obolibrary.org/obo/CL_0002183` -#### Removed -- [stem cell of gastric gland](http://purl.obolibrary.org/obo/CL_0002183) SubClassOf [mucous cell of stomach](http://purl.obolibrary.org/obo/CL_0002180) +- [striatal pthlh-expressing interneuron](http://purl.obolibrary.org/obo/CL_4042023) SubClassOf [CNS interneuron](http://purl.obolibrary.org/obo/CL_0000402) -- [stem cell of gastric gland](http://purl.obolibrary.org/obo/CL_0002183) SubClassOf [exocrine cell](http://purl.obolibrary.org/obo/CL_0000152) +- [striatal pthlh-expressing interneuron](http://purl.obolibrary.org/obo/CL_4042023) SubClassOf [RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000013502](http://purl.obolibrary.org/obo/PR_000013502) -#### Added -- [stem cell of gastric gland](http://purl.obolibrary.org/obo/CL_0002183) SubClassOf [epithelial cell of stomach](http://purl.obolibrary.org/obo/CL_0002178) +- [striatal pthlh-expressing interneuron](http://purl.obolibrary.org/obo/CL_4042023) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) +- [striatal pthlh-expressing interneuron](http://purl.obolibrary.org/obo/CL_4042023) SubClassOf [RO_0002100](http://purl.obolibrary.org/obo/RO_0002100) some [UBERON_0002435](http://purl.obolibrary.org/obo/UBERON_0002435) -### steroid hormone secreting cell `http://purl.obolibrary.org/obo/CL_0000174` -#### Removed -- [steroid hormone secreting cell](http://purl.obolibrary.org/obo/CL_0000174) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009106"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [striatal pthlh-expressing interneuron](http://purl.obolibrary.org/obo/CL_4042023) SubClassOf [RO_0002292](http://purl.obolibrary.org/obo/RO_0002292) some [PR_000013433](http://purl.obolibrary.org/obo/PR_000013433) -#### Added -- [steroid hormone secreting cell](http://purl.obolibrary.org/obo/CL_0000174) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009106"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [striatal pthlh-expressing interneuron](http://purl.obolibrary.org/obo/CL_4042023) SubClassOf [GABAergic interneuron](http://purl.obolibrary.org/obo/CL_0011005) -### stratified cuboidal epithelial cell `http://purl.obolibrary.org/obo/CL_0000241` -#### Removed -- [stratified cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000241) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009145"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### striated cell of salivary gland `http://purl.obolibrary.org/obo/CL_4052049` #### Added -- [stratified cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000241) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009145"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [striated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052049) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "SD cells"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:11590591"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [striated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052049) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) -### stratified epithelial cell `http://purl.obolibrary.org/obo/CL_0000079` -#### Removed -- [stratified epithelial cell](http://purl.obolibrary.org/obo/CL_0000079) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009042"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [striated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052049) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An columnar/cuboidal epithelial cell that is part of the striated duct of salivary gland, characterized by basal striations formed by infoldings of the plasma membrane. This cell play a crucial role in modifying the electrolyte composition and concentration of saliva through active ion transport, particularly the absorption of sodium and secretion of potassium."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30855909"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [stratified epithelial cell](http://purl.obolibrary.org/obo/CL_0000079) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009042"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:36726292"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34147989"^^[string](http://www.w3.org/2001/XMLSchema#string) -### stratified epithelial stem cell `http://purl.obolibrary.org/obo/CL_0000357` -#### Removed -- [stratified epithelial stem cell](http://purl.obolibrary.org/obo/CL_0000357) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009180"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [striated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052049) [contributor](http://purl.org/dc/terms/contributor) [0000-0003-4389-9821](https://orcid.org/0000-0003-4389-9821) -#### Added -- [stratified epithelial stem cell](http://purl.obolibrary.org/obo/CL_0000357) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009180"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [striated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052049) [has_broad_synonym](http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym) "striated duct cells"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:11590591"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [striated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052049) [label](http://www.w3.org/2000/01/rdf-schema#label) "striated cell of salivary gland"^^[string](http://www.w3.org/2001/XMLSchema#string) -### stratified keratinized epithelial stem cell `http://purl.obolibrary.org/obo/CL_1000083` -#### Removed -- [stratified keratinized epithelial stem cell](http://purl.obolibrary.org/obo/CL_1000083) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009371"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [striated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052049) [date](http://purl.org/dc/terms/date) "2024-09-11T10:00:25Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -#### Added -- [stratified keratinized epithelial stem cell](http://purl.obolibrary.org/obo/CL_1000083) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009371"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [striated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052049) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052049"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [striated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052049) -### stratified squamous epithelial cell `http://purl.obolibrary.org/obo/CL_0000240` -#### Removed -- [stratified squamous epithelial cell](http://purl.obolibrary.org/obo/CL_0000240) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009144"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [striated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052049) EquivalentTo [columnar/cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000075) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0014729](http://purl.obolibrary.org/obo/UBERON_0014729)) -#### Added -- [stratified squamous epithelial cell](http://purl.obolibrary.org/obo/CL_0000240) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009144"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [striated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052049) SubClassOf [duct epithelial cell](http://purl.obolibrary.org/obo/CL_0000068) +- [striated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052049) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0015766](http://purl.obolibrary.org/obo/UBERON_0015766) -### stretch receptor cell `http://purl.obolibrary.org/obo/CL_1000082` -#### Removed -- [stretch receptor cell](http://purl.obolibrary.org/obo/CL_1000082) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009370"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [striated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052049) SubClassOf [salivary gland glandular cell](http://purl.obolibrary.org/obo/CL_1001596) -#### Added -- [stretch receptor cell](http://purl.obolibrary.org/obo/CL_1000082) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009370"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [striated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052049) SubClassOf [RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_0036376](http://purl.obolibrary.org/obo/GO_0036376) +- [striated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052049) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0014729](http://purl.obolibrary.org/obo/UBERON_0014729) -### striated muscle cell `http://purl.obolibrary.org/obo/CL_0000737` -#### Removed -- [striated muscle cell](http://purl.obolibrary.org/obo/CL_0000737) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005784"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [striated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052049) SubClassOf [columnar/cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000075) -#### Added -- [striated muscle cell](http://purl.obolibrary.org/obo/CL_0000737) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005784"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [striated cell of salivary gland](http://purl.obolibrary.org/obo/CL_4052049) SubClassOf [RO_0002215](http://purl.obolibrary.org/obo/RO_0002215) some [GO_1990573](http://purl.obolibrary.org/obo/GO_1990573) -### stromal cell `http://purl.obolibrary.org/obo/CL_0000499` -#### Removed -- [stromal cell](http://purl.obolibrary.org/obo/CL_0000499) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009226"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### subepithelial intestinal fibroblast `http://purl.obolibrary.org/obo/CL_4052007` #### Added -- [stromal cell](http://purl.obolibrary.org/obo/CL_0000499) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009226"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) - +- [subepithelial intestinal fibroblast](http://purl.obolibrary.org/obo/CL_4052007) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) -### structural cell `http://purl.obolibrary.org/obo/CL_0000293` -#### Removed -- [structural cell](http://purl.obolibrary.org/obo/CL_0000293) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005745"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [subepithelial intestinal fibroblast](http://purl.obolibrary.org/obo/CL_4052007) [comment](http://www.w3.org/2000/01/rdf-schema#comment) "The S2 fibroblast population has been identified as a subset of intestinal fibroblasts located near the epithelial lining. This population is divided into two subtypes: S2a and S2b. S2a is involved in epithelial differentiation, while S2b, located at the top of the crypt, regulates intestinal stem cell proliferation, niche formation, and wound healing."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37495570"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [structural cell](http://purl.obolibrary.org/obo/CL_0000293) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005745"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33916891"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30270042"^^[string](http://www.w3.org/2001/XMLSchema#string) -### subset_property `http://www.geneontology.org/formats/oboInOwl#SubsetProperty` +- [subepithelial intestinal fibroblast](http://purl.obolibrary.org/obo/CL_4052007) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A fibroblast located adjacent to the intestinal epithelium in both the small intestine and colon, specifically around the crypts. This cell is characterized by the expression of PDGFRα and various collagen isoforms, including COL4A5 and COL4A6. It secretes signalling molecules like TGF-β, Wnt ligands, and BMPs, which are crucial for epithelial homeostasis, intestinal stem cell support, and basement membrane formation."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33916891"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [subset_property](http://www.geneontology.org/formats/oboInOwl#SubsetProperty) [label](http://www.w3.org/2000/01/rdf-schema#label) "subset_property"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30270042"^^[string](http://www.w3.org/2001/XMLSchema#string) -- AnnotationProperty: [subset_property](http://www.geneontology.org/formats/oboInOwl#SubsetProperty) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33430285"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37080817"^^[string](http://www.w3.org/2001/XMLSchema#string) -### substance P secreting cell `http://purl.obolibrary.org/obo/CL_0000505` -#### Removed -- [substance P secreting cell](http://purl.obolibrary.org/obo/CL_0000505) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009230"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [subepithelial intestinal fibroblast](http://purl.obolibrary.org/obo/CL_4052007) [date](http://purl.org/dc/terms/date) "2024-09-23T09:59:27Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -#### Added -- [substance P secreting cell](http://purl.obolibrary.org/obo/CL_0000505) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009230"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [subepithelial intestinal fibroblast](http://purl.obolibrary.org/obo/CL_4052007) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "S2 fibroblast"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33916891"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30270042"^^[string](http://www.w3.org/2001/XMLSchema#string) -### supporting cell `http://purl.obolibrary.org/obo/CL_0000630` -#### Removed -- [supporting cell](http://purl.obolibrary.org/obo/CL_0000630) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009387"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [subepithelial intestinal fibroblast](http://purl.obolibrary.org/obo/CL_4052007) [label](http://www.w3.org/2000/01/rdf-schema#label) "subepithelial intestinal fibroblast"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [supporting cell](http://purl.obolibrary.org/obo/CL_0000630) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009387"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [subepithelial intestinal fibroblast](http://purl.obolibrary.org/obo/CL_4052007) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "S2 mesenchymal cells"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:33916891"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [subepithelial intestinal fibroblast](http://purl.obolibrary.org/obo/CL_4052007) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052007"^^[string](http://www.w3.org/2001/XMLSchema#string) -### surface mucosal cell of stomach `http://purl.obolibrary.org/obo/CL_0002182` -#### Removed -- [surface mucosal cell of stomach](http://purl.obolibrary.org/obo/CL_0002182) SubClassOf [mucus secreting cell](http://purl.obolibrary.org/obo/CL_0000319) +- Class: [subepithelial intestinal fibroblast](http://purl.obolibrary.org/obo/CL_4052007) -#### Added -- [surface mucosal cell of stomach](http://purl.obolibrary.org/obo/CL_0002182) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0001276](http://purl.obolibrary.org/obo/UBERON_0001276) +- [subepithelial intestinal fibroblast](http://purl.obolibrary.org/obo/CL_4052007) SubClassOf [RO_0002220](http://purl.obolibrary.org/obo/RO_0002220) some [UBERON_0001277](http://purl.obolibrary.org/obo/UBERON_0001277) -- [surface mucosal cell of stomach](http://purl.obolibrary.org/obo/CL_0002182) SubClassOf [columnar/cuboidal epithelial cell](http://purl.obolibrary.org/obo/CL_0000075) +- [subepithelial intestinal fibroblast](http://purl.obolibrary.org/obo/CL_4052007) SubClassOf [fibroblast](http://purl.obolibrary.org/obo/CL_0000057) -### sustentacular cell `http://purl.obolibrary.org/obo/CL_0000703` -#### Removed -- [sustentacular cell](http://purl.obolibrary.org/obo/CL_0000703) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009302"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### substantia nigra dopaminergic neuron `http://purl.obolibrary.org/obo/CL_4042025` #### Added -- [sustentacular cell](http://purl.obolibrary.org/obo/CL_0000703) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009302"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [substantia nigra dopaminergic neuron](http://purl.obolibrary.org/obo/CL_4042025) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4042025"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [substantia nigra dopaminergic neuron](http://purl.obolibrary.org/obo/CL_4042025) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0098-8958](https://orcid.org/0000-0002-0098-8958) -### sympathetic cholinergic neuron `http://purl.obolibrary.org/obo/CL_3000003` -#### Removed -- [sympathetic cholinergic neuron](http://purl.obolibrary.org/obo/CL_3000003) [contributor](http://purl.org/dc/terms/contributor) [Q97529981](https://www.wikidata.org/entity/Q97529981) +- [substantia nigra dopaminergic neuron](http://purl.obolibrary.org/obo/CL_4042025) [label](http://www.w3.org/2000/01/rdf-schema#label) "substantia nigra dopaminergic neuron"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [sympathetic cholinergic neuron](http://purl.obolibrary.org/obo/CL_3000003) [contributor](http://purl.org/dc/terms/contributor) [Q97529981](http://www.wikidata.org/entity/Q97529981) +- [substantia nigra dopaminergic neuron](http://purl.obolibrary.org/obo/CL_4042025) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A midbrain dopaminergic neuron that has its soma located in a substantia nigra. This dopaminergic neuron type is highly metabolically active and it is involved in the regulation of movement, cognition, motivation and reward. Neurodegeneration of this dopaminergic neuronal type causes loss in fine motor control in Parkinson's Disease."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35308118"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:32826893"^^[string](http://www.w3.org/2001/XMLSchema#string) -### sympathetic neuron `http://purl.obolibrary.org/obo/CL_0011103` -#### Removed -- [sympathetic neuron](http://purl.obolibrary.org/obo/CL_0011103) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005777"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [substantia nigra dopaminergic neuron](http://purl.obolibrary.org/obo/CL_4042025) [has_narrow_synonym](http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym) "SNpc dopaminergic neuron"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:35308118"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [sympathetic neuron](http://purl.obolibrary.org/obo/CL_0011103) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005777"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [substantia nigra dopaminergic neuron](http://purl.obolibrary.org/obo/CL_4042025) [date](http://purl.org/dc/terms/date) "2024-09-16T13:09:29Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) +- Class: [substantia nigra dopaminergic neuron](http://purl.obolibrary.org/obo/CL_4042025) -### sympathetic noradrenergic neuron `http://purl.obolibrary.org/obo/CL_3000002` -#### Removed -- [sympathetic noradrenergic neuron](http://purl.obolibrary.org/obo/CL_3000002) [contributor](http://purl.org/dc/terms/contributor) [Q97529981](https://www.wikidata.org/entity/Q97529981) +- [substantia nigra dopaminergic neuron](http://purl.obolibrary.org/obo/CL_4042025) SubClassOf [midbrain dopaminergic neuron](http://purl.obolibrary.org/obo/CL_2000097) -#### Added -- [sympathetic noradrenergic neuron](http://purl.obolibrary.org/obo/CL_3000002) [contributor](http://purl.org/dc/terms/contributor) [Q97529981](http://www.wikidata.org/entity/Q97529981) +- [substantia nigra dopaminergic neuron](http://purl.obolibrary.org/obo/CL_4042025) SubClassOf [neuron of the substantia nigra](http://purl.obolibrary.org/obo/CL_0002614) -### synovial cell `http://purl.obolibrary.org/obo/CL_0000214` -#### Removed -- [synovial cell](http://purl.obolibrary.org/obo/CL_0000214) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009131"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### syncytial cell `http://purl.obolibrary.org/obo/CL_4052002` #### Added -- [synovial cell](http://purl.obolibrary.org/obo/CL_0000214) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009131"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [syncytial cell](http://purl.obolibrary.org/obo/CL_4052002) [id](http://www.geneontology.org/formats/oboInOwl#id) "CL:4052002"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [syncytial cell](http://purl.obolibrary.org/obo/CL_4052002) [contributor](http://purl.org/dc/terms/contributor) [0009-0000-8480-9277](https://orcid.org/0009-0000-8480-9277) -### taste receptor cell `http://purl.obolibrary.org/obo/CL_0000209` -#### Removed -- [taste receptor cell](http://purl.obolibrary.org/obo/CL_0000209) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009126"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [syncytial cell](http://purl.obolibrary.org/obo/CL_4052002) [has_related_synonym](http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym) "SC"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [has_synonym_type](http://www.geneontology.org/formats/oboInOwl#hasSynonymType) [OMO_0003000](http://purl.obolibrary.org/obo/OMO_0003000) -#### Added -- [taste receptor cell](http://purl.obolibrary.org/obo/CL_0000209) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009126"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:9067520"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [syncytial cell](http://purl.obolibrary.org/obo/CL_4052002) [date](http://purl.org/dc/terms/date) "2024-08-15T10:38:46Z"^^[dateTime](http://www.w3.org/2001/XMLSchema#dateTime) -### tendon cell `http://purl.obolibrary.org/obo/CL_0000388` -#### Removed -- [tendon cell](http://purl.obolibrary.org/obo/CL_0000388) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009189"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [syncytial cell](http://purl.obolibrary.org/obo/CL_4052002) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "syncytium"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "WBbt:0008074"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [tendon cell](http://purl.obolibrary.org/obo/CL_0000388) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009189"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [syncytial cell](http://purl.obolibrary.org/obo/CL_4052002) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A multinucleate cell formed by the fusion of multiple uninuclear cells through plasma membrane fusion. This process leads to a single large cell containing multiple nuclei within a shared cytoplasm."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Syncytium"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:20851884"^^[string](http://www.w3.org/2001/XMLSchema#string) -### terminal Schwann cell `http://purl.obolibrary.org/obo/CL_0000692` -#### Removed -- [terminal Schwann cell](http://purl.obolibrary.org/obo/CL_0000692) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009298"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [syncytial cell](http://purl.obolibrary.org/obo/CL_4052002) [label](http://www.w3.org/2000/01/rdf-schema#label) "syncytial cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [terminal Schwann cell](http://purl.obolibrary.org/obo/CL_0000692) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009298"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- Class: [syncytial cell](http://purl.obolibrary.org/obo/CL_4052002) +- [syncytial cell](http://purl.obolibrary.org/obo/CL_4052002) EquivalentTo [cell](http://purl.obolibrary.org/obo/CL_0000000) and ([RO_0000053](http://purl.obolibrary.org/obo/RO_0000053) some [PATO_0001908](http://purl.obolibrary.org/obo/PATO_0001908)) and ([RO_0002353](http://purl.obolibrary.org/obo/RO_0002353) some [GO_0000768](http://purl.obolibrary.org/obo/GO_0000768)) -### testosterone secreting cell `http://purl.obolibrary.org/obo/CL_0000177` -#### Removed -- [testosterone secreting cell](http://purl.obolibrary.org/obo/CL_0000177) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009107"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [syncytial cell](http://purl.obolibrary.org/obo/CL_4052002) SubClassOf [multinucleate cell](http://purl.obolibrary.org/obo/CL_0000228) -#### Added -- [testosterone secreting cell](http://purl.obolibrary.org/obo/CL_0000177) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009107"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [syncytial cell](http://purl.obolibrary.org/obo/CL_4052002) SubClassOf [RO_0002353](http://purl.obolibrary.org/obo/RO_0002353) some [GO_0000768](http://purl.obolibrary.org/obo/GO_0000768) +- [syncytial cell](http://purl.obolibrary.org/obo/CL_4052002) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) -### tether cell `http://purl.obolibrary.org/obo/CL_0002450` + +### syncytial epithelial cell `http://purl.obolibrary.org/obo/CL_0000420` #### Removed -- [tether cell](http://purl.obolibrary.org/obo/CL_0002450) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005565"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [syncytial epithelial cell](http://purl.obolibrary.org/obo/CL_0000420) SubClassOf [multinucleate cell](http://purl.obolibrary.org/obo/CL_0000228) #### Added -- [tether cell](http://purl.obolibrary.org/obo/CL_0002450) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005565"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [syncytial epithelial cell](http://purl.obolibrary.org/obo/CL_0000420) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An epithelial cell that forms a syncytium, which is a multinucleated cell resulting from the fusion of multiple cells."^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [syncytial epithelial cell](http://purl.obolibrary.org/obo/CL_0000420) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "Wikipedia:Syncytium"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [syncytial epithelial cell](http://purl.obolibrary.org/obo/CL_0000420) SubClassOf [syncytial cell](http://purl.obolibrary.org/obo/CL_4052002) -### theca cell `http://purl.obolibrary.org/obo/CL_0000503` + +### syncytiotrophoblast cell `http://purl.obolibrary.org/obo/CL_0000525` #### Removed -- [theca cell](http://purl.obolibrary.org/obo/CL_0000503) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009229"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [syncytiotrophoblast cell](http://purl.obolibrary.org/obo/CL_0000525) SubClassOf [multinucleate cell](http://purl.obolibrary.org/obo/CL_0000228) #### Added -- [theca cell](http://purl.obolibrary.org/obo/CL_0000503) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009229"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [syncytiotrophoblast cell](http://purl.obolibrary.org/obo/CL_0000525) SubClassOf [syncytial cell](http://purl.obolibrary.org/obo/CL_4052002) -### thecogen cell `http://purl.obolibrary.org/obo/CL_0000380` +### tanycyte `http://purl.obolibrary.org/obo/CL_0002085` #### Removed -- [thecogen cell](http://purl.obolibrary.org/obo/CL_0000380) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005173"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [tanycyte](http://purl.obolibrary.org/obo/CL_0002085) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stretch cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [tanycyte](http://purl.obolibrary.org/obo/CL_0002085) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "Specialized elongated ventricular ependymal cell that has processes that extend to the outer, or pial, surface of the CNS. Resemble spongioblasts seen in developing brain. Found in the adult brain in the third ventricle, cerebral aqueduct, spinal canal and floor of the fourth ventricle."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://neurolex.org/wiki/Category:Tanycyte"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [thecogen cell](http://purl.obolibrary.org/obo/CL_0000380) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005173"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [tanycyte](http://purl.obolibrary.org/obo/CL_0002085) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A specialized elongated ventricular ependymal cell that has processes that extend to the outer, or pial, surface of the CNS. A tanycyte is found in the adult brain, specifically in the third ventricle, cerebral aqueduct, spinal canal, and floor of the fourth ventricle. This cell type is involved in hormonal regulation, gatekeeping molecules between the bloodstream and cerebrospinal fluid, metabolic sensing, and regulating food intake."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "http://neurolex.org/wiki/Category:Tanycyte"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) -### thermoreceptor cell `http://purl.obolibrary.org/obo/CL_0000205` -#### Removed -- [thermoreceptor cell](http://purl.obolibrary.org/obo/CL_0000205) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009123"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [tanycyte](http://purl.obolibrary.org/obo/CL_0002085) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "stretch cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29351662"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [thermoreceptor cell](http://purl.obolibrary.org/obo/CL_0000205) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009123"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [tanycyte](http://purl.obolibrary.org/obo/CL_0002085) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004670](http://purl.obolibrary.org/obo/UBERON_0004670) -### thromboblast `http://purl.obolibrary.org/obo/CL_0000828` +### thymic nurse cell `http://purl.obolibrary.org/obo/CL_4030004` #### Removed -- [thromboblast](http://purl.obolibrary.org/obo/CL_0000828) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009351"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [thymic nurse cell](http://purl.obolibrary.org/obo/CL_4030004) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A large epithelial cell found in the thymus. This cell type may internalize thymocytes through extensions of plasma membrane. The cell surface and cytoplasmic vacuoles of a thymic nurse cell express MHC Class I and MHC Class II antigens. The interaction of these antigens with a developing thymocyte determines whether the thymocyte undergoes positive or negative selection."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://en.wikipedia.org/wiki/Thymic_nurse_cell"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0002-0819-0473"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [thromboblast](http://purl.obolibrary.org/obo/CL_0000828) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009351"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [thymic nurse cell](http://purl.obolibrary.org/obo/CL_4030004) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0819-0473](https://orcid.org/0000-0002-0819-0473) +- [thymic nurse cell](http://purl.obolibrary.org/obo/CL_4030004) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A large epithelial cell found in the thymus. This cell type may internalize thymocytes through extensions of plasma membrane. The cell surface and cytoplasmic vacuoles of a thymic nurse cell express MHC Class I and MHC Class II antigens. The interaction of these antigens with a developing thymocyte determines whether the thymocyte undergoes positive or negative selection."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://en.wikipedia.org/wiki/Thymic_nurse_cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -### thyroid hormone secreting cell `http://purl.obolibrary.org/obo/CL_0000452` -#### Removed -- [thyroid hormone secreting cell](http://purl.obolibrary.org/obo/CL_0000452) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009210"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +### tracheobronchial serous cell `http://purl.obolibrary.org/obo/CL_0019001` #### Added -- [thyroid hormone secreting cell](http://purl.obolibrary.org/obo/CL_0000452) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009210"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [tracheobronchial serous cell](http://purl.obolibrary.org/obo/CL_0019001) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### thyrotroph `http://purl.obolibrary.org/obo/CL_0000476` +### transit amplifying cell `http://purl.obolibrary.org/obo/CL_0009010` #### Removed -- [thyrotroph](http://purl.obolibrary.org/obo/CL_0000476) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009218"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [transit amplifying cell](http://purl.obolibrary.org/obo/CL_0009010) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) #### Added -- [thyrotroph](http://purl.obolibrary.org/obo/CL_0000476) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009218"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [transit amplifying cell](http://purl.obolibrary.org/obo/CL_0009010) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### tonsil germinal center B cell `http://purl.obolibrary.org/obo/CL_2000006` +### trophoblast cell `http://purl.obolibrary.org/obo/CL_0000351` #### Removed -- [tonsil germinal center B cell](http://purl.obolibrary.org/obo/CL_2000006) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +- [trophoblast cell](http://purl.obolibrary.org/obo/CL_0000351) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An extraembryonic cell that develops from a trophectodermal cell. This cell is found in the outer layer of the blastocyst and can invade other structures in the uterus once the blastocyst implants into the uterine wall. A trophoblast cell is involved in the implantation of the embryo into the uterine wall, placental formation, remodelling of maternal vasculature in the uterus, nutrient and gas exchange, hormone production, and immune modulation to support fetal development."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D014327"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [tonsil germinal center B cell](http://purl.obolibrary.org/obo/CL_2000006) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "doi:10.1007/978-3-030-84725-8"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) -### tormogen cell `http://purl.obolibrary.org/obo/CL_0000372` -#### Removed -- [tormogen cell](http://purl.obolibrary.org/obo/CL_0000372) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005171"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37630754"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [tormogen cell](http://purl.obolibrary.org/obo/CL_0000372) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005171"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [trophoblast cell](http://purl.obolibrary.org/obo/CL_0000351) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An extraembryonic cell that develops from a trophectodermal cell. This cell is found in the outer layer of the blastocyst and can invade other structures in the uterus once the blastocyst implants into the uterine wall. A trophoblast cell is involved in the implantation of the embryo into the uterine wall, placental formation, remodelling of maternal vasculature in the uterus, nutrient and gas exchange, hormone production, and immune modulation to support fetal development."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D014327"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.1007/978-3-030-84725-8"^^[string](http://www.w3.org/2001/XMLSchema#string) -### totipotent stem cell `http://purl.obolibrary.org/obo/CL_0000052` -#### Removed -- [totipotent stem cell](http://purl.obolibrary.org/obo/CL_0000052) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009024"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [totipotent stem cell](http://purl.obolibrary.org/obo/CL_0000052) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009024"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37630754"^^[string](http://www.w3.org/2001/XMLSchema#string) -### tracheobronchial goblet cell `http://purl.obolibrary.org/obo/CL_0019003` -#### Removed -- [tracheobronchial goblet cell](http://purl.obolibrary.org/obo/CL_0019003) EquivalentTo [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0007196](http://purl.obolibrary.org/obo/UBERON_0007196)) +### type A enteroendocrine cell `http://purl.obolibrary.org/obo/CL_0002067` #### Added -- [tracheobronchial goblet cell](http://purl.obolibrary.org/obo/CL_0019003) EquivalentTo [goblet cell](http://purl.obolibrary.org/obo/CL_0000160) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0008397](http://purl.obolibrary.org/obo/UBERON_0008397)) +- [type A enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0002067) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002067"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [type A enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0002067) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -### transitional epithelial cell `http://purl.obolibrary.org/obo/CL_0000244` -#### Removed -- [transitional epithelial cell](http://purl.obolibrary.org/obo/CL_0000244) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009148"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +Type A enteroendocrine cells, also known as alpha cells or A cells, are a species of endocrine cells primarily located in the pancreatic islets of Langerhans; they have also been identified within the lining of the stomach. Functionally, these cells are pivotal in glucose metabolism and homeostasis, accounting for about 20% of the total population of cells in the pancreatic islets. +The primary role of type A enteroendocrine cells involves the synthesis, storage, and secretion of the peptide hormone glucagon, which is critical in energy regulation throughout the body. In response to a decrease in blood glucose levels, the pancreatic A cells are stimulated to secrete glucagon into the bloodstream. Glucagon acts on its target cells, mainly in the liver, to stimulate glycogenolysis and gluconeogenesis processes, thereby increasing blood glucose levels back to normal. In this way, pancreatic A cells play an integral role in maintaining glucose homeostasis and preventing hypoglycemia. +Pancreatic A cells also participate in the local regulation of islet activities as glucagon acts through glucagon receptors on A, B and D type cells within the islets. Recent studies have also shown that Pancreatic A cells play a role in the generation and regeneration of B type cells. Following beta cell injuries pancreatic A cells increase in numbers and produce Glucagon-like peptide-1 (GLP-1), which increases the proliferation and cytoprotection of beta cells. In response to extreme injury of B type cells pancreatic A cells can transform (transdifferentiate) into functioning B type cells. +Until recently, glucagon has been considered a pancreas-specific hormone; however, extrapancreatic glucagon has been reported in patients who had undergone complete, and glucagon-positive cells been identified in the human stomach, indicating that Type A enteroendocrine cells are not restricted to the pancreas."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2337/dbi19-0002"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [transitional epithelial cell](http://purl.obolibrary.org/obo/CL_0000244) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009148"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.2337/db15-1541"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3389/fphys.2012.00349/full"^^[string](http://www.w3.org/2001/XMLSchema#string) -### transitional stage B cell `http://purl.obolibrary.org/obo/CL_0000818` -#### Removed -- [transitional stage B cell](http://purl.obolibrary.org/obo/CL_0000818) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009345"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.diabres.2018.06.013"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [transitional stage B cell](http://purl.obolibrary.org/obo/CL_0000818) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009345"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1210/en.2016-1748"^^[string](http://www.w3.org/2001/XMLSchema#string) -### trichogen cell `http://purl.obolibrary.org/obo/CL_0000374` -#### Removed -- [trichogen cell](http://purl.obolibrary.org/obo/CL_0000374) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005169"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +### type A synovial cell `http://purl.obolibrary.org/obo/CL_0002302` #### Added -- [trichogen cell](http://purl.obolibrary.org/obo/CL_0000374) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005169"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [type A synovial cell](http://purl.obolibrary.org/obo/CL_0002302) SubClassOf [squamous epithelial cell](http://purl.obolibrary.org/obo/CL_0000076) -### trophoblast cell `http://purl.obolibrary.org/obo/CL_0000351` +### type B synovial cell `http://purl.obolibrary.org/obo/CL_0002301` #### Removed -- [trophoblast cell](http://purl.obolibrary.org/obo/CL_0000351) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "trophoblastic cell"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [type B synovial cell](http://purl.obolibrary.org/obo/CL_0002301) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A resident stromal cell located in the synovial membrane and responsible for the production of immune-related cytokines and chemokines. This cell type secretes glycoproteins and hyaluronic acid, has abundant granular endoplasmic reticulum, but contains fewer vacuoles and vesicles."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34433485"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [trophoblast cell](http://purl.obolibrary.org/obo/CL_0000351) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A cell lining the outside of the blastocyst. After binding to the endometrium, trophoblast cells develop into two distinct layers, an inner layer of mononuclear cytotrophoblast cells and an outer layer of continuous multinuclear cytoplasm, the syncytiotrophoblast cells, which form the early fetal-maternal interface."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D014327"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34772990"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0517223651"^^[string](http://www.w3.org/2001/XMLSchema#string) - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [trophoblast cell](http://purl.obolibrary.org/obo/CL_0000351) SubClassOf [BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0000358](http://purl.obolibrary.org/obo/UBERON_0000358) + - [contributor](http://purl.org/dc/terms/contributor) "https://orcid.org/0000-0002-0819-0473"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [trophoblast cell](http://purl.obolibrary.org/obo/CL_0000351) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "An extraembryonic cell that develops from a trophectodermal cell. This cell is found in the outer layer of the blastocyst and can invade other structures in the uterus once the blastocyst implants into the uterine wall. A trophoblast cell is involved in the implantation of the embryo into the uterine wall, placental formation, remodelling of maternal vasculature in the uterus, nutrient and gas exchange, hormone production, and immune modulation to support fetal development."^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "MESH:D014327"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [type B synovial cell](http://purl.obolibrary.org/obo/CL_0002301) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A resident stromal cell located in the synovial membrane and responsible for the production of immune-related cytokines and chemokines. This cell type secretes glycoproteins and hyaluronic acid, has abundant granular endoplasmic reticulum, but contains fewer vacuoles and vesicles."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34433485"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [comment](http://www.w3.org/2000/01/rdf-schema#comment) "doi:10.1007/978-3-030-84725-8"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:34772990"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ISBN:0517223651"^^[string](http://www.w3.org/2001/XMLSchema#string) - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "GOC:tfm"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37630754"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [type B synovial cell](http://purl.obolibrary.org/obo/CL_0002301) [contributor](http://purl.org/dc/terms/contributor) [0000-0002-0819-0473](https://orcid.org/0000-0002-0819-0473) -- [trophoblast cell](http://purl.obolibrary.org/obo/CL_0000351) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "trophoblastic cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "doi:10.1007/978-3-030-84725-8"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [type B synovial cell](http://purl.obolibrary.org/obo/CL_0002301) SubClassOf [squamous epithelial cell](http://purl.obolibrary.org/obo/CL_0000076) -- [trophoblast cell](http://purl.obolibrary.org/obo/CL_0000351) SubClassOf [BFO_0000002](http://purl.obolibrary.org/obo/BFO_0000002) -- [trophoblast cell](http://purl.obolibrary.org/obo/CL_0000351) SubClassOf [RO_0002202](http://purl.obolibrary.org/obo/RO_0002202) some [trophectodermal cell](http://purl.obolibrary.org/obo/CL_1000274) +### type D enteroendocrine cell `http://purl.obolibrary.org/obo/CL_0000502` +#### Added +- [type D enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000502) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000502"^^[string](http://www.w3.org/2001/XMLSchema#string) -### type B pancreatic cell `http://purl.obolibrary.org/obo/CL_0000169` -#### Removed -- [type B pancreatic cell](http://purl.obolibrary.org/obo/CL_0000169) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009102"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [type D enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000502) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -#### Added -- [type B pancreatic cell](http://purl.obolibrary.org/obo/CL_0000169) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009102"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +Type D enteroendocrine cells, also known as D or delta cells, are specialized hormone-releasing cells found in the pancreas and also scattered throughout the lining of the gastrointestinal tract in mammals, notably within the stomach and the upper part of the small intestine known as the duodenum. The primary role of D cells is to produce and secrete somatostatin, a potent paracrine inhibitor. +In the gastrointestinal tract, somatostatin slows down digestion. It reduces gastric acid secretion and slows down the rate of gastric emptying, thereby prolonging and controling the digestive p. Functionally, these effects are aimed at sustaining nutrient absorption to optimize energy extraction from consumed food. +In the pancreas, D cells maintain a vital role in endocrine regulation. D cells in the pancreatic islands secrete somatostatin to inhibit the release of both insulin and glucagon from type A cells and B cells, glucoregulatory hormones that control blood sugar levels. Hence, D cells contribute considerably to the homeostasis of the body's metabolic processes. It is also noteworthy that dysfunctional D cells or irregular somatostatin signaling has been associated with certain pathologies such as neuroendocrine tumors and gastric ulcers."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1093/annonc/mdh216"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41574-018-0020-6"^^[string](http://www.w3.org/2001/XMLSchema#string) -### type D enteroendocrine cell `http://purl.obolibrary.org/obo/CL_0000502` -#### Removed -- [type D enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000502) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009228"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.pharmthera.2015.05.007"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [type D enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000502) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009228"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://www.sciencedirect.com/topics/neuroscience/somatostatin-cell"^^[string](http://www.w3.org/2001/XMLSchema#string) -### type G enteroendocrine cell `http://purl.obolibrary.org/obo/CL_0000508` -#### Removed -- [type G enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000508) SubClassOf [mucous cell of stomach](http://purl.obolibrary.org/obo/CL_0002180) +### type EC enteroendocrine cell `http://purl.obolibrary.org/obo/CL_0000577` #### Added -- [type G enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000508) SubClassOf [glandular epithelial cell of stomach](http://purl.obolibrary.org/obo/CL_0002659) +- [type EC enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000577) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000577"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [type EC enteroendocrine cell](http://purl.obolibrary.org/obo/CL_0000577) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -### type II cell of adrenal medulla `http://purl.obolibrary.org/obo/CL_0002082` -#### Removed -- [type II cell of adrenal medulla](http://purl.obolibrary.org/obo/CL_0002082) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "adremergic chromaffin cell"^^[string](http://www.w3.org/2001/XMLSchema#string) - -#### Added -- [type II cell of adrenal medulla](http://purl.obolibrary.org/obo/CL_0002082) [has_exact_synonym](http://www.geneontology.org/formats/oboInOwl#hasExactSynonym) "adrenergic chromaffin cell"^^[string](http://www.w3.org/2001/XMLSchema#string) +Type EC enteroendocrine cells, also known as enterochromaffin cells, are a vital hormone-secreting cell type found in the gastrointestinal tract. These cells are named after their location in the intestines (“entero”) and because they are stainable by chromium salts (“chromaffin”). +The primary function of type EC enteroendocrine cells is to act as chemosensors and lies in their capacity to produce and secrete serotonin, also known as 5-hydroxytryptamine (5-HT). Serotonin is a neurotransmitter that plays a significant role in modulating motility, secretion, vasodilation, perception of pain, and appetite in the gastrointestinal system. However, its function is not limited to the gastrointestinal tract; once secreted, serotonin is distributed via the bloodstream and contributes to regulating mood, appetite, and sleep in the brain. +Via specific chemosensory receptors type EC enteroendocrine cells are able to respond to various environmental, metabolic, and homeostatic stimuli and transduce information from the gut to the nervous system: Food intake, particularly the ingestion of fats and carbohydrates, prompts these cells to produce and release serotonin; the mechanical stimulus of food in the lumen can also trigger release. The distribution, function, and responsiveness of type EC cells reveal them as a crucial link between the intestinal environment, the nervous system, and the regulation of numerous bodily functions."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/0166-4328(96)00075-7"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1073/pnas.1804938115"^^[string](http://www.w3.org/2001/XMLSchema#string) -### umbilical artery endothelial cell `http://purl.obolibrary.org/obo/CL_2000052` -#### Removed -- [umbilical artery endothelial cell](http://purl.obolibrary.org/obo/CL_2000052) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41574-019-0168-8"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [umbilical artery endothelial cell](http://purl.obolibrary.org/obo/CL_2000052) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/j.cell.2017.05.034"^^[string](http://www.w3.org/2001/XMLSchema#string) -### unipolar neuron `http://purl.obolibrary.org/obo/CL_0000106` +### ureteral cell `http://purl.obolibrary.org/obo/CL_1000601` #### Removed -- [unipolar neuron](http://purl.obolibrary.org/obo/CL_0000106) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009058"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [ureteral cell](http://purl.obolibrary.org/obo/CL_1000601) SubClassOf [cell](http://purl.obolibrary.org/obo/CL_0000000) #### Added -- [unipolar neuron](http://purl.obolibrary.org/obo/CL_0000106) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009058"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [ureteral cell](http://purl.obolibrary.org/obo/CL_1000601) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) ### urothelial cell `http://purl.obolibrary.org/obo/CL_0000731` -#### Removed -- [urothelial cell](http://purl.obolibrary.org/obo/CL_0000731) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009308"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [urothelial cell](http://purl.obolibrary.org/obo/CL_0000731) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009308"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [urothelial cell](http://purl.obolibrary.org/obo/CL_0000731) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0000731"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [urothelial cell](http://purl.obolibrary.org/obo/CL_0000731) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -### vasa recta cell `http://purl.obolibrary.org/obo/CL_1001036` -#### Removed -- [vasa recta cell](http://purl.obolibrary.org/obo/CL_1001036) EquivalentTo [kidney capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1000892) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004726](http://purl.obolibrary.org/obo/UBERON_0004726)) - -- [vasa recta cell](http://purl.obolibrary.org/obo/CL_1001036) SubClassOf [kidney capillary endothelial cell](http://purl.obolibrary.org/obo/CL_1000892) - - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) +Urothelial cells are a unique type of epithelial cell found lining the urinary tract system. They form the urothelium, a specialized, multi-layered epithelium that lines major portions of the urinary tract, including the renal pelvis, ureters, bladder, and the proximal part of the urethra. The distinct characteristic of urothelial cells is their ability to stretch and contract depending on the volume of liquid they contain - a feature that facilitates the essential role they play in maintaining the functionality and integrity of the urinary system. +The primary function of urothelial cells is to provide an impermeable barrier to urine, preventing the toxic components present in the urine from seeping back into the body's bloodstream. The urothelium consists of a superficial umbrella cell layer, 1–2 layers of intermediate cells, and a basal cell layer. The umbrella layer is composed of large, mostly binucleated cells that are covered in an asymmetrical unit membrane, the uroplakin plaques. These plaques function to seal the apical membrane of the bladder from the toxic and highly variable contents of urine. The lipid bilayer structure of uroplakin plaques has an exceptionally high concentration of uroplakins that contribute to the barrier function of the urothelium. +Beyond their mechanical function, urothelial cells also play a role in sensing and signaling changes in the urinary system. They express a number of sensor molecules or respond to thermal, mechanical and chemical stimuli and can release chemical mediators. This allows them to act as sensory transducers because they detect changes in the filling state of the bladder and transmit this information to the nervous system. Moreover, these versatile cells contribute to the defense mechanism against urinary tract pathogens. They respond to bacterial infections by releasing chemical messengers, cytokines and chemokines, to attract immune cells, and also can engulf pathogens via endocytosis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/ncpuro0672"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [vasa recta cell](http://purl.obolibrary.org/obo/CL_1001036) SubClassOf [kidney venous blood vessel cell](http://purl.obolibrary.org/obo/CL_1000893) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/ki.2009.73"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [vasa recta cell](http://purl.obolibrary.org/obo/CL_1001036) EquivalentTo [microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000008) and ([BFO_0000050](http://purl.obolibrary.org/obo/BFO_0000050) some [UBERON_0004726](http://purl.obolibrary.org/obo/UBERON_0004726)) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41579-020-0324-0"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [vasa recta cell](http://purl.obolibrary.org/obo/CL_1001036) SubClassOf [microvascular endothelial cell](http://purl.obolibrary.org/obo/CL_2000008) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/physrev.00041.2019"^^[string](http://www.w3.org/2001/XMLSchema#string) -- [vasa recta cell](http://purl.obolibrary.org/obo/CL_1001036) SubClassOf [kidney medulla cell](http://purl.obolibrary.org/obo/CL_1000504) - - [is_inferred](http://www.geneontology.org/formats/oboInOwl#is_inferred) "true"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1002/nau.22195"^^[string](http://www.w3.org/2001/XMLSchema#string) -### vascular associated smooth muscle cell `http://purl.obolibrary.org/obo/CL_0000359` -#### Removed -- [vascular associated smooth muscle cell](http://purl.obolibrary.org/obo/CL_0000359) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009181"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### vaginal lubricant secreting cell `http://purl.obolibrary.org/obo/CL_0000436` #### Added -- [vascular associated smooth muscle cell](http://purl.obolibrary.org/obo/CL_0000359) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009181"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [vaginal lubricant secreting cell](http://purl.obolibrary.org/obo/CL_0000436) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### vascular lymphangioblast `http://purl.obolibrary.org/obo/CL_0005022` -#### Removed -- [vascular lymphangioblast](http://purl.obolibrary.org/obo/CL_0005022) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009395"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### vasa recta ascending limb cell `http://purl.obolibrary.org/obo/CL_1001131` #### Added -- [vascular lymphangioblast](http://purl.obolibrary.org/obo/CL_0005022) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009395"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [vasa recta ascending limb cell](http://purl.obolibrary.org/obo/CL_1001131) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1001131"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [vasa recta ascending limb cell](http://purl.obolibrary.org/obo/CL_1001131) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. -### ventricular cardiac muscle cell `http://purl.obolibrary.org/obo/CL_2000046` -#### Removed -- [ventricular cardiac muscle cell](http://purl.obolibrary.org/obo/CL_2000046) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](https://www.wikidata.org/entity/Q35563349) +The vasa recta ascending limb cells are specialized epithelial cells that are part of the vasa recta in the kidney, a crucial component of the renal medulla that functions as a counter-current exchanger to maintain the concentration gradient required for water reabsorption. These particular cells are located in the ascending limb of the vasa recta, which takes blood flow from the medulla back to the cortex. +The primary function of vasa recta ascending limb cells is to preserve the renal medulla's hypertonicity, necessary for the kidney's urine concentration mechanism. Unlike the vasa recta descending limb cells, the venous-like epithelial cells of the ascending vasa recta are highly fenestrated and lack pericyte coverage, which facilitates water reuptake. +As the blood flows through the ascending limb, it loses solutes and gains water, which is driven by the high solute concentration in the surrounding interstitium. This process acts in concert with cellular action in the descending limb and contributions from the so-called Loop of Henle, which helps with water and sodium chloride retrieval from the urine. +In the context of normal physiological processes, the function of the vasa recta ascending limb cells is essential in maintaining the body's overall fluid balance, electrolyte concentration, and systemic blood pressure. Any dysfunction in these cells may lead to impaired urine concentration or dilution capability of the kidney, potentially resulting in conditions like diabetes insipidus or hyponatremia."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1053/j.ajkd.2005.01.008"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [ventricular cardiac muscle cell](http://purl.obolibrary.org/obo/CL_2000046) [contributor](http://purl.org/dc/terms/contributor) [Q35563349](http://www.wikidata.org/entity/Q35563349) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/ajpregu.00657.2002"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1016/B978-0-323-35515-5.00009-9"^^[string](http://www.w3.org/2001/XMLSchema#string) -### visceral muscle cell `http://purl.obolibrary.org/obo/CL_0008007` -#### Removed -- [visceral muscle cell](http://purl.obolibrary.org/obo/CL_0008007) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005070"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/apha.12026"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [visceral muscle cell](http://purl.obolibrary.org/obo/CL_0008007) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00005070"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1081/jdi-100101958"^^[string](http://www.w3.org/2001/XMLSchema#string) -### visceromotor neuron `http://purl.obolibrary.org/obo/CL_0005025` -#### Removed -- [visceromotor neuron](http://purl.obolibrary.org/obo/CL_0005025) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005732"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### vasa recta descending limb cell `http://purl.obolibrary.org/obo/CL_1001285` #### Added -- [visceromotor neuron](http://purl.obolibrary.org/obo/CL_0005025) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005732"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [vasa recta descending limb cell](http://purl.obolibrary.org/obo/CL_1001285) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. +Vasa recta descending limb cells are specialized epithelial cells found in the vasa recta, a network of blood vessels in the renal medulla. These cells line the interior surface of the descending limb of the vasa recta and play a crucial role in the filtering and regulation of substances within the blood. +In contrast to vasa recta ascending limb cells, the arterial-like epithelial cells of the descending vasa recta are non-fenestrated and covered by a pericyte layer that regulates the medullary blood flow. They help keeping the body’s fluid and electrolyte balance in check through a process known as countercurrent exchange system, in which the cells of the descending limb are permeable to water but relatively impermeable to solutes, such as sodium and urea. As the blood descends into the medulla along its descending limb, water passively diffuses out of the vasa recta, concentrating the blood in solutes. +In addition to their central role in water and solute exchange, these cells contribute to maintaining the medullary osmotic gradient, a critical function to concentrate urine. The osmotic gradient is created by the counterflow of water and solutes between the descending and ascending limbs of the vasa recta and the adjacent Loop of Henle. The selective permeability of the descending limb cells allows them to maintain this gradient, which in turn helps to conserve water, a vital role in the overall function of the renal system. Thus, vasa recta descending limb cells have a significant function in renal physiology, particularly in osmoregulation and fluid balance."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1111/apha.12026#apha12026-bib-0039"^^[string](http://www.w3.org/2001/XMLSchema#string) -### visible light photoreceptor cell `http://purl.obolibrary.org/obo/CL_0000488` -#### Removed -- [visible light photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000488) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009219"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1053/j.ajkd.2005.01.008"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [visible light photoreceptor cell](http://purl.obolibrary.org/obo/CL_0000488) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009219"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1152/ajpregu.00657.2002"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1081/jdi-100101958"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [vasa recta descending limb cell](http://purl.obolibrary.org/obo/CL_1001285) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_1001285"^^[string](http://www.w3.org/2001/XMLSchema#string) -### visual pigment cell (sensu Nematoda and Protostomia) `http://purl.obolibrary.org/obo/CL_0001658` +### vascular leptomeningeal cell `http://purl.obolibrary.org/obo/CL_4023051` #### Removed -- [visual pigment cell (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0001658) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004230"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [vascular leptomeningeal cell](http://purl.obolibrary.org/obo/CL_4023051) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A type of mesothelial fibroblast that is derived from the neural crest, is localized on blood vessels, and is a key component of the pia and arachnoid membranes surrounding the brain."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27284195"^^[string](http://www.w3.org/2001/XMLSchema#string) -#### Added -- [visual pigment cell (sensu Nematoda and Protostomia)](http://purl.obolibrary.org/obo/CL_0001658) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "FBbt:00004230"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/ManualMappingCuration"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30096314"^^[string](http://www.w3.org/2001/XMLSchema#string) -### visual pigment cell (sensu Vertebrata) `http://purl.obolibrary.org/obo/CL_0000343` -#### Removed -- [visual pigment cell (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000343) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009171"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29443965"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [visual pigment cell (sensu Vertebrata)](http://purl.obolibrary.org/obo/CL_0000343) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009171"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [vascular leptomeningeal cell](http://purl.obolibrary.org/obo/CL_4023051) [definition](http://purl.obolibrary.org/obo/IAO_0000115) "A transcriptomically distinct type of mesothelial fibroblast that is derived from the neural crest, is localized on blood vessels, and is a key component of the pia and arachnoid membranes surrounding the brain. The standard transcriptomic reference data for this cell type can be found on the CellxGene census under the collection: 'Transcriptomic cytoarchitecture reveals principles of human neocortex organization', dataset: 'Supercluster: Non-neuronal cells', Author Categories: 'CrossArea_subclass', clusters VLMC."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:27284195"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:37824655"^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/e/5346f9c6-755e-4336-94cc-38706ec00c2f.cxg/"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:30096314"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "PMID:29443965"^^[string](http://www.w3.org/2001/XMLSchema#string) -### xanthoblast `http://purl.obolibrary.org/obo/CL_0005002` -#### Removed -- [xanthoblast](http://purl.obolibrary.org/obo/CL_0005002) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005245"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) + +### vein endothelial cell `http://purl.obolibrary.org/obo/CL_0002543` #### Added -- [xanthoblast](http://purl.obolibrary.org/obo/CL_0005002) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0005245"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [vein endothelial cell](http://purl.obolibrary.org/obo/CL_0002543) [description](http://purl.org/dc/terms/description) "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Vein endothelial cells form a thin layer of squamous cells, the endothelium, lining the interior surface of veins throughout the body. They shape the inner cellular lining of the entire vascular system, including the heart, playing a crucial role in blood circulation. The unique characteristic compact arrangement of these cells enables veins to act as a barrier between the blood (that can contain foreign substances) and the surrounding venous tissue and maintain the integrity of the vascular system. +The primary function of vein endothelial cells is to control the exchange of substances between the bloodstream and the surrounding tissues. They facilitate selective transportation of molecules depending on their size and solubility, including gases, nutrients, hormones, and waste products. Vein endothelial cells also play a protective role by inhibiting the translocation of toxins or pathogens from blood to tissues. Additionally, these cells are involved in blood coagulation and inflammation response, primarily by producing substances that inhibit blood clot formation under normal conditions and initiating clotting when necessary. +Another significant function of vein endothelial cells is the regulation of blood flow and blood pressure. They produce and release several substances, including nitric oxide and prostacyclin, which help in controlling vasodilation and vasoconstriction, thereby regulating blood pressure. These cells are also responsible for angiogenesis, the formation of new blood vessels, which is crucial during wound healing and in the formation of granulation tissue. Consequently, any dysfunction in vein endothelial cells can lead to severe health problems like atherosclerosis, hypertension, and thrombosis."^^[string](http://www.w3.org/2001/XMLSchema#string) + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1007/s00441-008-0706-5"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41598-021-01360-w"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.3390/ijms20184411"^^[string](http://www.w3.org/2001/XMLSchema#string) + + - [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "DOI:10.1038/s41569-022-00770-1"^^[string](http://www.w3.org/2001/XMLSchema#string) + +- [vein endothelial cell](http://purl.obolibrary.org/obo/CL_0002543) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "https://cellxgene.cziscience.com/cellguide/CL_0002543"^^[string](http://www.w3.org/2001/XMLSchema#string) ### xanthophore cell `http://purl.obolibrary.org/obo/CL_0000430` -#### Removed -- [xanthophore cell](http://purl.obolibrary.org/obo/CL_0000430) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009198"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) #### Added -- [xanthophore cell](http://purl.obolibrary.org/obo/CL_0000430) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0009198"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [xanthophore cell](http://purl.obolibrary.org/obo/CL_0000430) SubClassOf [eukaryotic cell](http://purl.obolibrary.org/obo/CL_0000255) -### yolk cell `http://purl.obolibrary.org/obo/CL_0000428` -#### Removed -- [yolk cell](http://purl.obolibrary.org/obo/CL_0000428) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0000084"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](http://purl.obolibrary.org/obo/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +### yolk sac hematopoietic stem cell `http://purl.obolibrary.org/obo/CL_0002354` #### Added -- [yolk cell](http://purl.obolibrary.org/obo/CL_0000428) [database_cross_reference](http://www.geneontology.org/formats/oboInOwl#hasDbXref) "ZFA:0000084"^^[string](http://www.w3.org/2001/XMLSchema#string) - - [mapping_justification](https://w3id.org/sssom/mapping_justification) "https://w3id.org/semapv/vocab/UnspecifiedMatching"^^[string](http://www.w3.org/2001/XMLSchema#string) +- [yolk sac hematopoietic stem cell](http://purl.obolibrary.org/obo/CL_0002354) SubClassOf [PR_000050567](http://purl.obolibrary.org/obo/PR_000050567) diff --git a/src/ontology/reports/cl-edit.owl-obo-report.tsv b/src/ontology/reports/cl-edit.owl-obo-report.tsv index 627326c2e..164583607 100644 --- a/src/ontology/reports/cl-edit.owl-obo-report.tsv +++ b/src/ontology/reports/cl-edit.owl-obo-report.tsv @@ -1,15 +1,12 @@ Level Rule Name Subject Property Value -WARN duplicate_scoped_synonym CL:4023064 oboInOwl:hasExactSynonym CGE interneuron -WARN duplicate_scoped_synonym CL:4023064 oboInOwl:hasRelatedSynonym CGE interneuron +WARN duplicate_label_synonym CL:1000347 oboInOwl:hasExactSynonym colonocyte WARN missing_definition CL:0000028 IAO:0000115 WARN missing_definition CL:0000030 IAO:0000115 WARN missing_definition CL:0000036 IAO:0000115 WARN missing_definition CL:0000054 IAO:0000115 WARN missing_definition CL:0000069 IAO:0000115 WARN missing_definition CL:0000072 IAO:0000115 -WARN missing_definition CL:0000076 IAO:0000115 WARN missing_definition CL:0000078 IAO:0000115 -WARN missing_definition CL:0000079 IAO:0000115 WARN missing_definition CL:0000095 IAO:0000115 WARN missing_definition CL:0000102 IAO:0000115 WARN missing_definition CL:0000109 IAO:0000115 @@ -28,8 +25,6 @@ WARN missing_definition CL:0000208 IAO:0000115 WARN missing_definition CL:0000217 IAO:0000115 WARN missing_definition CL:0000237 IAO:0000115 WARN missing_definition CL:0000238 IAO:0000115 -WARN missing_definition CL:0000240 IAO:0000115 -WARN missing_definition CL:0000241 IAO:0000115 WARN missing_definition CL:0000246 IAO:0000115 WARN missing_definition CL:0000249 IAO:0000115 WARN missing_definition CL:0000251 IAO:0000115 @@ -64,7 +59,6 @@ WARN missing_definition CL:0000406 IAO:0000115 WARN missing_definition CL:0000410 IAO:0000115 WARN missing_definition CL:0000416 IAO:0000115 WARN missing_definition CL:0000417 IAO:0000115 -WARN missing_definition CL:0000420 IAO:0000115 WARN missing_definition CL:0000423 IAO:0000115 WARN missing_definition CL:0000428 IAO:0000115 WARN missing_definition CL:0000435 IAO:0000115 @@ -160,6 +154,7 @@ INFO missing_superclass CL:0000020 rdfs:subClassOf INFO missing_superclass CL:0000048 rdfs:subClassOf INFO missing_superclass CL:0000064 rdfs:subClassOf INFO missing_superclass CL:0000067 rdfs:subClassOf +INFO missing_superclass CL:0000076 rdfs:subClassOf INFO missing_superclass CL:0000080 rdfs:subClassOf INFO missing_superclass CL:0000082 rdfs:subClassOf INFO missing_superclass CL:0000103 rdfs:subClassOf @@ -192,8 +187,10 @@ INFO missing_superclass CL:0000225 rdfs:subClassOf INFO missing_superclass CL:0000226 rdfs:subClassOf INFO missing_superclass CL:0000227 rdfs:subClassOf INFO missing_superclass CL:0000228 rdfs:subClassOf +INFO missing_superclass CL:0000240 rdfs:subClassOf INFO missing_superclass CL:0000255 rdfs:subClassOf INFO missing_superclass CL:0000295 rdfs:subClassOf +INFO missing_superclass CL:0000322 rdfs:subClassOf INFO missing_superclass CL:0000329 rdfs:subClassOf INFO missing_superclass CL:0000349 rdfs:subClassOf INFO missing_superclass CL:0000350 rdfs:subClassOf @@ -279,7 +276,6 @@ INFO missing_superclass CL:0002343 rdfs:subClassOf INFO missing_superclass CL:0002344 rdfs:subClassOf INFO missing_superclass CL:0002346 rdfs:subClassOf INFO missing_superclass CL:0002366 rdfs:subClassOf -INFO missing_superclass CL:0002372 rdfs:subClassOf INFO missing_superclass CL:0002374 rdfs:subClassOf INFO missing_superclass CL:0002426 rdfs:subClassOf INFO missing_superclass CL:0002438 rdfs:subClassOf @@ -319,6 +315,7 @@ INFO missing_superclass CL:0003001 rdfs:subClassOf INFO missing_superclass CL:0004246 rdfs:subClassOf INFO missing_superclass CL:0004247 rdfs:subClassOf INFO missing_superclass CL:0004250 rdfs:subClassOf +INFO missing_superclass CL:0005012 rdfs:subClassOf INFO missing_superclass CL:0005018 rdfs:subClassOf INFO missing_superclass CL:0005023 rdfs:subClassOf INFO missing_superclass CL:0008003 rdfs:subClassOf @@ -407,7 +404,6 @@ INFO missing_superclass CL:0009102 rdfs:subClassOf INFO missing_superclass CL:0009115 rdfs:subClassOf INFO missing_superclass CL:0010001 rdfs:subClassOf INFO missing_superclass CL:0010002 rdfs:subClassOf -INFO missing_superclass CL:0010003 rdfs:subClassOf INFO missing_superclass CL:0010004 rdfs:subClassOf INFO missing_superclass CL:0010005 rdfs:subClassOf INFO missing_superclass CL:0010006 rdfs:subClassOf @@ -461,6 +457,7 @@ INFO missing_superclass CL:1000222 rdfs:subClassOf INFO missing_superclass CL:1000236 rdfs:subClassOf INFO missing_superclass CL:1000239 rdfs:subClassOf INFO missing_superclass CL:1000245 rdfs:subClassOf +INFO missing_superclass CL:1000271 rdfs:subClassOf INFO missing_superclass CL:1000272 rdfs:subClassOf INFO missing_superclass CL:1000296 rdfs:subClassOf INFO missing_superclass CL:1000298 rdfs:subClassOf @@ -620,8 +617,6 @@ INFO missing_superclass CL:4023008 rdfs:subClassOf INFO missing_superclass CL:4023009 rdfs:subClassOf INFO missing_superclass CL:4023012 rdfs:subClassOf INFO missing_superclass CL:4023013 rdfs:subClassOf -INFO missing_superclass CL:4023017 rdfs:subClassOf -INFO missing_superclass CL:4023018 rdfs:subClassOf INFO missing_superclass CL:4023019 rdfs:subClassOf INFO missing_superclass CL:4023035 rdfs:subClassOf INFO missing_superclass CL:4023038 rdfs:subClassOf @@ -636,7 +631,6 @@ INFO missing_superclass CL:4023062 rdfs:subClassOf INFO missing_superclass CL:4023063 rdfs:subClassOf INFO missing_superclass CL:4023066 rdfs:subClassOf INFO missing_superclass CL:4023068 rdfs:subClassOf -INFO missing_superclass CL:4023069 rdfs:subClassOf INFO missing_superclass CL:4023072 rdfs:subClassOf INFO missing_superclass CL:4023074 rdfs:subClassOf INFO missing_superclass CL:4023076 rdfs:subClassOf @@ -749,3 +743,8 @@ INFO missing_superclass CL:4047002 rdfs:subClassOf INFO missing_superclass CL:4047003 rdfs:subClassOf INFO missing_superclass CL:4047004 rdfs:subClassOf INFO missing_superclass CL:4047005 rdfs:subClassOf +INFO missing_superclass CL:4047018 rdfs:subClassOf +INFO missing_superclass CL:4047019 rdfs:subClassOf +INFO missing_superclass CL:4047051 rdfs:subClassOf +INFO missing_superclass CL:4047052 rdfs:subClassOf +INFO missing_superclass CL:4052002 rdfs:subClassOf diff --git a/src/ontology/subsets/blood_and_immune_upper_slim.json b/src/ontology/subsets/blood_and_immune_upper_slim.json index 0f8e1a3e4..fdd02d37b 100644 --- a/src/ontology/subsets/blood_and_immune_upper_slim.json +++ b/src/ontology/subsets/blood_and_immune_upper_slim.json @@ -4,9 +4,9 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-08-16" + "val" : "2024-09-26" } ], - "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-08-16/subsets/blood_and_immune_upper_slim.owl" + "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-09-26/subsets/blood_and_immune_upper_slim.owl" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/CL_0000000", @@ -521,6 +521,10 @@ "lbl" : "squamous epithelial cell", "type" : "CLASS", "meta" : { + "definition" : { + "val" : "Any epithelial cell that is part of some squamous epithelium.", + "xrefs" : [ "FBC:Autogenerated" ] + }, "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-1249" @@ -719,10 +723,15 @@ "val" : "BTO:0001433" }, { "val" : "ZFA:0009064" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000113" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nMononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. \nIn addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses.\nMononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer." } ] } }, { @@ -1078,22 +1087,16 @@ "meta" : { "definition" : { "val" : "A cell with more than one nucleus.", - "xrefs" : [ "FB:ma" ] + "xrefs" : [ "FB:ma", "Wikipedia:Multinucleate" ] }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "syncitium" - }, { - "pred" : "hasExactSynonym", - "val" : "syncytial cell" + "val" : "multinucleated cells", + "xrefs" : [ "Wikipedia:Multinucleate" ] }, { "pred" : "hasExactSynonym", - "val" : "syncytium" - } ], - "xrefs" : [ { - "val" : "AEO:0000203" - }, { - "val" : "WBbt:0008074" + "val" : "polynuclear cells", + "xrefs" : [ "Wikipedia:Multinucleate" ] } ] } }, { @@ -1255,7 +1258,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "Any cell that only exists in Eukaryota.", + "val" : "Any cell that in taxon some Eukaryota.", "xrefs" : [ "FBC:Autogenerated" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], @@ -1884,8 +1887,8 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A phagocytic cell formed by the fusion of macrophages, occurs in chronic inflammatory responses to persistent microorganism such as M.tuberculosis, component of granulomas. Sometimes used to refer to megakaryocytes.", - "xrefs" : [ "GOC:add", "GOC:tfm", "ISBN:0702022918", "ISBN:0702024783" ] + "val" : "A phagocytic syncytial cell formed by the fusion of macrophages, occurs in chronic inflammatory responses to persistent microorganism such as M.tuberculosis, component of granulomas. Sometimes used to refer to megakaryocytes.", + "xrefs" : [ "GOC:add", "GOC:tfm", "ISBN:0702022918", "ISBN:0702024783", "PMID:33348900", "Wikipedia:Giant_cell" ] }, "comments" : [ "Role or process: Chronic infection, granulomatous inflammation. Consider also megakaryocyte (CL:0000556) as sometimes multinucleated giant cell is used to refer to this." ], "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim" ], @@ -1909,6 +1912,11 @@ "pred" : "hasExactSynonym", "val" : "syncytial giant cell", "xrefs" : [ "ISBN:0702022918", "ISBN:0702024783" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", + "pred" : "hasRelatedSynonym", + "val" : "MGC", + "xrefs" : [ "PMID:33348900" ] } ], "xrefs" : [ { "val" : "BTO:0003107" @@ -3452,27 +3460,6 @@ "val" : "2010-12-07T09:37:22Z" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/CL_0002546", - "lbl" : "embryonic blood vessel endothelial progenitor cell", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An endothelial progenitor cell that participates in angiogenesis during development.", - "xrefs" : [ "GOC:tfm" ] - }, - "comments" : [ "See CL:0002619." ], - "xrefs" : [ { - "val" : "ZFA:0005773" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0003-1980-3228" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2011-02-28T04:20:39Z" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/CL_0002679", "lbl" : "natural helper lymphocyte", @@ -3588,7 +3575,14 @@ "val" : "A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells.", "xrefs" : [ "https://orcid.org/0000-0001-5208-3432", "https://orcid.org/0000-0002-9900-7880" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "xrefs" : [ { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0011012" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." + } ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0011026", @@ -3809,6 +3803,33 @@ "val" : "2022-11-04T14:40:00Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_4052002", + "lbl" : "syncytial cell", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A multinucleate cell formed by the fusion of multiple uninuclear cells through plasma membrane fusion. This process leads to a single large cell containing multiple nuclei within a shared cytoplasm.", + "xrefs" : [ "PMID:20851884", "Wikipedia:Syncytium" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "syncytium", + "xrefs" : [ "WBbt:0008074" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", + "pred" : "hasRelatedSynonym", + "val" : "SC", + "xrefs" : [ "PMID:9067520" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0009-0000-8480-9277" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-08-15T10:38:46Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0000278", "lbl" : "mitotic cell cycle", @@ -3868,6 +3889,24 @@ "val" : "cellular_component" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0000768", + "lbl" : "syncytium formation by plasma membrane fusion", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells.", + "xrefs" : [ "GOC:mtg_muscle", "GOC:tb" ] + }, + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "cell fusion" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0000785", "lbl" : "chromatin", @@ -3892,6 +3931,9 @@ "val" : "NIF_Subcellular:sao1615953555" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28301" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "GO:0000789" }, { @@ -4986,7 +5028,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/GO_0002538", - "lbl" : "arachidonic acid metabolite production involved in inflammatory response", + "lbl" : "arachidonate metabolite production involved in inflammatory response", "type" : "CLASS", "meta" : { "definition" : { @@ -5000,11 +5042,17 @@ }, { "pred" : "hasBroadSynonym", "val" : "production of arachidonic acid metabolites involved in acute inflammatory response" + }, { + "pred" : "hasExactSynonym", + "val" : "arachidonic acid metabolite production involved in inflammatory response" }, { "pred" : "hasExactSynonym", "val" : "production of arachidonic acid metabolites involved in inflammatory response" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28648" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -6856,6 +6904,21 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0006949", + "lbl" : "syncytium formation", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane. Syncytia are normally derived from single cells that fuse or fail to complete cell division.", + "xrefs" : [ "ISBN:0198506732" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0006950", "lbl" : "response to stress", @@ -6865,7 +6928,6 @@ "val" : "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).", "xrefs" : [ "GOC:mah" ] }, - "comments" : [ "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC." ], "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_plant_ribbon" ], "synonyms" : [ { "pred" : "hasRelatedSynonym", @@ -6875,6 +6937,9 @@ "val" : "response to biotic stress" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/26810" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -6992,6 +7057,29 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0007009", + "lbl" : "plasma membrane organization", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the plasma membrane.", + "xrefs" : [ "GOC:dph", "GOC:jl", "GOC:mah" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "plasma membrane organisation" + }, { + "pred" : "hasRelatedSynonym", + "val" : "plasma membrane organization and biogenesis", + "xrefs" : [ "GOC:mah" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0007049", "lbl" : "cell cycle", @@ -7836,6 +7924,29 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0010256", + "lbl" : "endomembrane system organization", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endomembrane system.", + "xrefs" : [ "GOC:mah", "GOC:sm" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_drosophila" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "endomembrane organization" + }, { + "pred" : "hasExactSynonym", + "val" : "endomembrane system organisation", + "xrefs" : [ "GOC:mah" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0010324", "lbl" : "membrane invagination", @@ -8277,6 +8388,15 @@ "val" : "stem cell renewal" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_2" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_2157" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -9862,27 +9982,6 @@ "val" : "cellular_component" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0032993", - "lbl" : "protein-DNA complex", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A macromolecular complex containing both protein and DNA molecules.", - "xrefs" : [ "GOC:mah" ] - }, - "comments" : [ "Note that this term is intended to classify complexes that have DNA as one of the members of the complex, that is, the complex does not exist if DNA is not present. Protein complexes that interact with DNA e.g. transcription factor complexes should not be classified here." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "DNA-protein complex", - "xrefs" : [ "GOC:mah" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0033151", "lbl" : "V(D)J recombination", @@ -10732,6 +10831,7 @@ "val" : "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.", "xrefs" : [ "GOC:go_curators" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "membrane-enclosed organelle" @@ -10740,6 +10840,9 @@ "val" : "NIF_Subcellular:sao414196390" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28153" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -10753,7 +10856,7 @@ "val" : "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes.", "xrefs" : [ "GOC:go_curators" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_mouse" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_mouse" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "non-membrane-enclosed organelle" @@ -10767,6 +10870,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/21881" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28153" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -10781,8 +10887,11 @@ "val" : "Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.", "xrefs" : [ "GOC:go_curators" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_pir" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28153" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -10940,12 +11049,15 @@ "val" : "A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component.", "xrefs" : [ "GOC:jl", "GOC:mah" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_pir" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "cellular component biogenesis at cellular level" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/27194" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "GO:0071843" }, { @@ -11095,6 +11207,30 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0045026", + "lbl" : "plasma membrane fusion", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell.", + "xrefs" : [ "GOC:elh", "GOC:mtg_muscle" ] + }, + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "cell fusion" + }, { + "pred" : "hasBroadSynonym", + "val" : "cell-cell fusion" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0006947" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0045058", "lbl" : "T cell selection", @@ -11143,6 +11279,15 @@ "val" : "Wikipedia:Innate_immune_system" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_2" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_2157" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "GO:0002226" }, { @@ -13864,6 +14009,36 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0140253", + "lbl" : "cell-cell fusion", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A cellular process in which two or more cells combine together, their plasma membrane fusing, producing a single cell. In some cases, nuclei fuse, producing a polyploid cell, while in other cases, nuclei remain separate, producing a syncytium.", + "xrefs" : [ "Wikipedia:Cell_fusion" ] + }, + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "cell fusion" + }, { + "pred" : "hasExactSynonym", + "val" : "cell cell fusion" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/15939" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "pg" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-08-13T18:38:18Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0140352", "lbl" : "export from cell", @@ -18916,15 +19091,15 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/PR_000064867", - "lbl" : "protein-containing molecular entity", + "id" : "http://purl.obolibrary.org/obo/PR_000050567", + "lbl" : "protein-containing material entity", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A molecular entity that minimally consists of a protein.", + "val" : "A material entity that minimally consists of a protein.", "xrefs" : [ "PRO:DAN" ] }, - "comments" : [ "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565)." ], + "comments" : [ "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566)." ], "synonyms" : [ { "pred" : "hasNarrowSynonym", "val" : "protein", @@ -22055,7 +22230,7 @@ "val" : "The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO].", "xrefs" : [ "BIRNLEX:844", "ISBN:0-14-051288-8", "ISBN:3110148986", "NLM:nervous+system", "WB:rynl", "Wikipedia:Nervous_system", "ZFIN:curator" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#cumbo", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#cumbo", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "neurological system", @@ -22128,9 +22303,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -28047,7 +28219,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000050", - "lbl" : "part_of", + "lbl" : "part of", "type" : "PROPERTY", "propertyType" : "OBJECT", "meta" : { @@ -28070,9 +28242,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "part_of" @@ -28092,7 +28261,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000051", - "lbl" : "has_part", + "lbl" : "has part", "type" : "PROPERTY", "propertyType" : "OBJECT", "meta" : { @@ -28115,9 +28284,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_part" @@ -31982,6 +32148,10 @@ "id" : "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "type" : "PROPERTY", "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#gocheck_obsoletion_candidate", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/go#goslim_agr", "type" : "PROPERTY", @@ -32320,6 +32490,10 @@ "id" : "http://purl.org/dc/terms/date", "type" : "PROPERTY", "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/description", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/license", "type" : "PROPERTY", @@ -32345,12 +32519,10 @@ "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "lbl" : "created by", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "lbl" : "creation date", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { @@ -32443,7 +32615,6 @@ "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#id", - "lbl" : "id", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { @@ -32513,12 +32684,16 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000000", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_131567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000007", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0002321" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000034", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000034", "pred" : "is_a", @@ -32631,6 +32806,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000040", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000040", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -32736,7 +32915,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000066", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000066", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -32749,18 +32928,18 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000071", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0004638" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000071", - "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/CL_0002546" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000076", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000066" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000076", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0006914" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000080", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000080", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -32821,6 +33000,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000092", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000092", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -32871,6 +33054,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000094", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000094", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -32917,6 +33104,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000097", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0002274" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000097", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000097", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -32987,6 +33178,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000115", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000213" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000115", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000115", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -33033,6 +33228,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000187", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000183" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000187", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000187", "pred" : "is_a", @@ -33061,6 +33260,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000219", "pred" : "http://purl.obolibrary.org/obo/RO_0002215", "obj" : "http://purl.obolibrary.org/obo/GO_0048870" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000221", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000221", "pred" : "is_a", @@ -33069,6 +33272,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000221", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000924" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000222", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000222", "pred" : "is_a", @@ -33077,6 +33284,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000222", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000926" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000223", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000223", "pred" : "is_a", @@ -33093,6 +33304,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000225", "pred" : "http://purl.obolibrary.org/obo/RO_0000053", "obj" : "http://purl.obolibrary.org/obo/PATO_0001405" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000226", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000226", "pred" : "is_a", @@ -33101,6 +33316,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000226", "pred" : "http://purl.obolibrary.org/obo/RO_0000053", "obj" : "http://purl.obolibrary.org/obo/PATO_0001407" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000228", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000228", "pred" : "is_a", @@ -33239,7 +33458,7 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0000000" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000255", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000325", @@ -33291,7 +33510,7 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0010017" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000365", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000393", @@ -33309,6 +33528,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000451", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000145" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000451", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000451", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -33367,7 +33590,7 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000518", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000540", @@ -33419,6 +33642,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000547", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0002242" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000547", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000547", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -33493,6 +33720,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000549", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000549", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -33515,6 +33746,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000550", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000550", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -33661,6 +33896,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000557", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_1001610" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000557", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000557", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -33699,6 +33938,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000558", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000558", "pred" : "http://purl.obolibrary.org/obo/CL_4030046", @@ -33769,6 +34012,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000559", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000559", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -33795,6 +34042,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000566", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0011026" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000566", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000566", "pred" : "http://purl.obolibrary.org/obo/RO_0002104", @@ -33845,10 +34096,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000576", "pred" : "http://purl.obolibrary.org/obo/RO_0002215", "obj" : "http://purl.obolibrary.org/obo/GO_0043011" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000647", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000228" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000647", "pred" : "is_a", @@ -33859,6 +34106,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000647", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_4052002" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000647", "pred" : "http://purl.obolibrary.org/obo/RO_0000056", @@ -33875,6 +34126,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000680", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000055" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000680", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000680", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -33919,7 +34174,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0002405" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000738", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000738", @@ -33951,6 +34206,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000762", "pred" : "http://purl.obolibrary.org/obo/RO_0002215", "obj" : "http://purl.obolibrary.org/obo/GO_0007596" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000763", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000763", "pred" : "is_a", @@ -34207,6 +34466,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000786", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000786", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -34245,6 +34508,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000789", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000789", "pred" : "http://purl.obolibrary.org/obo/RO_0002104", @@ -34259,6 +34526,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000798", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000798", "pred" : "http://purl.obolibrary.org/obo/RO_0002104", @@ -34349,6 +34620,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000826", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000826", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -34423,6 +34698,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000831", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000831", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -34523,10 +34802,18 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000831", "pred" : "http://purl.obolibrary.org/obo/RO_0015016", "obj" : "http://purl.obolibrary.org/obo/PR_000007431" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000837", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000837", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0008001" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000837", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000837", "pred" : "http://purl.obolibrary.org/obo/CL_4030046", @@ -34651,6 +34938,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000889", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000889", "pred" : "http://purl.obolibrary.org/obo/RO_0000053", @@ -34806,7 +35097,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0001035", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0001035", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -34887,6 +35178,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0001200", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000945" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0001200", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0001200", "pred" : "http://purl.obolibrary.org/obo/CL_4030046", @@ -34945,6 +35240,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0002028", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0002191" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0002028", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002028", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -34981,6 +35280,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0002028", "pred" : "http://purl.obolibrary.org/obo/RO_0002215", "obj" : "http://purl.obolibrary.org/obo/GO_0060374" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0002031", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002031", "pred" : "is_a", @@ -34993,6 +35296,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0002031", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", "obj" : "http://purl.obolibrary.org/obo/CL_0002032" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0002032", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002032", "pred" : "is_a", @@ -35092,7 +35399,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002319", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002319", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -35100,7 +35407,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002320", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002320", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -35126,15 +35433,11 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002494", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002494", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0007100" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0002546", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000222" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002679", "pred" : "is_a", @@ -35145,6 +35448,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0002679", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002679", "pred" : "http://purl.obolibrary.org/obo/CL_4030046", @@ -35209,6 +35516,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0008019", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000219" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0008019", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0008019", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -35229,6 +35540,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0011012", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0002321" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0011026", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0011026", "pred" : "is_a", @@ -35329,6 +35644,14 @@ "sub" : "http://purl.obolibrary.org/obo/CL_4030029", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_2000001" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_4052002", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000228" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_4052002", + "pred" : "http://purl.obolibrary.org/obo/RO_0002353", + "obj" : "http://purl.obolibrary.org/obo/GO_0000768" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0000278", "pred" : "is_a", @@ -35353,10 +35676,18 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0000323", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0005773" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0000768", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0006949" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0000768", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0140253" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0000785", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0032993" + "obj" : "http://purl.obolibrary.org/obo/GO_0110165" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0000785", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -36189,8 +36520,8 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0043232" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0005840", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", - "obj" : "http://purl.obolibrary.org/obo/PR_000000001" + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0005840", "pred" : "http://purl.obolibrary.org/obo/RO_0002216", @@ -36387,6 +36718,18 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0006936", "pred" : "http://purl.obolibrary.org/obo/BFO_0000066", "obj" : "http://purl.obolibrary.org/obo/UBERON_0002385" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0006949", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0009987" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0006949", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0048646" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0006949", + "pred" : "http://purl.obolibrary.org/obo/RO_0002297", + "obj" : "http://purl.obolibrary.org/obo/CL_0000228" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0006950", "pred" : "is_a", @@ -36419,6 +36762,18 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0006996", "pred" : "http://purl.obolibrary.org/obo/RO_0002592", "obj" : "http://purl.obolibrary.org/obo/GO_0043226" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0007009", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0061024" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0007009", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/GO_0010256" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0007009", + "pred" : "http://purl.obolibrary.org/obo/RO_0002592", + "obj" : "http://purl.obolibrary.org/obo/GO_0005886" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0007049", "pred" : "is_a", @@ -36643,6 +36998,14 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0009987", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0008150" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0010256", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0016043" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0010256", + "pred" : "http://purl.obolibrary.org/obo/RO_0002592", + "obj" : "http://purl.obolibrary.org/obo/GO_0012505" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0010324", "pred" : "is_a", @@ -37273,12 +37636,8 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0005575" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0032991", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", - "obj" : "http://purl.obolibrary.org/obo/PR_000000001" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0032993", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0032991" + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0033151", "pred" : "is_a", @@ -37643,6 +38002,18 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0044419", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0008150" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0045026", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0007009" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0045026", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0061025" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0045026", + "pred" : "http://purl.obolibrary.org/obo/RO_0012008", + "obj" : "http://purl.obolibrary.org/obo/GO_0005886" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0045058", "pred" : "is_a", @@ -38499,6 +38870,10 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0098644", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0099080" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0098644", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0098644", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -38699,6 +39074,14 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0140112", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0044085" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0140253", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0009987" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0140253", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/GO_0045026" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0140352", "pred" : "is_a", @@ -39162,7 +39545,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/PR_000000001", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000064867" + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/PR_000000001", "pred" : "http://purl.obolibrary.org/obo/RO_0002353", @@ -39512,7 +39895,7 @@ "pred" : "http://purl.obolibrary.org/obo/RO_0002160", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { - "sub" : "http://purl.obolibrary.org/obo/PR_000064867", + "sub" : "http://purl.obolibrary.org/obo/PR_000050567", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { @@ -39635,7 +40018,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0001434" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000075", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000075", @@ -39737,7 +40120,7 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0007369" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000109", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000110", @@ -39757,7 +40140,7 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0001841" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000110", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000111", @@ -39773,7 +40156,7 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0048513" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000111", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", @@ -39781,12 +40164,16 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0004921" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", "obj" : "http://purl.obolibrary.org/obo/UBERON_0035804" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0000178", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000178", "pred" : "is_a", @@ -39839,7 +40226,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0002193" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000179", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000307", @@ -39859,7 +40246,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0011216" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000383", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000383", @@ -39967,6 +40354,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000481", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000479" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0000483", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000483", "pred" : "is_a", @@ -39981,7 +40372,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0005769" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000483", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208", "meta" : { "basicPropertyValues" : [ { @@ -40041,7 +40432,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0010316" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000923", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000924", @@ -40111,7 +40502,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0035804" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000930", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000948", @@ -40145,7 +40536,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0004151" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000948", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000948", @@ -40185,7 +40576,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000467" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001009", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001009", @@ -40217,7 +40608,7 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0000540" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001016", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001016", @@ -40264,7 +40655,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0001016" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001017", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001017", @@ -40342,7 +40733,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0004765" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001474", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001474", @@ -40364,7 +40755,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0001007" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001555", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001555", @@ -40396,6 +40787,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001630", "pred" : "http://purl.obolibrary.org/obo/RO_0002473", "obj" : "http://purl.obolibrary.org/obo/UBERON_0002385" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001969", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001969", "pred" : "is_a", @@ -40412,6 +40807,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001969", "pred" : "http://purl.obolibrary.org/obo/RO_0002221", "obj" : "http://purl.obolibrary.org/obo/CL_0000232" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", "pred" : "is_a", @@ -40489,7 +40888,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0012275" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001986", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001986", @@ -40569,7 +40968,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002193", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002204", @@ -40653,7 +41052,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0011137" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711", "meta" : { "basicPropertyValues" : [ { @@ -40705,7 +41104,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002329", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711", "meta" : { "basicPropertyValues" : [ { @@ -40750,7 +41149,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_89593" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", @@ -40841,7 +41240,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000479" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002384", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002385", @@ -40857,7 +41256,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0001015" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002385", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002385", @@ -40887,7 +41286,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002390", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002390", @@ -40925,7 +41324,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0001474" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002481", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002532", @@ -40987,7 +41386,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000926" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003068", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003068", @@ -41007,7 +41406,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0016879" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003075", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711", "meta" : { "basicPropertyValues" : [ { @@ -41104,7 +41503,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003081", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003081", @@ -41176,7 +41575,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003089", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742", "meta" : { "basicPropertyValues" : [ { @@ -41204,7 +41603,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000479" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003104", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003104", @@ -41386,6 +41785,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004291", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", "obj" : "http://purl.obolibrary.org/obo/UBERON_0004139" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004535", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004535", "pred" : "is_a", @@ -41402,6 +41805,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004535", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001981" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004537", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004537", "pred" : "is_a", @@ -41502,7 +41909,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004770", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004770", @@ -41542,7 +41949,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0003068" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004880", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004905", @@ -41574,7 +41981,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000060" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004923", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005061", @@ -41626,7 +42033,7 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0000187" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005090", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005157", @@ -41728,6 +42135,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0005764", "pred" : "http://purl.obolibrary.org/obo/RO_0002007", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", "pred" : "is_a", @@ -41748,7 +42159,7 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0005587" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", @@ -41842,7 +42253,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0005423" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006268", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006268", @@ -41872,7 +42283,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000307" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006595", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006595", @@ -41904,7 +42315,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000307" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006601", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006601", @@ -41920,7 +42331,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000307" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006603", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006603", @@ -41934,6 +42345,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0006914", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/CL_0000076" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0006965", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006965", "pred" : "is_a", @@ -42247,6 +42662,10 @@ "val" : "CARO" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0010210", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0010210", "pred" : "is_a", @@ -42429,7 +42848,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0011997", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0012275", @@ -42507,7 +42926,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000475" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0013701", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0013702", @@ -42557,7 +42976,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0015212", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0015228", @@ -43932,6 +44351,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0001981" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000076", + "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000066" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", + "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0006914" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000080", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ], @@ -44154,7 +44580,7 @@ "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000255", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002160", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002162", "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" } ] }, { @@ -44168,7 +44594,7 @@ "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000365", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0010017" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002160", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002162", "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" } ] }, { @@ -45086,9 +45512,6 @@ "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0002104", "fillerId" : "http://purl.obolibrary.org/obo/PR_000001002" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002162", - "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_40674" }, { "propertyId" : "http://purl.obolibrary.org/obo/RO_0002215", "fillerId" : "http://purl.obolibrary.org/obo/GO_0019724" @@ -45319,6 +45742,16 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0000178" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/CL_4052002", + "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000053", + "fillerId" : "http://purl.obolibrary.org/obo/PATO_0001908" + }, { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002353", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0000768" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0000278", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0007049" ], @@ -45333,6 +45766,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/GOREL_0002004", "fillerId" : "http://purl.obolibrary.org/obo/GO_0005634" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0000768", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0006949" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000051", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0045026" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0001677", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0022607" ], @@ -45662,6 +46102,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/GO_0097194" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0006949", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0048646" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002297", + "fillerId" : "http://purl.obolibrary.org/obo/CL_0000228" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0006996", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016043" ], @@ -45669,6 +46116,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002592", "fillerId" : "http://purl.obolibrary.org/obo/GO_0043226" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0007009", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016043" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002592", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0005886" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0007186", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0007165" ], @@ -45732,6 +46186,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002296", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0000479" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0010256", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016043" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002592", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0012505" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0012501", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008219" ], @@ -46145,6 +46606,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002592", "fillerId" : "http://purl.obolibrary.org/obo/GO_0032991" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045026", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009987" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0012008", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0005886" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045321", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0001775" ], diff --git a/src/ontology/subsets/blood_and_immune_upper_slim.obo b/src/ontology/subsets/blood_and_immune_upper_slim.obo index 0cc054eb5..e723d3ceb 100644 --- a/src/ontology/subsets/blood_and_immune_upper_slim.obo +++ b/src/ontology/subsets/blood_and_immune_upper_slim.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: cl/releases/2024-08-16/subsets/blood_and_immune_upper_slim.owl +data-version: cl/releases/2024-09-26/subsets/blood_and_immune_upper_slim.owl subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" subsetdef: attribute_slim "" @@ -19,6 +19,7 @@ subsetdef: eye_upper_slim "a subset of general classes related to specific cell subsetdef: functional_classification "" subsetdef: general_cell_types_upper_slim "a subset of general classes of cell types in the cell ontology." subsetdef: gocheck_do_not_annotate "" +subsetdef: gocheck_obsoletion_candidate "" subsetdef: goslim_agr "" subsetdef: goslim_candida "" subsetdef: goslim_chembl "" @@ -95,7 +96,7 @@ idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# idspace: sssom https://w3id.org/sssom/ idspace: terms http://purl.org/dc/terms/ ontology: cl/subsets/blood_and_immune_upper_slim -property_value: owl:versionInfo "2024-08-16" xsd:string +property_value: owl:versionInfo "2024-09-26" xsd:string [Term] id: CL:0000000 @@ -118,7 +119,7 @@ is_a: UBERON:0000061 ! anatomical structure disjoint_from: GO:0031012 ! extracellular matrix disjoint_from: GO:0032991 ! protein-containing complex disjoint_from: GO:0043226 ! organelle -relationship: RO:0002160 NCBITaxon:131567 ! only in taxon cellular organisms +relationship: RO:0002162 NCBITaxon:131567 ! in taxon cellular organisms [Term] id: CL:0000007 @@ -139,6 +140,7 @@ synonym: "animal stem cell" EXACT [] xref: CALOHA:TS-2086 xref: FMA:63368 xref: ZFA:0005957 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0011115 ! precursor cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0017145 ! stem cell division @@ -230,6 +232,7 @@ xref: FMA:83553 xref: ZFA:0009017 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0002194 {is_inferred="true"} ! monopoietic cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002194 ! monopoietic cell intersection_of: capable_of GO:0030224 ! monocyte differentiation intersection_of: has_part CL:0017503 ! basophilic cytoplasm @@ -398,7 +401,7 @@ xref: FBbt:00000124 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ xref: FMA:66768 xref: WBbt:0003672 xref: ZFA:0009034 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell disjoint_from: CL:0000738 ! leukocyte relationship: part_of UBERON:0000483 ! epithelium property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI @@ -415,23 +418,26 @@ is_a: CL:0002139 ! endothelial cell of vascular tree intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0001981 ! blood vessel relationship: part_of UBERON:0004638 ! blood vessel endothelium -relationship: RO:0002202 CL:0002546 ! develops from embryonic blood vessel endothelial progenitor cell property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000076 name: squamous epithelial cell +def: "Any epithelial cell that is part of some squamous epithelium." [FBC:Autogenerated] subset: cellxgene_subset xref: CALOHA:TS-1249 xref: ZFA:0009039 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell +intersection_of: CL:0000066 ! epithelial cell +intersection_of: part_of UBERON:0006914 ! squamous epithelium +relationship: part_of UBERON:0006914 ! squamous epithelium [Term] id: CL:0000080 name: circulating cell def: "A cell which moves among different tissues of the body, via blood, lymph, or other medium." [GOC:add] xref: ZFA:0009043 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0000179 ! haemolymphatic fluid relationship: part_of UBERON:0000179 ! haemolymphatic fluid @@ -491,6 +497,7 @@ xref: ZFA:0009047 {sssom:mapping_justification="https://w3id.org/semapv/vocab/Un is_a: CL:0000518 ! phagocyte (sensu Vertebrata) is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte is_a: CL:0001035 {is_inferred="true"} ! bone cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: capable_of GO:0045453 ! bone resorption intersection_of: has_part PR:000001850 ! cathepsin K @@ -527,6 +534,7 @@ xref: FMA:62854 xref: ZFA:0009048 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000081 ! blood cell is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: capable_of GO:0008015 ! blood circulation intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -564,6 +572,7 @@ xref: CALOHA:TS-0603 xref: FMA:66784 is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte is_a: CL:0002274 ! histamine secreting cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: capable_of GO:0002349 ! histamine production involved in inflammatory response intersection_of: capable_of GO:0002539 ! prostaglandin production involved in inflammatory response @@ -599,12 +608,14 @@ def: "A vertebrate phagocyte with a single nucleus." [GOC:add, GOC:tfm, ISBN:078 subset: cellxgene_subset subset: human_reference_atlas xref: BTO:0001433 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000113 xref: ZFA:0009064 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000518 {is_inferred="true"} ! phagocyte (sensu Vertebrata) is_a: CL:0000842 ! mononuclear cell intersection_of: CL:0000518 ! phagocyte (sensu Vertebrata) intersection_of: bearer_of PATO:0001407 ! mononucleate property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nMononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. \nIn addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses.\nMononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer." xsd:string {xref="DOI:10.1016/j.coi.2005.11.008", xref="DOI:10.1038/nri3087", xref="DOI:10.3389/fimmu.2019.01893"} [Term] id: CL:0000115 @@ -619,6 +630,7 @@ xref: CALOHA:TS-0278 xref: FMA:66772 xref: ZFA:0009065 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000213 ! lining cell +is_a: CL:0000255 ! eukaryotic cell relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell property_value: RO:0002175 NCBITaxon:9606 @@ -704,6 +716,7 @@ xref: FMA:67328 xref: WBbt:0003675 xref: ZFA:0009114 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000183 ! contractile cell +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000393 ! electrically responsive cell relationship: RO:0002202 CL:0000056 ! develops from myoblast property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI @@ -747,6 +760,7 @@ def: "A cell of the outer of the three germ layers of the embryo." [MESH:D004475 synonym: "ectoderm cell" EXACT [] xref: FMA:72549 xref: ZFA:0009137 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000924 ! ectoderm @@ -759,6 +773,7 @@ synonym: "mesoblast" EXACT [] synonym: "mesoderm cell" EXACT [] xref: FMA:72554 xref: ZFA:0009138 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000926 ! mesoderm @@ -769,6 +784,7 @@ def: "A cell of the inner of the three germ layers of the embryo." [MESH:D004707 synonym: "endoderm cell" EXACT [] xref: FMA:72555 xref: ZFA:0009139 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000925 ! endoderm @@ -788,6 +804,7 @@ relationship: bearer_of PATO:0001405 ! anucleate id: CL:0000226 name: single nucleate cell def: "A cell with a single nucleus." [FB:ma, GOC:tfm] +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002242 ! nucleate cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0001407 ! mononucleate @@ -796,12 +813,10 @@ relationship: bearer_of PATO:0001407 ! mononucleate [Term] id: CL:0000228 name: multinucleate cell -def: "A cell with more than one nucleus." [FB:ma] -synonym: "syncitium" EXACT [] -synonym: "syncytial cell" EXACT [] -synonym: "syncytium" EXACT [] -xref: AEO:0000203 -xref: WBbt:0008074 +def: "A cell with more than one nucleus." [FB:ma, Wikipedia:Multinucleate] +synonym: "multinucleated cells" EXACT [Wikipedia:Multinucleate] +synonym: "polynuclear cells" EXACT [Wikipedia:Multinucleate] +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002242 ! nucleate cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0001908 ! multinucleate @@ -926,13 +941,13 @@ property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000255 name: eukaryotic cell -def: "Any cell that only exists in Eukaryota." [FBC:Autogenerated] +def: "Any cell that in taxon some Eukaryota." [FBC:Autogenerated] subset: cellxgene_subset xref: MESH:D005057 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell -intersection_of: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota -relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +intersection_of: RO:0002162 NCBITaxon:2759 ! in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 ! in taxon Eukaryota [Term] id: CL:0000325 @@ -987,8 +1002,8 @@ is_a: CL:0000007 ! early embryonic cell (metazoa) is_a: CL:0000255 ! eukaryotic cell is_a: CL:0010017 ! zygote intersection_of: CL:0010017 ! zygote -intersection_of: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa -relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +intersection_of: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa [Term] id: CL:0000393 @@ -1020,6 +1035,7 @@ xref: MESH:D003713 xref: ZFA:0009209 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000113 ! mononuclear phagocyte is_a: CL:0000145 ! professional antigen presenting cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000738 ! leukocyte intersection_of: bearer_of PATO:0001407 ! mononucleate intersection_of: capable_of GO:0001816 ! cytokine production @@ -1073,7 +1089,7 @@ name: phagocyte (sensu Vertebrata) def: "A phagocyte in vertebrates that is able to phagocytosis." [GOC:tfm] is_a: CL:0000234 ! phagocyte is_a: CL:0000255 ! eukaryotic cell -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata [Term] id: CL:0000540 @@ -1135,6 +1151,7 @@ synonym: "rubriblast" EXACT [ISBN:0721601464] xref: FMA:83518 is_a: CL:0000764 {is_inferred="true"} ! erythroid lineage cell is_a: CL:0002242 ! nucleate cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000764 ! erythroid lineage cell intersection_of: bearer_of PATO:0002505 ! nucleated intersection_of: bearer_of PATO:0040072 ! high nuclear/cytoplasmic ratio @@ -1180,6 +1197,7 @@ synonym: "prorubricyte" EXACT [ISBN:0721601464] xref: FMA:83505 xref: ZFA:0005236 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000765 {is_inferred="true"} ! erythroblast +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017503 ! basophilic cytoplasm intersection_of: has_part GO:0000792 ! heterochromatin @@ -1201,6 +1219,7 @@ synonym: "rubricyte" EXACT [ISBN:0721601464] xref: FMA:83506 xref: ZFA:0005241 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000765 {is_inferred="true"} ! erythroblast +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017504 ! polychromatophilic cytoplasm intersection_of: has_part GO:0000792 ! heterochromatin @@ -1322,6 +1341,7 @@ is_a: CL:0000763 ! myeloid cell is_a: CL:0001012 ! CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor is_a: CL:0011026 ! progenitor cell is_a: CL:1001610 ! bone marrow hematopoietic cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002032 ! hematopoietic oligopotent progenitor cell intersection_of: capable_of GO:0030225 ! macrophage differentiation intersection_of: capable_of GO:0030851 ! granulocyte differentiation @@ -1351,6 +1371,7 @@ xref: CALOHA:TS-0864 xref: MESH:D012156 xref: ZFA:0009252 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000764 {is_inferred="true"} ! erythroid lineage cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000764 ! erythroid lineage cell intersection_of: capable_of GO:0071971 ! extracellular exosome assembly intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -1392,6 +1413,7 @@ xref: FMA:83551 xref: ZFA:0009253 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0002194 {is_inferred="true"} ! monopoietic cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002194 ! monopoietic cell intersection_of: capable_of GO:0030224 ! monocyte differentiation intersection_of: has_part GO:0042582 ! azurophil granule @@ -1411,6 +1433,7 @@ synonym: "chondroplast" EXACT [] xref: ZFA:0009258 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000134 {is_inferred="true"} ! mesenchymal stem cell is_a: CL:0011026 ! progenitor cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: RO:0002104 PR:000001444 ! has plasma membrane part cadherin-5 intersection_of: RO:0002104 PR:000002112 ! has plasma membrane part vascular endothelial growth factor receptor 2 @@ -1450,19 +1473,20 @@ property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000647 name: multinucleated giant cell -def: "A phagocytic cell formed by the fusion of macrophages, occurs in chronic inflammatory responses to persistent microorganism such as M.tuberculosis, component of granulomas. Sometimes used to refer to megakaryocytes." [GOC:add, GOC:tfm, ISBN:0702022918, ISBN:0702024783] +def: "A phagocytic syncytial cell formed by the fusion of macrophages, occurs in chronic inflammatory responses to persistent microorganism such as M.tuberculosis, component of granulomas. Sometimes used to refer to megakaryocytes." [GOC:add, GOC:tfm, ISBN:0702022918, ISBN:0702024783, PMID:33348900, Wikipedia:Giant_cell] comment: Role or process: Chronic infection, granulomatous inflammation. Consider also megakaryocyte (CL:0000556) as sometimes multinucleated giant cell is used to refer to this. subset: blood_and_immune_upper_slim synonym: "foreign body giant cell" EXACT [ISBN:0702022918, ISBN:0702024783] synonym: "Langerhans giant cell" EXACT [ISBN:0702022918, ISBN:0702024783] synonym: "macrophage polykaryon" EXACT [ISBN:0702022918, ISBN:0702024783] +synonym: "MGC" RELATED OMO:0003000 [PMID:33348900] synonym: "multinucleate giant cell" EXACT [ISBN:0702022918, ISBN:0702024783] synonym: "syncytial giant cell" EXACT [ISBN:0702022918, ISBN:0702024783] xref: BTO:0003107 xref: FMA:83035 xref: MESH:D015726 -is_a: CL:0000228 ! multinucleate cell is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte +is_a: CL:4052002 ! syncytial cell intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: bearer_of PATO:0001908 ! multinucleate intersection_of: participates_in GO:0002432 ! granuloma formation @@ -1478,6 +1502,7 @@ def: "A non-terminally differentiated cell that is capable of developing into a subset: cellxgene_subset xref: ZFA:0009291 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0011115 ! precursor cell intersection_of: RO:0002203 CL:0000187 ! develops into muscle cell relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell @@ -1519,7 +1544,7 @@ intersection_of: bearer_of PATO:0002505 ! nucleated intersection_of: capable_of GO:0001667 ! ameboidal-type cell migration relationship: capable_of GO:0001667 ! ameboidal-type cell migration relationship: part_of UBERON:0002405 ! immune system -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002202 CL:0000037 ! develops from hematopoietic stem cell property_value: RO:0002175 NCBITaxon:9606 @@ -1547,6 +1572,7 @@ xref: BTO:0001441 xref: CALOHA:TS-0647 xref: MESH:D022423 xref: ZFA:0009324 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000988 {is_inferred="true"} ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: RO:0002202 CL:0000049 ! develops from common myeloid progenitor @@ -1800,6 +1826,7 @@ xref: FMA:70574 xref: MESH:D010950 xref: ZFA:0009332 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000946 {is_inferred="true"} ! antibody secreting cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000946 ! antibody secreting cell intersection_of: CL:4030046 GO:0019814 ! lacks_plasma_membrane_part immunoglobulin complex intersection_of: CL:4030046 GO:0042613 ! lacks_plasma_membrane_part MHC class II protein complex @@ -1827,6 +1854,7 @@ synonym: "alpha-beta T-cell" EXACT [] synonym: "alpha-beta T-lymphocyte" EXACT [] xref: ZFA:0009335 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000084 {is_inferred="true"} ! T cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000084 ! T cell intersection_of: RO:0002104 GO:0042105 ! has plasma membrane part alpha-beta T cell receptor complex disjoint_from: CL:0000798 ! gamma-delta T cell @@ -1847,6 +1875,7 @@ synonym: "gammadelta T cell" EXACT [] synonym: "gd T cell" RELATED OMO:0003000 [] xref: ZFA:0009336 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000084 {is_inferred="true"} ! T cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000084 ! T cell intersection_of: RO:0002104 GO:0042106 ! has plasma membrane part gamma-delta T cell receptor complex relationship: RO:0002104 GO:0042106 ! has plasma membrane part gamma-delta T cell receptor complex @@ -1946,6 +1975,7 @@ synonym: "progenitor B-lymphocyte" EXACT [] xref: BTO:0003104 xref: ZFA:0009349 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000838 {is_inferred="true"} ! lymphoid lineage restricted progenitor cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: has_part PR:000001903 ! paired box protein PAX-5 intersection_of: has_part PR:000006611 ! DNA nucleotidylexotransferase @@ -1999,6 +2029,7 @@ synonym: "colony forming unit mast cell" RELATED [] synonym: "MCP" EXACT [] is_a: CL:0000763 ! myeloid cell is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: capable_of GO:0060374 ! mast cell differentiation intersection_of: CL:4030045 PR:000005307 ! lacks_part CCAAT/enhancer-binding protein alpha @@ -2063,7 +2094,9 @@ synonym: "MPP" EXACT [] xref: BTO:0000725 xref: CALOHA:TS-0448 xref: ZFA:0009354 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001402 ! multipotent intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -2160,6 +2193,7 @@ def: "An immature myeloid leukocyte of heterogeneous phenotype found particularl comment: Markers: Mouse: CD11b+GR1+CD31+; Human: CD34+ CD33+CD15-CD13+. (According to some reports in humans these cells are iNOS+ARG1+IL13+IFNg+); location: In cancerous tissue; in the blood and lymphoid organs in sepsis. subset: blood_and_immune_upper_slim is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: bearer_of PATO:0001501 ! immature intersection_of: capable_of GO:0050777 ! negative regulation of immune response @@ -2300,7 +2334,7 @@ name: bone cell def: "A connective tissue cell found in bone." [GO_REF:0000034, GOC:add] subset: general_cell_types_upper_slim subset: human_reference_atlas -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001474 ! bone element relationship: part_of UBERON:0001474 ! bone element @@ -2369,6 +2403,7 @@ name: lymphocyte of B lineage, CD19-positive def: "A lymphocyte of B lineage that is CD19-positive." [GOC:add] comment: Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells). Lymphocytes of B cell lineage can be distinguished from those of T cell lineage by their lack of CD3e (as part of the T cell receptor complex). is_a: CL:0000945 ! lymphocyte of B lineage +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000945 ! lymphocyte of B lineage intersection_of: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon intersection_of: RO:0002104 PR:000001002 ! has plasma membrane part CD19 molecule @@ -2392,7 +2427,6 @@ is_a: CL:0001200 ! lymphocyte of B lineage, CD19-positive intersection_of: CL:0001200 ! lymphocyte of B lineage, CD19-positive intersection_of: capable_of GO:0019724 ! B cell mediated immunity intersection_of: RO:0002104 PR:000001002 ! has plasma membrane part CD19 molecule -intersection_of: RO:0002162 NCBITaxon:40674 ! in taxon Mammalia property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 [Term] @@ -2422,6 +2456,7 @@ subset: cellxgene_subset synonym: "BMCP" EXACT [] is_a: CL:0000763 ! myeloid cell is_a: CL:0002191 ! granulocytopoietic cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: capable_of GO:0030221 ! basophil differentiation intersection_of: capable_of GO:0060374 ! mast cell differentiation @@ -2448,6 +2483,7 @@ id: CL:0002031 name: hematopoietic lineage restricted progenitor cell def: "A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells." [GOC:tfm, PMID:19022770] subset: blood_and_immune_upper_slim +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001400 ! unipotent @@ -2463,6 +2499,7 @@ name: hematopoietic oligopotent progenitor cell def: "A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities." [GOC:tfm, https://orcid.org/0000-0001-5208-3432, PMID:19022770] comment: This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). subset: blood_and_immune_upper_slim +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001401 ! oligopotent @@ -2584,7 +2621,7 @@ def: "A cell that is part of the nervous system." [GOC:tfm, ISBN:0618947256] subset: cellxgene_subset xref: CALOHA:TS-2040 xref: FMA:70333 -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001016 ! nervous system relationship: part_of UBERON:0001016 ! nervous system @@ -2600,7 +2637,7 @@ xref: CALOHA:TS-2096 xref: FMA:63875 xref: MESH:D003239 xref: ZFA:0009392 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0002384 ! connective tissue relationship: part_of UBERON:0002384 ! connective tissue @@ -2645,29 +2682,20 @@ xref: BTO:0001539 xref: CALOHA:TS-0115 xref: FMA:83808 xref: FMA:84791 -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0007100 ! primary circulatory organ relationship: part_of UBERON:0007100 ! primary circulatory organ property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-07T09:37:22Z -[Term] -id: CL:0002546 -name: embryonic blood vessel endothelial progenitor cell -def: "An endothelial progenitor cell that participates in angiogenesis during development." [GOC:tfm] -comment: See CL:0002619. -xref: ZFA:0005773 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000222 ! mesodermal cell -property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 -creation_date: 2011-02-28T04:20:39Z - [Term] id: CL:0002679 name: natural helper lymphocyte def: "A lymphocyte found in adipose tissue that lacks lineage markers of other lymphocytes but is capable of mediating TH2 cytokine responses. This cell type is found in fat associated lymphoid clusters, proliferates in response to IL2 and produce large amounts of TH2 cytokines such as IL5, IL6 and IL13" [GOC:tfm, PMID:20023630] subset: blood_and_immune_upper_slim is_a: CL:0000542 {is_inferred="true"} ! lymphocyte +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000542 ! lymphocyte intersection_of: CL:4030046 GO:0042105 ! lacks_plasma_membrane_part alpha-beta T cell receptor complex intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -2728,6 +2756,7 @@ subset: cellxgene_subset subset: human_reference_atlas synonym: "mesenchyme cell" EXACT [] is_a: CL:0000219 ! motile cell +is_a: CL:0000255 ! eukaryotic cell relationship: capable_of GO:0016477 ! cell migration relationship: part_of UBERON:0003104 ! mesenchyme property_value: RO:0002175 NCBITaxon:9606 @@ -2745,14 +2774,17 @@ id: CL:0011012 name: neural crest cell def: "A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells." [https://orcid.org/0000-0001-5208-3432, https://orcid.org/0000-0002-9900-7880] subset: cellxgene_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_0011012 is_a: CL:0000048 ! multi fate stem cell is_a: CL:0002321 ! embryonic cell (metazoa) +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." xsd:string {xref="DOI:10.1002/dvg.23276", xref="DOI:10.1242/dev.193193", xref="DOI:10.3389/fcell.2020.00635/full", xref="https://doi.org/10.1016/j.ydbio.2011.12.042"} [Term] id: CL:0011026 name: progenitor cell def: "A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses." [https://doi.org/10.1016/B978-0-12-409503-8.00002-0, ISBN:978-1-62808-994-3] subset: cellxgene_subset +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0011115 ! precursor cell intersection_of: CL:0011115 ! precursor cell intersection_of: RO:0002202 CL:0000034 ! develops from stem cell @@ -2885,6 +2917,20 @@ intersection_of: CL:0000542 ! lymphocyte intersection_of: part_of UBERON:0000178 ! blood property_value: terms:date "2022-11-04T14:40:00Z" xsd:dateTime +[Term] +id: CL:4052002 +name: syncytial cell +def: "A multinucleate cell formed by the fusion of multiple uninuclear cells through plasma membrane fusion. This process leads to a single large cell containing multiple nuclei within a shared cytoplasm." [PMID:20851884, Wikipedia:Syncytium] +synonym: "SC" RELATED OMO:0003000 [PMID:9067520] +synonym: "syncytium" EXACT [WBbt:0008074] +is_a: CL:0000228 ! multinucleate cell +intersection_of: CL:0000000 ! cell +intersection_of: bearer_of PATO:0001908 ! multinucleate +intersection_of: output_of GO:0000768 ! syncytium formation by plasma membrane fusion +relationship: output_of GO:0000768 ! syncytium formation by plasma membrane fusion +property_value: terms:contributor https://orcid.org/0009-0000-8480-9277 +property_value: terms:date "2024-08-15T10:38:46Z" xsd:dateTime + [Term] id: GO:0000278 name: mitotic cell cycle @@ -2924,6 +2970,17 @@ namespace: cellular_component def: "A vacuole that is maintained at an acidic pH and which contains degradative enzymes, including a wide variety of acid hydrolases." [GOC:krc] is_a: GO:0005773 ! vacuole +[Term] +id: GO:0000768 +name: syncytium formation by plasma membrane fusion +namespace: biological_process +def: "The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells." [GOC:mtg_muscle, GOC:tb] +synonym: "cell fusion" BROAD [] +is_a: GO:0006949 ! syncytium formation +is_a: GO:0140253 ! cell-cell fusion +intersection_of: GO:0006949 ! syncytium formation +intersection_of: has_part GO:0045026 ! plasma membrane fusion + [Term] id: GO:0000785 name: chromatin @@ -2937,8 +2994,9 @@ synonym: "chromosome scaffold" RELATED [] synonym: "cytoplasmic chromatin" NARROW [] synonym: "nuclear chromatin" NARROW [] xref: NIF_Subcellular:sao1615953555 -is_a: GO:0032993 ! protein-DNA complex +is_a: GO:0110165 ! cellular anatomical entity relationship: part_of GO:0005694 ! chromosome +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28301" xsd:anyURI [Term] id: GO:0000791 @@ -3516,13 +3574,15 @@ relationship: part_of GO:0006954 ! inflammatory response [Term] id: GO:0002538 -name: arachidonic acid metabolite production involved in inflammatory response +name: arachidonate metabolite production involved in inflammatory response namespace: biological_process def: "The synthesis or release of products of arachidonic acid metabolism following a stimulus as part of an inflammatory response, resulting in an increase in their intracellular or extracellular levels." [GOC:add, ISBN:0781735149] synonym: "arachidonic acid metabolite production involved in acute inflammatory response" BROAD [GOC:mah] +synonym: "arachidonic acid metabolite production involved in inflammatory response" EXACT [] synonym: "production of arachidonic acid metabolites involved in acute inflammatory response" BROAD [] synonym: "production of arachidonic acid metabolites involved in inflammatory response" EXACT [] is_a: GO:0002532 ! production of molecular mediator involved in inflammatory response +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28648" xsd:anyURI [Term] id: GO:0002539 @@ -3530,7 +3590,7 @@ name: prostaglandin production involved in inflammatory response namespace: biological_process def: "The synthesis or release of any prostaglandin following a stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels." [GOC:add, ISBN:0781735149] synonym: "prostaglandin production involved in acute inflammatory response" BROAD [] -is_a: GO:0002538 ! arachidonic acid metabolite production involved in inflammatory response +is_a: GO:0002538 ! arachidonate metabolite production involved in inflammatory response [Term] id: GO:0002544 @@ -4245,8 +4305,8 @@ synonym: "ribosomal RNA" RELATED [] xref: NIF_Subcellular:sao1429207766 xref: Wikipedia:Ribosome is_a: GO:0043232 ! intracellular non-membrane-bounded organelle +is_a: PR:000050567 ! protein-containing material entity relationship: capable_of_part_of GO:0006412 ! translation -relationship: has_part PR:000000001 ! protein [Term] id: GO:0005886 @@ -4589,12 +4649,23 @@ xref: Wikipedia:Muscle_contraction is_a: GO:0003012 ! muscle system process relationship: occurs_in UBERON:0002385 ! muscle tissue +[Term] +id: GO:0006949 +name: syncytium formation +namespace: biological_process +def: "The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane. Syncytia are normally derived from single cells that fuse or fail to complete cell division." [ISBN:0198506732] +subset: goslim_pir +is_a: GO:0009987 ! cellular process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +intersection_of: GO:0048646 ! anatomical structure formation involved in morphogenesis +intersection_of: results_in_formation_of CL:0000228 ! multinucleate cell +relationship: results_in_formation_of CL:0000228 ! multinucleate cell + [Term] id: GO:0006950 name: response to stress namespace: biological_process def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." [GOC:mah] -comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: goslim_candida subset: goslim_chembl subset: goslim_drosophila @@ -4604,6 +4675,7 @@ subset: goslim_plant_ribbon synonym: "response to abiotic stress" RELATED [] synonym: "response to biotic stress" RELATED [] is_a: GO:0050896 ! response to stimulus +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26810" xsd:anyURI [Term] id: GO:0006952 @@ -4661,6 +4733,20 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i created_by: jl creation_date: 2013-12-19T15:25:51Z +[Term] +id: GO:0007009 +name: plasma membrane organization +namespace: biological_process +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the plasma membrane." [GOC:dph, GOC:jl, GOC:mah] +subset: goslim_chembl +synonym: "plasma membrane organisation" EXACT [] +synonym: "plasma membrane organization and biogenesis" RELATED [GOC:mah] +is_a: GO:0061024 ! membrane organization +intersection_of: GO:0016043 ! cellular component organization +intersection_of: results_in_organization_of GO:0005886 ! plasma membrane +relationship: part_of GO:0010256 ! endomembrane system organization +relationship: results_in_organization_of GO:0005886 ! plasma membrane + [Term] id: GO:0007049 name: cell cycle @@ -5113,6 +5199,19 @@ is_a: GO:0008150 ! biological_process created_by: jl creation_date: 2012-12-11T16:56:55Z +[Term] +id: GO:0010256 +name: endomembrane system organization +namespace: biological_process +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endomembrane system." [GOC:mah, GOC:sm] +subset: goslim_drosophila +synonym: "endomembrane organization" EXACT [] +synonym: "endomembrane system organisation" EXACT [GOC:mah] +is_a: GO:0016043 ! cellular component organization +intersection_of: GO:0016043 ! cellular component organization +intersection_of: results_in_organization_of GO:0012505 ! endomembrane system +relationship: results_in_organization_of GO:0012505 ! endomembrane system + [Term] id: GO:0010324 name: membrane invagination @@ -5358,6 +5457,9 @@ is_a: GO:0051301 ! cell division intersection_of: GO:0051301 ! cell division intersection_of: has_primary_input CL:0000034 ! stem cell relationship: has_primary_input CL:0000034 ! stem cell +property_value: RO:0002161 NCBITaxon:2 +property_value: RO:0002161 NCBITaxon:2157 +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0019226 @@ -6215,18 +6317,8 @@ synonym: "protein complex" NARROW [] synonym: "protein containing complex" EXACT [] synonym: "protein-protein complex" NARROW [] is_a: GO:0005575 ! cellular_component +is_a: PR:000050567 ! protein-containing material entity disjoint_from: GO:0110165 ! cellular anatomical entity -relationship: has_part PR:000000001 ! protein - -[Term] -id: GO:0032993 -name: protein-DNA complex -namespace: cellular_component -def: "A macromolecular complex containing both protein and DNA molecules." [GOC:mah] -comment: Note that this term is intended to classify complexes that have DNA as one of the members of the complex, that is, the complex does not exist if DNA is not present. Protein complexes that interact with DNA e.g. transcription factor complexes should not be classified here. -subset: goslim_pir -synonym: "DNA-protein complex" EXACT [GOC:mah] -is_a: GO:0032991 ! protein-containing complex [Term] id: GO:0033151 @@ -6678,6 +6770,7 @@ id: GO:0043227 name: membrane-bounded organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane." [GOC:go_curators] +subset: gocheck_do_not_annotate synonym: "membrane-enclosed organelle" EXACT [] xref: NIF_Subcellular:sao414196390 is_a: GO:0043226 ! organelle @@ -6685,30 +6778,35 @@ intersection_of: GO:0043226 ! organelle intersection_of: has_part GO:0016020 ! membrane disjoint_from: GO:0043228 ! non-membrane-bounded organelle relationship: has_part GO:0016020 ! membrane +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI [Term] id: GO:0043228 name: non-membrane-bounded organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:go_curators] +subset: gocheck_do_not_annotate subset: goslim_mouse synonym: "biological condensate" RELATED [] synonym: "non-membrane-enclosed organelle" EXACT [] xref: NIF_Subcellular:sao1456184038 is_a: GO:0043226 ! organelle property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21881" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI [Term] id: GO:0043229 name: intracellular organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:go_curators] +subset: gocheck_do_not_annotate subset: goslim_pir is_a: GO:0043226 ! organelle intersection_of: GO:0043226 ! organelle intersection_of: part_of GO:0005622 ! intracellular anatomical structure disjoint_from: GO:0043230 ! extracellular organelle relationship: part_of GO:0005622 ! intracellular anatomical structure +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI [Term] id: GO:0043230 @@ -6798,9 +6896,11 @@ name: cellular component biogenesis namespace: biological_process alt_id: GO:0071843 def: "A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component." [GOC:jl, GOC:mah] +subset: gocheck_do_not_annotate subset: goslim_pir synonym: "cellular component biogenesis at cellular level" EXACT [] is_a: GO:0071840 ! cellular component organization or biogenesis +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27194" xsd:anyURI [Term] id: GO:0044207 @@ -6872,6 +6972,20 @@ is_a: GO:0008150 ! biological_process property_value: RO:0002161 NCBITaxon:4895 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20191" xsd:anyURI +[Term] +id: GO:0045026 +name: plasma membrane fusion +namespace: biological_process +alt_id: GO:0006947 +def: "The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell." [GOC:elh, GOC:mtg_muscle] +synonym: "cell fusion" BROAD [] +synonym: "cell-cell fusion" BROAD [] +is_a: GO:0007009 ! plasma membrane organization +is_a: GO:0061025 ! membrane fusion +intersection_of: GO:0009987 ! cellular process +intersection_of: results_in_fusion_of GO:0005886 ! plasma membrane +relationship: results_in_fusion_of GO:0005886 ! plasma membrane + [Term] id: GO:0045058 name: T cell selection @@ -6896,6 +7010,9 @@ synonym: "nonspecific immune response" EXACT [] xref: Wikipedia:Innate_immune_system is_a: GO:0006955 ! immune response is_a: GO:0140546 ! defense response to symbiont +property_value: RO:0002161 NCBITaxon:2 +property_value: RO:0002161 NCBITaxon:2157 +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0045190 @@ -8197,6 +8314,7 @@ def: "A complex of collagen trimers such as a fibril or collagen network." [GOC: synonym: "Supramolecular aggregate of collagen" EXACT [PMID:19693541] synonym: "Supramolecular collagen assembly" EXACT [PMID:21421911] is_a: GO:0099080 ! supramolecular complex +is_a: PR:000050567 ! protein-containing material entity relationship: has_part GO:0005581 ! collagen trimer relationship: part_of GO:0062023 ! collagen-containing extracellular matrix @@ -8453,6 +8571,19 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i created_by: pg creation_date: 2017-10-23T11:53:42Z +[Term] +id: GO:0140253 +name: cell-cell fusion +namespace: biological_process +def: "A cellular process in which two or more cells combine together, their plasma membrane fusing, producing a single cell. In some cases, nuclei fuse, producing a polyploid cell, while in other cases, nuclei remain separate, producing a syncytium." [Wikipedia:Cell_fusion] +synonym: "cell cell fusion" EXACT [] +synonym: "cell fusion" BROAD [] +is_a: GO:0009987 ! cellular process +relationship: has_part GO:0045026 ! plasma membrane fusion +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15939" xsd:anyURI +created_by: pg +creation_date: 2018-08-13T18:38:18Z + [Term] id: GO:0140352 name: export from cell @@ -9439,7 +9570,7 @@ comment: The definition above excludes protein complexes, which some also consid synonym: "native protein" NARROW [IEDB:BP] synonym: "natural protein" EXACT [PRO:DAN] is_a: PR:000018263 ! amino acid chain -is_a: PR:000064867 ! protein-containing molecular entity +is_a: PR:000050567 ! protein-containing material entity relationship: output_of GO:0006412 ! translation [Term] @@ -10615,11 +10746,11 @@ is_a: PR:000036194 ! eukaryotic protein relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa [Term] -id: PR:000064867 -name: protein-containing molecular entity +id: PR:000050567 +name: protein-containing material entity namespace: protein -def: "A molecular entity that minimally consists of a protein." [PRO:DAN] -comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). +def: "A material entity that minimally consists of a protein." [PRO:DAN] +comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566). synonym: "protein" NARROW [PRO:DAN] synonym: "protein aggregate" NARROW [PRO:DAN] synonym: "protein complex" NARROW [PRO:DAN] @@ -10849,7 +10980,7 @@ xref: SCTID:118966000 xref: UMLS:C1519343 {source="ncithesaurus:Skeletal_System_Part"} is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision relationship: part_of UBERON:0001434 ! skeletal system -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002473 UBERON:0004765 ! composed primarily of skeletal element [Term] @@ -11032,7 +11163,7 @@ is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000108 {source="BILS"} ! blastula stage relationship: RO:0002082 GO:0007369 ! simultaneous with gastrulation -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0000110 @@ -11048,7 +11179,7 @@ is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000109 ! gastrula stage relationship: RO:0002082 GO:0001841 ! simultaneous with neural tube formation -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: seeAlso "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/343" xsd:anyURI @@ -11068,7 +11199,7 @@ xref: Wikipedia:Organogenesis is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: RO:0002082 GO:0048513 ! simultaneous with animal organ development -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: seeAlso "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/533" xsd:anyURI @@ -11126,7 +11257,7 @@ xref: XAO:0003029 xref: ZFA:0000547 xref: ZFA:0000590 is_a: UBERON:0004921 ! subdivision of digestive tract -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002202 UBERON:0035804 ! develops from future mouth property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/661" xsd:anyURI @@ -11166,6 +11297,7 @@ xref: VHOG:0000224 xref: Wikipedia:Blood xref: XAO:0000124 xref: ZFA:0000007 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000179 ! haemolymphatic fluid relationship: has_part CL:0000232 {source="CL:tm"} ! erythrocyte relationship: has_part UBERON:0001969 ! blood plasma @@ -11186,7 +11318,7 @@ is_a: UBERON:0006314 ! bodily fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: part_of UBERON:0002193 ! hemolymphoid system relationship: part_of UBERON:0002193 ! hemolymphoid system -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: terms:contributor https://orcid.org/0000-0002-6601-2165 creation_date: 2009-04-08T04:38:19Z @@ -11244,7 +11376,7 @@ is_a: UBERON:0011216 ! organ system subdivision intersection_of: UBERON:0011216 ! organ system subdivision intersection_of: RO:0002473 UBERON:0001015 ! composed primarily of musculature relationship: capable_of GO:0003012 ! muscle system process -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002473 UBERON:0001015 ! composed primarily of musculature property_value: IAO:0000116 "consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77" xsd:string property_value: RO:0002161 NCBITaxon:6040 @@ -11658,12 +11790,13 @@ xref: VHOG:0000387 xref: Wikipedia:Epithelium xref: XAO:0003045 xref: ZFA:0001486 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: RO:0002473 CL:0000066 ! composed primarily of epithelial cell relationship: has_part GO:0005911 ! cell-cell junction relationship: has_part UBERON:0005769 ! basement membrane of epithelium -relationship: RO:0002160 NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! in taxon Metazoa relationship: RO:0002473 CL:0000066 ! composed primarily of epithelial cell property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI @@ -11820,7 +11953,7 @@ xref: Wikipedia:Germ_layer xref: XAO:0003011 xref: ZFA:0001122 is_a: UBERON:0010316 ! germ layer / neural crest -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0000924 @@ -11974,7 +12107,7 @@ xref: ZFA:0001290 is_a: UBERON:0013522 ! subdivision of tube relationship: part_of UBERON:0000924 ! ectoderm relationship: part_of UBERON:0035804 ! future mouth -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI property_value: IAO:0000116 "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" xsd:string @@ -12027,7 +12160,7 @@ intersection_of: UBERON:0007100 ! primary circulatory organ intersection_of: has_part UBERON:0004151 ! cardiac chamber relationship: has_part UBERON:0004151 ! cardiac chamber relationship: part_of UBERON:0015410 {source="MA"} ! heart plus pericardium -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002202 UBERON:0004141 ! develops from heart tube relationship: RO:0002433 UBERON:0004535 ! contributes to morphology of cardiovascular system property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/heart-female/v1.3/assets/3d-vh-f-heart.glb" xsd:anyURI @@ -12144,7 +12277,7 @@ disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system relationship: capable_of GO:0003013 ! circulatory system process -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} @@ -12194,7 +12327,6 @@ namespace: uberon def: "The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]." [BIRNLEX:844, ISBN:0-14-051288-8, ISBN:3110148986, NLM:nervous+system, WB:rynl, Wikipedia:Nervous_system, ZFIN:curator] subset: cumbo subset: efo_slim -subset: human_reference_atlas subset: pheno_slim subset: uberon_slim subset: vertebrate_core @@ -12235,14 +12367,13 @@ disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system relationship: capable_of GO:0050877 ! nervous system process relationship: has_part CL:0000540 ! neuron -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002473 CL:0002319 ! composed primarily of neural cell relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage relationship: RO:0002495 UBERON:0016880 {source="Bgee:AN"} ! immediate transformation of future nervous system property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:6040 -property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001017 @@ -12289,7 +12420,7 @@ xref: ZFA:0000012 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0011216 {source="FBbt", source="cjm"} ! organ system subdivision relationship: part_of UBERON:0001016 ! nervous system -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria relationship: RO:0002495 UBERON:0016879 {source="Bgee:AN"} ! immediate transformation of future central nervous system property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} property_value: RO:0002175 NCBITaxon:9606 @@ -12474,7 +12605,7 @@ intersection_of: UBERON:0004765 ! skeletal element intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue disjoint_from: UBERON:0001630 ! muscle organ disjoint_from: UBERON:0005090 ! muscle structure -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002473 UBERON:0002481 {source="VSAO-modified"} ! composed primarily of bone tissue [Term] @@ -12512,7 +12643,7 @@ xref: WBbt:0005743 xref: ZFA:0000112 is_a: UBERON:0000025 ! tube relationship: part_of UBERON:0001007 ! digestive system -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002176 UBERON:0000165 ! connects mouth relationship: RO:0002495 UBERON:0007026 {source="NCBIBook:NBK10107"} ! immediate transformation of presumptive gut property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} @@ -12572,6 +12703,7 @@ xref: MIAA:0000052 xref: NCIT:C13356 xref: UMLS:C0032105 {source="ncithesaurus:Plasma"} xref: Wikipedia:Blood_plasma +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000179 ! haemolymphatic fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: has_part GO:0005577 ! fibrinogen complex @@ -12620,6 +12752,7 @@ xref: VHOG:0001250 xref: Wikipedia:Blood_vessel xref: XAO:0001011 xref: ZFA:0005314 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000055 ! vessel is_a: UBERON:0004120 ! mesoderm-derived structure relationship: capable_of_part_of GO:0008015 ! blood circulation @@ -12657,7 +12790,7 @@ is_a: UBERON:0000487 {source="FMA-text-def", source="https://github.com/obopheno is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: RO:0002473 CL:0000115 ! composed primarily of endothelial cell -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002473 CL:0000115 ! composed primarily of endothelial cell property_value: RO:0002175 NCBITaxon:9606 @@ -12831,7 +12964,7 @@ xref: EMAPA:18765 xref: FMA:74562 xref: MA:0000013 is_a: UBERON:0000467 {source="MA"} ! anatomical system -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria [Term] id: UBERON:0002204 @@ -12971,7 +13104,7 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0011137 ! axial skeletal system relationship: produces PR:000014841 ! sonic hedgehog protein -relationship: RO:0002160 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! in taxon Chordata relationship: RO:0002202 UBERON:0004880 {source="ZFA"} ! develops from chordamesoderm relationship: RO:0002202 UBERON:0006267 {source="EHDAA2"} ! develops from notochordal plate relationship: RO:0002488 UBERON:0000068 ! existence starts during embryo stage @@ -13014,7 +13147,7 @@ xref: XAO:0000058 xref: ZFA:0000155 is_a: UBERON:0005423 ! developing anatomical structure is_a: UBERON:0007503 {source="EHDAA2"} ! epithelial vesicle -relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {source="GOTAX:0000352"} ! in taxon Chordata relationship: RO:0002202 UBERON:0003059 {source="ZFA"} ! develops from presomitic mesoderm property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:7712 {source="PMID:17237766"} @@ -13053,7 +13186,7 @@ is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0010316 ! germ layer / neural crest relationship: part_of UBERON:0002346 {source="XAO", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! neurectoderm -relationship: RO:0002160 NCBITaxon:89593 ! only in taxon Craniata +relationship: RO:0002162 NCBITaxon:89593 ! in taxon Craniata relationship: RO:0002202 UBERON:0003075 {source="BTO"} ! develops from neural plate relationship: RO:0002202 UBERON:0005062 {source="PMID:11523831"} ! develops from neural fold relationship: RO:0002473 CL:0000333 ! composed primarily of migratory neural crest cell @@ -13177,7 +13310,7 @@ xref: VSAO:0000017 xref: XAO:0001017 xref: ZFA:0001632 is_a: UBERON:0000479 ! tissue -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -13209,7 +13342,7 @@ intersection_of: UBERON:0000479 ! tissue intersection_of: RO:0002473 CL:0000187 ! composed primarily of muscle cell relationship: capable_of GO:0006936 ! muscle contraction relationship: part_of UBERON:0001015 ! musculature -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002473 CL:0000187 ! composed primarily of muscle cell [Term] @@ -13254,7 +13387,7 @@ is_a: UBERON:0000467 ! anatomical system is_a: UBERON:0004120 ! mesoderm-derived structure disjoint_from: UBERON:0002405 ! immune system relationship: part_of UBERON:0002193 {source="FMA"} ! hemolymphoid system -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002202 UBERON:0003061 ! develops from blood island property_value: RO:0002175 NCBITaxon:9606 @@ -13316,7 +13449,7 @@ xref: ZFA:0005621 is_a: UBERON:0004755 {source="VSAO"} ! skeletal tissue disjoint_from: UBERON:0005090 ! muscle structure relationship: part_of UBERON:0001474 ! bone element -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata property_value: IAO:0000116 "see https://github.com/obophenotype/uberon/issues/27" xsd:string [Term] @@ -13438,7 +13571,7 @@ xref: XAO:0000205 xref: ZFA:0001204 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0000926 ! mesoderm -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002202 UBERON:0000926 ! develops from mesoderm property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI @@ -13472,7 +13605,7 @@ xref: ZFA:0000132 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0016879 ! future central nervous system -relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {source="GOTAX:0000352"} ! in taxon Chordata relationship: RO:0002256 UBERON:0002328 {source="Wikipedia"} ! developmentally induced by notochord relationship: RO:0002495 UBERON:0007284 {source="Bgee:AN"} ! immediate transformation of presumptive neural plate property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI @@ -13539,7 +13672,7 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue relationship: part_of UBERON:0000926 {source="EHDAA2", source="VHOG"} ! mesoderm -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria relationship: RO:0002221 UBERON:0003887 ! surrounds intraembryonic coelom property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI @@ -13589,7 +13722,7 @@ xref: XAO:0000397 xref: ZFA:0001080 is_a: UBERON:0005856 {source="EHDAA2"} ! developing mesenchymal condensation is_a: UBERON:0007530 {source="EHDAA2"} ! migrating mesenchyme population -relationship: RO:0002160 NCBITaxon:7742 {source="VHOG:0000680"} ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 {source="VHOG:0000680"} ! in taxon Vertebrata relationship: RO:0002202 UBERON:0002329 {source="ZFA"} ! develops from somite property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI @@ -13644,7 +13777,7 @@ xref: ZFA:0000393 is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002328 GO:0032502 ! functionally related to developmental process relationship: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI @@ -13902,6 +14035,7 @@ xref: WikipediaCategory:Cardiovascular_system xref: XAO:0000100 xref: XAO:0001010 xref: ZFA:0000010 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000467 ! anatomical system intersection_of: UBERON:0000467 ! anatomical system intersection_of: has_part UBERON:0000948 ! heart @@ -13925,6 +14059,7 @@ synonym: "blood vessels" RELATED [TAO:0001079] synonym: "set of blood vessels" EXACT [] xref: TAO:0001079 xref: ZFA:0001079 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel @@ -14062,7 +14197,7 @@ is_a: UBERON:0034925 ! anatomical collection intersection_of: UBERON:0034925 ! anatomical collection intersection_of: RO:0002351 UBERON:0000982 ! has member skeletal joint relationship: part_of UBERON:0001434 {source="FMA"} ! skeletal system -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria relationship: RO:0002328 GO:0040011 ! functionally related to locomotion relationship: RO:0002351 UBERON:0000982 ! has member skeletal joint relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage @@ -14126,7 +14261,7 @@ xref: TAO:0000091 xref: ZFA:0000091 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0003068 ! axial mesoderm -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata [Term] id: UBERON:0004905 @@ -14169,7 +14304,7 @@ subset: upper_level xref: FMA:82485 is_a: UBERON:0000064 ! organ part relationship: part_of UBERON:0000060 ! anatomical wall -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0005061 @@ -14234,7 +14369,7 @@ synonym: "musculus" EXACT [FMA:30316] xref: FMA:30316 is_a: UBERON:0000061 ! anatomical structure relationship: has_part CL:0000187 ! muscle cell -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0005157 @@ -14398,11 +14533,12 @@ xref: NCIT:C13191 xref: SCTID:68989006 xref: UMLS:C0004799 {source="ncithesaurus:Basement_Membrane"} xref: Wikipedia:Basement_membrane +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005764 {source="FMA"} ! acellular membrane relationship: adjacent_to CL:0000066 ! epithelial cell relationship: has_part GO:0005587 ! collagen type IV trimer relationship: part_of UBERON:0000483 ! epithelium -relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa relationship: RO:0002473 GO:0005604 ! composed primarily of basement membrane property_value: RO:0002175 NCBITaxon:80999 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} @@ -14481,7 +14617,7 @@ xref: NCIT:C34232 xref: UMLS:C1518430 {source="ncithesaurus:Notochordal_Process"} xref: VHOG:0001213 is_a: UBERON:0005423 ! developing anatomical structure -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002202 UBERON:0000924 {source="EHDAA2"} ! develops from ectoderm [Term] @@ -14519,7 +14655,7 @@ intersection_of: UBERON:0006598 ! presumptive structure intersection_of: part_of UBERON:0000307 ! blastula intersection_of: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm relationship: part_of UBERON:0000307 ! blastula -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm [Term] @@ -14571,7 +14707,7 @@ intersection_of: UBERON:0006598 ! presumptive structure intersection_of: part_of UBERON:0000307 ! blastula intersection_of: RO:0002387 UBERON:0000924 ! has potential to develop into ectoderm relationship: part_of UBERON:0000307 ! blastula -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002387 UBERON:0000924 ! has potential to develop into ectoderm [Term] @@ -14589,7 +14725,7 @@ intersection_of: UBERON:0006598 ! presumptive structure intersection_of: part_of UBERON:0000307 ! blastula intersection_of: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm relationship: part_of UBERON:0000307 ! blastula -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm [Term] @@ -14616,6 +14752,7 @@ subset: efo_slim xref: EFO:0003709 xref: TAO:0005077 xref: ZFA:0005077 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005423 ! developing anatomical structure relationship: has_part CL:0000115 ! endothelial cell relationship: has_part CL:0000566 ! angioblastic mesenchymal cell @@ -14959,6 +15096,7 @@ synonym: "thrombus" EXACT [BTO:0000102] xref: BTO:0000102 xref: galen:BloodClot xref: Wikipedia:Thrombus +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000463 ! organism substance intersection_of: UBERON:0000463 ! organism substance intersection_of: output_of GO:0007596 ! blood coagulation @@ -15108,7 +15246,7 @@ synonym: "schizocoelom" NARROW [] xref: EHDAA2:0004731 xref: Wikipedia:Coelom is_a: UBERON:0000481 {source="EHDAA2"} ! multi-tissue structure -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria property_value: IAO:0000116 "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." xsd:string property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} @@ -15178,7 +15316,7 @@ namespace: uberon def: "A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages." [https://orcid.org/0000-0002-6601-2165] subset: non_informative is_a: UBERON:0000475 ! organism subdivision -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0013702 @@ -15243,7 +15381,7 @@ def: "Any structure that is placed on one side of the left-right axis of a bilat subset: grouping_class subset: non_informative is_a: UBERON:0000061 ! anatomical structure -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria [Term] id: UBERON:0015228 @@ -16766,9 +16904,7 @@ inverse_of: output_of ! output of [Typedef] id: has_part name: has part -name: has_part namespace: external -namespace: quality def: "a core relation that holds between a whole and its part" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology @@ -16973,9 +17109,7 @@ expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://p [Typedef] id: part_of name: part of -name: part_of namespace: external -namespace: quality def: "a core relation that holds between a part and its whole" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term diff --git a/src/ontology/subsets/blood_and_immune_upper_slim.owl b/src/ontology/subsets/blood_and_immune_upper_slim.owl index b38f201de..0fa546cf7 100644 --- a/src/ontology/subsets/blood_and_immune_upper_slim.owl +++ b/src/ontology/subsets/blood_and_immune_upper_slim.owl @@ -22,8 +22,8 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - 2024-08-16 + + 2024-09-26 @@ -392,6 +392,14 @@ WHERE { + + + + + + + + @@ -1038,6 +1046,12 @@ WHERE { + + + + + + @@ -1076,17 +1090,13 @@ WHERE { - - created by - + - - creation date - + @@ -1172,9 +1182,7 @@ WHERE { - - id - + @@ -1283,7 +1291,6 @@ WHERE { A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. BFO:0000050 external - quality part_of @@ -1292,7 +1299,6 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of part of part of - part_of http://www.obofoundry.org/ro/#OBO_REL:part_of @@ -1314,7 +1320,6 @@ A continuant cannot be part of an occurrent: use 'participates in'. An A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. BFO:0000051 external - quality has_part @@ -1322,7 +1327,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part has part has part - has_part @@ -4773,7 +4777,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -4854,6 +4858,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -5181,6 +5186,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -5673,7 +5679,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -5741,12 +5747,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - An endothelial cell that lines the vasculature. ZFA:0009036 @@ -5772,12 +5772,36 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + Any epithelial cell that is part of some squamous epithelium. CALOHA:TS-1249 ZFA:0009039 squamous epithelial cell + + + + Any epithelial cell that is part of some squamous epithelium. + FBC:Autogenerated + @@ -5801,7 +5825,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -5996,6 +6020,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6142,6 +6167,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6288,6 +6314,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6443,8 +6470,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different A vertebrate phagocyte with a single nucleus. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Mononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. +In addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses. +Mononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer. BTO:0001433 ZFA:0009064 + https://cellxgene.cziscience.com/cellguide/CL_0000113 mononuclear phagocyte @@ -6463,6 +6496,18 @@ Each of these 3 primitives can be composed to yield a cross-product of different GOC:tfm ISBN:0781735149 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Mononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. +In addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses. +Mononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer. + DOI:10.1016/j.coi.2005.11.008 + DOI:10.1038/nri3087 + DOI:10.3389/fimmu.2019.01893 + @@ -6476,6 +6521,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6748,6 +6794,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6903,6 +6950,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6934,6 +6982,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6967,6 +7016,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -7045,6 +7095,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -7079,6 +7130,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -7087,11 +7139,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell with more than one nucleus. - AEO:0000203 - WBbt:0008074 - syncitium - syncytial cell - syncytium + multinucleated cells + polynuclear cells multinucleate cell @@ -7099,6 +7148,19 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell with more than one nucleus. FB:ma + Wikipedia:Multinucleate + + + + + multinucleated cells + Wikipedia:Multinucleate + + + + + polynuclear cells + Wikipedia:Multinucleate @@ -7446,7 +7508,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -7455,11 +7517,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - Any cell that only exists in Eukaryota. + Any cell that in taxon some Eukaryota. MESH:D005057 eukaryotic cell @@ -7467,7 +7529,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - Any cell that only exists in Eukaryota. + Any cell that in taxon some Eukaryota. FBC:Autogenerated @@ -7611,7 +7673,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -7622,7 +7684,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -7744,6 +7806,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -7905,7 +7968,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -8130,6 +8193,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -8279,6 +8343,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -8375,6 +8440,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -8868,6 +8934,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -9054,6 +9121,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -9195,6 +9263,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -9269,6 +9338,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -9433,8 +9503,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -9453,7 +9523,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - A phagocytic cell formed by the fusion of macrophages, occurs in chronic inflammatory responses to persistent microorganism such as M.tuberculosis, component of granulomas. Sometimes used to refer to megakaryocytes. + A phagocytic syncytial cell formed by the fusion of macrophages, occurs in chronic inflammatory responses to persistent microorganism such as M.tuberculosis, component of granulomas. Sometimes used to refer to megakaryocytes. BTO:0003107 FMA:83035 MESH:D015726 @@ -9462,6 +9532,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different macrophage polykaryon multinucleate giant cell syncytial giant cell + MGC Role or process: Chronic infection, granulomatous inflammation. Consider also megakaryocyte (CL:0000556) as sometimes multinucleated giant cell is used to refer to this. multinucleated giant cell @@ -9475,11 +9546,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - A phagocytic cell formed by the fusion of macrophages, occurs in chronic inflammatory responses to persistent microorganism such as M.tuberculosis, component of granulomas. Sometimes used to refer to megakaryocytes. + A phagocytic syncytial cell formed by the fusion of macrophages, occurs in chronic inflammatory responses to persistent microorganism such as M.tuberculosis, component of granulomas. Sometimes used to refer to megakaryocytes. GOC:add GOC:tfm ISBN:0702022918 ISBN:0702024783 + PMID:33348900 + Wikipedia:Giant_cell @@ -9516,6 +9589,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different ISBN:0702022918 ISBN:0702024783 + + + + MGC + PMID:33348900 + + @@ -9534,6 +9614,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -9593,18 +9674,18 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009307 somatic stem cell - - - - ZFA:0009307 - - A stem cell that can give rise to cell types of the body other than those of the germ-line. GO:0048103 + + + + ZFA:0009307 + + @@ -9638,7 +9719,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -9767,6 +9848,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -10582,6 +10664,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -10687,6 +10770,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -10741,6 +10825,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -11089,6 +11174,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -11397,6 +11483,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -11646,7 +11733,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + @@ -11961,6 +12050,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -12444,7 +12534,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -12714,6 +12804,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -12757,10 +12848,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - @@ -12894,6 +12981,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -12982,6 +13070,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -13026,6 +13115,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -13389,7 +13479,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -13428,7 +13518,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -13549,7 +13639,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -13576,32 +13666,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - An endothelial progenitor cell that participates in angiogenesis during development. - - 2011-02-28T04:20:39Z - ZFA:0005773 - See CL:0002619. - embryonic blood vessel endothelial progenitor cell - - - - - An endothelial progenitor cell that participates in angiogenesis during development. - GOC:tfm - - - - - ZFA:0005773 - - - - - @@ -13653,6 +13717,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -13819,6 +13884,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -13859,6 +13925,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. +After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. +Disorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis. + https://cellxgene.cziscience.com/cellguide/CL_0011012 neural crest cell @@ -13869,6 +13941,19 @@ Each of these 3 primitives can be composed to yield a cross-product of different https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-9900-7880 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. +After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. +Disorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis. + DOI:10.1002/dvg.23276 + DOI:10.1242/dev.193193 + DOI:10.3389/fcell.2020.00635/full + https://doi.org/10.1016/j.ydbio.2011.12.042 + @@ -13886,6 +13971,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -14271,6 +14357,61 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + + + + + A multinucleate cell formed by the fusion of multiple uninuclear cells through plasma membrane fusion. This process leads to a single large cell containing multiple nuclei within a shared cytoplasm. + + 2024-08-15T10:38:46Z + syncytium + SC + syncytial cell + + + + + A multinucleate cell formed by the fusion of multiple uninuclear cells through plasma membrane fusion. This process leads to a single large cell containing multiple nuclei within a shared cytoplasm. + PMID:20851884 + Wikipedia:Syncytium + + + + + syncytium + WBbt:0008074 + + + + + SC + PMID:9067520 + + + + + @@ -14382,10 +14523,42 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells. + cell fusion + biological_process + GO:0000768 + syncytium formation by plasma membrane fusion + + + + + The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells. + GOC:mtg_muscle + GOC:tb + + + + - + @@ -14393,6 +14566,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome. + https://github.com/geneontology/go-ontology/issues/28301 GO:0000789 GO:0000790 GO:0005717 @@ -16136,12 +16310,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different The synthesis or release of products of arachidonic acid metabolism following a stimulus as part of an inflammatory response, resulting in an increase in their intracellular or extracellular levels. + https://github.com/geneontology/go-ontology/issues/28648 arachidonic acid metabolite production involved in acute inflammatory response production of arachidonic acid metabolites involved in acute inflammatory response + arachidonic acid metabolite production involved in inflammatory response production of arachidonic acid metabolites involved in inflammatory response biological_process GO:0002538 - arachidonic acid metabolite production involved in inflammatory response + arachidonate metabolite production involved in inflammatory response @@ -17424,32 +17600,32 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. Wikipedia:Collagen cellular_component GO:0005581 collagen trimer - + - + - + PMID:12382326 - + PMID:12382326 @@ -17902,12 +18078,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - + @@ -18730,11 +18901,49 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + + The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane. Syncytia are normally derived from single cells that fuse or fail to complete cell division. + biological_process + GO:0006949 + + syncytium formation + + + + + The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane. Syncytia are normally derived from single cells that fuse or fail to complete cell division. + ISBN:0198506732 + + + + Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). + https://github.com/geneontology/go-ontology/issues/26810 biological_process response to abiotic stress response to biotic stress @@ -18745,7 +18954,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to stress @@ -18897,6 +19105,58 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + + + + + + + A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the plasma membrane. + plasma membrane organisation + biological_process + plasma membrane organization and biogenesis + GO:0007009 + + plasma membrane organization + + + + + A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the plasma membrane. + GOC:dph + GOC:jl + GOC:mah + + + + + plasma membrane organization and biogenesis + GOC:mah + + + + @@ -19945,6 +20205,51 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endomembrane system. + endomembrane organization + endomembrane system organisation + biological_process + GO:0010256 + + endomembrane system organization + + + + + A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endomembrane system. + GOC:mah + GOC:sm + + + + + endomembrane system organisation + GOC:mah + + + + @@ -20534,6 +20839,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different The self-renewing division of a stem cell. A stem cell is an undifferentiated cell, in the embryo or adult, that can undergo unlimited division and give rise to one or several different cell types. + + + stem cell renewal biological_process GO:0017145 @@ -22837,12 +23145,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - + A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. GO:0043234 @@ -22872,33 +23175,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - A macromolecular complex containing both protein and DNA molecules. - DNA-protein complex - cellular_component - GO:0032993 - - Note that this term is intended to classify complexes that have DNA as one of the members of the complex, that is, the complex does not exist if DNA is not present. Protein complexes that interact with DNA e.g. transcription factor complexes should not be classified here. - protein-DNA complex - - - - - A macromolecular complex containing both protein and DNA molecules. - GOC:mah - - - - - DNA-protein complex - GOC:mah - - - - @@ -24135,10 +24411,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. + https://github.com/geneontology/go-ontology/issues/28153 NIF_Subcellular:sao414196390 membrane-enclosed organelle cellular_component GO:0043227 + membrane-bounded organelle @@ -24156,11 +24434,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. https://github.com/geneontology/go-ontology/issues/21881 + https://github.com/geneontology/go-ontology/issues/28153 NIF_Subcellular:sao1456184038 non-membrane-enclosed organelle cellular_component biological condensate GO:0043228 + non-membrane-bounded organelle @@ -24196,8 +24476,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. + https://github.com/geneontology/go-ontology/issues/28153 cellular_component GO:0043229 + intracellular organelle @@ -24445,10 +24727,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component. + https://github.com/geneontology/go-ontology/issues/27194 GO:0071843 cellular component biogenesis at cellular level biological_process GO:0044085 + cellular component biogenesis @@ -24598,6 +24882,46 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + + The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell. + GO:0006947 + cell fusion + cell-cell fusion + biological_process + GO:0045026 + plasma membrane fusion + + + + + The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell. + GOC:elh + GOC:mtg_muscle + + + + @@ -24639,6 +24963,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens. + + + GO:0002226 Wikipedia:Innate_immune_system innate immunity @@ -28234,6 +28561,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -29026,6 +29354,35 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + A cellular process in which two or more cells combine together, their plasma membrane fusing, producing a single cell. In some cases, nuclei fuse, producing a polyploid cell, while in other cases, nuclei remain separate, producing a syncytium. + https://github.com/geneontology/go-ontology/issues/15939 + pg + 2018-08-13T18:38:18Z + cell fusion + cell cell fusion + biological_process + GO:0140253 + cell-cell fusion + + + + + A cellular process in which two or more cells combine together, their plasma membrane fusing, producing a single cell. In some cases, nuclei fuse, producing a polyploid cell, while in other cases, nuclei remain separate, producing a syncytium. + Wikipedia:Cell_fusion + + + + @@ -31380,7 +31737,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -34539,51 +34896,51 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + - A molecular entity that minimally consists of a protein. + A material entity that minimally consists of a protein. protein protein aggregate protein complex protein-containing complex protein - PR:000064867 - Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). - protein-containing molecular entity + PR:000050567 + Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566). + protein-containing material entity - + - A molecular entity that minimally consists of a protein. + A material entity that minimally consists of a protein. PRO:DAN - + protein PRO:DAN - + protein aggregate PRO:DAN - + protein complex PRO:DAN - + protein-containing complex PRO:DAN @@ -35068,7 +35425,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -35444,7 +35801,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -35453,7 +35810,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -35480,14 +35837,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different gastrula stage - + - + BILS @@ -35559,7 +35916,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -35602,7 +35959,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -35636,7 +35993,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -35796,6 +36153,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -35803,15 +36161,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - - + + A fluid that is composed of blood plasma and erythrocytes. AAO:0000046 @@ -35848,34 +36206,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different blood - + - + - + - + CL:tm - + https://github.com/obophenotype/uberon/issues/1330 - + Bgee:AN @@ -35925,7 +36283,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -36030,7 +36388,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -36947,6 +37305,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -36960,7 +37319,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -37002,14 +37361,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg - - + + - + http://palaeos.com/metazoa/porifera/homoscleromorpha.html @@ -37338,7 +37697,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -37429,7 +37788,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. AAO:0000137 BILA:0000036 @@ -37464,14 +37823,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png - + - + Bgee:AN @@ -37511,7 +37870,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. AAO:0000139 BILA:0000038 @@ -37546,14 +37905,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png - + - + Bgee:AN @@ -37594,7 +37953,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The middle germ layer of the embryo, between the endoderm and ectoderm. UBERON:0003263 @@ -37635,14 +37994,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png - + - + Bgee:AN @@ -37697,7 +38056,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -37816,7 +38175,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -37825,7 +38184,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -37887,14 +38246,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different https://cdn.humanatlas.io/digital-objects/ref-organ/heart-female/v1.3/assets/3d-vh-f-heart.glb https://cdn.humanatlas.io/digital-objects/ref-organ/heart-male/v1.3/assets/3d-vh-m-heart.glb - + - + MA @@ -38120,7 +38479,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -38275,7 +38634,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -38297,14 +38656,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]. - AAO:0000324 BILA:0000079 BIRNLEX:844 @@ -38339,7 +38697,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0001016 - @@ -38347,14 +38704,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png - + - + Bgee:AN @@ -38416,11 +38773,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. @@ -38465,7 +38822,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different central nervous system - + @@ -38479,7 +38836,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Bgee:AN @@ -38863,11 +39220,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + Skeletal element that is composed of bone tissue. @@ -38909,14 +39266,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different bone element - + - + VSAO-modified @@ -38972,7 +39329,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -38982,7 +39339,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A tube extending from the mouth to the anus. @@ -39019,14 +39376,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different digestive tract - + - + NCBIBook:NBK10107 @@ -39171,6 +39528,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -39245,6 +39603,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -39253,8 +39612,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + @@ -39267,7 +39626,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -39321,34 +39680,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different blood vessel http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg - + - + - + - + AEO - + EHDAA2 - + GO:0072360 @@ -39410,7 +39769,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -39861,7 +40220,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -40182,9 +40541,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - + + + @@ -40232,15 +40591,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - - + + - + - + @@ -40259,19 +40618,19 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -40311,8 +40670,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. mesodermal cluster @@ -40350,11 +40709,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - - + + - + @@ -40367,13 +40726,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + GOTAX:0000352 - + ZFA @@ -40435,22 +40794,22 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + - - + + - + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. AAO:0010578 BTO:0001764 @@ -40483,45 +40842,45 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - + BTO - + PMID:11523831 - + PMID:11523831 @@ -40662,7 +41021,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -40718,14 +41077,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different bone marrow http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg - + - + FMA MA @@ -40773,7 +41132,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -40864,7 +41223,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -40937,10 +41296,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -40990,14 +41349,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different hematopoietic system - + - + FMA @@ -41095,7 +41454,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -41310,7 +41669,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. AAO:0011086 EFO:0001982 @@ -41333,14 +41692,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different presomitic mesoderm - + - + Bgee:AN @@ -41446,7 +41805,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -41494,9 +41853,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. AAO:0011072 BTO:0001765 @@ -41525,34 +41884,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - - + + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -41592,7 +41951,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. AAO:0010568 EFO:0003515 @@ -41618,7 +41977,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -41631,7 +41990,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Bgee:AN @@ -41678,10 +42037,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -41718,7 +42077,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -41731,7 +42090,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 VHOG @@ -41781,15 +42140,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + - + Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. should probably be merged with heart rudiment. AAO:0011044 @@ -41806,15 +42165,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different heart primordium - + - + - + @@ -41827,19 +42186,19 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + ZFA - + ZFA - + XAO @@ -41868,8 +42227,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. AAO:0010571 AEO:0000212 @@ -41893,11 +42252,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different sclerotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - - + + - + @@ -41916,13 +42275,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + VHOG:0000680 - + ZFA @@ -42006,7 +42365,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -42141,7 +42500,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults EHDAA:251 @@ -42156,14 +42515,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different intraembryonic coelom - + - + Wikipedia @@ -42458,8 +42817,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. XAO:0004185 first heart field @@ -42471,24 +42830,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0004140 primary heart field - + - + - + GO:0003128 - + https://orcid.org/0000-0003-3308-6245 @@ -42541,7 +42900,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + An epithelial tube that will give rise to the mature heart. AAO:0010411 EFO:0003526 @@ -42560,14 +42919,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different heart tube - + - + ZFA-modified @@ -42744,6 +43103,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -42840,6 +43200,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -43191,7 +43552,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. AAO:0011129 TAO:0001890 @@ -43205,14 +43566,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different skeletal element - + - + VSAO @@ -43239,10 +43600,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -43278,14 +43639,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0004770 articular system - + - + FMA @@ -43444,7 +43805,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -43610,7 +43971,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -43771,7 +44132,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -43999,7 +44360,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -44015,14 +44376,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different trunk mesenchyme - + - + EHDAA2 @@ -44139,7 +44500,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Multi-tissue structure that arises from the heart rudiment and will become the heart tube. EHDAA2:0001512 EHDAA:424 @@ -44157,14 +44518,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different primitive heart tube - + - + ZFA @@ -44231,6 +44592,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -44246,7 +44608,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -44330,7 +44692,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 @@ -44340,7 +44702,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0005856 developing mesenchymal condensation - + @@ -44359,7 +44721,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + AEO-modified-relation @@ -44453,7 +44815,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB EHDAA2:0001278 @@ -44467,7 +44829,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different notochordal plate - + @@ -44480,7 +44842,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 @@ -44504,11 +44866,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -44525,14 +44887,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -44635,7 +44997,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -44778,7 +45140,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -44842,7 +45204,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -44920,6 +45282,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -45421,7 +45784,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -45447,7 +45810,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different presumptive paraxial mesoderm - + @@ -45463,7 +45826,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + https://github.com/obophenotype/uberon/issues/1277 @@ -45539,7 +45902,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -45547,7 +45910,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0007524 dense mesenchyme tissue - + @@ -45560,7 +45923,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + AEO @@ -45663,7 +46026,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Anatomical system that consists of all blood and lymph vessels. consider merging with vasculature @@ -45680,14 +46043,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different vascular system - + - + MA @@ -45715,7 +46078,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -45732,14 +46095,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -45795,7 +46158,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -45803,14 +46166,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -45833,7 +46196,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EFO:0003704 TAO:0005041 ZFA:0005041 @@ -45843,14 +46206,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different anterior lateral plate mesoderm - + - + ZFA @@ -45964,6 +46327,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -45989,7 +46353,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -46009,14 +46373,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0010210 blood clot - + - + BTO @@ -46137,8 +46501,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. FMA:23879 SCTID:129140006 @@ -46150,11 +46514,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different subdivision of skeleton - + - + @@ -46167,13 +46531,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + UBERONREF:0000003 - + VSAO @@ -46234,7 +46598,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. axial skeletal system FMA:302077 @@ -46244,7 +46608,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different postcranial axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton - + @@ -46257,7 +46621,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + cjm @@ -46428,7 +46792,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -46530,7 +46894,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -46551,7 +46915,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0012429 hematopoietic tissue - + @@ -46564,7 +46928,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + defitional @@ -46697,7 +47061,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -46890,7 +47254,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -47115,7 +47479,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -47138,7 +47502,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0016887 entire extraembryonic component - + @@ -47151,7 +47515,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + AEO @@ -47565,72 +47929,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different /////////////////////////////////////////////////////////////////////////////////////// --> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - @@ -47671,6 +47969,454 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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+_:B219c8649X2Db5beX2D4319X2Dae80X2Db9cdc9e3289cgenid783 +_:B219c8649X2Db5beX2D4319X2Dae80X2Db9cdc9e3289cgenid798 +_:B219c8649X2Db5beX2D4319X2Dae80X2Db9cdc9e3289cgenid853 +_:B219c8649X2Db5beX2D4319X2Dae80X2Db9cdc9e3289cgenid885 +_:B219c8649X2Db5beX2D4319X2Dae80X2Db9cdc9e3289cgenid930 +_:B219c8649X2Db5beX2D4319X2Dae80X2Db9cdc9e3289cgenid944 +_:B219c8649X2Db5beX2D4319X2Dae80X2Db9cdc9e3289cgenid959 +_:B219c8649X2Db5beX2D4319X2Dae80X2Db9cdc9e3289cgenid976 +_:B219c8649X2Db5beX2D4319X2Dae80X2Db9cdc9e3289cgenid995 "cell" "early embryonic cell (metazoa)" "stem cell" @@ -515,7 +547,6 @@ _:Bd8962366X2Dda15X2D4a2dX2Da122X2D110badc7fe25genid994 "embryonic cell (metazoa)" "immature T cell" "cardiocyte" - "embryonic blood vessel endothelial progenitor cell" "natural helper lymphocyte" "skeletogenic cell" "premigratory neural crest cell" @@ -535,9 +566,11 @@ _:Bd8962366X2Dda15X2D4a2dX2Da122X2D110badc7fe25genid994 "bone marrow hematopoietic cell" "peripheral blood mononuclear cell" "blood lymphocyte" + "syncytial cell" "mitotic cell cycle" "nuclear division" "lytic vacuole" + "syncytium formation by plasma membrane fusion" "chromatin" "euchromatin" "heterochromatin" @@ -588,7 +621,7 @@ _:Bd8962366X2Dda15X2D4a2dX2Da122X2D110badc7fe25genid994 "immune system development" "leukocyte differentiation" "production of molecular mediator involved in inflammatory response" - "arachidonic acid metabolite production involved in inflammatory response" + "arachidonate metabolite production involved in inflammatory response" "prostaglandin production involved in inflammatory response" "chronic inflammatory response" "somatic diversification of immune receptors via germline recombination within a single locus" @@ -657,11 +690,13 @@ _:Bd8962366X2Dda15X2D4a2dX2Da122X2D110badc7fe25genid994 "cellular component disassembly involved in execution phase of apoptosis" "chemotaxis" "muscle contraction" + "syncytium formation" "response to stress" "defense response" "inflammatory response" "immune response" "organelle organization" + "plasma membrane organization" "cell cycle" "endomitotic cell cycle" "cell communication" @@ -693,6 +728,7 @@ _:Bd8962366X2Dda15X2D4a2dX2Da122X2D110badc7fe25genid994 "embryo development ending in birth or egg hatching" "tissue development" "cellular process" + "endomembrane system organization" "membrane invagination" "gene expression" "programmed cell death" @@ -772,7 +808,6 @@ _:Bd8962366X2Dda15X2D4a2dX2Da122X2D110badc7fe25genid994 "secretion by cell" "protein-containing complex disassembly" "protein-containing complex" - "protein-DNA complex" "V(D)J recombination" "immunoglobulin V(D)J recombination" "erythrocyte homeostasis" @@ -824,6 +859,7 @@ _:Bd8962366X2Dda15X2D4a2dX2Da122X2D110badc7fe25genid994 "primary metabolic process" "cellular biosynthetic process" "biological process involved in interspecies interaction between organisms" + "plasma membrane fusion" "T cell selection" "innate immune response" "isotype switching" @@ -947,6 +983,7 @@ _:Bd8962366X2Dda15X2D4a2dX2Da122X2D110badc7fe25genid994 "mitotic nuclear division" "exocytic process" "extracellular vesicle biogenesis" + "cell-cell fusion" "export from cell" "defense response to symbiont" "regulation of leukocyte differentiation" @@ -1127,7 +1164,7 @@ _:Bd8962366X2Dda15X2D4a2dX2Da122X2D110badc7fe25genid994 "G-protein coupled receptor" "eukaryotic protein" "cathepsin-like protease" - "protein-containing molecular entity" + "protein-containing material entity" "processual entity" "tube" "vessel" diff --git a/src/ontology/subsets/eye_upper_slim.json b/src/ontology/subsets/eye_upper_slim.json index b921f2954..27446ca77 100644 --- a/src/ontology/subsets/eye_upper_slim.json +++ b/src/ontology/subsets/eye_upper_slim.json @@ -4,9 +4,9 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-08-16" + "val" : "2024-09-26" } ], - "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-08-16/subsets/eye_upper_slim.owl" + "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-09-26/subsets/eye_upper_slim.owl" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/CL_0000000", @@ -535,6 +535,10 @@ "lbl" : "squamous epithelial cell", "type" : "CLASS", "meta" : { + "definition" : { + "val" : "Any epithelial cell that is part of some squamous epithelium.", + "xrefs" : [ "FBC:Autogenerated" ] + }, "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-1249" @@ -548,9 +552,10 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A flattened epithelial cell of mesenchymal origin that lines the serous cavity.", - "xrefs" : [ "GOC:tfm", "ISBN:0721662544" ] + "val" : "A flat, squamous-like epithelial cell of mesodermal origin. It forms the mesothelium, which lines the body's serous cavities including the pleural, peritoneal, and pericardial spaces. This cell plays a crucial role in synthesizing and secreting lubricants, such as glycosaminoglycans and surfactants, which minimize friction between adjacent tissues during movement.", + "xrefs" : [ "GOC:tfm", "ISBN:0721662544", "PMID:26106328" ] }, + "comments" : [ "Mesothelial cells, which morphologically resemble squamous epithelial cells, express both epithelial markers (cytokeratins) and mesenchymal markers (vimentin), reflecting their mesodermal origin. They feature surface microvilli and apical-basal polarity. Under certain conditions, they can undergo mesothelial-to-mesenchymal transition. These cells also produce extracellular matrix proteins, maintain serosal homeostasis, and facilitate fluid transport." ], "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -734,10 +739,15 @@ "val" : "FMA:54536" }, { "val" : "ZFA:0009073" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000125" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nGlial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons.\nThese different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning.\nOligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. \nMicroglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response.\nDespite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis." } ] } }, { @@ -1098,7 +1108,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A cell specialized to detect and transduce light.", + "val" : "A cell specialized in detecting light stimuli that are involved in visual perception.", "xrefs" : [ "MESH:D010786" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], @@ -1270,7 +1280,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "Any cell that only exists in Eukaryota.", + "val" : "Any cell that in taxon some Eukaryota.", "xrefs" : [ "FBC:Autogenerated" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], @@ -2601,6 +2611,8 @@ } ], "xrefs" : [ { "val" : "FMA:70606" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0002303" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", @@ -2608,6 +2620,9 @@ }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nPigmented ciliary epithelial cells, which are a type of pigment cell, have a crucial function within the eye's ciliary body. The ciliary body, located behind the iris, is one of the eye’s most vital structures and consists of two types of epithelial cells: the pigmented and the non-pigmented ciliary epithelial cells. The pigmented ciliary epithelial cells form the outer layer of the ciliary body and exhibit a black or brown pigmentation due to the melanin they contain.\nOne key function of pigmented ciliary epithelial cells is to aid in the formation of aqueous humor, an intraocular fluid that nourishes the cornea and lens, and maintains intraocular pressure which is essential for the eye’s shape and light refraction. These cells facilitate this function in conjunction with the non-pigmented ciliary epithelial cells. Together, the pigmented and non-pigmented ciliary epithelial cells form a bilayer epithelium that allows the secretion of aqueous humor through a bi-directional fluid transport mechanism.\nPigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, a physiological frontier that controls the entry and exit of various substances from the blood to the aqueous humor and vice versa. The pigmentation in these cells, intensified by melanin, helps to absorb scattered light coming into the eye, reducing any potential damage and glare." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-09-13T04:09:27Z" @@ -2800,27 +2815,6 @@ "val" : "2010-12-07T09:37:22Z" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/CL_0002546", - "lbl" : "embryonic blood vessel endothelial progenitor cell", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An endothelial progenitor cell that participates in angiogenesis during development.", - "xrefs" : [ "GOC:tfm" ] - }, - "comments" : [ "See CL:0002619." ], - "xrefs" : [ { - "val" : "ZFA:0005773" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0003-1980-3228" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2011-02-28T04:20:39Z" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/CL_0002565", "lbl" : "iris pigment epithelial cell", @@ -2852,12 +2846,18 @@ "xrefs" : [ "GOC:tfm" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "xrefs" : [ { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0002585" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nRetinal blood vessel endothelial cells constitute the innermost lining of the blood vessels found in the retina, the light-sensitive layer of tissue at the back of the eye. The primary role of these cells revolves around their location within the retinal vascular system, forming the structure of the blood-retinal barrier, a subset of the larger blood-ocular barrier system. \nThe endothelial cells are particularly involved in the growth of new retinal blood vessels from pre-existing ones (angiogenesis); this is critical in managing the amount of oxygen and essential nutrients delivered to the ocular tissues. They are crucial for maintaining homeostasis in the retinal environment by controlling the exchange of molecules between the blood and the retina. Furthermore, they mediate immune cell trafficking, supporting the immune privilege of the eye by preventing the unrestricted infiltration of inflammatory cells into the retina, thus maintaining ocular health and normal vision.\nThe malfunction or dysfunction of retinal blood vessel endothelial cells is implicated in numerous ocular pathologies, particularly diabetic retinopathy, which is one of the leading causes of blindness worldwide. In such conditions, the compromise in the integrity of the blood-retinal barrier and excess angiogenesis can lead to retinal edema and pathological neovascularization, resulting in vision loss." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2011-03-06T03:28:27Z" @@ -2877,6 +2877,8 @@ "val" : "BTO:0004910" }, { "val" : "FMA:75802" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0002586" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", @@ -2884,6 +2886,9 @@ }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nRetinal pigment epithelial (RPE) cells form a single layer of cells at the back of the eye sandwiched between the neurosensory retina and the choroid, playing a significant role in maintaining vision health. These pigment-laden cells are highly specialized and perform an array of metabolic and transport functions essential for the maintenance of the photoreceptor cells (rods and cones) in the retina. The pigmentation of RPE cells actively aids in the absorption of excess light and the prevention of light scattering, thus enhancing the eye's optical properties.\nThe retinal pigment epithelium forms a key part of the blood/retina barrier. The cells have long sheet-like microvilli on their apical membrane that project into the light-sensitive outer segments of the photoreceptors, forming a close structural interaction. The basolateral membrane of the RPE interacts with the underlying Bruch’s membrane, which separates the RPE cells from fenestrated endothelium of the choriocapillaris. \nRPE cells support the photoreceptor by providing them with oxygen and nutrients (such as glucose, retinol and fatty acids) and removing waste products. They also recycle the visual pigment, in a process called the \"visual cycle\", where the RPE cells play a vital role in the regeneration of visual pigment (11-cis retinol) following the absorption of light. This is essential for the maintenance of photoreceptor excitability.\nBeyond this, RPE cells take part in the phagocytosis process, where they digest the shed ends of photoreceptor outer segments, thus, preventing the build-up of waste residue that could otherwise harm retinal health. They also secrete various factors, including growth factors required to maintain the structural integrity of choriocapillaris endothelium and photoreceptors, as well as immunosuppressive factors that play an important role in establishing the immune privilege of the eye." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2011-03-06T03:37:09Z" @@ -3062,7 +3067,14 @@ "val" : "A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells.", "xrefs" : [ "https://orcid.org/0000-0001-5208-3432", "https://orcid.org/0000-0002-9900-7880" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "xrefs" : [ { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0011012" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." + } ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0011026", @@ -3330,6 +3342,9 @@ "val" : "NIF_Subcellular:sao1615953555" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28301" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "GO:0000789" }, { @@ -5831,6 +5846,15 @@ "val" : "stem cell renewal" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_2" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_2157" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -6790,27 +6814,6 @@ "val" : "cellular_component" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0032993", - "lbl" : "protein-DNA complex", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A macromolecular complex containing both protein and DNA molecules.", - "xrefs" : [ "GOC:mah" ] - }, - "comments" : [ "Note that this term is intended to classify complexes that have DNA as one of the members of the complex, that is, the complex does not exist if DNA is not present. Protein complexes that interact with DNA e.g. transcription factor complexes should not be classified here." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "DNA-protein complex", - "xrefs" : [ "GOC:mah" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0034101", "lbl" : "erythrocyte homeostasis", @@ -7276,6 +7279,7 @@ "val" : "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.", "xrefs" : [ "GOC:go_curators" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "membrane-enclosed organelle" @@ -7284,6 +7288,9 @@ "val" : "NIF_Subcellular:sao414196390" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28153" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -7297,7 +7304,7 @@ "val" : "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes.", "xrefs" : [ "GOC:go_curators" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_mouse" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_mouse" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "non-membrane-enclosed organelle" @@ -7311,6 +7318,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/21881" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28153" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -7325,8 +7335,11 @@ "val" : "Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.", "xrefs" : [ "GOC:go_curators" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_pir" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28153" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -7511,12 +7524,15 @@ "val" : "A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component.", "xrefs" : [ "GOC:jl", "GOC:mah" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_pir" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "cellular component biogenesis at cellular level" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/27194" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "GO:0071843" }, { @@ -8147,6 +8163,42 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0050908", + "lbl" : "detection of light stimulus involved in visual perception", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The series of events involved in visual perception in which a light stimulus is received and converted into a molecular signal.", + "xrefs" : [ "GOC:ai", "GOC:dos" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "sensory detection of light during visual perception" + }, { + "pred" : "hasExactSynonym", + "val" : "sensory detection of light stimulus during visual perception" + }, { + "pred" : "hasExactSynonym", + "val" : "sensory transduction of light during visual perception" + }, { + "pred" : "hasExactSynonym", + "val" : "sensory transduction of light stimulus during visual perception" + }, { + "pred" : "hasExactSynonym", + "val" : "visual perception, detection of light stimulus" + }, { + "pred" : "hasExactSynonym", + "val" : "visual perception, sensory transduction during perception of light" + }, { + "pred" : "hasExactSynonym", + "val" : "visual perception, sensory transduction of light stimulus" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0050953", "lbl" : "sensory perception of light stimulus", @@ -11443,7 +11495,7 @@ "meta" : { "definition" : { "val" : "A quality of a single cell inhering in the bearer by virtue of the bearer's size or shape or structure.", - "xrefs" : [ "ORCID:0000-0002-7073-9172" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "comments" : [ "Use this term for morphologies that can *only* inhere in a cell, e.g. morphological qualities inhering in a cell by virtue of the presence, location or shape of one or more cell parts." ], "basicPropertyValues" : [ { @@ -12590,15 +12642,15 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/PR_000064867", - "lbl" : "protein-containing molecular entity", + "id" : "http://purl.obolibrary.org/obo/PR_000050567", + "lbl" : "protein-containing material entity", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A molecular entity that minimally consists of a protein.", + "val" : "A material entity that minimally consists of a protein.", "xrefs" : [ "PRO:DAN" ] }, - "comments" : [ "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565)." ], + "comments" : [ "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566)." ], "synonyms" : [ { "pred" : "hasNarrowSynonym", "val" : "protein", @@ -17026,7 +17078,7 @@ "val" : "The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO].", "xrefs" : [ "BIRNLEX:844", "ISBN:0-14-051288-8", "ISBN:3110148986", "NLM:nervous+system", "WB:rynl", "Wikipedia:Nervous_system", "ZFIN:curator" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#cumbo", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#cumbo", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "neurological system", @@ -17099,9 +17151,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -30463,7 +30512,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000050", - "lbl" : "part_of", + "lbl" : "part of", "type" : "PROPERTY", "propertyType" : "OBJECT", "meta" : { @@ -30486,9 +30535,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "part_of" @@ -30508,7 +30554,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000051", - "lbl" : "has_part", + "lbl" : "has part", "type" : "PROPERTY", "propertyType" : "OBJECT", "meta" : { @@ -30531,9 +30577,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_part" @@ -34398,6 +34441,10 @@ "id" : "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "type" : "PROPERTY", "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#gocheck_obsoletion_candidate", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/go#goslim_agr", "type" : "PROPERTY", @@ -34736,6 +34783,10 @@ "id" : "http://purl.org/dc/terms/date", "type" : "PROPERTY", "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/description", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/license", "type" : "PROPERTY", @@ -34761,12 +34812,10 @@ "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "lbl" : "created by", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "lbl" : "creation date", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { @@ -34859,7 +34908,6 @@ "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#id", - "lbl" : "id", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { @@ -34929,7 +34977,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000000", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_131567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000005", @@ -34959,6 +35007,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000030", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000055" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000030", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000030", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -34973,8 +35025,12 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000031", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000034", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000034", "pred" : "is_a", @@ -35140,7 +35196,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000066", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000066", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -35153,10 +35209,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000071", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0004638" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000071", - "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/CL_0002546" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000075", "pred" : "is_a", @@ -35165,6 +35217,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000076", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000066" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000076", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0006914" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000077", "pred" : "is_a", @@ -35177,6 +35233,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000077", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0002078" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000077", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0001136" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000081", "pred" : "is_a", @@ -35223,6 +35283,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000115", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000213" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000115", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000115", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -35245,11 +35309,7 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0000095" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000123", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000255" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000123", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000123", @@ -35309,6 +35369,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000148", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000147" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000148", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000148", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -35337,6 +35401,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000187", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000183" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000187", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000187", "pred" : "is_a", @@ -35360,7 +35428,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000197", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000197", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -35372,17 +35440,15 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000210", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000006", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_inferred", - "val" : "true" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/CL_0000101" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000210", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0008028" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000210", "pred" : "http://purl.obolibrary.org/obo/RO_0002215", - "obj" : "http://purl.obolibrary.org/obo/GO_0050962" + "obj" : "http://purl.obolibrary.org/obo/GO_0050908" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000211", "pred" : "is_a", @@ -35403,6 +35469,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000219", "pred" : "http://purl.obolibrary.org/obo/RO_0002215", "obj" : "http://purl.obolibrary.org/obo/GO_0048870" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000221", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000221", "pred" : "is_a", @@ -35411,6 +35481,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000221", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000924" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000222", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000222", "pred" : "is_a", @@ -35419,6 +35493,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000222", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000926" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000223", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000223", "pred" : "is_a", @@ -35467,8 +35545,12 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0000000" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000255", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000287", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000006" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000287", "pred" : "is_a", @@ -35539,8 +35621,12 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000342", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000347", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000347", "pred" : "is_a", @@ -35553,6 +35639,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000347", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", "obj" : "http://purl.obolibrary.org/obo/CL_0000008" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000348", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000348", "pred" : "is_a", @@ -35583,7 +35673,7 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0010017" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000365", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000393", @@ -35659,6 +35749,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000547", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0002242" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000547", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000547", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -35733,6 +35827,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000549", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000549", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -35755,6 +35853,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000550", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000550", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -35895,6 +35997,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000558", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000558", "pred" : "http://purl.obolibrary.org/obo/CL_4030046", @@ -35985,6 +36091,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000566", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0011026" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000566", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000566", "pred" : "http://purl.obolibrary.org/obo/RO_0002104", @@ -36057,6 +36167,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000680", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000055" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000680", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000680", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -36129,6 +36243,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000748", "pred" : "http://purl.obolibrary.org/obo/RO_0002100", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001791" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000763", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000763", "pred" : "is_a", @@ -36221,10 +36339,18 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000765", "pred" : "http://purl.obolibrary.org/obo/RO_0002215", "obj" : "http://purl.obolibrary.org/obo/GO_0030218" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000837", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000837", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0008001" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000837", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000837", "pred" : "http://purl.obolibrary.org/obo/CL_4030046", @@ -36311,6 +36437,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000988", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0002031", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002031", "pred" : "is_a", @@ -36323,6 +36453,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0002031", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", "obj" : "http://purl.obolibrary.org/obo/CL_0002032" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0002032", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002032", "pred" : "is_a", @@ -36398,7 +36532,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002319", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002319", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -36406,7 +36540,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002320", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002320", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -36438,15 +36572,11 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002494", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002494", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0007100" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0002546", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000222" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002565", "pred" : "is_a", @@ -36557,6 +36687,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0008019", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000219" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0008019", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0008019", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -36611,6 +36745,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0011012", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0002321" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0011026", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0011026", "pred" : "is_a", @@ -36742,7 +36880,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GO_0000785", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0032993" + "obj" : "http://purl.obolibrary.org/obo/GO_0110165" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0000785", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -36991,8 +37129,8 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0043232" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0005840", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", - "obj" : "http://purl.obolibrary.org/obo/PR_000000001" + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0005840", "pred" : "http://purl.obolibrary.org/obo/RO_0002216", @@ -37767,12 +37905,8 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0005575" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0032991", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", - "obj" : "http://purl.obolibrary.org/obo/PR_000000001" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0032993", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0032991" + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0034101", "pred" : "is_a", @@ -38233,6 +38367,14 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0050906", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/GO_0007600" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0050908", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0050962" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0050908", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/GO_0007601" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0050953", "pred" : "is_a", @@ -38581,6 +38723,10 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0098644", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0099080" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0098644", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0098644", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -39184,7 +39330,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/PR_000000001", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000064867" + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/PR_000000001", "pred" : "http://purl.obolibrary.org/obo/RO_0002353", @@ -39314,7 +39460,7 @@ "pred" : "http://purl.obolibrary.org/obo/RO_0002160", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" }, { - "sub" : "http://purl.obolibrary.org/obo/PR_000064867", + "sub" : "http://purl.obolibrary.org/obo/PR_000050567", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { @@ -39387,8 +39533,12 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0007811" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000033", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0000042", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000042", "pred" : "is_a", @@ -39533,7 +39683,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0001434" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000075", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000075", @@ -39659,7 +39809,7 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0007369" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000109", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000110", @@ -39679,7 +39829,7 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0001841" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000110", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000111", @@ -39695,7 +39845,7 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0048513" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000111", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000122", @@ -39715,7 +39865,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000475" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000153", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000154", @@ -39723,7 +39873,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000475" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000154", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", @@ -39731,12 +39881,16 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0004921" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", "obj" : "http://purl.obolibrary.org/obo/UBERON_0035804" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0000178", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000178", "pred" : "is_a", @@ -39789,7 +39943,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0002193" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000179", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000307", @@ -39809,7 +39963,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0011216" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000383", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000383", @@ -39917,6 +40071,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000481", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000479" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0000483", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000483", "pred" : "is_a", @@ -39931,7 +40089,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0005769" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000483", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208", "meta" : { "basicPropertyValues" : [ { @@ -40003,7 +40161,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0010316" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000923", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000924", @@ -40073,7 +40231,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0035804" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000930", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000941", @@ -40141,7 +40299,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0004151" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000948", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000948", @@ -40217,6 +40375,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000959", "pred" : "http://purl.obolibrary.org/obo/uberon/core#extends_fibers_into", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001908" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0000964", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000964", "pred" : "is_a", @@ -40429,7 +40591,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000467" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001009", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001009", @@ -40461,7 +40623,7 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0000540" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001016", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001016", @@ -40508,7 +40670,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0001016" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001017", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001017", @@ -40632,7 +40794,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000475" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001137", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001434", @@ -40680,7 +40842,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0001007" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001555", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001555", @@ -41672,6 +41834,10 @@ "val" : "ZFA" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001969", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001969", "pred" : "is_a", @@ -41688,6 +41854,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001969", "pred" : "http://purl.obolibrary.org/obo/RO_0002221", "obj" : "http://purl.obolibrary.org/obo/CL_0000232" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", "pred" : "is_a", @@ -41789,7 +41959,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0012275" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001986", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001986", @@ -41813,7 +41983,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0002298" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002028", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_89593" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002028", @@ -41911,7 +42081,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002193", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002200", @@ -42095,7 +42265,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0011137" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711", "meta" : { "basicPropertyValues" : [ { @@ -42147,7 +42317,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002329", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711", "meta" : { "basicPropertyValues" : [ { @@ -42192,7 +42362,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_89593" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", @@ -42246,7 +42416,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000479" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002384", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002385", @@ -42262,7 +42432,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0001015" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002385", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002385", @@ -42292,7 +42462,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002390", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002390", @@ -42360,7 +42530,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000033" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002546", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711", "meta" : { "basicPropertyValues" : [ { @@ -42495,7 +42665,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000926" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003068", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003068", @@ -42634,7 +42804,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0016879" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003075", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711", "meta" : { "basicPropertyValues" : [ { @@ -42755,7 +42925,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003081", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003081", @@ -42827,7 +42997,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003089", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742", "meta" : { "basicPropertyValues" : [ { @@ -42897,7 +43067,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000479" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003104", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003104", @@ -43093,7 +43263,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000064" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003891", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003891", @@ -43525,6 +43695,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004456", "pred" : "http://purl.obolibrary.org/obo/RO_0002492", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000066" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004535", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004535", "pred" : "is_a", @@ -43541,6 +43715,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004535", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001981" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004537", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004537", "pred" : "is_a", @@ -43643,7 +43821,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004770", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004770", @@ -43683,7 +43861,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0003068" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004880", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004905", @@ -43715,7 +43893,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000060" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004923", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005061", @@ -43779,7 +43957,7 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0000187" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005090", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005157", @@ -44049,6 +44227,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0005764", "pred" : "http://purl.obolibrary.org/obo/RO_0002007", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", "pred" : "is_a", @@ -44069,7 +44251,7 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0005587" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", @@ -44109,6 +44291,10 @@ "val" : "AEO-modified-relation" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0005906", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005906", "pred" : "is_a", @@ -44201,7 +44387,7 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0043209" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006135", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006222", @@ -44305,7 +44491,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0005423" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006268", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006268", @@ -44355,7 +44541,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0004921" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006562", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006595", @@ -44367,7 +44553,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000307" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006595", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006595", @@ -44399,7 +44585,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000307" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006601", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006601", @@ -44415,7 +44601,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000307" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006603", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006603", @@ -44437,6 +44623,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0006914", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/CL_0000076" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0006965", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006965", "pred" : "is_a", @@ -45402,7 +45592,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0011997", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0012275", @@ -45412,6 +45602,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0012275", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0012430", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0012430", "pred" : "is_a", @@ -45490,7 +45684,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000475" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0013701", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0013702", @@ -45548,7 +45742,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0015212", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0015228", @@ -45746,7 +45940,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0015212" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0034713", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_89593" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0034713", @@ -47035,6 +47229,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0001981" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000076", + "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000066" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", + "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0006914" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000081", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000988" ], @@ -47088,7 +47289,7 @@ "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0002215", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0050962" + "fillerId" : "http://purl.obolibrary.org/obo/GO_0050908" } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000219", @@ -47120,7 +47321,7 @@ "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000255", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002160", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002162", "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" } ] }, { @@ -47155,7 +47356,7 @@ "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000365", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0010017" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002160", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002162", "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" } ] }, { @@ -48199,6 +48400,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/GO_0007600" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0050908", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009583" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0007601" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0050962", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009583" ], diff --git a/src/ontology/subsets/eye_upper_slim.obo b/src/ontology/subsets/eye_upper_slim.obo index 6947ccb4b..9b0a28e3c 100644 --- a/src/ontology/subsets/eye_upper_slim.obo +++ b/src/ontology/subsets/eye_upper_slim.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: cl/releases/2024-08-16/subsets/eye_upper_slim.owl +data-version: cl/releases/2024-09-26/subsets/eye_upper_slim.owl subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" subsetdef: attribute_slim "" @@ -19,6 +19,7 @@ subsetdef: eye_upper_slim "a subset of general classes related to specific cell subsetdef: functional_classification "" subsetdef: general_cell_types_upper_slim "a subset of general classes of cell types in the cell ontology." subsetdef: gocheck_do_not_annotate "" +subsetdef: gocheck_obsoletion_candidate "" subsetdef: goslim_agr "" subsetdef: goslim_candida "" subsetdef: goslim_chembl "" @@ -95,7 +96,7 @@ idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# idspace: sssom https://w3id.org/sssom/ idspace: terms http://purl.org/dc/terms/ ontology: cl/subsets/eye_upper_slim -property_value: owl:versionInfo "2024-08-16" xsd:string +property_value: owl:versionInfo "2024-09-26" xsd:string [Term] id: CL:0000000 @@ -118,7 +119,7 @@ is_a: UBERON:0000061 ! anatomical structure disjoint_from: GO:0031012 ! extracellular matrix disjoint_from: GO:0032991 ! protein-containing complex disjoint_from: GO:0043226 ! organelle -relationship: RO:0002160 NCBITaxon:131567 ! only in taxon cellular organisms +relationship: RO:0002162 NCBITaxon:131567 ! in taxon cellular organisms [Term] id: CL:0000005 @@ -163,6 +164,7 @@ name: glioblast subset: cellxgene_subset xref: ZFA:0009010 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell +is_a: CL:0000255 ! eukaryotic cell relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell [Term] @@ -176,7 +178,7 @@ xref: FMA:70563 xref: ZFA:0009011 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0000255 ! eukaryotic cell -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata [Term] id: CL:0000034 @@ -190,6 +192,7 @@ synonym: "animal stem cell" EXACT [] xref: CALOHA:TS-2086 xref: FMA:63368 xref: ZFA:0005957 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0011115 ! precursor cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0017145 ! stem cell division @@ -395,7 +398,7 @@ xref: FBbt:00000124 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ xref: FMA:66768 xref: WBbt:0003672 xref: ZFA:0009034 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell relationship: part_of UBERON:0000483 ! epithelium property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 @@ -411,7 +414,6 @@ is_a: CL:0002139 ! endothelial cell of vascular tree intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0001981 ! blood vessel relationship: part_of UBERON:0004638 ! blood vessel endothelium -relationship: RO:0002202 CL:0002546 ! develops from embryonic blood vessel endothelial progenitor cell property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -427,15 +429,20 @@ property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000076 name: squamous epithelial cell +def: "Any epithelial cell that is part of some squamous epithelium." [FBC:Autogenerated] subset: cellxgene_subset xref: CALOHA:TS-1249 xref: ZFA:0009039 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell +intersection_of: CL:0000066 ! epithelial cell +intersection_of: part_of UBERON:0006914 ! squamous epithelium +relationship: part_of UBERON:0006914 ! squamous epithelium [Term] id: CL:0000077 name: mesothelial cell -def: "A flattened epithelial cell of mesenchymal origin that lines the serous cavity." [GOC:tfm, ISBN:0721662544] +def: "A flat, squamous-like epithelial cell of mesodermal origin. It forms the mesothelium, which lines the body's serous cavities including the pleural, peritoneal, and pericardial spaces. This cell plays a crucial role in synthesizing and secreting lubricants, such as glycosaminoglycans and surfactants, which minimize friction between adjacent tissues during movement." [GOC:tfm, ISBN:0721662544, PMID:26106328] +comment: Mesothelial cells, which morphologically resemble squamous epithelial cells, express both epithelial markers (cytokeratins) and mesenchymal markers (vimentin), reflecting their mesodermal origin. They feature surface microvilli and apical-basal polarity. Under certain conditions, they can undergo mesothelial-to-mesenchymal transition. These cells also produce extracellular matrix proteins, maintain serosal homeostasis, and facilitate fluid transport. {xref="PMID:26106328"} subset: cellxgene_subset subset: human_reference_atlas synonym: "mesotheliocyte" EXACT [] @@ -444,6 +451,7 @@ xref: ZFA:0009040 {sssom:mapping_justification="https://w3id.org/semapv/vocab/Un is_a: CL:0000076 ! squamous epithelial cell is_a: CL:0000213 ! lining cell is_a: CL:0002078 ! meso-epithelial cell +relationship: part_of UBERON:0001136 ! mesothelium property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -524,6 +532,7 @@ xref: CALOHA:TS-0278 xref: FMA:66772 xref: ZFA:0009065 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000213 ! lining cell +is_a: CL:0000255 ! eukaryotic cell relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell property_value: RO:0002175 NCBITaxon:9606 @@ -540,8 +549,7 @@ id: CL:0000123 name: neuron associated cell (sensu Vertebrata) subset: cellxgene_subset is_a: CL:0000095 ! neuron associated cell -is_a: CL:0000255 ! eukaryotic cell -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell [Term] @@ -558,9 +566,11 @@ xref: BTO:0002606 xref: CALOHA:TS-0415 xref: FBbt:00005144 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:54536 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000125 xref: ZFA:0009073 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000095 ! neuron associated cell property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nGlial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons.\nThese different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning.\nOligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. \nMicroglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response.\nDespite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis." xsd:string {xref="DOI:10.1002/glia.24343", xref="DOI:10.1038/nn1988", xref="DOI:10.1101/cshperspect.a020602", xref="DOI:10.1126/science.aat0473", xref="DOI:10.3389/fncel.2017.00024"} [Term] id: CL:0000126 @@ -665,6 +675,7 @@ xref: MESH:D008544 xref: VHOG:0001679 xref: ZFA:0009091 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000147 ! pigment cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000147 ! pigment cell intersection_of: has_part GO:0042470 ! melanosome intersection_of: RO:0002202 CL:0000541 ! develops from melanoblast @@ -712,6 +723,7 @@ xref: FMA:67328 xref: WBbt:0003675 xref: ZFA:0009114 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000183 ! contractile cell +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000393 ! electrically responsive cell relationship: RO:0002202 CL:0000056 ! develops from myoblast property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI @@ -742,7 +754,7 @@ name: sensory receptor cell def: "A cell that is capable of detection of a stimulus involved in sensory perception." [] synonym: "receptor cell" EXACT [] xref: MESH:D011984 -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0050906 ! detection of stimulus involved in sensory perception intersection_of: part_of UBERON:0001032 ! sensory system @@ -752,17 +764,18 @@ relationship: part_of UBERON:0001032 ! sensory system [Term] id: CL:0000210 name: photoreceptor cell -def: "A cell specialized to detect and transduce light." [MESH:D010786] +def: "A cell specialized in detecting light stimuli that are involved in visual perception." [MESH:D010786] subset: cellxgene_subset xref: BTO:0001060 xref: CALOHA:TS-0868 xref: FBbt:00004211 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:86740 xref: ZFA:0009127 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000006 {is_inferred="true"} ! neuronal receptor cell +is_a: CL:0000101 ! sensory neuron +is_a: CL:0008028 ! visual system neuron intersection_of: CL:0000540 ! neuron -intersection_of: capable_of GO:0050962 ! detection of light stimulus involved in sensory perception -relationship: capable_of GO:0050962 ! detection of light stimulus involved in sensory perception +intersection_of: capable_of GO:0050908 ! detection of light stimulus involved in visual perception +relationship: capable_of GO:0050908 ! detection of light stimulus involved in visual perception property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg" xsd:anyURI [Term] @@ -804,6 +817,7 @@ def: "A cell of the outer of the three germ layers of the embryo." [MESH:D004475 synonym: "ectoderm cell" EXACT [] xref: FMA:72549 xref: ZFA:0009137 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000924 ! ectoderm @@ -816,6 +830,7 @@ synonym: "mesoblast" EXACT [] synonym: "mesoderm cell" EXACT [] xref: FMA:72554 xref: ZFA:0009138 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000926 ! mesoderm @@ -826,6 +841,7 @@ def: "A cell of the inner of the three germ layers of the embryo." [MESH:D004707 synonym: "endoderm cell" EXACT [] xref: FMA:72555 xref: ZFA:0009139 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000925 ! endoderm @@ -859,13 +875,13 @@ property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000255 name: eukaryotic cell -def: "Any cell that only exists in Eukaryota." [FBC:Autogenerated] +def: "Any cell that in taxon some Eukaryota." [FBC:Autogenerated] subset: cellxgene_subset xref: MESH:D005057 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell -intersection_of: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota -relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +intersection_of: RO:0002162 NCBITaxon:2759 ! in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 ! in taxon Eukaryota [Term] id: CL:0000287 @@ -875,6 +891,7 @@ subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas xref: ZFA:0009154 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000006 ! neuronal receptor cell is_a: CL:0000210 ! photoreceptor cell intersection_of: CL:0000210 ! photoreceptor cell intersection_of: part_of UBERON:0000970 ! eye @@ -948,7 +965,7 @@ def: "Any animal cell containing pigment granules." [GOC:tfm, ISBN:0721662544] xref: ZFA:0009170 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000147 ! pigment cell is_a: CL:0000255 ! eukaryotic cell -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata [Term] id: CL:0000347 @@ -956,6 +973,7 @@ name: scleral cell def: "A cell of the sclera of the eye." [GOC:add] subset: eye_upper_slim xref: ZFA:0009174 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000293 ! structural cell intersection_of: CL:0000293 ! structural cell intersection_of: part_of UBERON:0001773 ! sclera @@ -968,6 +986,7 @@ name: choroidal cell of the eye def: "A structural cell that is part of optic choroid." [GOC:add] subset: eye_upper_slim xref: ZFA:0009175 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000293 ! structural cell intersection_of: CL:0000293 ! structural cell intersection_of: part_of UBERON:0001776 ! optic choroid @@ -992,8 +1011,8 @@ is_a: CL:0000007 ! early embryonic cell (metazoa) is_a: CL:0000255 ! eukaryotic cell is_a: CL:0010017 ! zygote intersection_of: CL:0010017 ! zygote -intersection_of: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa -relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +intersection_of: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa [Term] id: CL:0000393 @@ -1100,6 +1119,7 @@ synonym: "rubriblast" EXACT [ISBN:0721601464] xref: FMA:83518 is_a: CL:0000764 {is_inferred="true"} ! erythroid lineage cell is_a: CL:0002242 ! nucleate cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000764 ! erythroid lineage cell intersection_of: bearer_of PATO:0002505 ! nucleated intersection_of: bearer_of PATO:0040072 ! high nuclear/cytoplasmic ratio @@ -1145,6 +1165,7 @@ synonym: "prorubricyte" EXACT [ISBN:0721601464] xref: FMA:83505 xref: ZFA:0005236 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000765 {is_inferred="true"} ! erythroblast +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017503 ! basophilic cytoplasm intersection_of: has_part GO:0000792 ! heterochromatin @@ -1166,6 +1187,7 @@ synonym: "rubricyte" EXACT [ISBN:0721601464] xref: FMA:83506 xref: ZFA:0005241 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000765 {is_inferred="true"} ! erythroblast +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017504 ! polychromatophilic cytoplasm intersection_of: has_part GO:0000792 ! heterochromatin @@ -1279,6 +1301,7 @@ xref: CALOHA:TS-0864 xref: MESH:D012156 xref: ZFA:0009252 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000764 {is_inferred="true"} ! erythroid lineage cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000764 ! erythroid lineage cell intersection_of: capable_of GO:0071971 ! extracellular exosome assembly intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -1338,6 +1361,7 @@ synonym: "chondroplast" EXACT [] xref: ZFA:0009258 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000134 {is_inferred="true"} ! mesenchymal stem cell is_a: CL:0011026 ! progenitor cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: RO:0002104 PR:000001444 ! has plasma membrane part cadherin-5 intersection_of: RO:0002104 PR:000002112 ! has plasma membrane part vascular endothelial growth factor receptor 2 @@ -1436,6 +1460,7 @@ def: "A non-terminally differentiated cell that is capable of developing into a subset: cellxgene_subset xref: ZFA:0009291 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0011115 ! precursor cell intersection_of: RO:0002203 CL:0000187 ! develops into muscle cell relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell @@ -1542,6 +1567,7 @@ xref: BTO:0001441 xref: CALOHA:TS-0647 xref: MESH:D022423 xref: ZFA:0009324 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000988 {is_inferred="true"} ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: RO:0002202 CL:0000049 ! develops from common myeloid progenitor @@ -1620,7 +1646,9 @@ synonym: "MPP" EXACT [] xref: BTO:0000725 xref: CALOHA:TS-0448 xref: ZFA:0009354 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001402 ! multipotent intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -1695,6 +1723,7 @@ id: CL:0002031 name: hematopoietic lineage restricted progenitor cell def: "A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells." [GOC:tfm, PMID:19022770] subset: blood_and_immune_upper_slim +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001400 ! unipotent @@ -1710,6 +1739,7 @@ name: hematopoietic oligopotent progenitor cell def: "A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities." [GOC:tfm, https://orcid.org/0000-0001-5208-3432, PMID:19022770] comment: This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). subset: blood_and_immune_upper_slim +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001401 ! oligopotent @@ -1803,10 +1833,12 @@ subset: eye_upper_slim subset: human_reference_atlas synonym: "PE cell" EXACT [https://doi.org/10.1016/j.exer.2003.09.021] xref: FMA:70606 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002303 is_a: CL:0000529 ! pigmented epithelial cell relationship: part_of UBERON:0001778 ! ciliary epithelium property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nPigmented ciliary epithelial cells, which are a type of pigment cell, have a crucial function within the eye's ciliary body. The ciliary body, located behind the iris, is one of the eye’s most vital structures and consists of two types of epithelial cells: the pigmented and the non-pigmented ciliary epithelial cells. The pigmented ciliary epithelial cells form the outer layer of the ciliary body and exhibit a black or brown pigmentation due to the melanin they contain.\nOne key function of pigmented ciliary epithelial cells is to aid in the formation of aqueous humor, an intraocular fluid that nourishes the cornea and lens, and maintains intraocular pressure which is essential for the eye’s shape and light refraction. These cells facilitate this function in conjunction with the non-pigmented ciliary epithelial cells. Together, the pigmented and non-pigmented ciliary epithelial cells form a bilayer epithelium that allows the secretion of aqueous humor through a bi-directional fluid transport mechanism.\nPigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, a physiological frontier that controls the entry and exit of various substances from the blood to the aqueous humor and vice versa. The pigmentation in these cells, intensified by melanin, helps to absorb scattered light coming into the eye, reducing any potential damage and glare." xsd:string {xref="DOI:10.1016/S1569-2590(05)10005-6", xref="DOI:10.1111/j.1444-0938.2002.tb02384.x"} creation_date: 2010-09-13T04:09:27Z [Term] @@ -1833,7 +1865,7 @@ def: "A cell that is part of the nervous system." [GOC:tfm, ISBN:0618947256] subset: cellxgene_subset xref: CALOHA:TS-2040 xref: FMA:70333 -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001016 ! nervous system relationship: part_of UBERON:0001016 ! nervous system @@ -1849,7 +1881,7 @@ xref: CALOHA:TS-2096 xref: FMA:63875 xref: MESH:D003239 xref: ZFA:0009392 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0002384 ! connective tissue relationship: part_of UBERON:0002384 ! connective tissue @@ -1908,23 +1940,13 @@ xref: BTO:0001539 xref: CALOHA:TS-0115 xref: FMA:83808 xref: FMA:84791 -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0007100 ! primary circulatory organ relationship: part_of UBERON:0007100 ! primary circulatory organ property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-07T09:37:22Z -[Term] -id: CL:0002546 -name: embryonic blood vessel endothelial progenitor cell -def: "An endothelial progenitor cell that participates in angiogenesis during development." [GOC:tfm] -comment: See CL:0002619. -xref: ZFA:0005773 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000222 ! mesodermal cell -property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 -creation_date: 2011-02-28T04:20:39Z - [Term] id: CL:0002565 name: iris pigment epithelial cell @@ -1947,6 +1969,7 @@ def: "A blood vessel endothelial cell that is part of the retina." [GOC:tfm] subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +xref: https://cellxgene.cziscience.com/cellguide/CL_0002585 is_a: CL:0000071 {is_inferred="true"} ! blood vessel endothelial cell is_a: CL:0009004 ! retinal cell intersection_of: CL:0000071 ! blood vessel endothelial cell @@ -1954,6 +1977,7 @@ intersection_of: part_of UBERON:0000966 ! retina relationship: part_of UBERON:0000966 ! retina property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nRetinal blood vessel endothelial cells constitute the innermost lining of the blood vessels found in the retina, the light-sensitive layer of tissue at the back of the eye. The primary role of these cells revolves around their location within the retinal vascular system, forming the structure of the blood-retinal barrier, a subset of the larger blood-ocular barrier system. \nThe endothelial cells are particularly involved in the growth of new retinal blood vessels from pre-existing ones (angiogenesis); this is critical in managing the amount of oxygen and essential nutrients delivered to the ocular tissues. They are crucial for maintaining homeostasis in the retinal environment by controlling the exchange of molecules between the blood and the retina. Furthermore, they mediate immune cell trafficking, supporting the immune privilege of the eye by preventing the unrestricted infiltration of inflammatory cells into the retina, thus maintaining ocular health and normal vision.\nThe malfunction or dysfunction of retinal blood vessel endothelial cells is implicated in numerous ocular pathologies, particularly diabetic retinopathy, which is one of the leading causes of blindness worldwide. In such conditions, the compromise in the integrity of the blood-retinal barrier and excess angiogenesis can lead to retinal edema and pathological neovascularization, resulting in vision loss." xsd:string {xref="DOI:0.1016/j.preteyeres.2015.08.001", xref="DOI:10.1016/j.preteyeres.2012.08.004", xref="DOI:10.1038/nature04482", xref="DOI:10.5301/EJO.2010.6049"} creation_date: 2011-03-06T03:28:27Z [Term] @@ -1965,6 +1989,7 @@ subset: eye_upper_slim subset: human_reference_atlas xref: BTO:0004910 xref: FMA:75802 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002586 is_a: CL:0000066 ! epithelial cell is_a: CL:0000149 ! visual pigment cell is_a: CL:0009004 ! retinal cell @@ -1974,6 +1999,7 @@ relationship: has_part GO:0042470 ! melanosome relationship: part_of UBERON:0001782 ! pigmented layer of retina property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nRetinal pigment epithelial (RPE) cells form a single layer of cells at the back of the eye sandwiched between the neurosensory retina and the choroid, playing a significant role in maintaining vision health. These pigment-laden cells are highly specialized and perform an array of metabolic and transport functions essential for the maintenance of the photoreceptor cells (rods and cones) in the retina. The pigmentation of RPE cells actively aids in the absorption of excess light and the prevention of light scattering, thus enhancing the eye's optical properties.\nThe retinal pigment epithelium forms a key part of the blood/retina barrier. The cells have long sheet-like microvilli on their apical membrane that project into the light-sensitive outer segments of the photoreceptors, forming a close structural interaction. The basolateral membrane of the RPE interacts with the underlying Bruch’s membrane, which separates the RPE cells from fenestrated endothelium of the choriocapillaris. \nRPE cells support the photoreceptor by providing them with oxygen and nutrients (such as glucose, retinol and fatty acids) and removing waste products. They also recycle the visual pigment, in a process called the \"visual cycle\", where the RPE cells play a vital role in the regeneration of visual pigment (11-cis retinol) following the absorption of light. This is essential for the maintenance of photoreceptor excitability.\nBeyond this, RPE cells take part in the phagocytosis process, where they digest the shed ends of photoreceptor outer segments, thus, preventing the build-up of waste residue that could otherwise harm retinal health. They also secrete various factors, including growth factors required to maintain the structural integrity of choriocapillaris endothelium and photoreceptors, as well as immunosuppressive factors that play an important role in establishing the immune privilege of the eye." xsd:string {xref="DOI:10.1111/febs.16018", xref="DOI:10.1152/physrev.00021.2004", xref="DOI:10.3389/fphar.2021.727870/full", xref="https://www.sciencedirect.com/topics/chemistry/retinal-pigment"} creation_date: 2011-03-06T03:37:09Z [Term] @@ -2038,6 +2064,7 @@ subset: cellxgene_subset subset: human_reference_atlas synonym: "mesenchyme cell" EXACT [] is_a: CL:0000219 ! motile cell +is_a: CL:0000255 ! eukaryotic cell relationship: capable_of GO:0016477 ! cell migration relationship: part_of UBERON:0003104 ! mesenchyme property_value: RO:0002175 NCBITaxon:9606 @@ -2088,14 +2115,17 @@ id: CL:0011012 name: neural crest cell def: "A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells." [https://orcid.org/0000-0001-5208-3432, https://orcid.org/0000-0002-9900-7880] subset: cellxgene_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_0011012 is_a: CL:0000048 ! multi fate stem cell is_a: CL:0002321 ! embryonic cell (metazoa) +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." xsd:string {xref="DOI:10.1002/dvg.23276", xref="DOI:10.1242/dev.193193", xref="DOI:10.3389/fcell.2020.00635/full", xref="https://doi.org/10.1016/j.ydbio.2011.12.042"} [Term] id: CL:0011026 name: progenitor cell def: "A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses." [https://doi.org/10.1016/B978-0-12-409503-8.00002-0, ISBN:978-1-62808-994-3] subset: cellxgene_subset +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0011115 ! precursor cell intersection_of: CL:0011115 ! precursor cell intersection_of: RO:0002202 CL:0000034 ! develops from stem cell @@ -2265,8 +2295,9 @@ synonym: "chromosome scaffold" RELATED [] synonym: "cytoplasmic chromatin" NARROW [] synonym: "nuclear chromatin" NARROW [] xref: NIF_Subcellular:sao1615953555 -is_a: GO:0032993 ! protein-DNA complex +is_a: GO:0110165 ! cellular anatomical entity relationship: part_of GO:0005694 ! chromosome +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28301" xsd:anyURI [Term] id: GO:0000792 @@ -2711,8 +2742,8 @@ synonym: "ribosomal RNA" RELATED [] xref: NIF_Subcellular:sao1429207766 xref: Wikipedia:Ribosome is_a: GO:0043232 ! intracellular non-membrane-bounded organelle +is_a: PR:000050567 ! protein-containing material entity relationship: capable_of_part_of GO:0006412 ! translation -relationship: has_part PR:000000001 ! protein [Term] id: GO:0005886 @@ -3652,6 +3683,9 @@ is_a: GO:0051301 ! cell division intersection_of: GO:0051301 ! cell division intersection_of: has_primary_input CL:0000034 ! stem cell relationship: has_primary_input CL:0000034 ! stem cell +property_value: RO:0002161 NCBITaxon:2 +property_value: RO:0002161 NCBITaxon:2157 +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0019226 @@ -4186,18 +4220,8 @@ synonym: "protein complex" NARROW [] synonym: "protein containing complex" EXACT [] synonym: "protein-protein complex" NARROW [] is_a: GO:0005575 ! cellular_component +is_a: PR:000050567 ! protein-containing material entity disjoint_from: GO:0110165 ! cellular anatomical entity -relationship: has_part PR:000000001 ! protein - -[Term] -id: GO:0032993 -name: protein-DNA complex -namespace: cellular_component -def: "A macromolecular complex containing both protein and DNA molecules." [GOC:mah] -comment: Note that this term is intended to classify complexes that have DNA as one of the members of the complex, that is, the complex does not exist if DNA is not present. Protein complexes that interact with DNA e.g. transcription factor complexes should not be classified here. -subset: goslim_pir -synonym: "DNA-protein complex" EXACT [GOC:mah] -is_a: GO:0032991 ! protein-containing complex [Term] id: GO:0034101 @@ -4448,6 +4472,7 @@ id: GO:0043227 name: membrane-bounded organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane." [GOC:go_curators] +subset: gocheck_do_not_annotate synonym: "membrane-enclosed organelle" EXACT [] xref: NIF_Subcellular:sao414196390 is_a: GO:0043226 ! organelle @@ -4455,30 +4480,35 @@ intersection_of: GO:0043226 ! organelle intersection_of: has_part GO:0016020 ! membrane disjoint_from: GO:0043228 ! non-membrane-bounded organelle relationship: has_part GO:0016020 ! membrane +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI [Term] id: GO:0043228 name: non-membrane-bounded organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:go_curators] +subset: gocheck_do_not_annotate subset: goslim_mouse synonym: "biological condensate" RELATED [] synonym: "non-membrane-enclosed organelle" EXACT [] xref: NIF_Subcellular:sao1456184038 is_a: GO:0043226 ! organelle property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21881" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI [Term] id: GO:0043229 name: intracellular organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:go_curators] +subset: gocheck_do_not_annotate subset: goslim_pir is_a: GO:0043226 ! organelle intersection_of: GO:0043226 ! organelle intersection_of: part_of GO:0005622 ! intracellular anatomical structure disjoint_from: GO:0043230 ! extracellular organelle relationship: part_of GO:0005622 ! intracellular anatomical structure +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI [Term] id: GO:0043230 @@ -4587,9 +4617,11 @@ name: cellular component biogenesis namespace: biological_process alt_id: GO:0071843 def: "A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component." [GOC:jl, GOC:mah] +subset: gocheck_do_not_annotate subset: goslim_pir synonym: "cellular component biogenesis at cellular level" EXACT [] is_a: GO:0071840 ! cellular component organization or biogenesis +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27194" xsd:anyURI [Term] id: GO:0044207 @@ -4954,6 +4986,23 @@ intersection_of: GO:0051606 ! detection of stimulus intersection_of: part_of GO:0007600 ! sensory perception relationship: part_of GO:0007600 ! sensory perception +[Term] +id: GO:0050908 +name: detection of light stimulus involved in visual perception +namespace: biological_process +def: "The series of events involved in visual perception in which a light stimulus is received and converted into a molecular signal." [GOC:ai, GOC:dos] +synonym: "sensory detection of light during visual perception" EXACT [] +synonym: "sensory detection of light stimulus during visual perception" EXACT [] +synonym: "sensory transduction of light during visual perception" EXACT [] +synonym: "sensory transduction of light stimulus during visual perception" EXACT [] +synonym: "visual perception, detection of light stimulus" EXACT [] +synonym: "visual perception, sensory transduction during perception of light" EXACT [] +synonym: "visual perception, sensory transduction of light stimulus" EXACT [] +is_a: GO:0050962 ! detection of light stimulus involved in sensory perception +intersection_of: GO:0009583 ! detection of light stimulus +intersection_of: part_of GO:0007601 ! visual perception +relationship: part_of GO:0007601 ! visual perception + [Term] id: GO:0050953 name: sensory perception of light stimulus @@ -5531,6 +5580,7 @@ def: "A complex of collagen trimers such as a fibril or collagen network." [GOC: synonym: "Supramolecular aggregate of collagen" EXACT [PMID:19693541] synonym: "Supramolecular collagen assembly" EXACT [PMID:21421911] is_a: GO:0099080 ! supramolecular complex +is_a: PR:000050567 ! protein-containing material entity relationship: has_part GO:0005581 ! collagen trimer relationship: part_of GO:0062023 ! collagen-containing extracellular matrix @@ -6631,7 +6681,7 @@ creation_date: 2014-12-12T08:43:17Z id: PATO:0010006 name: cell morphology namespace: quality -def: "A quality of a single cell inhering in the bearer by virtue of the bearer's size or shape or structure." [ORCID:0000-0002-7073-9172] +def: "A quality of a single cell inhering in the bearer by virtue of the bearer's size or shape or structure." [https://orcid.org/0000-0002-7073-9172] comment: Use this term for morphologies that can *only* inhere in a cell, e.g. morphological qualities inhering in a cell by virtue of the presence, location or shape of one or more cell parts. is_a: PATO:0000051 ! morphology property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 @@ -6718,7 +6768,7 @@ comment: The definition above excludes protein complexes, which some also consid synonym: "native protein" NARROW [IEDB:BP] synonym: "natural protein" EXACT [PRO:DAN] is_a: PR:000018263 ! amino acid chain -is_a: PR:000064867 ! protein-containing molecular entity +is_a: PR:000050567 ! protein-containing material entity relationship: output_of GO:0006412 ! translation [Term] @@ -7109,11 +7159,11 @@ intersection_of: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota [Term] -id: PR:000064867 -name: protein-containing molecular entity +id: PR:000050567 +name: protein-containing material entity namespace: protein -def: "A molecular entity that minimally consists of a protein." [PRO:DAN] -comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). +def: "A material entity that minimally consists of a protein." [PRO:DAN] +comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566). synonym: "protein" NARROW [PRO:DAN] synonym: "protein aggregate" NARROW [PRO:DAN] synonym: "protein complex" NARROW [PRO:DAN] @@ -7270,7 +7320,7 @@ xref: XAO:0003024 xref: ZFA:0001114 is_a: UBERON:0011676 ! subdivision of organism along main body axis relationship: part_of UBERON:0007811 ! craniocervical region -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria [Term] id: UBERON:0000042 @@ -7291,6 +7341,7 @@ xref: TAO:0005425 xref: UMLS:C0036760 {source="ncithesaurus:Serosa"} xref: Wikipedia:Serous_membrane xref: ZFA:0005425 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004120 ! mesoderm-derived structure relationship: has_part UBERON:0001136 ! mesothelium @@ -7538,7 +7589,7 @@ xref: SCTID:118966000 xref: UMLS:C1519343 {source="ncithesaurus:Skeletal_System_Part"} is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision relationship: part_of UBERON:0001434 ! skeletal system -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002473 UBERON:0004765 ! composed primarily of skeletal element [Term] @@ -7747,7 +7798,7 @@ is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000108 {source="BILS"} ! blastula stage relationship: RO:0002082 GO:0007369 ! simultaneous with gastrulation -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0000110 @@ -7763,7 +7814,7 @@ is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000109 ! gastrula stage relationship: RO:0002082 GO:0001841 ! simultaneous with neural tube formation -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: seeAlso "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/343" xsd:anyURI @@ -7783,7 +7834,7 @@ xref: Wikipedia:Organogenesis is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: RO:0002082 GO:0048513 ! simultaneous with animal organ development -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: seeAlso "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/533" xsd:anyURI @@ -7809,14 +7860,14 @@ name: anterior region of body namespace: uberon is_a: UBERON:0000475 ! organism subdivision disjoint_from: UBERON:0000154 {source="lexical"} ! posterior region of body -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria [Term] id: UBERON:0000154 name: posterior region of body namespace: uberon is_a: UBERON:0000475 ! organism subdivision -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria [Term] id: UBERON:0000165 @@ -7872,7 +7923,7 @@ xref: XAO:0003029 xref: ZFA:0000547 xref: ZFA:0000590 is_a: UBERON:0004921 ! subdivision of digestive tract -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002202 UBERON:0035804 ! develops from future mouth property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/661" xsd:anyURI @@ -7912,6 +7963,7 @@ xref: VHOG:0000224 xref: Wikipedia:Blood xref: XAO:0000124 xref: ZFA:0000007 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000179 ! haemolymphatic fluid relationship: has_part CL:0000232 {source="CL:tm"} ! erythrocyte relationship: has_part UBERON:0001969 ! blood plasma @@ -7932,7 +7984,7 @@ is_a: UBERON:0006314 ! bodily fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: part_of UBERON:0002193 ! hemolymphoid system relationship: part_of UBERON:0002193 ! hemolymphoid system -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: terms:contributor https://orcid.org/0000-0002-6601-2165 creation_date: 2009-04-08T04:38:19Z @@ -7990,7 +8042,7 @@ is_a: UBERON:0011216 ! organ system subdivision intersection_of: UBERON:0011216 ! organ system subdivision intersection_of: RO:0002473 UBERON:0001015 ! composed primarily of musculature relationship: capable_of GO:0003012 ! muscle system process -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002473 UBERON:0001015 ! composed primarily of musculature property_value: IAO:0000116 "consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77" xsd:string property_value: RO:0002161 NCBITaxon:6040 @@ -8404,12 +8456,13 @@ xref: VHOG:0000387 xref: Wikipedia:Epithelium xref: XAO:0003045 xref: ZFA:0001486 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: RO:0002473 CL:0000066 ! composed primarily of epithelial cell relationship: has_part GO:0005911 ! cell-cell junction relationship: has_part UBERON:0005769 ! basement membrane of epithelium -relationship: RO:0002160 NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! in taxon Metazoa relationship: RO:0002473 CL:0000066 ! composed primarily of epithelial cell property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI @@ -8612,7 +8665,7 @@ xref: Wikipedia:Germ_layer xref: XAO:0003011 xref: ZFA:0001122 is_a: UBERON:0010316 ! germ layer / neural crest -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0000924 @@ -8766,7 +8819,7 @@ xref: ZFA:0001290 is_a: UBERON:0013522 ! subdivision of tube relationship: part_of UBERON:0000924 ! ectoderm relationship: part_of UBERON:0035804 ! future mouth -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI property_value: IAO:0000116 "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" xsd:string @@ -8879,7 +8932,7 @@ intersection_of: UBERON:0007100 ! primary circulatory organ intersection_of: has_part UBERON:0004151 ! cardiac chamber relationship: has_part UBERON:0004151 ! cardiac chamber relationship: part_of UBERON:0015410 {source="MA"} ! heart plus pericardium -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002202 UBERON:0004141 ! develops from heart tube relationship: RO:0002433 UBERON:0004535 ! contributes to morphology of cardiovascular system property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/heart-female/v1.3/assets/3d-vh-f-heart.glb" xsd:anyURI @@ -9056,6 +9109,7 @@ xref: VHOG:0000164 xref: Wikipedia:Cornea xref: XAO:0000180 xref: ZFA:0000640 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0010000 ! multicellular anatomical structure is_a: UBERON:0010313 ! neural crest-derived structure relationship: has_part UBERON:0001772 ! corneal epithelium @@ -9311,7 +9365,7 @@ disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of GO:0003013 ! circulatory system process -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} @@ -9361,7 +9415,6 @@ namespace: uberon def: "The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]." [BIRNLEX:844, ISBN:0-14-051288-8, ISBN:3110148986, NLM:nervous+system, WB:rynl, Wikipedia:Nervous_system, ZFIN:curator] subset: cumbo subset: efo_slim -subset: human_reference_atlas subset: pheno_slim subset: uberon_slim subset: vertebrate_core @@ -9402,14 +9455,13 @@ disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of GO:0050877 ! nervous system process relationship: has_part CL:0000540 ! neuron -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002473 CL:0002319 ! composed primarily of neural cell relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage relationship: RO:0002495 UBERON:0016880 {source="Bgee:AN"} ! immediate transformation of future nervous system property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:6040 -property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001017 @@ -9456,7 +9508,7 @@ xref: ZFA:0000012 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0011216 {source="FBbt", source="cjm"} ! organ system subdivision relationship: part_of UBERON:0001016 ! nervous system -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria relationship: RO:0002495 UBERON:0016879 {source="Bgee:AN"} ! immediate transformation of future central nervous system property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} property_value: RO:0002175 NCBITaxon:9606 @@ -9743,7 +9795,7 @@ xref: SCTID:123961009 xref: UMLS:C0004600 {source="ncithesaurus:Back"} xref: Wikipedia:Dorsum_(anatomy) is_a: UBERON:0000475 ! organism subdivision -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/432px-Gray-back.PNG" xsd:anyURI [Term] @@ -9861,7 +9913,7 @@ xref: WBbt:0005743 xref: ZFA:0000112 is_a: UBERON:0000025 ! tube relationship: part_of UBERON:0001007 ! digestive system -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002176 UBERON:0000165 ! connects mouth relationship: RO:0002495 UBERON:0007026 {source="NCBIBook:NBK10107"} ! immediate transformation of presumptive gut property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} @@ -11254,6 +11306,7 @@ xref: MIAA:0000052 xref: NCIT:C13356 xref: UMLS:C0032105 {source="ncithesaurus:Plasma"} xref: Wikipedia:Blood_plasma +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000179 ! haemolymphatic fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: has_part GO:0005577 ! fibrinogen complex @@ -11302,6 +11355,7 @@ xref: VHOG:0001250 xref: Wikipedia:Blood_vessel xref: XAO:0001011 xref: ZFA:0005314 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000055 ! vessel is_a: UBERON:0004120 ! mesoderm-derived structure relationship: capable_of_part_of GO:0008015 ! blood circulation @@ -11374,7 +11428,7 @@ is_a: UBERON:0000487 {source="FMA-text-def", source="https://github.com/obopheno is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: RO:0002473 CL:0000115 ! composed primarily of endothelial cell -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002473 CL:0000115 ! composed primarily of endothelial cell property_value: RO:0002175 NCBITaxon:9606 @@ -11454,7 +11508,7 @@ xref: XAO:0000015 xref: ZFA:0000029 is_a: UBERON:0002616 ! regional part of brain relationship: overlaps UBERON:0002298 ! brainstem -relationship: RO:0002160 NCBITaxon:89593 ! only in taxon Craniata +relationship: RO:0002162 NCBITaxon:89593 ! in taxon Craniata relationship: RO:0002433 UBERON:0000955 ! contributes to morphology of brain relationship: RO:0002495 UBERON:0007277 {source="Bgee:AN"} ! immediate transformation of presumptive hindbrain property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI @@ -11658,7 +11712,7 @@ xref: EMAPA:18765 xref: FMA:74562 xref: MA:0000013 is_a: UBERON:0000467 {source="MA"} ! anatomical system -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria [Term] id: UBERON:0002200 @@ -11998,7 +12052,7 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0011137 ! axial skeletal system relationship: produces PR:000014841 ! sonic hedgehog protein -relationship: RO:0002160 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! in taxon Chordata relationship: RO:0002202 UBERON:0004880 {source="ZFA"} ! develops from chordamesoderm relationship: RO:0002202 UBERON:0006267 {source="EHDAA2"} ! develops from notochordal plate relationship: RO:0002488 UBERON:0000068 ! existence starts during embryo stage @@ -12041,7 +12095,7 @@ xref: XAO:0000058 xref: ZFA:0000155 is_a: UBERON:0005423 ! developing anatomical structure is_a: UBERON:0007503 {source="EHDAA2"} ! epithelial vesicle -relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {source="GOTAX:0000352"} ! in taxon Chordata relationship: RO:0002202 UBERON:0003059 {source="ZFA"} ! develops from presomitic mesoderm property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:7712 {source="PMID:17237766"} @@ -12080,7 +12134,7 @@ is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0010316 ! germ layer / neural crest relationship: part_of UBERON:0002346 {source="XAO", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! neurectoderm -relationship: RO:0002160 NCBITaxon:89593 ! only in taxon Craniata +relationship: RO:0002162 NCBITaxon:89593 ! in taxon Craniata relationship: RO:0002202 UBERON:0003075 {source="BTO"} ! develops from neural plate relationship: RO:0002202 UBERON:0005062 {source="PMID:11523831"} ! develops from neural fold relationship: RO:0002473 CL:0000333 ! composed primarily of migratory neural crest cell @@ -12156,7 +12210,7 @@ xref: VSAO:0000017 xref: XAO:0001017 xref: ZFA:0001632 is_a: UBERON:0000479 ! tissue -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -12189,7 +12243,7 @@ intersection_of: RO:0002473 CL:0000187 ! composed primarily of muscle cell disjoint_from: UBERON:0003714 ! neural tissue relationship: capable_of GO:0006936 ! muscle contraction relationship: part_of UBERON:0001015 ! musculature -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002473 CL:0000187 ! composed primarily of muscle cell [Term] @@ -12234,7 +12288,7 @@ is_a: UBERON:0000467 ! anatomical system is_a: UBERON:0004120 ! mesoderm-derived structure disjoint_from: UBERON:0004456 ! entire sense organ system relationship: part_of UBERON:0002193 {source="FMA"} ! hemolymphoid system -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002202 UBERON:0003061 ! develops from blood island property_value: RO:0002175 NCBITaxon:9606 @@ -12307,7 +12361,7 @@ xref: MIAA:0000369 xref: XAO:0000305 is_a: UBERON:0005085 {source="cjm"} ! ectodermal placode relationship: part_of UBERON:0000033 ! head -relationship: RO:0002160 NCBITaxon:7711 {source="PMID:11523831", source="PMID:22512454"} ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {source="PMID:11523831", source="PMID:22512454"} ! in taxon Chordata property_value: IAO:0000116 "Do not merge with neurogenic placode" xsd:string [Term] @@ -12496,7 +12550,7 @@ xref: XAO:0000205 xref: ZFA:0001204 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0000926 ! mesoderm -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002202 UBERON:0000926 ! develops from mesoderm property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI @@ -12627,7 +12681,7 @@ xref: ZFA:0000132 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0016879 ! future central nervous system -relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {source="GOTAX:0000352"} ! in taxon Chordata relationship: RO:0002256 UBERON:0002328 {source="Wikipedia"} ! developmentally induced by notochord relationship: RO:0002495 UBERON:0007284 {source="Bgee:AN"} ! immediate transformation of presumptive neural plate property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI @@ -12722,7 +12776,7 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue relationship: part_of UBERON:0000926 {source="EHDAA2", source="VHOG"} ! mesoderm -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria relationship: RO:0002221 UBERON:0003887 ! surrounds intraembryonic coelom property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI @@ -12772,7 +12826,7 @@ xref: XAO:0000397 xref: ZFA:0001080 is_a: UBERON:0005856 {source="EHDAA2"} ! developing mesenchymal condensation is_a: UBERON:0007530 {source="EHDAA2"} ! migrating mesenchyme population -relationship: RO:0002160 NCBITaxon:7742 {source="VHOG:0000680"} ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 {source="VHOG:0000680"} ! in taxon Vertebrata relationship: RO:0002202 UBERON:0002329 {source="ZFA"} ! develops from somite property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI @@ -12885,7 +12939,7 @@ xref: ZFA:0000393 is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002328 GO:0032502 ! functionally related to developmental process relationship: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI @@ -13146,7 +13200,7 @@ xref: FMA:81494 xref: NCIT:C67387 xref: UMLS:C0927195 {source="ncithesaurus:Stroma_Connective_Tissue"} is_a: UBERON:0000064 ! organ part -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002473 UBERON:0002384 ! composed primarily of connective tissue [Term] @@ -13661,6 +13715,7 @@ xref: WikipediaCategory:Cardiovascular_system xref: XAO:0000100 xref: XAO:0001010 xref: ZFA:0000010 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000467 ! anatomical system intersection_of: UBERON:0000467 ! anatomical system intersection_of: has_part UBERON:0000948 ! heart @@ -13684,6 +13739,7 @@ synonym: "blood vessels" RELATED [TAO:0001079] synonym: "set of blood vessels" EXACT [] xref: TAO:0001079 xref: ZFA:0001079 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel @@ -13833,7 +13889,7 @@ is_a: UBERON:0034925 ! anatomical collection intersection_of: UBERON:0034925 ! anatomical collection intersection_of: RO:0002351 UBERON:0000982 ! has member skeletal joint relationship: part_of UBERON:0001434 {source="FMA"} ! skeletal system -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria relationship: RO:0002328 GO:0040011 ! functionally related to locomotion relationship: RO:0002351 UBERON:0000982 ! has member skeletal joint relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage @@ -13897,7 +13953,7 @@ xref: TAO:0000091 xref: ZFA:0000091 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0003068 ! axial mesoderm -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata [Term] id: UBERON:0004905 @@ -13940,7 +13996,7 @@ subset: upper_level xref: FMA:82485 is_a: UBERON:0000064 ! organ part relationship: part_of UBERON:0000060 ! anatomical wall -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0005061 @@ -14017,7 +14073,7 @@ synonym: "musculus" EXACT [FMA:30316] xref: FMA:30316 is_a: UBERON:0000061 ! anatomical structure relationship: has_part CL:0000187 ! muscle cell -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0005157 @@ -14391,11 +14447,12 @@ xref: NCIT:C13191 xref: SCTID:68989006 xref: UMLS:C0004799 {source="ncithesaurus:Basement_Membrane"} xref: Wikipedia:Basement_membrane +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005764 {source="FMA"} ! acellular membrane relationship: adjacent_to CL:0000066 ! epithelial cell relationship: has_part GO:0005587 ! collagen type IV trimer relationship: part_of UBERON:0000483 ! epithelium -relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa relationship: RO:0002473 GO:0005604 ! composed primarily of basement membrane property_value: RO:0002175 NCBITaxon:80999 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} @@ -14420,6 +14477,7 @@ def: "Organ with organ cavity, which has as parts a serous membrane and a serous comment: See notes for serous membrane xref: FMA:9689 xref: SCTID:362890006 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000062 ! organ relationship: has_part UBERON:0000042 ! serous membrane relationship: has_part UBERON:0002553 ! anatomical cavity @@ -14504,7 +14562,7 @@ is_a: UBERON:0006134 ! nerve fiber intersection_of: UBERON:0006134 ! nerve fiber intersection_of: has_part GO:0043209 ! myelin sheath relationship: has_part GO:0043209 ! myelin sheath -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria property_value: IAO:0000116 "consider adding link to UBERON:0002316 ! white matter of neuraxis" xsd:string property_value: RO:0002161 NCBITaxon:117569 property_value: RO:0002161 NCBITaxon:7762 @@ -14644,7 +14702,7 @@ xref: NCIT:C34232 xref: UMLS:C1518430 {source="ncithesaurus:Notochordal_Process"} xref: VHOG:0001213 is_a: UBERON:0005423 ! developing anatomical structure -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002202 UBERON:0000924 {source="EHDAA2"} ! develops from ectoderm [Term] @@ -14712,7 +14770,7 @@ xref: MAT:0000049 xref: MESH:D010614 xref: MIAA:0000049 is_a: UBERON:0004921 ! subdivision of digestive tract -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria [Term] id: UBERON:0006595 @@ -14729,7 +14787,7 @@ intersection_of: UBERON:0006598 ! presumptive structure intersection_of: part_of UBERON:0000307 ! blastula intersection_of: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm relationship: part_of UBERON:0000307 ! blastula -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm [Term] @@ -14781,7 +14839,7 @@ intersection_of: UBERON:0006598 ! presumptive structure intersection_of: part_of UBERON:0000307 ! blastula intersection_of: RO:0002387 UBERON:0000924 ! has potential to develop into ectoderm relationship: part_of UBERON:0000307 ! blastula -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002387 UBERON:0000924 ! has potential to develop into ectoderm [Term] @@ -14799,7 +14857,7 @@ intersection_of: UBERON:0006598 ! presumptive structure intersection_of: part_of UBERON:0000307 ! blastula intersection_of: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm relationship: part_of UBERON:0000307 ! blastula -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm [Term] @@ -14840,6 +14898,7 @@ subset: efo_slim xref: EFO:0003709 xref: TAO:0005077 xref: ZFA:0005077 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005423 ! developing anatomical structure relationship: has_part CL:0000115 ! endothelial cell relationship: has_part CL:0000566 ! angioblastic mesenchymal cell @@ -15789,7 +15848,7 @@ synonym: "schizocoelom" NARROW [] xref: EHDAA2:0004731 xref: Wikipedia:Coelom is_a: UBERON:0000481 {source="EHDAA2"} ! multi-tissue structure -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria property_value: IAO:0000116 "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." xsd:string property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} @@ -15818,6 +15877,7 @@ synonym: "tunica fibrosa" BROAD [] xref: FMA:58102 xref: SCTID:361318005 xref: Wikipedia:Fibrous_tunic_of_eyeball +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004923 {source="FMA"} ! organ component layer is_a: UBERON:0010314 ! structure with developmental contribution from neural crest @@ -15870,7 +15930,7 @@ namespace: uberon def: "A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages." [https://orcid.org/0000-0002-6601-2165] subset: non_informative is_a: UBERON:0000475 ! organism subdivision -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0013702 @@ -15950,7 +16010,7 @@ def: "Any structure that is placed on one side of the left-right axis of a bilat subset: grouping_class subset: non_informative is_a: UBERON:0000061 ! anatomical structure -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria [Term] id: UBERON:0015228 @@ -16152,7 +16212,7 @@ synonym: "neuron projection bundle from brain" RELATED [http://orcid.org/0000-00 is_a: UBERON:0000122 ! neuron projection bundle is_a: UBERON:0015212 ! lateral structure relationship: extends_fibers_into UBERON:0000955 ! brain -relationship: RO:0002160 NCBITaxon:89593 ! only in taxon Craniata +relationship: RO:0002162 NCBITaxon:89593 ! in taxon Craniata property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -17643,9 +17703,7 @@ inverse_of: output_of ! output of [Typedef] id: has_part name: has part -name: has_part namespace: external -namespace: quality def: "a core relation that holds between a whole and its part" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology @@ -17850,9 +17908,7 @@ expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://p [Typedef] id: part_of name: part of -name: part_of namespace: external -namespace: quality def: "a core relation that holds between a part and its whole" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term diff --git a/src/ontology/subsets/eye_upper_slim.owl b/src/ontology/subsets/eye_upper_slim.owl index 69be33e39..394d31707 100644 --- a/src/ontology/subsets/eye_upper_slim.owl +++ b/src/ontology/subsets/eye_upper_slim.owl @@ -22,8 +22,8 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - 2024-08-16 + + 2024-09-26 @@ -392,6 +392,14 @@ WHERE { + + + + + + + + @@ -1038,6 +1046,12 @@ WHERE { + + + + + + @@ -1076,17 +1090,13 @@ WHERE { - - created by - + - - creation date - + @@ -1172,9 +1182,7 @@ WHERE { - - id - + @@ -1283,7 +1291,6 @@ WHERE { A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. BFO:0000050 external - quality part_of @@ -1292,7 +1299,6 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of part of part of - part_of http://www.obofoundry.org/ro/#OBO_REL:part_of @@ -1314,7 +1320,6 @@ A continuant cannot be part of an occurrent: use 'participates in'. An A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. BFO:0000051 external - quality has_part @@ -1322,7 +1327,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part has part has part - has_part @@ -4778,7 +4782,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -4945,6 +4949,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -4971,7 +4976,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -5013,6 +5018,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -5649,7 +5655,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -5716,12 +5722,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - An endothelial cell that lines the vasculature. ZFA:0009036 @@ -5774,12 +5774,36 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + Any epithelial cell that is part of some squamous epithelium. CALOHA:TS-1249 ZFA:0009039 squamous epithelial cell + + + + Any epithelial cell that is part of some squamous epithelium. + FBC:Autogenerated + @@ -5795,21 +5819,29 @@ Each of these 3 primitives can be composed to yield a cross-product of different - A flattened epithelial cell of mesenchymal origin that lines the serous cavity. + + + + + + + A flat, squamous-like epithelial cell of mesodermal origin. It forms the mesothelium, which lines the body's serous cavities including the pleural, peritoneal, and pericardial spaces. This cell plays a crucial role in synthesizing and secreting lubricants, such as glycosaminoglycans and surfactants, which minimize friction between adjacent tissues during movement. FMA:66773 ZFA:0009040 mesotheliocyte + Mesothelial cells, which morphologically resemble squamous epithelial cells, express both epithelial markers (cytokeratins) and mesenchymal markers (vimentin), reflecting their mesodermal origin. They feature surface microvilli and apical-basal polarity. Under certain conditions, they can undergo mesothelial-to-mesenchymal transition. These cells also produce extracellular matrix proteins, maintain serosal homeostasis, and facilitate fluid transport. mesothelial cell - A flattened epithelial cell of mesenchymal origin that lines the serous cavity. + A flat, squamous-like epithelial cell of mesodermal origin. It forms the mesothelium, which lines the body's serous cavities including the pleural, peritoneal, and pericardial spaces. This cell plays a crucial role in synthesizing and secreting lubricants, such as glycosaminoglycans and surfactants, which minimize friction between adjacent tissues during movement. GOC:tfm ISBN:0721662544 + PMID:26106328 @@ -5817,6 +5849,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009040 + + + + Mesothelial cells, which morphologically resemble squamous epithelial cells, express both epithelial markers (cytokeratins) and mesenchymal markers (vimentin), reflecting their mesodermal origin. They feature surface microvilli and apical-basal polarity. Under certain conditions, they can undergo mesothelial-to-mesenchymal transition. These cells also produce extracellular matrix proteins, maintain serosal homeostasis, and facilitate fluid transport. + PMID:26106328 + @@ -6025,6 +6063,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6094,10 +6133,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + @@ -6119,11 +6157,19 @@ Each of these 3 primitives can be composed to yield a cross-product of different A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Glial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons. +These different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning. +Oligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. +Microglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response. +Despite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis. BTO:0002606 CALOHA:TS-0415 FBbt:00005144 FMA:54536 ZFA:0009073 + https://cellxgene.cziscience.com/cellguide/CL_0000125 neuroglial cell neuroglia @@ -6138,6 +6184,22 @@ Each of these 3 primitives can be composed to yield a cross-product of different A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons. MESH:D009457 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Glial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons. +These different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning. +Oligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. +Microglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response. +Despite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis. + DOI:10.1002/glia.24343 + DOI:10.1038/nn1988 + DOI:10.1101/cshperspect.a020602 + DOI:10.1126/science.aat0473 + DOI:10.3389/fncel.2017.00024 + @@ -6450,6 +6512,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6559,6 +6622,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6674,7 +6738,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -6704,19 +6768,20 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + + - + - A cell specialized to detect and transduce light. + A cell specialized in detecting light stimuli that are involved in visual perception. BTO:0001060 CALOHA:TS-0868 FBbt:00004211 @@ -6726,16 +6791,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different photoreceptor cell https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg - - - - - true - - A cell specialized to detect and transduce light. + A cell specialized in detecting light stimuli that are involved in visual perception. MESH:D010786 @@ -6866,6 +6925,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6897,6 +6957,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6930,6 +6991,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -7051,7 +7113,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -7060,11 +7122,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - Any cell that only exists in Eukaryota. + Any cell that in taxon some Eukaryota. MESH:D005057 eukaryotic cell @@ -7072,7 +7134,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - Any cell that only exists in Eukaryota. + Any cell that in taxon some Eukaryota. FBC:Autogenerated @@ -7092,6 +7154,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -7304,7 +7367,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -7342,6 +7405,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -7389,6 +7453,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -7447,7 +7512,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -7458,7 +7523,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -7819,6 +7884,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -7968,6 +8034,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -8064,6 +8131,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -8574,6 +8642,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -8783,6 +8852,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -9083,6 +9153,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -9438,6 +9509,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -9768,7 +9840,9 @@ radial glial cells acting as neural progenitors throughout life. + + @@ -9999,6 +10073,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -10043,6 +10118,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -10286,8 +10362,14 @@ radial glial cells acting as neural progenitors throughout life. A cell that is part of pigmented ciliary epithelium. This cell type uptakes sodium and chloride ions from stromal interstitium and passes the ions to non-pigmented ciliary epithelial cells via gap junctions. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Pigmented ciliary epithelial cells, which are a type of pigment cell, have a crucial function within the eye's ciliary body. The ciliary body, located behind the iris, is one of the eye’s most vital structures and consists of two types of epithelial cells: the pigmented and the non-pigmented ciliary epithelial cells. The pigmented ciliary epithelial cells form the outer layer of the ciliary body and exhibit a black or brown pigmentation due to the melanin they contain. +One key function of pigmented ciliary epithelial cells is to aid in the formation of aqueous humor, an intraocular fluid that nourishes the cornea and lens, and maintains intraocular pressure which is essential for the eye’s shape and light refraction. These cells facilitate this function in conjunction with the non-pigmented ciliary epithelial cells. Together, the pigmented and non-pigmented ciliary epithelial cells form a bilayer epithelium that allows the secretion of aqueous humor through a bi-directional fluid transport mechanism. +Pigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, a physiological frontier that controls the entry and exit of various substances from the blood to the aqueous humor and vice versa. The pigmentation in these cells, intensified by melanin, helps to absorb scattered light coming into the eye, reducing any potential damage and glare. 2010-09-13T04:09:27Z FMA:70606 + https://cellxgene.cziscience.com/cellguide/CL_0002303 PE cell @@ -10301,6 +10383,17 @@ radial glial cells acting as neural progenitors throughout life. A cell that is part of pigmented ciliary epithelium. This cell type uptakes sodium and chloride ions from stromal interstitium and passes the ions to non-pigmented ciliary epithelial cells via gap junctions. PMID:15106942 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Pigmented ciliary epithelial cells, which are a type of pigment cell, have a crucial function within the eye's ciliary body. The ciliary body, located behind the iris, is one of the eye’s most vital structures and consists of two types of epithelial cells: the pigmented and the non-pigmented ciliary epithelial cells. The pigmented ciliary epithelial cells form the outer layer of the ciliary body and exhibit a black or brown pigmentation due to the melanin they contain. +One key function of pigmented ciliary epithelial cells is to aid in the formation of aqueous humor, an intraocular fluid that nourishes the cornea and lens, and maintains intraocular pressure which is essential for the eye’s shape and light refraction. These cells facilitate this function in conjunction with the non-pigmented ciliary epithelial cells. Together, the pigmented and non-pigmented ciliary epithelial cells form a bilayer epithelium that allows the secretion of aqueous humor through a bi-directional fluid transport mechanism. +Pigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, a physiological frontier that controls the entry and exit of various substances from the blood to the aqueous humor and vice versa. The pigmentation in these cells, intensified by melanin, helps to absorb scattered light coming into the eye, reducing any potential damage and glare. + DOI:10.1016/S1569-2590(05)10005-6 + DOI:10.1111/j.1444-0938.2002.tb02384.x + @@ -10381,7 +10474,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -10420,7 +10513,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -10575,7 +10668,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -10602,32 +10695,6 @@ radial glial cells acting as neural progenitors throughout life. - - - - - An endothelial progenitor cell that participates in angiogenesis during development. - - 2011-02-28T04:20:39Z - ZFA:0005773 - See CL:0002619. - embryonic blood vessel endothelial progenitor cell - - - - - An endothelial progenitor cell that participates in angiogenesis during development. - GOC:tfm - - - - - ZFA:0005773 - - - - - @@ -10698,7 +10765,13 @@ radial glial cells acting as neural progenitors throughout life. A blood vessel endothelial cell that is part of the retina. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Retinal blood vessel endothelial cells constitute the innermost lining of the blood vessels found in the retina, the light-sensitive layer of tissue at the back of the eye. The primary role of these cells revolves around their location within the retinal vascular system, forming the structure of the blood-retinal barrier, a subset of the larger blood-ocular barrier system. +The endothelial cells are particularly involved in the growth of new retinal blood vessels from pre-existing ones (angiogenesis); this is critical in managing the amount of oxygen and essential nutrients delivered to the ocular tissues. They are crucial for maintaining homeostasis in the retinal environment by controlling the exchange of molecules between the blood and the retina. Furthermore, they mediate immune cell trafficking, supporting the immune privilege of the eye by preventing the unrestricted infiltration of inflammatory cells into the retina, thus maintaining ocular health and normal vision. +The malfunction or dysfunction of retinal blood vessel endothelial cells is implicated in numerous ocular pathologies, particularly diabetic retinopathy, which is one of the leading causes of blindness worldwide. In such conditions, the compromise in the integrity of the blood-retinal barrier and excess angiogenesis can lead to retinal edema and pathological neovascularization, resulting in vision loss. 2011-03-06T03:28:27Z + https://cellxgene.cziscience.com/cellguide/CL_0002585 @@ -10716,6 +10789,19 @@ radial glial cells acting as neural progenitors throughout life. A blood vessel endothelial cell that is part of the retina. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Retinal blood vessel endothelial cells constitute the innermost lining of the blood vessels found in the retina, the light-sensitive layer of tissue at the back of the eye. The primary role of these cells revolves around their location within the retinal vascular system, forming the structure of the blood-retinal barrier, a subset of the larger blood-ocular barrier system. +The endothelial cells are particularly involved in the growth of new retinal blood vessels from pre-existing ones (angiogenesis); this is critical in managing the amount of oxygen and essential nutrients delivered to the ocular tissues. They are crucial for maintaining homeostasis in the retinal environment by controlling the exchange of molecules between the blood and the retina. Furthermore, they mediate immune cell trafficking, supporting the immune privilege of the eye by preventing the unrestricted infiltration of inflammatory cells into the retina, thus maintaining ocular health and normal vision. +The malfunction or dysfunction of retinal blood vessel endothelial cells is implicated in numerous ocular pathologies, particularly diabetic retinopathy, which is one of the leading causes of blindness worldwide. In such conditions, the compromise in the integrity of the blood-retinal barrier and excess angiogenesis can lead to retinal edema and pathological neovascularization, resulting in vision loss. + DOI:0.1016/j.preteyeres.2015.08.001 + DOI:10.1016/j.preteyeres.2012.08.004 + DOI:10.1038/nature04482 + DOI:10.5301/EJO.2010.6049 + @@ -10751,9 +10837,16 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell of the retinal pigmented epithelium. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Retinal pigment epithelial (RPE) cells form a single layer of cells at the back of the eye sandwiched between the neurosensory retina and the choroid, playing a significant role in maintaining vision health. These pigment-laden cells are highly specialized and perform an array of metabolic and transport functions essential for the maintenance of the photoreceptor cells (rods and cones) in the retina. The pigmentation of RPE cells actively aids in the absorption of excess light and the prevention of light scattering, thus enhancing the eye's optical properties. +The retinal pigment epithelium forms a key part of the blood/retina barrier. The cells have long sheet-like microvilli on their apical membrane that project into the light-sensitive outer segments of the photoreceptors, forming a close structural interaction. The basolateral membrane of the RPE interacts with the underlying Bruch’s membrane, which separates the RPE cells from fenestrated endothelium of the choriocapillaris. +RPE cells support the photoreceptor by providing them with oxygen and nutrients (such as glucose, retinol and fatty acids) and removing waste products. They also recycle the visual pigment, in a process called the "visual cycle", where the RPE cells play a vital role in the regeneration of visual pigment (11-cis retinol) following the absorption of light. This is essential for the maintenance of photoreceptor excitability. +Beyond this, RPE cells take part in the phagocytosis process, where they digest the shed ends of photoreceptor outer segments, thus, preventing the build-up of waste residue that could otherwise harm retinal health. They also secrete various factors, including growth factors required to maintain the structural integrity of choriocapillaris endothelium and photoreceptors, as well as immunosuppressive factors that play an important role in establishing the immune privilege of the eye. 2011-03-06T03:37:09Z BTO:0004910 FMA:75802 + https://cellxgene.cziscience.com/cellguide/CL_0002586 @@ -10765,6 +10858,20 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell of the retinal pigmented epithelium. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Retinal pigment epithelial (RPE) cells form a single layer of cells at the back of the eye sandwiched between the neurosensory retina and the choroid, playing a significant role in maintaining vision health. These pigment-laden cells are highly specialized and perform an array of metabolic and transport functions essential for the maintenance of the photoreceptor cells (rods and cones) in the retina. The pigmentation of RPE cells actively aids in the absorption of excess light and the prevention of light scattering, thus enhancing the eye's optical properties. +The retinal pigment epithelium forms a key part of the blood/retina barrier. The cells have long sheet-like microvilli on their apical membrane that project into the light-sensitive outer segments of the photoreceptors, forming a close structural interaction. The basolateral membrane of the RPE interacts with the underlying Bruch’s membrane, which separates the RPE cells from fenestrated endothelium of the choriocapillaris. +RPE cells support the photoreceptor by providing them with oxygen and nutrients (such as glucose, retinol and fatty acids) and removing waste products. They also recycle the visual pigment, in a process called the "visual cycle", where the RPE cells play a vital role in the regeneration of visual pigment (11-cis retinol) following the absorption of light. This is essential for the maintenance of photoreceptor excitability. +Beyond this, RPE cells take part in the phagocytosis process, where they digest the shed ends of photoreceptor outer segments, thus, preventing the build-up of waste residue that could otherwise harm retinal health. They also secrete various factors, including growth factors required to maintain the structural integrity of choriocapillaris endothelium and photoreceptors, as well as immunosuppressive factors that play an important role in establishing the immune privilege of the eye. + DOI:10.1111/febs.16018 + DOI:10.1152/physrev.00021.2004 + DOI:10.3389/fphar.2021.727870/full + https://www.sciencedirect.com/topics/chemistry/retinal-pigment + @@ -10955,6 +11062,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -11063,19 +11171,19 @@ radial glial cells acting as neural progenitors throughout life. - + Any photoreceptor cell that is part of some camera-type eye. camera type eye photoreceptor cell camera-type eye photoreceptor cell - + - + https://github.com/obophenotype/cell-ontology/issues/2245 @@ -11105,6 +11213,12 @@ radial glial cells acting as neural progenitors throughout life. A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. +After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. +Disorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis. + https://cellxgene.cziscience.com/cellguide/CL_0011012 neural crest cell @@ -11115,6 +11229,19 @@ radial glial cells acting as neural progenitors throughout life. https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-9900-7880 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. +After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. +Disorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis. + DOI:10.1002/dvg.23276 + DOI:10.1242/dev.193193 + DOI:10.3389/fcell.2020.00635/full + https://doi.org/10.1016/j.ydbio.2011.12.042 + @@ -11132,6 +11259,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -11641,7 +11769,7 @@ plexiform layer. - + @@ -11649,6 +11777,7 @@ plexiform layer. The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome. + https://github.com/geneontology/go-ontology/issues/28301 GO:0000789 GO:0000790 GO:0005717 @@ -12409,32 +12538,32 @@ plexiform layer. - - + + A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. Wikipedia:Collagen cellular_component GO:0005581 collagen trimer - + - + - + PMID:12382326 - + PMID:12382326 @@ -12744,12 +12873,7 @@ plexiform layer. - - - - - - + @@ -14948,6 +15072,9 @@ plexiform layer. The self-renewing division of a stem cell. A stem cell is an undifferentiated cell, in the embryo or adult, that can undergo unlimited division and give rise to one or several different cell types. + + + stem cell renewal biological_process GO:0017145 @@ -16375,12 +16502,7 @@ plexiform layer. - - - - - - + A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. GO:0043234 @@ -16410,33 +16532,6 @@ plexiform layer. - - - - - A macromolecular complex containing both protein and DNA molecules. - DNA-protein complex - cellular_component - GO:0032993 - - Note that this term is intended to classify complexes that have DNA as one of the members of the complex, that is, the complex does not exist if DNA is not present. Protein complexes that interact with DNA e.g. transcription factor complexes should not be classified here. - protein-DNA complex - - - - - A macromolecular complex containing both protein and DNA molecules. - GOC:mah - - - - - DNA-protein complex - GOC:mah - - - - @@ -17156,10 +17251,12 @@ plexiform layer. Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. + https://github.com/geneontology/go-ontology/issues/28153 NIF_Subcellular:sao414196390 membrane-enclosed organelle cellular_component GO:0043227 + membrane-bounded organelle @@ -17177,11 +17274,13 @@ plexiform layer. Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. https://github.com/geneontology/go-ontology/issues/21881 + https://github.com/geneontology/go-ontology/issues/28153 NIF_Subcellular:sao1456184038 non-membrane-enclosed organelle cellular_component biological condensate GO:0043228 + non-membrane-bounded organelle @@ -17217,8 +17316,10 @@ plexiform layer. Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. + https://github.com/geneontology/go-ontology/issues/28153 cellular_component GO:0043229 + intracellular organelle @@ -17535,10 +17636,12 @@ plexiform layer. A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component. + https://github.com/geneontology/go-ontology/issues/27194 GO:0071843 cellular component biogenesis at cellular level biological_process GO:0044085 + cellular component biogenesis @@ -18525,6 +18628,49 @@ plexiform layer. + + + + + + + + + + + + + + + + + + + + + + The series of events involved in visual perception in which a light stimulus is received and converted into a molecular signal. + sensory detection of light during visual perception + sensory detection of light stimulus during visual perception + sensory transduction of light during visual perception + sensory transduction of light stimulus during visual perception + visual perception, detection of light stimulus + visual perception, sensory transduction during perception of light + visual perception, sensory transduction of light stimulus + biological_process + GO:0050908 + detection of light stimulus involved in visual perception + + + + + The series of events involved in visual perception in which a light stimulus is received and converted into a molecular signal. + GOC:ai + GOC:dos + + + + @@ -20063,6 +20209,7 @@ plexiform layer. + @@ -22809,7 +22956,7 @@ plexiform layer. A quality of a single cell inhering in the bearer by virtue of the bearer's size or shape or structure. - ORCID:0000-0002-7073-9172 + https://orcid.org/0000-0002-7073-9172 @@ -22969,7 +23116,7 @@ plexiform layer. - + @@ -24035,51 +24182,51 @@ plexiform layer. - + - + - A molecular entity that minimally consists of a protein. + A material entity that minimally consists of a protein. protein protein aggregate protein complex protein-containing complex protein - PR:000064867 - Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). - protein-containing molecular entity + PR:000050567 + Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566). + protein-containing material entity - + - A molecular entity that minimally consists of a protein. + A material entity that minimally consists of a protein. PRO:DAN - + protein PRO:DAN - + protein aggregate PRO:DAN - + protein complex PRO:DAN - + protein-containing complex PRO:DAN @@ -24422,7 +24569,7 @@ plexiform layer. - + @@ -24498,6 +24645,7 @@ plexiform layer. + @@ -25103,7 +25251,7 @@ plexiform layer. - + @@ -25160,7 +25308,7 @@ plexiform layer. - + The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm. merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube) EHDAA2:0001968 @@ -25183,7 +25331,7 @@ plexiform layer. external ectoderm http://upload.wikimedia.org/wikipedia/commons/1/1d/Ectoderm.png - + @@ -25196,7 +25344,7 @@ plexiform layer. - + EHDAA2 @@ -25545,7 +25693,7 @@ plexiform layer. - + @@ -25554,7 +25702,7 @@ plexiform layer. - + @@ -25581,14 +25729,14 @@ plexiform layer. gastrula stage - + - + BILS @@ -25660,7 +25808,7 @@ plexiform layer. - + @@ -25703,7 +25851,7 @@ plexiform layer. - + @@ -25788,7 +25936,7 @@ plexiform layer. - + @@ -25812,7 +25960,7 @@ plexiform layer. - + @@ -25829,7 +25977,7 @@ plexiform layer. - + @@ -25989,6 +26137,7 @@ plexiform layer. + @@ -25996,15 +26145,15 @@ plexiform layer. - + - - + + A fluid that is composed of blood plasma and erythrocytes. AAO:0000046 @@ -26041,34 +26190,34 @@ plexiform layer. blood - + - + - + - + CL:tm - + https://github.com/obophenotype/uberon/issues/1330 - + Bgee:AN @@ -26118,7 +26267,7 @@ plexiform layer. - + @@ -26223,7 +26372,7 @@ plexiform layer. - + @@ -27140,6 +27289,7 @@ plexiform layer. + @@ -27153,7 +27303,7 @@ plexiform layer. - + @@ -27195,14 +27345,14 @@ plexiform layer. epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg - - + + - + http://palaeos.com/metazoa/porifera/homoscleromorpha.html @@ -27633,7 +27783,7 @@ plexiform layer. - + @@ -27724,7 +27874,7 @@ plexiform layer. - + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. AAO:0000137 BILA:0000036 @@ -27759,14 +27909,14 @@ plexiform layer. ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png - + - + Bgee:AN @@ -27806,7 +27956,7 @@ plexiform layer. - + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. AAO:0000139 BILA:0000038 @@ -27841,14 +27991,14 @@ plexiform layer. http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png - + - + Bgee:AN @@ -27889,7 +28039,7 @@ plexiform layer. - + The middle germ layer of the embryo, between the endoderm and ectoderm. UBERON:0003263 @@ -27930,14 +28080,14 @@ plexiform layer. mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png - + - + Bgee:AN @@ -27992,7 +28142,7 @@ plexiform layer. - + @@ -28125,7 +28275,7 @@ plexiform layer. - + @@ -28187,14 +28337,14 @@ plexiform layer. cranial nerve II - + - + EHDAA2 @@ -28304,7 +28454,7 @@ plexiform layer. - + @@ -28313,7 +28463,7 @@ plexiform layer. - + @@ -28375,14 +28525,14 @@ plexiform layer. https://cdn.humanatlas.io/digital-objects/ref-organ/heart-female/v1.3/assets/3d-vh-f-heart.glb https://cdn.humanatlas.io/digital-objects/ref-organ/heart-male/v1.3/assets/3d-vh-m-heart.glb - + - + MA @@ -28424,7 +28574,7 @@ plexiform layer. - + @@ -28443,7 +28593,7 @@ plexiform layer. - + The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. requires review for applicability to invertebrate structures, e.g. synganglion @@ -28502,11 +28652,11 @@ plexiform layer. https://cdn.humanatlas.io/digital-objects/ref-organ/brain-female/v1.4/assets/3d-allen-f-brain.glb https://cdn.humanatlas.io/digital-objects/ref-organ/brain-male/v1.4/assets/3d-allen-m-brain.glb - + - + @@ -28519,13 +28669,13 @@ plexiform layer. - + FMA - + Bgee:AN @@ -28775,11 +28925,12 @@ plexiform layer. + - - - + + + @@ -28863,34 +29014,34 @@ plexiform layer. cornea http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + - + - + MA - + MA - + FMA-isa @@ -29067,10 +29218,10 @@ plexiform layer. - - - - + + + + The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. @@ -29118,44 +29269,44 @@ plexiform layer. retina http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png - + - + - + - + - + FMA - + FMA - + FMA - + EHDAA2 @@ -29210,8 +29361,8 @@ plexiform layer. - - + + @@ -29243,24 +29394,24 @@ plexiform layer. eye - + - + - + PMID:21062451 - + PMID:21062451 @@ -29472,7 +29623,7 @@ plexiform layer. - + @@ -29627,7 +29778,7 @@ plexiform layer. - + @@ -29649,14 +29800,13 @@ plexiform layer. - + The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]. - AAO:0000324 BILA:0000079 BIRNLEX:844 @@ -29691,7 +29841,6 @@ plexiform layer. UBERON:0001016 - @@ -29699,14 +29848,14 @@ plexiform layer. http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png - + - + Bgee:AN @@ -29768,11 +29917,11 @@ plexiform layer. - + - + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. @@ -29817,7 +29966,7 @@ plexiform layer. central nervous system - + @@ -29831,7 +29980,7 @@ plexiform layer. - + Bgee:AN @@ -30484,7 +30633,7 @@ plexiform layer. - + Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. Wikipedia: The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri). AEO:0000111 BTO:0002422 @@ -30509,14 +30658,14 @@ plexiform layer. mesothelium http://upload.wikimedia.org/wikipedia/commons/2/25/Mesothelium_peritoneal_wash_high_mag.jpg - + - + FMA @@ -30541,7 +30690,7 @@ plexiform layer. - + @@ -30796,7 +30945,7 @@ plexiform layer. - + @@ -30806,7 +30955,7 @@ plexiform layer. - + A tube extending from the mouth to the anus. @@ -30843,14 +30992,14 @@ plexiform layer. digestive tract - + - + NCBIBook:NBK10107 @@ -30905,7 +31054,7 @@ plexiform layer. - + The ciliary muscle is a ring of smooth muscle in the middle layer of the eye that controls the eye's accommodation for viewing objects at varying distances and regulates the flow of aqueous humour through Schlemm's canal. [WP,unvetted]. BTO:0000654 @@ -30928,7 +31077,7 @@ plexiform layer. ciliary muscle http://upload.wikimedia.org/wikipedia/commons/2/28/Gray872.png - + @@ -30947,7 +31096,7 @@ plexiform layer. - + FMA @@ -31065,7 +31214,7 @@ plexiform layer. - + @@ -31111,14 +31260,14 @@ plexiform layer. eyelid https://upload.wikimedia.org/wikipedia/commons/8/84/Eye_makeup.jpg - + - + multiple @@ -31384,7 +31533,7 @@ plexiform layer. - + @@ -31423,14 +31572,14 @@ plexiform layer. iris - + - + XAO @@ -31484,7 +31633,7 @@ plexiform layer. - + @@ -31533,14 +31682,14 @@ plexiform layer. corneal epithelium http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png - + - + ISBN:0781772214 @@ -31628,15 +31777,15 @@ plexiform layer. - - + + - + @@ -31671,34 +31820,34 @@ plexiform layer. sclera http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + - + - + FMA - + ZFA - + ISBN:0781772214 @@ -31740,7 +31889,7 @@ plexiform layer. - + @@ -31778,14 +31927,14 @@ plexiform layer. ciliary body http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + ISBN:0781772214 @@ -31823,14 +31972,14 @@ plexiform layer. - + - + @@ -31891,24 +32040,24 @@ plexiform layer. optic choroid http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + - + MA - + Wikipedia @@ -32101,9 +32250,9 @@ plexiform layer. - - - + + + A double layer covering the ciliary body that produces aqueous humor. BTO:0001770 @@ -32123,15 +32272,15 @@ plexiform layer. ciliary epithelium - + - + - + @@ -32144,19 +32293,19 @@ plexiform layer. - + MA - + MP - + Wikipedia @@ -32272,7 +32421,7 @@ plexiform layer. - + @@ -32330,14 +32479,14 @@ plexiform layer. pigmented layer of retina http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png - + - + Wikipedia @@ -32413,7 +32562,7 @@ plexiform layer. - + @@ -32445,14 +32594,14 @@ plexiform layer. photoreceptor layer of retina http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png - + - + ZFA @@ -32945,7 +33094,7 @@ plexiform layer. - + @@ -33001,7 +33150,7 @@ plexiform layer. ganglionic layer of retina http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png - + @@ -33014,7 +33163,7 @@ plexiform layer. - + FMA @@ -33068,7 +33217,7 @@ plexiform layer. - + @@ -33123,14 +33272,14 @@ plexiform layer. nerve fiber layer of retina - + - + FMA @@ -33820,7 +33969,7 @@ plexiform layer. - + @@ -33852,14 +34001,14 @@ plexiform layer. anterior segment of eyeball http://upload.wikimedia.org/wikipedia/commons/b/ba/Cataract_in_human_eye.png - + - + FMA @@ -33903,7 +34052,7 @@ plexiform layer. - + @@ -33933,14 +34082,14 @@ plexiform layer. posterior segment of eyeball http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + FMA @@ -33977,9 +34126,9 @@ plexiform layer. - - - + + + @@ -34027,15 +34176,15 @@ plexiform layer. conjunctiva http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png - + - + - + @@ -34048,19 +34197,19 @@ plexiform layer. - + cjm - + MA - + ISBN:0781772214 @@ -34218,7 +34367,7 @@ plexiform layer. - + The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO]. developmental relationships need revised @@ -34264,14 +34413,14 @@ plexiform layer. midbrain http://upload.wikimedia.org/wikipedia/commons/f/f9/Human_brain_inferior_view_description.JPG - + - + Bgee:AN @@ -34742,7 +34891,7 @@ plexiform layer. - + Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP]. MTg @@ -34781,14 +34930,14 @@ plexiform layer. midbrain tegmentum http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray712.png - + - + ZFA @@ -34874,6 +35023,7 @@ plexiform layer. + @@ -34948,6 +35098,7 @@ plexiform layer. + @@ -34956,8 +35107,8 @@ plexiform layer. - - + + @@ -34970,7 +35121,7 @@ plexiform layer. - + @@ -35024,34 +35175,34 @@ plexiform layer. blood vessel http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg - + - + - + - + AEO - + EHDAA2 - + GO:0072360 @@ -35208,7 +35359,7 @@ plexiform layer. - + @@ -35370,7 +35521,7 @@ plexiform layer. - + @@ -35380,7 +35531,7 @@ plexiform layer. - + The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA]. @@ -35423,14 +35574,14 @@ plexiform layer. hindbrain http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg - + - + Bgee:AN @@ -35921,7 +36072,7 @@ plexiform layer. - + @@ -36061,7 +36212,7 @@ plexiform layer. - + Vasculature that is part of the eye region. FMA:74743 @@ -36083,14 +36234,14 @@ plexiform layer. https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-female/v1.3/assets/3d-vh-f-blood-vasculature.glb https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-male/v1.3/assets/3d-vh-m-blood-vasculature.glb - + - + ISBN:0781772214 @@ -36294,7 +36445,7 @@ plexiform layer. - + @@ -36368,14 +36519,14 @@ plexiform layer. https://cdn.humanatlas.io/digital-objects/ref-organ/spinal-cord-female/v1.1/assets/3d-vh-f-spinal-cord.glb https://cdn.humanatlas.io/digital-objects/ref-organ/spinal-cord-male/v1.1/assets/3d-vh-m-spinal-cord.glb - + - + ZFA @@ -36830,9 +36981,9 @@ plexiform layer. - - - + + + @@ -36880,15 +37031,15 @@ plexiform layer. notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - - + + - + - + @@ -36907,19 +37058,19 @@ plexiform layer. - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -36959,8 +37110,8 @@ plexiform layer. - - + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. mesodermal cluster @@ -36998,11 +37149,11 @@ plexiform layer. somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - - + + - + @@ -37015,13 +37166,13 @@ plexiform layer. - + GOTAX:0000352 - + ZFA @@ -37083,22 +37234,22 @@ plexiform layer. - + - + - - + + - + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. AAO:0010578 BTO:0001764 @@ -37131,45 +37282,45 @@ plexiform layer. http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - + BTO - + PMID:11523831 - + PMID:11523831 @@ -37290,7 +37441,7 @@ plexiform layer. - + @@ -37381,7 +37532,7 @@ plexiform layer. - + @@ -37455,10 +37606,10 @@ plexiform layer. - + - + @@ -37508,14 +37659,14 @@ plexiform layer. hematopoietic system - + - + FMA @@ -37555,8 +37706,8 @@ plexiform layer. - - + + @@ -37582,11 +37733,11 @@ plexiform layer. iris epithelium - + - + @@ -37599,13 +37750,13 @@ plexiform layer. - + MA - + MP @@ -37744,7 +37895,7 @@ plexiform layer. - + Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic. Do not merge with neurogenic placode ectodermal placode @@ -37761,8 +37912,8 @@ plexiform layer. cranial placode - - + + @@ -37774,7 +37925,7 @@ plexiform layer. - + PMID:11523831 PMID:22512454 @@ -37974,7 +38125,7 @@ plexiform layer. - + @@ -37987,7 +38138,7 @@ plexiform layer. - + The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate. consider adding class for organizer. Consider adding separate class for isthmus as a structure AAO:0011064 @@ -38016,24 +38167,24 @@ plexiform layer. midbrain-hindbrain boundary - + - + - + ZFA - + ZFA @@ -38155,7 +38306,7 @@ plexiform layer. - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. AAO:0011086 EFO:0001982 @@ -38178,14 +38329,14 @@ plexiform layer. presomitic mesoderm - + - + Bgee:AN @@ -38291,7 +38442,7 @@ plexiform layer. - + @@ -38352,7 +38503,7 @@ plexiform layer. - + @@ -38389,7 +38540,7 @@ plexiform layer. eye primordium - + @@ -38402,7 +38553,7 @@ plexiform layer. - + PMID:16496288 XAO @@ -38452,8 +38603,8 @@ plexiform layer. - - + + @@ -38481,24 +38632,24 @@ plexiform layer. optic cup - + - + - + ZFA - + ZFA @@ -38554,7 +38705,7 @@ plexiform layer. - + @@ -38592,7 +38743,7 @@ plexiform layer. lens placode http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png - + @@ -38605,7 +38756,7 @@ plexiform layer. - + ZFA @@ -38644,9 +38795,9 @@ plexiform layer. - - - + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. AAO:0011072 BTO:0001765 @@ -38675,34 +38826,34 @@ plexiform layer. neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - - + + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -38777,7 +38928,7 @@ plexiform layer. - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. AAO:0010568 EFO:0003515 @@ -38803,7 +38954,7 @@ plexiform layer. paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -38816,7 +38967,7 @@ plexiform layer. - + Bgee:AN @@ -38892,10 +39043,10 @@ plexiform layer. - + - + @@ -38932,7 +39083,7 @@ plexiform layer. lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -38945,7 +39096,7 @@ plexiform layer. - + EHDAA2 VHOG @@ -38995,15 +39146,15 @@ plexiform layer. - - + + - + Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. should probably be merged with heart rudiment. AAO:0011044 @@ -39020,15 +39171,15 @@ plexiform layer. heart primordium - + - + - + @@ -39041,19 +39192,19 @@ plexiform layer. - + ZFA - + ZFA - + XAO @@ -39082,8 +39233,8 @@ plexiform layer. - - + + Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. AAO:0010571 AEO:0000212 @@ -39107,11 +39258,11 @@ plexiform layer. sclerotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - - + + - + @@ -39130,13 +39281,13 @@ plexiform layer. - + VHOG:0000680 - + ZFA @@ -39367,7 +39518,7 @@ plexiform layer. - + @@ -39457,7 +39608,7 @@ plexiform layer. - + Mesenchyme that is part of a developing camera-type eye. TODO - change mesenchyme relationships to precursor_of EHDAA2:0000485 @@ -39469,14 +39620,14 @@ plexiform layer. UBERON:0003314 eye mesenchyme - + - + EHDAA2 @@ -40251,7 +40402,7 @@ plexiform layer. - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults EHDAA:251 @@ -40266,14 +40417,14 @@ plexiform layer. intraembryonic coelom - + - + Wikipedia @@ -40304,7 +40455,7 @@ plexiform layer. - + @@ -40366,7 +40517,7 @@ plexiform layer. - + The part of the retina that contains neurons and photoreceptor cells[GO]. AAO:0011095 @@ -40397,14 +40548,14 @@ plexiform layer. retinal neural layer - + - + Bgee:AN @@ -40657,7 +40808,7 @@ plexiform layer. - + The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium. consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure ependymal layer @@ -40674,7 +40825,7 @@ plexiform layer. neural tube ventricular layer - + @@ -40687,7 +40838,7 @@ plexiform layer. - + NCBIBook:NBK10047 @@ -41089,9 +41240,9 @@ plexiform layer. - - - + + + @@ -41123,34 +41274,34 @@ plexiform layer. optic vesicle http://upload.wikimedia.org/wikipedia/commons/e/e0/Gray863.png - + - + - + - + ZFA - + GO-def - + ZFA @@ -41246,8 +41397,8 @@ plexiform layer. - - + + A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. XAO:0004185 first heart field @@ -41259,24 +41410,24 @@ plexiform layer. UBERON:0004140 primary heart field - + - + - + GO:0003128 - + https://orcid.org/0000-0003-3308-6245 @@ -41329,7 +41480,7 @@ plexiform layer. - + An epithelial tube that will give rise to the mature heart. AAO:0010411 EFO:0003526 @@ -41348,14 +41499,14 @@ plexiform layer. heart tube - + - + ZFA-modified @@ -41432,7 +41583,7 @@ plexiform layer. - + @@ -41448,14 +41599,14 @@ plexiform layer. eye muscle - + - + MA @@ -41638,7 +41789,7 @@ plexiform layer. - + A transparent homogeneous acellular layer found between the substantia propria and the endothelial layer of the cornea[MP]. EMAPA:18804 @@ -41667,14 +41818,14 @@ plexiform layer. Descemet's membrane https://github.com/obophenotype/uberon/issues/15 - + - + Cline et al @@ -41933,6 +42084,7 @@ plexiform layer. + @@ -42029,6 +42181,7 @@ plexiform layer. + @@ -42424,7 +42577,7 @@ plexiform layer. - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. AAO:0011129 TAO:0001890 @@ -42438,14 +42591,14 @@ plexiform layer. skeletal element - + - + VSAO @@ -42472,10 +42625,10 @@ plexiform layer. - + - + @@ -42511,14 +42664,14 @@ plexiform layer. UBERON:0004770 articular system - + - + FMA @@ -42677,7 +42830,7 @@ plexiform layer. - + @@ -42843,7 +42996,7 @@ plexiform layer. - + @@ -43038,7 +43191,7 @@ plexiform layer. - + @@ -43370,7 +43523,7 @@ plexiform layer. - + Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells. EFO:0003492 EHDAA2:0000732 @@ -43391,14 +43544,14 @@ plexiform layer. head mesenchyme - + - + EHDAA2 @@ -43456,7 +43609,7 @@ plexiform layer. - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -43472,14 +43625,14 @@ plexiform layer. trunk mesenchyme - + - + EHDAA2 @@ -43994,7 +44147,7 @@ plexiform layer. - + Portion of tissue that is part of the eye and gives rise to the mature, fully layered cornea. TAO:0002188 ZFA:0001688 @@ -44002,7 +44155,7 @@ plexiform layer. UBERON:0005427 corneal primordium - + @@ -44021,7 +44174,7 @@ plexiform layer. - + ZFA @@ -44044,7 +44197,7 @@ plexiform layer. - + Multi-tissue structure that arises from the heart rudiment and will become the heart tube. EHDAA2:0001512 EHDAA:424 @@ -44062,14 +44215,14 @@ plexiform layer. primitive heart tube - + - + ZFA @@ -44160,6 +44313,7 @@ plexiform layer. + @@ -44175,7 +44329,7 @@ plexiform layer. - + @@ -44259,7 +44413,7 @@ plexiform layer. - + A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 @@ -44269,7 +44423,7 @@ plexiform layer. UBERON:0005856 developing mesenchymal condensation - + @@ -44288,7 +44442,7 @@ plexiform layer. - + AEO-modified-relation @@ -44309,6 +44463,7 @@ plexiform layer. + @@ -44345,8 +44500,8 @@ plexiform layer. - - + + @@ -44363,11 +44518,11 @@ plexiform layer. UBERON:0005908 conjunctival sac - + - + @@ -44380,13 +44535,13 @@ plexiform layer. - + FMA - + HPO:pr @@ -44578,7 +44733,7 @@ plexiform layer. - + @@ -44628,7 +44783,7 @@ plexiform layer. - + @@ -44651,14 +44806,14 @@ plexiform layer. future diencephalon - + - + EHDAA2 @@ -44834,7 +44989,7 @@ plexiform layer. - + @@ -44858,14 +45013,14 @@ plexiform layer. future spinal cord - + - + EHDAA2 @@ -44902,7 +45057,7 @@ plexiform layer. - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB EHDAA2:0001278 @@ -44916,7 +45071,7 @@ plexiform layer. notochordal plate - + @@ -44929,7 +45084,7 @@ plexiform layer. - + EHDAA2 @@ -44953,11 +45108,11 @@ plexiform layer. - + - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -44974,14 +45129,14 @@ plexiform layer. The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -45174,7 +45329,7 @@ plexiform layer. - + @@ -45226,7 +45381,7 @@ plexiform layer. - + @@ -45369,7 +45524,7 @@ plexiform layer. - + @@ -45433,7 +45588,7 @@ plexiform layer. - + @@ -45562,6 +45717,7 @@ plexiform layer. + @@ -46022,8 +46178,8 @@ plexiform layer. - - + + @@ -46049,24 +46205,24 @@ plexiform layer. presumptive hindbrain - + - + - + XAO-abduced - + cjm @@ -46117,7 +46273,7 @@ plexiform layer. - + @@ -46136,14 +46292,14 @@ plexiform layer. presumptive midbrain hindbrain boundary - + - + ZFA @@ -46289,7 +46445,7 @@ plexiform layer. - + @@ -46315,7 +46471,7 @@ plexiform layer. presumptive paraxial mesoderm - + @@ -46331,7 +46487,7 @@ plexiform layer. - + https://github.com/obophenotype/uberon/issues/1277 @@ -46413,7 +46569,7 @@ plexiform layer. - + A neural decussation that is part of a diencephalon. FMA:62446 diencephalon decussation @@ -46421,7 +46577,7 @@ plexiform layer. UBERON:0007425 decussation of diencephalon - + @@ -46434,7 +46590,7 @@ plexiform layer. - + Obol @@ -46509,7 +46665,7 @@ plexiform layer. - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -46517,7 +46673,7 @@ plexiform layer. UBERON:0007524 dense mesenchyme tissue - + @@ -46530,7 +46686,7 @@ plexiform layer. - + AEO @@ -46769,7 +46925,7 @@ plexiform layer. - + An axon tract that is part of a brain. the NIFSTD class 'nerve tract' is classified under 'regional part of brain', so it may seem like it belongs here, but actually includes spinal cord tracts FMA:83848 @@ -46779,14 +46935,14 @@ plexiform layer. UBERON:0007702 tract of brain - + - + cjm @@ -46814,7 +46970,7 @@ plexiform layer. - + Anatomical system that consists of all blood and lymph vessels. consider merging with vasculature @@ -46831,14 +46987,14 @@ plexiform layer. vascular system - + - + MA @@ -46959,7 +47115,7 @@ plexiform layer. - + @@ -46976,14 +47132,14 @@ plexiform layer. UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -47079,7 +47235,7 @@ plexiform layer. - + @@ -47095,14 +47251,14 @@ plexiform layer. UBERON:0009615 midbrain hindbrain boundary neural plate - + - + ZFA @@ -47135,14 +47291,14 @@ plexiform layer. - + - + @@ -47167,24 +47323,24 @@ plexiform layer. presumptive midbrain - + - + - + ZFA - + ZFA @@ -47230,7 +47386,7 @@ plexiform layer. - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -47238,14 +47394,14 @@ plexiform layer. UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -47268,7 +47424,7 @@ plexiform layer. - + EFO:0003704 TAO:0005041 ZFA:0005041 @@ -47278,14 +47434,14 @@ plexiform layer. anterior lateral plate mesoderm - + - + ZFA @@ -47341,14 +47497,14 @@ plexiform layer. - + EHDAA2:0001315 EHDAA:1122 uberon UBERON:0009920 optic neural crest - + @@ -47361,7 +47517,7 @@ plexiform layer. - + EHDAA2 @@ -47502,7 +47658,7 @@ plexiform layer. - + @@ -47525,14 +47681,14 @@ plexiform layer. eyeball of camera-type eye - + - + FMA @@ -47573,8 +47729,8 @@ plexiform layer. - - + + Portion of tissue that is dorsolateral to the floor plate and part of the midbrain. DHBA:12322 EFO:0003567 @@ -47588,11 +47744,11 @@ plexiform layer. midbrain basal plate - + - + @@ -47605,13 +47761,13 @@ plexiform layer. - + EHDAA2 - + ZFA @@ -47640,7 +47796,7 @@ plexiform layer. - + Portion of neural tube that gives rise to the midbrain. we follow ZFA in temporally dividing midbrain NT from presumptive midbrain, but in future this may be collapsed TAO:0007039 @@ -47649,14 +47805,14 @@ plexiform layer. UBERON:0010286 midbrain neural tube - + - + ZFA @@ -47959,8 +48115,8 @@ plexiform layer. - - + + Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. FMA:23879 SCTID:129140006 @@ -47972,11 +48128,11 @@ plexiform layer. subdivision of skeleton - + - + @@ -47989,13 +48145,13 @@ plexiform layer. - + UBERONREF:0000003 - + VSAO @@ -48056,7 +48212,7 @@ plexiform layer. - + Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. axial skeletal system FMA:302077 @@ -48066,7 +48222,7 @@ plexiform layer. postcranial axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton - + @@ -48079,7 +48235,7 @@ plexiform layer. - + cjm @@ -48201,7 +48357,7 @@ plexiform layer. - + AAO:0010038 EMAPA:18808 FMA:49150 @@ -48211,14 +48367,14 @@ plexiform layer. UBERON:0011222 intra-ocular muscle - + - + EMAPA @@ -48480,7 +48636,7 @@ plexiform layer. - + @@ -48522,7 +48678,7 @@ plexiform layer. anterior uvea - + @@ -48535,7 +48691,7 @@ plexiform layer. - + MP @@ -48577,7 +48733,7 @@ plexiform layer. - + @@ -48666,6 +48822,7 @@ plexiform layer. + @@ -48861,7 +49018,7 @@ plexiform layer. - + @@ -49090,7 +49247,7 @@ plexiform layer. - + @@ -49328,7 +49485,7 @@ plexiform layer. - + @@ -49351,7 +49508,7 @@ plexiform layer. UBERON:0016887 entire extraembryonic component - + @@ -49364,7 +49521,7 @@ plexiform layer. - + AEO @@ -49708,7 +49865,7 @@ plexiform layer. - + @@ -50350,6 +50507,454 @@ plexiform layer. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/ontology/subsets/eye_upper_slim.tsv b/src/ontology/subsets/eye_upper_slim.tsv index af5171f4d..114a1bbfa 100644 --- a/src/ontology/subsets/eye_upper_slim.tsv +++ b/src/ontology/subsets/eye_upper_slim.tsv @@ -1,315 +1,349 @@ ?x ?label -_:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid1001 -_:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid1016 -_:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid1022 -_:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid1031 -_:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid1037 -_:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid1043 -_:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid1051 -_:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid1058 -_:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid1065 -_:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid1074 -_:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid1088 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+_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid767 +_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid786 +_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid802 +_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid809 +_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid820 +_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid826 +_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid843 +_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid849 +_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid858 +_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid868 +_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid916 +_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid966 +_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid976 +_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid983 +_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid990 +_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid997 "cell" "neural crest derived fibroblast" "neuronal receptor cell" @@ -428,7 +462,6 @@ _:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid990 "keratocyte" "retinal melanocyte" "cardiocyte" - "embryonic blood vessel endothelial progenitor cell" "iris pigment epithelial cell" "retinal blood vessel endothelial cell" "retinal pigment epithelial cell" @@ -592,7 +625,6 @@ _:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid990 "secretion by cell" "protein-containing complex disassembly" "protein-containing complex" - "protein-DNA complex" "erythrocyte homeostasis" "monoatomic ion transmembrane transport" "tube formation" @@ -652,6 +684,7 @@ _:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid990 "nervous system process" "response to stimulus" "detection of stimulus involved in sensory perception" + "detection of light stimulus involved in visual perception" "sensory perception of light stimulus" "detection of light stimulus involved in sensory perception" "localization" @@ -842,7 +875,7 @@ _:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid990 "integrin alpha" "Mus musculus protein" "eukaryotic protein" - "protein-containing molecular entity" + "protein-containing material entity" "processual entity" "camera-type eye" "sense organ" diff --git a/src/ontology/subsets/general_cell_types_upper_slim.json b/src/ontology/subsets/general_cell_types_upper_slim.json index 31ba38f2e..6a4f6cb9e 100644 --- a/src/ontology/subsets/general_cell_types_upper_slim.json +++ b/src/ontology/subsets/general_cell_types_upper_slim.json @@ -4,9 +4,9 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-08-16" + "val" : "2024-09-26" } ], - "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-08-16/subsets/general_cell_types_upper_slim.owl" + "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-09-26/subsets/general_cell_types_upper_slim.owl" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/CL_0000000", @@ -41,24 +41,6 @@ "val" : "ZFA:0009000" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/CL_0000006", - "lbl" : "neuronal receptor cell", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any sensory receptor cell that is a(n) neuron and is capable of some detection of stimulus involved in sensory perception.", - "xrefs" : [ "FBC:Autogenerated" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "neuronal receptor cell (sensu Animalia)" - } ], - "xrefs" : [ { - "val" : "ZFA:0009001" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000007", "lbl" : "early embryonic cell (metazoa)", @@ -675,10 +657,15 @@ "val" : "BTO:0001433" }, { "val" : "ZFA:0009064" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000113" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nMononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. \nIn addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses.\nMononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer." } ] } }, { @@ -709,10 +696,15 @@ "val" : "FMA:54536" }, { "val" : "ZFA:0009073" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000125" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nGlial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons.\nThese different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning.\nOligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. \nMicroglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response.\nDespite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis." } ] } }, { @@ -1090,29 +1082,13 @@ "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/CL_0000197", - "lbl" : "sensory receptor cell", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A cell that is capable of detection of a stimulus involved in sensory perception." - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "receptor cell" - } ], - "xrefs" : [ { - "val" : "MESH:D011984" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000210", "lbl" : "photoreceptor cell", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A cell specialized to detect and transduce light.", + "val" : "A cell specialized in detecting light stimuli that are involved in visual perception.", "xrefs" : [ "MESH:D010786" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], @@ -1236,22 +1212,16 @@ "meta" : { "definition" : { "val" : "A cell with more than one nucleus.", - "xrefs" : [ "FB:ma" ] + "xrefs" : [ "FB:ma", "Wikipedia:Multinucleate" ] }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "syncitium" + "val" : "multinucleated cells", + "xrefs" : [ "Wikipedia:Multinucleate" ] }, { "pred" : "hasExactSynonym", - "val" : "syncytial cell" - }, { - "pred" : "hasExactSynonym", - "val" : "syncytium" - } ], - "xrefs" : [ { - "val" : "AEO:0000203" - }, { - "val" : "WBbt:0008074" + "val" : "polynuclear cells", + "xrefs" : [ "Wikipedia:Multinucleate" ] } ] } }, { @@ -1351,7 +1321,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "Any cell that only exists in Eukaryota.", + "val" : "Any cell that in taxon some Eukaryota.", "xrefs" : [ "FBC:Autogenerated" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], @@ -2731,15 +2701,17 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A transversely striated, synctial muscle cell, formed by the fusion of myoblasts.", + "val" : "A transversely striated, multinucleated syncytial muscle cell, formed by the fusion of myoblasts during muscle development.", "xrefs" : [ "GOC:dos", "GOC:tfm", "ISBN:0323052908", "PMID:22274696" ] }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "myotubule" + "val" : "myofiber", + "xrefs" : [ "FBbt:00005812" ] }, { "pred" : "hasExactSynonym", - "val" : "single cell sarcomere" + "val" : "myofibril", + "xrefs" : [ "FBbt:00005812" ] } ], "xrefs" : [ { "val" : "FBbt:00005812" @@ -2892,6 +2864,23 @@ "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_0008028", + "lbl" : "visual system neuron", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any neuron that is capable of part of some visual perception.", + "xrefs" : [ "FBC:Autogenerated" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-07-09T19:12:36Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/CL_0009004", "lbl" : "retinal cell", @@ -2944,7 +2933,14 @@ "val" : "A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells.", "xrefs" : [ "https://orcid.org/0000-0001-5208-3432", "https://orcid.org/0000-0002-9900-7880" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "xrefs" : [ { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0011012" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." + } ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0011026", @@ -3029,6 +3025,33 @@ "val" : "CALOHA:TS-2109" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_4052002", + "lbl" : "syncytial cell", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A multinucleate cell formed by the fusion of multiple uninuclear cells through plasma membrane fusion. This process leads to a single large cell containing multiple nuclei within a shared cytoplasm.", + "xrefs" : [ "PMID:20851884", "Wikipedia:Syncytium" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "syncytium", + "xrefs" : [ "WBbt:0008074" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", + "pred" : "hasRelatedSynonym", + "val" : "SC", + "xrefs" : [ "PMID:9067520" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0009-0000-8480-9277" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-08-15T10:38:46Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0000323", "lbl" : "lytic vacuole", @@ -3043,6 +3066,24 @@ "val" : "cellular_component" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0000768", + "lbl" : "syncytium formation by plasma membrane fusion", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells.", + "xrefs" : [ "GOC:mtg_muscle", "GOC:tb" ] + }, + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "cell fusion" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0000785", "lbl" : "chromatin", @@ -3067,6 +3108,9 @@ "val" : "NIF_Subcellular:sao1615953555" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28301" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "GO:0000789" }, { @@ -4768,6 +4812,21 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0006949", + "lbl" : "syncytium formation", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane. Syncytia are normally derived from single cells that fuse or fail to complete cell division.", + "xrefs" : [ "ISBN:0198506732" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0006955", "lbl" : "immune response", @@ -4826,6 +4885,29 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0007009", + "lbl" : "plasma membrane organization", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the plasma membrane.", + "xrefs" : [ "GOC:dph", "GOC:jl", "GOC:mah" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "plasma membrane organisation" + }, { + "pred" : "hasRelatedSynonym", + "val" : "plasma membrane organization and biogenesis", + "xrefs" : [ "GOC:mah" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0007154", "lbl" : "cell communication", @@ -5634,6 +5716,29 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0010256", + "lbl" : "endomembrane system organization", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endomembrane system.", + "xrefs" : [ "GOC:mah", "GOC:sm" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_drosophila" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "endomembrane organization" + }, { + "pred" : "hasExactSynonym", + "val" : "endomembrane system organisation", + "xrefs" : [ "GOC:mah" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0010324", "lbl" : "membrane invagination", @@ -5995,6 +6100,15 @@ "val" : "stem cell renewal" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_2" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_2157" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -7142,27 +7256,6 @@ "val" : "cellular_component" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0032993", - "lbl" : "protein-DNA complex", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A macromolecular complex containing both protein and DNA molecules.", - "xrefs" : [ "GOC:mah" ] - }, - "comments" : [ "Note that this term is intended to classify complexes that have DNA as one of the members of the complex, that is, the complex does not exist if DNA is not present. Protein complexes that interact with DNA e.g. transcription factor complexes should not be classified here." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "DNA-protein complex", - "xrefs" : [ "GOC:mah" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0033151", "lbl" : "V(D)J recombination", @@ -7640,6 +7733,7 @@ "val" : "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.", "xrefs" : [ "GOC:go_curators" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "membrane-enclosed organelle" @@ -7648,6 +7742,9 @@ "val" : "NIF_Subcellular:sao414196390" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28153" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -7661,7 +7758,7 @@ "val" : "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes.", "xrefs" : [ "GOC:go_curators" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_mouse" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_mouse" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "non-membrane-enclosed organelle" @@ -7675,6 +7772,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/21881" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28153" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -7689,8 +7789,11 @@ "val" : "Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.", "xrefs" : [ "GOC:go_curators" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_pir" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28153" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -7839,12 +7942,15 @@ "val" : "A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component.", "xrefs" : [ "GOC:jl", "GOC:mah" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_pir" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "cellular component biogenesis at cellular level" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/27194" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "GO:0071843" }, { @@ -7994,6 +8100,30 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0045026", + "lbl" : "plasma membrane fusion", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell.", + "xrefs" : [ "GOC:elh", "GOC:mtg_muscle" ] + }, + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "cell fusion" + }, { + "pred" : "hasBroadSynonym", + "val" : "cell-cell fusion" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0006947" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0045087", "lbl" : "innate immune response", @@ -8015,6 +8145,15 @@ "val" : "Wikipedia:Innate_immune_system" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_2" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_2157" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "GO:0002226" }, { @@ -8715,6 +8854,42 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0050908", + "lbl" : "detection of light stimulus involved in visual perception", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The series of events involved in visual perception in which a light stimulus is received and converted into a molecular signal.", + "xrefs" : [ "GOC:ai", "GOC:dos" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "sensory detection of light during visual perception" + }, { + "pred" : "hasExactSynonym", + "val" : "sensory detection of light stimulus during visual perception" + }, { + "pred" : "hasExactSynonym", + "val" : "sensory transduction of light during visual perception" + }, { + "pred" : "hasExactSynonym", + "val" : "sensory transduction of light stimulus during visual perception" + }, { + "pred" : "hasExactSynonym", + "val" : "visual perception, detection of light stimulus" + }, { + "pred" : "hasExactSynonym", + "val" : "visual perception, sensory transduction during perception of light" + }, { + "pred" : "hasExactSynonym", + "val" : "visual perception, sensory transduction of light stimulus" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0050953", "lbl" : "sensory perception of light stimulus", @@ -9938,6 +10113,36 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0140253", + "lbl" : "cell-cell fusion", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A cellular process in which two or more cells combine together, their plasma membrane fusing, producing a single cell. In some cases, nuclei fuse, producing a polyploid cell, while in other cases, nuclei remain separate, producing a syncytium.", + "xrefs" : [ "Wikipedia:Cell_fusion" ] + }, + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "cell fusion" + }, { + "pred" : "hasExactSynonym", + "val" : "cell cell fusion" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/15939" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "pg" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-08-13T18:38:18Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0140352", "lbl" : "export from cell", @@ -13541,15 +13746,15 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/PR_000064867", - "lbl" : "protein-containing molecular entity", + "id" : "http://purl.obolibrary.org/obo/PR_000050567", + "lbl" : "protein-containing material entity", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A molecular entity that minimally consists of a protein.", + "val" : "A material entity that minimally consists of a protein.", "xrefs" : [ "PRO:DAN" ] }, - "comments" : [ "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565)." ], + "comments" : [ "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566)." ], "synonyms" : [ { "pred" : "hasNarrowSynonym", "val" : "protein", @@ -16844,7 +17049,7 @@ "val" : "The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO].", "xrefs" : [ "BIRNLEX:844", "ISBN:0-14-051288-8", "ISBN:3110148986", "NLM:nervous+system", "WB:rynl", "Wikipedia:Nervous_system", "ZFIN:curator" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#cumbo", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#cumbo", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "neurological system", @@ -16917,9 +17122,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -22124,7 +22326,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000050", - "lbl" : "part_of", + "lbl" : "part of", "type" : "PROPERTY", "propertyType" : "OBJECT", "meta" : { @@ -22147,9 +22349,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "part_of" @@ -22169,7 +22368,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000051", - "lbl" : "has_part", + "lbl" : "has part", "type" : "PROPERTY", "propertyType" : "OBJECT", "meta" : { @@ -22192,9 +22391,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_part" @@ -26059,6 +26255,10 @@ "id" : "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "type" : "PROPERTY", "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#gocheck_obsoletion_candidate", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/go#goslim_agr", "type" : "PROPERTY", @@ -26397,6 +26597,10 @@ "id" : "http://purl.org/dc/terms/date", "type" : "PROPERTY", "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/description", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/license", "type" : "PROPERTY", @@ -26422,12 +26626,10 @@ "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "lbl" : "created by", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "lbl" : "creation date", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { @@ -26520,7 +26722,6 @@ "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#id", - "lbl" : "id", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { @@ -26590,20 +26791,16 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000000", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_131567" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000006", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000101" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000006", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000197" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000007", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0002321" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000034", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000034", "pred" : "is_a", @@ -26706,6 +26903,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000040", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000040", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -26785,7 +26986,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000066", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000066", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -26850,6 +27051,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000092", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000092", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -26900,6 +27105,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000094", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000094", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -27016,6 +27225,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000148", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000147" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000148", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000148", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -27040,6 +27253,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000152", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000151" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000152", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000152", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -27048,6 +27265,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000163", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000151" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000163", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000163", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -27060,6 +27281,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000187", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000183" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000187", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000187", "pred" : "is_a", @@ -27071,7 +27296,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000188", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000188", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -27089,31 +27314,17 @@ "pred" : "http://purl.obolibrary.org/obo/RO_0002202", "obj" : "http://purl.obolibrary.org/obo/CL_0000514" }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000197", + "sub" : "http://purl.obolibrary.org/obo/CL_0000210", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000197", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0001032" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000197", - "pred" : "http://purl.obolibrary.org/obo/RO_0002215", - "obj" : "http://purl.obolibrary.org/obo/GO_0050906" + "obj" : "http://purl.obolibrary.org/obo/CL_0000101" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000210", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000006", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_inferred", - "val" : "true" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/CL_0008028" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000210", "pred" : "http://purl.obolibrary.org/obo/RO_0002215", - "obj" : "http://purl.obolibrary.org/obo/GO_0050962" + "obj" : "http://purl.obolibrary.org/obo/GO_0050908" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000211", "pred" : "is_a", @@ -27126,6 +27337,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000219", "pred" : "http://purl.obolibrary.org/obo/RO_0002215", "obj" : "http://purl.obolibrary.org/obo/GO_0048870" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000221", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000221", "pred" : "is_a", @@ -27134,6 +27349,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000221", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000924" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000222", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000222", "pred" : "is_a", @@ -27142,6 +27361,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000222", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000926" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000223", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000223", "pred" : "is_a", @@ -27150,6 +27373,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000223", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000925" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000226", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000226", "pred" : "is_a", @@ -27158,6 +27385,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000226", "pred" : "http://purl.obolibrary.org/obo/RO_0000053", "obj" : "http://purl.obolibrary.org/obo/PATO_0001407" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000228", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000228", "pred" : "is_a", @@ -27228,7 +27459,7 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0000000" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000255", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000325", @@ -27257,7 +27488,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000349", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000349", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -27294,7 +27525,7 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0010017" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000365", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000393", @@ -27312,6 +27543,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000451", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000145" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000451", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000451", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -27402,7 +27637,7 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000518", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000526", @@ -27476,6 +27711,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000557", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_1001610" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000557", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000557", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -27518,6 +27757,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000559", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000559", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -27544,6 +27787,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000566", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0011026" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000566", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000566", "pred" : "http://purl.obolibrary.org/obo/RO_0002104", @@ -27622,6 +27869,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000680", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000055" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000680", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000680", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -27678,7 +27929,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0002405" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000738", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000738", @@ -27708,6 +27959,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000746", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", "obj" : "http://purl.obolibrary.org/obo/CL_0000513" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000763", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000763", "pred" : "is_a", @@ -27768,6 +28023,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000825", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000825", "pred" : "http://purl.obolibrary.org/obo/CL_4030046", @@ -27806,6 +28065,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000826", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000826", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -27840,10 +28103,18 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000827", "pred" : "http://purl.obolibrary.org/obo/RO_0002215", "obj" : "http://purl.obolibrary.org/obo/GO_0030217" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000837", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000837", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0008001" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000837", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000837", "pred" : "http://purl.obolibrary.org/obo/CL_4030046", @@ -27997,7 +28268,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0001035", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0001035", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -28112,6 +28383,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0002009", "pred" : "http://purl.obolibrary.org/obo/RO_0002215", "obj" : "http://purl.obolibrary.org/obo/GO_0043011" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0002031", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002031", "pred" : "is_a", @@ -28124,6 +28399,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0002031", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", "obj" : "http://purl.obolibrary.org/obo/CL_0002032" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0002032", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002032", "pred" : "is_a", @@ -28183,7 +28462,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002319", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002319", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -28191,7 +28470,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002320", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002320", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -28203,11 +28482,11 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002372", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000228" + "obj" : "http://purl.obolibrary.org/obo/CL_0000737" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002372", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000737" + "obj" : "http://purl.obolibrary.org/obo/CL_4052002" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002372", "pred" : "http://purl.obolibrary.org/obo/RO_0000053", @@ -28215,7 +28494,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002494", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002494", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -28268,6 +28547,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0008019", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000219" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0008019", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0008019", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -28276,6 +28559,14 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0008019", "pred" : "http://purl.obolibrary.org/obo/RO_0002215", "obj" : "http://purl.obolibrary.org/obo/GO_0016477" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0008028", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000540" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0008028", + "pred" : "http://purl.obolibrary.org/obo/RO_0002216", + "obj" : "http://purl.obolibrary.org/obo/GO_0007601" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0009004", "pred" : "is_a", @@ -28304,6 +28595,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0011012", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0002321" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0011026", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0011026", "pred" : "is_a", @@ -28348,14 +28643,30 @@ "sub" : "http://purl.obolibrary.org/obo/CL_1001610", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0012429" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_4052002", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000228" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_4052002", + "pred" : "http://purl.obolibrary.org/obo/RO_0002353", + "obj" : "http://purl.obolibrary.org/obo/GO_0000768" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0000323", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0005773" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0000768", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0006949" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0000768", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0140253" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0000785", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0032993" + "obj" : "http://purl.obolibrary.org/obo/GO_0110165" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0000785", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -28930,6 +29241,18 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0006936", "pred" : "http://purl.obolibrary.org/obo/BFO_0000066", "obj" : "http://purl.obolibrary.org/obo/UBERON_0002385" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0006949", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0009987" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0006949", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0048646" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0006949", + "pred" : "http://purl.obolibrary.org/obo/RO_0002297", + "obj" : "http://purl.obolibrary.org/obo/CL_0000228" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0006955", "pred" : "is_a", @@ -28946,6 +29269,18 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0006996", "pred" : "http://purl.obolibrary.org/obo/RO_0002592", "obj" : "http://purl.obolibrary.org/obo/GO_0043226" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0007009", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0061024" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0007009", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/GO_0010256" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0007009", + "pred" : "http://purl.obolibrary.org/obo/RO_0002592", + "obj" : "http://purl.obolibrary.org/obo/GO_0005886" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0007154", "pred" : "is_a", @@ -29166,6 +29501,14 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0009987", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0008150" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0010256", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0016043" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0010256", + "pred" : "http://purl.obolibrary.org/obo/RO_0002592", + "obj" : "http://purl.obolibrary.org/obo/GO_0012505" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0010324", "pred" : "is_a", @@ -29632,12 +29975,8 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0005575" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0032991", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", - "obj" : "http://purl.obolibrary.org/obo/PR_000000001" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0032993", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0032991" + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0033151", "pred" : "is_a", @@ -29906,6 +30245,18 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0044419", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0008150" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0045026", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0007009" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0045026", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0061025" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0045026", + "pred" : "http://purl.obolibrary.org/obo/RO_0012008", + "obj" : "http://purl.obolibrary.org/obo/GO_0005886" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0045087", "pred" : "is_a", @@ -30218,6 +30569,14 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0050906", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/GO_0007600" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0050908", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0050962" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0050908", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/GO_0007601" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0050953", "pred" : "is_a", @@ -30482,6 +30841,10 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0098644", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0099080" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0098644", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0098644", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -30658,6 +31021,14 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0140029", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/GO_0006887" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0140253", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0009987" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0140253", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/GO_0045026" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0140352", "pred" : "is_a", @@ -31033,7 +31404,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/PR_000000001", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000064867" + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/PR_000000001", "pred" : "http://purl.obolibrary.org/obo/RO_0002353", @@ -31267,7 +31638,7 @@ "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PR_000001006" }, { - "sub" : "http://purl.obolibrary.org/obo/PR_000064867", + "sub" : "http://purl.obolibrary.org/obo/PR_000050567", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { @@ -31326,7 +31697,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000043", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000043", @@ -31336,6 +31707,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000043", "pred" : "http://purl.obolibrary.org/obo/RO_0002176", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001630" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0000058", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000058", "pred" : "is_a", @@ -31456,7 +31831,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0001434" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000075", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000075", @@ -31558,7 +31933,7 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0007369" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000109", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000110", @@ -31578,7 +31953,7 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0001841" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000110", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000111", @@ -31594,7 +31969,7 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0048513" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000111", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", @@ -31602,7 +31977,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0004921" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", @@ -31626,7 +32001,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0011216" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000383", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000383", @@ -31742,6 +32117,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000481", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000479" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0000483", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000483", "pred" : "is_a", @@ -31756,7 +32135,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0005769" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000483", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208", "meta" : { "basicPropertyValues" : [ { @@ -31794,7 +32173,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0010316" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000923", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000924", @@ -31864,7 +32243,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0035804" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000930", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000949", @@ -31872,7 +32251,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0015204" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000949", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000949", @@ -31944,7 +32323,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000467" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001009", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001009", @@ -31976,7 +32355,7 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0000540" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001016", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001016", @@ -32023,7 +32402,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0001016" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001017", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001017", @@ -32135,7 +32514,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0004765" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001474", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001474", @@ -32157,7 +32536,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0001007" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001555", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001555", @@ -32233,7 +32612,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002193", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002204", @@ -32293,7 +32672,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0011137" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711", "meta" : { "basicPropertyValues" : [ { @@ -32345,7 +32724,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002329", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711", "meta" : { "basicPropertyValues" : [ { @@ -32363,13 +32742,17 @@ "val" : "ZFA" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0002330", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002330", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000467" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002330", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002330", @@ -32406,7 +32789,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_89593" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", @@ -32454,6 +32837,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002346", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/CL_0000133" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0002365", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002365", "pred" : "is_a", @@ -32521,7 +32908,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000479" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002384", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002385", @@ -32537,7 +32924,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0001015" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002385", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002385", @@ -32567,7 +32954,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002390", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002390", @@ -32605,7 +32992,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0001474" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002481", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002530", @@ -32613,7 +33000,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000062" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002530", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002530", @@ -32683,7 +33070,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000926" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003068", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003068", @@ -32703,7 +33090,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0016879" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003075", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711", "meta" : { "basicPropertyValues" : [ { @@ -32800,7 +33187,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003081", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003081", @@ -32840,7 +33227,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000479" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003104", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003104", @@ -33049,7 +33436,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004770", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004770", @@ -33073,7 +33460,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0003068" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004880", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004905", @@ -33105,7 +33492,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000060" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004923", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005061", @@ -33157,7 +33544,7 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0000187" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005090", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005157", @@ -33225,6 +33612,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0005764", "pred" : "http://purl.obolibrary.org/obo/RO_0002007", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", "pred" : "is_a", @@ -33245,7 +33636,7 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0005587" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", @@ -33293,7 +33684,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0005423" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006268", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006268", @@ -33315,7 +33706,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000307" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006595", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006595", @@ -33339,7 +33730,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000307" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006601", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006601", @@ -33355,7 +33746,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000307" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006603", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006603", @@ -33487,6 +33878,10 @@ "val" : "AEO" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0007845", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007845", "pred" : "is_a", @@ -33687,6 +34082,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0011822", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/GO_0071953" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0011823", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0011823", "pred" : "is_a", @@ -33695,6 +34094,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0011823", "pred" : "http://purl.obolibrary.org/obo/RO_0002473", "obj" : "http://purl.obolibrary.org/obo/UBERON_0011860" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0011860", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0011860", "pred" : "is_a", @@ -33757,7 +34160,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0011997", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0012429", @@ -33827,7 +34230,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000475" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0013701", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0013702", @@ -33857,7 +34260,7 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0000100" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0014892", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0014892", @@ -33889,7 +34292,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0015212", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0015228", @@ -35189,13 +35592,6 @@ "obj" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to" } ], "logicalDefinitionAxioms" : [ { - "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000006", - "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000197", "http://purl.obolibrary.org/obo/CL_0000540" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002215", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0050906" - } ] - }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000034", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ], "restrictions" : [ { @@ -35415,22 +35811,12 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0001134" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000197", - "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0001032" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002215", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0050906" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000210", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0002215", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0050962" + "fillerId" : "http://purl.obolibrary.org/obo/GO_0050908" } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000219", @@ -35484,7 +35870,7 @@ "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000255", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002160", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002162", "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" } ] }, { @@ -35505,7 +35891,7 @@ "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000365", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0010017" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002160", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002162", "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" } ] }, { @@ -36052,6 +36438,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_8600004" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/CL_0008028", + "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002216", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0007601" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0009004", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0002319" ], @@ -36101,6 +36494,23 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0002371" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/CL_4052002", + "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000053", + "fillerId" : "http://purl.obolibrary.org/obo/PATO_0001908" + }, { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002353", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0000768" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0000768", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0006949" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000051", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0045026" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0001677", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0022607" ], @@ -36248,6 +36658,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0012008", "fillerId" : "http://purl.obolibrary.org/obo/GO_0012506" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0006949", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0048646" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002297", + "fillerId" : "http://purl.obolibrary.org/obo/CL_0000228" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0006996", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016043" ], @@ -36255,6 +36672,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002592", "fillerId" : "http://purl.obolibrary.org/obo/GO_0043226" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0007009", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016043" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002592", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0005886" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0007275", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0048856" ], @@ -36304,6 +36728,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002296", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0000479" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0010256", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016043" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002592", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0012505" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0012506", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016020" ], @@ -36577,6 +37008,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002592", "fillerId" : "http://purl.obolibrary.org/obo/GO_0032991" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045026", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009987" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0012008", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0005886" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045321", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0001775" ], @@ -36724,6 +37162,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/GO_0007600" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0050908", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009583" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0007601" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0050962", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009583" ], diff --git a/src/ontology/subsets/general_cell_types_upper_slim.obo b/src/ontology/subsets/general_cell_types_upper_slim.obo index 90957720c..9c6b81e98 100644 --- a/src/ontology/subsets/general_cell_types_upper_slim.obo +++ b/src/ontology/subsets/general_cell_types_upper_slim.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: cl/releases/2024-08-16/subsets/general_cell_types_upper_slim.owl +data-version: cl/releases/2024-09-26/subsets/general_cell_types_upper_slim.owl subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" subsetdef: attribute_slim "" @@ -19,6 +19,7 @@ subsetdef: eye_upper_slim "a subset of general classes related to specific cell subsetdef: functional_classification "" subsetdef: general_cell_types_upper_slim "a subset of general classes of cell types in the cell ontology." subsetdef: gocheck_do_not_annotate "" +subsetdef: gocheck_obsoletion_candidate "" subsetdef: goslim_agr "" subsetdef: goslim_candida "" subsetdef: goslim_chembl "" @@ -95,7 +96,7 @@ idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# idspace: sssom https://w3id.org/sssom/ idspace: terms http://purl.org/dc/terms/ ontology: cl/subsets/general_cell_types_upper_slim -property_value: owl:versionInfo "2024-08-16" xsd:string +property_value: owl:versionInfo "2024-09-26" xsd:string [Term] id: CL:0000000 @@ -118,20 +119,7 @@ is_a: UBERON:0000061 ! anatomical structure disjoint_from: GO:0031012 ! extracellular matrix disjoint_from: GO:0032991 ! protein-containing complex disjoint_from: GO:0043226 ! organelle -relationship: RO:0002160 NCBITaxon:131567 ! only in taxon cellular organisms - -[Term] -id: CL:0000006 -name: neuronal receptor cell -def: "Any sensory receptor cell that is a(n) neuron and is capable of some detection of stimulus involved in sensory perception." [FBC:Autogenerated] -subset: cellxgene_subset -synonym: "neuronal receptor cell (sensu Animalia)" EXACT [] -xref: ZFA:0009001 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000101 ! sensory neuron -is_a: CL:0000197 ! sensory receptor cell -intersection_of: CL:0000197 ! sensory receptor cell -intersection_of: CL:0000540 ! neuron -intersection_of: capable_of GO:0050906 ! detection of stimulus involved in sensory perception +relationship: RO:0002162 NCBITaxon:131567 ! in taxon cellular organisms [Term] id: CL:0000007 @@ -152,6 +140,7 @@ synonym: "animal stem cell" EXACT [] xref: CALOHA:TS-2086 xref: FMA:63368 xref: ZFA:0005957 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0011115 ! precursor cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0017145 ! stem cell division @@ -236,6 +225,7 @@ xref: FMA:83553 xref: ZFA:0009017 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0002194 {is_inferred="true"} ! monopoietic cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002194 ! monopoietic cell intersection_of: capable_of GO:0030224 ! monocyte differentiation intersection_of: has_part CL:0017503 ! basophilic cytoplasm @@ -376,7 +366,7 @@ xref: FBbt:00000124 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ xref: FMA:66768 xref: WBbt:0003672 xref: ZFA:0009034 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell disjoint_from: CL:0000738 ! leukocyte relationship: part_of UBERON:0000483 ! epithelium property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI @@ -447,6 +437,7 @@ xref: ZFA:0009047 {sssom:mapping_justification="https://w3id.org/semapv/vocab/Un is_a: CL:0000518 ! phagocyte (sensu Vertebrata) is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte is_a: CL:0001035 {is_inferred="true"} ! bone cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: capable_of GO:0045453 ! bone resorption intersection_of: has_part PR:000001850 ! cathepsin K @@ -483,6 +474,7 @@ xref: FMA:62854 xref: ZFA:0009048 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000081 ! blood cell is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: capable_of GO:0008015 ! blood circulation intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -549,12 +541,14 @@ def: "A vertebrate phagocyte with a single nucleus." [GOC:add, GOC:tfm, ISBN:078 subset: cellxgene_subset subset: human_reference_atlas xref: BTO:0001433 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000113 xref: ZFA:0009064 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000518 {is_inferred="true"} ! phagocyte (sensu Vertebrata) is_a: CL:0000842 ! mononuclear cell intersection_of: CL:0000518 ! phagocyte (sensu Vertebrata) intersection_of: bearer_of PATO:0001407 ! mononucleate property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nMononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. \nIn addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses.\nMononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer." xsd:string {xref="DOI:10.1016/j.coi.2005.11.008", xref="DOI:10.1038/nri3087", xref="DOI:10.3389/fimmu.2019.01893"} [Term] id: CL:0000125 @@ -570,9 +564,11 @@ xref: BTO:0002606 xref: CALOHA:TS-0415 xref: FBbt:00005144 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:54536 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000125 xref: ZFA:0009073 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000095 ! neuron associated cell property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nGlial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons.\nThese different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning.\nOligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. \nMicroglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response.\nDespite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis." xsd:string {xref="DOI:10.1002/glia.24343", xref="DOI:10.1038/nn1988", xref="DOI:10.1101/cshperspect.a020602", xref="DOI:10.1126/science.aat0473", xref="DOI:10.3389/fncel.2017.00024"} [Term] id: CL:0000133 @@ -665,6 +661,7 @@ xref: MESH:D008544 xref: VHOG:0001679 xref: ZFA:0009091 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000147 ! pigment cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000147 ! pigment cell intersection_of: has_part GO:0042470 ! melanosome intersection_of: RO:0002202 CL:0000541 ! develops from melanoblast @@ -698,6 +695,7 @@ subset: general_cell_types_upper_slim xref: FMA:16014 xref: ZFA:0009092 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000151 ! secretory cell intersection_of: part_of UBERON:0002365 ! exocrine gland relationship: part_of UBERON:0002365 ! exocrine gland @@ -713,6 +711,7 @@ synonym: "endocrinocyte" EXACT [] xref: FMA:83809 xref: ZFA:0009096 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell +is_a: CL:0000255 ! eukaryotic cell relationship: part_of UBERON:0000949 ! endocrine system property_value: RO:0002175 NCBITaxon:9606 @@ -738,6 +737,7 @@ xref: FMA:67328 xref: WBbt:0003675 xref: ZFA:0009114 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000183 ! contractile cell +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000393 ! electrically responsive cell relationship: RO:0002202 CL:0000056 ! develops from myoblast property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI @@ -754,7 +754,7 @@ xref: BTO:0004392 xref: CALOHA:TS-2158 xref: FMA:9727 xref: ZFA:0009115 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001134 ! skeletal muscle tissue relationship: part_of UBERON:0001134 ! skeletal muscle tissue @@ -780,33 +780,21 @@ is_a: CL:0008007 ! visceral muscle cell relationship: RO:0002202 CL:0000514 ! develops from smooth muscle myoblast property_value: RO:0002175 NCBITaxon:9606 -[Term] -id: CL:0000197 -name: sensory receptor cell -def: "A cell that is capable of detection of a stimulus involved in sensory perception." [] -synonym: "receptor cell" EXACT [] -xref: MESH:D011984 -is_a: CL:0000000 ! cell -intersection_of: CL:0000000 ! cell -intersection_of: capable_of GO:0050906 ! detection of stimulus involved in sensory perception -intersection_of: part_of UBERON:0001032 ! sensory system -relationship: capable_of GO:0050906 ! detection of stimulus involved in sensory perception -relationship: part_of UBERON:0001032 ! sensory system - [Term] id: CL:0000210 name: photoreceptor cell -def: "A cell specialized to detect and transduce light." [MESH:D010786] +def: "A cell specialized in detecting light stimuli that are involved in visual perception." [MESH:D010786] subset: cellxgene_subset xref: BTO:0001060 xref: CALOHA:TS-0868 xref: FBbt:00004211 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:86740 xref: ZFA:0009127 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000006 {is_inferred="true"} ! neuronal receptor cell +is_a: CL:0000101 ! sensory neuron +is_a: CL:0008028 ! visual system neuron intersection_of: CL:0000540 ! neuron -intersection_of: capable_of GO:0050962 ! detection of light stimulus involved in sensory perception -relationship: capable_of GO:0050962 ! detection of light stimulus involved in sensory perception +intersection_of: capable_of GO:0050908 ! detection of light stimulus involved in visual perception +relationship: capable_of GO:0050908 ! detection of light stimulus involved in visual perception property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg" xsd:anyURI [Term] @@ -833,6 +821,7 @@ def: "A cell of the outer of the three germ layers of the embryo." [MESH:D004475 synonym: "ectoderm cell" EXACT [] xref: FMA:72549 xref: ZFA:0009137 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000924 ! ectoderm @@ -845,6 +834,7 @@ synonym: "mesoblast" EXACT [] synonym: "mesoderm cell" EXACT [] xref: FMA:72554 xref: ZFA:0009138 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000926 ! mesoderm @@ -855,6 +845,7 @@ def: "A cell of the inner of the three germ layers of the embryo." [MESH:D004707 synonym: "endoderm cell" EXACT [] xref: FMA:72555 xref: ZFA:0009139 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000925 ! endoderm @@ -862,6 +853,7 @@ relationship: part_of UBERON:0000925 ! endoderm id: CL:0000226 name: single nucleate cell def: "A cell with a single nucleus." [FB:ma, GOC:tfm] +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002242 ! nucleate cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0001407 ! mononucleate @@ -870,12 +862,10 @@ relationship: bearer_of PATO:0001407 ! mononucleate [Term] id: CL:0000228 name: multinucleate cell -def: "A cell with more than one nucleus." [FB:ma] -synonym: "syncitium" EXACT [] -synonym: "syncytial cell" EXACT [] -synonym: "syncytium" EXACT [] -xref: AEO:0000203 -xref: WBbt:0008074 +def: "A cell with more than one nucleus." [FB:ma, Wikipedia:Multinucleate] +synonym: "multinucleated cells" EXACT [Wikipedia:Multinucleate] +synonym: "polynuclear cells" EXACT [Wikipedia:Multinucleate] +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002242 ! nucleate cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0001908 ! multinucleate @@ -950,13 +940,13 @@ property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000255 name: eukaryotic cell -def: "Any cell that only exists in Eukaryota." [FBC:Autogenerated] +def: "Any cell that in taxon some Eukaryota." [FBC:Autogenerated] subset: cellxgene_subset xref: MESH:D005057 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell -intersection_of: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota -relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +intersection_of: RO:0002162 NCBITaxon:2759 ! in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 ! in taxon Eukaryota [Term] id: CL:0000325 @@ -988,7 +978,7 @@ name: extraembryonic cell def: "Any cell that is part of some extraembryonic structure." [FBC:Autogenerated] subset: general_cell_types_upper_slim xref: ZFA:0009176 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0000478 ! extraembryonic structure relationship: part_of UBERON:0000478 ! extraembryonic structure @@ -1023,8 +1013,8 @@ is_a: CL:0000007 ! early embryonic cell (metazoa) is_a: CL:0000255 ! eukaryotic cell is_a: CL:0010017 ! zygote intersection_of: CL:0010017 ! zygote -intersection_of: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa -relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +intersection_of: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa [Term] id: CL:0000393 @@ -1056,6 +1046,7 @@ xref: MESH:D003713 xref: ZFA:0009209 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000113 ! mononuclear phagocyte is_a: CL:0000145 ! professional antigen presenting cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000738 ! leukocyte intersection_of: bearer_of PATO:0001407 ! mononucleate intersection_of: capable_of GO:0001816 ! cytokine production @@ -1149,7 +1140,7 @@ name: phagocyte (sensu Vertebrata) def: "A phagocyte in vertebrates that is able to phagocytosis." [GOC:tfm] is_a: CL:0000234 ! phagocyte is_a: CL:0000255 ! eukaryotic cell -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata [Term] id: CL:0000526 @@ -1250,6 +1241,7 @@ is_a: CL:0000763 ! myeloid cell is_a: CL:0001012 ! CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor is_a: CL:0011026 ! progenitor cell is_a: CL:1001610 ! bone marrow hematopoietic cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002032 ! hematopoietic oligopotent progenitor cell intersection_of: capable_of GO:0030225 ! macrophage differentiation intersection_of: capable_of GO:0030851 ! granulocyte differentiation @@ -1280,6 +1272,7 @@ xref: FMA:83551 xref: ZFA:0009253 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0002194 {is_inferred="true"} ! monopoietic cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002194 ! monopoietic cell intersection_of: capable_of GO:0030224 ! monocyte differentiation intersection_of: has_part GO:0042582 ! azurophil granule @@ -1299,6 +1292,7 @@ synonym: "chondroplast" EXACT [] xref: ZFA:0009258 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000134 {is_inferred="true"} ! mesenchymal stem cell is_a: CL:0011026 ! progenitor cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: RO:0002104 PR:000001444 ! has plasma membrane part cadherin-5 intersection_of: RO:0002104 PR:000002112 ! has plasma membrane part vascular endothelial growth factor receptor 2 @@ -1375,6 +1369,7 @@ def: "A non-terminally differentiated cell that is capable of developing into a subset: cellxgene_subset xref: ZFA:0009291 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0011115 ! precursor cell intersection_of: RO:0002203 CL:0000187 ! develops into muscle cell relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell @@ -1432,7 +1427,7 @@ intersection_of: bearer_of PATO:0002505 ! nucleated intersection_of: capable_of GO:0001667 ! ameboidal-type cell migration relationship: capable_of GO:0001667 ! ameboidal-type cell migration relationship: part_of UBERON:0002405 ! immune system -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002202 CL:0000037 ! develops from hematopoietic stem cell property_value: RO:0002175 NCBITaxon:9606 @@ -1476,6 +1471,7 @@ xref: BTO:0001441 xref: CALOHA:TS-0647 xref: MESH:D022423 xref: ZFA:0009324 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000988 {is_inferred="true"} ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: RO:0002202 CL:0000049 ! develops from common myeloid progenitor @@ -1523,6 +1519,7 @@ synonym: "preNK cell" RELATED [PMID:11532393] synonym: "pro-natural killer cell" EXACT [] xref: ZFA:0009348 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000838 {is_inferred="true"} ! lymphoid lineage restricted progenitor cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: CL:4030046 PR:000001874 ! lacks_plasma_membrane_part KLRB1-like protein intersection_of: CL:4030046 PR:000002065 ! lacks_plasma_membrane_part mast/stem cell growth factor receptor @@ -1557,6 +1554,7 @@ synonym: "progenitor B-lymphocyte" EXACT [] xref: BTO:0003104 xref: ZFA:0009349 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000838 {is_inferred="true"} ! lymphoid lineage restricted progenitor cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: has_part PR:000001903 ! paired box protein PAX-5 intersection_of: has_part PR:000006611 ! DNA nucleotidylexotransferase @@ -1597,7 +1595,9 @@ synonym: "MPP" EXACT [] xref: BTO:0000725 xref: CALOHA:TS-0448 xref: ZFA:0009354 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001402 ! multipotent intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -1745,7 +1745,7 @@ name: bone cell def: "A connective tissue cell found in bone." [GO_REF:0000034, GOC:add] subset: general_cell_types_upper_slim subset: human_reference_atlas -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001474 ! bone element relationship: part_of UBERON:0001474 ! bone element @@ -1844,6 +1844,7 @@ id: CL:0002031 name: hematopoietic lineage restricted progenitor cell def: "A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells." [GOC:tfm, PMID:19022770] subset: blood_and_immune_upper_slim +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001400 ! unipotent @@ -1859,6 +1860,7 @@ name: hematopoietic oligopotent progenitor cell def: "A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities." [GOC:tfm, https://orcid.org/0000-0001-5208-3432, PMID:19022770] comment: This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). subset: blood_and_immune_upper_slim +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001401 ! oligopotent @@ -1927,7 +1929,7 @@ def: "A cell that is part of the nervous system." [GOC:tfm, ISBN:0618947256] subset: cellxgene_subset xref: CALOHA:TS-2040 xref: FMA:70333 -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001016 ! nervous system relationship: part_of UBERON:0001016 ! nervous system @@ -1943,7 +1945,7 @@ xref: CALOHA:TS-2096 xref: FMA:63875 xref: MESH:D003239 xref: ZFA:0009392 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0002384 ! connective tissue relationship: part_of UBERON:0002384 ! connective tissue @@ -1965,12 +1967,12 @@ creation_date: 2010-09-15T03:39:21Z [Term] id: CL:0002372 name: myotube -def: "A transversely striated, synctial muscle cell, formed by the fusion of myoblasts." [GOC:dos, GOC:tfm, ISBN:0323052908, PMID:22274696] -synonym: "myotubule" EXACT [] -synonym: "single cell sarcomere" EXACT [] +def: "A transversely striated, multinucleated syncytial muscle cell, formed by the fusion of myoblasts during muscle development." [GOC:dos, GOC:tfm, ISBN:0323052908, PMID:22274696] +synonym: "myofiber" EXACT [FBbt:00005812] +synonym: "myofibril" EXACT [FBbt:00005812] xref: FBbt:00005812 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} -is_a: CL:0000228 ! multinucleate cell is_a: CL:0000737 ! striated muscle cell +is_a: CL:4052002 ! syncytial cell intersection_of: CL:0000187 ! muscle cell intersection_of: bearer_of PATO:0001908 ! multinucleate intersection_of: bearer_of PATO:0002478 ! transversely striated @@ -1989,7 +1991,7 @@ xref: BTO:0001539 xref: CALOHA:TS-0115 xref: FMA:83808 xref: FMA:84791 -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0007100 ! primary circulatory organ relationship: part_of UBERON:0007100 ! primary circulatory organ @@ -2063,10 +2065,22 @@ subset: cellxgene_subset subset: human_reference_atlas synonym: "mesenchyme cell" EXACT [] is_a: CL:0000219 ! motile cell +is_a: CL:0000255 ! eukaryotic cell relationship: capable_of GO:0016477 ! cell migration relationship: part_of UBERON:0003104 ! mesenchyme property_value: RO:0002175 NCBITaxon:9606 +[Term] +id: CL:0008028 +name: visual system neuron +def: "Any neuron that is capable of part of some visual perception." [FBC:Autogenerated] +is_a: CL:0000540 ! neuron +intersection_of: CL:0000540 ! neuron +intersection_of: capable_of_part_of GO:0007601 ! visual perception +relationship: capable_of_part_of GO:0007601 ! visual perception +property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 +creation_date: 2017-07-09T19:12:36Z + [Term] id: CL:0009004 name: retinal cell @@ -2101,14 +2115,17 @@ id: CL:0011012 name: neural crest cell def: "A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells." [https://orcid.org/0000-0001-5208-3432, https://orcid.org/0000-0002-9900-7880] subset: cellxgene_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_0011012 is_a: CL:0000048 ! multi fate stem cell is_a: CL:0002321 ! embryonic cell (metazoa) +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." xsd:string {xref="DOI:10.1002/dvg.23276", xref="DOI:10.1242/dev.193193", xref="DOI:10.3389/fcell.2020.00635/full", xref="https://doi.org/10.1016/j.ydbio.2011.12.042"} [Term] id: CL:0011026 name: progenitor cell def: "A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses." [https://doi.org/10.1016/B978-0-12-409503-8.00002-0, ISBN:978-1-62808-994-3] subset: cellxgene_subset +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0011115 ! precursor cell intersection_of: CL:0011115 ! precursor cell intersection_of: RO:0002202 CL:0000034 ! develops from stem cell @@ -2161,6 +2178,20 @@ intersection_of: CL:0000988 ! hematopoietic cell intersection_of: part_of UBERON:0002371 ! bone marrow relationship: part_of UBERON:0012429 ! hematopoietic tissue +[Term] +id: CL:4052002 +name: syncytial cell +def: "A multinucleate cell formed by the fusion of multiple uninuclear cells through plasma membrane fusion. This process leads to a single large cell containing multiple nuclei within a shared cytoplasm." [PMID:20851884, Wikipedia:Syncytium] +synonym: "SC" RELATED OMO:0003000 [PMID:9067520] +synonym: "syncytium" EXACT [WBbt:0008074] +is_a: CL:0000228 ! multinucleate cell +intersection_of: CL:0000000 ! cell +intersection_of: bearer_of PATO:0001908 ! multinucleate +intersection_of: output_of GO:0000768 ! syncytium formation by plasma membrane fusion +relationship: output_of GO:0000768 ! syncytium formation by plasma membrane fusion +property_value: terms:contributor https://orcid.org/0009-0000-8480-9277 +property_value: terms:date "2024-08-15T10:38:46Z" xsd:dateTime + [Term] id: GO:0000323 name: lytic vacuole @@ -2168,6 +2199,17 @@ namespace: cellular_component def: "A vacuole that is maintained at an acidic pH and which contains degradative enzymes, including a wide variety of acid hydrolases." [GOC:krc] is_a: GO:0005773 ! vacuole +[Term] +id: GO:0000768 +name: syncytium formation by plasma membrane fusion +namespace: biological_process +def: "The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells." [GOC:mtg_muscle, GOC:tb] +synonym: "cell fusion" BROAD [] +is_a: GO:0006949 ! syncytium formation +is_a: GO:0140253 ! cell-cell fusion +intersection_of: GO:0006949 ! syncytium formation +intersection_of: has_part GO:0045026 ! plasma membrane fusion + [Term] id: GO:0000785 name: chromatin @@ -2181,8 +2223,9 @@ synonym: "chromosome scaffold" RELATED [] synonym: "cytoplasmic chromatin" NARROW [] synonym: "nuclear chromatin" NARROW [] xref: NIF_Subcellular:sao1615953555 -is_a: GO:0032993 ! protein-DNA complex +is_a: GO:0110165 ! cellular anatomical entity relationship: part_of GO:0005694 ! chromosome +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28301" xsd:anyURI [Term] id: GO:0000791 @@ -3158,6 +3201,18 @@ xref: Wikipedia:Muscle_contraction is_a: GO:0003012 ! muscle system process relationship: occurs_in UBERON:0002385 ! muscle tissue +[Term] +id: GO:0006949 +name: syncytium formation +namespace: biological_process +def: "The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane. Syncytia are normally derived from single cells that fuse or fail to complete cell division." [ISBN:0198506732] +subset: goslim_pir +is_a: GO:0009987 ! cellular process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +intersection_of: GO:0048646 ! anatomical structure formation involved in morphogenesis +intersection_of: results_in_formation_of CL:0000228 ! multinucleate cell +relationship: results_in_formation_of CL:0000228 ! multinucleate cell + [Term] id: GO:0006955 name: immune response @@ -3189,6 +3244,20 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i created_by: jl creation_date: 2013-12-19T15:25:51Z +[Term] +id: GO:0007009 +name: plasma membrane organization +namespace: biological_process +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the plasma membrane." [GOC:dph, GOC:jl, GOC:mah] +subset: goslim_chembl +synonym: "plasma membrane organisation" EXACT [] +synonym: "plasma membrane organization and biogenesis" RELATED [GOC:mah] +is_a: GO:0061024 ! membrane organization +intersection_of: GO:0016043 ! cellular component organization +intersection_of: results_in_organization_of GO:0005886 ! plasma membrane +relationship: part_of GO:0010256 ! endomembrane system organization +relationship: results_in_organization_of GO:0005886 ! plasma membrane + [Term] id: GO:0007154 name: cell communication @@ -3618,6 +3687,19 @@ is_a: GO:0008150 ! biological_process created_by: jl creation_date: 2012-12-11T16:56:55Z +[Term] +id: GO:0010256 +name: endomembrane system organization +namespace: biological_process +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endomembrane system." [GOC:mah, GOC:sm] +subset: goslim_drosophila +synonym: "endomembrane organization" EXACT [] +synonym: "endomembrane system organisation" EXACT [GOC:mah] +is_a: GO:0016043 ! cellular component organization +intersection_of: GO:0016043 ! cellular component organization +intersection_of: results_in_organization_of GO:0012505 ! endomembrane system +relationship: results_in_organization_of GO:0012505 ! endomembrane system + [Term] id: GO:0010324 name: membrane invagination @@ -3816,6 +3898,9 @@ is_a: GO:0051301 ! cell division intersection_of: GO:0051301 ! cell division intersection_of: has_primary_input CL:0000034 ! stem cell relationship: has_primary_input CL:0000034 ! stem cell +property_value: RO:0002161 NCBITaxon:2 +property_value: RO:0002161 NCBITaxon:2157 +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0019226 @@ -4454,18 +4539,8 @@ synonym: "protein complex" NARROW [] synonym: "protein containing complex" EXACT [] synonym: "protein-protein complex" NARROW [] is_a: GO:0005575 ! cellular_component +is_a: PR:000050567 ! protein-containing material entity disjoint_from: GO:0110165 ! cellular anatomical entity -relationship: has_part PR:000000001 ! protein - -[Term] -id: GO:0032993 -name: protein-DNA complex -namespace: cellular_component -def: "A macromolecular complex containing both protein and DNA molecules." [GOC:mah] -comment: Note that this term is intended to classify complexes that have DNA as one of the members of the complex, that is, the complex does not exist if DNA is not present. Protein complexes that interact with DNA e.g. transcription factor complexes should not be classified here. -subset: goslim_pir -synonym: "DNA-protein complex" EXACT [GOC:mah] -is_a: GO:0032991 ! protein-containing complex [Term] id: GO:0033151 @@ -4721,6 +4796,7 @@ id: GO:0043227 name: membrane-bounded organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane." [GOC:go_curators] +subset: gocheck_do_not_annotate synonym: "membrane-enclosed organelle" EXACT [] xref: NIF_Subcellular:sao414196390 is_a: GO:0043226 ! organelle @@ -4728,29 +4804,34 @@ intersection_of: GO:0043226 ! organelle intersection_of: has_part GO:0016020 ! membrane disjoint_from: GO:0043228 ! non-membrane-bounded organelle relationship: has_part GO:0016020 ! membrane +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI [Term] id: GO:0043228 name: non-membrane-bounded organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:go_curators] +subset: gocheck_do_not_annotate subset: goslim_mouse synonym: "biological condensate" RELATED [] synonym: "non-membrane-enclosed organelle" EXACT [] xref: NIF_Subcellular:sao1456184038 is_a: GO:0043226 ! organelle property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21881" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI [Term] id: GO:0043229 name: intracellular organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:go_curators] +subset: gocheck_do_not_annotate subset: goslim_pir is_a: GO:0043226 ! organelle intersection_of: GO:0043226 ! organelle intersection_of: part_of GO:0005622 ! intracellular anatomical structure relationship: part_of GO:0005622 ! intracellular anatomical structure +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI [Term] id: GO:0043231 @@ -4832,9 +4913,11 @@ name: cellular component biogenesis namespace: biological_process alt_id: GO:0071843 def: "A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component." [GOC:jl, GOC:mah] +subset: gocheck_do_not_annotate subset: goslim_pir synonym: "cellular component biogenesis at cellular level" EXACT [] is_a: GO:0071840 ! cellular component organization or biogenesis +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27194" xsd:anyURI [Term] id: GO:0044207 @@ -4906,6 +4989,20 @@ is_a: GO:0008150 ! biological_process property_value: RO:0002161 NCBITaxon:4895 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20191" xsd:anyURI +[Term] +id: GO:0045026 +name: plasma membrane fusion +namespace: biological_process +alt_id: GO:0006947 +def: "The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell." [GOC:elh, GOC:mtg_muscle] +synonym: "cell fusion" BROAD [] +synonym: "cell-cell fusion" BROAD [] +is_a: GO:0007009 ! plasma membrane organization +is_a: GO:0061025 ! membrane fusion +intersection_of: GO:0009987 ! cellular process +intersection_of: results_in_fusion_of GO:0005886 ! plasma membrane +relationship: results_in_fusion_of GO:0005886 ! plasma membrane + [Term] id: GO:0045087 name: innate immune response @@ -4917,6 +5014,9 @@ synonym: "nonspecific immune response" EXACT [] xref: Wikipedia:Innate_immune_system is_a: GO:0006955 ! immune response is_a: GO:0140546 ! defense response to symbiont +property_value: RO:0002161 NCBITaxon:2 +property_value: RO:0002161 NCBITaxon:2157 +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0045202 @@ -5348,6 +5448,23 @@ intersection_of: GO:0051606 ! detection of stimulus intersection_of: part_of GO:0007600 ! sensory perception relationship: part_of GO:0007600 ! sensory perception +[Term] +id: GO:0050908 +name: detection of light stimulus involved in visual perception +namespace: biological_process +def: "The series of events involved in visual perception in which a light stimulus is received and converted into a molecular signal." [GOC:ai, GOC:dos] +synonym: "sensory detection of light during visual perception" EXACT [] +synonym: "sensory detection of light stimulus during visual perception" EXACT [] +synonym: "sensory transduction of light during visual perception" EXACT [] +synonym: "sensory transduction of light stimulus during visual perception" EXACT [] +synonym: "visual perception, detection of light stimulus" EXACT [] +synonym: "visual perception, sensory transduction during perception of light" EXACT [] +synonym: "visual perception, sensory transduction of light stimulus" EXACT [] +is_a: GO:0050962 ! detection of light stimulus involved in sensory perception +intersection_of: GO:0009583 ! detection of light stimulus +intersection_of: part_of GO:0007601 ! visual perception +relationship: part_of GO:0007601 ! visual perception + [Term] id: GO:0050953 name: sensory perception of light stimulus @@ -5827,6 +5944,7 @@ def: "A complex of collagen trimers such as a fibril or collagen network." [GOC: synonym: "Supramolecular aggregate of collagen" EXACT [PMID:19693541] synonym: "Supramolecular collagen assembly" EXACT [PMID:21421911] is_a: GO:0099080 ! supramolecular complex +is_a: PR:000050567 ! protein-containing material entity relationship: has_part GO:0005581 ! collagen trimer relationship: part_of GO:0062023 ! collagen-containing extracellular matrix @@ -6041,6 +6159,19 @@ relationship: part_of GO:0006887 ! exocytosis created_by: pg creation_date: 2017-05-15T13:20:45Z +[Term] +id: GO:0140253 +name: cell-cell fusion +namespace: biological_process +def: "A cellular process in which two or more cells combine together, their plasma membrane fusing, producing a single cell. In some cases, nuclei fuse, producing a polyploid cell, while in other cases, nuclei remain separate, producing a syncytium." [Wikipedia:Cell_fusion] +synonym: "cell cell fusion" EXACT [] +synonym: "cell fusion" BROAD [] +is_a: GO:0009987 ! cellular process +relationship: has_part GO:0045026 ! plasma membrane fusion +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15939" xsd:anyURI +created_by: pg +creation_date: 2018-08-13T18:38:18Z + [Term] id: GO:0140352 name: export from cell @@ -6867,7 +6998,7 @@ comment: The definition above excludes protein complexes, which some also consid synonym: "native protein" NARROW [IEDB:BP] synonym: "natural protein" EXACT [PRO:DAN] is_a: PR:000018263 ! amino acid chain -is_a: PR:000064867 ! protein-containing molecular entity +is_a: PR:000050567 ! protein-containing material entity relationship: output_of GO:0006412 ! translation [Term] @@ -7609,11 +7740,11 @@ synonym: "PTPRC/iso:CD45R" EXACT PRO-short-label [PRO:DNx] is_a: PR:000001006 ! receptor-type tyrosine-protein phosphatase C [Term] -id: PR:000064867 -name: protein-containing molecular entity +id: PR:000050567 +name: protein-containing material entity namespace: protein -def: "A molecular entity that minimally consists of a protein." [PRO:DAN] -comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). +def: "A material entity that minimally consists of a protein." [PRO:DAN] +comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566). synonym: "protein" NARROW [PRO:DAN] synonym: "protein aggregate" NARROW [PRO:DAN] synonym: "protein complex" NARROW [PRO:DAN] @@ -7718,7 +7849,7 @@ xref: ZFA:0005647 is_a: UBERON:0007846 {source="VSAO"} ! dense regular connective tissue relationship: has_part CL:0000327 {source="AEO"} ! extracellular matrix secreting cell relationship: part_of UBERON:0002204 {source="OG"} ! musculoskeletal system -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002176 UBERON:0001474 ! connects bone element relationship: RO:0002176 UBERON:0001630 ! connects muscle organ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg" xsd:anyURI @@ -7744,6 +7875,7 @@ xref: UMLS:C0687028 {source="ncithesaurus:Duct"} xref: Wikipedia:Duct_(anatomy) xref: XAO:0004000 xref: ZFA:0005171 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000063 ! organ subunit relationship: has_part UBERON:0034969 ! epithelial layer of duct relationship: RO:0000086 PATO:0002299 ! has quality tubular @@ -7946,7 +8078,7 @@ xref: SCTID:118966000 xref: UMLS:C1519343 {source="ncithesaurus:Skeletal_System_Part"} is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision relationship: part_of UBERON:0001434 ! skeletal system -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002473 UBERON:0004765 ! composed primarily of skeletal element [Term] @@ -8129,7 +8261,7 @@ is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000108 {source="BILS"} ! blastula stage relationship: RO:0002082 GO:0007369 ! simultaneous with gastrulation -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0000110 @@ -8145,7 +8277,7 @@ is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000109 ! gastrula stage relationship: RO:0002082 GO:0001841 ! simultaneous with neural tube formation -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: seeAlso "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/343" xsd:anyURI @@ -8165,7 +8297,7 @@ xref: Wikipedia:Organogenesis is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: RO:0002082 GO:0048513 ! simultaneous with animal organ development -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: seeAlso "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/533" xsd:anyURI @@ -8223,7 +8355,7 @@ xref: XAO:0003029 xref: ZFA:0000547 xref: ZFA:0000590 is_a: UBERON:0004921 ! subdivision of digestive tract -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002202 UBERON:0035804 ! develops from future mouth property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/661" xsd:anyURI @@ -8282,7 +8414,7 @@ is_a: UBERON:0011216 ! organ system subdivision intersection_of: UBERON:0011216 ! organ system subdivision intersection_of: RO:0002473 UBERON:0001015 ! composed primarily of musculature relationship: capable_of GO:0003012 ! muscle system process -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002473 UBERON:0001015 ! composed primarily of musculature property_value: IAO:0000116 "consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77" xsd:string property_value: RO:0002161 NCBITaxon:6040 @@ -8731,6 +8863,7 @@ xref: VHOG:0000387 xref: Wikipedia:Epithelium xref: XAO:0003045 xref: ZFA:0001486 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: RO:0002473 CL:0000066 ! composed primarily of epithelial cell @@ -8738,7 +8871,7 @@ union_of: UBERON:0000486 ! multilaminar epithelium union_of: UBERON:0000490 ! unilaminar epithelium relationship: has_part GO:0005911 ! cell-cell junction relationship: has_part UBERON:0005769 ! basement membrane of epithelium -relationship: RO:0002160 NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! in taxon Metazoa relationship: RO:0002473 CL:0000066 ! composed primarily of epithelial cell property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI @@ -8871,7 +9004,7 @@ xref: Wikipedia:Germ_layer xref: XAO:0003011 xref: ZFA:0001122 is_a: UBERON:0010316 ! germ layer / neural crest -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0000924 @@ -9025,7 +9158,7 @@ xref: ZFA:0001290 is_a: UBERON:0013522 ! subdivision of tube relationship: part_of UBERON:0000924 ! ectoderm relationship: part_of UBERON:0035804 ! future mouth -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI property_value: IAO:0000116 "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" xsd:string @@ -9070,7 +9203,7 @@ disjoint_from: UBERON:0002330 ! exocrine system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0004456 ! entire sense organ system -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002473 UBERON:0002368 ! composed primarily of endocrine gland relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage @@ -9217,7 +9350,7 @@ disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of GO:0003013 ! circulatory system process -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} @@ -9267,7 +9400,6 @@ namespace: uberon def: "The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]." [BIRNLEX:844, ISBN:0-14-051288-8, ISBN:3110148986, NLM:nervous+system, WB:rynl, Wikipedia:Nervous_system, ZFIN:curator] subset: cumbo subset: efo_slim -subset: human_reference_atlas subset: pheno_slim subset: uberon_slim subset: vertebrate_core @@ -9310,14 +9442,13 @@ disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of GO:0050877 ! nervous system process relationship: has_part CL:0000540 ! neuron -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002473 CL:0002319 ! composed primarily of neural cell relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage relationship: RO:0002495 UBERON:0016880 {source="Bgee:AN"} ! immediate transformation of future nervous system property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:6040 -property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001017 @@ -9364,7 +9495,7 @@ xref: ZFA:0000012 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0011216 {source="FBbt", source="cjm"} ! organ system subdivision relationship: part_of UBERON:0001016 ! nervous system -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria relationship: RO:0002495 UBERON:0016879 {source="Bgee:AN"} ! immediate transformation of future central nervous system property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} property_value: RO:0002175 NCBITaxon:9606 @@ -9645,7 +9776,7 @@ intersection_of: UBERON:0004765 ! skeletal element intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue disjoint_from: UBERON:0001630 ! muscle organ disjoint_from: UBERON:0005090 ! muscle structure -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002473 UBERON:0002481 {source="VSAO-modified"} ! composed primarily of bone tissue [Term] @@ -9683,7 +9814,7 @@ xref: WBbt:0005743 xref: ZFA:0000112 is_a: UBERON:0000025 ! tube relationship: part_of UBERON:0001007 ! digestive system -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002176 UBERON:0000165 ! connects mouth relationship: RO:0002495 UBERON:0007026 {source="NCBIBook:NBK10107"} ! immediate transformation of presumptive gut property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} @@ -9854,7 +9985,7 @@ xref: EMAPA:18765 xref: FMA:74562 xref: MA:0000013 is_a: UBERON:0000467 {source="MA"} ! anatomical system -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria [Term] id: UBERON:0002204 @@ -9929,7 +10060,7 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0011137 ! axial skeletal system relationship: produces PR:000014841 ! sonic hedgehog protein -relationship: RO:0002160 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! in taxon Chordata relationship: RO:0002202 UBERON:0004880 {source="ZFA"} ! develops from chordamesoderm relationship: RO:0002202 UBERON:0006267 {source="EHDAA2"} ! develops from notochordal plate relationship: RO:0002488 UBERON:0000068 ! existence starts during embryo stage @@ -9972,7 +10103,7 @@ xref: XAO:0000058 xref: ZFA:0000155 is_a: UBERON:0005423 ! developing anatomical structure is_a: UBERON:0007503 {source="EHDAA2"} ! epithelial vesicle -relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {source="GOTAX:0000352"} ! in taxon Chordata relationship: RO:0002202 UBERON:0003059 {source="ZFA"} ! develops from presomitic mesoderm property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:7712 {source="PMID:17237766"} @@ -9994,11 +10125,12 @@ xref: NCIT:C12957 xref: UMLS:C1516995 {source="ncithesaurus:Exocrine_System"} xref: Wikipedia:Exocrine_gland xref: WikipediaCategory:Exocrine_system +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000467 ! anatomical system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0004456 ! entire sense organ system -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002473 UBERON:0002365 ! composed primarily of exocrine gland relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage @@ -10036,7 +10168,7 @@ is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0010316 ! germ layer / neural crest relationship: part_of UBERON:0002346 {source="XAO", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! neurectoderm -relationship: RO:0002160 NCBITaxon:89593 ! only in taxon Craniata +relationship: RO:0002162 NCBITaxon:89593 ! in taxon Craniata relationship: RO:0002202 UBERON:0003075 {source="BTO"} ! develops from neural plate relationship: RO:0002202 UBERON:0005062 {source="PMID:11523831"} ! develops from neural fold relationship: RO:0002473 CL:0000333 ! composed primarily of migratory neural crest cell @@ -10103,6 +10235,7 @@ xref: NCIT:C12712 xref: SCTID:115976003 xref: UMLS:C0015282 {source="ncithesaurus:Exocrine_Gland"} xref: Wikipedia:Exocrine_gland +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002530 ! gland intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0002330 ! exocrine system @@ -10222,7 +10355,7 @@ xref: VSAO:0000017 xref: XAO:0001017 xref: ZFA:0001632 is_a: UBERON:0000479 ! tissue -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -10254,7 +10387,7 @@ intersection_of: UBERON:0000479 ! tissue intersection_of: RO:0002473 CL:0000187 ! composed primarily of muscle cell relationship: capable_of GO:0006936 ! muscle contraction relationship: part_of UBERON:0001015 ! musculature -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002473 CL:0000187 ! composed primarily of muscle cell [Term] @@ -10300,7 +10433,7 @@ is_a: UBERON:0004120 ! mesoderm-derived structure disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: part_of UBERON:0002193 {source="FMA"} ! hemolymphoid system -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002202 UBERON:0003061 ! develops from blood island property_value: RO:0002175 NCBITaxon:9606 @@ -10363,7 +10496,7 @@ xref: ZFA:0005621 is_a: UBERON:0004755 {source="VSAO"} ! skeletal tissue disjoint_from: UBERON:0005090 ! muscle structure relationship: part_of UBERON:0001474 ! bone element -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata property_value: IAO:0000116 "see https://github.com/obophenotype/uberon/issues/27" xsd:string [Term] @@ -10400,7 +10533,7 @@ xref: WikipediaCategory:Glands is_a: UBERON:0000062 ! organ relationship: capable_of GO:0046903 ! secretion relationship: produces UBERON:0000463 ! organism substance -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/a1/Gray1026.png" xsd:anyURI [Term] @@ -10522,7 +10655,7 @@ xref: XAO:0000205 xref: ZFA:0001204 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0000926 ! mesoderm -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002202 UBERON:0000926 ! develops from mesoderm property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI @@ -10556,7 +10689,7 @@ xref: ZFA:0000132 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0016879 ! future central nervous system -relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {source="GOTAX:0000352"} ! in taxon Chordata relationship: RO:0002256 UBERON:0002328 {source="Wikipedia"} ! developmentally induced by notochord relationship: RO:0002495 UBERON:0007284 {source="Bgee:AN"} ! immediate transformation of presumptive neural plate property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI @@ -10623,7 +10756,7 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue relationship: part_of UBERON:0000926 {source="EHDAA2", source="VHOG"} ! mesoderm -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria relationship: RO:0002221 UBERON:0003887 ! surrounds intraembryonic coelom property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI @@ -10716,7 +10849,7 @@ xref: ZFA:0000393 is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002328 GO:0032502 ! functionally related to developmental process relationship: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI @@ -10979,7 +11112,7 @@ is_a: UBERON:0034925 ! anatomical collection intersection_of: UBERON:0034925 ! anatomical collection intersection_of: RO:0002351 UBERON:0000982 ! has member skeletal joint relationship: part_of UBERON:0001434 {source="FMA"} ! skeletal system -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria relationship: RO:0002328 GO:0040011 ! functionally related to locomotion relationship: RO:0002351 UBERON:0000982 ! has member skeletal joint relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage @@ -11001,7 +11134,7 @@ xref: TAO:0000091 xref: ZFA:0000091 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0003068 ! axial mesoderm -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata [Term] id: UBERON:0004905 @@ -11044,7 +11177,7 @@ subset: upper_level xref: FMA:82485 is_a: UBERON:0000064 ! organ part relationship: part_of UBERON:0000060 ! anatomical wall -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0005061 @@ -11109,7 +11242,7 @@ synonym: "musculus" EXACT [FMA:30316] xref: FMA:30316 is_a: UBERON:0000061 ! anatomical structure relationship: has_part CL:0000187 ! muscle cell -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0005157 @@ -11221,11 +11354,12 @@ xref: NCIT:C13191 xref: SCTID:68989006 xref: UMLS:C0004799 {source="ncithesaurus:Basement_Membrane"} xref: Wikipedia:Basement_membrane +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005764 {source="FMA"} ! acellular membrane relationship: adjacent_to CL:0000066 ! epithelial cell relationship: has_part GO:0005587 ! collagen type IV trimer relationship: part_of UBERON:0000483 ! epithelium -relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa relationship: RO:0002473 GO:0005604 ! composed primarily of basement membrane property_value: RO:0002175 NCBITaxon:80999 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} @@ -11265,7 +11399,7 @@ xref: NCIT:C34232 xref: UMLS:C1518430 {source="ncithesaurus:Notochordal_Process"} xref: VHOG:0001213 is_a: UBERON:0005423 ! developing anatomical structure -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002202 UBERON:0000924 {source="EHDAA2"} ! develops from ectoderm [Term] @@ -11283,7 +11417,7 @@ intersection_of: UBERON:0006598 ! presumptive structure intersection_of: part_of UBERON:0000307 ! blastula intersection_of: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm relationship: part_of UBERON:0000307 ! blastula -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm [Term] @@ -11320,7 +11454,7 @@ intersection_of: UBERON:0006598 ! presumptive structure intersection_of: part_of UBERON:0000307 ! blastula intersection_of: RO:0002387 UBERON:0000924 ! has potential to develop into ectoderm relationship: part_of UBERON:0000307 ! blastula -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002387 UBERON:0000924 ! has potential to develop into ectoderm [Term] @@ -11338,7 +11472,7 @@ intersection_of: UBERON:0006598 ! presumptive structure intersection_of: part_of UBERON:0000307 ! blastula intersection_of: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm relationship: part_of UBERON:0000307 ! blastula -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm [Term] @@ -11502,6 +11636,7 @@ name: regular connective tissue namespace: uberon def: "Connective tissue, which consists of fibroblasts, the intercellular matrix of which contains a regular network of collagen and elastic fiber bundles. Examples: bone (tissue), cartilage (tissue), dense regular connective tissue." [FMA:20103] xref: FMA:20103 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002384 {source="FMA"} ! connective tissue disjoint_from: UBERON:0011821 ! irregular connective tissue relationship: has_part CL:0000057 ! fibroblast @@ -11695,6 +11830,7 @@ xref: AAO:0000121 xref: NCIT:C32450 xref: UMLS:C1511770 {source="ncithesaurus:Dense_Connective_Tissue"} xref: Wikipedia:Dense_connective_tissue +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002384 ! connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: RO:0002473 UBERON:0011860 ! composed primarily of collection of collagen fibrils @@ -11709,6 +11845,7 @@ xref: FMA:63212 xref: MESH:D024022 xref: NCIT:C32339 xref: NIF_Subcellular:sao7547390221 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000476 {source="ZFA"} ! acellular anatomical structure relationship: RO:0002473 GO:0005581 ! composed primarily of collagen trimer relationship: RO:0002473 GO:0098643 ! composed primarily of banded collagen fibril @@ -11744,7 +11881,7 @@ synonym: "schizocoelom" NARROW [] xref: EHDAA2:0004731 xref: Wikipedia:Coelom is_a: UBERON:0000481 {source="EHDAA2"} ! multi-tissue structure -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria property_value: IAO:0000116 "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." xsd:string property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} @@ -11801,7 +11938,7 @@ namespace: uberon def: "A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages." [https://orcid.org/0000-0002-6601-2165] subset: non_informative is_a: UBERON:0000475 ! organism subdivision -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0013702 @@ -11851,7 +11988,7 @@ intersection_of: RO:0002219 UBERON:0011899 ! surrounded by epimysium intersection_of: RO:0002473 UBERON:0001134 ! composed primarily of skeletal muscle tissue relationship: part_of UBERON:0018254 ! skeletal musculature relationship: RO:0002103 CL:0000100 ! synapsed by motor neuron -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002202 UBERON:0003082 ! develops from myotome relationship: RO:0002219 UBERON:0011899 ! surrounded by epimysium relationship: RO:0002473 UBERON:0001134 ! composed primarily of skeletal muscle tissue @@ -11885,7 +12022,7 @@ def: "Any structure that is placed on one side of the left-right axis of a bilat subset: grouping_class subset: non_informative is_a: UBERON:0000061 ! anatomical structure -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria [Term] id: UBERON:0015228 @@ -13456,9 +13593,7 @@ inverse_of: output_of ! output of [Typedef] id: has_part name: has part -name: has_part namespace: external -namespace: quality def: "a core relation that holds between a whole and its part" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology @@ -13663,9 +13798,7 @@ expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://p [Typedef] id: part_of name: part of -name: part_of namespace: external -namespace: quality def: "a core relation that holds between a part and its whole" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term diff --git a/src/ontology/subsets/general_cell_types_upper_slim.owl b/src/ontology/subsets/general_cell_types_upper_slim.owl index 0df0a51ec..8065f3828 100644 --- a/src/ontology/subsets/general_cell_types_upper_slim.owl +++ b/src/ontology/subsets/general_cell_types_upper_slim.owl @@ -22,8 +22,8 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - 2024-08-16 + + 2024-09-26 @@ -392,6 +392,14 @@ WHERE { + + + + + + + + @@ -1038,6 +1046,12 @@ WHERE { + + + + + + @@ -1076,17 +1090,13 @@ WHERE { - - created by - + - - creation date - + @@ -1172,9 +1182,7 @@ WHERE { - - id - + @@ -1283,7 +1291,6 @@ WHERE { A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. BFO:0000050 external - quality part_of @@ -1292,7 +1299,6 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of part of part of - part_of http://www.obofoundry.org/ro/#OBO_REL:part_of @@ -1314,7 +1320,6 @@ A continuant cannot be part of an occurrent: use 'participates in'. An A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. BFO:0000051 external - quality has_part @@ -1322,7 +1327,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part has part has part - has_part @@ -4768,7 +4772,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -4812,44 +4816,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - Any sensory receptor cell that is a(n) neuron and is capable of some detection of stimulus involved in sensory perception. - ZFA:0009001 - neuronal receptor cell (sensu Animalia) - - neuronal receptor cell - - - - - Any sensory receptor cell that is a(n) neuron and is capable of some detection of stimulus involved in sensory perception. - FBC:Autogenerated - - - - - ZFA:0009001 - - - - - @@ -4887,6 +4853,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -5189,6 +5156,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -5604,7 +5572,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -5847,6 +5815,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -5993,6 +5962,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6204,8 +6174,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different A vertebrate phagocyte with a single nucleus. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Mononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. +In addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses. +Mononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer. BTO:0001433 ZFA:0009064 + https://cellxgene.cziscience.com/cellguide/CL_0000113 mononuclear phagocyte @@ -6224,6 +6200,18 @@ Each of these 3 primitives can be composed to yield a cross-product of different GOC:tfm ISBN:0781735149 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Mononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. +In addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses. +Mononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer. + DOI:10.1016/j.coi.2005.11.008 + DOI:10.1038/nri3087 + DOI:10.3389/fimmu.2019.01893 + @@ -6239,11 +6227,19 @@ Each of these 3 primitives can be composed to yield a cross-product of different A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Glial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons. +These different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning. +Oligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. +Microglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response. +Despite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis. BTO:0002606 CALOHA:TS-0415 FBbt:00005144 FMA:54536 ZFA:0009073 + https://cellxgene.cziscience.com/cellguide/CL_0000125 neuroglial cell neuroglia @@ -6258,6 +6254,22 @@ Each of these 3 primitives can be composed to yield a cross-product of different A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons. MESH:D009457 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Glial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons. +These different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning. +Oligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. +Microglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response. +Despite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis. + DOI:10.1002/glia.24343 + DOI:10.1038/nn1988 + DOI:10.1101/cshperspect.a020602 + DOI:10.1126/science.aat0473 + DOI:10.3389/fncel.2017.00024 + @@ -6534,6 +6546,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6637,6 +6650,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6689,6 +6703,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6757,6 +6772,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6813,7 +6829,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -6902,45 +6918,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A cell that is capable of detection of a stimulus involved in sensory perception. - MESH:D011984 - receptor cell - sensory receptor cell - - - - @@ -6950,19 +6927,20 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + + - + - A cell specialized to detect and transduce light. + A cell specialized in detecting light stimuli that are involved in visual perception. BTO:0001060 CALOHA:TS-0868 FBbt:00004211 @@ -6972,16 +6950,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different photoreceptor cell https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg - - - - - true - - A cell specialized to detect and transduce light. + A cell specialized in detecting light stimuli that are involved in visual perception. MESH:D010786 @@ -7065,6 +7037,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -7096,6 +7069,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -7129,6 +7103,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -7171,6 +7146,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -7205,6 +7181,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -7213,11 +7190,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell with more than one nucleus. - AEO:0000203 - WBbt:0008074 - syncitium - syncytial cell - syncytium + multinucleated cells + polynuclear cells multinucleate cell @@ -7225,6 +7199,19 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell with more than one nucleus. FB:ma + Wikipedia:Multinucleate + + + + + multinucleated cells + Wikipedia:Multinucleate + + + + + polynuclear cells + Wikipedia:Multinucleate @@ -7424,7 +7411,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -7433,11 +7420,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - Any cell that only exists in Eukaryota. + Any cell that in taxon some Eukaryota. MESH:D005057 eukaryotic cell @@ -7445,7 +7432,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - Any cell that only exists in Eukaryota. + Any cell that in taxon some Eukaryota. FBC:Autogenerated @@ -7530,7 +7517,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -7625,7 +7612,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -7636,7 +7623,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -7758,6 +7745,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -8046,7 +8034,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -8327,6 +8315,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -8474,6 +8463,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -8548,6 +8538,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -8805,6 +8796,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -8964,7 +8956,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -9122,6 +9114,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -9295,6 +9288,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -9417,6 +9411,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -9626,7 +9621,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + @@ -10058,7 +10055,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -10420,6 +10417,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -10464,6 +10462,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -10678,7 +10677,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -10717,7 +10716,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -10800,26 +10799,26 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - A transversely striated, synctial muscle cell, formed by the fusion of myoblasts. + A transversely striated, multinucleated syncytial muscle cell, formed by the fusion of myoblasts during muscle development. 2010-09-24T01:13:01Z FBbt:00005812 - myotubule - single cell sarcomere + myofiber + myofibril myotube - A transversely striated, synctial muscle cell, formed by the fusion of myoblasts. + A transversely striated, multinucleated syncytial muscle cell, formed by the fusion of myoblasts during muscle development. GOC:dos GOC:tfm ISBN:0323052908 @@ -10831,6 +10830,18 @@ Each of these 3 primitives can be composed to yield a cross-product of different FBbt:00005812 + + + + myofiber + FBbt:00005812 + + + + + myofibril + FBbt:00005812 + @@ -10848,7 +10859,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -11064,6 +11075,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -11086,6 +11098,41 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + Any neuron that is capable of part of some visual perception. + + 2017-07-09T19:12:36Z + visual system neuron + + + + + Any neuron that is capable of part of some visual perception. + FBC:Autogenerated + + + + @@ -11173,6 +11220,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. +After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. +Disorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis. + https://cellxgene.cziscience.com/cellguide/CL_0011012 neural crest cell @@ -11183,6 +11236,19 @@ Each of these 3 primitives can be composed to yield a cross-product of different https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-9900-7880 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. +After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. +Disorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis. + DOI:10.1002/dvg.23276 + DOI:10.1242/dev.193193 + DOI:10.3389/fcell.2020.00635/full + https://doi.org/10.1016/j.ydbio.2011.12.042 + @@ -11200,6 +11266,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -11376,6 +11443,61 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + + + + + A multinucleate cell formed by the fusion of multiple uninuclear cells through plasma membrane fusion. This process leads to a single large cell containing multiple nuclei within a shared cytoplasm. + + 2024-08-15T10:38:46Z + syncytium + SC + syncytial cell + + + + + A multinucleate cell formed by the fusion of multiple uninuclear cells through plasma membrane fusion. This process leads to a single large cell containing multiple nuclei within a shared cytoplasm. + PMID:20851884 + Wikipedia:Syncytium + + + + + syncytium + WBbt:0008074 + + + + + SC + PMID:9067520 + + + + + @@ -11394,10 +11516,42 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells. + cell fusion + biological_process + GO:0000768 + syncytium formation by plasma membrane fusion + + + + + The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells. + GOC:mtg_muscle + GOC:tb + + + + - + @@ -11405,6 +11559,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome. + https://github.com/geneontology/go-ontology/issues/28301 GO:0000789 GO:0000790 GO:0005717 @@ -12879,32 +13034,32 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. Wikipedia:Collagen cellular_component GO:0005581 collagen trimer - + - + - + PMID:12382326 - + PMID:12382326 @@ -13869,6 +14024,43 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + + The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane. Syncytia are normally derived from single cells that fuse or fail to complete cell division. + biological_process + GO:0006949 + + syncytium formation + + + + + The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane. Syncytia are normally derived from single cells that fuse or fail to complete cell division. + ISBN:0198506732 + + + + @@ -13951,6 +14143,58 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + + + + + + + A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the plasma membrane. + plasma membrane organisation + biological_process + plasma membrane organization and biogenesis + GO:0007009 + + plasma membrane organization + + + + + A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the plasma membrane. + GOC:dph + GOC:jl + GOC:mah + + + + + plasma membrane organization and biogenesis + GOC:mah + + + + @@ -14926,6 +15170,51 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endomembrane system. + endomembrane organization + endomembrane system organisation + biological_process + GO:0010256 + + endomembrane system organization + + + + + A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endomembrane system. + GOC:mah + GOC:sm + + + + + endomembrane system organisation + GOC:mah + + + + @@ -15420,6 +15709,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different The self-renewing division of a stem cell. A stem cell is an undifferentiated cell, in the embryo or adult, that can undergo unlimited division and give rise to one or several different cell types. + + + stem cell renewal biological_process GO:0017145 @@ -17052,12 +17344,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - + A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. GO:0043234 @@ -17087,33 +17374,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - A macromolecular complex containing both protein and DNA molecules. - DNA-protein complex - cellular_component - GO:0032993 - - Note that this term is intended to classify complexes that have DNA as one of the members of the complex, that is, the complex does not exist if DNA is not present. Protein complexes that interact with DNA e.g. transcription factor complexes should not be classified here. - protein-DNA complex - - - - - A macromolecular complex containing both protein and DNA molecules. - GOC:mah - - - - - DNA-protein complex - GOC:mah - - - - @@ -17829,10 +18089,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. + https://github.com/geneontology/go-ontology/issues/28153 NIF_Subcellular:sao414196390 membrane-enclosed organelle cellular_component GO:0043227 + membrane-bounded organelle @@ -17850,11 +18112,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. https://github.com/geneontology/go-ontology/issues/21881 + https://github.com/geneontology/go-ontology/issues/28153 NIF_Subcellular:sao1456184038 non-membrane-enclosed organelle cellular_component biological condensate GO:0043228 + non-membrane-bounded organelle @@ -17889,8 +18153,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. + https://github.com/geneontology/go-ontology/issues/28153 cellular_component GO:0043229 + intracellular organelle @@ -18111,10 +18377,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component. + https://github.com/geneontology/go-ontology/issues/27194 GO:0071843 cellular component biogenesis at cellular level biological_process GO:0044085 + cellular component biogenesis @@ -18264,12 +18532,55 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + + The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell. + GO:0006947 + cell fusion + cell-cell fusion + biological_process + GO:0045026 + plasma membrane fusion + + + + + The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell. + GOC:elh + GOC:mtg_muscle + + + + Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens. + + + GO:0002226 Wikipedia:Innate_immune_system innate immunity @@ -19537,6 +19848,49 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + The series of events involved in visual perception in which a light stimulus is received and converted into a molecular signal. + sensory detection of light during visual perception + sensory detection of light stimulus during visual perception + sensory transduction of light during visual perception + sensory transduction of light stimulus during visual perception + visual perception, detection of light stimulus + visual perception, sensory transduction during perception of light + visual perception, sensory transduction of light stimulus + biological_process + GO:0050908 + detection of light stimulus involved in visual perception + + + + + The series of events involved in visual perception in which a light stimulus is received and converted into a molecular signal. + GOC:ai + GOC:dos + + + + @@ -20796,6 +21150,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -21486,6 +21841,35 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + A cellular process in which two or more cells combine together, their plasma membrane fusing, producing a single cell. In some cases, nuclei fuse, producing a polyploid cell, while in other cases, nuclei remain separate, producing a syncytium. + https://github.com/geneontology/go-ontology/issues/15939 + pg + 2018-08-13T18:38:18Z + cell fusion + cell cell fusion + biological_process + GO:0140253 + cell-cell fusion + + + + + A cellular process in which two or more cells combine together, their plasma membrane fusing, producing a single cell. In some cases, nuclei fuse, producing a polyploid cell, while in other cases, nuclei remain separate, producing a syncytium. + Wikipedia:Cell_fusion + + + + @@ -23417,7 +23801,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -25442,51 +25826,51 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + - A molecular entity that minimally consists of a protein. + A material entity that minimally consists of a protein. protein protein aggregate protein complex protein-containing complex protein - PR:000064867 - Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). - protein-containing molecular entity + PR:000050567 + Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566). + protein-containing material entity - + - A molecular entity that minimally consists of a protein. + A material entity that minimally consists of a protein. PRO:DAN - + protein PRO:DAN - + protein aggregate PRO:DAN - + protein complex PRO:DAN - + protein-containing complex PRO:DAN @@ -25697,11 +26081,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + - + @@ -25746,11 +26130,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different tendon http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg - + - + @@ -25763,13 +26147,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + OG - + AEO @@ -25806,6 +26190,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -26298,7 +26683,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -26674,7 +27059,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -26683,7 +27068,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -26710,14 +27095,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different gastrula stage - + - + BILS @@ -26789,7 +27174,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -26832,7 +27217,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -26866,7 +27251,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -27105,7 +27490,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -28111,6 +28496,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -28124,7 +28510,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -28166,14 +28552,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg - - + + - + http://palaeos.com/metazoa/porifera/homoscleromorpha.html @@ -28425,7 +28811,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -28516,7 +28902,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. AAO:0000137 BILA:0000036 @@ -28551,14 +28937,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png - + - + Bgee:AN @@ -28598,7 +28984,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. AAO:0000139 BILA:0000038 @@ -28633,14 +29019,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png - + - + Bgee:AN @@ -28681,7 +29067,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The middle germ layer of the embryo, between the endoderm and ectoderm. UBERON:0003263 @@ -28722,14 +29108,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png - + - + Bgee:AN @@ -28784,7 +29170,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -28891,7 +29277,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -28985,8 +29371,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + @@ -29018,24 +29404,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different eye - + - + - + PMID:21062451 - + PMID:21062451 @@ -29250,7 +29636,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -29407,7 +29793,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -29429,7 +29815,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -29438,7 +29824,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]. - AAO:0000324 BILA:0000079 BIRNLEX:844 @@ -29473,7 +29858,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0001016 - @@ -29481,14 +29865,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png - + - + Bgee:AN @@ -29550,11 +29934,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. @@ -29599,7 +29983,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different central nervous system - + @@ -29613,7 +29997,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Bgee:AN @@ -30329,11 +30713,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + Skeletal element that is composed of bone tissue. @@ -30375,14 +30759,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different bone element - + - + VSAO-modified @@ -30438,7 +30822,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -30448,7 +30832,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A tube extending from the mouth to the anus. @@ -30485,14 +30869,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different digestive tract - + - + NCBIBook:NBK10107 @@ -30899,7 +31283,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -31021,9 +31405,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - + + + @@ -31071,15 +31455,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - - + + - + - + @@ -31098,19 +31482,19 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -31150,8 +31534,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. mesodermal cluster @@ -31189,11 +31573,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - - + + - + @@ -31206,13 +31590,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + GOTAX:0000352 - + ZFA @@ -31271,10 +31655,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different + - + @@ -31337,22 +31722,22 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + - - + + - + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. AAO:0010578 BTO:0001764 @@ -31385,45 +31770,45 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - + BTO - + PMID:11523831 - + PMID:11523831 @@ -31552,6 +31937,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -31730,7 +32116,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -31786,14 +32172,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different bone marrow http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg - + - + FMA MA @@ -31841,7 +32227,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -31932,7 +32318,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -32005,10 +32391,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -32059,14 +32445,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different hematopoietic system - + - + FMA @@ -32165,7 +32551,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -32250,7 +32636,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -32476,7 +32862,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. AAO:0011086 EFO:0001982 @@ -32499,14 +32885,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different presomitic mesoderm - + - + Bgee:AN @@ -32612,7 +32998,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -32660,9 +33046,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. AAO:0011072 BTO:0001765 @@ -32691,34 +33077,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - - + + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -32758,7 +33144,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. AAO:0010568 EFO:0003515 @@ -32784,7 +33170,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -32797,7 +33183,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Bgee:AN @@ -32844,10 +33230,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -32884,7 +33270,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -32897,7 +33283,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 VHOG @@ -32947,7 +33333,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -32988,7 +33374,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different myotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + @@ -33001,7 +33387,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2-abduced @@ -33083,7 +33469,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -33161,7 +33547,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults EHDAA:251 @@ -33176,14 +33562,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different intraembryonic coelom - + - + Wikipedia @@ -33485,7 +33871,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The bilaminar epithelium formed from the myotome and dermatome. AAO:0010572 AEO:0000214 @@ -33503,7 +33889,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0004290 dermomyotome - + @@ -33522,7 +33908,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 ZFA @@ -33853,7 +34239,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. AAO:0011129 TAO:0001890 @@ -33867,14 +34253,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different skeletal element - + - + VSAO @@ -33901,10 +34287,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -33940,14 +34326,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0004770 articular system - + - + FMA @@ -33989,7 +34375,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -34155,7 +34541,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -34316,7 +34702,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -34388,7 +34774,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -34404,14 +34790,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different trunk mesenchyme - + - + EHDAA2 @@ -34619,6 +35005,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -34634,7 +35021,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -34720,7 +35107,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB EHDAA2:0001278 @@ -34734,7 +35121,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different notochordal plate - + @@ -34747,7 +35134,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 @@ -34771,11 +35158,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -34792,14 +35179,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -34844,7 +35231,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -34953,7 +35340,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -35017,7 +35404,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -35410,7 +35797,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -35436,7 +35823,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different presumptive paraxial mesoderm - + @@ -35452,7 +35839,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + https://github.com/obophenotype/uberon/issues/1277 @@ -35501,7 +35888,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -35509,7 +35896,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0007524 dense mesenchyme tissue - + @@ -35522,7 +35909,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + AEO @@ -35537,6 +35924,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -35680,7 +36068,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -35697,14 +36085,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -35726,7 +36114,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -35734,14 +36122,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -36150,6 +36538,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -36185,6 +36574,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -36221,7 +36611,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -36245,7 +36635,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0011899 epimysium - + @@ -36258,7 +36648,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + FMA @@ -36295,7 +36685,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -36364,7 +36754,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -36385,7 +36775,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0012429 hematopoietic tissue - + @@ -36398,7 +36788,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + defitional @@ -36531,7 +36921,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -36639,7 +37029,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -36768,7 +37158,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -36953,7 +37343,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -36976,7 +37366,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0016887 entire extraembryonic component - + @@ -36989,7 +37379,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + AEO @@ -37075,7 +37465,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -37092,14 +37482,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different skeletal musculature - + - + MA @@ -37576,48 +37966,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different /////////////////////////////////////////////////////////////////////////////////////// --> - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - @@ -37648,6 +37996,454 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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+_:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid762 +_:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid783 +_:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid791 +_:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid798 +_:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid808 +_:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid821 +_:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid837 +_:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid845 +_:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid852 +_:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid862 +_:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid889 +_:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid906 +_:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid915 +_:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid965 +_:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid973 +_:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid981 +_:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid993 "cell" - "neuronal receptor cell" "early embryonic cell (metazoa)" "stem cell" "hematopoietic stem cell" @@ -313,7 +346,6 @@ _:B993c35aeX2D65c9X2D47bfX2Dbc91X2D1922643fd86cgenid993 "muscle cell" "cell of skeletal muscle" "smooth muscle cell" - "sensory receptor cell" "photoreceptor cell" "electrically active cell" "motile cell" @@ -394,6 +426,7 @@ _:B993c35aeX2D65c9X2D47bfX2Dbc91X2D1922643fd86cgenid993 "skeletal muscle fiber" "visceral muscle cell" "mesenchymal cell" + "visual system neuron" "retinal cell" "zygote" "cardiac myoblast" @@ -403,7 +436,9 @@ _:B993c35aeX2D65c9X2D47bfX2Dbc91X2D1922643fd86cgenid993 "neutrophillic cytoplasm" "basophilic cytoplasm" "bone marrow hematopoietic cell" + "syncytial cell" "lytic vacuole" + "syncytium formation by plasma membrane fusion" "chromatin" "euchromatin" "heterochromatin" @@ -474,8 +509,10 @@ _:B993c35aeX2D65c9X2D47bfX2Dbc91X2D1922643fd86cgenid993 "vesicle fusion" "phagocytosis" "muscle contraction" + "syncytium formation" "immune response" "organelle organization" + "plasma membrane organization" "cell communication" "cell-cell signaling" "chemical synaptic transmission" @@ -509,6 +546,7 @@ _:B993c35aeX2D65c9X2D47bfX2Dbc91X2D1922643fd86cgenid993 "tissue development" "hormone transport" "cellular process" + "endomembrane system organization" "membrane invagination" "gene expression" "regulation of hormone levels" @@ -567,7 +605,6 @@ _:B993c35aeX2D65c9X2D47bfX2Dbc91X2D1922643fd86cgenid993 "secretion by cell" "protein-containing complex disassembly" "protein-containing complex" - "protein-DNA complex" "V(D)J recombination" "immunoglobulin V(D)J recombination" "monoatomic ion transmembrane transport" @@ -603,6 +640,7 @@ _:B993c35aeX2D65c9X2D47bfX2Dbc91X2D1922643fd86cgenid993 "primary metabolic process" "cellular biosynthetic process" "biological process involved in interspecies interaction between organisms" + "plasma membrane fusion" "innate immune response" "synapse" "leukocyte activation" @@ -639,6 +677,7 @@ _:B993c35aeX2D65c9X2D47bfX2Dbc91X2D1922643fd86cgenid993 "nervous system process" "response to stimulus" "detection of stimulus involved in sensory perception" + "detection of light stimulus involved in visual perception" "sensory perception of light stimulus" "detection of light stimulus involved in sensory perception" "localization" @@ -694,6 +733,7 @@ _:B993c35aeX2D65c9X2D47bfX2Dbc91X2D1922643fd86cgenid993 "plasma membrane bounded cell projection" "plasma membrane bounded cell projection organization" "exocytic process" + "cell-cell fusion" "export from cell" "defense response to symbiont" "regulation of leukocyte differentiation" @@ -831,7 +871,7 @@ _:B993c35aeX2D65c9X2D47bfX2Dbc91X2D1922643fd86cgenid993 "eukaryotic protein" "cathepsin-like protease" "receptor-type tyrosine-protein phosphatase C isoform CD45R" - "protein-containing molecular entity" + "protein-containing material entity" "processual entity" "sense organ" "tube" diff --git a/src/ontology/subsets/kidney_upper_slim.json b/src/ontology/subsets/kidney_upper_slim.json index 5bc36508b..ddee7b988 100644 --- a/src/ontology/subsets/kidney_upper_slim.json +++ b/src/ontology/subsets/kidney_upper_slim.json @@ -4,9 +4,9 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-08-16" + "val" : "2024-09-26" } ], - "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-08-16/subsets/kidney_upper_slim.owl" + "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-09-26/subsets/kidney_upper_slim.owl" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/CL_0000000", @@ -491,6 +491,10 @@ "lbl" : "squamous epithelial cell", "type" : "CLASS", "meta" : { + "definition" : { + "val" : "Any epithelial cell that is part of some squamous epithelium.", + "xrefs" : [ "FBC:Autogenerated" ] + }, "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-1249" @@ -899,7 +903,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "Any cell that only exists in Eukaryota.", + "val" : "Any cell that in taxon some Eukaryota.", "xrefs" : [ "FBC:Autogenerated" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], @@ -1441,6 +1445,12 @@ } ], "xrefs" : [ { "val" : "ZFA:0009286" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000666" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nFenestrated cells are specialized epithelial cells that are characterized by a distinctive structural feature, fenestrations or tiny pores, which allow an exchange of substances such as fluids, nutrients, and waste between blood vessels and the surrounding tissue environments. These cells are present in various types of epithelial tissues in the human body, including the intestinal tract, endocrine glands, and certain parts of the renal system. \nThere are multiple types of endothelial cell fenestrations. The most common type is found in systemic capillaries of the endocrine tissue (e.g., pancreatic islets), gastrointestinal mucosa, and renal peritubular capillaries. Here, the fenestrated cells have fenestrations in their peripheral cytoplasm with a unique thin and permeable diaphragm that provides a high degree of selectivity, blocking the passage of larger molecules while allowing the free movement of smaller ones. In contrast, other types of fenestrations, such as the discontinuous epithelium of the liver sinusoidal endothelial cells, do not have diaphragms. \nCharacteristically, fenestrated cells play a vital role in the filtering process of body systems. They are a key part of the glomeruli in the kidneys where blood is filtered under high pressure. The fenestrations present in the endothelial cells lining the capillaries of the glomerulus allow the free passage of water and small solute molecules towards the Bowman's capsule, leaving behind larger proteins and cells in the blood, thereby aiding in the filtration and waste removal process. \nIn the endocrine system, fenestrated cells in glandular capillaries allow the prompt release of hormones into the bloodstream. These cells have tightly clustered fenestrations which increase the surface area available for passive diffusion, improving the efficiency of hormone secretion. In villi of the small intestine, these cells increase absorption efficiency, permitting the exchange of water, electrolytes, and nutrients.\nOverall, fenestrated cells contribute immensely to important physiological processes of filtration, absorption, and secretion, primarily connecting our body's circulation system with the surrounding tissues and organs." } ] } }, { @@ -2080,27 +2090,6 @@ "val" : "2011-02-08T10:46:34Z" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/CL_0002546", - "lbl" : "embryonic blood vessel endothelial progenitor cell", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An endothelial progenitor cell that participates in angiogenesis during development.", - "xrefs" : [ "GOC:tfm" ] - }, - "comments" : [ "See CL:0002619." ], - "xrefs" : [ { - "val" : "ZFA:0005773" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0003-1980-3228" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2011-02-28T04:20:39Z" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/CL_0002584", "lbl" : "renal cortical epithelial cell", @@ -2159,6 +2148,12 @@ "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], "xrefs" : [ { "val" : "ZFA:0005322" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0005009" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nRenal principal cells are the major cell type in the initial collecting tubule and the cortical and outer medullary collecting ducts, as well as the connecting tubule, in the nephrons of the kidneys.\nA key function of renal principal cells is the regulation of water balance in the body. These cells express aquaporin-2 (AQP2) water channels, which facilitate the reabsorption of water from the fluid within the renal tubule lumen back into the blood. The translocation of AQP2 to the cell membrane is controlled by the hormone vasopressin: In response to high vasopressin levels, AQP2 moves to the cell membrane, allowing water to pass through effectively and be reabsorbed, therefore concentrating the urine. Conversely, in low vasopressin conditions, AQP2 is removed from the membrane, reducing water reabsorption and diluting the urine. \nRenal principal cells are also involved in the regulation of sodium and potassium levels in the body. They have sodium channels (ENaC) in their luminal membranes which permit the reabsorption of sodium ions from the tubule fluid back into the blood, resulting in a net reabsorption of sodium ions into the systemic circulation. This process is controlled, in part, by the hormone aldosterone. Additionally, renal principal cells contain potassium channels that facilitate the secretion of potassium ions into the urine. The activities of these channels, in coordination with other cell types in the nephron, are critical for maintaining electrolyte balance and overall body homeostasis." } ] } }, { @@ -2282,7 +2277,14 @@ "val" : "A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells.", "xrefs" : [ "https://orcid.org/0000-0001-5208-3432", "https://orcid.org/0000-0002-9900-7880" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "xrefs" : [ { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0011012" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." + } ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0011026", @@ -2423,10 +2425,15 @@ "val" : "FMA:70982" }, { "val" : "KUPO:0001059" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_1000454" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nKidney collecting duct epithelial cells are a specialized type of cells that form an integral part of the renal system. Located in the collecting duct system of the kidneys, these cells are responsible for one of the final steps in the process of urine formation, and they are instrumental in the fine tuning of the volume and composition of urine by reabsorbing water and certain solutes back into the bloodstream.\nThese cells express specific channels and carriers that actively and passively transport ions and water. They also have channels on their membranes, such as sodium channels and potassium channels, involved in reabsorbing or secreting these electrolytes depending upon the body's needs. The function of renal collecting duct epithelial cells can be regulated by a variety of hormones, including vasopressin (antidiuretic hormone), which can modulate the ion channels and carriers and hence indirectly influence body fluid homeostasis.\nAside from their function in ion and water balance, kidney collecting duct epithelial cells also aid in maintaining the body's acid-base balance. They have specialized functionality to secret hydrogen ions into the tubular lumen, which contributes to acid excretion. Any dysfunction may have serious implications and lead to various renal or systemic diseases, exemplifying the importance of these cells in maintaining overall body homeostasis." } ] } }, { @@ -2921,6 +2928,9 @@ "val" : "NIF_Subcellular:sao1615953555" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28301" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "GO:0000789" }, { @@ -3139,7 +3149,7 @@ "val" : "A slow mechanism of blood pressure regulation that responds to changes in pressure resulting from fluid and salt intake by modulating the quantity of blood in the circulatory system.", "xrefs" : [ "GOC:dph", "GOC:tb", "ISBN:0721643949" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_obsoletion_candidate" ], "synonyms" : [ { "pred" : "hasRelatedSynonym", "val" : "renal blood volume control of blood pressure" @@ -4533,6 +4543,15 @@ "val" : "gametogenesis" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_2" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_2157" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "GO:0009552" }, { @@ -5503,6 +5522,15 @@ "val" : "stem cell renewal" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_2" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_2157" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -6448,27 +6476,6 @@ "val" : "cellular_component" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0032993", - "lbl" : "protein-DNA complex", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A macromolecular complex containing both protein and DNA molecules.", - "xrefs" : [ "GOC:mah" ] - }, - "comments" : [ "Note that this term is intended to classify complexes that have DNA as one of the members of the complex, that is, the complex does not exist if DNA is not present. Protein complexes that interact with DNA e.g. transcription factor complexes should not be classified here." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "DNA-protein complex", - "xrefs" : [ "GOC:mah" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0033036", "lbl" : "macromolecule localization", @@ -6642,6 +6649,15 @@ "xrefs" : [ "PMID:19129259" ] } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_2" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_2157" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "bf" }, { @@ -6883,6 +6899,7 @@ "val" : "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.", "xrefs" : [ "GOC:go_curators" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "membrane-enclosed organelle" @@ -6891,6 +6908,9 @@ "val" : "NIF_Subcellular:sao414196390" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28153" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -6904,7 +6924,7 @@ "val" : "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes.", "xrefs" : [ "GOC:go_curators" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_mouse" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_mouse" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "non-membrane-enclosed organelle" @@ -6918,6 +6938,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/21881" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28153" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -6932,8 +6955,11 @@ "val" : "Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.", "xrefs" : [ "GOC:go_curators" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_pir" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28153" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -7090,12 +7116,15 @@ "val" : "A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component.", "xrefs" : [ "GOC:jl", "GOC:mah" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_pir" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "cellular component biogenesis at cellular level" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/27194" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "GO:0071843" }, { @@ -11928,15 +11957,15 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/PR_000064867", - "lbl" : "protein-containing molecular entity", + "id" : "http://purl.obolibrary.org/obo/PR_000050567", + "lbl" : "protein-containing material entity", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A molecular entity that minimally consists of a protein.", + "val" : "A material entity that minimally consists of a protein.", "xrefs" : [ "PRO:DAN" ] }, - "comments" : [ "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565)." ], + "comments" : [ "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566)." ], "synonyms" : [ { "pred" : "hasNarrowSynonym", "val" : "protein", @@ -16773,7 +16802,7 @@ "val" : "The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO].", "xrefs" : [ "BIRNLEX:844", "ISBN:0-14-051288-8", "ISBN:3110148986", "NLM:nervous+system", "WB:rynl", "Wikipedia:Nervous_system", "ZFIN:curator" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#cumbo", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#cumbo", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "neurological system", @@ -16846,9 +16875,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -29093,7 +29119,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000050", - "lbl" : "part_of", + "lbl" : "part of", "type" : "PROPERTY", "propertyType" : "OBJECT", "meta" : { @@ -29116,9 +29142,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "part_of" @@ -29138,7 +29161,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000051", - "lbl" : "has_part", + "lbl" : "has part", "type" : "PROPERTY", "propertyType" : "OBJECT", "meta" : { @@ -29161,9 +29184,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_part" @@ -33028,6 +33048,10 @@ "id" : "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "type" : "PROPERTY", "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#gocheck_obsoletion_candidate", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/go#goslim_agr", "type" : "PROPERTY", @@ -33366,6 +33390,10 @@ "id" : "http://purl.org/dc/terms/date", "type" : "PROPERTY", "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/description", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/license", "type" : "PROPERTY", @@ -33391,12 +33419,10 @@ "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "lbl" : "created by", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "lbl" : "creation date", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { @@ -33489,7 +33515,6 @@ "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#id", - "lbl" : "id", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { @@ -33559,12 +33584,16 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000000", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_131567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000007", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0002321" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000034", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000034", "pred" : "is_a", @@ -33738,7 +33767,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000066", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000066", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -33759,10 +33788,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000071", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0004638" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000071", - "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/CL_0002546" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000072", "pred" : "is_a", @@ -33779,6 +33804,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000076", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000066" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000076", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0006914" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000081", "pred" : "is_a", @@ -33797,6 +33826,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000115", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000213" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000115", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000115", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -33843,6 +33876,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000187", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000183" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000187", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000187", "pred" : "is_a", @@ -33883,6 +33920,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000219", "pred" : "http://purl.obolibrary.org/obo/RO_0002215", "obj" : "http://purl.obolibrary.org/obo/GO_0048870" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000221", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000221", "pred" : "is_a", @@ -33891,6 +33932,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000221", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000924" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000222", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000222", "pred" : "is_a", @@ -33899,6 +33944,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000222", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000926" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000223", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000223", "pred" : "is_a", @@ -33947,7 +33996,7 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0000000" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000255", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000329", @@ -33995,7 +34044,7 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0010017" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000365", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000393", @@ -34043,6 +34092,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000547", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0002242" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000547", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000547", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -34117,6 +34170,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000549", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000549", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -34139,6 +34196,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000550", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000550", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -34279,6 +34340,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000558", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000558", "pred" : "http://purl.obolibrary.org/obo/CL_4030046", @@ -34349,6 +34414,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000566", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0011026" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000566", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000566", "pred" : "http://purl.obolibrary.org/obo/RO_0002104", @@ -34435,6 +34504,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000680", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000055" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000680", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000680", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -34451,6 +34524,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000723", "pred" : "http://purl.obolibrary.org/obo/RO_0002215", "obj" : "http://purl.obolibrary.org/obo/GO_0048103" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000763", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000763", "pred" : "is_a", @@ -34543,10 +34620,18 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000765", "pred" : "http://purl.obolibrary.org/obo/RO_0002215", "obj" : "http://purl.obolibrary.org/obo/GO_0030218" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000837", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000837", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0008001" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000837", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000837", "pred" : "http://purl.obolibrary.org/obo/CL_4030046", @@ -34633,6 +34718,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000988", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0002031", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002031", "pred" : "is_a", @@ -34645,6 +34734,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0002031", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", "obj" : "http://purl.obolibrary.org/obo/CL_0002032" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0002032", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002032", "pred" : "is_a", @@ -34719,6 +34812,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0002188", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0002681" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0002188", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002188", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -34782,7 +34879,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002319", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002319", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -34790,7 +34887,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002320", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002320", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -34802,7 +34899,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002494", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002494", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -34821,10 +34918,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0002546", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000222" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002584", "pred" : "is_a", @@ -34897,6 +34990,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0008019", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000219" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0008019", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0008019", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -34921,6 +35018,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0011012", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0002321" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0011026", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0011026", "pred" : "is_a", @@ -35016,7 +35117,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_1000497", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_1000497", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -35318,7 +35419,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_4030031", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_4030031", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -35354,7 +35455,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GO_0000785", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0032993" + "obj" : "http://purl.obolibrary.org/obo/GO_0110165" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0000785", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -35707,8 +35808,8 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0043232" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0005840", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", - "obj" : "http://purl.obolibrary.org/obo/PR_000000001" + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0005840", "pred" : "http://purl.obolibrary.org/obo/RO_0002216", @@ -36427,12 +36528,8 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0005575" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0032991", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", - "obj" : "http://purl.obolibrary.org/obo/PR_000000001" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0032993", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0032991" + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0033036", "pred" : "is_a", @@ -37149,6 +37246,10 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0098644", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0099080" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0098644", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0098644", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -37680,7 +37781,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/PR_000000001", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000064867" + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/PR_000000001", "pred" : "http://purl.obolibrary.org/obo/RO_0002353", @@ -37818,7 +37919,7 @@ "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { - "sub" : "http://purl.obolibrary.org/obo/PR_000064867", + "sub" : "http://purl.obolibrary.org/obo/PR_000050567", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { @@ -37839,7 +37940,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000475" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000026", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000055", @@ -37937,6 +38038,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000057", "pred" : "http://purl.obolibrary.org/obo/uberon/core#channels_from", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001255" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0000058", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000058", "pred" : "is_a", @@ -38086,7 +38191,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0001434" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000075", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000075", @@ -38294,7 +38399,7 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0007369" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000109", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000110", @@ -38314,7 +38419,7 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0001841" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000110", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000111", @@ -38330,7 +38435,7 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0048513" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000111", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000119", @@ -38342,7 +38447,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000475" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000154", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000158", @@ -38382,7 +38487,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000162", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000163", @@ -38432,7 +38537,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000164", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000164", @@ -38448,7 +38553,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0004921" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", @@ -38462,6 +38567,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000174", "pred" : "http://purl.obolibrary.org/obo/RO_0002353", "obj" : "http://purl.obolibrary.org/obo/GO_0007588" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0000178", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000178", "pred" : "is_a", @@ -38514,7 +38623,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0002193" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000179", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000307", @@ -38534,7 +38643,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000064" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000353", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000353", @@ -38566,7 +38675,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0011216" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000383", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000383", @@ -38682,6 +38791,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000481", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000479" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0000483", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000483", "pred" : "is_a", @@ -38696,7 +38809,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0005769" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000483", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208", "meta" : { "basicPropertyValues" : [ { @@ -38770,7 +38883,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000916", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000922", @@ -38790,7 +38903,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0010316" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000923", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000924", @@ -38860,7 +38973,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0035804" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000930", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000931", @@ -38888,7 +39001,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000931", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000931", @@ -38930,7 +39043,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0004151" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000948", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000948", @@ -38954,7 +39067,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000471" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000958", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000958", @@ -39022,7 +39135,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_8450002" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001008", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001008", @@ -39038,7 +39151,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000467" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001009", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001009", @@ -39070,7 +39183,7 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0000540" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001016", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001016", @@ -39117,7 +39230,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0001016" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001017", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001017", @@ -39758,7 +39871,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0001007" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001555", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001555", @@ -39842,6 +39955,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001915", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001982" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001969", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001969", "pred" : "is_a", @@ -39900,6 +40017,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001980", "pred" : "http://purl.obolibrary.org/obo/RO_0002433", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001637" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", "pred" : "is_a", @@ -39989,7 +40110,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0012275" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001986", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001986", @@ -40087,7 +40208,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000026" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002091", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7776" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002091", @@ -40125,7 +40246,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002113", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002113", @@ -40193,7 +40314,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002193", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002201", @@ -40239,6 +40360,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002224", "pred" : "http://purl.obolibrary.org/obo/RO_0002572", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000915" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0002303", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002303", "pred" : "is_a", @@ -40381,7 +40506,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0011137" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711", "meta" : { "basicPropertyValues" : [ { @@ -40433,7 +40558,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002329", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711", "meta" : { "basicPropertyValues" : [ { @@ -40502,7 +40627,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_89593" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", @@ -40568,7 +40693,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000479" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002384", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002385", @@ -40584,7 +40709,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0001015" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002385", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002385", @@ -40614,7 +40739,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002390", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002390", @@ -40774,7 +40899,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000926" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003068", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003068", @@ -40822,7 +40947,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0016879" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003075", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711", "meta" : { "basicPropertyValues" : [ { @@ -40919,7 +41044,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003081", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003081", @@ -40991,7 +41116,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003089", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742", "meta" : { "basicPropertyValues" : [ { @@ -41019,7 +41144,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000479" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003104", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003104", @@ -41191,7 +41316,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000064" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003891", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003891", @@ -41603,6 +41728,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004341", "pred" : "http://purl.obolibrary.org/obo/RO_0002387", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000926" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004535", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004535", "pred" : "is_a", @@ -41619,6 +41748,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004535", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001981" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004537", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004537", "pred" : "is_a", @@ -41627,6 +41760,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004537", "pred" : "http://purl.obolibrary.org/obo/RO_0002473", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001981" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004572", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004572", "pred" : "is_a", @@ -41641,6 +41778,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004572", "pred" : "http://purl.obolibrary.org/obo/RO_0002351", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001637" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004582", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004582", "pred" : "is_a", @@ -41775,7 +41916,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004770", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004770", @@ -41907,7 +42048,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0003068" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004880", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004905", @@ -41939,7 +42080,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000060" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004923", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005061", @@ -42007,7 +42148,7 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0000187" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005090", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005095", @@ -42353,6 +42494,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0005764", "pred" : "http://purl.obolibrary.org/obo/RO_0002007", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", "pred" : "is_a", @@ -42373,7 +42518,7 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0005587" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", @@ -42534,7 +42679,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0005423" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006268", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006268", @@ -42604,7 +42749,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000307" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006595", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006595", @@ -42636,7 +42781,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000307" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006601", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006601", @@ -42652,7 +42797,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000307" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006603", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006603", @@ -42700,6 +42845,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0006914", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/CL_0000076" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0006965", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006965", "pred" : "is_a", @@ -43001,7 +43150,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0010707" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007823", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007823", @@ -43163,7 +43312,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0006555" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0009773", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0009856", @@ -43409,7 +43558,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0015212" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0010707", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0010707", @@ -43601,7 +43750,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0011997", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0012274", @@ -43745,7 +43894,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000475" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0013701", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0013702", @@ -43803,7 +43952,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0015212", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0015228", @@ -45237,6 +45386,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0001981" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000076", + "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000066" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", + "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0006914" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000081", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000988" ], @@ -45288,7 +45444,7 @@ "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000255", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002160", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002162", "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" } ] }, { @@ -45302,7 +45458,7 @@ "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000365", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0010017" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002160", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002162", "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" } ] }, { diff --git a/src/ontology/subsets/kidney_upper_slim.obo b/src/ontology/subsets/kidney_upper_slim.obo index 467009d20..abc4ba250 100644 --- a/src/ontology/subsets/kidney_upper_slim.obo +++ b/src/ontology/subsets/kidney_upper_slim.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: cl/releases/2024-08-16/subsets/kidney_upper_slim.owl +data-version: cl/releases/2024-09-26/subsets/kidney_upper_slim.owl subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" subsetdef: attribute_slim "" @@ -19,6 +19,7 @@ subsetdef: eye_upper_slim "a subset of general classes related to specific cell subsetdef: functional_classification "" subsetdef: general_cell_types_upper_slim "a subset of general classes of cell types in the cell ontology." subsetdef: gocheck_do_not_annotate "" +subsetdef: gocheck_obsoletion_candidate "" subsetdef: goslim_agr "" subsetdef: goslim_candida "" subsetdef: goslim_chembl "" @@ -95,7 +96,7 @@ idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# idspace: sssom https://w3id.org/sssom/ idspace: terms http://purl.org/dc/terms/ ontology: cl/subsets/kidney_upper_slim -property_value: owl:versionInfo "2024-08-16" xsd:string +property_value: owl:versionInfo "2024-09-26" xsd:string [Term] id: CL:0000000 @@ -118,7 +119,7 @@ is_a: UBERON:0000061 ! anatomical structure disjoint_from: GO:0031012 ! extracellular matrix disjoint_from: GO:0032991 ! protein-containing complex disjoint_from: GO:0043226 ! organelle -relationship: RO:0002160 NCBITaxon:131567 ! only in taxon cellular organisms +relationship: RO:0002162 NCBITaxon:131567 ! in taxon cellular organisms [Term] id: CL:0000007 @@ -139,6 +140,7 @@ synonym: "animal stem cell" EXACT [] xref: CALOHA:TS-2086 xref: FMA:63368 xref: ZFA:0005957 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0011115 ! precursor cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0017145 ! stem cell division @@ -355,7 +357,7 @@ xref: FBbt:00000124 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ xref: FMA:66768 xref: WBbt:0003672 xref: ZFA:0009034 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell relationship: part_of UBERON:0000483 ! epithelium property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 @@ -382,7 +384,6 @@ is_a: CL:0002139 ! endothelial cell of vascular tree intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0001981 ! blood vessel relationship: part_of UBERON:0004638 ! blood vessel endothelium -relationship: RO:0002202 CL:0002546 ! develops from embryonic blood vessel endothelial progenitor cell property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -404,10 +405,14 @@ property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000076 name: squamous epithelial cell +def: "Any epithelial cell that is part of some squamous epithelium." [FBC:Autogenerated] subset: cellxgene_subset xref: CALOHA:TS-1249 xref: ZFA:0009039 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell +intersection_of: CL:0000066 ! epithelial cell +intersection_of: part_of UBERON:0006914 ! squamous epithelium +relationship: part_of UBERON:0006914 ! squamous epithelium [Term] id: CL:0000081 @@ -436,6 +441,7 @@ xref: CALOHA:TS-0278 xref: FMA:66772 xref: ZFA:0009065 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000213 ! lining cell +is_a: CL:0000255 ! eukaryotic cell relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell property_value: RO:0002175 NCBITaxon:9606 @@ -516,6 +522,7 @@ xref: FMA:67328 xref: WBbt:0003675 xref: ZFA:0009114 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000183 ! contractile cell +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000393 ! electrically responsive cell relationship: RO:0002202 CL:0000056 ! develops from myoblast property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI @@ -579,6 +586,7 @@ def: "A cell of the outer of the three germ layers of the embryo." [MESH:D004475 synonym: "ectoderm cell" EXACT [] xref: FMA:72549 xref: ZFA:0009137 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000924 ! ectoderm @@ -591,6 +599,7 @@ synonym: "mesoblast" EXACT [] synonym: "mesoderm cell" EXACT [] xref: FMA:72554 xref: ZFA:0009138 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000926 ! mesoderm @@ -601,6 +610,7 @@ def: "A cell of the inner of the three germ layers of the embryo." [MESH:D004707 synonym: "endoderm cell" EXACT [] xref: FMA:72555 xref: ZFA:0009139 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000925 ! endoderm @@ -634,13 +644,13 @@ property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000255 name: eukaryotic cell -def: "Any cell that only exists in Eukaryota." [FBC:Autogenerated] +def: "Any cell that in taxon some Eukaryota." [FBC:Autogenerated] subset: cellxgene_subset xref: MESH:D005057 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell -intersection_of: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota -relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +intersection_of: RO:0002162 NCBITaxon:2759 ! in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 ! in taxon Eukaryota [Term] id: CL:0000329 @@ -688,8 +698,8 @@ is_a: CL:0000007 ! early embryonic cell (metazoa) is_a: CL:0000255 ! eukaryotic cell is_a: CL:0010017 ! zygote intersection_of: CL:0010017 ! zygote -intersection_of: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa -relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +intersection_of: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa [Term] id: CL:0000393 @@ -753,6 +763,7 @@ synonym: "rubriblast" EXACT [ISBN:0721601464] xref: FMA:83518 is_a: CL:0000764 {is_inferred="true"} ! erythroid lineage cell is_a: CL:0002242 ! nucleate cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000764 ! erythroid lineage cell intersection_of: bearer_of PATO:0002505 ! nucleated intersection_of: bearer_of PATO:0040072 ! high nuclear/cytoplasmic ratio @@ -798,6 +809,7 @@ synonym: "prorubricyte" EXACT [ISBN:0721601464] xref: FMA:83505 xref: ZFA:0005236 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000765 {is_inferred="true"} ! erythroblast +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017503 ! basophilic cytoplasm intersection_of: has_part GO:0000792 ! heterochromatin @@ -819,6 +831,7 @@ synonym: "rubricyte" EXACT [ISBN:0721601464] xref: FMA:83506 xref: ZFA:0005241 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000765 {is_inferred="true"} ! erythroblast +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017504 ! polychromatophilic cytoplasm intersection_of: has_part GO:0000792 ! heterochromatin @@ -932,6 +945,7 @@ xref: CALOHA:TS-0864 xref: MESH:D012156 xref: ZFA:0009252 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000764 {is_inferred="true"} ! erythroid lineage cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000764 ! erythroid lineage cell intersection_of: capable_of GO:0071971 ! extracellular exosome assembly intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -971,6 +985,7 @@ synonym: "chondroplast" EXACT [] xref: ZFA:0009258 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000134 {is_inferred="true"} ! mesenchymal stem cell is_a: CL:0011026 ! progenitor cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: RO:0002104 PR:000001444 ! has plasma membrane part cadherin-5 intersection_of: RO:0002104 PR:000002112 ! has plasma membrane part vascular endothelial growth factor receptor 2 @@ -1042,11 +1057,13 @@ name: fenestrated endothelial cell def: "An endothelial cell that has small pores, or fenestrations, which allow for the efficient exchange of substances between the blood and surrounding tissues." [DOI:10.1007/978-3-211-99390-3_133] subset: cellxgene_subset synonym: "window cell" EXACT [] +xref: https://cellxgene.cziscience.com/cellguide/CL_0000666 xref: ZFA:0009286 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000115 ! endothelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: bearer_of PATO:0002064 ! fenestrated relationship: bearer_of PATO:0002064 ! fenestrated +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nFenestrated cells are specialized epithelial cells that are characterized by a distinctive structural feature, fenestrations or tiny pores, which allow an exchange of substances such as fluids, nutrients, and waste between blood vessels and the surrounding tissue environments. These cells are present in various types of epithelial tissues in the human body, including the intestinal tract, endocrine glands, and certain parts of the renal system. \nThere are multiple types of endothelial cell fenestrations. The most common type is found in systemic capillaries of the endocrine tissue (e.g., pancreatic islets), gastrointestinal mucosa, and renal peritubular capillaries. Here, the fenestrated cells have fenestrations in their peripheral cytoplasm with a unique thin and permeable diaphragm that provides a high degree of selectivity, blocking the passage of larger molecules while allowing the free movement of smaller ones. In contrast, other types of fenestrations, such as the discontinuous epithelium of the liver sinusoidal endothelial cells, do not have diaphragms. \nCharacteristically, fenestrated cells play a vital role in the filtering process of body systems. They are a key part of the glomeruli in the kidneys where blood is filtered under high pressure. The fenestrations present in the endothelial cells lining the capillaries of the glomerulus allow the free passage of water and small solute molecules towards the Bowman's capsule, leaving behind larger proteins and cells in the blood, thereby aiding in the filtration and waste removal process. \nIn the endocrine system, fenestrated cells in glandular capillaries allow the prompt release of hormones into the bloodstream. These cells have tightly clustered fenestrations which increase the surface area available for passive diffusion, improving the efficiency of hormone secretion. In villi of the small intestine, these cells increase absorption efficiency, permitting the exchange of water, electrolytes, and nutrients.\nOverall, fenestrated cells contribute immensely to important physiological processes of filtration, absorption, and secretion, primarily connecting our body's circulation system with the surrounding tissues and organs." xsd:string {xref="DOI:10.1002/ar.1092200109", xref="DOI:10.1016/0306-4522(86)90162-4", xref="DOI:10.1016/j.devcel.2012.11.003", xref="DOI:10.1038/s41467-022-31571-2", xref="DOI:10.1152/ajprenal.90601.2008"} [Term] id: CL:0000669 @@ -1077,6 +1094,7 @@ def: "A non-terminally differentiated cell that is capable of developing into a subset: cellxgene_subset xref: ZFA:0009291 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0011115 ! precursor cell intersection_of: RO:0002203 CL:0000187 ! develops into muscle cell relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell @@ -1103,6 +1121,7 @@ xref: BTO:0001441 xref: CALOHA:TS-0647 xref: MESH:D022423 xref: ZFA:0009324 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000988 {is_inferred="true"} ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: RO:0002202 CL:0000049 ! develops from common myeloid progenitor @@ -1181,7 +1200,9 @@ synonym: "MPP" EXACT [] xref: BTO:0000725 xref: CALOHA:TS-0448 xref: ZFA:0009354 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001402 ! multipotent intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -1256,6 +1277,7 @@ id: CL:0002031 name: hematopoietic lineage restricted progenitor cell def: "A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells." [GOC:tfm, PMID:19022770] subset: blood_and_immune_upper_slim +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001400 ! unipotent @@ -1271,6 +1293,7 @@ name: hematopoietic oligopotent progenitor cell def: "A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities." [GOC:tfm, https://orcid.org/0000-0001-5208-3432, PMID:19022770] comment: This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). subset: blood_and_immune_upper_slim +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001401 ! oligopotent @@ -1368,6 +1391,7 @@ xref: BTO:0004632 xref: FMA:70970 is_a: CL:0000666 ! fenestrated endothelial cell is_a: CL:0002681 ! kidney cortical cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0000074 ! renal glomerulus relationship: has_part GO:0036053 ! glomerular endothelium fenestra @@ -1428,7 +1452,7 @@ def: "A cell that is part of the nervous system." [GOC:tfm, ISBN:0618947256] subset: cellxgene_subset xref: CALOHA:TS-2040 xref: FMA:70333 -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001016 ! nervous system relationship: part_of UBERON:0001016 ! nervous system @@ -1444,7 +1468,7 @@ xref: CALOHA:TS-2096 xref: FMA:63875 xref: MESH:D003239 xref: ZFA:0009392 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0002384 ! connective tissue relationship: part_of UBERON:0002384 ! connective tissue @@ -1473,7 +1497,7 @@ xref: BTO:0001539 xref: CALOHA:TS-0115 xref: FMA:83808 xref: FMA:84791 -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0007100 ! primary circulatory organ relationship: part_of UBERON:0007100 ! primary circulatory organ @@ -1494,16 +1518,6 @@ intersection_of: part_of UBERON:0002113 ! kidney property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-08T10:46:34Z -[Term] -id: CL:0002546 -name: embryonic blood vessel endothelial progenitor cell -def: "An endothelial progenitor cell that participates in angiogenesis during development." [GOC:tfm] -comment: See CL:0002619. -xref: ZFA:0005773 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000222 ! mesodermal cell -property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 -creation_date: 2011-02-28T04:20:39Z - [Term] id: CL:0002584 name: renal cortical epithelial cell @@ -1538,9 +1552,11 @@ id: CL:0005009 name: renal principal cell def: "A cuboidal epithelial cell of the kidney which regulates sodium and potassium balance. The activity of sodium and potassium channels on the apical membrane of the cell is regulated by aldosterone and vasopressin. In mammals this cell type is located in the renal collecting duct system." [CL:CVS] subset: cellxgene_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_0005009 xref: ZFA:0005322 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000075 ! columnar/cuboidal epithelial cell is_a: CL:0002518 ! kidney epithelial cell +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nRenal principal cells are the major cell type in the initial collecting tubule and the cortical and outer medullary collecting ducts, as well as the connecting tubule, in the nephrons of the kidneys.\nA key function of renal principal cells is the regulation of water balance in the body. These cells express aquaporin-2 (AQP2) water channels, which facilitate the reabsorption of water from the fluid within the renal tubule lumen back into the blood. The translocation of AQP2 to the cell membrane is controlled by the hormone vasopressin: In response to high vasopressin levels, AQP2 moves to the cell membrane, allowing water to pass through effectively and be reabsorbed, therefore concentrating the urine. Conversely, in low vasopressin conditions, AQP2 is removed from the membrane, reducing water reabsorption and diluting the urine. \nRenal principal cells are also involved in the regulation of sodium and potassium levels in the body. They have sodium channels (ENaC) in their luminal membranes which permit the reabsorption of sodium ions from the tubule fluid back into the blood, resulting in a net reabsorption of sodium ions into the systemic circulation. This process is controlled, in part, by the hormone aldosterone. Additionally, renal principal cells contain potassium channels that facilitate the secretion of potassium ions into the urine. The activities of these channels, in coordination with other cell types in the nephron, are critical for maintaining electrolyte balance and overall body homeostasis." xsd:string {xref="DOI:10.1016/j.krcp.2013.07.005", xref="DOI:10.2215/CJN.05760513", xref="DOI:10.2215/CJN.08580813"} [Term] id: CL:0007004 @@ -1584,6 +1600,7 @@ subset: cellxgene_subset subset: human_reference_atlas synonym: "mesenchyme cell" EXACT [] is_a: CL:0000219 ! motile cell +is_a: CL:0000255 ! eukaryotic cell relationship: capable_of GO:0016477 ! cell migration relationship: part_of UBERON:0003104 ! mesenchyme property_value: RO:0002175 NCBITaxon:9606 @@ -1614,14 +1631,17 @@ id: CL:0011012 name: neural crest cell def: "A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells." [https://orcid.org/0000-0001-5208-3432, https://orcid.org/0000-0002-9900-7880] subset: cellxgene_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_0011012 is_a: CL:0000048 ! multi fate stem cell is_a: CL:0002321 ! embryonic cell (metazoa) +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." xsd:string {xref="DOI:10.1002/dvg.23276", xref="DOI:10.1242/dev.193193", xref="DOI:10.3389/fcell.2020.00635/full", xref="https://doi.org/10.1016/j.ydbio.2011.12.042"} [Term] id: CL:0011026 name: progenitor cell def: "A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses." [https://doi.org/10.1016/B978-0-12-409503-8.00002-0, ISBN:978-1-62808-994-3] subset: cellxgene_subset +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0011115 ! precursor cell intersection_of: CL:0011115 ! precursor cell intersection_of: RO:0002202 CL:0000034 ! develops from stem cell @@ -1708,6 +1728,7 @@ subset: human_reference_atlas subset: kidney_upper_slim synonym: "epithelial cell of renal collecting tubule" EXACT [FMA:70982] xref: FMA:70982 +xref: https://cellxgene.cziscience.com/cellguide/CL_1000454 xref: KUPO:0001059 is_a: CL:0000072 {is_inferred="true"} ! non-branched duct epithelial cell is_a: CL:1000449 ! epithelial cell of nephron @@ -1715,6 +1736,7 @@ is_a: CL:1001225 {is_inferred="true"} ! kidney collecting duct cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001232 ! collecting duct of renal tubule property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nKidney collecting duct epithelial cells are a specialized type of cells that form an integral part of the renal system. Located in the collecting duct system of the kidneys, these cells are responsible for one of the final steps in the process of urine formation, and they are instrumental in the fine tuning of the volume and composition of urine by reabsorbing water and certain solutes back into the bloodstream.\nThese cells express specific channels and carriers that actively and passively transport ions and water. They also have channels on their membranes, such as sodium channels and potassium channels, involved in reabsorbing or secreting these electrolytes depending upon the body's needs. The function of renal collecting duct epithelial cells can be regulated by a variety of hormones, including vasopressin (antidiuretic hormone), which can modulate the ion channels and carriers and hence indirectly influence body fluid homeostasis.\nAside from their function in ion and water balance, kidney collecting duct epithelial cells also aid in maintaining the body's acid-base balance. They have specialized functionality to secret hydrogen ions into the tubular lumen, which contributes to acid excretion. Any dysfunction may have serious implications and lead to various renal or systemic diseases, exemplifying the importance of these cells in maintaining overall body homeostasis." xsd:string {xref="DOI:10.1016/j.ajpath.2014.01.014", xref="DOI:10.1016/j.semnephrol.2019.04.005", xref="DOI:10.2215/CJN.05760513", xref="DOI:10.2215/CJN.08880914"} [Term] id: CL:1000494 @@ -1738,7 +1760,7 @@ def: "A cell that is part of a kidney." [] subset: cellxgene_subset xref: KUPO:0001010 xref: ZFA:0009389 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0002113 ! kidney relationship: part_of UBERON:0002113 ! kidney @@ -2034,7 +2056,7 @@ creation_date: 2014-06-04T15:07:42Z id: CL:4030031 name: interstitial cell def: "Any cell that is located within the interstitium between the cells most prominent in defining a given tissue. \"Interstitial cell\" is a morphological term and refers to a variety of cells with differing origins and phenotypes." [PMID:24987007] -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0005169 ! interstitial tissue relationship: part_of UBERON:0005169 ! interstitial tissue @@ -2096,8 +2118,9 @@ synonym: "chromosome scaffold" RELATED [] synonym: "cytoplasmic chromatin" NARROW [] synonym: "nuclear chromatin" NARROW [] xref: NIF_Subcellular:sao1615953555 -is_a: GO:0032993 ! protein-DNA complex +is_a: GO:0110165 ! cellular anatomical entity relationship: part_of GO:0005694 ! chromosome +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28301" xsd:anyURI [Term] id: GO:0000792 @@ -2217,7 +2240,7 @@ id: GO:0001977 name: renal system process involved in regulation of blood volume namespace: biological_process def: "A slow mechanism of blood pressure regulation that responds to changes in pressure resulting from fluid and salt intake by modulating the quantity of blood in the circulatory system." [GOC:dph, GOC:tb, ISBN:0721643949] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "renal blood volume control of blood pressure" RELATED [] synonym: "renal regulation of blood volume" RELATED [GOC:dph, GOC:tb] is_a: GO:0003071 ! renal system process involved in regulation of systemic arterial blood pressure @@ -2667,8 +2690,8 @@ synonym: "ribosomal RNA" RELATED [] xref: NIF_Subcellular:sao1429207766 xref: Wikipedia:Ribosome is_a: GO:0043232 ! intracellular non-membrane-bounded organelle +is_a: PR:000050567 ! protein-containing material entity relationship: capable_of_part_of GO:0006412 ! translation -relationship: has_part PR:000000001 ! protein [Term] id: GO:0005886 @@ -3022,6 +3045,9 @@ def: "The generation and maintenance of gametes in a multicellular organism. A g synonym: "gametogenesis" RELATED [] is_a: GO:0048609 ! multicellular organismal reproductive process relationship: part_of GO:0019953 ! sexual reproduction +property_value: RO:0002161 NCBITaxon:2 +property_value: RO:0002161 NCBITaxon:2157 +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0007369 @@ -3535,6 +3561,9 @@ is_a: GO:0051301 ! cell division intersection_of: GO:0051301 ! cell division intersection_of: has_primary_input CL:0000034 ! stem cell relationship: has_primary_input CL:0000034 ! stem cell +property_value: RO:0002161 NCBITaxon:2 +property_value: RO:0002161 NCBITaxon:2157 +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0019226 @@ -4060,18 +4089,8 @@ synonym: "protein complex" NARROW [] synonym: "protein containing complex" EXACT [] synonym: "protein-protein complex" NARROW [] is_a: GO:0005575 ! cellular_component +is_a: PR:000050567 ! protein-containing material entity disjoint_from: GO:0110165 ! cellular anatomical entity -relationship: has_part PR:000000001 ! protein - -[Term] -id: GO:0032993 -name: protein-DNA complex -namespace: cellular_component -def: "A macromolecular complex containing both protein and DNA molecules." [GOC:mah] -comment: Note that this term is intended to classify complexes that have DNA as one of the members of the complex, that is, the complex does not exist if DNA is not present. Protein complexes that interact with DNA e.g. transcription factor complexes should not be classified here. -subset: goslim_pir -synonym: "DNA-protein complex" EXACT [GOC:mah] -is_a: GO:0032991 ! protein-containing complex [Term] id: GO:0033036 @@ -4165,6 +4184,9 @@ def: "A large plasma membrane-lined circular pore that perforates the flattened synonym: "GEnC fenestration" EXACT [PMID:19129259] synonym: "glomerular endothelial cell fenestration" EXACT [PMID:19129259] is_a: GO:0046930 ! pore complex +property_value: RO:0002161 NCBITaxon:2 +property_value: RO:0002161 NCBITaxon:2157 +property_value: RO:0002161 NCBITaxon:4751 created_by: bf creation_date: 2011-12-12T10:53:24Z @@ -4294,6 +4316,7 @@ id: GO:0043227 name: membrane-bounded organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane." [GOC:go_curators] +subset: gocheck_do_not_annotate synonym: "membrane-enclosed organelle" EXACT [] xref: NIF_Subcellular:sao414196390 is_a: GO:0043226 ! organelle @@ -4301,30 +4324,35 @@ intersection_of: GO:0043226 ! organelle intersection_of: has_part GO:0016020 ! membrane disjoint_from: GO:0043228 ! non-membrane-bounded organelle relationship: has_part GO:0016020 ! membrane +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI [Term] id: GO:0043228 name: non-membrane-bounded organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:go_curators] +subset: gocheck_do_not_annotate subset: goslim_mouse synonym: "biological condensate" RELATED [] synonym: "non-membrane-enclosed organelle" EXACT [] xref: NIF_Subcellular:sao1456184038 is_a: GO:0043226 ! organelle property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21881" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI [Term] id: GO:0043229 name: intracellular organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:go_curators] +subset: gocheck_do_not_annotate subset: goslim_pir is_a: GO:0043226 ! organelle intersection_of: GO:0043226 ! organelle intersection_of: part_of GO:0005622 ! intracellular anatomical structure disjoint_from: GO:0043230 ! extracellular organelle relationship: part_of GO:0005622 ! intracellular anatomical structure +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI [Term] id: GO:0043230 @@ -4413,9 +4441,11 @@ name: cellular component biogenesis namespace: biological_process alt_id: GO:0071843 def: "A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component." [GOC:jl, GOC:mah] +subset: gocheck_do_not_annotate subset: goslim_pir synonym: "cellular component biogenesis at cellular level" EXACT [] is_a: GO:0071840 ! cellular component organization or biogenesis +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27194" xsd:anyURI [Term] id: GO:0044207 @@ -5312,6 +5342,7 @@ def: "A complex of collagen trimers such as a fibril or collagen network." [GOC: synonym: "Supramolecular aggregate of collagen" EXACT [PMID:19693541] synonym: "Supramolecular collagen assembly" EXACT [PMID:21421911] is_a: GO:0099080 ! supramolecular complex +is_a: PR:000050567 ! protein-containing material entity relationship: has_part GO:0005581 ! collagen trimer relationship: part_of GO:0062023 ! collagen-containing extracellular matrix @@ -6378,7 +6409,7 @@ comment: The definition above excludes protein complexes, which some also consid synonym: "native protein" NARROW [IEDB:BP] synonym: "natural protein" EXACT [PRO:DAN] is_a: PR:000018263 ! amino acid chain -is_a: PR:000064867 ! protein-containing molecular entity +is_a: PR:000050567 ! protein-containing material entity relationship: output_of GO:0006412 ! translation [Term] @@ -6789,11 +6820,11 @@ synonym: "fam:angiotensinogenase" EXACT PRO-short-label [PRO:DAN] is_a: PR:000000001 ! protein [Term] -id: PR:000064867 -name: protein-containing molecular entity +id: PR:000050567 +name: protein-containing material entity namespace: protein -def: "A molecular entity that minimally consists of a protein." [PRO:DAN] -comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). +def: "A material entity that minimally consists of a protein." [PRO:DAN] +comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566). synonym: "protein" NARROW [PRO:DAN] synonym: "protein aggregate" NARROW [PRO:DAN] synonym: "protein complex" NARROW [PRO:DAN] @@ -6858,7 +6889,7 @@ xref: VSAO:0000075 xref: Wikipedia:Appendage xref: XAO:0000218 is_a: UBERON:0000475 ! organism subdivision -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0000055 @@ -6978,6 +7009,7 @@ xref: UMLS:C0687028 {source="ncithesaurus:Duct"} xref: Wikipedia:Duct_(anatomy) xref: XAO:0004000 xref: ZFA:0005171 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000063 ! organ subunit relationship: has_part UBERON:0034969 ! epithelial layer of duct relationship: RO:0000086 PATO:0002299 ! has quality tubular @@ -7223,7 +7255,7 @@ xref: SCTID:118966000 xref: UMLS:C1519343 {source="ncithesaurus:Skeletal_System_Part"} is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision relationship: part_of UBERON:0001434 ! skeletal system -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002473 UBERON:0004765 ! composed primarily of skeletal element [Term] @@ -7531,7 +7563,7 @@ is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000108 {source="BILS"} ! blastula stage relationship: RO:0002082 GO:0007369 ! simultaneous with gastrulation -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0000110 @@ -7547,7 +7579,7 @@ is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000109 ! gastrula stage relationship: RO:0002082 GO:0001841 ! simultaneous with neural tube formation -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: seeAlso "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/343" xsd:anyURI @@ -7567,7 +7599,7 @@ xref: Wikipedia:Organogenesis is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: RO:0002082 GO:0048513 ! simultaneous with animal organ development -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: seeAlso "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/533" xsd:anyURI @@ -7590,7 +7622,7 @@ id: UBERON:0000154 name: posterior region of body namespace: uberon is_a: UBERON:0000475 ! organism subdivision -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria [Term] id: UBERON:0000158 @@ -7639,7 +7671,7 @@ xref: ZFA:0005781 is_a: UBERON:0013522 ! subdivision of tube relationship: part_of UBERON:0001555 {source="ZFA"} ! digestive tract relationship: part_of UBERON:0004122 {source="AAO"} ! genitourinary system -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata property_value: IAO:0000116 "adding df link to embryonic cloaca leads to a cycle in uberon-simple, as cloaca is a suberclass of embryonic cloaca" xsd:string [Term] @@ -7680,7 +7712,7 @@ xref: VHOG:0000414 xref: Wikipedia:Definitive_urogenital_sinus is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0000163 {source="MP-def"} ! embryonic cloaca -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002202 UBERON:0003064 ! develops from intermediate mesoderm relationship: RO:0002433 UBERON:0000163 ! contributes to morphology of embryonic cloaca property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png" xsd:anyURI @@ -7739,7 +7771,7 @@ xref: XAO:0003029 xref: ZFA:0000547 xref: ZFA:0000590 is_a: UBERON:0004921 ! subdivision of digestive tract -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002202 UBERON:0035804 ! develops from future mouth property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/661" xsd:anyURI @@ -7801,6 +7833,7 @@ xref: VHOG:0000224 xref: Wikipedia:Blood xref: XAO:0000124 xref: ZFA:0000007 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000179 ! haemolymphatic fluid relationship: has_part CL:0000232 {source="CL:tm"} ! erythrocyte relationship: has_part UBERON:0001969 ! blood plasma @@ -7821,7 +7854,7 @@ is_a: UBERON:0006314 ! bodily fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: part_of UBERON:0002193 ! hemolymphoid system relationship: part_of UBERON:0002193 ! hemolymphoid system -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: terms:contributor https://orcid.org/0000-0002-6601-2165 creation_date: 2009-04-08T04:38:19Z @@ -7872,7 +7905,7 @@ xref: Wikipedia:Parenchyma is_a: UBERON:0000064 ! organ part disjoint_from: UBERON:0003891 ! stroma relationship: capable_of GO:0032501 ! multicellular organismal process -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0000362 @@ -7948,7 +7981,7 @@ is_a: UBERON:0011216 ! organ system subdivision intersection_of: UBERON:0011216 ! organ system subdivision intersection_of: RO:0002473 UBERON:0001015 ! composed primarily of musculature relationship: capable_of GO:0003012 ! muscle system process -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002473 UBERON:0001015 ! composed primarily of musculature property_value: IAO:0000116 "consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77" xsd:string property_value: RO:0002161 NCBITaxon:6040 @@ -8382,12 +8415,13 @@ xref: VHOG:0000387 xref: Wikipedia:Epithelium xref: XAO:0003045 xref: ZFA:0001486 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: RO:0002473 CL:0000066 ! composed primarily of epithelial cell relationship: has_part GO:0005911 ! cell-cell junction relationship: has_part UBERON:0005769 ! basement membrane of epithelium -relationship: RO:0002160 NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! in taxon Metazoa relationship: RO:0002473 CL:0000066 ! composed primarily of epithelial cell property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI @@ -8552,7 +8586,7 @@ xref: SCTID:302553009 xref: Wikipedia:Abdomen is_a: UBERON:0009569 ! subdivision of trunk relationship: part_of UBERON:0002417 {source="MA"} ! abdominal segment of trunk -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata property_value: IAO:0000116 "Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class" xsd:string [Term] @@ -8633,7 +8667,7 @@ xref: Wikipedia:Germ_layer xref: XAO:0003011 xref: ZFA:0001122 is_a: UBERON:0010316 ! germ layer / neural crest -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0000924 @@ -8787,7 +8821,7 @@ xref: ZFA:0001290 is_a: UBERON:0013522 ! subdivision of tube relationship: part_of UBERON:0000924 ! ectoderm relationship: part_of UBERON:0035804 ! future mouth -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI property_value: IAO:0000116 "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" xsd:string @@ -8816,7 +8850,7 @@ xref: ZFA:0000066 is_a: UBERON:0016566 {source="EHDAA2"} ! pit relationship: part_of UBERON:0007026 ! presumptive gut relationship: RO:0001025 UBERON:0012469 {source="EHDAA2"} ! located in external anal region -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002202 UBERON:0000924 ! develops from ectoderm relationship: RO:0002387 UBERON:0001353 ! has potential to develop into anal region property_value: IAO:0000116 "removed WBbt:0006795 'proctodeum' - junction between the alimentary and genital tracts in the male." xsd:string @@ -8871,7 +8905,7 @@ intersection_of: UBERON:0007100 ! primary circulatory organ intersection_of: has_part UBERON:0004151 ! cardiac chamber relationship: has_part UBERON:0004151 ! cardiac chamber relationship: part_of UBERON:0015410 {source="MA"} ! heart plus pericardium -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002202 UBERON:0004141 ! develops from heart tube relationship: RO:0002433 UBERON:0004535 ! contributes to morphology of cardiovascular system property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/heart-female/v1.3/assets/3d-vh-f-heart.glb" xsd:anyURI @@ -8907,7 +8941,7 @@ synonym: "medulla" EXACT [FMA:61108] xref: FMA:61108 xref: galen:Medulla is_a: UBERON:0000471 ! compound organ component -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002219 UBERON:0001851 ! surrounded by cortex [Term] @@ -9149,7 +9183,7 @@ is_a: UBERON:8450002 ! excretory system intersection_of: UBERON:8450002 ! excretory system intersection_of: capable_of GO:0097254 ! renal tubular secretion relationship: capable_of GO:0097254 ! renal tubular secretion -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage property_value: RO:0002161 NCBITaxon:110815 {source="Wikipedia"} property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} @@ -9174,7 +9208,7 @@ disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:8450002 ! excretory system relationship: capable_of GO:0003013 ! circulatory system process -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} @@ -9224,7 +9258,6 @@ namespace: uberon def: "The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]." [BIRNLEX:844, ISBN:0-14-051288-8, ISBN:3110148986, NLM:nervous+system, WB:rynl, Wikipedia:Nervous_system, ZFIN:curator] subset: cumbo subset: efo_slim -subset: human_reference_atlas subset: pheno_slim subset: uberon_slim subset: vertebrate_core @@ -9265,14 +9298,13 @@ disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:8450002 ! excretory system relationship: capable_of GO:0050877 ! nervous system process relationship: has_part CL:0000540 ! neuron -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002473 CL:0002319 ! composed primarily of neural cell relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage relationship: RO:0002495 UBERON:0016880 {source="Bgee:AN"} ! immediate transformation of future nervous system property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:6040 -property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001017 @@ -9319,7 +9351,7 @@ xref: ZFA:0000012 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0011216 {source="FBbt", source="cjm"} ! organ system subdivision relationship: part_of UBERON:0001016 ! nervous system -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria relationship: RO:0002495 UBERON:0016879 {source="Bgee:AN"} ! immediate transformation of future central nervous system property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} property_value: RO:0002175 NCBITaxon:9606 @@ -10286,7 +10318,7 @@ xref: WBbt:0005743 xref: ZFA:0000112 is_a: UBERON:0000025 ! tube relationship: part_of UBERON:0001007 ! digestive system -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002176 UBERON:0000165 ! connects mouth relationship: RO:0002495 UBERON:0007026 {source="NCBIBook:NBK10107"} ! immediate transformation of presumptive gut property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} @@ -10491,6 +10523,7 @@ xref: MIAA:0000052 xref: NCIT:C13356 xref: UMLS:C0032105 {source="ncithesaurus:Plasma"} xref: Wikipedia:Blood_plasma +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000179 ! haemolymphatic fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: has_part GO:0005577 ! fibrinogen complex @@ -10600,6 +10633,7 @@ xref: VHOG:0001250 xref: Wikipedia:Blood_vessel xref: XAO:0001011 xref: ZFA:0005314 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000055 ! vessel is_a: UBERON:0004120 ! mesoderm-derived structure relationship: capable_of_part_of GO:0008015 ! blood circulation @@ -10677,7 +10711,7 @@ is_a: UBERON:0000487 {source="FMA-text-def", source="https://github.com/obopheno is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: RO:0002473 CL:0000115 ! composed primarily of endothelial cell -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002473 CL:0000115 ! composed primarily of endothelial cell property_value: RO:0002175 NCBITaxon:9606 @@ -10907,7 +10941,7 @@ xref: XAO:0003166 is_a: UBERON:0010912 ! subdivision of skeleton relationship: overlaps UBERON:0000026 ! appendage relationship: part_of UBERON:0011249 ! appendicular skeletal system -relationship: RO:0002160 NCBITaxon:7776 ! only in taxon Gnathostomata +relationship: RO:0002162 NCBITaxon:7776 ! in taxon Gnathostomata relationship: RO:0002433 UBERON:0001434 ! contributes to morphology of skeletal system property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/7c/Appendicular_skeleton_diagram.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 @@ -10976,7 +11010,7 @@ is_a: UBERON:0000489 ! cavitated compound organ is_a: UBERON:0005172 ! abdomen element is_a: UBERON:0015212 ! lateral structure relationship: part_of UBERON:0011143 {source="FMA"} ! upper urinary tract -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002202 UBERON:0003918 ! develops from kidney mesenchyme relationship: RO:0002202 UBERON:0005095 ! develops from kidney rudiment relationship: RO:0002433 UBERON:0001008 ! contributes to morphology of renal system @@ -11036,7 +11070,7 @@ xref: EMAPA:18765 xref: FMA:74562 xref: MA:0000013 is_a: UBERON:0000467 {source="MA"} ! anatomical system -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria [Term] id: UBERON:0002201 @@ -11142,6 +11176,7 @@ xref: NCIT:C32891 xref: SCTID:362219002 xref: UMLS:C0022445 {source="ncithesaurus:Juxtaglomerular_Apparatus"} xref: Wikipedia:Juxtaglomerular_apparatus +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000061 ! anatomical structure relationship: capable_of GO:0003093 {source="GO"} ! regulation of glomerular filtration relationship: has_part CL:0000648 ! kidney granular cell @@ -11268,7 +11303,7 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0011137 ! axial skeletal system relationship: produces PR:000014841 ! sonic hedgehog protein -relationship: RO:0002160 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! in taxon Chordata relationship: RO:0002202 UBERON:0004880 {source="ZFA"} ! develops from chordamesoderm relationship: RO:0002202 UBERON:0006267 {source="EHDAA2"} ! develops from notochordal plate relationship: RO:0002488 UBERON:0000068 ! existence starts during embryo stage @@ -11311,7 +11346,7 @@ xref: XAO:0000058 xref: ZFA:0000155 is_a: UBERON:0005423 ! developing anatomical structure is_a: UBERON:0007503 {source="EHDAA2"} ! epithelial vesicle -relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {source="GOTAX:0000352"} ! in taxon Chordata relationship: RO:0002202 UBERON:0003059 {source="ZFA"} ! develops from presomitic mesoderm property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:7712 {source="PMID:17237766"} @@ -11371,7 +11406,7 @@ is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0010316 ! germ layer / neural crest relationship: part_of UBERON:0002346 {source="XAO", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! neurectoderm -relationship: RO:0002160 NCBITaxon:89593 ! only in taxon Craniata +relationship: RO:0002162 NCBITaxon:89593 ! in taxon Craniata relationship: RO:0002202 UBERON:0003075 {source="BTO"} ! develops from neural plate relationship: RO:0002202 UBERON:0005062 {source="PMID:11523831"} ! develops from neural fold relationship: RO:0002473 CL:0000333 ! composed primarily of migratory neural crest cell @@ -11478,7 +11513,7 @@ xref: VSAO:0000017 xref: XAO:0001017 xref: ZFA:0001632 is_a: UBERON:0000479 ! tissue -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -11510,7 +11545,7 @@ intersection_of: UBERON:0000479 ! tissue intersection_of: RO:0002473 CL:0000187 ! composed primarily of muscle cell relationship: capable_of GO:0006936 ! muscle contraction relationship: part_of UBERON:0001015 ! musculature -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002473 CL:0000187 ! composed primarily of muscle cell [Term] @@ -11555,7 +11590,7 @@ is_a: UBERON:0000467 ! anatomical system is_a: UBERON:0004120 ! mesoderm-derived structure disjoint_from: UBERON:8450002 ! excretory system relationship: part_of UBERON:0002193 {source="FMA"} ! hemolymphoid system -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002202 UBERON:0003061 ! develops from blood island property_value: RO:0002175 NCBITaxon:9606 @@ -11752,7 +11787,7 @@ xref: XAO:0000205 xref: ZFA:0001204 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0000926 ! mesoderm -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002202 UBERON:0000926 ! develops from mesoderm property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI @@ -11819,7 +11854,7 @@ xref: ZFA:0000132 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0016879 ! future central nervous system -relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {source="GOTAX:0000352"} ! in taxon Chordata relationship: RO:0002256 UBERON:0002328 {source="Wikipedia"} ! developmentally induced by notochord relationship: RO:0002495 UBERON:0007284 {source="Bgee:AN"} ! immediate transformation of presumptive neural plate property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI @@ -11886,7 +11921,7 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue relationship: part_of UBERON:0000926 {source="EHDAA2", source="VHOG"} ! mesoderm -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria relationship: RO:0002221 UBERON:0003887 ! surrounds intraembryonic coelom property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI @@ -11936,7 +11971,7 @@ xref: XAO:0000397 xref: ZFA:0001080 is_a: UBERON:0005856 {source="EHDAA2"} ! developing mesenchymal condensation is_a: UBERON:0007530 {source="EHDAA2"} ! migrating mesenchyme population -relationship: RO:0002160 NCBITaxon:7742 {source="VHOG:0000680"} ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 {source="VHOG:0000680"} ! in taxon Vertebrata relationship: RO:0002202 UBERON:0002329 {source="ZFA"} ! develops from somite property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI @@ -11991,7 +12026,7 @@ xref: ZFA:0000393 is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002328 GO:0032502 ! functionally related to developmental process relationship: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI @@ -12250,7 +12285,7 @@ xref: FMA:81494 xref: NCIT:C67387 xref: UMLS:C0927195 {source="ncithesaurus:Stroma_Connective_Tissue"} is_a: UBERON:0000064 ! organ part -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002473 UBERON:0002384 ! composed primarily of connective tissue [Term] @@ -12865,6 +12900,7 @@ xref: WikipediaCategory:Cardiovascular_system xref: XAO:0000100 xref: XAO:0001010 xref: ZFA:0000010 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000467 ! anatomical system intersection_of: UBERON:0000467 ! anatomical system intersection_of: has_part UBERON:0000948 ! heart @@ -12888,6 +12924,7 @@ synonym: "blood vessels" RELATED [TAO:0001079] synonym: "set of blood vessels" EXACT [] xref: TAO:0001079 xref: ZFA:0001079 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel @@ -12911,6 +12948,7 @@ xref: EMAPA:16371 xref: MA:0002719 xref: SCTID:362030008 xref: VHOG:0000273 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0007798 {source="MA"} ! vascular system relationship: RO:0002351 UBERON:0001637 ! has member artery property_value: RO:0002175 NCBITaxon:9606 @@ -12931,6 +12969,7 @@ xref: NCIT:C33858 xref: SCTID:362060003 xref: UMLS:C1267406 {source="ncithesaurus:Venous_System"} xref: VHOG:0000277 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0007798 {source="MA"} ! vascular system relationship: RO:0002473 UBERON:0001638 ! composed primarily of vein property_value: RO:0002175 NCBITaxon:9606 @@ -13108,7 +13147,7 @@ is_a: UBERON:0034925 ! anatomical collection intersection_of: UBERON:0034925 ! anatomical collection intersection_of: RO:0002351 UBERON:0000982 ! has member skeletal joint relationship: part_of UBERON:0001434 {source="FMA"} ! skeletal system -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria relationship: RO:0002328 GO:0040011 ! functionally related to locomotion relationship: RO:0002351 UBERON:0000982 ! has member skeletal joint relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage @@ -13265,7 +13304,7 @@ xref: TAO:0000091 xref: ZFA:0000091 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0003068 ! axial mesoderm -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata [Term] id: UBERON:0004905 @@ -13308,7 +13347,7 @@ subset: upper_level xref: FMA:82485 is_a: UBERON:0000064 ! organ part relationship: part_of UBERON:0000060 ! anatomical wall -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0005061 @@ -13393,7 +13432,7 @@ synonym: "musculus" EXACT [FMA:30316] xref: FMA:30316 is_a: UBERON:0000061 ! anatomical structure relationship: has_part CL:0000187 ! muscle cell -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0005095 @@ -13873,11 +13912,12 @@ xref: NCIT:C13191 xref: SCTID:68989006 xref: UMLS:C0004799 {source="ncithesaurus:Basement_Membrane"} xref: Wikipedia:Basement_membrane +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005764 {source="FMA"} ! acellular membrane relationship: adjacent_to CL:0000066 ! epithelial cell relationship: has_part GO:0005587 ! collagen type IV trimer relationship: part_of UBERON:0000483 ! epithelium -relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa relationship: RO:0002473 GO:0005604 ! composed primarily of basement membrane property_value: RO:0002175 NCBITaxon:80999 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} @@ -14026,7 +14066,7 @@ xref: NCIT:C34232 xref: UMLS:C1518430 {source="ncithesaurus:Notochordal_Process"} xref: VHOG:0001213 is_a: UBERON:0005423 ! developing anatomical structure -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002202 UBERON:0000924 {source="EHDAA2"} ! develops from ectoderm [Term] @@ -14131,7 +14171,7 @@ intersection_of: UBERON:0006598 ! presumptive structure intersection_of: part_of UBERON:0000307 ! blastula intersection_of: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm relationship: part_of UBERON:0000307 ! blastula -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm [Term] @@ -14183,7 +14223,7 @@ intersection_of: UBERON:0006598 ! presumptive structure intersection_of: part_of UBERON:0000307 ! blastula intersection_of: RO:0002387 UBERON:0000924 ! has potential to develop into ectoderm relationship: part_of UBERON:0000307 ! blastula -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002387 UBERON:0000924 ! has potential to develop into ectoderm [Term] @@ -14201,7 +14241,7 @@ intersection_of: UBERON:0006598 ! presumptive structure intersection_of: part_of UBERON:0000307 ! blastula intersection_of: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm relationship: part_of UBERON:0000307 ! blastula -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm [Term] @@ -14270,6 +14310,7 @@ subset: efo_slim xref: EFO:0003709 xref: TAO:0005077 xref: ZFA:0005077 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005423 ! developing anatomical structure relationship: has_part CL:0000115 ! endothelial cell relationship: has_part CL:0000566 ! angioblastic mesenchymal cell @@ -14601,7 +14642,7 @@ is_a: UBERON:0000475 ! organism subdivision intersection_of: UBERON:0000475 ! organism subdivision intersection_of: RO:0002551 UBERON:0010719 ! has skeleton girdle skeleton relationship: part_of UBERON:0010707 ! appendage girdle complex -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002551 UBERON:0010719 ! has skeleton girdle skeleton [Term] @@ -14757,7 +14798,7 @@ synonym: "renal tubule (generic)" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "tubule of excretory system" EXACT [https://orcid.org/0000-0002-6601-2165, OBOL:automatic] is_a: UBERON:0003914 ! epithelial tube is_a: UBERON:0006555 ! excretory tube -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria [Term] id: UBERON:0009856 @@ -14987,7 +15028,7 @@ xref: FMA:7182 xref: VSAO:0000214 is_a: UBERON:0000475 ! organism subdivision is_a: UBERON:0015212 ! lateral structure -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002328 GO:0040011 ! functionally related to locomotion property_value: IAO:0000116 "It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO]" xsd:string property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 @@ -15168,7 +15209,7 @@ synonym: "schizocoelom" NARROW [] xref: EHDAA2:0004731 xref: Wikipedia:Coelom is_a: UBERON:0000481 {source="EHDAA2"} ! multi-tissue structure -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria property_value: IAO:0000116 "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." xsd:string property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} @@ -15288,7 +15329,7 @@ namespace: uberon def: "A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages." [https://orcid.org/0000-0002-6601-2165] subset: non_informative is_a: UBERON:0000475 ! organism subdivision -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0013702 @@ -15372,7 +15413,7 @@ def: "Any structure that is placed on one side of the left-right axis of a bilat subset: grouping_class subset: non_informative is_a: UBERON:0000061 ! anatomical structure -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria [Term] id: UBERON:0015228 @@ -17011,9 +17052,7 @@ inverse_of: output_of ! output of [Typedef] id: has_part name: has part -name: has_part namespace: external -namespace: quality def: "a core relation that holds between a whole and its part" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology @@ -17218,9 +17257,7 @@ expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://p [Typedef] id: part_of name: part of -name: part_of namespace: external -namespace: quality def: "a core relation that holds between a part and its whole" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term diff --git a/src/ontology/subsets/kidney_upper_slim.owl b/src/ontology/subsets/kidney_upper_slim.owl index 68c9d4c93..ae3211d54 100644 --- a/src/ontology/subsets/kidney_upper_slim.owl +++ b/src/ontology/subsets/kidney_upper_slim.owl @@ -22,8 +22,8 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - 2024-08-16 + + 2024-09-26 @@ -392,6 +392,14 @@ WHERE { + + + + + + + + @@ -1038,6 +1046,12 @@ WHERE { + + + + + + @@ -1076,17 +1090,13 @@ WHERE { - - created by - + - - creation date - + @@ -1172,9 +1182,7 @@ WHERE { - - id - + @@ -1283,7 +1291,6 @@ WHERE { A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. BFO:0000050 external - quality part_of @@ -1292,7 +1299,6 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of part of part of - part_of http://www.obofoundry.org/ro/#OBO_REL:part_of @@ -1314,7 +1320,6 @@ A continuant cannot be part of an occurrent: use 'participates in'. An A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. BFO:0000051 external - quality has_part @@ -1322,7 +1327,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part has part has part - has_part @@ -4773,7 +4777,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -4854,6 +4858,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -5523,7 +5528,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -5631,12 +5636,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - An endothelial cell that lines the vasculature. ZFA:0009036 @@ -5699,12 +5698,36 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + Any epithelial cell that is part of some squamous epithelium. CALOHA:TS-1249 ZFA:0009039 squamous epithelial cell + + + + Any epithelial cell that is part of some squamous epithelium. + FBC:Autogenerated + @@ -5769,6 +5792,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6023,6 +6047,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6233,6 +6258,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6264,6 +6290,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6297,6 +6324,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6418,7 +6446,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -6427,11 +6455,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - Any cell that only exists in Eukaryota. + Any cell that in taxon some Eukaryota. MESH:D005057 eukaryotic cell @@ -6439,7 +6467,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - Any cell that only exists in Eukaryota. + Any cell that in taxon some Eukaryota. FBC:Autogenerated @@ -6566,7 +6594,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -6577,7 +6605,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -6821,6 +6849,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6970,6 +6999,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -7066,6 +7096,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -7576,6 +7607,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -7717,6 +7749,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -7944,7 +7977,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different An endothelial cell that has small pores, or fenestrations, which allow for the efficient exchange of substances between the blood and surrounding tissues. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Fenestrated cells are specialized epithelial cells that are characterized by a distinctive structural feature, fenestrations or tiny pores, which allow an exchange of substances such as fluids, nutrients, and waste between blood vessels and the surrounding tissue environments. These cells are present in various types of epithelial tissues in the human body, including the intestinal tract, endocrine glands, and certain parts of the renal system. +There are multiple types of endothelial cell fenestrations. The most common type is found in systemic capillaries of the endocrine tissue (e.g., pancreatic islets), gastrointestinal mucosa, and renal peritubular capillaries. Here, the fenestrated cells have fenestrations in their peripheral cytoplasm with a unique thin and permeable diaphragm that provides a high degree of selectivity, blocking the passage of larger molecules while allowing the free movement of smaller ones. In contrast, other types of fenestrations, such as the discontinuous epithelium of the liver sinusoidal endothelial cells, do not have diaphragms. +Characteristically, fenestrated cells play a vital role in the filtering process of body systems. They are a key part of the glomeruli in the kidneys where blood is filtered under high pressure. The fenestrations present in the endothelial cells lining the capillaries of the glomerulus allow the free passage of water and small solute molecules towards the Bowman's capsule, leaving behind larger proteins and cells in the blood, thereby aiding in the filtration and waste removal process. +In the endocrine system, fenestrated cells in glandular capillaries allow the prompt release of hormones into the bloodstream. These cells have tightly clustered fenestrations which increase the surface area available for passive diffusion, improving the efficiency of hormone secretion. In villi of the small intestine, these cells increase absorption efficiency, permitting the exchange of water, electrolytes, and nutrients. +Overall, fenestrated cells contribute immensely to important physiological processes of filtration, absorption, and secretion, primarily connecting our body's circulation system with the surrounding tissues and organs. ZFA:0009286 + https://cellxgene.cziscience.com/cellguide/CL_0000666 window cell fenestrated endothelial cell @@ -7955,6 +7996,22 @@ Each of these 3 primitives can be composed to yield a cross-product of different An endothelial cell that has small pores, or fenestrations, which allow for the efficient exchange of substances between the blood and surrounding tissues. DOI:10.1007/978-3-211-99390-3_133 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Fenestrated cells are specialized epithelial cells that are characterized by a distinctive structural feature, fenestrations or tiny pores, which allow an exchange of substances such as fluids, nutrients, and waste between blood vessels and the surrounding tissue environments. These cells are present in various types of epithelial tissues in the human body, including the intestinal tract, endocrine glands, and certain parts of the renal system. +There are multiple types of endothelial cell fenestrations. The most common type is found in systemic capillaries of the endocrine tissue (e.g., pancreatic islets), gastrointestinal mucosa, and renal peritubular capillaries. Here, the fenestrated cells have fenestrations in their peripheral cytoplasm with a unique thin and permeable diaphragm that provides a high degree of selectivity, blocking the passage of larger molecules while allowing the free movement of smaller ones. In contrast, other types of fenestrations, such as the discontinuous epithelium of the liver sinusoidal endothelial cells, do not have diaphragms. +Characteristically, fenestrated cells play a vital role in the filtering process of body systems. They are a key part of the glomeruli in the kidneys where blood is filtered under high pressure. The fenestrations present in the endothelial cells lining the capillaries of the glomerulus allow the free passage of water and small solute molecules towards the Bowman's capsule, leaving behind larger proteins and cells in the blood, thereby aiding in the filtration and waste removal process. +In the endocrine system, fenestrated cells in glandular capillaries allow the prompt release of hormones into the bloodstream. These cells have tightly clustered fenestrations which increase the surface area available for passive diffusion, improving the efficiency of hormone secretion. In villi of the small intestine, these cells increase absorption efficiency, permitting the exchange of water, electrolytes, and nutrients. +Overall, fenestrated cells contribute immensely to important physiological processes of filtration, absorption, and secretion, primarily connecting our body's circulation system with the surrounding tissues and organs. + DOI:10.1002/ar.1092200109 + DOI:10.1016/0306-4522(86)90162-4 + DOI:10.1016/j.devcel.2012.11.003 + DOI:10.1038/s41467-022-31571-2 + DOI:10.1152/ajprenal.90601.2008 + @@ -8029,6 +8086,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -8117,6 +8175,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -8447,7 +8506,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + @@ -8678,6 +8739,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -8722,6 +8784,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -8977,6 +9040,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -9163,7 +9227,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -9202,7 +9266,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -9277,7 +9341,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -9350,32 +9414,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - An endothelial progenitor cell that participates in angiogenesis during development. - - 2011-02-28T04:20:39Z - ZFA:0005773 - See CL:0002619. - embryonic blood vessel endothelial progenitor cell - - - - - An endothelial progenitor cell that participates in angiogenesis during development. - GOC:tfm - - - - - ZFA:0005773 - - - - - @@ -9470,7 +9508,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cuboidal epithelial cell of the kidney which regulates sodium and potassium balance. The activity of sodium and potassium channels on the apical membrane of the cell is regulated by aldosterone and vasopressin. In mammals this cell type is located in the renal collecting duct system. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Renal principal cells are the major cell type in the initial collecting tubule and the cortical and outer medullary collecting ducts, as well as the connecting tubule, in the nephrons of the kidneys. +A key function of renal principal cells is the regulation of water balance in the body. These cells express aquaporin-2 (AQP2) water channels, which facilitate the reabsorption of water from the fluid within the renal tubule lumen back into the blood. The translocation of AQP2 to the cell membrane is controlled by the hormone vasopressin: In response to high vasopressin levels, AQP2 moves to the cell membrane, allowing water to pass through effectively and be reabsorbed, therefore concentrating the urine. Conversely, in low vasopressin conditions, AQP2 is removed from the membrane, reducing water reabsorption and diluting the urine. +Renal principal cells are also involved in the regulation of sodium and potassium levels in the body. They have sodium channels (ENaC) in their luminal membranes which permit the reabsorption of sodium ions from the tubule fluid back into the blood, resulting in a net reabsorption of sodium ions into the systemic circulation. This process is controlled, in part, by the hormone aldosterone. Additionally, renal principal cells contain potassium channels that facilitate the secretion of potassium ions into the urine. The activities of these channels, in coordination with other cell types in the nephron, are critical for maintaining electrolyte balance and overall body homeostasis. ZFA:0005322 + https://cellxgene.cziscience.com/cellguide/CL_0005009 renal principal cell @@ -9480,6 +9524,18 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cuboidal epithelial cell of the kidney which regulates sodium and potassium balance. The activity of sodium and potassium channels on the apical membrane of the cell is regulated by aldosterone and vasopressin. In mammals this cell type is located in the renal collecting duct system. CL:CVS + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Renal principal cells are the major cell type in the initial collecting tubule and the cortical and outer medullary collecting ducts, as well as the connecting tubule, in the nephrons of the kidneys. +A key function of renal principal cells is the regulation of water balance in the body. These cells express aquaporin-2 (AQP2) water channels, which facilitate the reabsorption of water from the fluid within the renal tubule lumen back into the blood. The translocation of AQP2 to the cell membrane is controlled by the hormone vasopressin: In response to high vasopressin levels, AQP2 moves to the cell membrane, allowing water to pass through effectively and be reabsorbed, therefore concentrating the urine. Conversely, in low vasopressin conditions, AQP2 is removed from the membrane, reducing water reabsorption and diluting the urine. +Renal principal cells are also involved in the regulation of sodium and potassium levels in the body. They have sodium channels (ENaC) in their luminal membranes which permit the reabsorption of sodium ions from the tubule fluid back into the blood, resulting in a net reabsorption of sodium ions into the systemic circulation. This process is controlled, in part, by the hormone aldosterone. Additionally, renal principal cells contain potassium channels that facilitate the secretion of potassium ions into the urine. The activities of these channels, in coordination with other cell types in the nephron, are critical for maintaining electrolyte balance and overall body homeostasis. + DOI:10.1016/j.krcp.2013.07.005 + DOI:10.2215/CJN.05760513 + DOI:10.2215/CJN.08580813 + @@ -9603,6 +9659,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -9672,6 +9729,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. +After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. +Disorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis. + https://cellxgene.cziscience.com/cellguide/CL_0011012 neural crest cell @@ -9682,6 +9745,19 @@ Each of these 3 primitives can be composed to yield a cross-product of different https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-9900-7880 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. +After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. +Disorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis. + DOI:10.1002/dvg.23276 + DOI:10.1242/dev.193193 + DOI:10.3389/fcell.2020.00635/full + https://doi.org/10.1016/j.ydbio.2011.12.042 + @@ -9699,6 +9775,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -9961,20 +10038,20 @@ Each of these 3 primitives can be composed to yield a cross-product of different An epithelial cell that is part of the collecting duct of renal tubule. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Kidney collecting duct epithelial cells are a specialized type of cells that form an integral part of the renal system. Located in the collecting duct system of the kidneys, these cells are responsible for one of the final steps in the process of urine formation, and they are instrumental in the fine tuning of the volume and composition of urine by reabsorbing water and certain solutes back into the bloodstream. +These cells express specific channels and carriers that actively and passively transport ions and water. They also have channels on their membranes, such as sodium channels and potassium channels, involved in reabsorbing or secreting these electrolytes depending upon the body's needs. The function of renal collecting duct epithelial cells can be regulated by a variety of hormones, including vasopressin (antidiuretic hormone), which can modulate the ion channels and carriers and hence indirectly influence body fluid homeostasis. +Aside from their function in ion and water balance, kidney collecting duct epithelial cells also aid in maintaining the body's acid-base balance. They have specialized functionality to secret hydrogen ions into the tubular lumen, which contributes to acid excretion. Any dysfunction may have serious implications and lead to various renal or systemic diseases, exemplifying the importance of these cells in maintaining overall body homeostasis. FMA:70982 KUPO:0001059 + https://cellxgene.cziscience.com/cellguide/CL_1000454 epithelial cell of renal collecting tubule kidney collecting duct epithelial cell - - - - - true - @@ -9987,12 +10064,31 @@ Each of these 3 primitives can be composed to yield a cross-product of different An epithelial cell that is part of the collecting duct of renal tubule. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Kidney collecting duct epithelial cells are a specialized type of cells that form an integral part of the renal system. Located in the collecting duct system of the kidneys, these cells are responsible for one of the final steps in the process of urine formation, and they are instrumental in the fine tuning of the volume and composition of urine by reabsorbing water and certain solutes back into the bloodstream. +These cells express specific channels and carriers that actively and passively transport ions and water. They also have channels on their membranes, such as sodium channels and potassium channels, involved in reabsorbing or secreting these electrolytes depending upon the body's needs. The function of renal collecting duct epithelial cells can be regulated by a variety of hormones, including vasopressin (antidiuretic hormone), which can modulate the ion channels and carriers and hence indirectly influence body fluid homeostasis. +Aside from their function in ion and water balance, kidney collecting duct epithelial cells also aid in maintaining the body's acid-base balance. They have specialized functionality to secret hydrogen ions into the tubular lumen, which contributes to acid excretion. Any dysfunction may have serious implications and lead to various renal or systemic diseases, exemplifying the importance of these cells in maintaining overall body homeostasis. + DOI:10.1016/j.ajpath.2014.01.014 + DOI:10.1016/j.semnephrol.2019.04.005 + DOI:10.2215/CJN.05760513 + DOI:10.2215/CJN.08880914 + epithelial cell of renal collecting tubule FMA:70982 + + + + + true + @@ -10049,7 +10145,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -10986,7 +11082,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -11138,7 +11234,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -11146,6 +11242,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome. + https://github.com/geneontology/go-ontology/issues/28301 GO:0000789 GO:0000790 GO:0005717 @@ -11550,7 +11647,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different renal blood volume control of blood pressure renal regulation of blood volume GO:0001977 - + renal system process involved in regulation of blood volume @@ -12267,32 +12364,32 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. Wikipedia:Collagen cellular_component GO:0005581 collagen trimer - + - + - + PMID:12382326 - + PMID:12382326 @@ -12602,12 +12699,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - + @@ -13445,6 +13537,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different The generation and maintenance of gametes in a multicellular organism. A gamete is a haploid reproductive cell. + + + GO:0009552 biological_process gametogenesis @@ -14673,6 +14768,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different The self-renewing division of a stem cell. A stem cell is an undifferentiated cell, in the embryo or adult, that can undergo unlimited division and give rise to one or several different cell types. + + + stem cell renewal biological_process GO:0017145 @@ -16054,12 +16152,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - + A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. GO:0043234 @@ -16089,33 +16182,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - A macromolecular complex containing both protein and DNA molecules. - DNA-protein complex - cellular_component - GO:0032993 - - Note that this term is intended to classify complexes that have DNA as one of the members of the complex, that is, the complex does not exist if DNA is not present. Protein complexes that interact with DNA e.g. transcription factor complexes should not be classified here. - protein-DNA complex - - - - - A macromolecular complex containing both protein and DNA molecules. - GOC:mah - - - - - DNA-protein complex - GOC:mah - - - - @@ -16411,6 +16477,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different A large plasma membrane-lined circular pore that perforates the flattened glomerular endothelium and, unlike those of other fenestrated capillaries, is not spanned by diaphragms; the density and size of glomerular fenestrae account, at least in part, for the high permeability of the glomerular capillary wall to water and small solutes. + + + bf 2011-12-12T10:53:24Z GEnC fenestration @@ -16748,10 +16817,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. + https://github.com/geneontology/go-ontology/issues/28153 NIF_Subcellular:sao414196390 membrane-enclosed organelle cellular_component GO:0043227 + membrane-bounded organelle @@ -16769,11 +16840,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. https://github.com/geneontology/go-ontology/issues/21881 + https://github.com/geneontology/go-ontology/issues/28153 NIF_Subcellular:sao1456184038 non-membrane-enclosed organelle cellular_component biological condensate GO:0043228 + non-membrane-bounded organelle @@ -16809,8 +16882,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. + https://github.com/geneontology/go-ontology/issues/28153 cellular_component GO:0043229 + intracellular organelle @@ -17057,10 +17132,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component. + https://github.com/geneontology/go-ontology/issues/27194 GO:0071843 cellular component biogenesis at cellular level biological_process GO:0044085 + cellular component biogenesis @@ -19432,6 +19509,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -22011,7 +22089,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -23133,51 +23211,51 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + - A molecular entity that minimally consists of a protein. + A material entity that minimally consists of a protein. protein protein aggregate protein complex protein-containing complex protein - PR:000064867 - Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). - protein-containing molecular entity + PR:000050567 + Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566). + protein-containing material entity - + - A molecular entity that minimally consists of a protein. + A material entity that minimally consists of a protein. PRO:DAN - + protein PRO:DAN - + protein aggregate PRO:DAN - + protein complex PRO:DAN - + protein-containing complex PRO:DAN @@ -23259,7 +23337,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -23380,7 +23458,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -23434,14 +23512,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different ureter https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg - + - + GO @@ -23491,7 +23569,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -23539,14 +23617,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different urethra https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png - + - + Wikipedia @@ -23568,6 +23646,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -24053,7 +24132,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -24103,14 +24182,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg - + - + FMA MA @@ -24192,7 +24271,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -24373,14 +24452,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -24412,24 +24491,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different metanephros - + - + - + GO - + ISBN:9780878932504 @@ -24544,8 +24623,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + An epithelial swelling on the Wolffian duct that elongates to invade the adjacent metanephric mesenchyme[MP]. BTO:0001646 EHDAA2:0002140 @@ -24569,11 +24648,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different ureteric bud - + - + @@ -24586,13 +24665,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 - + ISBN:9780878932504 @@ -24973,7 +25052,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -24982,7 +25061,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -25009,14 +25088,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different gastrula stage - + - + BILS @@ -25088,7 +25167,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -25131,7 +25210,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -25196,7 +25275,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -25276,11 +25355,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + - + @@ -25303,24 +25382,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0000162 cloaca - + - + - + ZFA - + AAO @@ -25361,8 +25440,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + @@ -25380,24 +25459,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different embryonic cloaca - + - + - + EHDAA2 - + EHDAA2 @@ -25420,10 +25499,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -25459,14 +25538,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different primitive urogenital sinus http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png - + - + MP-def @@ -25515,7 +25594,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -25741,6 +25820,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -25748,15 +25828,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - - + + A fluid that is composed of blood plasma and erythrocytes. AAO:0000046 @@ -25793,34 +25873,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different blood - + - + - + - + CL:tm - + https://github.com/obophenotype/uberon/issues/1330 - + Bgee:AN @@ -25870,7 +25950,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -25964,7 +26044,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -26188,7 +26268,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -27149,6 +27229,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -27162,7 +27243,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -27204,14 +27285,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg - - + + - + http://palaeos.com/metazoa/porifera/homoscleromorpha.html @@ -27569,10 +27650,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -27604,14 +27685,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different abdomen - + - + MA @@ -27749,7 +27830,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -27840,7 +27921,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. AAO:0000137 BILA:0000036 @@ -27875,14 +27956,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png - + - + Bgee:AN @@ -27922,7 +28003,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. AAO:0000139 BILA:0000038 @@ -27957,14 +28038,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png - + - + Bgee:AN @@ -28005,7 +28086,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The middle germ layer of the embryo, between the endoderm and ectoderm. UBERON:0003263 @@ -28046,14 +28127,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png - + - + Bgee:AN @@ -28108,7 +28189,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -28219,10 +28300,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -28262,7 +28343,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different proctodeum https://github.com/obophenotype/uberon/issues/685 - + @@ -28275,7 +28356,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 @@ -28337,7 +28418,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -28346,7 +28427,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -28408,14 +28489,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different https://cdn.humanatlas.io/digital-objects/ref-organ/heart-female/v1.3/assets/3d-vh-f-heart.glb https://cdn.humanatlas.io/digital-objects/ref-organ/heart-male/v1.3/assets/3d-vh-m-heart.glb - + - + MA @@ -28500,7 +28581,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -28969,7 +29050,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -29092,7 +29173,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -29247,7 +29328,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -29269,14 +29350,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]. - AAO:0000324 BILA:0000079 BIRNLEX:844 @@ -29311,7 +29391,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0001016 - @@ -29319,14 +29398,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png - + - + Bgee:AN @@ -29388,11 +29467,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. @@ -29437,7 +29516,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different central nervous system - + @@ -29451,7 +29530,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Bgee:AN @@ -29648,7 +29727,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -29682,14 +29761,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different hindgut http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray472.png - + - + Wikipedia @@ -30180,14 +30259,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -30239,24 +30318,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different renal pelvis https://upload.wikimedia.org/wikipedia/commons/c/c0/Illu_kidney2.jpg - + - + - + MA - + FMA @@ -30302,7 +30381,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -30338,14 +30417,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-male-right/v1.3/assets/3d-vh-m-kidney-r.glb https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg - + - + FMA @@ -30381,7 +30460,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -30426,14 +30505,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different renal corpuscle https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg - + - + MA ZFA @@ -30507,7 +30586,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -30549,14 +30628,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different glomerular capsule http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg - + - + Wikipedia @@ -30646,10 +30725,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -30693,7 +30772,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different nephron tubule - + @@ -30702,14 +30781,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + GO MA ZFA @@ -30723,7 +30802,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + ZFA @@ -30937,7 +31016,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -30984,7 +31063,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different https://cdn.humanatlas.io/digital-objects/ref-organ/urinary-bladder-male/v1.2/assets/3d-vh-m-urinary-bladder.glb https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg - + @@ -30997,7 +31076,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + FMA @@ -31127,7 +31206,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -31140,7 +31219,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The basic functional unit of the kidney. its chief function is to regulate the concentration of water and soluble substances like sodium salts by filtering the blood, reabsorbing what is needed and excreting the rest as urine. A nephron eliminates wastes from the body, regulates blood volume and blood pressure, controls levels of electrolytes and metabolites, and regulates blood pH. Its functions are vital to life and are regulated by the endocrine system by hormones such as antidiuretic hormone, aldosterone, and parathyroid hormone.[WP]. kidney terms require review for cross-vertebrate compatibility and developmental relationships. @@ -31171,24 +31250,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different nephron http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + - + - + FMA - + Bgee:AN @@ -31239,14 +31318,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -31282,11 +31361,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different proximal convoluted tubule http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + - + @@ -31299,13 +31378,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + GO - + Wikipedia @@ -31437,7 +31516,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -31464,7 +31543,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different descending limb of loop of Henle http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + @@ -31477,7 +31556,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + FMA @@ -31501,14 +31580,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -31553,11 +31632,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different proximal straight tubule - + - + @@ -31570,13 +31649,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + MA - + MA @@ -31618,7 +31697,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -31654,7 +31733,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different distal convoluted tubule https://upload.wikimedia.org/wikipedia/commons/2/21/Kidney_nephron.png - + @@ -31667,7 +31746,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EMAPA GO MA-modified-from-isa @@ -31942,7 +32021,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -31965,14 +32044,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different kidney arcuate artery https://upload.wikimedia.org/wikipedia/commons/8/87/2610_The_Kidney.jpg - + - + MA @@ -32003,7 +32082,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -32013,7 +32092,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A tube extending from the mouth to the anus. @@ -32050,14 +32129,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different digestive tract - + - + NCBIBook:NBK10107 @@ -32535,6 +32614,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -32762,6 +32842,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -32770,8 +32851,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + @@ -32784,7 +32865,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -32838,34 +32919,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different blood vessel http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg - + - + - + - + AEO - + EHDAA2 - + GO:0072360 @@ -33008,7 +33089,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -33569,7 +33650,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -33722,10 +33803,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -33774,14 +33855,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different kidney - + - + FMA @@ -33816,8 +33897,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + @@ -33855,11 +33936,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different Once the more complex mesonephros forms the pronephros undergoes apoptosis in amphibians. In fishes the nephron degenerates but the organ remains and becomes a component of the immune system[Wikipedia:Pronephros]. // TODO - check developmental relationships. Note that we previously include the ZFA/XAO terms under the more specific 'pronephric kidney', but these are now merged. TODO GCI: relationship: capable_of GO:0030104 pronephros - + - + @@ -33872,13 +33953,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + OG - + ZFA @@ -33927,7 +34008,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -34204,8 +34285,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + - + @@ -34224,7 +34306,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + An anatomical structure which consists of juxtaglomerular cells, extraglomerular mesangial cells and the macula densa. The juxtaglomerular apparatus lies adjacent to the glomerulus and regulates kidney function by maintaining the blood flow to the kidney and the filtration rate[GO]. a microscopic structure in the kidney, which regulates the function of each nephron. The juxtaglomerular apparatus is named for its proximity to the glomerulus: it is found between the vascular pole of the renal corpuscle and the returning distal convoluted tubule of the same nephron. This location is critical to its function in regulating renal blood flow and glomerular filtration rate. The three cellular components of the apparatus are the macula densa, extraglomerular mesangial cells, and juxtaglomerular cells (also known as granular cells)[WP]. BTO:0005157 @@ -34246,24 +34328,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different juxtaglomerular apparatus - + - + - + MA - + GO @@ -34387,8 +34469,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + @@ -34405,24 +34487,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different EDITOR_NOTE check MA part_ofs - should be spatially disjoint from renal glomerulus? extraglomerular mesangium - + - + - + MA - + MA @@ -34564,9 +34646,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - + + + @@ -34614,15 +34696,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - - + + - + - + @@ -34641,19 +34723,19 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -34693,8 +34775,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. mesodermal cluster @@ -34732,11 +34814,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - - + + - + @@ -34749,13 +34831,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + GOTAX:0000352 - + ZFA @@ -34815,8 +34897,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + The macula densa is an area of specialized cells in the distal tubule that makes contact with the vascular pole of the glomerulus[GO]. BTO:0003940 @@ -34834,24 +34916,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different macula densa - + - + - + MA - + GO @@ -34876,22 +34958,22 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + - - + + - + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. AAO:0010578 BTO:0001764 @@ -34924,45 +35006,45 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - + BTO - + PMID:11523831 - + PMID:11523831 @@ -35162,7 +35244,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -35253,7 +35335,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -35326,10 +35408,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -35379,14 +35461,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different hematopoietic system - + - + FMA @@ -35604,7 +35686,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. AAO:0011086 EFO:0001982 @@ -35627,14 +35709,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different presomitic mesoderm - + - + Bgee:AN @@ -35675,8 +35757,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + In mammals, the pronephric duct is the predecessor of the Wolffian duct[WP]. AAO:0011088 NCIT:C34279 @@ -35695,11 +35777,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different The pronephric duct collects the filtrate from the pronephric tubules and opens to the exterior of the pronephric kidney[GOC:mtg_kidney_jan10, PMID:15647339, XAO:0000063, ZFA:0000150] pronephric duct - + - + @@ -35712,13 +35794,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Wikipedia - + XAO @@ -35824,9 +35906,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - + + + @@ -35865,34 +35947,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different intermediate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + - + AAO - + EMAPA - + XAO @@ -35948,7 +36030,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -36001,7 +36083,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Paired organ that connects the primitive kidney Wolffian body (or mesonephros) to the cloaca and serves as the anlage for certain male reproductive organs. the Wolffian duct is what remains of the pronephric duct after the atrophy of the pronephros[WP]. In Zebrafish: Duct of the adult kidney (mesonephros), present bilaterally ventral to the somites and leading to the cloacal chamber[ZFA]. Consider adding subclasses for male and female specific variants TODO - mesonephric portion of the nephric duct @@ -36030,7 +36112,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different mesonephric duct http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png - + @@ -36043,7 +36125,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 @@ -36097,9 +36179,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. AAO:0011072 BTO:0001765 @@ -36128,34 +36210,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - - + + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -36195,7 +36277,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. AAO:0010568 EFO:0003515 @@ -36221,7 +36303,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -36234,7 +36316,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Bgee:AN @@ -36281,10 +36363,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -36321,7 +36403,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -36334,7 +36416,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 VHOG @@ -36384,15 +36466,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + - + Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. should probably be merged with heart rudiment. AAO:0011044 @@ -36409,15 +36491,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different heart primordium - + - + - + @@ -36430,19 +36512,19 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + ZFA - + ZFA - + XAO @@ -36471,8 +36553,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. AAO:0010571 AEO:0000212 @@ -36496,11 +36578,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different sclerotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - - + + - + @@ -36519,13 +36601,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + VHOG:0000680 - + ZFA @@ -36609,7 +36691,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -36770,7 +36852,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -36796,14 +36878,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different Genes: The positional specification of the metanephrogenic mesenchyme is negatively regulated by Foxc1 and Foxc2. Next the permanent kidney forming metanephrogenic mesenchyme is specified by Hox11 genes. The competence to respond to ureteric bud inducers is regulated by WT1. GDNF secretion restricted to posterior region by Robo2 and Sprouty1. The receptors for GDNF are synthesized in the nephric ducts and later in ureteric buds [ISBN:9780878932504 "Developmental Biology"] metanephric mesenchyme - + - + ISBN:9780878932504 @@ -37491,7 +37573,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults EHDAA:251 @@ -37506,14 +37588,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different intraembryonic coelom - + - + Wikipedia @@ -37544,7 +37626,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -38093,8 +38175,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + In mammals, the proximal tubule is a nephron tubule that connects Bowman's capsule to the loop of Henle. It has a brush border epithelial morphology[GO]. TODO - ensure definition works across species. @@ -38111,24 +38193,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different proximal tubule - + - + - + GO - + GO @@ -38187,7 +38269,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The intermediate tubule is a nephron tubule that lies between the proximal and distal tubules. TODO - check for applicability across species FMA:17718 @@ -38197,14 +38279,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0004136 intermediate tubule - + - + FMA @@ -38280,8 +38362,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. XAO:0004185 first heart field @@ -38293,24 +38375,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0004140 primary heart field - + - + - + GO:0003128 - + https://orcid.org/0000-0003-3308-6245 @@ -38363,7 +38445,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + An epithelial tube that will give rise to the mature heart. AAO:0010411 EFO:0003526 @@ -38382,14 +38464,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different heart tube - + - + ZFA-modified @@ -38611,8 +38693,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + The comma-shaped body is the precursor structure to the S-shaped body that contributes to the morphogenesis of the nephron. EMAPA:27681 ZFA:0005588 @@ -38622,24 +38704,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different comma-shaped body - + - + - + cjm - + ZFA @@ -38661,8 +38743,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + The S-shaped body is the successor of the comma-shaped body that contributes to the morphogenesis of the nephron. TODO EMAPA:27756 @@ -38674,24 +38756,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different S-shaped body - + - + - + cjm - + GO @@ -39103,7 +39185,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -39141,14 +39223,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different glomerular capillary - + - + https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -39394,6 +39476,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -39490,6 +39573,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -39531,6 +39615,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -39572,6 +39657,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -39688,7 +39774,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -39725,14 +39811,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different renal afferent arteriole http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + - + Wikipedia @@ -40092,7 +40178,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. AAO:0011129 TAO:0001890 @@ -40106,14 +40192,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different skeletal element - + - + VSAO @@ -40140,10 +40226,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -40179,14 +40265,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0004770 articular system - + - + FMA @@ -40484,7 +40570,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -40505,14 +40591,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different somatopleure http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png - + - + EHDAA2 @@ -40578,9 +40664,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - + + + @@ -40600,34 +40686,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different urogenital fold - + - + - + - + EHDAA2 - + Wikipedia - + EHDAA2 @@ -40673,7 +40759,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -40839,7 +40925,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -41070,7 +41156,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -41102,7 +41188,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Missing definition for term UBERON:0005095. Please replace it using linked reference. class added for consistency with GO - consider merging with kidney mesenchyme. uberon @@ -41110,14 +41196,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0005095 kidney rudiment - + - + GO @@ -41233,7 +41319,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The connecting tubule is a tubular segment of the nephron; it connects the distal convoluted tubule to the collecting duct[GO]. BTO:0004539 @@ -41251,14 +41337,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different renal connecting tubule http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + - + Wikipedia @@ -41989,7 +42075,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -42005,14 +42091,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different trunk mesenchyme - + - + EHDAA2 @@ -42129,7 +42215,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Multi-tissue structure that arises from the heart rudiment and will become the heart tube. EHDAA2:0001512 EHDAA:424 @@ -42147,14 +42233,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different primitive heart tube - + - + ZFA @@ -42182,7 +42268,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -42209,7 +42295,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different gonad primordium - + @@ -42222,7 +42308,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + ZFA @@ -42281,14 +42367,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + A mesoderm that has the potential to develop into a pronephros. AAO:0011090 EFO:0003479 @@ -42306,24 +42392,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different the intermediate mesoderm of the chick embryo acquires its ability to form kidneys through its interactions with the paraxial mesoderm [ISBN:9780878932504 "Developmental Biology", PMID:10720431 "Signals from trunk paraxial mesoderm induce pronephros formation in chick intermediate mesoderm"]. These interactions induce the expression of TFs including Lim1, Pax2 and Pax6 that cause the intermediate mesoderm to form the kidney pronephric mesoderm - + - + - + ZFA - + Bgee:AN @@ -42370,7 +42456,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -42387,14 +42473,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different glomerular tuft - + - + Wikipedia @@ -42534,6 +42620,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -42549,7 +42636,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -42644,7 +42731,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -42672,14 +42759,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different glomerular basement membrane http://upload.wikimedia.org/wikipedia/commons/d/de/PhysiologieGlom%C3%A9rulaire.png - + - + true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -42764,7 +42851,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 @@ -42774,7 +42861,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0005856 developing mesenchymal condensation - + @@ -42793,7 +42880,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + AEO-modified-relation @@ -42890,7 +42977,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -42929,14 +43016,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different cloacal membrane http://upload.wikimedia.org/wikipedia/commons/d/d2/Gray991.png - + - + Wikipedia @@ -42970,7 +43057,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB EHDAA2:0001278 @@ -42984,7 +43071,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different notochordal plate - + @@ -42997,7 +43084,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 @@ -43021,11 +43108,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -43042,14 +43129,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -43342,7 +43429,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -43485,7 +43572,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -43549,7 +43636,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -43593,7 +43680,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A region of nephron tubule that is part of a cortex of kidney. EMAPA:18976 MA:0002609 @@ -43603,14 +43690,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0006853 renal cortex tubule - + - + MA @@ -43781,6 +43868,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -44282,7 +44370,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -44308,7 +44396,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different presumptive paraxial mesoderm - + @@ -44324,7 +44412,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + https://github.com/obophenotype/uberon/issues/1277 @@ -44485,7 +44573,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -44493,7 +44581,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0007524 dense mesenchyme tissue - + @@ -44506,7 +44594,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + AEO @@ -44720,7 +44808,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Anatomical system that consists of all blood and lymph vessels. consider merging with vasculature @@ -44737,14 +44825,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different vascular system - + - + MA @@ -44785,7 +44873,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -44882,7 +44970,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -44920,14 +45008,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different pelvic girdle skeleton http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png - + - + PMID:21455939 @@ -45010,7 +45098,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The functional tissue of the kidney, consisting of the nephrons. BTO:0003604 FMA:15574 @@ -45021,7 +45109,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0008987 renal parenchyma - + @@ -45034,7 +45122,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + FMA @@ -45104,7 +45192,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -45121,14 +45209,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -45247,7 +45335,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -45255,14 +45343,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -45287,7 +45375,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -45361,7 +45449,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EFO:0003704 TAO:0005041 ZFA:0005041 @@ -45371,14 +45459,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different anterior lateral plate mesoderm - + - + ZFA @@ -45699,7 +45787,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -45717,14 +45805,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0010227 future cardiac atrium - + - + ZFA @@ -45867,7 +45955,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -45881,7 +45969,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0010377 mesenchyme from somatopleure - + @@ -45894,7 +45982,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 @@ -45910,7 +45998,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses. MESH:D055806 TAO:0005251 @@ -45920,14 +46008,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0010523 microcirculatory vessel - + - + ZFA @@ -45960,7 +46048,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -45976,7 +46064,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0010532 primitive nephron - + @@ -45989,7 +46077,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 @@ -46005,7 +46093,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -46016,7 +46104,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0010536 nephron progenitor - + @@ -46029,7 +46117,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + cjm @@ -46042,7 +46130,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -46272,8 +46360,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. FMA:23879 SCTID:129140006 @@ -46285,11 +46373,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different subdivision of skeleton - + - + @@ -46302,13 +46390,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + UBERONREF:0000003 - + VSAO @@ -46369,7 +46457,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. axial skeletal system FMA:302077 @@ -46379,7 +46467,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different postcranial axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton - + @@ -46392,7 +46480,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + cjm @@ -46416,7 +46504,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -46441,14 +46529,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different upper urinary tract - + - + FMA @@ -46645,7 +46733,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -46766,7 +46854,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -46781,14 +46869,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different We presume this is distinct from AAO:0001003, an external integumentary structure - check with amphibian anatomy ontology developers. AO notes: the text def states mesenchymal swelling, EHDAA2 splits into mesenchymal and epithelial parts embryonic cloacal fold - + - + EHDAA2 @@ -46811,20 +46899,20 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2:0004588 uberon UBERON:0012361 internal anal region - + - + EHDAA2 @@ -46834,20 +46922,20 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2:0004589 uberon UBERON:0012469 external anal region - + - + EHDAA2 @@ -46874,7 +46962,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -46894,14 +46982,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different skeleton of pelvic complex - + - + FMA @@ -46953,7 +47041,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The precursor of the urethra. SCTID:361531004 Wikipedia:Urethral_groove @@ -46964,14 +47052,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0013241 embryonic urethral groove - + - + Wikipedia @@ -47075,7 +47163,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -47321,7 +47409,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -47542,7 +47630,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -47565,7 +47653,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0016887 entire extraembryonic component - + @@ -47578,7 +47666,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + AEO @@ -47989,7 +48077,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The upper tract of the renal system. The renal pelvis is the large cavity in the middle of each kidney. Urine drains from each kidney through a long tube called the ureter, into the bladder, where it is stored until it is passed from the body through the urethra. NCIT:C54419 @@ -48000,14 +48088,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different renal pelvis/ureter - + - + NCIT @@ -48348,6 +48436,454 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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+_:B869127b4X2D9725X2D463eX2Dbe79X2D2d475f23f3cfgenid939 +_:B869127b4X2D9725X2D463eX2Dbe79X2D2d475f23f3cfgenid952 +_:B869127b4X2D9725X2D463eX2Dbe79X2D2d475f23f3cfgenid958 +_:B869127b4X2D9725X2D463eX2Dbe79X2D2d475f23f3cfgenid964 +_:B869127b4X2D9725X2D463eX2Dbe79X2D2d475f23f3cfgenid970 +_:B869127b4X2D9725X2D463eX2Dbe79X2D2d475f23f3cfgenid976 +_:B869127b4X2D9725X2D463eX2Dbe79X2D2d475f23f3cfgenid982 +_:B869127b4X2D9725X2D463eX2Dbe79X2D2d475f23f3cfgenid988 +_:B869127b4X2D9725X2D463eX2Dbe79X2D2d475f23f3cfgenid995 "cell" "early embryonic cell (metazoa)" "stem cell" @@ -416,7 +449,6 @@ _:B37f46b34X2Dd719X2D4ca1X2D82faX2Db899d54442eagenid997 "embryonic cell (metazoa)" "cardiocyte" "kidney epithelial cell" - "embryonic blood vessel endothelial progenitor cell" "renal cortical epithelial cell" "squamous endothelial cell" "kidney cortical cell" @@ -603,7 +635,6 @@ _:B37f46b34X2Dd719X2D4ca1X2D82faX2Db899d54442eagenid997 "secretion by cell" "protein-containing complex disassembly" "protein-containing complex" - "protein-DNA complex" "macromolecule localization" "erythrocyte homeostasis" "monoatomic ion transmembrane transport" @@ -838,7 +869,7 @@ _:B37f46b34X2Dd719X2D4ca1X2D82faX2Db899d54442eagenid997 "Mus musculus protein" "eukaryotic protein" "angiotensinogenase" - "protein-containing molecular entity" + "protein-containing material entity" "processual entity" "tube" "appendage" diff --git a/subsets/blood_and_immune_upper_slim.json b/subsets/blood_and_immune_upper_slim.json index 0f8e1a3e4..fdd02d37b 100644 --- a/subsets/blood_and_immune_upper_slim.json +++ b/subsets/blood_and_immune_upper_slim.json @@ -4,9 +4,9 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-08-16" + "val" : "2024-09-26" } ], - "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-08-16/subsets/blood_and_immune_upper_slim.owl" + "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-09-26/subsets/blood_and_immune_upper_slim.owl" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/CL_0000000", @@ -521,6 +521,10 @@ "lbl" : "squamous epithelial cell", "type" : "CLASS", "meta" : { + "definition" : { + "val" : "Any epithelial cell that is part of some squamous epithelium.", + "xrefs" : [ "FBC:Autogenerated" ] + }, "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-1249" @@ -719,10 +723,15 @@ "val" : "BTO:0001433" }, { "val" : "ZFA:0009064" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000113" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nMononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. \nIn addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses.\nMononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer." } ] } }, { @@ -1078,22 +1087,16 @@ "meta" : { "definition" : { "val" : "A cell with more than one nucleus.", - "xrefs" : [ "FB:ma" ] + "xrefs" : [ "FB:ma", "Wikipedia:Multinucleate" ] }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "syncitium" - }, { - "pred" : "hasExactSynonym", - "val" : "syncytial cell" + "val" : "multinucleated cells", + "xrefs" : [ "Wikipedia:Multinucleate" ] }, { "pred" : "hasExactSynonym", - "val" : "syncytium" - } ], - "xrefs" : [ { - "val" : "AEO:0000203" - }, { - "val" : "WBbt:0008074" + "val" : "polynuclear cells", + "xrefs" : [ "Wikipedia:Multinucleate" ] } ] } }, { @@ -1255,7 +1258,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "Any cell that only exists in Eukaryota.", + "val" : "Any cell that in taxon some Eukaryota.", "xrefs" : [ "FBC:Autogenerated" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], @@ -1884,8 +1887,8 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A phagocytic cell formed by the fusion of macrophages, occurs in chronic inflammatory responses to persistent microorganism such as M.tuberculosis, component of granulomas. Sometimes used to refer to megakaryocytes.", - "xrefs" : [ "GOC:add", "GOC:tfm", "ISBN:0702022918", "ISBN:0702024783" ] + "val" : "A phagocytic syncytial cell formed by the fusion of macrophages, occurs in chronic inflammatory responses to persistent microorganism such as M.tuberculosis, component of granulomas. Sometimes used to refer to megakaryocytes.", + "xrefs" : [ "GOC:add", "GOC:tfm", "ISBN:0702022918", "ISBN:0702024783", "PMID:33348900", "Wikipedia:Giant_cell" ] }, "comments" : [ "Role or process: Chronic infection, granulomatous inflammation. Consider also megakaryocyte (CL:0000556) as sometimes multinucleated giant cell is used to refer to this." ], "subsets" : [ "http://purl.obolibrary.org/obo/cl#blood_and_immune_upper_slim" ], @@ -1909,6 +1912,11 @@ "pred" : "hasExactSynonym", "val" : "syncytial giant cell", "xrefs" : [ "ISBN:0702022918", "ISBN:0702024783" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", + "pred" : "hasRelatedSynonym", + "val" : "MGC", + "xrefs" : [ "PMID:33348900" ] } ], "xrefs" : [ { "val" : "BTO:0003107" @@ -3452,27 +3460,6 @@ "val" : "2010-12-07T09:37:22Z" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/CL_0002546", - "lbl" : "embryonic blood vessel endothelial progenitor cell", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An endothelial progenitor cell that participates in angiogenesis during development.", - "xrefs" : [ "GOC:tfm" ] - }, - "comments" : [ "See CL:0002619." ], - "xrefs" : [ { - "val" : "ZFA:0005773" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0003-1980-3228" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2011-02-28T04:20:39Z" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/CL_0002679", "lbl" : "natural helper lymphocyte", @@ -3588,7 +3575,14 @@ "val" : "A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells.", "xrefs" : [ "https://orcid.org/0000-0001-5208-3432", "https://orcid.org/0000-0002-9900-7880" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "xrefs" : [ { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0011012" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." + } ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0011026", @@ -3809,6 +3803,33 @@ "val" : "2022-11-04T14:40:00Z" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_4052002", + "lbl" : "syncytial cell", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A multinucleate cell formed by the fusion of multiple uninuclear cells through plasma membrane fusion. This process leads to a single large cell containing multiple nuclei within a shared cytoplasm.", + "xrefs" : [ "PMID:20851884", "Wikipedia:Syncytium" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "syncytium", + "xrefs" : [ "WBbt:0008074" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", + "pred" : "hasRelatedSynonym", + "val" : "SC", + "xrefs" : [ "PMID:9067520" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0009-0000-8480-9277" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-08-15T10:38:46Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0000278", "lbl" : "mitotic cell cycle", @@ -3868,6 +3889,24 @@ "val" : "cellular_component" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0000768", + "lbl" : "syncytium formation by plasma membrane fusion", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells.", + "xrefs" : [ "GOC:mtg_muscle", "GOC:tb" ] + }, + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "cell fusion" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0000785", "lbl" : "chromatin", @@ -3892,6 +3931,9 @@ "val" : "NIF_Subcellular:sao1615953555" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28301" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "GO:0000789" }, { @@ -4986,7 +5028,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/GO_0002538", - "lbl" : "arachidonic acid metabolite production involved in inflammatory response", + "lbl" : "arachidonate metabolite production involved in inflammatory response", "type" : "CLASS", "meta" : { "definition" : { @@ -5000,11 +5042,17 @@ }, { "pred" : "hasBroadSynonym", "val" : "production of arachidonic acid metabolites involved in acute inflammatory response" + }, { + "pred" : "hasExactSynonym", + "val" : "arachidonic acid metabolite production involved in inflammatory response" }, { "pred" : "hasExactSynonym", "val" : "production of arachidonic acid metabolites involved in inflammatory response" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28648" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -6856,6 +6904,21 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0006949", + "lbl" : "syncytium formation", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane. Syncytia are normally derived from single cells that fuse or fail to complete cell division.", + "xrefs" : [ "ISBN:0198506732" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0006950", "lbl" : "response to stress", @@ -6865,7 +6928,6 @@ "val" : "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).", "xrefs" : [ "GOC:mah" ] }, - "comments" : [ "Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC." ], "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_candida", "http://purl.obolibrary.org/obo/go#goslim_chembl", "http://purl.obolibrary.org/obo/go#goslim_drosophila", "http://purl.obolibrary.org/obo/go#goslim_metagenomics", "http://purl.obolibrary.org/obo/go#goslim_plant", "http://purl.obolibrary.org/obo/go#goslim_plant_ribbon" ], "synonyms" : [ { "pred" : "hasRelatedSynonym", @@ -6875,6 +6937,9 @@ "val" : "response to biotic stress" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/26810" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -6992,6 +7057,29 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0007009", + "lbl" : "plasma membrane organization", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the plasma membrane.", + "xrefs" : [ "GOC:dph", "GOC:jl", "GOC:mah" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "plasma membrane organisation" + }, { + "pred" : "hasRelatedSynonym", + "val" : "plasma membrane organization and biogenesis", + "xrefs" : [ "GOC:mah" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0007049", "lbl" : "cell cycle", @@ -7836,6 +7924,29 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0010256", + "lbl" : "endomembrane system organization", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endomembrane system.", + "xrefs" : [ "GOC:mah", "GOC:sm" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_drosophila" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "endomembrane organization" + }, { + "pred" : "hasExactSynonym", + "val" : "endomembrane system organisation", + "xrefs" : [ "GOC:mah" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0010324", "lbl" : "membrane invagination", @@ -8277,6 +8388,15 @@ "val" : "stem cell renewal" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_2" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_2157" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -9862,27 +9982,6 @@ "val" : "cellular_component" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0032993", - "lbl" : "protein-DNA complex", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A macromolecular complex containing both protein and DNA molecules.", - "xrefs" : [ "GOC:mah" ] - }, - "comments" : [ "Note that this term is intended to classify complexes that have DNA as one of the members of the complex, that is, the complex does not exist if DNA is not present. Protein complexes that interact with DNA e.g. transcription factor complexes should not be classified here." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "DNA-protein complex", - "xrefs" : [ "GOC:mah" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0033151", "lbl" : "V(D)J recombination", @@ -10732,6 +10831,7 @@ "val" : "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.", "xrefs" : [ "GOC:go_curators" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "membrane-enclosed organelle" @@ -10740,6 +10840,9 @@ "val" : "NIF_Subcellular:sao414196390" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28153" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -10753,7 +10856,7 @@ "val" : "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes.", "xrefs" : [ "GOC:go_curators" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_mouse" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_mouse" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "non-membrane-enclosed organelle" @@ -10767,6 +10870,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/21881" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28153" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -10781,8 +10887,11 @@ "val" : "Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.", "xrefs" : [ "GOC:go_curators" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_pir" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28153" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -10940,12 +11049,15 @@ "val" : "A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component.", "xrefs" : [ "GOC:jl", "GOC:mah" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_pir" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "cellular component biogenesis at cellular level" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/27194" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "GO:0071843" }, { @@ -11095,6 +11207,30 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0045026", + "lbl" : "plasma membrane fusion", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell.", + "xrefs" : [ "GOC:elh", "GOC:mtg_muscle" ] + }, + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "cell fusion" + }, { + "pred" : "hasBroadSynonym", + "val" : "cell-cell fusion" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0006947" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0045058", "lbl" : "T cell selection", @@ -11143,6 +11279,15 @@ "val" : "Wikipedia:Innate_immune_system" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_2" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_2157" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "GO:0002226" }, { @@ -13864,6 +14009,36 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0140253", + "lbl" : "cell-cell fusion", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A cellular process in which two or more cells combine together, their plasma membrane fusing, producing a single cell. In some cases, nuclei fuse, producing a polyploid cell, while in other cases, nuclei remain separate, producing a syncytium.", + "xrefs" : [ "Wikipedia:Cell_fusion" ] + }, + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "cell fusion" + }, { + "pred" : "hasExactSynonym", + "val" : "cell cell fusion" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/15939" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "pg" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-08-13T18:38:18Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0140352", "lbl" : "export from cell", @@ -18916,15 +19091,15 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/PR_000064867", - "lbl" : "protein-containing molecular entity", + "id" : "http://purl.obolibrary.org/obo/PR_000050567", + "lbl" : "protein-containing material entity", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A molecular entity that minimally consists of a protein.", + "val" : "A material entity that minimally consists of a protein.", "xrefs" : [ "PRO:DAN" ] }, - "comments" : [ "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565)." ], + "comments" : [ "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566)." ], "synonyms" : [ { "pred" : "hasNarrowSynonym", "val" : "protein", @@ -22055,7 +22230,7 @@ "val" : "The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO].", "xrefs" : [ "BIRNLEX:844", "ISBN:0-14-051288-8", "ISBN:3110148986", "NLM:nervous+system", "WB:rynl", "Wikipedia:Nervous_system", "ZFIN:curator" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#cumbo", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#cumbo", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "neurological system", @@ -22128,9 +22303,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -28047,7 +28219,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000050", - "lbl" : "part_of", + "lbl" : "part of", "type" : "PROPERTY", "propertyType" : "OBJECT", "meta" : { @@ -28070,9 +28242,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "part_of" @@ -28092,7 +28261,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000051", - "lbl" : "has_part", + "lbl" : "has part", "type" : "PROPERTY", "propertyType" : "OBJECT", "meta" : { @@ -28115,9 +28284,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_part" @@ -31982,6 +32148,10 @@ "id" : "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "type" : "PROPERTY", "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#gocheck_obsoletion_candidate", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/go#goslim_agr", "type" : "PROPERTY", @@ -32320,6 +32490,10 @@ "id" : "http://purl.org/dc/terms/date", "type" : "PROPERTY", "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/description", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/license", "type" : "PROPERTY", @@ -32345,12 +32519,10 @@ "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "lbl" : "created by", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "lbl" : "creation date", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { @@ -32443,7 +32615,6 @@ "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#id", - "lbl" : "id", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { @@ -32513,12 +32684,16 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000000", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_131567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000007", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0002321" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000034", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000034", "pred" : "is_a", @@ -32631,6 +32806,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000040", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000040", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -32736,7 +32915,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000066", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000066", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -32749,18 +32928,18 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000071", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0004638" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000071", - "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/CL_0002546" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000076", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000066" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000076", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0006914" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000080", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000080", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -32821,6 +33000,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000092", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000092", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -32871,6 +33054,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000094", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000094", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -32917,6 +33104,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000097", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0002274" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000097", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000097", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -32987,6 +33178,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000115", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000213" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000115", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000115", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -33033,6 +33228,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000187", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000183" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000187", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000187", "pred" : "is_a", @@ -33061,6 +33260,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000219", "pred" : "http://purl.obolibrary.org/obo/RO_0002215", "obj" : "http://purl.obolibrary.org/obo/GO_0048870" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000221", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000221", "pred" : "is_a", @@ -33069,6 +33272,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000221", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000924" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000222", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000222", "pred" : "is_a", @@ -33077,6 +33284,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000222", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000926" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000223", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000223", "pred" : "is_a", @@ -33093,6 +33304,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000225", "pred" : "http://purl.obolibrary.org/obo/RO_0000053", "obj" : "http://purl.obolibrary.org/obo/PATO_0001405" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000226", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000226", "pred" : "is_a", @@ -33101,6 +33316,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000226", "pred" : "http://purl.obolibrary.org/obo/RO_0000053", "obj" : "http://purl.obolibrary.org/obo/PATO_0001407" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000228", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000228", "pred" : "is_a", @@ -33239,7 +33458,7 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0000000" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000255", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000325", @@ -33291,7 +33510,7 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0010017" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000365", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000393", @@ -33309,6 +33528,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000451", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000145" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000451", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000451", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -33367,7 +33590,7 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000518", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000540", @@ -33419,6 +33642,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000547", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0002242" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000547", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000547", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -33493,6 +33720,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000549", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000549", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -33515,6 +33746,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000550", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000550", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -33661,6 +33896,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000557", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_1001610" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000557", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000557", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -33699,6 +33938,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000558", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000558", "pred" : "http://purl.obolibrary.org/obo/CL_4030046", @@ -33769,6 +34012,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000559", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000559", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -33795,6 +34042,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000566", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0011026" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000566", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000566", "pred" : "http://purl.obolibrary.org/obo/RO_0002104", @@ -33845,10 +34096,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000576", "pred" : "http://purl.obolibrary.org/obo/RO_0002215", "obj" : "http://purl.obolibrary.org/obo/GO_0043011" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000647", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000228" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000647", "pred" : "is_a", @@ -33859,6 +34106,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000647", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_4052002" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000647", "pred" : "http://purl.obolibrary.org/obo/RO_0000056", @@ -33875,6 +34126,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000680", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000055" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000680", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000680", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -33919,7 +34174,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0002405" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000738", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000738", @@ -33951,6 +34206,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000762", "pred" : "http://purl.obolibrary.org/obo/RO_0002215", "obj" : "http://purl.obolibrary.org/obo/GO_0007596" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000763", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000763", "pred" : "is_a", @@ -34207,6 +34466,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000786", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000786", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -34245,6 +34508,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000789", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000789", "pred" : "http://purl.obolibrary.org/obo/RO_0002104", @@ -34259,6 +34526,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000798", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000798", "pred" : "http://purl.obolibrary.org/obo/RO_0002104", @@ -34349,6 +34620,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000826", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000826", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -34423,6 +34698,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000831", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000831", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -34523,10 +34802,18 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000831", "pred" : "http://purl.obolibrary.org/obo/RO_0015016", "obj" : "http://purl.obolibrary.org/obo/PR_000007431" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000837", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000837", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0008001" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000837", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000837", "pred" : "http://purl.obolibrary.org/obo/CL_4030046", @@ -34651,6 +34938,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000889", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000889", "pred" : "http://purl.obolibrary.org/obo/RO_0000053", @@ -34806,7 +35097,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0001035", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0001035", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -34887,6 +35178,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0001200", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000945" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0001200", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0001200", "pred" : "http://purl.obolibrary.org/obo/CL_4030046", @@ -34945,6 +35240,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0002028", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0002191" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0002028", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002028", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -34981,6 +35280,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0002028", "pred" : "http://purl.obolibrary.org/obo/RO_0002215", "obj" : "http://purl.obolibrary.org/obo/GO_0060374" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0002031", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002031", "pred" : "is_a", @@ -34993,6 +35296,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0002031", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", "obj" : "http://purl.obolibrary.org/obo/CL_0002032" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0002032", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002032", "pred" : "is_a", @@ -35092,7 +35399,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002319", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002319", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -35100,7 +35407,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002320", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002320", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -35126,15 +35433,11 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002494", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002494", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0007100" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0002546", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000222" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002679", "pred" : "is_a", @@ -35145,6 +35448,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0002679", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002679", "pred" : "http://purl.obolibrary.org/obo/CL_4030046", @@ -35209,6 +35516,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0008019", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000219" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0008019", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0008019", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -35229,6 +35540,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0011012", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0002321" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0011026", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0011026", "pred" : "is_a", @@ -35329,6 +35644,14 @@ "sub" : "http://purl.obolibrary.org/obo/CL_4030029", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_2000001" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_4052002", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000228" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_4052002", + "pred" : "http://purl.obolibrary.org/obo/RO_0002353", + "obj" : "http://purl.obolibrary.org/obo/GO_0000768" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0000278", "pred" : "is_a", @@ -35353,10 +35676,18 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0000323", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0005773" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0000768", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0006949" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0000768", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0140253" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0000785", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0032993" + "obj" : "http://purl.obolibrary.org/obo/GO_0110165" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0000785", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -36189,8 +36520,8 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0043232" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0005840", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", - "obj" : "http://purl.obolibrary.org/obo/PR_000000001" + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0005840", "pred" : "http://purl.obolibrary.org/obo/RO_0002216", @@ -36387,6 +36718,18 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0006936", "pred" : "http://purl.obolibrary.org/obo/BFO_0000066", "obj" : "http://purl.obolibrary.org/obo/UBERON_0002385" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0006949", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0009987" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0006949", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0048646" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0006949", + "pred" : "http://purl.obolibrary.org/obo/RO_0002297", + "obj" : "http://purl.obolibrary.org/obo/CL_0000228" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0006950", "pred" : "is_a", @@ -36419,6 +36762,18 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0006996", "pred" : "http://purl.obolibrary.org/obo/RO_0002592", "obj" : "http://purl.obolibrary.org/obo/GO_0043226" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0007009", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0061024" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0007009", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/GO_0010256" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0007009", + "pred" : "http://purl.obolibrary.org/obo/RO_0002592", + "obj" : "http://purl.obolibrary.org/obo/GO_0005886" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0007049", "pred" : "is_a", @@ -36643,6 +36998,14 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0009987", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0008150" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0010256", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0016043" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0010256", + "pred" : "http://purl.obolibrary.org/obo/RO_0002592", + "obj" : "http://purl.obolibrary.org/obo/GO_0012505" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0010324", "pred" : "is_a", @@ -37273,12 +37636,8 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0005575" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0032991", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", - "obj" : "http://purl.obolibrary.org/obo/PR_000000001" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0032993", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0032991" + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0033151", "pred" : "is_a", @@ -37643,6 +38002,18 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0044419", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0008150" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0045026", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0007009" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0045026", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0061025" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0045026", + "pred" : "http://purl.obolibrary.org/obo/RO_0012008", + "obj" : "http://purl.obolibrary.org/obo/GO_0005886" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0045058", "pred" : "is_a", @@ -38499,6 +38870,10 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0098644", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0099080" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0098644", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0098644", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -38699,6 +39074,14 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0140112", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0044085" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0140253", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0009987" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0140253", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/GO_0045026" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0140352", "pred" : "is_a", @@ -39162,7 +39545,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/PR_000000001", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000064867" + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/PR_000000001", "pred" : "http://purl.obolibrary.org/obo/RO_0002353", @@ -39512,7 +39895,7 @@ "pred" : "http://purl.obolibrary.org/obo/RO_0002160", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { - "sub" : "http://purl.obolibrary.org/obo/PR_000064867", + "sub" : "http://purl.obolibrary.org/obo/PR_000050567", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { @@ -39635,7 +40018,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0001434" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000075", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000075", @@ -39737,7 +40120,7 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0007369" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000109", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000110", @@ -39757,7 +40140,7 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0001841" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000110", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000111", @@ -39773,7 +40156,7 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0048513" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000111", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", @@ -39781,12 +40164,16 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0004921" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", "obj" : "http://purl.obolibrary.org/obo/UBERON_0035804" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0000178", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000178", "pred" : "is_a", @@ -39839,7 +40226,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0002193" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000179", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000307", @@ -39859,7 +40246,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0011216" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000383", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000383", @@ -39967,6 +40354,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000481", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000479" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0000483", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000483", "pred" : "is_a", @@ -39981,7 +40372,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0005769" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000483", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208", "meta" : { "basicPropertyValues" : [ { @@ -40041,7 +40432,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0010316" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000923", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000924", @@ -40111,7 +40502,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0035804" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000930", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000948", @@ -40145,7 +40536,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0004151" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000948", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000948", @@ -40185,7 +40576,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000467" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001009", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001009", @@ -40217,7 +40608,7 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0000540" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001016", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001016", @@ -40264,7 +40655,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0001016" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001017", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001017", @@ -40342,7 +40733,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0004765" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001474", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001474", @@ -40364,7 +40755,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0001007" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001555", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001555", @@ -40396,6 +40787,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001630", "pred" : "http://purl.obolibrary.org/obo/RO_0002473", "obj" : "http://purl.obolibrary.org/obo/UBERON_0002385" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001969", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001969", "pred" : "is_a", @@ -40412,6 +40807,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001969", "pred" : "http://purl.obolibrary.org/obo/RO_0002221", "obj" : "http://purl.obolibrary.org/obo/CL_0000232" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", "pred" : "is_a", @@ -40489,7 +40888,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0012275" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001986", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001986", @@ -40569,7 +40968,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002193", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002204", @@ -40653,7 +41052,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0011137" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711", "meta" : { "basicPropertyValues" : [ { @@ -40705,7 +41104,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002329", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711", "meta" : { "basicPropertyValues" : [ { @@ -40750,7 +41149,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_89593" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", @@ -40841,7 +41240,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000479" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002384", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002385", @@ -40857,7 +41256,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0001015" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002385", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002385", @@ -40887,7 +41286,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002390", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002390", @@ -40925,7 +41324,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0001474" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002481", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002532", @@ -40987,7 +41386,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000926" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003068", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003068", @@ -41007,7 +41406,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0016879" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003075", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711", "meta" : { "basicPropertyValues" : [ { @@ -41104,7 +41503,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003081", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003081", @@ -41176,7 +41575,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003089", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742", "meta" : { "basicPropertyValues" : [ { @@ -41204,7 +41603,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000479" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003104", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003104", @@ -41386,6 +41785,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004291", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", "obj" : "http://purl.obolibrary.org/obo/UBERON_0004139" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004535", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004535", "pred" : "is_a", @@ -41402,6 +41805,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004535", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001981" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004537", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004537", "pred" : "is_a", @@ -41502,7 +41909,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004770", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004770", @@ -41542,7 +41949,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0003068" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004880", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004905", @@ -41574,7 +41981,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000060" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004923", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005061", @@ -41626,7 +42033,7 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0000187" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005090", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005157", @@ -41728,6 +42135,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0005764", "pred" : "http://purl.obolibrary.org/obo/RO_0002007", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", "pred" : "is_a", @@ -41748,7 +42159,7 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0005587" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", @@ -41842,7 +42253,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0005423" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006268", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006268", @@ -41872,7 +42283,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000307" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006595", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006595", @@ -41904,7 +42315,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000307" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006601", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006601", @@ -41920,7 +42331,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000307" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006603", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006603", @@ -41934,6 +42345,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0006914", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/CL_0000076" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0006965", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006965", "pred" : "is_a", @@ -42247,6 +42662,10 @@ "val" : "CARO" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0010210", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0010210", "pred" : "is_a", @@ -42429,7 +42848,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0011997", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0012275", @@ -42507,7 +42926,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000475" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0013701", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0013702", @@ -42557,7 +42976,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0015212", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0015228", @@ -43932,6 +44351,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0001981" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000076", + "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000066" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", + "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0006914" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000080", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ], @@ -44154,7 +44580,7 @@ "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000255", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002160", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002162", "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" } ] }, { @@ -44168,7 +44594,7 @@ "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000365", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0010017" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002160", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002162", "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" } ] }, { @@ -45086,9 +45512,6 @@ "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0002104", "fillerId" : "http://purl.obolibrary.org/obo/PR_000001002" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002162", - "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_40674" }, { "propertyId" : "http://purl.obolibrary.org/obo/RO_0002215", "fillerId" : "http://purl.obolibrary.org/obo/GO_0019724" @@ -45319,6 +45742,16 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0000178" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/CL_4052002", + "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000053", + "fillerId" : "http://purl.obolibrary.org/obo/PATO_0001908" + }, { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002353", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0000768" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0000278", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0007049" ], @@ -45333,6 +45766,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/GOREL_0002004", "fillerId" : "http://purl.obolibrary.org/obo/GO_0005634" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0000768", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0006949" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000051", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0045026" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0001677", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0022607" ], @@ -45662,6 +46102,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/GO_0097194" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0006949", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0048646" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002297", + "fillerId" : "http://purl.obolibrary.org/obo/CL_0000228" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0006996", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016043" ], @@ -45669,6 +46116,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002592", "fillerId" : "http://purl.obolibrary.org/obo/GO_0043226" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0007009", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016043" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002592", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0005886" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0007186", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0007165" ], @@ -45732,6 +46186,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002296", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0000479" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0010256", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016043" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002592", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0012505" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0012501", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0008219" ], @@ -46145,6 +46606,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002592", "fillerId" : "http://purl.obolibrary.org/obo/GO_0032991" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045026", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009987" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0012008", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0005886" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045321", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0001775" ], diff --git a/subsets/blood_and_immune_upper_slim.obo b/subsets/blood_and_immune_upper_slim.obo index 0cc054eb5..e723d3ceb 100644 --- a/subsets/blood_and_immune_upper_slim.obo +++ b/subsets/blood_and_immune_upper_slim.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: cl/releases/2024-08-16/subsets/blood_and_immune_upper_slim.owl +data-version: cl/releases/2024-09-26/subsets/blood_and_immune_upper_slim.owl subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" subsetdef: attribute_slim "" @@ -19,6 +19,7 @@ subsetdef: eye_upper_slim "a subset of general classes related to specific cell subsetdef: functional_classification "" subsetdef: general_cell_types_upper_slim "a subset of general classes of cell types in the cell ontology." subsetdef: gocheck_do_not_annotate "" +subsetdef: gocheck_obsoletion_candidate "" subsetdef: goslim_agr "" subsetdef: goslim_candida "" subsetdef: goslim_chembl "" @@ -95,7 +96,7 @@ idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# idspace: sssom https://w3id.org/sssom/ idspace: terms http://purl.org/dc/terms/ ontology: cl/subsets/blood_and_immune_upper_slim -property_value: owl:versionInfo "2024-08-16" xsd:string +property_value: owl:versionInfo "2024-09-26" xsd:string [Term] id: CL:0000000 @@ -118,7 +119,7 @@ is_a: UBERON:0000061 ! anatomical structure disjoint_from: GO:0031012 ! extracellular matrix disjoint_from: GO:0032991 ! protein-containing complex disjoint_from: GO:0043226 ! organelle -relationship: RO:0002160 NCBITaxon:131567 ! only in taxon cellular organisms +relationship: RO:0002162 NCBITaxon:131567 ! in taxon cellular organisms [Term] id: CL:0000007 @@ -139,6 +140,7 @@ synonym: "animal stem cell" EXACT [] xref: CALOHA:TS-2086 xref: FMA:63368 xref: ZFA:0005957 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0011115 ! precursor cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0017145 ! stem cell division @@ -230,6 +232,7 @@ xref: FMA:83553 xref: ZFA:0009017 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0002194 {is_inferred="true"} ! monopoietic cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002194 ! monopoietic cell intersection_of: capable_of GO:0030224 ! monocyte differentiation intersection_of: has_part CL:0017503 ! basophilic cytoplasm @@ -398,7 +401,7 @@ xref: FBbt:00000124 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ xref: FMA:66768 xref: WBbt:0003672 xref: ZFA:0009034 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell disjoint_from: CL:0000738 ! leukocyte relationship: part_of UBERON:0000483 ! epithelium property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI @@ -415,23 +418,26 @@ is_a: CL:0002139 ! endothelial cell of vascular tree intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0001981 ! blood vessel relationship: part_of UBERON:0004638 ! blood vessel endothelium -relationship: RO:0002202 CL:0002546 ! develops from embryonic blood vessel endothelial progenitor cell property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000076 name: squamous epithelial cell +def: "Any epithelial cell that is part of some squamous epithelium." [FBC:Autogenerated] subset: cellxgene_subset xref: CALOHA:TS-1249 xref: ZFA:0009039 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell +intersection_of: CL:0000066 ! epithelial cell +intersection_of: part_of UBERON:0006914 ! squamous epithelium +relationship: part_of UBERON:0006914 ! squamous epithelium [Term] id: CL:0000080 name: circulating cell def: "A cell which moves among different tissues of the body, via blood, lymph, or other medium." [GOC:add] xref: ZFA:0009043 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0000179 ! haemolymphatic fluid relationship: part_of UBERON:0000179 ! haemolymphatic fluid @@ -491,6 +497,7 @@ xref: ZFA:0009047 {sssom:mapping_justification="https://w3id.org/semapv/vocab/Un is_a: CL:0000518 ! phagocyte (sensu Vertebrata) is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte is_a: CL:0001035 {is_inferred="true"} ! bone cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: capable_of GO:0045453 ! bone resorption intersection_of: has_part PR:000001850 ! cathepsin K @@ -527,6 +534,7 @@ xref: FMA:62854 xref: ZFA:0009048 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000081 ! blood cell is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: capable_of GO:0008015 ! blood circulation intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -564,6 +572,7 @@ xref: CALOHA:TS-0603 xref: FMA:66784 is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte is_a: CL:0002274 ! histamine secreting cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: capable_of GO:0002349 ! histamine production involved in inflammatory response intersection_of: capable_of GO:0002539 ! prostaglandin production involved in inflammatory response @@ -599,12 +608,14 @@ def: "A vertebrate phagocyte with a single nucleus." [GOC:add, GOC:tfm, ISBN:078 subset: cellxgene_subset subset: human_reference_atlas xref: BTO:0001433 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000113 xref: ZFA:0009064 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000518 {is_inferred="true"} ! phagocyte (sensu Vertebrata) is_a: CL:0000842 ! mononuclear cell intersection_of: CL:0000518 ! phagocyte (sensu Vertebrata) intersection_of: bearer_of PATO:0001407 ! mononucleate property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nMononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. \nIn addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses.\nMononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer." xsd:string {xref="DOI:10.1016/j.coi.2005.11.008", xref="DOI:10.1038/nri3087", xref="DOI:10.3389/fimmu.2019.01893"} [Term] id: CL:0000115 @@ -619,6 +630,7 @@ xref: CALOHA:TS-0278 xref: FMA:66772 xref: ZFA:0009065 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000213 ! lining cell +is_a: CL:0000255 ! eukaryotic cell relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell property_value: RO:0002175 NCBITaxon:9606 @@ -704,6 +716,7 @@ xref: FMA:67328 xref: WBbt:0003675 xref: ZFA:0009114 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000183 ! contractile cell +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000393 ! electrically responsive cell relationship: RO:0002202 CL:0000056 ! develops from myoblast property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI @@ -747,6 +760,7 @@ def: "A cell of the outer of the three germ layers of the embryo." [MESH:D004475 synonym: "ectoderm cell" EXACT [] xref: FMA:72549 xref: ZFA:0009137 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000924 ! ectoderm @@ -759,6 +773,7 @@ synonym: "mesoblast" EXACT [] synonym: "mesoderm cell" EXACT [] xref: FMA:72554 xref: ZFA:0009138 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000926 ! mesoderm @@ -769,6 +784,7 @@ def: "A cell of the inner of the three germ layers of the embryo." [MESH:D004707 synonym: "endoderm cell" EXACT [] xref: FMA:72555 xref: ZFA:0009139 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000925 ! endoderm @@ -788,6 +804,7 @@ relationship: bearer_of PATO:0001405 ! anucleate id: CL:0000226 name: single nucleate cell def: "A cell with a single nucleus." [FB:ma, GOC:tfm] +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002242 ! nucleate cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0001407 ! mononucleate @@ -796,12 +813,10 @@ relationship: bearer_of PATO:0001407 ! mononucleate [Term] id: CL:0000228 name: multinucleate cell -def: "A cell with more than one nucleus." [FB:ma] -synonym: "syncitium" EXACT [] -synonym: "syncytial cell" EXACT [] -synonym: "syncytium" EXACT [] -xref: AEO:0000203 -xref: WBbt:0008074 +def: "A cell with more than one nucleus." [FB:ma, Wikipedia:Multinucleate] +synonym: "multinucleated cells" EXACT [Wikipedia:Multinucleate] +synonym: "polynuclear cells" EXACT [Wikipedia:Multinucleate] +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002242 ! nucleate cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0001908 ! multinucleate @@ -926,13 +941,13 @@ property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000255 name: eukaryotic cell -def: "Any cell that only exists in Eukaryota." [FBC:Autogenerated] +def: "Any cell that in taxon some Eukaryota." [FBC:Autogenerated] subset: cellxgene_subset xref: MESH:D005057 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell -intersection_of: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota -relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +intersection_of: RO:0002162 NCBITaxon:2759 ! in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 ! in taxon Eukaryota [Term] id: CL:0000325 @@ -987,8 +1002,8 @@ is_a: CL:0000007 ! early embryonic cell (metazoa) is_a: CL:0000255 ! eukaryotic cell is_a: CL:0010017 ! zygote intersection_of: CL:0010017 ! zygote -intersection_of: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa -relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +intersection_of: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa [Term] id: CL:0000393 @@ -1020,6 +1035,7 @@ xref: MESH:D003713 xref: ZFA:0009209 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000113 ! mononuclear phagocyte is_a: CL:0000145 ! professional antigen presenting cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000738 ! leukocyte intersection_of: bearer_of PATO:0001407 ! mononucleate intersection_of: capable_of GO:0001816 ! cytokine production @@ -1073,7 +1089,7 @@ name: phagocyte (sensu Vertebrata) def: "A phagocyte in vertebrates that is able to phagocytosis." [GOC:tfm] is_a: CL:0000234 ! phagocyte is_a: CL:0000255 ! eukaryotic cell -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata [Term] id: CL:0000540 @@ -1135,6 +1151,7 @@ synonym: "rubriblast" EXACT [ISBN:0721601464] xref: FMA:83518 is_a: CL:0000764 {is_inferred="true"} ! erythroid lineage cell is_a: CL:0002242 ! nucleate cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000764 ! erythroid lineage cell intersection_of: bearer_of PATO:0002505 ! nucleated intersection_of: bearer_of PATO:0040072 ! high nuclear/cytoplasmic ratio @@ -1180,6 +1197,7 @@ synonym: "prorubricyte" EXACT [ISBN:0721601464] xref: FMA:83505 xref: ZFA:0005236 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000765 {is_inferred="true"} ! erythroblast +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017503 ! basophilic cytoplasm intersection_of: has_part GO:0000792 ! heterochromatin @@ -1201,6 +1219,7 @@ synonym: "rubricyte" EXACT [ISBN:0721601464] xref: FMA:83506 xref: ZFA:0005241 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000765 {is_inferred="true"} ! erythroblast +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017504 ! polychromatophilic cytoplasm intersection_of: has_part GO:0000792 ! heterochromatin @@ -1322,6 +1341,7 @@ is_a: CL:0000763 ! myeloid cell is_a: CL:0001012 ! CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor is_a: CL:0011026 ! progenitor cell is_a: CL:1001610 ! bone marrow hematopoietic cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002032 ! hematopoietic oligopotent progenitor cell intersection_of: capable_of GO:0030225 ! macrophage differentiation intersection_of: capable_of GO:0030851 ! granulocyte differentiation @@ -1351,6 +1371,7 @@ xref: CALOHA:TS-0864 xref: MESH:D012156 xref: ZFA:0009252 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000764 {is_inferred="true"} ! erythroid lineage cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000764 ! erythroid lineage cell intersection_of: capable_of GO:0071971 ! extracellular exosome assembly intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -1392,6 +1413,7 @@ xref: FMA:83551 xref: ZFA:0009253 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0002194 {is_inferred="true"} ! monopoietic cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002194 ! monopoietic cell intersection_of: capable_of GO:0030224 ! monocyte differentiation intersection_of: has_part GO:0042582 ! azurophil granule @@ -1411,6 +1433,7 @@ synonym: "chondroplast" EXACT [] xref: ZFA:0009258 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000134 {is_inferred="true"} ! mesenchymal stem cell is_a: CL:0011026 ! progenitor cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: RO:0002104 PR:000001444 ! has plasma membrane part cadherin-5 intersection_of: RO:0002104 PR:000002112 ! has plasma membrane part vascular endothelial growth factor receptor 2 @@ -1450,19 +1473,20 @@ property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000647 name: multinucleated giant cell -def: "A phagocytic cell formed by the fusion of macrophages, occurs in chronic inflammatory responses to persistent microorganism such as M.tuberculosis, component of granulomas. Sometimes used to refer to megakaryocytes." [GOC:add, GOC:tfm, ISBN:0702022918, ISBN:0702024783] +def: "A phagocytic syncytial cell formed by the fusion of macrophages, occurs in chronic inflammatory responses to persistent microorganism such as M.tuberculosis, component of granulomas. Sometimes used to refer to megakaryocytes." [GOC:add, GOC:tfm, ISBN:0702022918, ISBN:0702024783, PMID:33348900, Wikipedia:Giant_cell] comment: Role or process: Chronic infection, granulomatous inflammation. Consider also megakaryocyte (CL:0000556) as sometimes multinucleated giant cell is used to refer to this. subset: blood_and_immune_upper_slim synonym: "foreign body giant cell" EXACT [ISBN:0702022918, ISBN:0702024783] synonym: "Langerhans giant cell" EXACT [ISBN:0702022918, ISBN:0702024783] synonym: "macrophage polykaryon" EXACT [ISBN:0702022918, ISBN:0702024783] +synonym: "MGC" RELATED OMO:0003000 [PMID:33348900] synonym: "multinucleate giant cell" EXACT [ISBN:0702022918, ISBN:0702024783] synonym: "syncytial giant cell" EXACT [ISBN:0702022918, ISBN:0702024783] xref: BTO:0003107 xref: FMA:83035 xref: MESH:D015726 -is_a: CL:0000228 ! multinucleate cell is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte +is_a: CL:4052002 ! syncytial cell intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: bearer_of PATO:0001908 ! multinucleate intersection_of: participates_in GO:0002432 ! granuloma formation @@ -1478,6 +1502,7 @@ def: "A non-terminally differentiated cell that is capable of developing into a subset: cellxgene_subset xref: ZFA:0009291 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0011115 ! precursor cell intersection_of: RO:0002203 CL:0000187 ! develops into muscle cell relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell @@ -1519,7 +1544,7 @@ intersection_of: bearer_of PATO:0002505 ! nucleated intersection_of: capable_of GO:0001667 ! ameboidal-type cell migration relationship: capable_of GO:0001667 ! ameboidal-type cell migration relationship: part_of UBERON:0002405 ! immune system -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002202 CL:0000037 ! develops from hematopoietic stem cell property_value: RO:0002175 NCBITaxon:9606 @@ -1547,6 +1572,7 @@ xref: BTO:0001441 xref: CALOHA:TS-0647 xref: MESH:D022423 xref: ZFA:0009324 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000988 {is_inferred="true"} ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: RO:0002202 CL:0000049 ! develops from common myeloid progenitor @@ -1800,6 +1826,7 @@ xref: FMA:70574 xref: MESH:D010950 xref: ZFA:0009332 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000946 {is_inferred="true"} ! antibody secreting cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000946 ! antibody secreting cell intersection_of: CL:4030046 GO:0019814 ! lacks_plasma_membrane_part immunoglobulin complex intersection_of: CL:4030046 GO:0042613 ! lacks_plasma_membrane_part MHC class II protein complex @@ -1827,6 +1854,7 @@ synonym: "alpha-beta T-cell" EXACT [] synonym: "alpha-beta T-lymphocyte" EXACT [] xref: ZFA:0009335 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000084 {is_inferred="true"} ! T cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000084 ! T cell intersection_of: RO:0002104 GO:0042105 ! has plasma membrane part alpha-beta T cell receptor complex disjoint_from: CL:0000798 ! gamma-delta T cell @@ -1847,6 +1875,7 @@ synonym: "gammadelta T cell" EXACT [] synonym: "gd T cell" RELATED OMO:0003000 [] xref: ZFA:0009336 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000084 {is_inferred="true"} ! T cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000084 ! T cell intersection_of: RO:0002104 GO:0042106 ! has plasma membrane part gamma-delta T cell receptor complex relationship: RO:0002104 GO:0042106 ! has plasma membrane part gamma-delta T cell receptor complex @@ -1946,6 +1975,7 @@ synonym: "progenitor B-lymphocyte" EXACT [] xref: BTO:0003104 xref: ZFA:0009349 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000838 {is_inferred="true"} ! lymphoid lineage restricted progenitor cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: has_part PR:000001903 ! paired box protein PAX-5 intersection_of: has_part PR:000006611 ! DNA nucleotidylexotransferase @@ -1999,6 +2029,7 @@ synonym: "colony forming unit mast cell" RELATED [] synonym: "MCP" EXACT [] is_a: CL:0000763 ! myeloid cell is_a: CL:0000839 {is_inferred="true"} ! myeloid lineage restricted progenitor cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: capable_of GO:0060374 ! mast cell differentiation intersection_of: CL:4030045 PR:000005307 ! lacks_part CCAAT/enhancer-binding protein alpha @@ -2063,7 +2094,9 @@ synonym: "MPP" EXACT [] xref: BTO:0000725 xref: CALOHA:TS-0448 xref: ZFA:0009354 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001402 ! multipotent intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -2160,6 +2193,7 @@ def: "An immature myeloid leukocyte of heterogeneous phenotype found particularl comment: Markers: Mouse: CD11b+GR1+CD31+; Human: CD34+ CD33+CD15-CD13+. (According to some reports in humans these cells are iNOS+ARG1+IL13+IFNg+); location: In cancerous tissue; in the blood and lymphoid organs in sepsis. subset: blood_and_immune_upper_slim is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: bearer_of PATO:0001501 ! immature intersection_of: capable_of GO:0050777 ! negative regulation of immune response @@ -2300,7 +2334,7 @@ name: bone cell def: "A connective tissue cell found in bone." [GO_REF:0000034, GOC:add] subset: general_cell_types_upper_slim subset: human_reference_atlas -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001474 ! bone element relationship: part_of UBERON:0001474 ! bone element @@ -2369,6 +2403,7 @@ name: lymphocyte of B lineage, CD19-positive def: "A lymphocyte of B lineage that is CD19-positive." [GOC:add] comment: Types of B lineage lymphocytes include B cells and antibody secreting cells (plasmablasts and plasma cells). Lymphocytes of B cell lineage can be distinguished from those of T cell lineage by their lack of CD3e (as part of the T cell receptor complex). is_a: CL:0000945 ! lymphocyte of B lineage +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000945 ! lymphocyte of B lineage intersection_of: CL:4030046 PR:000001020 ! lacks_plasma_membrane_part CD3 epsilon intersection_of: RO:0002104 PR:000001002 ! has plasma membrane part CD19 molecule @@ -2392,7 +2427,6 @@ is_a: CL:0001200 ! lymphocyte of B lineage, CD19-positive intersection_of: CL:0001200 ! lymphocyte of B lineage, CD19-positive intersection_of: capable_of GO:0019724 ! B cell mediated immunity intersection_of: RO:0002104 PR:000001002 ! has plasma membrane part CD19 molecule -intersection_of: RO:0002162 NCBITaxon:40674 ! in taxon Mammalia property_value: terms:contributor https://orcid.org/0000-0001-9990-8331 [Term] @@ -2422,6 +2456,7 @@ subset: cellxgene_subset synonym: "BMCP" EXACT [] is_a: CL:0000763 ! myeloid cell is_a: CL:0002191 ! granulocytopoietic cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000839 ! myeloid lineage restricted progenitor cell intersection_of: capable_of GO:0030221 ! basophil differentiation intersection_of: capable_of GO:0060374 ! mast cell differentiation @@ -2448,6 +2483,7 @@ id: CL:0002031 name: hematopoietic lineage restricted progenitor cell def: "A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells." [GOC:tfm, PMID:19022770] subset: blood_and_immune_upper_slim +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001400 ! unipotent @@ -2463,6 +2499,7 @@ name: hematopoietic oligopotent progenitor cell def: "A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities." [GOC:tfm, https://orcid.org/0000-0001-5208-3432, PMID:19022770] comment: This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). subset: blood_and_immune_upper_slim +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001401 ! oligopotent @@ -2584,7 +2621,7 @@ def: "A cell that is part of the nervous system." [GOC:tfm, ISBN:0618947256] subset: cellxgene_subset xref: CALOHA:TS-2040 xref: FMA:70333 -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001016 ! nervous system relationship: part_of UBERON:0001016 ! nervous system @@ -2600,7 +2637,7 @@ xref: CALOHA:TS-2096 xref: FMA:63875 xref: MESH:D003239 xref: ZFA:0009392 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0002384 ! connective tissue relationship: part_of UBERON:0002384 ! connective tissue @@ -2645,29 +2682,20 @@ xref: BTO:0001539 xref: CALOHA:TS-0115 xref: FMA:83808 xref: FMA:84791 -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0007100 ! primary circulatory organ relationship: part_of UBERON:0007100 ! primary circulatory organ property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-07T09:37:22Z -[Term] -id: CL:0002546 -name: embryonic blood vessel endothelial progenitor cell -def: "An endothelial progenitor cell that participates in angiogenesis during development." [GOC:tfm] -comment: See CL:0002619. -xref: ZFA:0005773 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000222 ! mesodermal cell -property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 -creation_date: 2011-02-28T04:20:39Z - [Term] id: CL:0002679 name: natural helper lymphocyte def: "A lymphocyte found in adipose tissue that lacks lineage markers of other lymphocytes but is capable of mediating TH2 cytokine responses. This cell type is found in fat associated lymphoid clusters, proliferates in response to IL2 and produce large amounts of TH2 cytokines such as IL5, IL6 and IL13" [GOC:tfm, PMID:20023630] subset: blood_and_immune_upper_slim is_a: CL:0000542 {is_inferred="true"} ! lymphocyte +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000542 ! lymphocyte intersection_of: CL:4030046 GO:0042105 ! lacks_plasma_membrane_part alpha-beta T cell receptor complex intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -2728,6 +2756,7 @@ subset: cellxgene_subset subset: human_reference_atlas synonym: "mesenchyme cell" EXACT [] is_a: CL:0000219 ! motile cell +is_a: CL:0000255 ! eukaryotic cell relationship: capable_of GO:0016477 ! cell migration relationship: part_of UBERON:0003104 ! mesenchyme property_value: RO:0002175 NCBITaxon:9606 @@ -2745,14 +2774,17 @@ id: CL:0011012 name: neural crest cell def: "A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells." [https://orcid.org/0000-0001-5208-3432, https://orcid.org/0000-0002-9900-7880] subset: cellxgene_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_0011012 is_a: CL:0000048 ! multi fate stem cell is_a: CL:0002321 ! embryonic cell (metazoa) +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." xsd:string {xref="DOI:10.1002/dvg.23276", xref="DOI:10.1242/dev.193193", xref="DOI:10.3389/fcell.2020.00635/full", xref="https://doi.org/10.1016/j.ydbio.2011.12.042"} [Term] id: CL:0011026 name: progenitor cell def: "A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses." [https://doi.org/10.1016/B978-0-12-409503-8.00002-0, ISBN:978-1-62808-994-3] subset: cellxgene_subset +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0011115 ! precursor cell intersection_of: CL:0011115 ! precursor cell intersection_of: RO:0002202 CL:0000034 ! develops from stem cell @@ -2885,6 +2917,20 @@ intersection_of: CL:0000542 ! lymphocyte intersection_of: part_of UBERON:0000178 ! blood property_value: terms:date "2022-11-04T14:40:00Z" xsd:dateTime +[Term] +id: CL:4052002 +name: syncytial cell +def: "A multinucleate cell formed by the fusion of multiple uninuclear cells through plasma membrane fusion. This process leads to a single large cell containing multiple nuclei within a shared cytoplasm." [PMID:20851884, Wikipedia:Syncytium] +synonym: "SC" RELATED OMO:0003000 [PMID:9067520] +synonym: "syncytium" EXACT [WBbt:0008074] +is_a: CL:0000228 ! multinucleate cell +intersection_of: CL:0000000 ! cell +intersection_of: bearer_of PATO:0001908 ! multinucleate +intersection_of: output_of GO:0000768 ! syncytium formation by plasma membrane fusion +relationship: output_of GO:0000768 ! syncytium formation by plasma membrane fusion +property_value: terms:contributor https://orcid.org/0009-0000-8480-9277 +property_value: terms:date "2024-08-15T10:38:46Z" xsd:dateTime + [Term] id: GO:0000278 name: mitotic cell cycle @@ -2924,6 +2970,17 @@ namespace: cellular_component def: "A vacuole that is maintained at an acidic pH and which contains degradative enzymes, including a wide variety of acid hydrolases." [GOC:krc] is_a: GO:0005773 ! vacuole +[Term] +id: GO:0000768 +name: syncytium formation by plasma membrane fusion +namespace: biological_process +def: "The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells." [GOC:mtg_muscle, GOC:tb] +synonym: "cell fusion" BROAD [] +is_a: GO:0006949 ! syncytium formation +is_a: GO:0140253 ! cell-cell fusion +intersection_of: GO:0006949 ! syncytium formation +intersection_of: has_part GO:0045026 ! plasma membrane fusion + [Term] id: GO:0000785 name: chromatin @@ -2937,8 +2994,9 @@ synonym: "chromosome scaffold" RELATED [] synonym: "cytoplasmic chromatin" NARROW [] synonym: "nuclear chromatin" NARROW [] xref: NIF_Subcellular:sao1615953555 -is_a: GO:0032993 ! protein-DNA complex +is_a: GO:0110165 ! cellular anatomical entity relationship: part_of GO:0005694 ! chromosome +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28301" xsd:anyURI [Term] id: GO:0000791 @@ -3516,13 +3574,15 @@ relationship: part_of GO:0006954 ! inflammatory response [Term] id: GO:0002538 -name: arachidonic acid metabolite production involved in inflammatory response +name: arachidonate metabolite production involved in inflammatory response namespace: biological_process def: "The synthesis or release of products of arachidonic acid metabolism following a stimulus as part of an inflammatory response, resulting in an increase in their intracellular or extracellular levels." [GOC:add, ISBN:0781735149] synonym: "arachidonic acid metabolite production involved in acute inflammatory response" BROAD [GOC:mah] +synonym: "arachidonic acid metabolite production involved in inflammatory response" EXACT [] synonym: "production of arachidonic acid metabolites involved in acute inflammatory response" BROAD [] synonym: "production of arachidonic acid metabolites involved in inflammatory response" EXACT [] is_a: GO:0002532 ! production of molecular mediator involved in inflammatory response +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28648" xsd:anyURI [Term] id: GO:0002539 @@ -3530,7 +3590,7 @@ name: prostaglandin production involved in inflammatory response namespace: biological_process def: "The synthesis or release of any prostaglandin following a stimulus as part of an inflammatory response, resulting in an increase in its intracellular or extracellular levels." [GOC:add, ISBN:0781735149] synonym: "prostaglandin production involved in acute inflammatory response" BROAD [] -is_a: GO:0002538 ! arachidonic acid metabolite production involved in inflammatory response +is_a: GO:0002538 ! arachidonate metabolite production involved in inflammatory response [Term] id: GO:0002544 @@ -4245,8 +4305,8 @@ synonym: "ribosomal RNA" RELATED [] xref: NIF_Subcellular:sao1429207766 xref: Wikipedia:Ribosome is_a: GO:0043232 ! intracellular non-membrane-bounded organelle +is_a: PR:000050567 ! protein-containing material entity relationship: capable_of_part_of GO:0006412 ! translation -relationship: has_part PR:000000001 ! protein [Term] id: GO:0005886 @@ -4589,12 +4649,23 @@ xref: Wikipedia:Muscle_contraction is_a: GO:0003012 ! muscle system process relationship: occurs_in UBERON:0002385 ! muscle tissue +[Term] +id: GO:0006949 +name: syncytium formation +namespace: biological_process +def: "The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane. Syncytia are normally derived from single cells that fuse or fail to complete cell division." [ISBN:0198506732] +subset: goslim_pir +is_a: GO:0009987 ! cellular process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +intersection_of: GO:0048646 ! anatomical structure formation involved in morphogenesis +intersection_of: results_in_formation_of CL:0000228 ! multinucleate cell +relationship: results_in_formation_of CL:0000228 ! multinucleate cell + [Term] id: GO:0006950 name: response to stress namespace: biological_process def: "Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation)." [GOC:mah] -comment: Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. subset: goslim_candida subset: goslim_chembl subset: goslim_drosophila @@ -4604,6 +4675,7 @@ subset: goslim_plant_ribbon synonym: "response to abiotic stress" RELATED [] synonym: "response to biotic stress" RELATED [] is_a: GO:0050896 ! response to stimulus +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/26810" xsd:anyURI [Term] id: GO:0006952 @@ -4661,6 +4733,20 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i created_by: jl creation_date: 2013-12-19T15:25:51Z +[Term] +id: GO:0007009 +name: plasma membrane organization +namespace: biological_process +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the plasma membrane." [GOC:dph, GOC:jl, GOC:mah] +subset: goslim_chembl +synonym: "plasma membrane organisation" EXACT [] +synonym: "plasma membrane organization and biogenesis" RELATED [GOC:mah] +is_a: GO:0061024 ! membrane organization +intersection_of: GO:0016043 ! cellular component organization +intersection_of: results_in_organization_of GO:0005886 ! plasma membrane +relationship: part_of GO:0010256 ! endomembrane system organization +relationship: results_in_organization_of GO:0005886 ! plasma membrane + [Term] id: GO:0007049 name: cell cycle @@ -5113,6 +5199,19 @@ is_a: GO:0008150 ! biological_process created_by: jl creation_date: 2012-12-11T16:56:55Z +[Term] +id: GO:0010256 +name: endomembrane system organization +namespace: biological_process +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endomembrane system." [GOC:mah, GOC:sm] +subset: goslim_drosophila +synonym: "endomembrane organization" EXACT [] +synonym: "endomembrane system organisation" EXACT [GOC:mah] +is_a: GO:0016043 ! cellular component organization +intersection_of: GO:0016043 ! cellular component organization +intersection_of: results_in_organization_of GO:0012505 ! endomembrane system +relationship: results_in_organization_of GO:0012505 ! endomembrane system + [Term] id: GO:0010324 name: membrane invagination @@ -5358,6 +5457,9 @@ is_a: GO:0051301 ! cell division intersection_of: GO:0051301 ! cell division intersection_of: has_primary_input CL:0000034 ! stem cell relationship: has_primary_input CL:0000034 ! stem cell +property_value: RO:0002161 NCBITaxon:2 +property_value: RO:0002161 NCBITaxon:2157 +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0019226 @@ -6215,18 +6317,8 @@ synonym: "protein complex" NARROW [] synonym: "protein containing complex" EXACT [] synonym: "protein-protein complex" NARROW [] is_a: GO:0005575 ! cellular_component +is_a: PR:000050567 ! protein-containing material entity disjoint_from: GO:0110165 ! cellular anatomical entity -relationship: has_part PR:000000001 ! protein - -[Term] -id: GO:0032993 -name: protein-DNA complex -namespace: cellular_component -def: "A macromolecular complex containing both protein and DNA molecules." [GOC:mah] -comment: Note that this term is intended to classify complexes that have DNA as one of the members of the complex, that is, the complex does not exist if DNA is not present. Protein complexes that interact with DNA e.g. transcription factor complexes should not be classified here. -subset: goslim_pir -synonym: "DNA-protein complex" EXACT [GOC:mah] -is_a: GO:0032991 ! protein-containing complex [Term] id: GO:0033151 @@ -6678,6 +6770,7 @@ id: GO:0043227 name: membrane-bounded organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane." [GOC:go_curators] +subset: gocheck_do_not_annotate synonym: "membrane-enclosed organelle" EXACT [] xref: NIF_Subcellular:sao414196390 is_a: GO:0043226 ! organelle @@ -6685,30 +6778,35 @@ intersection_of: GO:0043226 ! organelle intersection_of: has_part GO:0016020 ! membrane disjoint_from: GO:0043228 ! non-membrane-bounded organelle relationship: has_part GO:0016020 ! membrane +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI [Term] id: GO:0043228 name: non-membrane-bounded organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:go_curators] +subset: gocheck_do_not_annotate subset: goslim_mouse synonym: "biological condensate" RELATED [] synonym: "non-membrane-enclosed organelle" EXACT [] xref: NIF_Subcellular:sao1456184038 is_a: GO:0043226 ! organelle property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21881" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI [Term] id: GO:0043229 name: intracellular organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:go_curators] +subset: gocheck_do_not_annotate subset: goslim_pir is_a: GO:0043226 ! organelle intersection_of: GO:0043226 ! organelle intersection_of: part_of GO:0005622 ! intracellular anatomical structure disjoint_from: GO:0043230 ! extracellular organelle relationship: part_of GO:0005622 ! intracellular anatomical structure +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI [Term] id: GO:0043230 @@ -6798,9 +6896,11 @@ name: cellular component biogenesis namespace: biological_process alt_id: GO:0071843 def: "A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component." [GOC:jl, GOC:mah] +subset: gocheck_do_not_annotate subset: goslim_pir synonym: "cellular component biogenesis at cellular level" EXACT [] is_a: GO:0071840 ! cellular component organization or biogenesis +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27194" xsd:anyURI [Term] id: GO:0044207 @@ -6872,6 +6972,20 @@ is_a: GO:0008150 ! biological_process property_value: RO:0002161 NCBITaxon:4895 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20191" xsd:anyURI +[Term] +id: GO:0045026 +name: plasma membrane fusion +namespace: biological_process +alt_id: GO:0006947 +def: "The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell." [GOC:elh, GOC:mtg_muscle] +synonym: "cell fusion" BROAD [] +synonym: "cell-cell fusion" BROAD [] +is_a: GO:0007009 ! plasma membrane organization +is_a: GO:0061025 ! membrane fusion +intersection_of: GO:0009987 ! cellular process +intersection_of: results_in_fusion_of GO:0005886 ! plasma membrane +relationship: results_in_fusion_of GO:0005886 ! plasma membrane + [Term] id: GO:0045058 name: T cell selection @@ -6896,6 +7010,9 @@ synonym: "nonspecific immune response" EXACT [] xref: Wikipedia:Innate_immune_system is_a: GO:0006955 ! immune response is_a: GO:0140546 ! defense response to symbiont +property_value: RO:0002161 NCBITaxon:2 +property_value: RO:0002161 NCBITaxon:2157 +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0045190 @@ -8197,6 +8314,7 @@ def: "A complex of collagen trimers such as a fibril or collagen network." [GOC: synonym: "Supramolecular aggregate of collagen" EXACT [PMID:19693541] synonym: "Supramolecular collagen assembly" EXACT [PMID:21421911] is_a: GO:0099080 ! supramolecular complex +is_a: PR:000050567 ! protein-containing material entity relationship: has_part GO:0005581 ! collagen trimer relationship: part_of GO:0062023 ! collagen-containing extracellular matrix @@ -8453,6 +8571,19 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i created_by: pg creation_date: 2017-10-23T11:53:42Z +[Term] +id: GO:0140253 +name: cell-cell fusion +namespace: biological_process +def: "A cellular process in which two or more cells combine together, their plasma membrane fusing, producing a single cell. In some cases, nuclei fuse, producing a polyploid cell, while in other cases, nuclei remain separate, producing a syncytium." [Wikipedia:Cell_fusion] +synonym: "cell cell fusion" EXACT [] +synonym: "cell fusion" BROAD [] +is_a: GO:0009987 ! cellular process +relationship: has_part GO:0045026 ! plasma membrane fusion +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15939" xsd:anyURI +created_by: pg +creation_date: 2018-08-13T18:38:18Z + [Term] id: GO:0140352 name: export from cell @@ -9439,7 +9570,7 @@ comment: The definition above excludes protein complexes, which some also consid synonym: "native protein" NARROW [IEDB:BP] synonym: "natural protein" EXACT [PRO:DAN] is_a: PR:000018263 ! amino acid chain -is_a: PR:000064867 ! protein-containing molecular entity +is_a: PR:000050567 ! protein-containing material entity relationship: output_of GO:0006412 ! translation [Term] @@ -10615,11 +10746,11 @@ is_a: PR:000036194 ! eukaryotic protein relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa [Term] -id: PR:000064867 -name: protein-containing molecular entity +id: PR:000050567 +name: protein-containing material entity namespace: protein -def: "A molecular entity that minimally consists of a protein." [PRO:DAN] -comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). +def: "A material entity that minimally consists of a protein." [PRO:DAN] +comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566). synonym: "protein" NARROW [PRO:DAN] synonym: "protein aggregate" NARROW [PRO:DAN] synonym: "protein complex" NARROW [PRO:DAN] @@ -10849,7 +10980,7 @@ xref: SCTID:118966000 xref: UMLS:C1519343 {source="ncithesaurus:Skeletal_System_Part"} is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision relationship: part_of UBERON:0001434 ! skeletal system -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002473 UBERON:0004765 ! composed primarily of skeletal element [Term] @@ -11032,7 +11163,7 @@ is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000108 {source="BILS"} ! blastula stage relationship: RO:0002082 GO:0007369 ! simultaneous with gastrulation -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0000110 @@ -11048,7 +11179,7 @@ is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000109 ! gastrula stage relationship: RO:0002082 GO:0001841 ! simultaneous with neural tube formation -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: seeAlso "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/343" xsd:anyURI @@ -11068,7 +11199,7 @@ xref: Wikipedia:Organogenesis is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: RO:0002082 GO:0048513 ! simultaneous with animal organ development -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: seeAlso "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/533" xsd:anyURI @@ -11126,7 +11257,7 @@ xref: XAO:0003029 xref: ZFA:0000547 xref: ZFA:0000590 is_a: UBERON:0004921 ! subdivision of digestive tract -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002202 UBERON:0035804 ! develops from future mouth property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/661" xsd:anyURI @@ -11166,6 +11297,7 @@ xref: VHOG:0000224 xref: Wikipedia:Blood xref: XAO:0000124 xref: ZFA:0000007 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000179 ! haemolymphatic fluid relationship: has_part CL:0000232 {source="CL:tm"} ! erythrocyte relationship: has_part UBERON:0001969 ! blood plasma @@ -11186,7 +11318,7 @@ is_a: UBERON:0006314 ! bodily fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: part_of UBERON:0002193 ! hemolymphoid system relationship: part_of UBERON:0002193 ! hemolymphoid system -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: terms:contributor https://orcid.org/0000-0002-6601-2165 creation_date: 2009-04-08T04:38:19Z @@ -11244,7 +11376,7 @@ is_a: UBERON:0011216 ! organ system subdivision intersection_of: UBERON:0011216 ! organ system subdivision intersection_of: RO:0002473 UBERON:0001015 ! composed primarily of musculature relationship: capable_of GO:0003012 ! muscle system process -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002473 UBERON:0001015 ! composed primarily of musculature property_value: IAO:0000116 "consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77" xsd:string property_value: RO:0002161 NCBITaxon:6040 @@ -11658,12 +11790,13 @@ xref: VHOG:0000387 xref: Wikipedia:Epithelium xref: XAO:0003045 xref: ZFA:0001486 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: RO:0002473 CL:0000066 ! composed primarily of epithelial cell relationship: has_part GO:0005911 ! cell-cell junction relationship: has_part UBERON:0005769 ! basement membrane of epithelium -relationship: RO:0002160 NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! in taxon Metazoa relationship: RO:0002473 CL:0000066 ! composed primarily of epithelial cell property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI @@ -11820,7 +11953,7 @@ xref: Wikipedia:Germ_layer xref: XAO:0003011 xref: ZFA:0001122 is_a: UBERON:0010316 ! germ layer / neural crest -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0000924 @@ -11974,7 +12107,7 @@ xref: ZFA:0001290 is_a: UBERON:0013522 ! subdivision of tube relationship: part_of UBERON:0000924 ! ectoderm relationship: part_of UBERON:0035804 ! future mouth -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI property_value: IAO:0000116 "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" xsd:string @@ -12027,7 +12160,7 @@ intersection_of: UBERON:0007100 ! primary circulatory organ intersection_of: has_part UBERON:0004151 ! cardiac chamber relationship: has_part UBERON:0004151 ! cardiac chamber relationship: part_of UBERON:0015410 {source="MA"} ! heart plus pericardium -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002202 UBERON:0004141 ! develops from heart tube relationship: RO:0002433 UBERON:0004535 ! contributes to morphology of cardiovascular system property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/heart-female/v1.3/assets/3d-vh-f-heart.glb" xsd:anyURI @@ -12144,7 +12277,7 @@ disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system relationship: capable_of GO:0003013 ! circulatory system process -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} @@ -12194,7 +12327,6 @@ namespace: uberon def: "The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]." [BIRNLEX:844, ISBN:0-14-051288-8, ISBN:3110148986, NLM:nervous+system, WB:rynl, Wikipedia:Nervous_system, ZFIN:curator] subset: cumbo subset: efo_slim -subset: human_reference_atlas subset: pheno_slim subset: uberon_slim subset: vertebrate_core @@ -12235,14 +12367,13 @@ disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system relationship: capable_of GO:0050877 ! nervous system process relationship: has_part CL:0000540 ! neuron -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002473 CL:0002319 ! composed primarily of neural cell relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage relationship: RO:0002495 UBERON:0016880 {source="Bgee:AN"} ! immediate transformation of future nervous system property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:6040 -property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001017 @@ -12289,7 +12420,7 @@ xref: ZFA:0000012 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0011216 {source="FBbt", source="cjm"} ! organ system subdivision relationship: part_of UBERON:0001016 ! nervous system -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria relationship: RO:0002495 UBERON:0016879 {source="Bgee:AN"} ! immediate transformation of future central nervous system property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} property_value: RO:0002175 NCBITaxon:9606 @@ -12474,7 +12605,7 @@ intersection_of: UBERON:0004765 ! skeletal element intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue disjoint_from: UBERON:0001630 ! muscle organ disjoint_from: UBERON:0005090 ! muscle structure -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002473 UBERON:0002481 {source="VSAO-modified"} ! composed primarily of bone tissue [Term] @@ -12512,7 +12643,7 @@ xref: WBbt:0005743 xref: ZFA:0000112 is_a: UBERON:0000025 ! tube relationship: part_of UBERON:0001007 ! digestive system -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002176 UBERON:0000165 ! connects mouth relationship: RO:0002495 UBERON:0007026 {source="NCBIBook:NBK10107"} ! immediate transformation of presumptive gut property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} @@ -12572,6 +12703,7 @@ xref: MIAA:0000052 xref: NCIT:C13356 xref: UMLS:C0032105 {source="ncithesaurus:Plasma"} xref: Wikipedia:Blood_plasma +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000179 ! haemolymphatic fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: has_part GO:0005577 ! fibrinogen complex @@ -12620,6 +12752,7 @@ xref: VHOG:0001250 xref: Wikipedia:Blood_vessel xref: XAO:0001011 xref: ZFA:0005314 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000055 ! vessel is_a: UBERON:0004120 ! mesoderm-derived structure relationship: capable_of_part_of GO:0008015 ! blood circulation @@ -12657,7 +12790,7 @@ is_a: UBERON:0000487 {source="FMA-text-def", source="https://github.com/obopheno is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: RO:0002473 CL:0000115 ! composed primarily of endothelial cell -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002473 CL:0000115 ! composed primarily of endothelial cell property_value: RO:0002175 NCBITaxon:9606 @@ -12831,7 +12964,7 @@ xref: EMAPA:18765 xref: FMA:74562 xref: MA:0000013 is_a: UBERON:0000467 {source="MA"} ! anatomical system -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria [Term] id: UBERON:0002204 @@ -12971,7 +13104,7 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0011137 ! axial skeletal system relationship: produces PR:000014841 ! sonic hedgehog protein -relationship: RO:0002160 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! in taxon Chordata relationship: RO:0002202 UBERON:0004880 {source="ZFA"} ! develops from chordamesoderm relationship: RO:0002202 UBERON:0006267 {source="EHDAA2"} ! develops from notochordal plate relationship: RO:0002488 UBERON:0000068 ! existence starts during embryo stage @@ -13014,7 +13147,7 @@ xref: XAO:0000058 xref: ZFA:0000155 is_a: UBERON:0005423 ! developing anatomical structure is_a: UBERON:0007503 {source="EHDAA2"} ! epithelial vesicle -relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {source="GOTAX:0000352"} ! in taxon Chordata relationship: RO:0002202 UBERON:0003059 {source="ZFA"} ! develops from presomitic mesoderm property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:7712 {source="PMID:17237766"} @@ -13053,7 +13186,7 @@ is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0010316 ! germ layer / neural crest relationship: part_of UBERON:0002346 {source="XAO", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! neurectoderm -relationship: RO:0002160 NCBITaxon:89593 ! only in taxon Craniata +relationship: RO:0002162 NCBITaxon:89593 ! in taxon Craniata relationship: RO:0002202 UBERON:0003075 {source="BTO"} ! develops from neural plate relationship: RO:0002202 UBERON:0005062 {source="PMID:11523831"} ! develops from neural fold relationship: RO:0002473 CL:0000333 ! composed primarily of migratory neural crest cell @@ -13177,7 +13310,7 @@ xref: VSAO:0000017 xref: XAO:0001017 xref: ZFA:0001632 is_a: UBERON:0000479 ! tissue -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -13209,7 +13342,7 @@ intersection_of: UBERON:0000479 ! tissue intersection_of: RO:0002473 CL:0000187 ! composed primarily of muscle cell relationship: capable_of GO:0006936 ! muscle contraction relationship: part_of UBERON:0001015 ! musculature -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002473 CL:0000187 ! composed primarily of muscle cell [Term] @@ -13254,7 +13387,7 @@ is_a: UBERON:0000467 ! anatomical system is_a: UBERON:0004120 ! mesoderm-derived structure disjoint_from: UBERON:0002405 ! immune system relationship: part_of UBERON:0002193 {source="FMA"} ! hemolymphoid system -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002202 UBERON:0003061 ! develops from blood island property_value: RO:0002175 NCBITaxon:9606 @@ -13316,7 +13449,7 @@ xref: ZFA:0005621 is_a: UBERON:0004755 {source="VSAO"} ! skeletal tissue disjoint_from: UBERON:0005090 ! muscle structure relationship: part_of UBERON:0001474 ! bone element -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata property_value: IAO:0000116 "see https://github.com/obophenotype/uberon/issues/27" xsd:string [Term] @@ -13438,7 +13571,7 @@ xref: XAO:0000205 xref: ZFA:0001204 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0000926 ! mesoderm -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002202 UBERON:0000926 ! develops from mesoderm property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI @@ -13472,7 +13605,7 @@ xref: ZFA:0000132 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0016879 ! future central nervous system -relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {source="GOTAX:0000352"} ! in taxon Chordata relationship: RO:0002256 UBERON:0002328 {source="Wikipedia"} ! developmentally induced by notochord relationship: RO:0002495 UBERON:0007284 {source="Bgee:AN"} ! immediate transformation of presumptive neural plate property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI @@ -13539,7 +13672,7 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue relationship: part_of UBERON:0000926 {source="EHDAA2", source="VHOG"} ! mesoderm -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria relationship: RO:0002221 UBERON:0003887 ! surrounds intraembryonic coelom property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI @@ -13589,7 +13722,7 @@ xref: XAO:0000397 xref: ZFA:0001080 is_a: UBERON:0005856 {source="EHDAA2"} ! developing mesenchymal condensation is_a: UBERON:0007530 {source="EHDAA2"} ! migrating mesenchyme population -relationship: RO:0002160 NCBITaxon:7742 {source="VHOG:0000680"} ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 {source="VHOG:0000680"} ! in taxon Vertebrata relationship: RO:0002202 UBERON:0002329 {source="ZFA"} ! develops from somite property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI @@ -13644,7 +13777,7 @@ xref: ZFA:0000393 is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002328 GO:0032502 ! functionally related to developmental process relationship: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI @@ -13902,6 +14035,7 @@ xref: WikipediaCategory:Cardiovascular_system xref: XAO:0000100 xref: XAO:0001010 xref: ZFA:0000010 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000467 ! anatomical system intersection_of: UBERON:0000467 ! anatomical system intersection_of: has_part UBERON:0000948 ! heart @@ -13925,6 +14059,7 @@ synonym: "blood vessels" RELATED [TAO:0001079] synonym: "set of blood vessels" EXACT [] xref: TAO:0001079 xref: ZFA:0001079 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel @@ -14062,7 +14197,7 @@ is_a: UBERON:0034925 ! anatomical collection intersection_of: UBERON:0034925 ! anatomical collection intersection_of: RO:0002351 UBERON:0000982 ! has member skeletal joint relationship: part_of UBERON:0001434 {source="FMA"} ! skeletal system -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria relationship: RO:0002328 GO:0040011 ! functionally related to locomotion relationship: RO:0002351 UBERON:0000982 ! has member skeletal joint relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage @@ -14126,7 +14261,7 @@ xref: TAO:0000091 xref: ZFA:0000091 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0003068 ! axial mesoderm -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata [Term] id: UBERON:0004905 @@ -14169,7 +14304,7 @@ subset: upper_level xref: FMA:82485 is_a: UBERON:0000064 ! organ part relationship: part_of UBERON:0000060 ! anatomical wall -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0005061 @@ -14234,7 +14369,7 @@ synonym: "musculus" EXACT [FMA:30316] xref: FMA:30316 is_a: UBERON:0000061 ! anatomical structure relationship: has_part CL:0000187 ! muscle cell -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0005157 @@ -14398,11 +14533,12 @@ xref: NCIT:C13191 xref: SCTID:68989006 xref: UMLS:C0004799 {source="ncithesaurus:Basement_Membrane"} xref: Wikipedia:Basement_membrane +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005764 {source="FMA"} ! acellular membrane relationship: adjacent_to CL:0000066 ! epithelial cell relationship: has_part GO:0005587 ! collagen type IV trimer relationship: part_of UBERON:0000483 ! epithelium -relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa relationship: RO:0002473 GO:0005604 ! composed primarily of basement membrane property_value: RO:0002175 NCBITaxon:80999 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} @@ -14481,7 +14617,7 @@ xref: NCIT:C34232 xref: UMLS:C1518430 {source="ncithesaurus:Notochordal_Process"} xref: VHOG:0001213 is_a: UBERON:0005423 ! developing anatomical structure -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002202 UBERON:0000924 {source="EHDAA2"} ! develops from ectoderm [Term] @@ -14519,7 +14655,7 @@ intersection_of: UBERON:0006598 ! presumptive structure intersection_of: part_of UBERON:0000307 ! blastula intersection_of: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm relationship: part_of UBERON:0000307 ! blastula -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm [Term] @@ -14571,7 +14707,7 @@ intersection_of: UBERON:0006598 ! presumptive structure intersection_of: part_of UBERON:0000307 ! blastula intersection_of: RO:0002387 UBERON:0000924 ! has potential to develop into ectoderm relationship: part_of UBERON:0000307 ! blastula -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002387 UBERON:0000924 ! has potential to develop into ectoderm [Term] @@ -14589,7 +14725,7 @@ intersection_of: UBERON:0006598 ! presumptive structure intersection_of: part_of UBERON:0000307 ! blastula intersection_of: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm relationship: part_of UBERON:0000307 ! blastula -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm [Term] @@ -14616,6 +14752,7 @@ subset: efo_slim xref: EFO:0003709 xref: TAO:0005077 xref: ZFA:0005077 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005423 ! developing anatomical structure relationship: has_part CL:0000115 ! endothelial cell relationship: has_part CL:0000566 ! angioblastic mesenchymal cell @@ -14959,6 +15096,7 @@ synonym: "thrombus" EXACT [BTO:0000102] xref: BTO:0000102 xref: galen:BloodClot xref: Wikipedia:Thrombus +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000463 ! organism substance intersection_of: UBERON:0000463 ! organism substance intersection_of: output_of GO:0007596 ! blood coagulation @@ -15108,7 +15246,7 @@ synonym: "schizocoelom" NARROW [] xref: EHDAA2:0004731 xref: Wikipedia:Coelom is_a: UBERON:0000481 {source="EHDAA2"} ! multi-tissue structure -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria property_value: IAO:0000116 "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." xsd:string property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} @@ -15178,7 +15316,7 @@ namespace: uberon def: "A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages." [https://orcid.org/0000-0002-6601-2165] subset: non_informative is_a: UBERON:0000475 ! organism subdivision -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0013702 @@ -15243,7 +15381,7 @@ def: "Any structure that is placed on one side of the left-right axis of a bilat subset: grouping_class subset: non_informative is_a: UBERON:0000061 ! anatomical structure -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria [Term] id: UBERON:0015228 @@ -16766,9 +16904,7 @@ inverse_of: output_of ! output of [Typedef] id: has_part name: has part -name: has_part namespace: external -namespace: quality def: "a core relation that holds between a whole and its part" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology @@ -16973,9 +17109,7 @@ expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://p [Typedef] id: part_of name: part of -name: part_of namespace: external -namespace: quality def: "a core relation that holds between a part and its whole" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term diff --git a/subsets/blood_and_immune_upper_slim.owl b/subsets/blood_and_immune_upper_slim.owl index b38f201de..0fa546cf7 100644 --- a/subsets/blood_and_immune_upper_slim.owl +++ b/subsets/blood_and_immune_upper_slim.owl @@ -22,8 +22,8 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - 2024-08-16 + + 2024-09-26 @@ -392,6 +392,14 @@ WHERE { + + + + + + + + @@ -1038,6 +1046,12 @@ WHERE { + + + + + + @@ -1076,17 +1090,13 @@ WHERE { - - created by - + - - creation date - + @@ -1172,9 +1182,7 @@ WHERE { - - id - + @@ -1283,7 +1291,6 @@ WHERE { A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. BFO:0000050 external - quality part_of @@ -1292,7 +1299,6 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of part of part of - part_of http://www.obofoundry.org/ro/#OBO_REL:part_of @@ -1314,7 +1320,6 @@ A continuant cannot be part of an occurrent: use 'participates in'. An A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. BFO:0000051 external - quality has_part @@ -1322,7 +1327,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part has part has part - has_part @@ -4773,7 +4777,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -4854,6 +4858,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -5181,6 +5186,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -5673,7 +5679,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -5741,12 +5747,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - An endothelial cell that lines the vasculature. ZFA:0009036 @@ -5772,12 +5772,36 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + Any epithelial cell that is part of some squamous epithelium. CALOHA:TS-1249 ZFA:0009039 squamous epithelial cell + + + + Any epithelial cell that is part of some squamous epithelium. + FBC:Autogenerated + @@ -5801,7 +5825,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -5996,6 +6020,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6142,6 +6167,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6288,6 +6314,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6443,8 +6470,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different A vertebrate phagocyte with a single nucleus. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Mononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. +In addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses. +Mononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer. BTO:0001433 ZFA:0009064 + https://cellxgene.cziscience.com/cellguide/CL_0000113 mononuclear phagocyte @@ -6463,6 +6496,18 @@ Each of these 3 primitives can be composed to yield a cross-product of different GOC:tfm ISBN:0781735149 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Mononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. +In addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses. +Mononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer. + DOI:10.1016/j.coi.2005.11.008 + DOI:10.1038/nri3087 + DOI:10.3389/fimmu.2019.01893 + @@ -6476,6 +6521,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6748,6 +6794,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6903,6 +6950,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6934,6 +6982,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6967,6 +7016,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -7045,6 +7095,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -7079,6 +7130,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -7087,11 +7139,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell with more than one nucleus. - AEO:0000203 - WBbt:0008074 - syncitium - syncytial cell - syncytium + multinucleated cells + polynuclear cells multinucleate cell @@ -7099,6 +7148,19 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell with more than one nucleus. FB:ma + Wikipedia:Multinucleate + + + + + multinucleated cells + Wikipedia:Multinucleate + + + + + polynuclear cells + Wikipedia:Multinucleate @@ -7446,7 +7508,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -7455,11 +7517,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - Any cell that only exists in Eukaryota. + Any cell that in taxon some Eukaryota. MESH:D005057 eukaryotic cell @@ -7467,7 +7529,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - Any cell that only exists in Eukaryota. + Any cell that in taxon some Eukaryota. FBC:Autogenerated @@ -7611,7 +7673,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -7622,7 +7684,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -7744,6 +7806,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -7905,7 +7968,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -8130,6 +8193,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -8279,6 +8343,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -8375,6 +8440,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -8868,6 +8934,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -9054,6 +9121,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -9195,6 +9263,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -9269,6 +9338,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -9433,8 +9503,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -9453,7 +9523,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - A phagocytic cell formed by the fusion of macrophages, occurs in chronic inflammatory responses to persistent microorganism such as M.tuberculosis, component of granulomas. Sometimes used to refer to megakaryocytes. + A phagocytic syncytial cell formed by the fusion of macrophages, occurs in chronic inflammatory responses to persistent microorganism such as M.tuberculosis, component of granulomas. Sometimes used to refer to megakaryocytes. BTO:0003107 FMA:83035 MESH:D015726 @@ -9462,6 +9532,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different macrophage polykaryon multinucleate giant cell syncytial giant cell + MGC Role or process: Chronic infection, granulomatous inflammation. Consider also megakaryocyte (CL:0000556) as sometimes multinucleated giant cell is used to refer to this. multinucleated giant cell @@ -9475,11 +9546,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - A phagocytic cell formed by the fusion of macrophages, occurs in chronic inflammatory responses to persistent microorganism such as M.tuberculosis, component of granulomas. Sometimes used to refer to megakaryocytes. + A phagocytic syncytial cell formed by the fusion of macrophages, occurs in chronic inflammatory responses to persistent microorganism such as M.tuberculosis, component of granulomas. Sometimes used to refer to megakaryocytes. GOC:add GOC:tfm ISBN:0702022918 ISBN:0702024783 + PMID:33348900 + Wikipedia:Giant_cell @@ -9516,6 +9589,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different ISBN:0702022918 ISBN:0702024783 + + + + MGC + PMID:33348900 + + @@ -9534,6 +9614,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -9593,18 +9674,18 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009307 somatic stem cell - - - - ZFA:0009307 - - A stem cell that can give rise to cell types of the body other than those of the germ-line. GO:0048103 + + + + ZFA:0009307 + + @@ -9638,7 +9719,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -9767,6 +9848,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -10582,6 +10664,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -10687,6 +10770,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -10741,6 +10825,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -11089,6 +11174,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -11397,6 +11483,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -11646,7 +11733,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + @@ -11961,6 +12050,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -12444,7 +12534,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -12714,6 +12804,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -12757,10 +12848,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - @@ -12894,6 +12981,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -12982,6 +13070,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -13026,6 +13115,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -13389,7 +13479,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -13428,7 +13518,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -13549,7 +13639,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -13576,32 +13666,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - An endothelial progenitor cell that participates in angiogenesis during development. - - 2011-02-28T04:20:39Z - ZFA:0005773 - See CL:0002619. - embryonic blood vessel endothelial progenitor cell - - - - - An endothelial progenitor cell that participates in angiogenesis during development. - GOC:tfm - - - - - ZFA:0005773 - - - - - @@ -13653,6 +13717,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -13819,6 +13884,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -13859,6 +13925,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. +After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. +Disorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis. + https://cellxgene.cziscience.com/cellguide/CL_0011012 neural crest cell @@ -13869,6 +13941,19 @@ Each of these 3 primitives can be composed to yield a cross-product of different https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-9900-7880 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. +After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. +Disorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis. + DOI:10.1002/dvg.23276 + DOI:10.1242/dev.193193 + DOI:10.3389/fcell.2020.00635/full + https://doi.org/10.1016/j.ydbio.2011.12.042 + @@ -13886,6 +13971,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -14271,6 +14357,61 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + + + + + A multinucleate cell formed by the fusion of multiple uninuclear cells through plasma membrane fusion. This process leads to a single large cell containing multiple nuclei within a shared cytoplasm. + + 2024-08-15T10:38:46Z + syncytium + SC + syncytial cell + + + + + A multinucleate cell formed by the fusion of multiple uninuclear cells through plasma membrane fusion. This process leads to a single large cell containing multiple nuclei within a shared cytoplasm. + PMID:20851884 + Wikipedia:Syncytium + + + + + syncytium + WBbt:0008074 + + + + + SC + PMID:9067520 + + + + + @@ -14382,10 +14523,42 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells. + cell fusion + biological_process + GO:0000768 + syncytium formation by plasma membrane fusion + + + + + The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells. + GOC:mtg_muscle + GOC:tb + + + + - + @@ -14393,6 +14566,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome. + https://github.com/geneontology/go-ontology/issues/28301 GO:0000789 GO:0000790 GO:0005717 @@ -16136,12 +16310,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different The synthesis or release of products of arachidonic acid metabolism following a stimulus as part of an inflammatory response, resulting in an increase in their intracellular or extracellular levels. + https://github.com/geneontology/go-ontology/issues/28648 arachidonic acid metabolite production involved in acute inflammatory response production of arachidonic acid metabolites involved in acute inflammatory response + arachidonic acid metabolite production involved in inflammatory response production of arachidonic acid metabolites involved in inflammatory response biological_process GO:0002538 - arachidonic acid metabolite production involved in inflammatory response + arachidonate metabolite production involved in inflammatory response @@ -17424,32 +17600,32 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. Wikipedia:Collagen cellular_component GO:0005581 collagen trimer - + - + - + PMID:12382326 - + PMID:12382326 @@ -17902,12 +18078,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - + @@ -18730,11 +18901,49 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + + The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane. Syncytia are normally derived from single cells that fuse or fail to complete cell division. + biological_process + GO:0006949 + + syncytium formation + + + + + The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane. Syncytia are normally derived from single cells that fuse or fail to complete cell division. + ISBN:0198506732 + + + + Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation). + https://github.com/geneontology/go-ontology/issues/26810 biological_process response to abiotic stress response to biotic stress @@ -18745,7 +18954,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to stress @@ -18897,6 +19105,58 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + + + + + + + A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the plasma membrane. + plasma membrane organisation + biological_process + plasma membrane organization and biogenesis + GO:0007009 + + plasma membrane organization + + + + + A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the plasma membrane. + GOC:dph + GOC:jl + GOC:mah + + + + + plasma membrane organization and biogenesis + GOC:mah + + + + @@ -19945,6 +20205,51 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endomembrane system. + endomembrane organization + endomembrane system organisation + biological_process + GO:0010256 + + endomembrane system organization + + + + + A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endomembrane system. + GOC:mah + GOC:sm + + + + + endomembrane system organisation + GOC:mah + + + + @@ -20534,6 +20839,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different The self-renewing division of a stem cell. A stem cell is an undifferentiated cell, in the embryo or adult, that can undergo unlimited division and give rise to one or several different cell types. + + + stem cell renewal biological_process GO:0017145 @@ -22837,12 +23145,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - + A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. GO:0043234 @@ -22872,33 +23175,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - A macromolecular complex containing both protein and DNA molecules. - DNA-protein complex - cellular_component - GO:0032993 - - Note that this term is intended to classify complexes that have DNA as one of the members of the complex, that is, the complex does not exist if DNA is not present. Protein complexes that interact with DNA e.g. transcription factor complexes should not be classified here. - protein-DNA complex - - - - - A macromolecular complex containing both protein and DNA molecules. - GOC:mah - - - - - DNA-protein complex - GOC:mah - - - - @@ -24135,10 +24411,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. + https://github.com/geneontology/go-ontology/issues/28153 NIF_Subcellular:sao414196390 membrane-enclosed organelle cellular_component GO:0043227 + membrane-bounded organelle @@ -24156,11 +24434,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. https://github.com/geneontology/go-ontology/issues/21881 + https://github.com/geneontology/go-ontology/issues/28153 NIF_Subcellular:sao1456184038 non-membrane-enclosed organelle cellular_component biological condensate GO:0043228 + non-membrane-bounded organelle @@ -24196,8 +24476,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. + https://github.com/geneontology/go-ontology/issues/28153 cellular_component GO:0043229 + intracellular organelle @@ -24445,10 +24727,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component. + https://github.com/geneontology/go-ontology/issues/27194 GO:0071843 cellular component biogenesis at cellular level biological_process GO:0044085 + cellular component biogenesis @@ -24598,6 +24882,46 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + + The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell. + GO:0006947 + cell fusion + cell-cell fusion + biological_process + GO:0045026 + plasma membrane fusion + + + + + The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell. + GOC:elh + GOC:mtg_muscle + + + + @@ -24639,6 +24963,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens. + + + GO:0002226 Wikipedia:Innate_immune_system innate immunity @@ -28234,6 +28561,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -29026,6 +29354,35 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + A cellular process in which two or more cells combine together, their plasma membrane fusing, producing a single cell. In some cases, nuclei fuse, producing a polyploid cell, while in other cases, nuclei remain separate, producing a syncytium. + https://github.com/geneontology/go-ontology/issues/15939 + pg + 2018-08-13T18:38:18Z + cell fusion + cell cell fusion + biological_process + GO:0140253 + cell-cell fusion + + + + + A cellular process in which two or more cells combine together, their plasma membrane fusing, producing a single cell. In some cases, nuclei fuse, producing a polyploid cell, while in other cases, nuclei remain separate, producing a syncytium. + Wikipedia:Cell_fusion + + + + @@ -31380,7 +31737,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -34539,51 +34896,51 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + - A molecular entity that minimally consists of a protein. + A material entity that minimally consists of a protein. protein protein aggregate protein complex protein-containing complex protein - PR:000064867 - Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). - protein-containing molecular entity + PR:000050567 + Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566). + protein-containing material entity - + - A molecular entity that minimally consists of a protein. + A material entity that minimally consists of a protein. PRO:DAN - + protein PRO:DAN - + protein aggregate PRO:DAN - + protein complex PRO:DAN - + protein-containing complex PRO:DAN @@ -35068,7 +35425,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -35444,7 +35801,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -35453,7 +35810,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -35480,14 +35837,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different gastrula stage - + - + BILS @@ -35559,7 +35916,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -35602,7 +35959,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -35636,7 +35993,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -35796,6 +36153,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -35803,15 +36161,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - - + + A fluid that is composed of blood plasma and erythrocytes. AAO:0000046 @@ -35848,34 +36206,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different blood - + - + - + - + CL:tm - + https://github.com/obophenotype/uberon/issues/1330 - + Bgee:AN @@ -35925,7 +36283,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -36030,7 +36388,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -36947,6 +37305,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -36960,7 +37319,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -37002,14 +37361,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg - - + + - + http://palaeos.com/metazoa/porifera/homoscleromorpha.html @@ -37338,7 +37697,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -37429,7 +37788,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. AAO:0000137 BILA:0000036 @@ -37464,14 +37823,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png - + - + Bgee:AN @@ -37511,7 +37870,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. AAO:0000139 BILA:0000038 @@ -37546,14 +37905,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png - + - + Bgee:AN @@ -37594,7 +37953,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The middle germ layer of the embryo, between the endoderm and ectoderm. UBERON:0003263 @@ -37635,14 +37994,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png - + - + Bgee:AN @@ -37697,7 +38056,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -37816,7 +38175,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -37825,7 +38184,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -37887,14 +38246,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different https://cdn.humanatlas.io/digital-objects/ref-organ/heart-female/v1.3/assets/3d-vh-f-heart.glb https://cdn.humanatlas.io/digital-objects/ref-organ/heart-male/v1.3/assets/3d-vh-m-heart.glb - + - + MA @@ -38120,7 +38479,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -38275,7 +38634,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -38297,14 +38656,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]. - AAO:0000324 BILA:0000079 BIRNLEX:844 @@ -38339,7 +38697,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0001016 - @@ -38347,14 +38704,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png - + - + Bgee:AN @@ -38416,11 +38773,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. @@ -38465,7 +38822,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different central nervous system - + @@ -38479,7 +38836,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Bgee:AN @@ -38863,11 +39220,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + Skeletal element that is composed of bone tissue. @@ -38909,14 +39266,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different bone element - + - + VSAO-modified @@ -38972,7 +39329,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -38982,7 +39339,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A tube extending from the mouth to the anus. @@ -39019,14 +39376,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different digestive tract - + - + NCBIBook:NBK10107 @@ -39171,6 +39528,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -39245,6 +39603,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -39253,8 +39612,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + @@ -39267,7 +39626,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -39321,34 +39680,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different blood vessel http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg - + - + - + - + AEO - + EHDAA2 - + GO:0072360 @@ -39410,7 +39769,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -39861,7 +40220,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -40182,9 +40541,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - + + + @@ -40232,15 +40591,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - - + + - + - + @@ -40259,19 +40618,19 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -40311,8 +40670,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. mesodermal cluster @@ -40350,11 +40709,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - - + + - + @@ -40367,13 +40726,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + GOTAX:0000352 - + ZFA @@ -40435,22 +40794,22 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + - - + + - + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. AAO:0010578 BTO:0001764 @@ -40483,45 +40842,45 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - + BTO - + PMID:11523831 - + PMID:11523831 @@ -40662,7 +41021,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -40718,14 +41077,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different bone marrow http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg - + - + FMA MA @@ -40773,7 +41132,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -40864,7 +41223,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -40937,10 +41296,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -40990,14 +41349,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different hematopoietic system - + - + FMA @@ -41095,7 +41454,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -41310,7 +41669,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. AAO:0011086 EFO:0001982 @@ -41333,14 +41692,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different presomitic mesoderm - + - + Bgee:AN @@ -41446,7 +41805,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -41494,9 +41853,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. AAO:0011072 BTO:0001765 @@ -41525,34 +41884,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - - + + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -41592,7 +41951,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. AAO:0010568 EFO:0003515 @@ -41618,7 +41977,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -41631,7 +41990,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Bgee:AN @@ -41678,10 +42037,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -41718,7 +42077,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -41731,7 +42090,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 VHOG @@ -41781,15 +42140,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + - + Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. should probably be merged with heart rudiment. AAO:0011044 @@ -41806,15 +42165,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different heart primordium - + - + - + @@ -41827,19 +42186,19 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + ZFA - + ZFA - + XAO @@ -41868,8 +42227,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. AAO:0010571 AEO:0000212 @@ -41893,11 +42252,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different sclerotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - - + + - + @@ -41916,13 +42275,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + VHOG:0000680 - + ZFA @@ -42006,7 +42365,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -42141,7 +42500,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults EHDAA:251 @@ -42156,14 +42515,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different intraembryonic coelom - + - + Wikipedia @@ -42458,8 +42817,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. XAO:0004185 first heart field @@ -42471,24 +42830,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0004140 primary heart field - + - + - + GO:0003128 - + https://orcid.org/0000-0003-3308-6245 @@ -42541,7 +42900,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + An epithelial tube that will give rise to the mature heart. AAO:0010411 EFO:0003526 @@ -42560,14 +42919,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different heart tube - + - + ZFA-modified @@ -42744,6 +43103,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -42840,6 +43200,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -43191,7 +43552,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. AAO:0011129 TAO:0001890 @@ -43205,14 +43566,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different skeletal element - + - + VSAO @@ -43239,10 +43600,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -43278,14 +43639,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0004770 articular system - + - + FMA @@ -43444,7 +43805,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -43610,7 +43971,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -43771,7 +44132,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -43999,7 +44360,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -44015,14 +44376,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different trunk mesenchyme - + - + EHDAA2 @@ -44139,7 +44500,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Multi-tissue structure that arises from the heart rudiment and will become the heart tube. EHDAA2:0001512 EHDAA:424 @@ -44157,14 +44518,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different primitive heart tube - + - + ZFA @@ -44231,6 +44592,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -44246,7 +44608,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -44330,7 +44692,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 @@ -44340,7 +44702,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0005856 developing mesenchymal condensation - + @@ -44359,7 +44721,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + AEO-modified-relation @@ -44453,7 +44815,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB EHDAA2:0001278 @@ -44467,7 +44829,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different notochordal plate - + @@ -44480,7 +44842,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 @@ -44504,11 +44866,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -44525,14 +44887,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -44635,7 +44997,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -44778,7 +45140,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -44842,7 +45204,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -44920,6 +45282,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -45421,7 +45784,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -45447,7 +45810,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different presumptive paraxial mesoderm - + @@ -45463,7 +45826,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + https://github.com/obophenotype/uberon/issues/1277 @@ -45539,7 +45902,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -45547,7 +45910,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0007524 dense mesenchyme tissue - + @@ -45560,7 +45923,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + AEO @@ -45663,7 +46026,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Anatomical system that consists of all blood and lymph vessels. consider merging with vasculature @@ -45680,14 +46043,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different vascular system - + - + MA @@ -45715,7 +46078,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -45732,14 +46095,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -45795,7 +46158,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -45803,14 +46166,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -45833,7 +46196,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EFO:0003704 TAO:0005041 ZFA:0005041 @@ -45843,14 +46206,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different anterior lateral plate mesoderm - + - + ZFA @@ -45964,6 +46327,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -45989,7 +46353,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -46009,14 +46373,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0010210 blood clot - + - + BTO @@ -46137,8 +46501,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. FMA:23879 SCTID:129140006 @@ -46150,11 +46514,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different subdivision of skeleton - + - + @@ -46167,13 +46531,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + UBERONREF:0000003 - + VSAO @@ -46234,7 +46598,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. axial skeletal system FMA:302077 @@ -46244,7 +46608,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different postcranial axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton - + @@ -46257,7 +46621,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + cjm @@ -46428,7 +46792,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -46530,7 +46894,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -46551,7 +46915,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0012429 hematopoietic tissue - + @@ -46564,7 +46928,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + defitional @@ -46697,7 +47061,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -46890,7 +47254,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -47115,7 +47479,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -47138,7 +47502,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0016887 entire extraembryonic component - + @@ -47151,7 +47515,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + AEO @@ -47565,72 +47929,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different /////////////////////////////////////////////////////////////////////////////////////// --> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - @@ -47671,6 +47969,454 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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+_:B219c8649X2Db5beX2D4319X2Dae80X2Db9cdc9e3289cgenid798 +_:B219c8649X2Db5beX2D4319X2Dae80X2Db9cdc9e3289cgenid853 +_:B219c8649X2Db5beX2D4319X2Dae80X2Db9cdc9e3289cgenid885 +_:B219c8649X2Db5beX2D4319X2Dae80X2Db9cdc9e3289cgenid930 +_:B219c8649X2Db5beX2D4319X2Dae80X2Db9cdc9e3289cgenid944 +_:B219c8649X2Db5beX2D4319X2Dae80X2Db9cdc9e3289cgenid959 +_:B219c8649X2Db5beX2D4319X2Dae80X2Db9cdc9e3289cgenid976 +_:B219c8649X2Db5beX2D4319X2Dae80X2Db9cdc9e3289cgenid995 "cell" "early embryonic cell (metazoa)" "stem cell" @@ -515,7 +547,6 @@ _:Bd8962366X2Dda15X2D4a2dX2Da122X2D110badc7fe25genid994 "embryonic cell (metazoa)" "immature T cell" "cardiocyte" - "embryonic blood vessel endothelial progenitor cell" "natural helper lymphocyte" "skeletogenic cell" "premigratory neural crest cell" @@ -535,9 +566,11 @@ _:Bd8962366X2Dda15X2D4a2dX2Da122X2D110badc7fe25genid994 "bone marrow hematopoietic cell" "peripheral blood mononuclear cell" "blood lymphocyte" + "syncytial cell" "mitotic cell cycle" "nuclear division" "lytic vacuole" + "syncytium formation by plasma membrane fusion" "chromatin" "euchromatin" "heterochromatin" @@ -588,7 +621,7 @@ _:Bd8962366X2Dda15X2D4a2dX2Da122X2D110badc7fe25genid994 "immune system development" "leukocyte differentiation" "production of molecular mediator involved in inflammatory response" - "arachidonic acid metabolite production involved in inflammatory response" + "arachidonate metabolite production involved in inflammatory response" "prostaglandin production involved in inflammatory response" "chronic inflammatory response" "somatic diversification of immune receptors via germline recombination within a single locus" @@ -657,11 +690,13 @@ _:Bd8962366X2Dda15X2D4a2dX2Da122X2D110badc7fe25genid994 "cellular component disassembly involved in execution phase of apoptosis" "chemotaxis" "muscle contraction" + "syncytium formation" "response to stress" "defense response" "inflammatory response" "immune response" "organelle organization" + "plasma membrane organization" "cell cycle" "endomitotic cell cycle" "cell communication" @@ -693,6 +728,7 @@ _:Bd8962366X2Dda15X2D4a2dX2Da122X2D110badc7fe25genid994 "embryo development ending in birth or egg hatching" "tissue development" "cellular process" + "endomembrane system organization" "membrane invagination" "gene expression" "programmed cell death" @@ -772,7 +808,6 @@ _:Bd8962366X2Dda15X2D4a2dX2Da122X2D110badc7fe25genid994 "secretion by cell" "protein-containing complex disassembly" "protein-containing complex" - "protein-DNA complex" "V(D)J recombination" "immunoglobulin V(D)J recombination" "erythrocyte homeostasis" @@ -824,6 +859,7 @@ _:Bd8962366X2Dda15X2D4a2dX2Da122X2D110badc7fe25genid994 "primary metabolic process" "cellular biosynthetic process" "biological process involved in interspecies interaction between organisms" + "plasma membrane fusion" "T cell selection" "innate immune response" "isotype switching" @@ -947,6 +983,7 @@ _:Bd8962366X2Dda15X2D4a2dX2Da122X2D110badc7fe25genid994 "mitotic nuclear division" "exocytic process" "extracellular vesicle biogenesis" + "cell-cell fusion" "export from cell" "defense response to symbiont" "regulation of leukocyte differentiation" @@ -1127,7 +1164,7 @@ _:Bd8962366X2Dda15X2D4a2dX2Da122X2D110badc7fe25genid994 "G-protein coupled receptor" "eukaryotic protein" "cathepsin-like protease" - "protein-containing molecular entity" + "protein-containing material entity" "processual entity" "tube" "vessel" diff --git a/subsets/eye_upper_slim.json b/subsets/eye_upper_slim.json index b921f2954..27446ca77 100644 --- a/subsets/eye_upper_slim.json +++ b/subsets/eye_upper_slim.json @@ -4,9 +4,9 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-08-16" + "val" : "2024-09-26" } ], - "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-08-16/subsets/eye_upper_slim.owl" + "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-09-26/subsets/eye_upper_slim.owl" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/CL_0000000", @@ -535,6 +535,10 @@ "lbl" : "squamous epithelial cell", "type" : "CLASS", "meta" : { + "definition" : { + "val" : "Any epithelial cell that is part of some squamous epithelium.", + "xrefs" : [ "FBC:Autogenerated" ] + }, "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-1249" @@ -548,9 +552,10 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A flattened epithelial cell of mesenchymal origin that lines the serous cavity.", - "xrefs" : [ "GOC:tfm", "ISBN:0721662544" ] + "val" : "A flat, squamous-like epithelial cell of mesodermal origin. It forms the mesothelium, which lines the body's serous cavities including the pleural, peritoneal, and pericardial spaces. This cell plays a crucial role in synthesizing and secreting lubricants, such as glycosaminoglycans and surfactants, which minimize friction between adjacent tissues during movement.", + "xrefs" : [ "GOC:tfm", "ISBN:0721662544", "PMID:26106328" ] }, + "comments" : [ "Mesothelial cells, which morphologically resemble squamous epithelial cells, express both epithelial markers (cytokeratins) and mesenchymal markers (vimentin), reflecting their mesodermal origin. They feature surface microvilli and apical-basal polarity. Under certain conditions, they can undergo mesothelial-to-mesenchymal transition. These cells also produce extracellular matrix proteins, maintain serosal homeostasis, and facilitate fluid transport." ], "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], "synonyms" : [ { "pred" : "hasExactSynonym", @@ -734,10 +739,15 @@ "val" : "FMA:54536" }, { "val" : "ZFA:0009073" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000125" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nGlial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons.\nThese different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning.\nOligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. \nMicroglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response.\nDespite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis." } ] } }, { @@ -1098,7 +1108,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A cell specialized to detect and transduce light.", + "val" : "A cell specialized in detecting light stimuli that are involved in visual perception.", "xrefs" : [ "MESH:D010786" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], @@ -1270,7 +1280,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "Any cell that only exists in Eukaryota.", + "val" : "Any cell that in taxon some Eukaryota.", "xrefs" : [ "FBC:Autogenerated" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], @@ -2601,6 +2611,8 @@ } ], "xrefs" : [ { "val" : "FMA:70606" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0002303" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", @@ -2608,6 +2620,9 @@ }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nPigmented ciliary epithelial cells, which are a type of pigment cell, have a crucial function within the eye's ciliary body. The ciliary body, located behind the iris, is one of the eye’s most vital structures and consists of two types of epithelial cells: the pigmented and the non-pigmented ciliary epithelial cells. The pigmented ciliary epithelial cells form the outer layer of the ciliary body and exhibit a black or brown pigmentation due to the melanin they contain.\nOne key function of pigmented ciliary epithelial cells is to aid in the formation of aqueous humor, an intraocular fluid that nourishes the cornea and lens, and maintains intraocular pressure which is essential for the eye’s shape and light refraction. These cells facilitate this function in conjunction with the non-pigmented ciliary epithelial cells. Together, the pigmented and non-pigmented ciliary epithelial cells form a bilayer epithelium that allows the secretion of aqueous humor through a bi-directional fluid transport mechanism.\nPigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, a physiological frontier that controls the entry and exit of various substances from the blood to the aqueous humor and vice versa. The pigmentation in these cells, intensified by melanin, helps to absorb scattered light coming into the eye, reducing any potential damage and glare." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2010-09-13T04:09:27Z" @@ -2800,27 +2815,6 @@ "val" : "2010-12-07T09:37:22Z" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/CL_0002546", - "lbl" : "embryonic blood vessel endothelial progenitor cell", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An endothelial progenitor cell that participates in angiogenesis during development.", - "xrefs" : [ "GOC:tfm" ] - }, - "comments" : [ "See CL:0002619." ], - "xrefs" : [ { - "val" : "ZFA:0005773" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0003-1980-3228" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2011-02-28T04:20:39Z" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/CL_0002565", "lbl" : "iris pigment epithelial cell", @@ -2852,12 +2846,18 @@ "xrefs" : [ "GOC:tfm" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset", "http://purl.obolibrary.org/obo/cl#eye_upper_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas" ], + "xrefs" : [ { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0002585" + } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nRetinal blood vessel endothelial cells constitute the innermost lining of the blood vessels found in the retina, the light-sensitive layer of tissue at the back of the eye. The primary role of these cells revolves around their location within the retinal vascular system, forming the structure of the blood-retinal barrier, a subset of the larger blood-ocular barrier system. \nThe endothelial cells are particularly involved in the growth of new retinal blood vessels from pre-existing ones (angiogenesis); this is critical in managing the amount of oxygen and essential nutrients delivered to the ocular tissues. They are crucial for maintaining homeostasis in the retinal environment by controlling the exchange of molecules between the blood and the retina. Furthermore, they mediate immune cell trafficking, supporting the immune privilege of the eye by preventing the unrestricted infiltration of inflammatory cells into the retina, thus maintaining ocular health and normal vision.\nThe malfunction or dysfunction of retinal blood vessel endothelial cells is implicated in numerous ocular pathologies, particularly diabetic retinopathy, which is one of the leading causes of blindness worldwide. In such conditions, the compromise in the integrity of the blood-retinal barrier and excess angiogenesis can lead to retinal edema and pathological neovascularization, resulting in vision loss." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2011-03-06T03:28:27Z" @@ -2877,6 +2877,8 @@ "val" : "BTO:0004910" }, { "val" : "FMA:75802" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0002586" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", @@ -2884,6 +2886,9 @@ }, { "pred" : "http://purl.org/dc/terms/contributor", "val" : "https://orcid.org/0000-0003-1980-3228" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nRetinal pigment epithelial (RPE) cells form a single layer of cells at the back of the eye sandwiched between the neurosensory retina and the choroid, playing a significant role in maintaining vision health. These pigment-laden cells are highly specialized and perform an array of metabolic and transport functions essential for the maintenance of the photoreceptor cells (rods and cones) in the retina. The pigmentation of RPE cells actively aids in the absorption of excess light and the prevention of light scattering, thus enhancing the eye's optical properties.\nThe retinal pigment epithelium forms a key part of the blood/retina barrier. The cells have long sheet-like microvilli on their apical membrane that project into the light-sensitive outer segments of the photoreceptors, forming a close structural interaction. The basolateral membrane of the RPE interacts with the underlying Bruch’s membrane, which separates the RPE cells from fenestrated endothelium of the choriocapillaris. \nRPE cells support the photoreceptor by providing them with oxygen and nutrients (such as glucose, retinol and fatty acids) and removing waste products. They also recycle the visual pigment, in a process called the \"visual cycle\", where the RPE cells play a vital role in the regeneration of visual pigment (11-cis retinol) following the absorption of light. This is essential for the maintenance of photoreceptor excitability.\nBeyond this, RPE cells take part in the phagocytosis process, where they digest the shed ends of photoreceptor outer segments, thus, preventing the build-up of waste residue that could otherwise harm retinal health. They also secrete various factors, including growth factors required to maintain the structural integrity of choriocapillaris endothelium and photoreceptors, as well as immunosuppressive factors that play an important role in establishing the immune privilege of the eye." }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", "val" : "2011-03-06T03:37:09Z" @@ -3062,7 +3067,14 @@ "val" : "A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells.", "xrefs" : [ "https://orcid.org/0000-0001-5208-3432", "https://orcid.org/0000-0002-9900-7880" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "xrefs" : [ { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0011012" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." + } ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0011026", @@ -3330,6 +3342,9 @@ "val" : "NIF_Subcellular:sao1615953555" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28301" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "GO:0000789" }, { @@ -5831,6 +5846,15 @@ "val" : "stem cell renewal" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_2" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_2157" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -6790,27 +6814,6 @@ "val" : "cellular_component" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0032993", - "lbl" : "protein-DNA complex", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A macromolecular complex containing both protein and DNA molecules.", - "xrefs" : [ "GOC:mah" ] - }, - "comments" : [ "Note that this term is intended to classify complexes that have DNA as one of the members of the complex, that is, the complex does not exist if DNA is not present. Protein complexes that interact with DNA e.g. transcription factor complexes should not be classified here." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "DNA-protein complex", - "xrefs" : [ "GOC:mah" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0034101", "lbl" : "erythrocyte homeostasis", @@ -7276,6 +7279,7 @@ "val" : "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.", "xrefs" : [ "GOC:go_curators" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "membrane-enclosed organelle" @@ -7284,6 +7288,9 @@ "val" : "NIF_Subcellular:sao414196390" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28153" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -7297,7 +7304,7 @@ "val" : "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes.", "xrefs" : [ "GOC:go_curators" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_mouse" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_mouse" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "non-membrane-enclosed organelle" @@ -7311,6 +7318,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/21881" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28153" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -7325,8 +7335,11 @@ "val" : "Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.", "xrefs" : [ "GOC:go_curators" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_pir" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28153" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -7511,12 +7524,15 @@ "val" : "A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component.", "xrefs" : [ "GOC:jl", "GOC:mah" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_pir" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "cellular component biogenesis at cellular level" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/27194" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "GO:0071843" }, { @@ -8147,6 +8163,42 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0050908", + "lbl" : "detection of light stimulus involved in visual perception", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The series of events involved in visual perception in which a light stimulus is received and converted into a molecular signal.", + "xrefs" : [ "GOC:ai", "GOC:dos" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "sensory detection of light during visual perception" + }, { + "pred" : "hasExactSynonym", + "val" : "sensory detection of light stimulus during visual perception" + }, { + "pred" : "hasExactSynonym", + "val" : "sensory transduction of light during visual perception" + }, { + "pred" : "hasExactSynonym", + "val" : "sensory transduction of light stimulus during visual perception" + }, { + "pred" : "hasExactSynonym", + "val" : "visual perception, detection of light stimulus" + }, { + "pred" : "hasExactSynonym", + "val" : "visual perception, sensory transduction during perception of light" + }, { + "pred" : "hasExactSynonym", + "val" : "visual perception, sensory transduction of light stimulus" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0050953", "lbl" : "sensory perception of light stimulus", @@ -11443,7 +11495,7 @@ "meta" : { "definition" : { "val" : "A quality of a single cell inhering in the bearer by virtue of the bearer's size or shape or structure.", - "xrefs" : [ "ORCID:0000-0002-7073-9172" ] + "xrefs" : [ "https://orcid.org/0000-0002-7073-9172" ] }, "comments" : [ "Use this term for morphologies that can *only* inhere in a cell, e.g. morphological qualities inhering in a cell by virtue of the presence, location or shape of one or more cell parts." ], "basicPropertyValues" : [ { @@ -12590,15 +12642,15 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/PR_000064867", - "lbl" : "protein-containing molecular entity", + "id" : "http://purl.obolibrary.org/obo/PR_000050567", + "lbl" : "protein-containing material entity", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A molecular entity that minimally consists of a protein.", + "val" : "A material entity that minimally consists of a protein.", "xrefs" : [ "PRO:DAN" ] }, - "comments" : [ "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565)." ], + "comments" : [ "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566)." ], "synonyms" : [ { "pred" : "hasNarrowSynonym", "val" : "protein", @@ -17026,7 +17078,7 @@ "val" : "The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO].", "xrefs" : [ "BIRNLEX:844", "ISBN:0-14-051288-8", "ISBN:3110148986", "NLM:nervous+system", "WB:rynl", "Wikipedia:Nervous_system", "ZFIN:curator" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#cumbo", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#cumbo", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "neurological system", @@ -17099,9 +17151,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -30463,7 +30512,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000050", - "lbl" : "part_of", + "lbl" : "part of", "type" : "PROPERTY", "propertyType" : "OBJECT", "meta" : { @@ -30486,9 +30535,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "part_of" @@ -30508,7 +30554,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000051", - "lbl" : "has_part", + "lbl" : "has part", "type" : "PROPERTY", "propertyType" : "OBJECT", "meta" : { @@ -30531,9 +30577,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_part" @@ -34398,6 +34441,10 @@ "id" : "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "type" : "PROPERTY", "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#gocheck_obsoletion_candidate", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/go#goslim_agr", "type" : "PROPERTY", @@ -34736,6 +34783,10 @@ "id" : "http://purl.org/dc/terms/date", "type" : "PROPERTY", "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/description", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/license", "type" : "PROPERTY", @@ -34761,12 +34812,10 @@ "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "lbl" : "created by", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "lbl" : "creation date", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { @@ -34859,7 +34908,6 @@ "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#id", - "lbl" : "id", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { @@ -34929,7 +34977,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000000", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_131567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000005", @@ -34959,6 +35007,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000030", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000055" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000030", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000030", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -34973,8 +35025,12 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000031", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000034", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000034", "pred" : "is_a", @@ -35140,7 +35196,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000066", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000066", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -35153,10 +35209,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000071", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0004638" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000071", - "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/CL_0002546" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000075", "pred" : "is_a", @@ -35165,6 +35217,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000076", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000066" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000076", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0006914" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000077", "pred" : "is_a", @@ -35177,6 +35233,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000077", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0002078" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000077", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0001136" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000081", "pred" : "is_a", @@ -35223,6 +35283,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000115", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000213" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000115", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000115", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -35245,11 +35309,7 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0000095" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000123", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000255" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000123", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000123", @@ -35309,6 +35369,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000148", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000147" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000148", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000148", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -35337,6 +35401,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000187", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000183" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000187", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000187", "pred" : "is_a", @@ -35360,7 +35428,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000197", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000197", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -35372,17 +35440,15 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000210", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000006", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_inferred", - "val" : "true" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/CL_0000101" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000210", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0008028" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000210", "pred" : "http://purl.obolibrary.org/obo/RO_0002215", - "obj" : "http://purl.obolibrary.org/obo/GO_0050962" + "obj" : "http://purl.obolibrary.org/obo/GO_0050908" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000211", "pred" : "is_a", @@ -35403,6 +35469,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000219", "pred" : "http://purl.obolibrary.org/obo/RO_0002215", "obj" : "http://purl.obolibrary.org/obo/GO_0048870" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000221", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000221", "pred" : "is_a", @@ -35411,6 +35481,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000221", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000924" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000222", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000222", "pred" : "is_a", @@ -35419,6 +35493,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000222", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000926" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000223", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000223", "pred" : "is_a", @@ -35467,8 +35545,12 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0000000" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000255", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000287", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000006" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000287", "pred" : "is_a", @@ -35539,8 +35621,12 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000342", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000347", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000347", "pred" : "is_a", @@ -35553,6 +35639,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000347", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", "obj" : "http://purl.obolibrary.org/obo/CL_0000008" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000348", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000348", "pred" : "is_a", @@ -35583,7 +35673,7 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0010017" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000365", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000393", @@ -35659,6 +35749,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000547", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0002242" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000547", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000547", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -35733,6 +35827,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000549", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000549", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -35755,6 +35853,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000550", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000550", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -35895,6 +35997,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000558", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000558", "pred" : "http://purl.obolibrary.org/obo/CL_4030046", @@ -35985,6 +36091,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000566", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0011026" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000566", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000566", "pred" : "http://purl.obolibrary.org/obo/RO_0002104", @@ -36057,6 +36167,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000680", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000055" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000680", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000680", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -36129,6 +36243,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000748", "pred" : "http://purl.obolibrary.org/obo/RO_0002100", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001791" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000763", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000763", "pred" : "is_a", @@ -36221,10 +36339,18 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000765", "pred" : "http://purl.obolibrary.org/obo/RO_0002215", "obj" : "http://purl.obolibrary.org/obo/GO_0030218" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000837", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000837", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0008001" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000837", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000837", "pred" : "http://purl.obolibrary.org/obo/CL_4030046", @@ -36311,6 +36437,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000988", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0002031", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002031", "pred" : "is_a", @@ -36323,6 +36453,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0002031", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", "obj" : "http://purl.obolibrary.org/obo/CL_0002032" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0002032", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002032", "pred" : "is_a", @@ -36398,7 +36532,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002319", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002319", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -36406,7 +36540,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002320", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002320", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -36438,15 +36572,11 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002494", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002494", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0007100" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0002546", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000222" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002565", "pred" : "is_a", @@ -36557,6 +36687,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0008019", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000219" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0008019", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0008019", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -36611,6 +36745,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0011012", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0002321" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0011026", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0011026", "pred" : "is_a", @@ -36742,7 +36880,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GO_0000785", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0032993" + "obj" : "http://purl.obolibrary.org/obo/GO_0110165" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0000785", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -36991,8 +37129,8 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0043232" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0005840", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", - "obj" : "http://purl.obolibrary.org/obo/PR_000000001" + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0005840", "pred" : "http://purl.obolibrary.org/obo/RO_0002216", @@ -37767,12 +37905,8 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0005575" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0032991", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", - "obj" : "http://purl.obolibrary.org/obo/PR_000000001" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0032993", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0032991" + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0034101", "pred" : "is_a", @@ -38233,6 +38367,14 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0050906", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/GO_0007600" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0050908", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0050962" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0050908", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/GO_0007601" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0050953", "pred" : "is_a", @@ -38581,6 +38723,10 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0098644", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0099080" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0098644", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0098644", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -39184,7 +39330,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/PR_000000001", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000064867" + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/PR_000000001", "pred" : "http://purl.obolibrary.org/obo/RO_0002353", @@ -39314,7 +39460,7 @@ "pred" : "http://purl.obolibrary.org/obo/RO_0002160", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" }, { - "sub" : "http://purl.obolibrary.org/obo/PR_000064867", + "sub" : "http://purl.obolibrary.org/obo/PR_000050567", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { @@ -39387,8 +39533,12 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0007811" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000033", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0000042", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000042", "pred" : "is_a", @@ -39533,7 +39683,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0001434" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000075", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000075", @@ -39659,7 +39809,7 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0007369" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000109", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000110", @@ -39679,7 +39829,7 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0001841" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000110", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000111", @@ -39695,7 +39845,7 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0048513" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000111", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000122", @@ -39715,7 +39865,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000475" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000153", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000154", @@ -39723,7 +39873,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000475" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000154", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", @@ -39731,12 +39881,16 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0004921" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", "obj" : "http://purl.obolibrary.org/obo/UBERON_0035804" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0000178", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000178", "pred" : "is_a", @@ -39789,7 +39943,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0002193" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000179", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000307", @@ -39809,7 +39963,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0011216" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000383", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000383", @@ -39917,6 +40071,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000481", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000479" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0000483", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000483", "pred" : "is_a", @@ -39931,7 +40089,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0005769" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000483", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208", "meta" : { "basicPropertyValues" : [ { @@ -40003,7 +40161,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0010316" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000923", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000924", @@ -40073,7 +40231,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0035804" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000930", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000941", @@ -40141,7 +40299,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0004151" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000948", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000948", @@ -40217,6 +40375,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000959", "pred" : "http://purl.obolibrary.org/obo/uberon/core#extends_fibers_into", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001908" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0000964", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000964", "pred" : "is_a", @@ -40429,7 +40591,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000467" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001009", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001009", @@ -40461,7 +40623,7 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0000540" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001016", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001016", @@ -40508,7 +40670,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0001016" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001017", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001017", @@ -40632,7 +40794,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000475" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001137", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001434", @@ -40680,7 +40842,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0001007" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001555", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001555", @@ -41672,6 +41834,10 @@ "val" : "ZFA" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001969", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001969", "pred" : "is_a", @@ -41688,6 +41854,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001969", "pred" : "http://purl.obolibrary.org/obo/RO_0002221", "obj" : "http://purl.obolibrary.org/obo/CL_0000232" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", "pred" : "is_a", @@ -41789,7 +41959,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0012275" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001986", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001986", @@ -41813,7 +41983,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0002298" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002028", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_89593" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002028", @@ -41911,7 +42081,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002193", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002200", @@ -42095,7 +42265,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0011137" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711", "meta" : { "basicPropertyValues" : [ { @@ -42147,7 +42317,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002329", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711", "meta" : { "basicPropertyValues" : [ { @@ -42192,7 +42362,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_89593" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", @@ -42246,7 +42416,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000479" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002384", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002385", @@ -42262,7 +42432,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0001015" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002385", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002385", @@ -42292,7 +42462,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002390", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002390", @@ -42360,7 +42530,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000033" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002546", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711", "meta" : { "basicPropertyValues" : [ { @@ -42495,7 +42665,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000926" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003068", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003068", @@ -42634,7 +42804,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0016879" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003075", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711", "meta" : { "basicPropertyValues" : [ { @@ -42755,7 +42925,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003081", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003081", @@ -42827,7 +42997,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003089", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742", "meta" : { "basicPropertyValues" : [ { @@ -42897,7 +43067,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000479" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003104", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003104", @@ -43093,7 +43263,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000064" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003891", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003891", @@ -43525,6 +43695,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004456", "pred" : "http://purl.obolibrary.org/obo/RO_0002492", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000066" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004535", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004535", "pred" : "is_a", @@ -43541,6 +43715,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004535", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001981" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004537", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004537", "pred" : "is_a", @@ -43643,7 +43821,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004770", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004770", @@ -43683,7 +43861,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0003068" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004880", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004905", @@ -43715,7 +43893,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000060" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004923", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005061", @@ -43779,7 +43957,7 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0000187" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005090", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005157", @@ -44049,6 +44227,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0005764", "pred" : "http://purl.obolibrary.org/obo/RO_0002007", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", "pred" : "is_a", @@ -44069,7 +44251,7 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0005587" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", @@ -44109,6 +44291,10 @@ "val" : "AEO-modified-relation" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0005906", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005906", "pred" : "is_a", @@ -44201,7 +44387,7 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0043209" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006135", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006222", @@ -44305,7 +44491,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0005423" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006268", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006268", @@ -44355,7 +44541,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0004921" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006562", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006595", @@ -44367,7 +44553,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000307" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006595", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006595", @@ -44399,7 +44585,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000307" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006601", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006601", @@ -44415,7 +44601,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000307" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006603", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006603", @@ -44437,6 +44623,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0006914", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/CL_0000076" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0006965", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006965", "pred" : "is_a", @@ -45402,7 +45592,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0011997", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0012275", @@ -45412,6 +45602,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0012275", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0004120" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0012430", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0012430", "pred" : "is_a", @@ -45490,7 +45684,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000475" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0013701", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0013702", @@ -45548,7 +45742,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0015212", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0015228", @@ -45746,7 +45940,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0015212" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0034713", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_89593" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0034713", @@ -47035,6 +47229,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0001981" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000076", + "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000066" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", + "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0006914" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000081", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000988" ], @@ -47088,7 +47289,7 @@ "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0002215", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0050962" + "fillerId" : "http://purl.obolibrary.org/obo/GO_0050908" } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000219", @@ -47120,7 +47321,7 @@ "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000255", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002160", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002162", "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" } ] }, { @@ -47155,7 +47356,7 @@ "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000365", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0010017" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002160", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002162", "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" } ] }, { @@ -48199,6 +48400,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/GO_0007600" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0050908", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009583" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0007601" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0050962", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009583" ], diff --git a/subsets/eye_upper_slim.obo b/subsets/eye_upper_slim.obo index 6947ccb4b..9b0a28e3c 100644 --- a/subsets/eye_upper_slim.obo +++ b/subsets/eye_upper_slim.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: cl/releases/2024-08-16/subsets/eye_upper_slim.owl +data-version: cl/releases/2024-09-26/subsets/eye_upper_slim.owl subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" subsetdef: attribute_slim "" @@ -19,6 +19,7 @@ subsetdef: eye_upper_slim "a subset of general classes related to specific cell subsetdef: functional_classification "" subsetdef: general_cell_types_upper_slim "a subset of general classes of cell types in the cell ontology." subsetdef: gocheck_do_not_annotate "" +subsetdef: gocheck_obsoletion_candidate "" subsetdef: goslim_agr "" subsetdef: goslim_candida "" subsetdef: goslim_chembl "" @@ -95,7 +96,7 @@ idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# idspace: sssom https://w3id.org/sssom/ idspace: terms http://purl.org/dc/terms/ ontology: cl/subsets/eye_upper_slim -property_value: owl:versionInfo "2024-08-16" xsd:string +property_value: owl:versionInfo "2024-09-26" xsd:string [Term] id: CL:0000000 @@ -118,7 +119,7 @@ is_a: UBERON:0000061 ! anatomical structure disjoint_from: GO:0031012 ! extracellular matrix disjoint_from: GO:0032991 ! protein-containing complex disjoint_from: GO:0043226 ! organelle -relationship: RO:0002160 NCBITaxon:131567 ! only in taxon cellular organisms +relationship: RO:0002162 NCBITaxon:131567 ! in taxon cellular organisms [Term] id: CL:0000005 @@ -163,6 +164,7 @@ name: glioblast subset: cellxgene_subset xref: ZFA:0009010 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell +is_a: CL:0000255 ! eukaryotic cell relationship: RO:0002202 CL:0000133 ! develops from neurectodermal cell [Term] @@ -176,7 +178,7 @@ xref: FMA:70563 xref: ZFA:0009011 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell is_a: CL:0000255 ! eukaryotic cell -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata [Term] id: CL:0000034 @@ -190,6 +192,7 @@ synonym: "animal stem cell" EXACT [] xref: CALOHA:TS-2086 xref: FMA:63368 xref: ZFA:0005957 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0011115 ! precursor cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0017145 ! stem cell division @@ -395,7 +398,7 @@ xref: FBbt:00000124 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ xref: FMA:66768 xref: WBbt:0003672 xref: ZFA:0009034 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell relationship: part_of UBERON:0000483 ! epithelium property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 @@ -411,7 +414,6 @@ is_a: CL:0002139 ! endothelial cell of vascular tree intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0001981 ! blood vessel relationship: part_of UBERON:0004638 ! blood vessel endothelium -relationship: RO:0002202 CL:0002546 ! develops from embryonic blood vessel endothelial progenitor cell property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -427,15 +429,20 @@ property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000076 name: squamous epithelial cell +def: "Any epithelial cell that is part of some squamous epithelium." [FBC:Autogenerated] subset: cellxgene_subset xref: CALOHA:TS-1249 xref: ZFA:0009039 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell +intersection_of: CL:0000066 ! epithelial cell +intersection_of: part_of UBERON:0006914 ! squamous epithelium +relationship: part_of UBERON:0006914 ! squamous epithelium [Term] id: CL:0000077 name: mesothelial cell -def: "A flattened epithelial cell of mesenchymal origin that lines the serous cavity." [GOC:tfm, ISBN:0721662544] +def: "A flat, squamous-like epithelial cell of mesodermal origin. It forms the mesothelium, which lines the body's serous cavities including the pleural, peritoneal, and pericardial spaces. This cell plays a crucial role in synthesizing and secreting lubricants, such as glycosaminoglycans and surfactants, which minimize friction between adjacent tissues during movement." [GOC:tfm, ISBN:0721662544, PMID:26106328] +comment: Mesothelial cells, which morphologically resemble squamous epithelial cells, express both epithelial markers (cytokeratins) and mesenchymal markers (vimentin), reflecting their mesodermal origin. They feature surface microvilli and apical-basal polarity. Under certain conditions, they can undergo mesothelial-to-mesenchymal transition. These cells also produce extracellular matrix proteins, maintain serosal homeostasis, and facilitate fluid transport. {xref="PMID:26106328"} subset: cellxgene_subset subset: human_reference_atlas synonym: "mesotheliocyte" EXACT [] @@ -444,6 +451,7 @@ xref: ZFA:0009040 {sssom:mapping_justification="https://w3id.org/semapv/vocab/Un is_a: CL:0000076 ! squamous epithelial cell is_a: CL:0000213 ! lining cell is_a: CL:0002078 ! meso-epithelial cell +relationship: part_of UBERON:0001136 ! mesothelium property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -524,6 +532,7 @@ xref: CALOHA:TS-0278 xref: FMA:66772 xref: ZFA:0009065 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000213 ! lining cell +is_a: CL:0000255 ! eukaryotic cell relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell property_value: RO:0002175 NCBITaxon:9606 @@ -540,8 +549,7 @@ id: CL:0000123 name: neuron associated cell (sensu Vertebrata) subset: cellxgene_subset is_a: CL:0000095 ! neuron associated cell -is_a: CL:0000255 ! eukaryotic cell -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002202 CL:0000333 ! develops from migratory neural crest cell [Term] @@ -558,9 +566,11 @@ xref: BTO:0002606 xref: CALOHA:TS-0415 xref: FBbt:00005144 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:54536 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000125 xref: ZFA:0009073 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000095 ! neuron associated cell property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nGlial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons.\nThese different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning.\nOligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. \nMicroglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response.\nDespite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis." xsd:string {xref="DOI:10.1002/glia.24343", xref="DOI:10.1038/nn1988", xref="DOI:10.1101/cshperspect.a020602", xref="DOI:10.1126/science.aat0473", xref="DOI:10.3389/fncel.2017.00024"} [Term] id: CL:0000126 @@ -665,6 +675,7 @@ xref: MESH:D008544 xref: VHOG:0001679 xref: ZFA:0009091 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000147 ! pigment cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000147 ! pigment cell intersection_of: has_part GO:0042470 ! melanosome intersection_of: RO:0002202 CL:0000541 ! develops from melanoblast @@ -712,6 +723,7 @@ xref: FMA:67328 xref: WBbt:0003675 xref: ZFA:0009114 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000183 ! contractile cell +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000393 ! electrically responsive cell relationship: RO:0002202 CL:0000056 ! develops from myoblast property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI @@ -742,7 +754,7 @@ name: sensory receptor cell def: "A cell that is capable of detection of a stimulus involved in sensory perception." [] synonym: "receptor cell" EXACT [] xref: MESH:D011984 -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0050906 ! detection of stimulus involved in sensory perception intersection_of: part_of UBERON:0001032 ! sensory system @@ -752,17 +764,18 @@ relationship: part_of UBERON:0001032 ! sensory system [Term] id: CL:0000210 name: photoreceptor cell -def: "A cell specialized to detect and transduce light." [MESH:D010786] +def: "A cell specialized in detecting light stimuli that are involved in visual perception." [MESH:D010786] subset: cellxgene_subset xref: BTO:0001060 xref: CALOHA:TS-0868 xref: FBbt:00004211 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:86740 xref: ZFA:0009127 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000006 {is_inferred="true"} ! neuronal receptor cell +is_a: CL:0000101 ! sensory neuron +is_a: CL:0008028 ! visual system neuron intersection_of: CL:0000540 ! neuron -intersection_of: capable_of GO:0050962 ! detection of light stimulus involved in sensory perception -relationship: capable_of GO:0050962 ! detection of light stimulus involved in sensory perception +intersection_of: capable_of GO:0050908 ! detection of light stimulus involved in visual perception +relationship: capable_of GO:0050908 ! detection of light stimulus involved in visual perception property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg" xsd:anyURI [Term] @@ -804,6 +817,7 @@ def: "A cell of the outer of the three germ layers of the embryo." [MESH:D004475 synonym: "ectoderm cell" EXACT [] xref: FMA:72549 xref: ZFA:0009137 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000924 ! ectoderm @@ -816,6 +830,7 @@ synonym: "mesoblast" EXACT [] synonym: "mesoderm cell" EXACT [] xref: FMA:72554 xref: ZFA:0009138 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000926 ! mesoderm @@ -826,6 +841,7 @@ def: "A cell of the inner of the three germ layers of the embryo." [MESH:D004707 synonym: "endoderm cell" EXACT [] xref: FMA:72555 xref: ZFA:0009139 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000925 ! endoderm @@ -859,13 +875,13 @@ property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000255 name: eukaryotic cell -def: "Any cell that only exists in Eukaryota." [FBC:Autogenerated] +def: "Any cell that in taxon some Eukaryota." [FBC:Autogenerated] subset: cellxgene_subset xref: MESH:D005057 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell -intersection_of: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota -relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +intersection_of: RO:0002162 NCBITaxon:2759 ! in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 ! in taxon Eukaryota [Term] id: CL:0000287 @@ -875,6 +891,7 @@ subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas xref: ZFA:0009154 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000006 ! neuronal receptor cell is_a: CL:0000210 ! photoreceptor cell intersection_of: CL:0000210 ! photoreceptor cell intersection_of: part_of UBERON:0000970 ! eye @@ -948,7 +965,7 @@ def: "Any animal cell containing pigment granules." [GOC:tfm, ISBN:0721662544] xref: ZFA:0009170 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000147 ! pigment cell is_a: CL:0000255 ! eukaryotic cell -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata [Term] id: CL:0000347 @@ -956,6 +973,7 @@ name: scleral cell def: "A cell of the sclera of the eye." [GOC:add] subset: eye_upper_slim xref: ZFA:0009174 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000293 ! structural cell intersection_of: CL:0000293 ! structural cell intersection_of: part_of UBERON:0001773 ! sclera @@ -968,6 +986,7 @@ name: choroidal cell of the eye def: "A structural cell that is part of optic choroid." [GOC:add] subset: eye_upper_slim xref: ZFA:0009175 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000293 ! structural cell intersection_of: CL:0000293 ! structural cell intersection_of: part_of UBERON:0001776 ! optic choroid @@ -992,8 +1011,8 @@ is_a: CL:0000007 ! early embryonic cell (metazoa) is_a: CL:0000255 ! eukaryotic cell is_a: CL:0010017 ! zygote intersection_of: CL:0010017 ! zygote -intersection_of: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa -relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +intersection_of: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa [Term] id: CL:0000393 @@ -1100,6 +1119,7 @@ synonym: "rubriblast" EXACT [ISBN:0721601464] xref: FMA:83518 is_a: CL:0000764 {is_inferred="true"} ! erythroid lineage cell is_a: CL:0002242 ! nucleate cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000764 ! erythroid lineage cell intersection_of: bearer_of PATO:0002505 ! nucleated intersection_of: bearer_of PATO:0040072 ! high nuclear/cytoplasmic ratio @@ -1145,6 +1165,7 @@ synonym: "prorubricyte" EXACT [ISBN:0721601464] xref: FMA:83505 xref: ZFA:0005236 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000765 {is_inferred="true"} ! erythroblast +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017503 ! basophilic cytoplasm intersection_of: has_part GO:0000792 ! heterochromatin @@ -1166,6 +1187,7 @@ synonym: "rubricyte" EXACT [ISBN:0721601464] xref: FMA:83506 xref: ZFA:0005241 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000765 {is_inferred="true"} ! erythroblast +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017504 ! polychromatophilic cytoplasm intersection_of: has_part GO:0000792 ! heterochromatin @@ -1279,6 +1301,7 @@ xref: CALOHA:TS-0864 xref: MESH:D012156 xref: ZFA:0009252 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000764 {is_inferred="true"} ! erythroid lineage cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000764 ! erythroid lineage cell intersection_of: capable_of GO:0071971 ! extracellular exosome assembly intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -1338,6 +1361,7 @@ synonym: "chondroplast" EXACT [] xref: ZFA:0009258 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000134 {is_inferred="true"} ! mesenchymal stem cell is_a: CL:0011026 ! progenitor cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: RO:0002104 PR:000001444 ! has plasma membrane part cadherin-5 intersection_of: RO:0002104 PR:000002112 ! has plasma membrane part vascular endothelial growth factor receptor 2 @@ -1436,6 +1460,7 @@ def: "A non-terminally differentiated cell that is capable of developing into a subset: cellxgene_subset xref: ZFA:0009291 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0011115 ! precursor cell intersection_of: RO:0002203 CL:0000187 ! develops into muscle cell relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell @@ -1542,6 +1567,7 @@ xref: BTO:0001441 xref: CALOHA:TS-0647 xref: MESH:D022423 xref: ZFA:0009324 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000988 {is_inferred="true"} ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: RO:0002202 CL:0000049 ! develops from common myeloid progenitor @@ -1620,7 +1646,9 @@ synonym: "MPP" EXACT [] xref: BTO:0000725 xref: CALOHA:TS-0448 xref: ZFA:0009354 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001402 ! multipotent intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -1695,6 +1723,7 @@ id: CL:0002031 name: hematopoietic lineage restricted progenitor cell def: "A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells." [GOC:tfm, PMID:19022770] subset: blood_and_immune_upper_slim +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001400 ! unipotent @@ -1710,6 +1739,7 @@ name: hematopoietic oligopotent progenitor cell def: "A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities." [GOC:tfm, https://orcid.org/0000-0001-5208-3432, PMID:19022770] comment: This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). subset: blood_and_immune_upper_slim +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001401 ! oligopotent @@ -1803,10 +1833,12 @@ subset: eye_upper_slim subset: human_reference_atlas synonym: "PE cell" EXACT [https://doi.org/10.1016/j.exer.2003.09.021] xref: FMA:70606 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002303 is_a: CL:0000529 ! pigmented epithelial cell relationship: part_of UBERON:0001778 ! ciliary epithelium property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nPigmented ciliary epithelial cells, which are a type of pigment cell, have a crucial function within the eye's ciliary body. The ciliary body, located behind the iris, is one of the eye’s most vital structures and consists of two types of epithelial cells: the pigmented and the non-pigmented ciliary epithelial cells. The pigmented ciliary epithelial cells form the outer layer of the ciliary body and exhibit a black or brown pigmentation due to the melanin they contain.\nOne key function of pigmented ciliary epithelial cells is to aid in the formation of aqueous humor, an intraocular fluid that nourishes the cornea and lens, and maintains intraocular pressure which is essential for the eye’s shape and light refraction. These cells facilitate this function in conjunction with the non-pigmented ciliary epithelial cells. Together, the pigmented and non-pigmented ciliary epithelial cells form a bilayer epithelium that allows the secretion of aqueous humor through a bi-directional fluid transport mechanism.\nPigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, a physiological frontier that controls the entry and exit of various substances from the blood to the aqueous humor and vice versa. The pigmentation in these cells, intensified by melanin, helps to absorb scattered light coming into the eye, reducing any potential damage and glare." xsd:string {xref="DOI:10.1016/S1569-2590(05)10005-6", xref="DOI:10.1111/j.1444-0938.2002.tb02384.x"} creation_date: 2010-09-13T04:09:27Z [Term] @@ -1833,7 +1865,7 @@ def: "A cell that is part of the nervous system." [GOC:tfm, ISBN:0618947256] subset: cellxgene_subset xref: CALOHA:TS-2040 xref: FMA:70333 -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001016 ! nervous system relationship: part_of UBERON:0001016 ! nervous system @@ -1849,7 +1881,7 @@ xref: CALOHA:TS-2096 xref: FMA:63875 xref: MESH:D003239 xref: ZFA:0009392 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0002384 ! connective tissue relationship: part_of UBERON:0002384 ! connective tissue @@ -1908,23 +1940,13 @@ xref: BTO:0001539 xref: CALOHA:TS-0115 xref: FMA:83808 xref: FMA:84791 -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0007100 ! primary circulatory organ relationship: part_of UBERON:0007100 ! primary circulatory organ property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2010-12-07T09:37:22Z -[Term] -id: CL:0002546 -name: embryonic blood vessel endothelial progenitor cell -def: "An endothelial progenitor cell that participates in angiogenesis during development." [GOC:tfm] -comment: See CL:0002619. -xref: ZFA:0005773 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000222 ! mesodermal cell -property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 -creation_date: 2011-02-28T04:20:39Z - [Term] id: CL:0002565 name: iris pigment epithelial cell @@ -1947,6 +1969,7 @@ def: "A blood vessel endothelial cell that is part of the retina." [GOC:tfm] subset: cellxgene_subset subset: eye_upper_slim subset: human_reference_atlas +xref: https://cellxgene.cziscience.com/cellguide/CL_0002585 is_a: CL:0000071 {is_inferred="true"} ! blood vessel endothelial cell is_a: CL:0009004 ! retinal cell intersection_of: CL:0000071 ! blood vessel endothelial cell @@ -1954,6 +1977,7 @@ intersection_of: part_of UBERON:0000966 ! retina relationship: part_of UBERON:0000966 ! retina property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nRetinal blood vessel endothelial cells constitute the innermost lining of the blood vessels found in the retina, the light-sensitive layer of tissue at the back of the eye. The primary role of these cells revolves around their location within the retinal vascular system, forming the structure of the blood-retinal barrier, a subset of the larger blood-ocular barrier system. \nThe endothelial cells are particularly involved in the growth of new retinal blood vessels from pre-existing ones (angiogenesis); this is critical in managing the amount of oxygen and essential nutrients delivered to the ocular tissues. They are crucial for maintaining homeostasis in the retinal environment by controlling the exchange of molecules between the blood and the retina. Furthermore, they mediate immune cell trafficking, supporting the immune privilege of the eye by preventing the unrestricted infiltration of inflammatory cells into the retina, thus maintaining ocular health and normal vision.\nThe malfunction or dysfunction of retinal blood vessel endothelial cells is implicated in numerous ocular pathologies, particularly diabetic retinopathy, which is one of the leading causes of blindness worldwide. In such conditions, the compromise in the integrity of the blood-retinal barrier and excess angiogenesis can lead to retinal edema and pathological neovascularization, resulting in vision loss." xsd:string {xref="DOI:0.1016/j.preteyeres.2015.08.001", xref="DOI:10.1016/j.preteyeres.2012.08.004", xref="DOI:10.1038/nature04482", xref="DOI:10.5301/EJO.2010.6049"} creation_date: 2011-03-06T03:28:27Z [Term] @@ -1965,6 +1989,7 @@ subset: eye_upper_slim subset: human_reference_atlas xref: BTO:0004910 xref: FMA:75802 +xref: https://cellxgene.cziscience.com/cellguide/CL_0002586 is_a: CL:0000066 ! epithelial cell is_a: CL:0000149 ! visual pigment cell is_a: CL:0009004 ! retinal cell @@ -1974,6 +1999,7 @@ relationship: has_part GO:0042470 ! melanosome relationship: part_of UBERON:0001782 ! pigmented layer of retina property_value: RO:0002175 NCBITaxon:9606 property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nRetinal pigment epithelial (RPE) cells form a single layer of cells at the back of the eye sandwiched between the neurosensory retina and the choroid, playing a significant role in maintaining vision health. These pigment-laden cells are highly specialized and perform an array of metabolic and transport functions essential for the maintenance of the photoreceptor cells (rods and cones) in the retina. The pigmentation of RPE cells actively aids in the absorption of excess light and the prevention of light scattering, thus enhancing the eye's optical properties.\nThe retinal pigment epithelium forms a key part of the blood/retina barrier. The cells have long sheet-like microvilli on their apical membrane that project into the light-sensitive outer segments of the photoreceptors, forming a close structural interaction. The basolateral membrane of the RPE interacts with the underlying Bruch’s membrane, which separates the RPE cells from fenestrated endothelium of the choriocapillaris. \nRPE cells support the photoreceptor by providing them with oxygen and nutrients (such as glucose, retinol and fatty acids) and removing waste products. They also recycle the visual pigment, in a process called the \"visual cycle\", where the RPE cells play a vital role in the regeneration of visual pigment (11-cis retinol) following the absorption of light. This is essential for the maintenance of photoreceptor excitability.\nBeyond this, RPE cells take part in the phagocytosis process, where they digest the shed ends of photoreceptor outer segments, thus, preventing the build-up of waste residue that could otherwise harm retinal health. They also secrete various factors, including growth factors required to maintain the structural integrity of choriocapillaris endothelium and photoreceptors, as well as immunosuppressive factors that play an important role in establishing the immune privilege of the eye." xsd:string {xref="DOI:10.1111/febs.16018", xref="DOI:10.1152/physrev.00021.2004", xref="DOI:10.3389/fphar.2021.727870/full", xref="https://www.sciencedirect.com/topics/chemistry/retinal-pigment"} creation_date: 2011-03-06T03:37:09Z [Term] @@ -2038,6 +2064,7 @@ subset: cellxgene_subset subset: human_reference_atlas synonym: "mesenchyme cell" EXACT [] is_a: CL:0000219 ! motile cell +is_a: CL:0000255 ! eukaryotic cell relationship: capable_of GO:0016477 ! cell migration relationship: part_of UBERON:0003104 ! mesenchyme property_value: RO:0002175 NCBITaxon:9606 @@ -2088,14 +2115,17 @@ id: CL:0011012 name: neural crest cell def: "A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells." [https://orcid.org/0000-0001-5208-3432, https://orcid.org/0000-0002-9900-7880] subset: cellxgene_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_0011012 is_a: CL:0000048 ! multi fate stem cell is_a: CL:0002321 ! embryonic cell (metazoa) +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." xsd:string {xref="DOI:10.1002/dvg.23276", xref="DOI:10.1242/dev.193193", xref="DOI:10.3389/fcell.2020.00635/full", xref="https://doi.org/10.1016/j.ydbio.2011.12.042"} [Term] id: CL:0011026 name: progenitor cell def: "A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses." [https://doi.org/10.1016/B978-0-12-409503-8.00002-0, ISBN:978-1-62808-994-3] subset: cellxgene_subset +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0011115 ! precursor cell intersection_of: CL:0011115 ! precursor cell intersection_of: RO:0002202 CL:0000034 ! develops from stem cell @@ -2265,8 +2295,9 @@ synonym: "chromosome scaffold" RELATED [] synonym: "cytoplasmic chromatin" NARROW [] synonym: "nuclear chromatin" NARROW [] xref: NIF_Subcellular:sao1615953555 -is_a: GO:0032993 ! protein-DNA complex +is_a: GO:0110165 ! cellular anatomical entity relationship: part_of GO:0005694 ! chromosome +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28301" xsd:anyURI [Term] id: GO:0000792 @@ -2711,8 +2742,8 @@ synonym: "ribosomal RNA" RELATED [] xref: NIF_Subcellular:sao1429207766 xref: Wikipedia:Ribosome is_a: GO:0043232 ! intracellular non-membrane-bounded organelle +is_a: PR:000050567 ! protein-containing material entity relationship: capable_of_part_of GO:0006412 ! translation -relationship: has_part PR:000000001 ! protein [Term] id: GO:0005886 @@ -3652,6 +3683,9 @@ is_a: GO:0051301 ! cell division intersection_of: GO:0051301 ! cell division intersection_of: has_primary_input CL:0000034 ! stem cell relationship: has_primary_input CL:0000034 ! stem cell +property_value: RO:0002161 NCBITaxon:2 +property_value: RO:0002161 NCBITaxon:2157 +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0019226 @@ -4186,18 +4220,8 @@ synonym: "protein complex" NARROW [] synonym: "protein containing complex" EXACT [] synonym: "protein-protein complex" NARROW [] is_a: GO:0005575 ! cellular_component +is_a: PR:000050567 ! protein-containing material entity disjoint_from: GO:0110165 ! cellular anatomical entity -relationship: has_part PR:000000001 ! protein - -[Term] -id: GO:0032993 -name: protein-DNA complex -namespace: cellular_component -def: "A macromolecular complex containing both protein and DNA molecules." [GOC:mah] -comment: Note that this term is intended to classify complexes that have DNA as one of the members of the complex, that is, the complex does not exist if DNA is not present. Protein complexes that interact with DNA e.g. transcription factor complexes should not be classified here. -subset: goslim_pir -synonym: "DNA-protein complex" EXACT [GOC:mah] -is_a: GO:0032991 ! protein-containing complex [Term] id: GO:0034101 @@ -4448,6 +4472,7 @@ id: GO:0043227 name: membrane-bounded organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane." [GOC:go_curators] +subset: gocheck_do_not_annotate synonym: "membrane-enclosed organelle" EXACT [] xref: NIF_Subcellular:sao414196390 is_a: GO:0043226 ! organelle @@ -4455,30 +4480,35 @@ intersection_of: GO:0043226 ! organelle intersection_of: has_part GO:0016020 ! membrane disjoint_from: GO:0043228 ! non-membrane-bounded organelle relationship: has_part GO:0016020 ! membrane +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI [Term] id: GO:0043228 name: non-membrane-bounded organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:go_curators] +subset: gocheck_do_not_annotate subset: goslim_mouse synonym: "biological condensate" RELATED [] synonym: "non-membrane-enclosed organelle" EXACT [] xref: NIF_Subcellular:sao1456184038 is_a: GO:0043226 ! organelle property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21881" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI [Term] id: GO:0043229 name: intracellular organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:go_curators] +subset: gocheck_do_not_annotate subset: goslim_pir is_a: GO:0043226 ! organelle intersection_of: GO:0043226 ! organelle intersection_of: part_of GO:0005622 ! intracellular anatomical structure disjoint_from: GO:0043230 ! extracellular organelle relationship: part_of GO:0005622 ! intracellular anatomical structure +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI [Term] id: GO:0043230 @@ -4587,9 +4617,11 @@ name: cellular component biogenesis namespace: biological_process alt_id: GO:0071843 def: "A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component." [GOC:jl, GOC:mah] +subset: gocheck_do_not_annotate subset: goslim_pir synonym: "cellular component biogenesis at cellular level" EXACT [] is_a: GO:0071840 ! cellular component organization or biogenesis +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27194" xsd:anyURI [Term] id: GO:0044207 @@ -4954,6 +4986,23 @@ intersection_of: GO:0051606 ! detection of stimulus intersection_of: part_of GO:0007600 ! sensory perception relationship: part_of GO:0007600 ! sensory perception +[Term] +id: GO:0050908 +name: detection of light stimulus involved in visual perception +namespace: biological_process +def: "The series of events involved in visual perception in which a light stimulus is received and converted into a molecular signal." [GOC:ai, GOC:dos] +synonym: "sensory detection of light during visual perception" EXACT [] +synonym: "sensory detection of light stimulus during visual perception" EXACT [] +synonym: "sensory transduction of light during visual perception" EXACT [] +synonym: "sensory transduction of light stimulus during visual perception" EXACT [] +synonym: "visual perception, detection of light stimulus" EXACT [] +synonym: "visual perception, sensory transduction during perception of light" EXACT [] +synonym: "visual perception, sensory transduction of light stimulus" EXACT [] +is_a: GO:0050962 ! detection of light stimulus involved in sensory perception +intersection_of: GO:0009583 ! detection of light stimulus +intersection_of: part_of GO:0007601 ! visual perception +relationship: part_of GO:0007601 ! visual perception + [Term] id: GO:0050953 name: sensory perception of light stimulus @@ -5531,6 +5580,7 @@ def: "A complex of collagen trimers such as a fibril or collagen network." [GOC: synonym: "Supramolecular aggregate of collagen" EXACT [PMID:19693541] synonym: "Supramolecular collagen assembly" EXACT [PMID:21421911] is_a: GO:0099080 ! supramolecular complex +is_a: PR:000050567 ! protein-containing material entity relationship: has_part GO:0005581 ! collagen trimer relationship: part_of GO:0062023 ! collagen-containing extracellular matrix @@ -6631,7 +6681,7 @@ creation_date: 2014-12-12T08:43:17Z id: PATO:0010006 name: cell morphology namespace: quality -def: "A quality of a single cell inhering in the bearer by virtue of the bearer's size or shape or structure." [ORCID:0000-0002-7073-9172] +def: "A quality of a single cell inhering in the bearer by virtue of the bearer's size or shape or structure." [https://orcid.org/0000-0002-7073-9172] comment: Use this term for morphologies that can *only* inhere in a cell, e.g. morphological qualities inhering in a cell by virtue of the presence, location or shape of one or more cell parts. is_a: PATO:0000051 ! morphology property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 @@ -6718,7 +6768,7 @@ comment: The definition above excludes protein complexes, which some also consid synonym: "native protein" NARROW [IEDB:BP] synonym: "natural protein" EXACT [PRO:DAN] is_a: PR:000018263 ! amino acid chain -is_a: PR:000064867 ! protein-containing molecular entity +is_a: PR:000050567 ! protein-containing material entity relationship: output_of GO:0006412 ! translation [Term] @@ -7109,11 +7159,11 @@ intersection_of: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota [Term] -id: PR:000064867 -name: protein-containing molecular entity +id: PR:000050567 +name: protein-containing material entity namespace: protein -def: "A molecular entity that minimally consists of a protein." [PRO:DAN] -comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). +def: "A material entity that minimally consists of a protein." [PRO:DAN] +comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566). synonym: "protein" NARROW [PRO:DAN] synonym: "protein aggregate" NARROW [PRO:DAN] synonym: "protein complex" NARROW [PRO:DAN] @@ -7270,7 +7320,7 @@ xref: XAO:0003024 xref: ZFA:0001114 is_a: UBERON:0011676 ! subdivision of organism along main body axis relationship: part_of UBERON:0007811 ! craniocervical region -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria [Term] id: UBERON:0000042 @@ -7291,6 +7341,7 @@ xref: TAO:0005425 xref: UMLS:C0036760 {source="ncithesaurus:Serosa"} xref: Wikipedia:Serous_membrane xref: ZFA:0005425 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000481 ! multi-tissue structure is_a: UBERON:0004120 ! mesoderm-derived structure relationship: has_part UBERON:0001136 ! mesothelium @@ -7538,7 +7589,7 @@ xref: SCTID:118966000 xref: UMLS:C1519343 {source="ncithesaurus:Skeletal_System_Part"} is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision relationship: part_of UBERON:0001434 ! skeletal system -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002473 UBERON:0004765 ! composed primarily of skeletal element [Term] @@ -7747,7 +7798,7 @@ is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000108 {source="BILS"} ! blastula stage relationship: RO:0002082 GO:0007369 ! simultaneous with gastrulation -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0000110 @@ -7763,7 +7814,7 @@ is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000109 ! gastrula stage relationship: RO:0002082 GO:0001841 ! simultaneous with neural tube formation -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: seeAlso "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/343" xsd:anyURI @@ -7783,7 +7834,7 @@ xref: Wikipedia:Organogenesis is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: RO:0002082 GO:0048513 ! simultaneous with animal organ development -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: seeAlso "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/533" xsd:anyURI @@ -7809,14 +7860,14 @@ name: anterior region of body namespace: uberon is_a: UBERON:0000475 ! organism subdivision disjoint_from: UBERON:0000154 {source="lexical"} ! posterior region of body -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria [Term] id: UBERON:0000154 name: posterior region of body namespace: uberon is_a: UBERON:0000475 ! organism subdivision -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria [Term] id: UBERON:0000165 @@ -7872,7 +7923,7 @@ xref: XAO:0003029 xref: ZFA:0000547 xref: ZFA:0000590 is_a: UBERON:0004921 ! subdivision of digestive tract -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002202 UBERON:0035804 ! develops from future mouth property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/661" xsd:anyURI @@ -7912,6 +7963,7 @@ xref: VHOG:0000224 xref: Wikipedia:Blood xref: XAO:0000124 xref: ZFA:0000007 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000179 ! haemolymphatic fluid relationship: has_part CL:0000232 {source="CL:tm"} ! erythrocyte relationship: has_part UBERON:0001969 ! blood plasma @@ -7932,7 +7984,7 @@ is_a: UBERON:0006314 ! bodily fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: part_of UBERON:0002193 ! hemolymphoid system relationship: part_of UBERON:0002193 ! hemolymphoid system -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: terms:contributor https://orcid.org/0000-0002-6601-2165 creation_date: 2009-04-08T04:38:19Z @@ -7990,7 +8042,7 @@ is_a: UBERON:0011216 ! organ system subdivision intersection_of: UBERON:0011216 ! organ system subdivision intersection_of: RO:0002473 UBERON:0001015 ! composed primarily of musculature relationship: capable_of GO:0003012 ! muscle system process -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002473 UBERON:0001015 ! composed primarily of musculature property_value: IAO:0000116 "consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77" xsd:string property_value: RO:0002161 NCBITaxon:6040 @@ -8404,12 +8456,13 @@ xref: VHOG:0000387 xref: Wikipedia:Epithelium xref: XAO:0003045 xref: ZFA:0001486 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: RO:0002473 CL:0000066 ! composed primarily of epithelial cell relationship: has_part GO:0005911 ! cell-cell junction relationship: has_part UBERON:0005769 ! basement membrane of epithelium -relationship: RO:0002160 NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! in taxon Metazoa relationship: RO:0002473 CL:0000066 ! composed primarily of epithelial cell property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI @@ -8612,7 +8665,7 @@ xref: Wikipedia:Germ_layer xref: XAO:0003011 xref: ZFA:0001122 is_a: UBERON:0010316 ! germ layer / neural crest -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0000924 @@ -8766,7 +8819,7 @@ xref: ZFA:0001290 is_a: UBERON:0013522 ! subdivision of tube relationship: part_of UBERON:0000924 ! ectoderm relationship: part_of UBERON:0035804 ! future mouth -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI property_value: IAO:0000116 "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" xsd:string @@ -8879,7 +8932,7 @@ intersection_of: UBERON:0007100 ! primary circulatory organ intersection_of: has_part UBERON:0004151 ! cardiac chamber relationship: has_part UBERON:0004151 ! cardiac chamber relationship: part_of UBERON:0015410 {source="MA"} ! heart plus pericardium -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002202 UBERON:0004141 ! develops from heart tube relationship: RO:0002433 UBERON:0004535 ! contributes to morphology of cardiovascular system property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/heart-female/v1.3/assets/3d-vh-f-heart.glb" xsd:anyURI @@ -9056,6 +9109,7 @@ xref: VHOG:0000164 xref: Wikipedia:Cornea xref: XAO:0000180 xref: ZFA:0000640 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0010000 ! multicellular anatomical structure is_a: UBERON:0010313 ! neural crest-derived structure relationship: has_part UBERON:0001772 ! corneal epithelium @@ -9311,7 +9365,7 @@ disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of GO:0003013 ! circulatory system process -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} @@ -9361,7 +9415,6 @@ namespace: uberon def: "The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]." [BIRNLEX:844, ISBN:0-14-051288-8, ISBN:3110148986, NLM:nervous+system, WB:rynl, Wikipedia:Nervous_system, ZFIN:curator] subset: cumbo subset: efo_slim -subset: human_reference_atlas subset: pheno_slim subset: uberon_slim subset: vertebrate_core @@ -9402,14 +9455,13 @@ disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of GO:0050877 ! nervous system process relationship: has_part CL:0000540 ! neuron -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002473 CL:0002319 ! composed primarily of neural cell relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage relationship: RO:0002495 UBERON:0016880 {source="Bgee:AN"} ! immediate transformation of future nervous system property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:6040 -property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001017 @@ -9456,7 +9508,7 @@ xref: ZFA:0000012 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0011216 {source="FBbt", source="cjm"} ! organ system subdivision relationship: part_of UBERON:0001016 ! nervous system -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria relationship: RO:0002495 UBERON:0016879 {source="Bgee:AN"} ! immediate transformation of future central nervous system property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} property_value: RO:0002175 NCBITaxon:9606 @@ -9743,7 +9795,7 @@ xref: SCTID:123961009 xref: UMLS:C0004600 {source="ncithesaurus:Back"} xref: Wikipedia:Dorsum_(anatomy) is_a: UBERON:0000475 ! organism subdivision -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/e/ee/432px-Gray-back.PNG" xsd:anyURI [Term] @@ -9861,7 +9913,7 @@ xref: WBbt:0005743 xref: ZFA:0000112 is_a: UBERON:0000025 ! tube relationship: part_of UBERON:0001007 ! digestive system -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002176 UBERON:0000165 ! connects mouth relationship: RO:0002495 UBERON:0007026 {source="NCBIBook:NBK10107"} ! immediate transformation of presumptive gut property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} @@ -11254,6 +11306,7 @@ xref: MIAA:0000052 xref: NCIT:C13356 xref: UMLS:C0032105 {source="ncithesaurus:Plasma"} xref: Wikipedia:Blood_plasma +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000179 ! haemolymphatic fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: has_part GO:0005577 ! fibrinogen complex @@ -11302,6 +11355,7 @@ xref: VHOG:0001250 xref: Wikipedia:Blood_vessel xref: XAO:0001011 xref: ZFA:0005314 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000055 ! vessel is_a: UBERON:0004120 ! mesoderm-derived structure relationship: capable_of_part_of GO:0008015 ! blood circulation @@ -11374,7 +11428,7 @@ is_a: UBERON:0000487 {source="FMA-text-def", source="https://github.com/obopheno is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: RO:0002473 CL:0000115 ! composed primarily of endothelial cell -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002473 CL:0000115 ! composed primarily of endothelial cell property_value: RO:0002175 NCBITaxon:9606 @@ -11454,7 +11508,7 @@ xref: XAO:0000015 xref: ZFA:0000029 is_a: UBERON:0002616 ! regional part of brain relationship: overlaps UBERON:0002298 ! brainstem -relationship: RO:0002160 NCBITaxon:89593 ! only in taxon Craniata +relationship: RO:0002162 NCBITaxon:89593 ! in taxon Craniata relationship: RO:0002433 UBERON:0000955 ! contributes to morphology of brain relationship: RO:0002495 UBERON:0007277 {source="Bgee:AN"} ! immediate transformation of presumptive hindbrain property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg" xsd:anyURI @@ -11658,7 +11712,7 @@ xref: EMAPA:18765 xref: FMA:74562 xref: MA:0000013 is_a: UBERON:0000467 {source="MA"} ! anatomical system -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria [Term] id: UBERON:0002200 @@ -11998,7 +12052,7 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0011137 ! axial skeletal system relationship: produces PR:000014841 ! sonic hedgehog protein -relationship: RO:0002160 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! in taxon Chordata relationship: RO:0002202 UBERON:0004880 {source="ZFA"} ! develops from chordamesoderm relationship: RO:0002202 UBERON:0006267 {source="EHDAA2"} ! develops from notochordal plate relationship: RO:0002488 UBERON:0000068 ! existence starts during embryo stage @@ -12041,7 +12095,7 @@ xref: XAO:0000058 xref: ZFA:0000155 is_a: UBERON:0005423 ! developing anatomical structure is_a: UBERON:0007503 {source="EHDAA2"} ! epithelial vesicle -relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {source="GOTAX:0000352"} ! in taxon Chordata relationship: RO:0002202 UBERON:0003059 {source="ZFA"} ! develops from presomitic mesoderm property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:7712 {source="PMID:17237766"} @@ -12080,7 +12134,7 @@ is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0010316 ! germ layer / neural crest relationship: part_of UBERON:0002346 {source="XAO", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! neurectoderm -relationship: RO:0002160 NCBITaxon:89593 ! only in taxon Craniata +relationship: RO:0002162 NCBITaxon:89593 ! in taxon Craniata relationship: RO:0002202 UBERON:0003075 {source="BTO"} ! develops from neural plate relationship: RO:0002202 UBERON:0005062 {source="PMID:11523831"} ! develops from neural fold relationship: RO:0002473 CL:0000333 ! composed primarily of migratory neural crest cell @@ -12156,7 +12210,7 @@ xref: VSAO:0000017 xref: XAO:0001017 xref: ZFA:0001632 is_a: UBERON:0000479 ! tissue -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -12189,7 +12243,7 @@ intersection_of: RO:0002473 CL:0000187 ! composed primarily of muscle cell disjoint_from: UBERON:0003714 ! neural tissue relationship: capable_of GO:0006936 ! muscle contraction relationship: part_of UBERON:0001015 ! musculature -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002473 CL:0000187 ! composed primarily of muscle cell [Term] @@ -12234,7 +12288,7 @@ is_a: UBERON:0000467 ! anatomical system is_a: UBERON:0004120 ! mesoderm-derived structure disjoint_from: UBERON:0004456 ! entire sense organ system relationship: part_of UBERON:0002193 {source="FMA"} ! hemolymphoid system -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002202 UBERON:0003061 ! develops from blood island property_value: RO:0002175 NCBITaxon:9606 @@ -12307,7 +12361,7 @@ xref: MIAA:0000369 xref: XAO:0000305 is_a: UBERON:0005085 {source="cjm"} ! ectodermal placode relationship: part_of UBERON:0000033 ! head -relationship: RO:0002160 NCBITaxon:7711 {source="PMID:11523831", source="PMID:22512454"} ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {source="PMID:11523831", source="PMID:22512454"} ! in taxon Chordata property_value: IAO:0000116 "Do not merge with neurogenic placode" xsd:string [Term] @@ -12496,7 +12550,7 @@ xref: XAO:0000205 xref: ZFA:0001204 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0000926 ! mesoderm -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002202 UBERON:0000926 ! develops from mesoderm property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI @@ -12627,7 +12681,7 @@ xref: ZFA:0000132 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0016879 ! future central nervous system -relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {source="GOTAX:0000352"} ! in taxon Chordata relationship: RO:0002256 UBERON:0002328 {source="Wikipedia"} ! developmentally induced by notochord relationship: RO:0002495 UBERON:0007284 {source="Bgee:AN"} ! immediate transformation of presumptive neural plate property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI @@ -12722,7 +12776,7 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue relationship: part_of UBERON:0000926 {source="EHDAA2", source="VHOG"} ! mesoderm -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria relationship: RO:0002221 UBERON:0003887 ! surrounds intraembryonic coelom property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI @@ -12772,7 +12826,7 @@ xref: XAO:0000397 xref: ZFA:0001080 is_a: UBERON:0005856 {source="EHDAA2"} ! developing mesenchymal condensation is_a: UBERON:0007530 {source="EHDAA2"} ! migrating mesenchyme population -relationship: RO:0002160 NCBITaxon:7742 {source="VHOG:0000680"} ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 {source="VHOG:0000680"} ! in taxon Vertebrata relationship: RO:0002202 UBERON:0002329 {source="ZFA"} ! develops from somite property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI @@ -12885,7 +12939,7 @@ xref: ZFA:0000393 is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002328 GO:0032502 ! functionally related to developmental process relationship: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI @@ -13146,7 +13200,7 @@ xref: FMA:81494 xref: NCIT:C67387 xref: UMLS:C0927195 {source="ncithesaurus:Stroma_Connective_Tissue"} is_a: UBERON:0000064 ! organ part -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002473 UBERON:0002384 ! composed primarily of connective tissue [Term] @@ -13661,6 +13715,7 @@ xref: WikipediaCategory:Cardiovascular_system xref: XAO:0000100 xref: XAO:0001010 xref: ZFA:0000010 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000467 ! anatomical system intersection_of: UBERON:0000467 ! anatomical system intersection_of: has_part UBERON:0000948 ! heart @@ -13684,6 +13739,7 @@ synonym: "blood vessels" RELATED [TAO:0001079] synonym: "set of blood vessels" EXACT [] xref: TAO:0001079 xref: ZFA:0001079 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel @@ -13833,7 +13889,7 @@ is_a: UBERON:0034925 ! anatomical collection intersection_of: UBERON:0034925 ! anatomical collection intersection_of: RO:0002351 UBERON:0000982 ! has member skeletal joint relationship: part_of UBERON:0001434 {source="FMA"} ! skeletal system -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria relationship: RO:0002328 GO:0040011 ! functionally related to locomotion relationship: RO:0002351 UBERON:0000982 ! has member skeletal joint relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage @@ -13897,7 +13953,7 @@ xref: TAO:0000091 xref: ZFA:0000091 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0003068 ! axial mesoderm -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata [Term] id: UBERON:0004905 @@ -13940,7 +13996,7 @@ subset: upper_level xref: FMA:82485 is_a: UBERON:0000064 ! organ part relationship: part_of UBERON:0000060 ! anatomical wall -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0005061 @@ -14017,7 +14073,7 @@ synonym: "musculus" EXACT [FMA:30316] xref: FMA:30316 is_a: UBERON:0000061 ! anatomical structure relationship: has_part CL:0000187 ! muscle cell -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0005157 @@ -14391,11 +14447,12 @@ xref: NCIT:C13191 xref: SCTID:68989006 xref: UMLS:C0004799 {source="ncithesaurus:Basement_Membrane"} xref: Wikipedia:Basement_membrane +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005764 {source="FMA"} ! acellular membrane relationship: adjacent_to CL:0000066 ! epithelial cell relationship: has_part GO:0005587 ! collagen type IV trimer relationship: part_of UBERON:0000483 ! epithelium -relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa relationship: RO:0002473 GO:0005604 ! composed primarily of basement membrane property_value: RO:0002175 NCBITaxon:80999 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} @@ -14420,6 +14477,7 @@ def: "Organ with organ cavity, which has as parts a serous membrane and a serous comment: See notes for serous membrane xref: FMA:9689 xref: SCTID:362890006 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000062 ! organ relationship: has_part UBERON:0000042 ! serous membrane relationship: has_part UBERON:0002553 ! anatomical cavity @@ -14504,7 +14562,7 @@ is_a: UBERON:0006134 ! nerve fiber intersection_of: UBERON:0006134 ! nerve fiber intersection_of: has_part GO:0043209 ! myelin sheath relationship: has_part GO:0043209 ! myelin sheath -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria property_value: IAO:0000116 "consider adding link to UBERON:0002316 ! white matter of neuraxis" xsd:string property_value: RO:0002161 NCBITaxon:117569 property_value: RO:0002161 NCBITaxon:7762 @@ -14644,7 +14702,7 @@ xref: NCIT:C34232 xref: UMLS:C1518430 {source="ncithesaurus:Notochordal_Process"} xref: VHOG:0001213 is_a: UBERON:0005423 ! developing anatomical structure -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002202 UBERON:0000924 {source="EHDAA2"} ! develops from ectoderm [Term] @@ -14712,7 +14770,7 @@ xref: MAT:0000049 xref: MESH:D010614 xref: MIAA:0000049 is_a: UBERON:0004921 ! subdivision of digestive tract -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria [Term] id: UBERON:0006595 @@ -14729,7 +14787,7 @@ intersection_of: UBERON:0006598 ! presumptive structure intersection_of: part_of UBERON:0000307 ! blastula intersection_of: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm relationship: part_of UBERON:0000307 ! blastula -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm [Term] @@ -14781,7 +14839,7 @@ intersection_of: UBERON:0006598 ! presumptive structure intersection_of: part_of UBERON:0000307 ! blastula intersection_of: RO:0002387 UBERON:0000924 ! has potential to develop into ectoderm relationship: part_of UBERON:0000307 ! blastula -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002387 UBERON:0000924 ! has potential to develop into ectoderm [Term] @@ -14799,7 +14857,7 @@ intersection_of: UBERON:0006598 ! presumptive structure intersection_of: part_of UBERON:0000307 ! blastula intersection_of: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm relationship: part_of UBERON:0000307 ! blastula -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm [Term] @@ -14840,6 +14898,7 @@ subset: efo_slim xref: EFO:0003709 xref: TAO:0005077 xref: ZFA:0005077 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005423 ! developing anatomical structure relationship: has_part CL:0000115 ! endothelial cell relationship: has_part CL:0000566 ! angioblastic mesenchymal cell @@ -15789,7 +15848,7 @@ synonym: "schizocoelom" NARROW [] xref: EHDAA2:0004731 xref: Wikipedia:Coelom is_a: UBERON:0000481 {source="EHDAA2"} ! multi-tissue structure -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria property_value: IAO:0000116 "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." xsd:string property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} @@ -15818,6 +15877,7 @@ synonym: "tunica fibrosa" BROAD [] xref: FMA:58102 xref: SCTID:361318005 xref: Wikipedia:Fibrous_tunic_of_eyeball +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0004923 {source="FMA"} ! organ component layer is_a: UBERON:0010314 ! structure with developmental contribution from neural crest @@ -15870,7 +15930,7 @@ namespace: uberon def: "A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages." [https://orcid.org/0000-0002-6601-2165] subset: non_informative is_a: UBERON:0000475 ! organism subdivision -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0013702 @@ -15950,7 +16010,7 @@ def: "Any structure that is placed on one side of the left-right axis of a bilat subset: grouping_class subset: non_informative is_a: UBERON:0000061 ! anatomical structure -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria [Term] id: UBERON:0015228 @@ -16152,7 +16212,7 @@ synonym: "neuron projection bundle from brain" RELATED [http://orcid.org/0000-00 is_a: UBERON:0000122 ! neuron projection bundle is_a: UBERON:0015212 ! lateral structure relationship: extends_fibers_into UBERON:0000955 ! brain -relationship: RO:0002160 NCBITaxon:89593 ! only in taxon Craniata +relationship: RO:0002162 NCBITaxon:89593 ! in taxon Craniata property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -17643,9 +17703,7 @@ inverse_of: output_of ! output of [Typedef] id: has_part name: has part -name: has_part namespace: external -namespace: quality def: "a core relation that holds between a whole and its part" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology @@ -17850,9 +17908,7 @@ expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://p [Typedef] id: part_of name: part of -name: part_of namespace: external -namespace: quality def: "a core relation that holds between a part and its whole" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term diff --git a/subsets/eye_upper_slim.owl b/subsets/eye_upper_slim.owl index 69be33e39..394d31707 100644 --- a/subsets/eye_upper_slim.owl +++ b/subsets/eye_upper_slim.owl @@ -22,8 +22,8 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - 2024-08-16 + + 2024-09-26 @@ -392,6 +392,14 @@ WHERE { + + + + + + + + @@ -1038,6 +1046,12 @@ WHERE { + + + + + + @@ -1076,17 +1090,13 @@ WHERE { - - created by - + - - creation date - + @@ -1172,9 +1182,7 @@ WHERE { - - id - + @@ -1283,7 +1291,6 @@ WHERE { A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. BFO:0000050 external - quality part_of @@ -1292,7 +1299,6 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of part of part of - part_of http://www.obofoundry.org/ro/#OBO_REL:part_of @@ -1314,7 +1320,6 @@ A continuant cannot be part of an occurrent: use 'participates in'. An A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. BFO:0000051 external - quality has_part @@ -1322,7 +1327,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part has part has part - has_part @@ -4778,7 +4782,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -4945,6 +4949,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -4971,7 +4976,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -5013,6 +5018,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -5649,7 +5655,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -5716,12 +5722,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - An endothelial cell that lines the vasculature. ZFA:0009036 @@ -5774,12 +5774,36 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + Any epithelial cell that is part of some squamous epithelium. CALOHA:TS-1249 ZFA:0009039 squamous epithelial cell + + + + Any epithelial cell that is part of some squamous epithelium. + FBC:Autogenerated + @@ -5795,21 +5819,29 @@ Each of these 3 primitives can be composed to yield a cross-product of different - A flattened epithelial cell of mesenchymal origin that lines the serous cavity. + + + + + + + A flat, squamous-like epithelial cell of mesodermal origin. It forms the mesothelium, which lines the body's serous cavities including the pleural, peritoneal, and pericardial spaces. This cell plays a crucial role in synthesizing and secreting lubricants, such as glycosaminoglycans and surfactants, which minimize friction between adjacent tissues during movement. FMA:66773 ZFA:0009040 mesotheliocyte + Mesothelial cells, which morphologically resemble squamous epithelial cells, express both epithelial markers (cytokeratins) and mesenchymal markers (vimentin), reflecting their mesodermal origin. They feature surface microvilli and apical-basal polarity. Under certain conditions, they can undergo mesothelial-to-mesenchymal transition. These cells also produce extracellular matrix proteins, maintain serosal homeostasis, and facilitate fluid transport. mesothelial cell - A flattened epithelial cell of mesenchymal origin that lines the serous cavity. + A flat, squamous-like epithelial cell of mesodermal origin. It forms the mesothelium, which lines the body's serous cavities including the pleural, peritoneal, and pericardial spaces. This cell plays a crucial role in synthesizing and secreting lubricants, such as glycosaminoglycans and surfactants, which minimize friction between adjacent tissues during movement. GOC:tfm ISBN:0721662544 + PMID:26106328 @@ -5817,6 +5849,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different ZFA:0009040 + + + + Mesothelial cells, which morphologically resemble squamous epithelial cells, express both epithelial markers (cytokeratins) and mesenchymal markers (vimentin), reflecting their mesodermal origin. They feature surface microvilli and apical-basal polarity. Under certain conditions, they can undergo mesothelial-to-mesenchymal transition. These cells also produce extracellular matrix proteins, maintain serosal homeostasis, and facilitate fluid transport. + PMID:26106328 + @@ -6025,6 +6063,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6094,10 +6133,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + @@ -6119,11 +6157,19 @@ Each of these 3 primitives can be composed to yield a cross-product of different A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Glial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons. +These different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning. +Oligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. +Microglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response. +Despite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis. BTO:0002606 CALOHA:TS-0415 FBbt:00005144 FMA:54536 ZFA:0009073 + https://cellxgene.cziscience.com/cellguide/CL_0000125 neuroglial cell neuroglia @@ -6138,6 +6184,22 @@ Each of these 3 primitives can be composed to yield a cross-product of different A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons. MESH:D009457 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Glial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons. +These different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning. +Oligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. +Microglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response. +Despite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis. + DOI:10.1002/glia.24343 + DOI:10.1038/nn1988 + DOI:10.1101/cshperspect.a020602 + DOI:10.1126/science.aat0473 + DOI:10.3389/fncel.2017.00024 + @@ -6450,6 +6512,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6559,6 +6622,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6674,7 +6738,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -6704,19 +6768,20 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + + - + - A cell specialized to detect and transduce light. + A cell specialized in detecting light stimuli that are involved in visual perception. BTO:0001060 CALOHA:TS-0868 FBbt:00004211 @@ -6726,16 +6791,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different photoreceptor cell https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg - - - - - true - - A cell specialized to detect and transduce light. + A cell specialized in detecting light stimuli that are involved in visual perception. MESH:D010786 @@ -6866,6 +6925,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6897,6 +6957,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6930,6 +6991,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -7051,7 +7113,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -7060,11 +7122,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - Any cell that only exists in Eukaryota. + Any cell that in taxon some Eukaryota. MESH:D005057 eukaryotic cell @@ -7072,7 +7134,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - Any cell that only exists in Eukaryota. + Any cell that in taxon some Eukaryota. FBC:Autogenerated @@ -7092,6 +7154,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -7304,7 +7367,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -7342,6 +7405,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -7389,6 +7453,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -7447,7 +7512,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -7458,7 +7523,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -7819,6 +7884,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -7968,6 +8034,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -8064,6 +8131,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -8574,6 +8642,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -8783,6 +8852,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -9083,6 +9153,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -9438,6 +9509,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -9768,7 +9840,9 @@ radial glial cells acting as neural progenitors throughout life. + + @@ -9999,6 +10073,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -10043,6 +10118,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -10286,8 +10362,14 @@ radial glial cells acting as neural progenitors throughout life. A cell that is part of pigmented ciliary epithelium. This cell type uptakes sodium and chloride ions from stromal interstitium and passes the ions to non-pigmented ciliary epithelial cells via gap junctions. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Pigmented ciliary epithelial cells, which are a type of pigment cell, have a crucial function within the eye's ciliary body. The ciliary body, located behind the iris, is one of the eye’s most vital structures and consists of two types of epithelial cells: the pigmented and the non-pigmented ciliary epithelial cells. The pigmented ciliary epithelial cells form the outer layer of the ciliary body and exhibit a black or brown pigmentation due to the melanin they contain. +One key function of pigmented ciliary epithelial cells is to aid in the formation of aqueous humor, an intraocular fluid that nourishes the cornea and lens, and maintains intraocular pressure which is essential for the eye’s shape and light refraction. These cells facilitate this function in conjunction with the non-pigmented ciliary epithelial cells. Together, the pigmented and non-pigmented ciliary epithelial cells form a bilayer epithelium that allows the secretion of aqueous humor through a bi-directional fluid transport mechanism. +Pigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, a physiological frontier that controls the entry and exit of various substances from the blood to the aqueous humor and vice versa. The pigmentation in these cells, intensified by melanin, helps to absorb scattered light coming into the eye, reducing any potential damage and glare. 2010-09-13T04:09:27Z FMA:70606 + https://cellxgene.cziscience.com/cellguide/CL_0002303 PE cell @@ -10301,6 +10383,17 @@ radial glial cells acting as neural progenitors throughout life. A cell that is part of pigmented ciliary epithelium. This cell type uptakes sodium and chloride ions from stromal interstitium and passes the ions to non-pigmented ciliary epithelial cells via gap junctions. PMID:15106942 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Pigmented ciliary epithelial cells, which are a type of pigment cell, have a crucial function within the eye's ciliary body. The ciliary body, located behind the iris, is one of the eye’s most vital structures and consists of two types of epithelial cells: the pigmented and the non-pigmented ciliary epithelial cells. The pigmented ciliary epithelial cells form the outer layer of the ciliary body and exhibit a black or brown pigmentation due to the melanin they contain. +One key function of pigmented ciliary epithelial cells is to aid in the formation of aqueous humor, an intraocular fluid that nourishes the cornea and lens, and maintains intraocular pressure which is essential for the eye’s shape and light refraction. These cells facilitate this function in conjunction with the non-pigmented ciliary epithelial cells. Together, the pigmented and non-pigmented ciliary epithelial cells form a bilayer epithelium that allows the secretion of aqueous humor through a bi-directional fluid transport mechanism. +Pigmented ciliary epithelial cells also contribute to the blood-aqueous barrier, a physiological frontier that controls the entry and exit of various substances from the blood to the aqueous humor and vice versa. The pigmentation in these cells, intensified by melanin, helps to absorb scattered light coming into the eye, reducing any potential damage and glare. + DOI:10.1016/S1569-2590(05)10005-6 + DOI:10.1111/j.1444-0938.2002.tb02384.x + @@ -10381,7 +10474,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -10420,7 +10513,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -10575,7 +10668,7 @@ radial glial cells acting as neural progenitors throughout life. - + @@ -10602,32 +10695,6 @@ radial glial cells acting as neural progenitors throughout life. - - - - - An endothelial progenitor cell that participates in angiogenesis during development. - - 2011-02-28T04:20:39Z - ZFA:0005773 - See CL:0002619. - embryonic blood vessel endothelial progenitor cell - - - - - An endothelial progenitor cell that participates in angiogenesis during development. - GOC:tfm - - - - - ZFA:0005773 - - - - - @@ -10698,7 +10765,13 @@ radial glial cells acting as neural progenitors throughout life. A blood vessel endothelial cell that is part of the retina. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Retinal blood vessel endothelial cells constitute the innermost lining of the blood vessels found in the retina, the light-sensitive layer of tissue at the back of the eye. The primary role of these cells revolves around their location within the retinal vascular system, forming the structure of the blood-retinal barrier, a subset of the larger blood-ocular barrier system. +The endothelial cells are particularly involved in the growth of new retinal blood vessels from pre-existing ones (angiogenesis); this is critical in managing the amount of oxygen and essential nutrients delivered to the ocular tissues. They are crucial for maintaining homeostasis in the retinal environment by controlling the exchange of molecules between the blood and the retina. Furthermore, they mediate immune cell trafficking, supporting the immune privilege of the eye by preventing the unrestricted infiltration of inflammatory cells into the retina, thus maintaining ocular health and normal vision. +The malfunction or dysfunction of retinal blood vessel endothelial cells is implicated in numerous ocular pathologies, particularly diabetic retinopathy, which is one of the leading causes of blindness worldwide. In such conditions, the compromise in the integrity of the blood-retinal barrier and excess angiogenesis can lead to retinal edema and pathological neovascularization, resulting in vision loss. 2011-03-06T03:28:27Z + https://cellxgene.cziscience.com/cellguide/CL_0002585 @@ -10716,6 +10789,19 @@ radial glial cells acting as neural progenitors throughout life. A blood vessel endothelial cell that is part of the retina. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Retinal blood vessel endothelial cells constitute the innermost lining of the blood vessels found in the retina, the light-sensitive layer of tissue at the back of the eye. The primary role of these cells revolves around their location within the retinal vascular system, forming the structure of the blood-retinal barrier, a subset of the larger blood-ocular barrier system. +The endothelial cells are particularly involved in the growth of new retinal blood vessels from pre-existing ones (angiogenesis); this is critical in managing the amount of oxygen and essential nutrients delivered to the ocular tissues. They are crucial for maintaining homeostasis in the retinal environment by controlling the exchange of molecules between the blood and the retina. Furthermore, they mediate immune cell trafficking, supporting the immune privilege of the eye by preventing the unrestricted infiltration of inflammatory cells into the retina, thus maintaining ocular health and normal vision. +The malfunction or dysfunction of retinal blood vessel endothelial cells is implicated in numerous ocular pathologies, particularly diabetic retinopathy, which is one of the leading causes of blindness worldwide. In such conditions, the compromise in the integrity of the blood-retinal barrier and excess angiogenesis can lead to retinal edema and pathological neovascularization, resulting in vision loss. + DOI:0.1016/j.preteyeres.2015.08.001 + DOI:10.1016/j.preteyeres.2012.08.004 + DOI:10.1038/nature04482 + DOI:10.5301/EJO.2010.6049 + @@ -10751,9 +10837,16 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell of the retinal pigmented epithelium. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Retinal pigment epithelial (RPE) cells form a single layer of cells at the back of the eye sandwiched between the neurosensory retina and the choroid, playing a significant role in maintaining vision health. These pigment-laden cells are highly specialized and perform an array of metabolic and transport functions essential for the maintenance of the photoreceptor cells (rods and cones) in the retina. The pigmentation of RPE cells actively aids in the absorption of excess light and the prevention of light scattering, thus enhancing the eye's optical properties. +The retinal pigment epithelium forms a key part of the blood/retina barrier. The cells have long sheet-like microvilli on their apical membrane that project into the light-sensitive outer segments of the photoreceptors, forming a close structural interaction. The basolateral membrane of the RPE interacts with the underlying Bruch’s membrane, which separates the RPE cells from fenestrated endothelium of the choriocapillaris. +RPE cells support the photoreceptor by providing them with oxygen and nutrients (such as glucose, retinol and fatty acids) and removing waste products. They also recycle the visual pigment, in a process called the "visual cycle", where the RPE cells play a vital role in the regeneration of visual pigment (11-cis retinol) following the absorption of light. This is essential for the maintenance of photoreceptor excitability. +Beyond this, RPE cells take part in the phagocytosis process, where they digest the shed ends of photoreceptor outer segments, thus, preventing the build-up of waste residue that could otherwise harm retinal health. They also secrete various factors, including growth factors required to maintain the structural integrity of choriocapillaris endothelium and photoreceptors, as well as immunosuppressive factors that play an important role in establishing the immune privilege of the eye. 2011-03-06T03:37:09Z BTO:0004910 FMA:75802 + https://cellxgene.cziscience.com/cellguide/CL_0002586 @@ -10765,6 +10858,20 @@ radial glial cells acting as neural progenitors throughout life. An epithelial cell of the retinal pigmented epithelium. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Retinal pigment epithelial (RPE) cells form a single layer of cells at the back of the eye sandwiched between the neurosensory retina and the choroid, playing a significant role in maintaining vision health. These pigment-laden cells are highly specialized and perform an array of metabolic and transport functions essential for the maintenance of the photoreceptor cells (rods and cones) in the retina. The pigmentation of RPE cells actively aids in the absorption of excess light and the prevention of light scattering, thus enhancing the eye's optical properties. +The retinal pigment epithelium forms a key part of the blood/retina barrier. The cells have long sheet-like microvilli on their apical membrane that project into the light-sensitive outer segments of the photoreceptors, forming a close structural interaction. The basolateral membrane of the RPE interacts with the underlying Bruch’s membrane, which separates the RPE cells from fenestrated endothelium of the choriocapillaris. +RPE cells support the photoreceptor by providing them with oxygen and nutrients (such as glucose, retinol and fatty acids) and removing waste products. They also recycle the visual pigment, in a process called the "visual cycle", where the RPE cells play a vital role in the regeneration of visual pigment (11-cis retinol) following the absorption of light. This is essential for the maintenance of photoreceptor excitability. +Beyond this, RPE cells take part in the phagocytosis process, where they digest the shed ends of photoreceptor outer segments, thus, preventing the build-up of waste residue that could otherwise harm retinal health. They also secrete various factors, including growth factors required to maintain the structural integrity of choriocapillaris endothelium and photoreceptors, as well as immunosuppressive factors that play an important role in establishing the immune privilege of the eye. + DOI:10.1111/febs.16018 + DOI:10.1152/physrev.00021.2004 + DOI:10.3389/fphar.2021.727870/full + https://www.sciencedirect.com/topics/chemistry/retinal-pigment + @@ -10955,6 +11062,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -11063,19 +11171,19 @@ radial glial cells acting as neural progenitors throughout life. - + Any photoreceptor cell that is part of some camera-type eye. camera type eye photoreceptor cell camera-type eye photoreceptor cell - + - + https://github.com/obophenotype/cell-ontology/issues/2245 @@ -11105,6 +11213,12 @@ radial glial cells acting as neural progenitors throughout life. A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. +After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. +Disorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis. + https://cellxgene.cziscience.com/cellguide/CL_0011012 neural crest cell @@ -11115,6 +11229,19 @@ radial glial cells acting as neural progenitors throughout life. https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-9900-7880 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. +After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. +Disorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis. + DOI:10.1002/dvg.23276 + DOI:10.1242/dev.193193 + DOI:10.3389/fcell.2020.00635/full + https://doi.org/10.1016/j.ydbio.2011.12.042 + @@ -11132,6 +11259,7 @@ radial glial cells acting as neural progenitors throughout life. + @@ -11641,7 +11769,7 @@ plexiform layer. - + @@ -11649,6 +11777,7 @@ plexiform layer. The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome. + https://github.com/geneontology/go-ontology/issues/28301 GO:0000789 GO:0000790 GO:0005717 @@ -12409,32 +12538,32 @@ plexiform layer. - - + + A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. Wikipedia:Collagen cellular_component GO:0005581 collagen trimer - + - + - + PMID:12382326 - + PMID:12382326 @@ -12744,12 +12873,7 @@ plexiform layer. - - - - - - + @@ -14948,6 +15072,9 @@ plexiform layer. The self-renewing division of a stem cell. A stem cell is an undifferentiated cell, in the embryo or adult, that can undergo unlimited division and give rise to one or several different cell types. + + + stem cell renewal biological_process GO:0017145 @@ -16375,12 +16502,7 @@ plexiform layer. - - - - - - + A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. GO:0043234 @@ -16410,33 +16532,6 @@ plexiform layer. - - - - - A macromolecular complex containing both protein and DNA molecules. - DNA-protein complex - cellular_component - GO:0032993 - - Note that this term is intended to classify complexes that have DNA as one of the members of the complex, that is, the complex does not exist if DNA is not present. Protein complexes that interact with DNA e.g. transcription factor complexes should not be classified here. - protein-DNA complex - - - - - A macromolecular complex containing both protein and DNA molecules. - GOC:mah - - - - - DNA-protein complex - GOC:mah - - - - @@ -17156,10 +17251,12 @@ plexiform layer. Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. + https://github.com/geneontology/go-ontology/issues/28153 NIF_Subcellular:sao414196390 membrane-enclosed organelle cellular_component GO:0043227 + membrane-bounded organelle @@ -17177,11 +17274,13 @@ plexiform layer. Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. https://github.com/geneontology/go-ontology/issues/21881 + https://github.com/geneontology/go-ontology/issues/28153 NIF_Subcellular:sao1456184038 non-membrane-enclosed organelle cellular_component biological condensate GO:0043228 + non-membrane-bounded organelle @@ -17217,8 +17316,10 @@ plexiform layer. Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. + https://github.com/geneontology/go-ontology/issues/28153 cellular_component GO:0043229 + intracellular organelle @@ -17535,10 +17636,12 @@ plexiform layer. A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component. + https://github.com/geneontology/go-ontology/issues/27194 GO:0071843 cellular component biogenesis at cellular level biological_process GO:0044085 + cellular component biogenesis @@ -18525,6 +18628,49 @@ plexiform layer. + + + + + + + + + + + + + + + + + + + + + + The series of events involved in visual perception in which a light stimulus is received and converted into a molecular signal. + sensory detection of light during visual perception + sensory detection of light stimulus during visual perception + sensory transduction of light during visual perception + sensory transduction of light stimulus during visual perception + visual perception, detection of light stimulus + visual perception, sensory transduction during perception of light + visual perception, sensory transduction of light stimulus + biological_process + GO:0050908 + detection of light stimulus involved in visual perception + + + + + The series of events involved in visual perception in which a light stimulus is received and converted into a molecular signal. + GOC:ai + GOC:dos + + + + @@ -20063,6 +20209,7 @@ plexiform layer. + @@ -22809,7 +22956,7 @@ plexiform layer. A quality of a single cell inhering in the bearer by virtue of the bearer's size or shape or structure. - ORCID:0000-0002-7073-9172 + https://orcid.org/0000-0002-7073-9172 @@ -22969,7 +23116,7 @@ plexiform layer. - + @@ -24035,51 +24182,51 @@ plexiform layer. - + - + - A molecular entity that minimally consists of a protein. + A material entity that minimally consists of a protein. protein protein aggregate protein complex protein-containing complex protein - PR:000064867 - Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). - protein-containing molecular entity + PR:000050567 + Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566). + protein-containing material entity - + - A molecular entity that minimally consists of a protein. + A material entity that minimally consists of a protein. PRO:DAN - + protein PRO:DAN - + protein aggregate PRO:DAN - + protein complex PRO:DAN - + protein-containing complex PRO:DAN @@ -24422,7 +24569,7 @@ plexiform layer. - + @@ -24498,6 +24645,7 @@ plexiform layer. + @@ -25103,7 +25251,7 @@ plexiform layer. - + @@ -25160,7 +25308,7 @@ plexiform layer. - + The surface (external) layer of ectoderm which begins to proliferate shortly after separation from the neuroectoderm. merge with non-neural. In vertebrates, the ectoderm has three parts: external ectoderm (also known as surface ectoderm), the neurectoderm (neural crest, and neural tube) EHDAA2:0001968 @@ -25183,7 +25331,7 @@ plexiform layer. external ectoderm http://upload.wikimedia.org/wikipedia/commons/1/1d/Ectoderm.png - + @@ -25196,7 +25344,7 @@ plexiform layer. - + EHDAA2 @@ -25545,7 +25693,7 @@ plexiform layer. - + @@ -25554,7 +25702,7 @@ plexiform layer. - + @@ -25581,14 +25729,14 @@ plexiform layer. gastrula stage - + - + BILS @@ -25660,7 +25808,7 @@ plexiform layer. - + @@ -25703,7 +25851,7 @@ plexiform layer. - + @@ -25788,7 +25936,7 @@ plexiform layer. - + @@ -25812,7 +25960,7 @@ plexiform layer. - + @@ -25829,7 +25977,7 @@ plexiform layer. - + @@ -25989,6 +26137,7 @@ plexiform layer. + @@ -25996,15 +26145,15 @@ plexiform layer. - + - - + + A fluid that is composed of blood plasma and erythrocytes. AAO:0000046 @@ -26041,34 +26190,34 @@ plexiform layer. blood - + - + - + - + CL:tm - + https://github.com/obophenotype/uberon/issues/1330 - + Bgee:AN @@ -26118,7 +26267,7 @@ plexiform layer. - + @@ -26223,7 +26372,7 @@ plexiform layer. - + @@ -27140,6 +27289,7 @@ plexiform layer. + @@ -27153,7 +27303,7 @@ plexiform layer. - + @@ -27195,14 +27345,14 @@ plexiform layer. epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg - - + + - + http://palaeos.com/metazoa/porifera/homoscleromorpha.html @@ -27633,7 +27783,7 @@ plexiform layer. - + @@ -27724,7 +27874,7 @@ plexiform layer. - + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. AAO:0000137 BILA:0000036 @@ -27759,14 +27909,14 @@ plexiform layer. ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png - + - + Bgee:AN @@ -27806,7 +27956,7 @@ plexiform layer. - + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. AAO:0000139 BILA:0000038 @@ -27841,14 +27991,14 @@ plexiform layer. http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png - + - + Bgee:AN @@ -27889,7 +28039,7 @@ plexiform layer. - + The middle germ layer of the embryo, between the endoderm and ectoderm. UBERON:0003263 @@ -27930,14 +28080,14 @@ plexiform layer. mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png - + - + Bgee:AN @@ -27992,7 +28142,7 @@ plexiform layer. - + @@ -28125,7 +28275,7 @@ plexiform layer. - + @@ -28187,14 +28337,14 @@ plexiform layer. cranial nerve II - + - + EHDAA2 @@ -28304,7 +28454,7 @@ plexiform layer. - + @@ -28313,7 +28463,7 @@ plexiform layer. - + @@ -28375,14 +28525,14 @@ plexiform layer. https://cdn.humanatlas.io/digital-objects/ref-organ/heart-female/v1.3/assets/3d-vh-f-heart.glb https://cdn.humanatlas.io/digital-objects/ref-organ/heart-male/v1.3/assets/3d-vh-m-heart.glb - + - + MA @@ -28424,7 +28574,7 @@ plexiform layer. - + @@ -28443,7 +28593,7 @@ plexiform layer. - + The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. requires review for applicability to invertebrate structures, e.g. synganglion @@ -28502,11 +28652,11 @@ plexiform layer. https://cdn.humanatlas.io/digital-objects/ref-organ/brain-female/v1.4/assets/3d-allen-f-brain.glb https://cdn.humanatlas.io/digital-objects/ref-organ/brain-male/v1.4/assets/3d-allen-m-brain.glb - + - + @@ -28519,13 +28669,13 @@ plexiform layer. - + FMA - + Bgee:AN @@ -28775,11 +28925,12 @@ plexiform layer. + - - - + + + @@ -28863,34 +29014,34 @@ plexiform layer. cornea http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + - + - + MA - + MA - + FMA-isa @@ -29067,10 +29218,10 @@ plexiform layer. - - - - + + + + The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates. @@ -29118,44 +29269,44 @@ plexiform layer. retina http://upload.wikimedia.org/wikipedia/commons/e/ed/Human_eye_cross-sectional_view_grayscale.png - + - + - + - + - + FMA - + FMA - + FMA - + EHDAA2 @@ -29210,8 +29361,8 @@ plexiform layer. - - + + @@ -29243,24 +29394,24 @@ plexiform layer. eye - + - + - + PMID:21062451 - + PMID:21062451 @@ -29472,7 +29623,7 @@ plexiform layer. - + @@ -29627,7 +29778,7 @@ plexiform layer. - + @@ -29649,14 +29800,13 @@ plexiform layer. - + The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]. - AAO:0000324 BILA:0000079 BIRNLEX:844 @@ -29691,7 +29841,6 @@ plexiform layer. UBERON:0001016 - @@ -29699,14 +29848,14 @@ plexiform layer. http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png - + - + Bgee:AN @@ -29768,11 +29917,11 @@ plexiform layer. - + - + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. @@ -29817,7 +29966,7 @@ plexiform layer. central nervous system - + @@ -29831,7 +29980,7 @@ plexiform layer. - + Bgee:AN @@ -30484,7 +30633,7 @@ plexiform layer. - + Simple squamous epithelium of mesodermal origin which lines serous membranes. Examples: mesothelium of pleura, mesothelium of peritoneum[FMA]. Wikipedia: The mesothelium is a membrane that forms the lining of several body cavities: the pleura (thoracal cavity), peritoneum (abdominal cavity including the mesentery) and pericardium (heart sac). Mesothelial tissue also surrounds the male internal reproductive organs (the tunica vaginalis testis) and covers the internal reproductive organs of women (the tunica serosa uteri). AEO:0000111 BTO:0002422 @@ -30509,14 +30658,14 @@ plexiform layer. mesothelium http://upload.wikimedia.org/wikipedia/commons/2/25/Mesothelium_peritoneal_wash_high_mag.jpg - + - + FMA @@ -30541,7 +30690,7 @@ plexiform layer. - + @@ -30796,7 +30945,7 @@ plexiform layer. - + @@ -30806,7 +30955,7 @@ plexiform layer. - + A tube extending from the mouth to the anus. @@ -30843,14 +30992,14 @@ plexiform layer. digestive tract - + - + NCBIBook:NBK10107 @@ -30905,7 +31054,7 @@ plexiform layer. - + The ciliary muscle is a ring of smooth muscle in the middle layer of the eye that controls the eye's accommodation for viewing objects at varying distances and regulates the flow of aqueous humour through Schlemm's canal. [WP,unvetted]. BTO:0000654 @@ -30928,7 +31077,7 @@ plexiform layer. ciliary muscle http://upload.wikimedia.org/wikipedia/commons/2/28/Gray872.png - + @@ -30947,7 +31096,7 @@ plexiform layer. - + FMA @@ -31065,7 +31214,7 @@ plexiform layer. - + @@ -31111,14 +31260,14 @@ plexiform layer. eyelid https://upload.wikimedia.org/wikipedia/commons/8/84/Eye_makeup.jpg - + - + multiple @@ -31384,7 +31533,7 @@ plexiform layer. - + @@ -31423,14 +31572,14 @@ plexiform layer. iris - + - + XAO @@ -31484,7 +31633,7 @@ plexiform layer. - + @@ -31533,14 +31682,14 @@ plexiform layer. corneal epithelium http://upload.wikimedia.org/wikipedia/commons/6/66/Gray871.png - + - + ISBN:0781772214 @@ -31628,15 +31777,15 @@ plexiform layer. - - + + - + @@ -31671,34 +31820,34 @@ plexiform layer. sclera http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + - + - + FMA - + ZFA - + ISBN:0781772214 @@ -31740,7 +31889,7 @@ plexiform layer. - + @@ -31778,14 +31927,14 @@ plexiform layer. ciliary body http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + ISBN:0781772214 @@ -31823,14 +31972,14 @@ plexiform layer. - + - + @@ -31891,24 +32040,24 @@ plexiform layer. optic choroid http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + - + MA - + Wikipedia @@ -32101,9 +32250,9 @@ plexiform layer. - - - + + + A double layer covering the ciliary body that produces aqueous humor. BTO:0001770 @@ -32123,15 +32272,15 @@ plexiform layer. ciliary epithelium - + - + - + @@ -32144,19 +32293,19 @@ plexiform layer. - + MA - + MP - + Wikipedia @@ -32272,7 +32421,7 @@ plexiform layer. - + @@ -32330,14 +32479,14 @@ plexiform layer. pigmented layer of retina http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png - + - + Wikipedia @@ -32413,7 +32562,7 @@ plexiform layer. - + @@ -32445,14 +32594,14 @@ plexiform layer. photoreceptor layer of retina http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png - + - + ZFA @@ -32945,7 +33094,7 @@ plexiform layer. - + @@ -33001,7 +33150,7 @@ plexiform layer. ganglionic layer of retina http://upload.wikimedia.org/wikipedia/commons/5/55/Gray881.png - + @@ -33014,7 +33163,7 @@ plexiform layer. - + FMA @@ -33068,7 +33217,7 @@ plexiform layer. - + @@ -33123,14 +33272,14 @@ plexiform layer. nerve fiber layer of retina - + - + FMA @@ -33820,7 +33969,7 @@ plexiform layer. - + @@ -33852,14 +34001,14 @@ plexiform layer. anterior segment of eyeball http://upload.wikimedia.org/wikipedia/commons/b/ba/Cataract_in_human_eye.png - + - + FMA @@ -33903,7 +34052,7 @@ plexiform layer. - + @@ -33933,14 +34082,14 @@ plexiform layer. posterior segment of eyeball http://upload.wikimedia.org/wikipedia/commons/1/1e/Schematic_diagram_of_the_human_eye_en.svg - + - + FMA @@ -33977,9 +34126,9 @@ plexiform layer. - - - + + + @@ -34027,15 +34176,15 @@ plexiform layer. conjunctiva http://upload.wikimedia.org/wikipedia/commons/5/55/Gray883.png - + - + - + @@ -34048,19 +34197,19 @@ plexiform layer. - + cjm - + MA - + ISBN:0781772214 @@ -34218,7 +34367,7 @@ plexiform layer. - + The midbrain is the middle division of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes a ventral part containing the cerebral peduncles and a dorsal tectum containing the corpora quadrigemina and that surrounds the aqueduct of Sylvius connecting the third and fourth ventricles)[GO]. developmental relationships need revised @@ -34264,14 +34413,14 @@ plexiform layer. midbrain http://upload.wikimedia.org/wikipedia/commons/f/f9/Human_brain_inferior_view_description.JPG - + - + Bgee:AN @@ -34742,7 +34891,7 @@ plexiform layer. - + Ventral part of the midbrain, separated from the hindbrain by the isthmus[ISBN:0471888893]. Subdivision of the midbrain lying anterior to the tectum and posterior to the substantia nigra and cerebral peduncle[FMA] The part of the midbrain extending from the substantia nigra to the cerebral aqueduct in a horizontal section of the midbrain. It forms the floor of the midbrain that surrounds the cerebral aqueduct[WP]. MTg @@ -34781,14 +34930,14 @@ plexiform layer. midbrain tegmentum http://upload.wikimedia.org/wikipedia/commons/b/b6/Gray712.png - + - + ZFA @@ -34874,6 +35023,7 @@ plexiform layer. + @@ -34948,6 +35098,7 @@ plexiform layer. + @@ -34956,8 +35107,8 @@ plexiform layer. - - + + @@ -34970,7 +35121,7 @@ plexiform layer. - + @@ -35024,34 +35175,34 @@ plexiform layer. blood vessel http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg - + - + - + - + AEO - + EHDAA2 - + GO:0072360 @@ -35208,7 +35359,7 @@ plexiform layer. - + @@ -35370,7 +35521,7 @@ plexiform layer. - + @@ -35380,7 +35531,7 @@ plexiform layer. - + The most posterior of the three principal regions of the brain. In mammals and birds the hindbrain is divided into a rostral metencephalon and a caudal myelencephalon. In zebrafish, with the exception of the cerebellum, the ventral remainder of the metencephalon can be separated only arbitrarily from the more caudal myelencephalic portion of the medulla oblongata (From: Neuroanatomy of the Zebrafish Brain)[ZFA]. Organ component of neuraxis that has as its parts the pons, cerebellum and medulla oblongata[FMA]. @@ -35423,14 +35574,14 @@ plexiform layer. hindbrain http://upload.wikimedia.org/wikipedia/commons/5/54/EmbryonicBrain.svg - + - + Bgee:AN @@ -35921,7 +36072,7 @@ plexiform layer. - + @@ -36061,7 +36212,7 @@ plexiform layer. - + Vasculature that is part of the eye region. FMA:74743 @@ -36083,14 +36234,14 @@ plexiform layer. https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-female/v1.3/assets/3d-vh-f-blood-vasculature.glb https://cdn.humanatlas.io/digital-objects/ref-organ/blood-vasculature-male/v1.3/assets/3d-vh-m-blood-vasculature.glb - + - + ISBN:0781772214 @@ -36294,7 +36445,7 @@ plexiform layer. - + @@ -36368,14 +36519,14 @@ plexiform layer. https://cdn.humanatlas.io/digital-objects/ref-organ/spinal-cord-female/v1.1/assets/3d-vh-f-spinal-cord.glb https://cdn.humanatlas.io/digital-objects/ref-organ/spinal-cord-male/v1.1/assets/3d-vh-m-spinal-cord.glb - + - + ZFA @@ -36830,9 +36981,9 @@ plexiform layer. - - - + + + @@ -36880,15 +37031,15 @@ plexiform layer. notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - - + + - + - + @@ -36907,19 +37058,19 @@ plexiform layer. - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -36959,8 +37110,8 @@ plexiform layer. - - + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. mesodermal cluster @@ -36998,11 +37149,11 @@ plexiform layer. somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - - + + - + @@ -37015,13 +37166,13 @@ plexiform layer. - + GOTAX:0000352 - + ZFA @@ -37083,22 +37234,22 @@ plexiform layer. - + - + - - + + - + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. AAO:0010578 BTO:0001764 @@ -37131,45 +37282,45 @@ plexiform layer. http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - + BTO - + PMID:11523831 - + PMID:11523831 @@ -37290,7 +37441,7 @@ plexiform layer. - + @@ -37381,7 +37532,7 @@ plexiform layer. - + @@ -37455,10 +37606,10 @@ plexiform layer. - + - + @@ -37508,14 +37659,14 @@ plexiform layer. hematopoietic system - + - + FMA @@ -37555,8 +37706,8 @@ plexiform layer. - - + + @@ -37582,11 +37733,11 @@ plexiform layer. iris epithelium - + - + @@ -37599,13 +37750,13 @@ plexiform layer. - + MA - + MP @@ -37744,7 +37895,7 @@ plexiform layer. - + Ectodermal placode that develops in the head into a part of the sensory nervous system. With a few exceptions (lens, adenohypophyseal), cranial placodes are neurogenic. Do not merge with neurogenic placode ectodermal placode @@ -37761,8 +37912,8 @@ plexiform layer. cranial placode - - + + @@ -37774,7 +37925,7 @@ plexiform layer. - + PMID:11523831 PMID:22512454 @@ -37974,7 +38125,7 @@ plexiform layer. - + @@ -37987,7 +38138,7 @@ plexiform layer. - + The part of the brain that is the morphological boundary between the midbrain and hindbrain and that is the location of an organizing center which patterns the midbrain and hindbrain primordia of the neural plate. consider adding class for organizer. Consider adding separate class for isthmus as a structure AAO:0011064 @@ -38016,24 +38167,24 @@ plexiform layer. midbrain-hindbrain boundary - + - + - + ZFA - + ZFA @@ -38155,7 +38306,7 @@ plexiform layer. - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. AAO:0011086 EFO:0001982 @@ -38178,14 +38329,14 @@ plexiform layer. presomitic mesoderm - + - + Bgee:AN @@ -38291,7 +38442,7 @@ plexiform layer. - + @@ -38352,7 +38503,7 @@ plexiform layer. - + @@ -38389,7 +38540,7 @@ plexiform layer. eye primordium - + @@ -38402,7 +38553,7 @@ plexiform layer. - + PMID:16496288 XAO @@ -38452,8 +38603,8 @@ plexiform layer. - - + + @@ -38481,24 +38632,24 @@ plexiform layer. optic cup - + - + - + ZFA - + ZFA @@ -38554,7 +38705,7 @@ plexiform layer. - + @@ -38592,7 +38743,7 @@ plexiform layer. lens placode http://upload.wikimedia.org/wikipedia/commons/2/2f/Gray864.png - + @@ -38605,7 +38756,7 @@ plexiform layer. - + ZFA @@ -38644,9 +38795,9 @@ plexiform layer. - - - + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. AAO:0011072 BTO:0001765 @@ -38675,34 +38826,34 @@ plexiform layer. neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - - + + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -38777,7 +38928,7 @@ plexiform layer. - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. AAO:0010568 EFO:0003515 @@ -38803,7 +38954,7 @@ plexiform layer. paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -38816,7 +38967,7 @@ plexiform layer. - + Bgee:AN @@ -38892,10 +39043,10 @@ plexiform layer. - + - + @@ -38932,7 +39083,7 @@ plexiform layer. lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -38945,7 +39096,7 @@ plexiform layer. - + EHDAA2 VHOG @@ -38995,15 +39146,15 @@ plexiform layer. - - + + - + Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. should probably be merged with heart rudiment. AAO:0011044 @@ -39020,15 +39171,15 @@ plexiform layer. heart primordium - + - + - + @@ -39041,19 +39192,19 @@ plexiform layer. - + ZFA - + ZFA - + XAO @@ -39082,8 +39233,8 @@ plexiform layer. - - + + Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. AAO:0010571 AEO:0000212 @@ -39107,11 +39258,11 @@ plexiform layer. sclerotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - - + + - + @@ -39130,13 +39281,13 @@ plexiform layer. - + VHOG:0000680 - + ZFA @@ -39367,7 +39518,7 @@ plexiform layer. - + @@ -39457,7 +39608,7 @@ plexiform layer. - + Mesenchyme that is part of a developing camera-type eye. TODO - change mesenchyme relationships to precursor_of EHDAA2:0000485 @@ -39469,14 +39620,14 @@ plexiform layer. UBERON:0003314 eye mesenchyme - + - + EHDAA2 @@ -40251,7 +40402,7 @@ plexiform layer. - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults EHDAA:251 @@ -40266,14 +40417,14 @@ plexiform layer. intraembryonic coelom - + - + Wikipedia @@ -40304,7 +40455,7 @@ plexiform layer. - + @@ -40366,7 +40517,7 @@ plexiform layer. - + The part of the retina that contains neurons and photoreceptor cells[GO]. AAO:0011095 @@ -40397,14 +40548,14 @@ plexiform layer. retinal neural layer - + - + Bgee:AN @@ -40657,7 +40808,7 @@ plexiform layer. - + The layer of undifferentiated, proliferating cells that line the neural tube lumen that is the immediate transformation of the germinal neuroepithelium. consider merging with 'ventricular zone'; note that the MA class probably does not belong here, as this is an embryonic structure ependymal layer @@ -40674,7 +40825,7 @@ plexiform layer. neural tube ventricular layer - + @@ -40687,7 +40838,7 @@ plexiform layer. - + NCBIBook:NBK10047 @@ -41089,9 +41240,9 @@ plexiform layer. - - - + + + @@ -41123,34 +41274,34 @@ plexiform layer. optic vesicle http://upload.wikimedia.org/wikipedia/commons/e/e0/Gray863.png - + - + - + - + ZFA - + GO-def - + ZFA @@ -41246,8 +41397,8 @@ plexiform layer. - - + + A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. XAO:0004185 first heart field @@ -41259,24 +41410,24 @@ plexiform layer. UBERON:0004140 primary heart field - + - + - + GO:0003128 - + https://orcid.org/0000-0003-3308-6245 @@ -41329,7 +41480,7 @@ plexiform layer. - + An epithelial tube that will give rise to the mature heart. AAO:0010411 EFO:0003526 @@ -41348,14 +41499,14 @@ plexiform layer. heart tube - + - + ZFA-modified @@ -41432,7 +41583,7 @@ plexiform layer. - + @@ -41448,14 +41599,14 @@ plexiform layer. eye muscle - + - + MA @@ -41638,7 +41789,7 @@ plexiform layer. - + A transparent homogeneous acellular layer found between the substantia propria and the endothelial layer of the cornea[MP]. EMAPA:18804 @@ -41667,14 +41818,14 @@ plexiform layer. Descemet's membrane https://github.com/obophenotype/uberon/issues/15 - + - + Cline et al @@ -41933,6 +42084,7 @@ plexiform layer. + @@ -42029,6 +42181,7 @@ plexiform layer. + @@ -42424,7 +42577,7 @@ plexiform layer. - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. AAO:0011129 TAO:0001890 @@ -42438,14 +42591,14 @@ plexiform layer. skeletal element - + - + VSAO @@ -42472,10 +42625,10 @@ plexiform layer. - + - + @@ -42511,14 +42664,14 @@ plexiform layer. UBERON:0004770 articular system - + - + FMA @@ -42677,7 +42830,7 @@ plexiform layer. - + @@ -42843,7 +42996,7 @@ plexiform layer. - + @@ -43038,7 +43191,7 @@ plexiform layer. - + @@ -43370,7 +43523,7 @@ plexiform layer. - + Portion of primordial embryonic connective tissue of the developing head, consisting of mesenchymal cells supported in interlaminar jelly, that derive mostly from the mesoderm and contribute to head connective tissue, bone and musculature in conjunction with cranial neural crest cells. EFO:0003492 EHDAA2:0000732 @@ -43391,14 +43544,14 @@ plexiform layer. head mesenchyme - + - + EHDAA2 @@ -43456,7 +43609,7 @@ plexiform layer. - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -43472,14 +43625,14 @@ plexiform layer. trunk mesenchyme - + - + EHDAA2 @@ -43994,7 +44147,7 @@ plexiform layer. - + Portion of tissue that is part of the eye and gives rise to the mature, fully layered cornea. TAO:0002188 ZFA:0001688 @@ -44002,7 +44155,7 @@ plexiform layer. UBERON:0005427 corneal primordium - + @@ -44021,7 +44174,7 @@ plexiform layer. - + ZFA @@ -44044,7 +44197,7 @@ plexiform layer. - + Multi-tissue structure that arises from the heart rudiment and will become the heart tube. EHDAA2:0001512 EHDAA:424 @@ -44062,14 +44215,14 @@ plexiform layer. primitive heart tube - + - + ZFA @@ -44160,6 +44313,7 @@ plexiform layer. + @@ -44175,7 +44329,7 @@ plexiform layer. - + @@ -44259,7 +44413,7 @@ plexiform layer. - + A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 @@ -44269,7 +44423,7 @@ plexiform layer. UBERON:0005856 developing mesenchymal condensation - + @@ -44288,7 +44442,7 @@ plexiform layer. - + AEO-modified-relation @@ -44309,6 +44463,7 @@ plexiform layer. + @@ -44345,8 +44500,8 @@ plexiform layer. - - + + @@ -44363,11 +44518,11 @@ plexiform layer. UBERON:0005908 conjunctival sac - + - + @@ -44380,13 +44535,13 @@ plexiform layer. - + FMA - + HPO:pr @@ -44578,7 +44733,7 @@ plexiform layer. - + @@ -44628,7 +44783,7 @@ plexiform layer. - + @@ -44651,14 +44806,14 @@ plexiform layer. future diencephalon - + - + EHDAA2 @@ -44834,7 +44989,7 @@ plexiform layer. - + @@ -44858,14 +45013,14 @@ plexiform layer. future spinal cord - + - + EHDAA2 @@ -44902,7 +45057,7 @@ plexiform layer. - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB EHDAA2:0001278 @@ -44916,7 +45071,7 @@ plexiform layer. notochordal plate - + @@ -44929,7 +45084,7 @@ plexiform layer. - + EHDAA2 @@ -44953,11 +45108,11 @@ plexiform layer. - + - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -44974,14 +45129,14 @@ plexiform layer. The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -45174,7 +45329,7 @@ plexiform layer. - + @@ -45226,7 +45381,7 @@ plexiform layer. - + @@ -45369,7 +45524,7 @@ plexiform layer. - + @@ -45433,7 +45588,7 @@ plexiform layer. - + @@ -45562,6 +45717,7 @@ plexiform layer. + @@ -46022,8 +46178,8 @@ plexiform layer. - - + + @@ -46049,24 +46205,24 @@ plexiform layer. presumptive hindbrain - + - + - + XAO-abduced - + cjm @@ -46117,7 +46273,7 @@ plexiform layer. - + @@ -46136,14 +46292,14 @@ plexiform layer. presumptive midbrain hindbrain boundary - + - + ZFA @@ -46289,7 +46445,7 @@ plexiform layer. - + @@ -46315,7 +46471,7 @@ plexiform layer. presumptive paraxial mesoderm - + @@ -46331,7 +46487,7 @@ plexiform layer. - + https://github.com/obophenotype/uberon/issues/1277 @@ -46413,7 +46569,7 @@ plexiform layer. - + A neural decussation that is part of a diencephalon. FMA:62446 diencephalon decussation @@ -46421,7 +46577,7 @@ plexiform layer. UBERON:0007425 decussation of diencephalon - + @@ -46434,7 +46590,7 @@ plexiform layer. - + Obol @@ -46509,7 +46665,7 @@ plexiform layer. - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -46517,7 +46673,7 @@ plexiform layer. UBERON:0007524 dense mesenchyme tissue - + @@ -46530,7 +46686,7 @@ plexiform layer. - + AEO @@ -46769,7 +46925,7 @@ plexiform layer. - + An axon tract that is part of a brain. the NIFSTD class 'nerve tract' is classified under 'regional part of brain', so it may seem like it belongs here, but actually includes spinal cord tracts FMA:83848 @@ -46779,14 +46935,14 @@ plexiform layer. UBERON:0007702 tract of brain - + - + cjm @@ -46814,7 +46970,7 @@ plexiform layer. - + Anatomical system that consists of all blood and lymph vessels. consider merging with vasculature @@ -46831,14 +46987,14 @@ plexiform layer. vascular system - + - + MA @@ -46959,7 +47115,7 @@ plexiform layer. - + @@ -46976,14 +47132,14 @@ plexiform layer. UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -47079,7 +47235,7 @@ plexiform layer. - + @@ -47095,14 +47251,14 @@ plexiform layer. UBERON:0009615 midbrain hindbrain boundary neural plate - + - + ZFA @@ -47135,14 +47291,14 @@ plexiform layer. - + - + @@ -47167,24 +47323,24 @@ plexiform layer. presumptive midbrain - + - + - + ZFA - + ZFA @@ -47230,7 +47386,7 @@ plexiform layer. - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -47238,14 +47394,14 @@ plexiform layer. UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -47268,7 +47424,7 @@ plexiform layer. - + EFO:0003704 TAO:0005041 ZFA:0005041 @@ -47278,14 +47434,14 @@ plexiform layer. anterior lateral plate mesoderm - + - + ZFA @@ -47341,14 +47497,14 @@ plexiform layer. - + EHDAA2:0001315 EHDAA:1122 uberon UBERON:0009920 optic neural crest - + @@ -47361,7 +47517,7 @@ plexiform layer. - + EHDAA2 @@ -47502,7 +47658,7 @@ plexiform layer. - + @@ -47525,14 +47681,14 @@ plexiform layer. eyeball of camera-type eye - + - + FMA @@ -47573,8 +47729,8 @@ plexiform layer. - - + + Portion of tissue that is dorsolateral to the floor plate and part of the midbrain. DHBA:12322 EFO:0003567 @@ -47588,11 +47744,11 @@ plexiform layer. midbrain basal plate - + - + @@ -47605,13 +47761,13 @@ plexiform layer. - + EHDAA2 - + ZFA @@ -47640,7 +47796,7 @@ plexiform layer. - + Portion of neural tube that gives rise to the midbrain. we follow ZFA in temporally dividing midbrain NT from presumptive midbrain, but in future this may be collapsed TAO:0007039 @@ -47649,14 +47805,14 @@ plexiform layer. UBERON:0010286 midbrain neural tube - + - + ZFA @@ -47959,8 +48115,8 @@ plexiform layer. - - + + Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. FMA:23879 SCTID:129140006 @@ -47972,11 +48128,11 @@ plexiform layer. subdivision of skeleton - + - + @@ -47989,13 +48145,13 @@ plexiform layer. - + UBERONREF:0000003 - + VSAO @@ -48056,7 +48212,7 @@ plexiform layer. - + Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. axial skeletal system FMA:302077 @@ -48066,7 +48222,7 @@ plexiform layer. postcranial axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton - + @@ -48079,7 +48235,7 @@ plexiform layer. - + cjm @@ -48201,7 +48357,7 @@ plexiform layer. - + AAO:0010038 EMAPA:18808 FMA:49150 @@ -48211,14 +48367,14 @@ plexiform layer. UBERON:0011222 intra-ocular muscle - + - + EMAPA @@ -48480,7 +48636,7 @@ plexiform layer. - + @@ -48522,7 +48678,7 @@ plexiform layer. anterior uvea - + @@ -48535,7 +48691,7 @@ plexiform layer. - + MP @@ -48577,7 +48733,7 @@ plexiform layer. - + @@ -48666,6 +48822,7 @@ plexiform layer. + @@ -48861,7 +49018,7 @@ plexiform layer. - + @@ -49090,7 +49247,7 @@ plexiform layer. - + @@ -49328,7 +49485,7 @@ plexiform layer. - + @@ -49351,7 +49508,7 @@ plexiform layer. UBERON:0016887 entire extraembryonic component - + @@ -49364,7 +49521,7 @@ plexiform layer. - + AEO @@ -49708,7 +49865,7 @@ plexiform layer. - + @@ -50350,6 +50507,454 @@ plexiform layer. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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+_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid786 +_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid802 +_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid809 +_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid820 +_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid826 +_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid843 +_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid849 +_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid858 +_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid868 +_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid916 +_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid966 +_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid976 +_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid983 +_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid990 +_:B53189381X2D873cX2D4ec4X2Daff8X2D63fc38c8481egenid997 "cell" "neural crest derived fibroblast" "neuronal receptor cell" @@ -428,7 +462,6 @@ _:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid990 "keratocyte" "retinal melanocyte" "cardiocyte" - "embryonic blood vessel endothelial progenitor cell" "iris pigment epithelial cell" "retinal blood vessel endothelial cell" "retinal pigment epithelial cell" @@ -592,7 +625,6 @@ _:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid990 "secretion by cell" "protein-containing complex disassembly" "protein-containing complex" - "protein-DNA complex" "erythrocyte homeostasis" "monoatomic ion transmembrane transport" "tube formation" @@ -652,6 +684,7 @@ _:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid990 "nervous system process" "response to stimulus" "detection of stimulus involved in sensory perception" + "detection of light stimulus involved in visual perception" "sensory perception of light stimulus" "detection of light stimulus involved in sensory perception" "localization" @@ -842,7 +875,7 @@ _:B06857fcdX2Da49bX2D4244X2D8d0aX2D56b2175d8de8genid990 "integrin alpha" "Mus musculus protein" "eukaryotic protein" - "protein-containing molecular entity" + "protein-containing material entity" "processual entity" "camera-type eye" "sense organ" diff --git a/subsets/general_cell_types_upper_slim.json b/subsets/general_cell_types_upper_slim.json index 31ba38f2e..6a4f6cb9e 100644 --- a/subsets/general_cell_types_upper_slim.json +++ b/subsets/general_cell_types_upper_slim.json @@ -4,9 +4,9 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-08-16" + "val" : "2024-09-26" } ], - "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-08-16/subsets/general_cell_types_upper_slim.owl" + "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-09-26/subsets/general_cell_types_upper_slim.owl" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/CL_0000000", @@ -41,24 +41,6 @@ "val" : "ZFA:0009000" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/CL_0000006", - "lbl" : "neuronal receptor cell", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "Any sensory receptor cell that is a(n) neuron and is capable of some detection of stimulus involved in sensory perception.", - "xrefs" : [ "FBC:Autogenerated" ] - }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "neuronal receptor cell (sensu Animalia)" - } ], - "xrefs" : [ { - "val" : "ZFA:0009001" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000007", "lbl" : "early embryonic cell (metazoa)", @@ -675,10 +657,15 @@ "val" : "BTO:0001433" }, { "val" : "ZFA:0009064" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000113" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nMononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. \nIn addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses.\nMononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer." } ] } }, { @@ -709,10 +696,15 @@ "val" : "FMA:54536" }, { "val" : "ZFA:0009073" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000125" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nGlial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons.\nThese different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning.\nOligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. \nMicroglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response.\nDespite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis." } ] } }, { @@ -1090,29 +1082,13 @@ "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/CL_0000197", - "lbl" : "sensory receptor cell", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A cell that is capable of detection of a stimulus involved in sensory perception." - }, - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "receptor cell" - } ], - "xrefs" : [ { - "val" : "MESH:D011984" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/CL_0000210", "lbl" : "photoreceptor cell", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A cell specialized to detect and transduce light.", + "val" : "A cell specialized in detecting light stimuli that are involved in visual perception.", "xrefs" : [ "MESH:D010786" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], @@ -1236,22 +1212,16 @@ "meta" : { "definition" : { "val" : "A cell with more than one nucleus.", - "xrefs" : [ "FB:ma" ] + "xrefs" : [ "FB:ma", "Wikipedia:Multinucleate" ] }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "syncitium" + "val" : "multinucleated cells", + "xrefs" : [ "Wikipedia:Multinucleate" ] }, { "pred" : "hasExactSynonym", - "val" : "syncytial cell" - }, { - "pred" : "hasExactSynonym", - "val" : "syncytium" - } ], - "xrefs" : [ { - "val" : "AEO:0000203" - }, { - "val" : "WBbt:0008074" + "val" : "polynuclear cells", + "xrefs" : [ "Wikipedia:Multinucleate" ] } ] } }, { @@ -1351,7 +1321,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "Any cell that only exists in Eukaryota.", + "val" : "Any cell that in taxon some Eukaryota.", "xrefs" : [ "FBC:Autogenerated" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], @@ -2731,15 +2701,17 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "A transversely striated, synctial muscle cell, formed by the fusion of myoblasts.", + "val" : "A transversely striated, multinucleated syncytial muscle cell, formed by the fusion of myoblasts during muscle development.", "xrefs" : [ "GOC:dos", "GOC:tfm", "ISBN:0323052908", "PMID:22274696" ] }, "synonyms" : [ { "pred" : "hasExactSynonym", - "val" : "myotubule" + "val" : "myofiber", + "xrefs" : [ "FBbt:00005812" ] }, { "pred" : "hasExactSynonym", - "val" : "single cell sarcomere" + "val" : "myofibril", + "xrefs" : [ "FBbt:00005812" ] } ], "xrefs" : [ { "val" : "FBbt:00005812" @@ -2892,6 +2864,23 @@ "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_0008028", + "lbl" : "visual system neuron", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "Any neuron that is capable of part of some visual perception.", + "xrefs" : [ "FBC:Autogenerated" ] + }, + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0000-0002-7073-9172" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2017-07-09T19:12:36Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/CL_0009004", "lbl" : "retinal cell", @@ -2944,7 +2933,14 @@ "val" : "A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells.", "xrefs" : [ "https://orcid.org/0000-0001-5208-3432", "https://orcid.org/0000-0002-9900-7880" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "xrefs" : [ { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0011012" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." + } ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0011026", @@ -3029,6 +3025,33 @@ "val" : "CALOHA:TS-2109" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/CL_4052002", + "lbl" : "syncytial cell", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A multinucleate cell formed by the fusion of multiple uninuclear cells through plasma membrane fusion. This process leads to a single large cell containing multiple nuclei within a shared cytoplasm.", + "xrefs" : [ "PMID:20851884", "Wikipedia:Syncytium" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "syncytium", + "xrefs" : [ "WBbt:0008074" ] + }, { + "synonymType" : "http://purl.obolibrary.org/obo/OMO_0003000", + "pred" : "hasRelatedSynonym", + "val" : "SC", + "xrefs" : [ "PMID:9067520" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/contributor", + "val" : "https://orcid.org/0009-0000-8480-9277" + }, { + "pred" : "http://purl.org/dc/terms/date", + "val" : "2024-08-15T10:38:46Z" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0000323", "lbl" : "lytic vacuole", @@ -3043,6 +3066,24 @@ "val" : "cellular_component" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0000768", + "lbl" : "syncytium formation by plasma membrane fusion", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells.", + "xrefs" : [ "GOC:mtg_muscle", "GOC:tb" ] + }, + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "cell fusion" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0000785", "lbl" : "chromatin", @@ -3067,6 +3108,9 @@ "val" : "NIF_Subcellular:sao1615953555" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28301" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "GO:0000789" }, { @@ -4768,6 +4812,21 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0006949", + "lbl" : "syncytium formation", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane. Syncytia are normally derived from single cells that fuse or fail to complete cell division.", + "xrefs" : [ "ISBN:0198506732" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0006955", "lbl" : "immune response", @@ -4826,6 +4885,29 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0007009", + "lbl" : "plasma membrane organization", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the plasma membrane.", + "xrefs" : [ "GOC:dph", "GOC:jl", "GOC:mah" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_chembl" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "plasma membrane organisation" + }, { + "pred" : "hasRelatedSynonym", + "val" : "plasma membrane organization and biogenesis", + "xrefs" : [ "GOC:mah" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0007154", "lbl" : "cell communication", @@ -5634,6 +5716,29 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0010256", + "lbl" : "endomembrane system organization", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endomembrane system.", + "xrefs" : [ "GOC:mah", "GOC:sm" ] + }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_drosophila" ], + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "endomembrane organization" + }, { + "pred" : "hasExactSynonym", + "val" : "endomembrane system organisation", + "xrefs" : [ "GOC:mah" ] + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0010324", "lbl" : "membrane invagination", @@ -5995,6 +6100,15 @@ "val" : "stem cell renewal" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_2" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_2157" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -7142,27 +7256,6 @@ "val" : "cellular_component" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0032993", - "lbl" : "protein-DNA complex", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A macromolecular complex containing both protein and DNA molecules.", - "xrefs" : [ "GOC:mah" ] - }, - "comments" : [ "Note that this term is intended to classify complexes that have DNA as one of the members of the complex, that is, the complex does not exist if DNA is not present. Protein complexes that interact with DNA e.g. transcription factor complexes should not be classified here." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "DNA-protein complex", - "xrefs" : [ "GOC:mah" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0033151", "lbl" : "V(D)J recombination", @@ -7640,6 +7733,7 @@ "val" : "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.", "xrefs" : [ "GOC:go_curators" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "membrane-enclosed organelle" @@ -7648,6 +7742,9 @@ "val" : "NIF_Subcellular:sao414196390" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28153" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -7661,7 +7758,7 @@ "val" : "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes.", "xrefs" : [ "GOC:go_curators" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_mouse" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_mouse" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "non-membrane-enclosed organelle" @@ -7675,6 +7772,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/21881" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28153" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -7689,8 +7789,11 @@ "val" : "Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.", "xrefs" : [ "GOC:go_curators" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_pir" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28153" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -7839,12 +7942,15 @@ "val" : "A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component.", "xrefs" : [ "GOC:jl", "GOC:mah" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_pir" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "cellular component biogenesis at cellular level" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/27194" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "GO:0071843" }, { @@ -7994,6 +8100,30 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0045026", + "lbl" : "plasma membrane fusion", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell.", + "xrefs" : [ "GOC:elh", "GOC:mtg_muscle" ] + }, + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "cell fusion" + }, { + "pred" : "hasBroadSynonym", + "val" : "cell-cell fusion" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", + "val" : "GO:0006947" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0045087", "lbl" : "innate immune response", @@ -8015,6 +8145,15 @@ "val" : "Wikipedia:Innate_immune_system" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_2" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_2157" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "GO:0002226" }, { @@ -8715,6 +8854,42 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0050908", + "lbl" : "detection of light stimulus involved in visual perception", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "The series of events involved in visual perception in which a light stimulus is received and converted into a molecular signal.", + "xrefs" : [ "GOC:ai", "GOC:dos" ] + }, + "synonyms" : [ { + "pred" : "hasExactSynonym", + "val" : "sensory detection of light during visual perception" + }, { + "pred" : "hasExactSynonym", + "val" : "sensory detection of light stimulus during visual perception" + }, { + "pred" : "hasExactSynonym", + "val" : "sensory transduction of light during visual perception" + }, { + "pred" : "hasExactSynonym", + "val" : "sensory transduction of light stimulus during visual perception" + }, { + "pred" : "hasExactSynonym", + "val" : "visual perception, detection of light stimulus" + }, { + "pred" : "hasExactSynonym", + "val" : "visual perception, sensory transduction during perception of light" + }, { + "pred" : "hasExactSynonym", + "val" : "visual perception, sensory transduction of light stimulus" + } ], + "basicPropertyValues" : [ { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0050953", "lbl" : "sensory perception of light stimulus", @@ -9938,6 +10113,36 @@ "val" : "biological_process" } ] } + }, { + "id" : "http://purl.obolibrary.org/obo/GO_0140253", + "lbl" : "cell-cell fusion", + "type" : "CLASS", + "meta" : { + "definition" : { + "val" : "A cellular process in which two or more cells combine together, their plasma membrane fusing, producing a single cell. In some cases, nuclei fuse, producing a polyploid cell, while in other cases, nuclei remain separate, producing a syncytium.", + "xrefs" : [ "Wikipedia:Cell_fusion" ] + }, + "synonyms" : [ { + "pred" : "hasBroadSynonym", + "val" : "cell fusion" + }, { + "pred" : "hasExactSynonym", + "val" : "cell cell fusion" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/15939" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", + "val" : "pg" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", + "val" : "2018-08-13T18:38:18Z" + }, { + "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", + "val" : "biological_process" + } ] + } }, { "id" : "http://purl.obolibrary.org/obo/GO_0140352", "lbl" : "export from cell", @@ -13541,15 +13746,15 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/PR_000064867", - "lbl" : "protein-containing molecular entity", + "id" : "http://purl.obolibrary.org/obo/PR_000050567", + "lbl" : "protein-containing material entity", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A molecular entity that minimally consists of a protein.", + "val" : "A material entity that minimally consists of a protein.", "xrefs" : [ "PRO:DAN" ] }, - "comments" : [ "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565)." ], + "comments" : [ "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566)." ], "synonyms" : [ { "pred" : "hasNarrowSynonym", "val" : "protein", @@ -16844,7 +17049,7 @@ "val" : "The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO].", "xrefs" : [ "BIRNLEX:844", "ISBN:0-14-051288-8", "ISBN:3110148986", "NLM:nervous+system", "WB:rynl", "Wikipedia:Nervous_system", "ZFIN:curator" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#cumbo", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#cumbo", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "neurological system", @@ -16917,9 +17122,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -22124,7 +22326,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000050", - "lbl" : "part_of", + "lbl" : "part of", "type" : "PROPERTY", "propertyType" : "OBJECT", "meta" : { @@ -22147,9 +22349,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "part_of" @@ -22169,7 +22368,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000051", - "lbl" : "has_part", + "lbl" : "has part", "type" : "PROPERTY", "propertyType" : "OBJECT", "meta" : { @@ -22192,9 +22391,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_part" @@ -26059,6 +26255,10 @@ "id" : "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "type" : "PROPERTY", "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#gocheck_obsoletion_candidate", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/go#goslim_agr", "type" : "PROPERTY", @@ -26397,6 +26597,10 @@ "id" : "http://purl.org/dc/terms/date", "type" : "PROPERTY", "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/description", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/license", "type" : "PROPERTY", @@ -26422,12 +26626,10 @@ "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "lbl" : "created by", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "lbl" : "creation date", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { @@ -26520,7 +26722,6 @@ "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#id", - "lbl" : "id", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { @@ -26590,20 +26791,16 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000000", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_131567" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000006", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000101" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000006", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000197" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000007", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0002321" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000034", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000034", "pred" : "is_a", @@ -26706,6 +26903,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000040", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000040", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -26785,7 +26986,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000066", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000066", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -26850,6 +27051,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000092", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000092", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -26900,6 +27105,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000094", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000094", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -27016,6 +27225,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000148", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000147" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000148", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000148", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -27040,6 +27253,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000152", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000151" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000152", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000152", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -27048,6 +27265,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000163", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000151" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000163", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000163", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -27060,6 +27281,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000187", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000183" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000187", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000187", "pred" : "is_a", @@ -27071,7 +27296,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000188", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000188", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -27089,31 +27314,17 @@ "pred" : "http://purl.obolibrary.org/obo/RO_0002202", "obj" : "http://purl.obolibrary.org/obo/CL_0000514" }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000197", + "sub" : "http://purl.obolibrary.org/obo/CL_0000210", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000197", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", - "obj" : "http://purl.obolibrary.org/obo/UBERON_0001032" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000197", - "pred" : "http://purl.obolibrary.org/obo/RO_0002215", - "obj" : "http://purl.obolibrary.org/obo/GO_0050906" + "obj" : "http://purl.obolibrary.org/obo/CL_0000101" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000210", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000006", - "meta" : { - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#is_inferred", - "val" : "true" - } ] - } + "obj" : "http://purl.obolibrary.org/obo/CL_0008028" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000210", "pred" : "http://purl.obolibrary.org/obo/RO_0002215", - "obj" : "http://purl.obolibrary.org/obo/GO_0050962" + "obj" : "http://purl.obolibrary.org/obo/GO_0050908" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000211", "pred" : "is_a", @@ -27126,6 +27337,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000219", "pred" : "http://purl.obolibrary.org/obo/RO_0002215", "obj" : "http://purl.obolibrary.org/obo/GO_0048870" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000221", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000221", "pred" : "is_a", @@ -27134,6 +27349,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000221", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000924" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000222", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000222", "pred" : "is_a", @@ -27142,6 +27361,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000222", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000926" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000223", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000223", "pred" : "is_a", @@ -27150,6 +27373,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000223", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000925" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000226", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000226", "pred" : "is_a", @@ -27158,6 +27385,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000226", "pred" : "http://purl.obolibrary.org/obo/RO_0000053", "obj" : "http://purl.obolibrary.org/obo/PATO_0001407" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000228", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000228", "pred" : "is_a", @@ -27228,7 +27459,7 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0000000" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000255", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000325", @@ -27257,7 +27488,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000349", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000349", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -27294,7 +27525,7 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0010017" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000365", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000393", @@ -27312,6 +27543,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000451", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000145" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000451", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000451", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -27402,7 +27637,7 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000518", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000526", @@ -27476,6 +27711,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000557", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_1001610" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000557", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000557", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -27518,6 +27757,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000559", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000559", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -27544,6 +27787,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000566", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0011026" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000566", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000566", "pred" : "http://purl.obolibrary.org/obo/RO_0002104", @@ -27622,6 +27869,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000680", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000055" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000680", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000680", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -27678,7 +27929,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0002405" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000738", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000738", @@ -27708,6 +27959,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000746", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", "obj" : "http://purl.obolibrary.org/obo/CL_0000513" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000763", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000763", "pred" : "is_a", @@ -27768,6 +28023,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000825", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000825", "pred" : "http://purl.obolibrary.org/obo/CL_4030046", @@ -27806,6 +28065,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000826", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000826", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -27840,10 +28103,18 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000827", "pred" : "http://purl.obolibrary.org/obo/RO_0002215", "obj" : "http://purl.obolibrary.org/obo/GO_0030217" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000837", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000837", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0008001" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000837", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000837", "pred" : "http://purl.obolibrary.org/obo/CL_4030046", @@ -27997,7 +28268,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0001035", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0001035", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -28112,6 +28383,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0002009", "pred" : "http://purl.obolibrary.org/obo/RO_0002215", "obj" : "http://purl.obolibrary.org/obo/GO_0043011" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0002031", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002031", "pred" : "is_a", @@ -28124,6 +28399,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0002031", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", "obj" : "http://purl.obolibrary.org/obo/CL_0002032" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0002032", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002032", "pred" : "is_a", @@ -28183,7 +28462,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002319", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002319", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -28191,7 +28470,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002320", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002320", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -28203,11 +28482,11 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002372", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000228" + "obj" : "http://purl.obolibrary.org/obo/CL_0000737" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002372", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000737" + "obj" : "http://purl.obolibrary.org/obo/CL_4052002" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002372", "pred" : "http://purl.obolibrary.org/obo/RO_0000053", @@ -28215,7 +28494,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002494", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002494", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -28268,6 +28547,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0008019", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000219" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0008019", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0008019", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -28276,6 +28559,14 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0008019", "pred" : "http://purl.obolibrary.org/obo/RO_0002215", "obj" : "http://purl.obolibrary.org/obo/GO_0016477" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0008028", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000540" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0008028", + "pred" : "http://purl.obolibrary.org/obo/RO_0002216", + "obj" : "http://purl.obolibrary.org/obo/GO_0007601" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0009004", "pred" : "is_a", @@ -28304,6 +28595,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0011012", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0002321" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0011026", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0011026", "pred" : "is_a", @@ -28348,14 +28643,30 @@ "sub" : "http://purl.obolibrary.org/obo/CL_1001610", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0012429" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_4052002", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000228" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_4052002", + "pred" : "http://purl.obolibrary.org/obo/RO_0002353", + "obj" : "http://purl.obolibrary.org/obo/GO_0000768" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0000323", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0005773" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0000768", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0006949" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0000768", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0140253" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0000785", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0032993" + "obj" : "http://purl.obolibrary.org/obo/GO_0110165" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0000785", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -28930,6 +29241,18 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0006936", "pred" : "http://purl.obolibrary.org/obo/BFO_0000066", "obj" : "http://purl.obolibrary.org/obo/UBERON_0002385" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0006949", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0009987" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0006949", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0048646" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0006949", + "pred" : "http://purl.obolibrary.org/obo/RO_0002297", + "obj" : "http://purl.obolibrary.org/obo/CL_0000228" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0006955", "pred" : "is_a", @@ -28946,6 +29269,18 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0006996", "pred" : "http://purl.obolibrary.org/obo/RO_0002592", "obj" : "http://purl.obolibrary.org/obo/GO_0043226" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0007009", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0061024" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0007009", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/GO_0010256" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0007009", + "pred" : "http://purl.obolibrary.org/obo/RO_0002592", + "obj" : "http://purl.obolibrary.org/obo/GO_0005886" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0007154", "pred" : "is_a", @@ -29166,6 +29501,14 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0009987", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0008150" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0010256", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0016043" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0010256", + "pred" : "http://purl.obolibrary.org/obo/RO_0002592", + "obj" : "http://purl.obolibrary.org/obo/GO_0012505" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0010324", "pred" : "is_a", @@ -29632,12 +29975,8 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0005575" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0032991", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", - "obj" : "http://purl.obolibrary.org/obo/PR_000000001" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0032993", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0032991" + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0033151", "pred" : "is_a", @@ -29906,6 +30245,18 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0044419", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0008150" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0045026", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0007009" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0045026", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0061025" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0045026", + "pred" : "http://purl.obolibrary.org/obo/RO_0012008", + "obj" : "http://purl.obolibrary.org/obo/GO_0005886" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0045087", "pred" : "is_a", @@ -30218,6 +30569,14 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0050906", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/GO_0007600" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0050908", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0050962" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0050908", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/GO_0007601" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0050953", "pred" : "is_a", @@ -30482,6 +30841,10 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0098644", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0099080" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0098644", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0098644", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -30658,6 +31021,14 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0140029", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/GO_0006887" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0140253", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/GO_0009987" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0140253", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", + "obj" : "http://purl.obolibrary.org/obo/GO_0045026" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0140352", "pred" : "is_a", @@ -31033,7 +31404,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/PR_000000001", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000064867" + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/PR_000000001", "pred" : "http://purl.obolibrary.org/obo/RO_0002353", @@ -31267,7 +31638,7 @@ "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PR_000001006" }, { - "sub" : "http://purl.obolibrary.org/obo/PR_000064867", + "sub" : "http://purl.obolibrary.org/obo/PR_000050567", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { @@ -31326,7 +31697,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000043", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000043", @@ -31336,6 +31707,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000043", "pred" : "http://purl.obolibrary.org/obo/RO_0002176", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001630" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0000058", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000058", "pred" : "is_a", @@ -31456,7 +31831,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0001434" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000075", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000075", @@ -31558,7 +31933,7 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0007369" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000109", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000110", @@ -31578,7 +31953,7 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0001841" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000110", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000111", @@ -31594,7 +31969,7 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0048513" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000111", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", @@ -31602,7 +31977,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0004921" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", @@ -31626,7 +32001,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0011216" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000383", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000383", @@ -31742,6 +32117,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000481", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000479" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0000483", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000483", "pred" : "is_a", @@ -31756,7 +32135,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0005769" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000483", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208", "meta" : { "basicPropertyValues" : [ { @@ -31794,7 +32173,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0010316" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000923", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000924", @@ -31864,7 +32243,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0035804" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000930", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000949", @@ -31872,7 +32251,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0015204" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000949", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000949", @@ -31944,7 +32323,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000467" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001009", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001009", @@ -31976,7 +32355,7 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0000540" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001016", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001016", @@ -32023,7 +32402,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0001016" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001017", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001017", @@ -32135,7 +32514,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0004765" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001474", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001474", @@ -32157,7 +32536,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0001007" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001555", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001555", @@ -32233,7 +32612,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002193", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002204", @@ -32293,7 +32672,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0011137" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711", "meta" : { "basicPropertyValues" : [ { @@ -32345,7 +32724,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002329", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711", "meta" : { "basicPropertyValues" : [ { @@ -32363,13 +32742,17 @@ "val" : "ZFA" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0002330", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002330", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000467" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002330", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002330", @@ -32406,7 +32789,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_89593" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", @@ -32454,6 +32837,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002346", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/CL_0000133" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0002365", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002365", "pred" : "is_a", @@ -32521,7 +32908,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000479" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002384", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002385", @@ -32537,7 +32924,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0001015" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002385", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002385", @@ -32567,7 +32954,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002390", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002390", @@ -32605,7 +32992,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0001474" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002481", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002530", @@ -32613,7 +33000,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000062" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002530", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002530", @@ -32683,7 +33070,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000926" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003068", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003068", @@ -32703,7 +33090,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0016879" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003075", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711", "meta" : { "basicPropertyValues" : [ { @@ -32800,7 +33187,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003081", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003081", @@ -32840,7 +33227,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000479" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003104", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003104", @@ -33049,7 +33436,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004770", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004770", @@ -33073,7 +33460,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0003068" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004880", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004905", @@ -33105,7 +33492,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000060" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004923", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005061", @@ -33157,7 +33544,7 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0000187" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005090", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005157", @@ -33225,6 +33612,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0005764", "pred" : "http://purl.obolibrary.org/obo/RO_0002007", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", "pred" : "is_a", @@ -33245,7 +33636,7 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0005587" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", @@ -33293,7 +33684,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0005423" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006268", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006268", @@ -33315,7 +33706,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000307" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006595", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006595", @@ -33339,7 +33730,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000307" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006601", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006601", @@ -33355,7 +33746,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000307" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006603", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006603", @@ -33487,6 +33878,10 @@ "val" : "AEO" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0007845", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007845", "pred" : "is_a", @@ -33687,6 +34082,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0011822", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/GO_0071953" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0011823", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0011823", "pred" : "is_a", @@ -33695,6 +34094,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0011823", "pred" : "http://purl.obolibrary.org/obo/RO_0002473", "obj" : "http://purl.obolibrary.org/obo/UBERON_0011860" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0011860", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0011860", "pred" : "is_a", @@ -33757,7 +34160,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0011997", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0012429", @@ -33827,7 +34230,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000475" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0013701", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0013702", @@ -33857,7 +34260,7 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0000100" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0014892", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0014892", @@ -33889,7 +34292,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0015212", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0015228", @@ -35189,13 +35592,6 @@ "obj" : "http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to" } ], "logicalDefinitionAxioms" : [ { - "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000006", - "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000197", "http://purl.obolibrary.org/obo/CL_0000540" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002215", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0050906" - } ] - }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000034", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ], "restrictions" : [ { @@ -35415,22 +35811,12 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0001134" } ] - }, { - "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000197", - "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ], - "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", - "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0001032" - }, { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002215", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0050906" - } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000210", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ], "restrictions" : [ { "propertyId" : "http://purl.obolibrary.org/obo/RO_0002215", - "fillerId" : "http://purl.obolibrary.org/obo/GO_0050962" + "fillerId" : "http://purl.obolibrary.org/obo/GO_0050908" } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000219", @@ -35484,7 +35870,7 @@ "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000255", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002160", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002162", "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" } ] }, { @@ -35505,7 +35891,7 @@ "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000365", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0010017" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002160", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002162", "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" } ] }, { @@ -36052,6 +36438,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_8600004" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/CL_0008028", + "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000540" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002216", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0007601" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0009004", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0002319" ], @@ -36101,6 +36494,23 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0002371" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/CL_4052002", + "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0000053", + "fillerId" : "http://purl.obolibrary.org/obo/PATO_0001908" + }, { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002353", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0000768" + } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0000768", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0006949" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000051", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0045026" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0001677", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0022607" ], @@ -36248,6 +36658,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0012008", "fillerId" : "http://purl.obolibrary.org/obo/GO_0012506" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0006949", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0048646" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002297", + "fillerId" : "http://purl.obolibrary.org/obo/CL_0000228" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0006996", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016043" ], @@ -36255,6 +36672,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002592", "fillerId" : "http://purl.obolibrary.org/obo/GO_0043226" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0007009", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016043" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002592", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0005886" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0007275", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0048856" ], @@ -36304,6 +36728,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002296", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0000479" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0010256", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016043" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002592", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0012505" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0012506", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0016020" ], @@ -36577,6 +37008,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/RO_0002592", "fillerId" : "http://purl.obolibrary.org/obo/GO_0032991" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045026", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009987" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/RO_0012008", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0005886" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0045321", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0001775" ], @@ -36724,6 +37162,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/GO_0007600" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/GO_0050908", + "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009583" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", + "fillerId" : "http://purl.obolibrary.org/obo/GO_0007601" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/GO_0050962", "genusIds" : [ "http://purl.obolibrary.org/obo/GO_0009583" ], diff --git a/subsets/general_cell_types_upper_slim.obo b/subsets/general_cell_types_upper_slim.obo index 90957720c..9c6b81e98 100644 --- a/subsets/general_cell_types_upper_slim.obo +++ b/subsets/general_cell_types_upper_slim.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: cl/releases/2024-08-16/subsets/general_cell_types_upper_slim.owl +data-version: cl/releases/2024-09-26/subsets/general_cell_types_upper_slim.owl subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" subsetdef: attribute_slim "" @@ -19,6 +19,7 @@ subsetdef: eye_upper_slim "a subset of general classes related to specific cell subsetdef: functional_classification "" subsetdef: general_cell_types_upper_slim "a subset of general classes of cell types in the cell ontology." subsetdef: gocheck_do_not_annotate "" +subsetdef: gocheck_obsoletion_candidate "" subsetdef: goslim_agr "" subsetdef: goslim_candida "" subsetdef: goslim_chembl "" @@ -95,7 +96,7 @@ idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# idspace: sssom https://w3id.org/sssom/ idspace: terms http://purl.org/dc/terms/ ontology: cl/subsets/general_cell_types_upper_slim -property_value: owl:versionInfo "2024-08-16" xsd:string +property_value: owl:versionInfo "2024-09-26" xsd:string [Term] id: CL:0000000 @@ -118,20 +119,7 @@ is_a: UBERON:0000061 ! anatomical structure disjoint_from: GO:0031012 ! extracellular matrix disjoint_from: GO:0032991 ! protein-containing complex disjoint_from: GO:0043226 ! organelle -relationship: RO:0002160 NCBITaxon:131567 ! only in taxon cellular organisms - -[Term] -id: CL:0000006 -name: neuronal receptor cell -def: "Any sensory receptor cell that is a(n) neuron and is capable of some detection of stimulus involved in sensory perception." [FBC:Autogenerated] -subset: cellxgene_subset -synonym: "neuronal receptor cell (sensu Animalia)" EXACT [] -xref: ZFA:0009001 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000101 ! sensory neuron -is_a: CL:0000197 ! sensory receptor cell -intersection_of: CL:0000197 ! sensory receptor cell -intersection_of: CL:0000540 ! neuron -intersection_of: capable_of GO:0050906 ! detection of stimulus involved in sensory perception +relationship: RO:0002162 NCBITaxon:131567 ! in taxon cellular organisms [Term] id: CL:0000007 @@ -152,6 +140,7 @@ synonym: "animal stem cell" EXACT [] xref: CALOHA:TS-2086 xref: FMA:63368 xref: ZFA:0005957 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0011115 ! precursor cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0017145 ! stem cell division @@ -236,6 +225,7 @@ xref: FMA:83553 xref: ZFA:0009017 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0002194 {is_inferred="true"} ! monopoietic cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002194 ! monopoietic cell intersection_of: capable_of GO:0030224 ! monocyte differentiation intersection_of: has_part CL:0017503 ! basophilic cytoplasm @@ -376,7 +366,7 @@ xref: FBbt:00000124 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ xref: FMA:66768 xref: WBbt:0003672 xref: ZFA:0009034 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell disjoint_from: CL:0000738 ! leukocyte relationship: part_of UBERON:0000483 ! epithelium property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI @@ -447,6 +437,7 @@ xref: ZFA:0009047 {sssom:mapping_justification="https://w3id.org/semapv/vocab/Un is_a: CL:0000518 ! phagocyte (sensu Vertebrata) is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte is_a: CL:0001035 {is_inferred="true"} ! bone cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: capable_of GO:0045453 ! bone resorption intersection_of: has_part PR:000001850 ! cathepsin K @@ -483,6 +474,7 @@ xref: FMA:62854 xref: ZFA:0009048 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000081 ! blood cell is_a: CL:0000766 {is_inferred="true"} ! myeloid leukocyte +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000766 ! myeloid leukocyte intersection_of: capable_of GO:0008015 ! blood circulation intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -549,12 +541,14 @@ def: "A vertebrate phagocyte with a single nucleus." [GOC:add, GOC:tfm, ISBN:078 subset: cellxgene_subset subset: human_reference_atlas xref: BTO:0001433 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000113 xref: ZFA:0009064 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000518 {is_inferred="true"} ! phagocyte (sensu Vertebrata) is_a: CL:0000842 ! mononuclear cell intersection_of: CL:0000518 ! phagocyte (sensu Vertebrata) intersection_of: bearer_of PATO:0001407 ! mononucleate property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nMononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. \nIn addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses.\nMononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer." xsd:string {xref="DOI:10.1016/j.coi.2005.11.008", xref="DOI:10.1038/nri3087", xref="DOI:10.3389/fimmu.2019.01893"} [Term] id: CL:0000125 @@ -570,9 +564,11 @@ xref: BTO:0002606 xref: CALOHA:TS-0415 xref: FBbt:00005144 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:54536 +xref: https://cellxgene.cziscience.com/cellguide/CL_0000125 xref: ZFA:0009073 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000095 ! neuron associated cell property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nGlial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons.\nThese different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning.\nOligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. \nMicroglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response.\nDespite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis." xsd:string {xref="DOI:10.1002/glia.24343", xref="DOI:10.1038/nn1988", xref="DOI:10.1101/cshperspect.a020602", xref="DOI:10.1126/science.aat0473", xref="DOI:10.3389/fncel.2017.00024"} [Term] id: CL:0000133 @@ -665,6 +661,7 @@ xref: MESH:D008544 xref: VHOG:0001679 xref: ZFA:0009091 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000147 ! pigment cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000147 ! pigment cell intersection_of: has_part GO:0042470 ! melanosome intersection_of: RO:0002202 CL:0000541 ! develops from melanoblast @@ -698,6 +695,7 @@ subset: general_cell_types_upper_slim xref: FMA:16014 xref: ZFA:0009092 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000151 ! secretory cell intersection_of: part_of UBERON:0002365 ! exocrine gland relationship: part_of UBERON:0002365 ! exocrine gland @@ -713,6 +711,7 @@ synonym: "endocrinocyte" EXACT [] xref: FMA:83809 xref: ZFA:0009096 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000151 ! secretory cell +is_a: CL:0000255 ! eukaryotic cell relationship: part_of UBERON:0000949 ! endocrine system property_value: RO:0002175 NCBITaxon:9606 @@ -738,6 +737,7 @@ xref: FMA:67328 xref: WBbt:0003675 xref: ZFA:0009114 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000183 ! contractile cell +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000393 ! electrically responsive cell relationship: RO:0002202 CL:0000056 ! develops from myoblast property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI @@ -754,7 +754,7 @@ xref: BTO:0004392 xref: CALOHA:TS-2158 xref: FMA:9727 xref: ZFA:0009115 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001134 ! skeletal muscle tissue relationship: part_of UBERON:0001134 ! skeletal muscle tissue @@ -780,33 +780,21 @@ is_a: CL:0008007 ! visceral muscle cell relationship: RO:0002202 CL:0000514 ! develops from smooth muscle myoblast property_value: RO:0002175 NCBITaxon:9606 -[Term] -id: CL:0000197 -name: sensory receptor cell -def: "A cell that is capable of detection of a stimulus involved in sensory perception." [] -synonym: "receptor cell" EXACT [] -xref: MESH:D011984 -is_a: CL:0000000 ! cell -intersection_of: CL:0000000 ! cell -intersection_of: capable_of GO:0050906 ! detection of stimulus involved in sensory perception -intersection_of: part_of UBERON:0001032 ! sensory system -relationship: capable_of GO:0050906 ! detection of stimulus involved in sensory perception -relationship: part_of UBERON:0001032 ! sensory system - [Term] id: CL:0000210 name: photoreceptor cell -def: "A cell specialized to detect and transduce light." [MESH:D010786] +def: "A cell specialized in detecting light stimuli that are involved in visual perception." [MESH:D010786] subset: cellxgene_subset xref: BTO:0001060 xref: CALOHA:TS-0868 xref: FBbt:00004211 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} xref: FMA:86740 xref: ZFA:0009127 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000006 {is_inferred="true"} ! neuronal receptor cell +is_a: CL:0000101 ! sensory neuron +is_a: CL:0008028 ! visual system neuron intersection_of: CL:0000540 ! neuron -intersection_of: capable_of GO:0050962 ! detection of light stimulus involved in sensory perception -relationship: capable_of GO:0050962 ! detection of light stimulus involved in sensory perception +intersection_of: capable_of GO:0050908 ! detection of light stimulus involved in visual perception +relationship: capable_of GO:0050908 ! detection of light stimulus involved in visual perception property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg" xsd:anyURI [Term] @@ -833,6 +821,7 @@ def: "A cell of the outer of the three germ layers of the embryo." [MESH:D004475 synonym: "ectoderm cell" EXACT [] xref: FMA:72549 xref: ZFA:0009137 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000924 ! ectoderm @@ -845,6 +834,7 @@ synonym: "mesoblast" EXACT [] synonym: "mesoderm cell" EXACT [] xref: FMA:72554 xref: ZFA:0009138 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000926 ! mesoderm @@ -855,6 +845,7 @@ def: "A cell of the inner of the three germ layers of the embryo." [MESH:D004707 synonym: "endoderm cell" EXACT [] xref: FMA:72555 xref: ZFA:0009139 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000925 ! endoderm @@ -862,6 +853,7 @@ relationship: part_of UBERON:0000925 ! endoderm id: CL:0000226 name: single nucleate cell def: "A cell with a single nucleus." [FB:ma, GOC:tfm] +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002242 ! nucleate cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0001407 ! mononucleate @@ -870,12 +862,10 @@ relationship: bearer_of PATO:0001407 ! mononucleate [Term] id: CL:0000228 name: multinucleate cell -def: "A cell with more than one nucleus." [FB:ma] -synonym: "syncitium" EXACT [] -synonym: "syncytial cell" EXACT [] -synonym: "syncytium" EXACT [] -xref: AEO:0000203 -xref: WBbt:0008074 +def: "A cell with more than one nucleus." [FB:ma, Wikipedia:Multinucleate] +synonym: "multinucleated cells" EXACT [Wikipedia:Multinucleate] +synonym: "polynuclear cells" EXACT [Wikipedia:Multinucleate] +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002242 ! nucleate cell intersection_of: CL:0000000 ! cell intersection_of: bearer_of PATO:0001908 ! multinucleate @@ -950,13 +940,13 @@ property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000255 name: eukaryotic cell -def: "Any cell that only exists in Eukaryota." [FBC:Autogenerated] +def: "Any cell that in taxon some Eukaryota." [FBC:Autogenerated] subset: cellxgene_subset xref: MESH:D005057 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell -intersection_of: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota -relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +intersection_of: RO:0002162 NCBITaxon:2759 ! in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 ! in taxon Eukaryota [Term] id: CL:0000325 @@ -988,7 +978,7 @@ name: extraembryonic cell def: "Any cell that is part of some extraembryonic structure." [FBC:Autogenerated] subset: general_cell_types_upper_slim xref: ZFA:0009176 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0000478 ! extraembryonic structure relationship: part_of UBERON:0000478 ! extraembryonic structure @@ -1023,8 +1013,8 @@ is_a: CL:0000007 ! early embryonic cell (metazoa) is_a: CL:0000255 ! eukaryotic cell is_a: CL:0010017 ! zygote intersection_of: CL:0010017 ! zygote -intersection_of: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa -relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +intersection_of: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa [Term] id: CL:0000393 @@ -1056,6 +1046,7 @@ xref: MESH:D003713 xref: ZFA:0009209 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000113 ! mononuclear phagocyte is_a: CL:0000145 ! professional antigen presenting cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000738 ! leukocyte intersection_of: bearer_of PATO:0001407 ! mononucleate intersection_of: capable_of GO:0001816 ! cytokine production @@ -1149,7 +1140,7 @@ name: phagocyte (sensu Vertebrata) def: "A phagocyte in vertebrates that is able to phagocytosis." [GOC:tfm] is_a: CL:0000234 ! phagocyte is_a: CL:0000255 ! eukaryotic cell -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata [Term] id: CL:0000526 @@ -1250,6 +1241,7 @@ is_a: CL:0000763 ! myeloid cell is_a: CL:0001012 ! CD7-negative lymphoid progenitor OR granulocyte monocyte progenitor is_a: CL:0011026 ! progenitor cell is_a: CL:1001610 ! bone marrow hematopoietic cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002032 ! hematopoietic oligopotent progenitor cell intersection_of: capable_of GO:0030225 ! macrophage differentiation intersection_of: capable_of GO:0030851 ! granulocyte differentiation @@ -1280,6 +1272,7 @@ xref: FMA:83551 xref: ZFA:0009253 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000763 ! myeloid cell is_a: CL:0002194 {is_inferred="true"} ! monopoietic cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0002194 ! monopoietic cell intersection_of: capable_of GO:0030224 ! monocyte differentiation intersection_of: has_part GO:0042582 ! azurophil granule @@ -1299,6 +1292,7 @@ synonym: "chondroplast" EXACT [] xref: ZFA:0009258 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000134 {is_inferred="true"} ! mesenchymal stem cell is_a: CL:0011026 ! progenitor cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: RO:0002104 PR:000001444 ! has plasma membrane part cadherin-5 intersection_of: RO:0002104 PR:000002112 ! has plasma membrane part vascular endothelial growth factor receptor 2 @@ -1375,6 +1369,7 @@ def: "A non-terminally differentiated cell that is capable of developing into a subset: cellxgene_subset xref: ZFA:0009291 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0011115 ! precursor cell intersection_of: RO:0002203 CL:0000187 ! develops into muscle cell relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell @@ -1432,7 +1427,7 @@ intersection_of: bearer_of PATO:0002505 ! nucleated intersection_of: capable_of GO:0001667 ! ameboidal-type cell migration relationship: capable_of GO:0001667 ! ameboidal-type cell migration relationship: part_of UBERON:0002405 ! immune system -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002202 CL:0000037 ! develops from hematopoietic stem cell property_value: RO:0002175 NCBITaxon:9606 @@ -1476,6 +1471,7 @@ xref: BTO:0001441 xref: CALOHA:TS-0647 xref: MESH:D022423 xref: ZFA:0009324 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000988 {is_inferred="true"} ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: RO:0002202 CL:0000049 ! develops from common myeloid progenitor @@ -1523,6 +1519,7 @@ synonym: "preNK cell" RELATED [PMID:11532393] synonym: "pro-natural killer cell" EXACT [] xref: ZFA:0009348 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000838 {is_inferred="true"} ! lymphoid lineage restricted progenitor cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: CL:4030046 PR:000001874 ! lacks_plasma_membrane_part KLRB1-like protein intersection_of: CL:4030046 PR:000002065 ! lacks_plasma_membrane_part mast/stem cell growth factor receptor @@ -1557,6 +1554,7 @@ synonym: "progenitor B-lymphocyte" EXACT [] xref: BTO:0003104 xref: ZFA:0009349 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000838 {is_inferred="true"} ! lymphoid lineage restricted progenitor cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000838 ! lymphoid lineage restricted progenitor cell intersection_of: has_part PR:000001903 ! paired box protein PAX-5 intersection_of: has_part PR:000006611 ! DNA nucleotidylexotransferase @@ -1597,7 +1595,9 @@ synonym: "MPP" EXACT [] xref: BTO:0000725 xref: CALOHA:TS-0448 xref: ZFA:0009354 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001402 ! multipotent intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -1745,7 +1745,7 @@ name: bone cell def: "A connective tissue cell found in bone." [GO_REF:0000034, GOC:add] subset: general_cell_types_upper_slim subset: human_reference_atlas -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001474 ! bone element relationship: part_of UBERON:0001474 ! bone element @@ -1844,6 +1844,7 @@ id: CL:0002031 name: hematopoietic lineage restricted progenitor cell def: "A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells." [GOC:tfm, PMID:19022770] subset: blood_and_immune_upper_slim +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001400 ! unipotent @@ -1859,6 +1860,7 @@ name: hematopoietic oligopotent progenitor cell def: "A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities." [GOC:tfm, https://orcid.org/0000-0001-5208-3432, PMID:19022770] comment: This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). subset: blood_and_immune_upper_slim +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001401 ! oligopotent @@ -1927,7 +1929,7 @@ def: "A cell that is part of the nervous system." [GOC:tfm, ISBN:0618947256] subset: cellxgene_subset xref: CALOHA:TS-2040 xref: FMA:70333 -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001016 ! nervous system relationship: part_of UBERON:0001016 ! nervous system @@ -1943,7 +1945,7 @@ xref: CALOHA:TS-2096 xref: FMA:63875 xref: MESH:D003239 xref: ZFA:0009392 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0002384 ! connective tissue relationship: part_of UBERON:0002384 ! connective tissue @@ -1965,12 +1967,12 @@ creation_date: 2010-09-15T03:39:21Z [Term] id: CL:0002372 name: myotube -def: "A transversely striated, synctial muscle cell, formed by the fusion of myoblasts." [GOC:dos, GOC:tfm, ISBN:0323052908, PMID:22274696] -synonym: "myotubule" EXACT [] -synonym: "single cell sarcomere" EXACT [] +def: "A transversely striated, multinucleated syncytial muscle cell, formed by the fusion of myoblasts during muscle development." [GOC:dos, GOC:tfm, ISBN:0323052908, PMID:22274696] +synonym: "myofiber" EXACT [FBbt:00005812] +synonym: "myofibril" EXACT [FBbt:00005812] xref: FBbt:00005812 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ManualMappingCuration"} -is_a: CL:0000228 ! multinucleate cell is_a: CL:0000737 ! striated muscle cell +is_a: CL:4052002 ! syncytial cell intersection_of: CL:0000187 ! muscle cell intersection_of: bearer_of PATO:0001908 ! multinucleate intersection_of: bearer_of PATO:0002478 ! transversely striated @@ -1989,7 +1991,7 @@ xref: BTO:0001539 xref: CALOHA:TS-0115 xref: FMA:83808 xref: FMA:84791 -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0007100 ! primary circulatory organ relationship: part_of UBERON:0007100 ! primary circulatory organ @@ -2063,10 +2065,22 @@ subset: cellxgene_subset subset: human_reference_atlas synonym: "mesenchyme cell" EXACT [] is_a: CL:0000219 ! motile cell +is_a: CL:0000255 ! eukaryotic cell relationship: capable_of GO:0016477 ! cell migration relationship: part_of UBERON:0003104 ! mesenchyme property_value: RO:0002175 NCBITaxon:9606 +[Term] +id: CL:0008028 +name: visual system neuron +def: "Any neuron that is capable of part of some visual perception." [FBC:Autogenerated] +is_a: CL:0000540 ! neuron +intersection_of: CL:0000540 ! neuron +intersection_of: capable_of_part_of GO:0007601 ! visual perception +relationship: capable_of_part_of GO:0007601 ! visual perception +property_value: terms:contributor https://orcid.org/0000-0002-7073-9172 +creation_date: 2017-07-09T19:12:36Z + [Term] id: CL:0009004 name: retinal cell @@ -2101,14 +2115,17 @@ id: CL:0011012 name: neural crest cell def: "A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells." [https://orcid.org/0000-0001-5208-3432, https://orcid.org/0000-0002-9900-7880] subset: cellxgene_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_0011012 is_a: CL:0000048 ! multi fate stem cell is_a: CL:0002321 ! embryonic cell (metazoa) +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." xsd:string {xref="DOI:10.1002/dvg.23276", xref="DOI:10.1242/dev.193193", xref="DOI:10.3389/fcell.2020.00635/full", xref="https://doi.org/10.1016/j.ydbio.2011.12.042"} [Term] id: CL:0011026 name: progenitor cell def: "A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses." [https://doi.org/10.1016/B978-0-12-409503-8.00002-0, ISBN:978-1-62808-994-3] subset: cellxgene_subset +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0011115 ! precursor cell intersection_of: CL:0011115 ! precursor cell intersection_of: RO:0002202 CL:0000034 ! develops from stem cell @@ -2161,6 +2178,20 @@ intersection_of: CL:0000988 ! hematopoietic cell intersection_of: part_of UBERON:0002371 ! bone marrow relationship: part_of UBERON:0012429 ! hematopoietic tissue +[Term] +id: CL:4052002 +name: syncytial cell +def: "A multinucleate cell formed by the fusion of multiple uninuclear cells through plasma membrane fusion. This process leads to a single large cell containing multiple nuclei within a shared cytoplasm." [PMID:20851884, Wikipedia:Syncytium] +synonym: "SC" RELATED OMO:0003000 [PMID:9067520] +synonym: "syncytium" EXACT [WBbt:0008074] +is_a: CL:0000228 ! multinucleate cell +intersection_of: CL:0000000 ! cell +intersection_of: bearer_of PATO:0001908 ! multinucleate +intersection_of: output_of GO:0000768 ! syncytium formation by plasma membrane fusion +relationship: output_of GO:0000768 ! syncytium formation by plasma membrane fusion +property_value: terms:contributor https://orcid.org/0009-0000-8480-9277 +property_value: terms:date "2024-08-15T10:38:46Z" xsd:dateTime + [Term] id: GO:0000323 name: lytic vacuole @@ -2168,6 +2199,17 @@ namespace: cellular_component def: "A vacuole that is maintained at an acidic pH and which contains degradative enzymes, including a wide variety of acid hydrolases." [GOC:krc] is_a: GO:0005773 ! vacuole +[Term] +id: GO:0000768 +name: syncytium formation by plasma membrane fusion +namespace: biological_process +def: "The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells." [GOC:mtg_muscle, GOC:tb] +synonym: "cell fusion" BROAD [] +is_a: GO:0006949 ! syncytium formation +is_a: GO:0140253 ! cell-cell fusion +intersection_of: GO:0006949 ! syncytium formation +intersection_of: has_part GO:0045026 ! plasma membrane fusion + [Term] id: GO:0000785 name: chromatin @@ -2181,8 +2223,9 @@ synonym: "chromosome scaffold" RELATED [] synonym: "cytoplasmic chromatin" NARROW [] synonym: "nuclear chromatin" NARROW [] xref: NIF_Subcellular:sao1615953555 -is_a: GO:0032993 ! protein-DNA complex +is_a: GO:0110165 ! cellular anatomical entity relationship: part_of GO:0005694 ! chromosome +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28301" xsd:anyURI [Term] id: GO:0000791 @@ -3158,6 +3201,18 @@ xref: Wikipedia:Muscle_contraction is_a: GO:0003012 ! muscle system process relationship: occurs_in UBERON:0002385 ! muscle tissue +[Term] +id: GO:0006949 +name: syncytium formation +namespace: biological_process +def: "The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane. Syncytia are normally derived from single cells that fuse or fail to complete cell division." [ISBN:0198506732] +subset: goslim_pir +is_a: GO:0009987 ! cellular process +is_a: GO:0048646 ! anatomical structure formation involved in morphogenesis +intersection_of: GO:0048646 ! anatomical structure formation involved in morphogenesis +intersection_of: results_in_formation_of CL:0000228 ! multinucleate cell +relationship: results_in_formation_of CL:0000228 ! multinucleate cell + [Term] id: GO:0006955 name: immune response @@ -3189,6 +3244,20 @@ property_value: term_tracker_item "https://github.com/geneontology/go-ontology/i created_by: jl creation_date: 2013-12-19T15:25:51Z +[Term] +id: GO:0007009 +name: plasma membrane organization +namespace: biological_process +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the plasma membrane." [GOC:dph, GOC:jl, GOC:mah] +subset: goslim_chembl +synonym: "plasma membrane organisation" EXACT [] +synonym: "plasma membrane organization and biogenesis" RELATED [GOC:mah] +is_a: GO:0061024 ! membrane organization +intersection_of: GO:0016043 ! cellular component organization +intersection_of: results_in_organization_of GO:0005886 ! plasma membrane +relationship: part_of GO:0010256 ! endomembrane system organization +relationship: results_in_organization_of GO:0005886 ! plasma membrane + [Term] id: GO:0007154 name: cell communication @@ -3618,6 +3687,19 @@ is_a: GO:0008150 ! biological_process created_by: jl creation_date: 2012-12-11T16:56:55Z +[Term] +id: GO:0010256 +name: endomembrane system organization +namespace: biological_process +def: "A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endomembrane system." [GOC:mah, GOC:sm] +subset: goslim_drosophila +synonym: "endomembrane organization" EXACT [] +synonym: "endomembrane system organisation" EXACT [GOC:mah] +is_a: GO:0016043 ! cellular component organization +intersection_of: GO:0016043 ! cellular component organization +intersection_of: results_in_organization_of GO:0012505 ! endomembrane system +relationship: results_in_organization_of GO:0012505 ! endomembrane system + [Term] id: GO:0010324 name: membrane invagination @@ -3816,6 +3898,9 @@ is_a: GO:0051301 ! cell division intersection_of: GO:0051301 ! cell division intersection_of: has_primary_input CL:0000034 ! stem cell relationship: has_primary_input CL:0000034 ! stem cell +property_value: RO:0002161 NCBITaxon:2 +property_value: RO:0002161 NCBITaxon:2157 +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0019226 @@ -4454,18 +4539,8 @@ synonym: "protein complex" NARROW [] synonym: "protein containing complex" EXACT [] synonym: "protein-protein complex" NARROW [] is_a: GO:0005575 ! cellular_component +is_a: PR:000050567 ! protein-containing material entity disjoint_from: GO:0110165 ! cellular anatomical entity -relationship: has_part PR:000000001 ! protein - -[Term] -id: GO:0032993 -name: protein-DNA complex -namespace: cellular_component -def: "A macromolecular complex containing both protein and DNA molecules." [GOC:mah] -comment: Note that this term is intended to classify complexes that have DNA as one of the members of the complex, that is, the complex does not exist if DNA is not present. Protein complexes that interact with DNA e.g. transcription factor complexes should not be classified here. -subset: goslim_pir -synonym: "DNA-protein complex" EXACT [GOC:mah] -is_a: GO:0032991 ! protein-containing complex [Term] id: GO:0033151 @@ -4721,6 +4796,7 @@ id: GO:0043227 name: membrane-bounded organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane." [GOC:go_curators] +subset: gocheck_do_not_annotate synonym: "membrane-enclosed organelle" EXACT [] xref: NIF_Subcellular:sao414196390 is_a: GO:0043226 ! organelle @@ -4728,29 +4804,34 @@ intersection_of: GO:0043226 ! organelle intersection_of: has_part GO:0016020 ! membrane disjoint_from: GO:0043228 ! non-membrane-bounded organelle relationship: has_part GO:0016020 ! membrane +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI [Term] id: GO:0043228 name: non-membrane-bounded organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:go_curators] +subset: gocheck_do_not_annotate subset: goslim_mouse synonym: "biological condensate" RELATED [] synonym: "non-membrane-enclosed organelle" EXACT [] xref: NIF_Subcellular:sao1456184038 is_a: GO:0043226 ! organelle property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21881" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI [Term] id: GO:0043229 name: intracellular organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:go_curators] +subset: gocheck_do_not_annotate subset: goslim_pir is_a: GO:0043226 ! organelle intersection_of: GO:0043226 ! organelle intersection_of: part_of GO:0005622 ! intracellular anatomical structure relationship: part_of GO:0005622 ! intracellular anatomical structure +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI [Term] id: GO:0043231 @@ -4832,9 +4913,11 @@ name: cellular component biogenesis namespace: biological_process alt_id: GO:0071843 def: "A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component." [GOC:jl, GOC:mah] +subset: gocheck_do_not_annotate subset: goslim_pir synonym: "cellular component biogenesis at cellular level" EXACT [] is_a: GO:0071840 ! cellular component organization or biogenesis +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27194" xsd:anyURI [Term] id: GO:0044207 @@ -4906,6 +4989,20 @@ is_a: GO:0008150 ! biological_process property_value: RO:0002161 NCBITaxon:4895 property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/20191" xsd:anyURI +[Term] +id: GO:0045026 +name: plasma membrane fusion +namespace: biological_process +alt_id: GO:0006947 +def: "The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell." [GOC:elh, GOC:mtg_muscle] +synonym: "cell fusion" BROAD [] +synonym: "cell-cell fusion" BROAD [] +is_a: GO:0007009 ! plasma membrane organization +is_a: GO:0061025 ! membrane fusion +intersection_of: GO:0009987 ! cellular process +intersection_of: results_in_fusion_of GO:0005886 ! plasma membrane +relationship: results_in_fusion_of GO:0005886 ! plasma membrane + [Term] id: GO:0045087 name: innate immune response @@ -4917,6 +5014,9 @@ synonym: "nonspecific immune response" EXACT [] xref: Wikipedia:Innate_immune_system is_a: GO:0006955 ! immune response is_a: GO:0140546 ! defense response to symbiont +property_value: RO:0002161 NCBITaxon:2 +property_value: RO:0002161 NCBITaxon:2157 +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0045202 @@ -5348,6 +5448,23 @@ intersection_of: GO:0051606 ! detection of stimulus intersection_of: part_of GO:0007600 ! sensory perception relationship: part_of GO:0007600 ! sensory perception +[Term] +id: GO:0050908 +name: detection of light stimulus involved in visual perception +namespace: biological_process +def: "The series of events involved in visual perception in which a light stimulus is received and converted into a molecular signal." [GOC:ai, GOC:dos] +synonym: "sensory detection of light during visual perception" EXACT [] +synonym: "sensory detection of light stimulus during visual perception" EXACT [] +synonym: "sensory transduction of light during visual perception" EXACT [] +synonym: "sensory transduction of light stimulus during visual perception" EXACT [] +synonym: "visual perception, detection of light stimulus" EXACT [] +synonym: "visual perception, sensory transduction during perception of light" EXACT [] +synonym: "visual perception, sensory transduction of light stimulus" EXACT [] +is_a: GO:0050962 ! detection of light stimulus involved in sensory perception +intersection_of: GO:0009583 ! detection of light stimulus +intersection_of: part_of GO:0007601 ! visual perception +relationship: part_of GO:0007601 ! visual perception + [Term] id: GO:0050953 name: sensory perception of light stimulus @@ -5827,6 +5944,7 @@ def: "A complex of collagen trimers such as a fibril or collagen network." [GOC: synonym: "Supramolecular aggregate of collagen" EXACT [PMID:19693541] synonym: "Supramolecular collagen assembly" EXACT [PMID:21421911] is_a: GO:0099080 ! supramolecular complex +is_a: PR:000050567 ! protein-containing material entity relationship: has_part GO:0005581 ! collagen trimer relationship: part_of GO:0062023 ! collagen-containing extracellular matrix @@ -6041,6 +6159,19 @@ relationship: part_of GO:0006887 ! exocytosis created_by: pg creation_date: 2017-05-15T13:20:45Z +[Term] +id: GO:0140253 +name: cell-cell fusion +namespace: biological_process +def: "A cellular process in which two or more cells combine together, their plasma membrane fusing, producing a single cell. In some cases, nuclei fuse, producing a polyploid cell, while in other cases, nuclei remain separate, producing a syncytium." [Wikipedia:Cell_fusion] +synonym: "cell cell fusion" EXACT [] +synonym: "cell fusion" BROAD [] +is_a: GO:0009987 ! cellular process +relationship: has_part GO:0045026 ! plasma membrane fusion +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/15939" xsd:anyURI +created_by: pg +creation_date: 2018-08-13T18:38:18Z + [Term] id: GO:0140352 name: export from cell @@ -6867,7 +6998,7 @@ comment: The definition above excludes protein complexes, which some also consid synonym: "native protein" NARROW [IEDB:BP] synonym: "natural protein" EXACT [PRO:DAN] is_a: PR:000018263 ! amino acid chain -is_a: PR:000064867 ! protein-containing molecular entity +is_a: PR:000050567 ! protein-containing material entity relationship: output_of GO:0006412 ! translation [Term] @@ -7609,11 +7740,11 @@ synonym: "PTPRC/iso:CD45R" EXACT PRO-short-label [PRO:DNx] is_a: PR:000001006 ! receptor-type tyrosine-protein phosphatase C [Term] -id: PR:000064867 -name: protein-containing molecular entity +id: PR:000050567 +name: protein-containing material entity namespace: protein -def: "A molecular entity that minimally consists of a protein." [PRO:DAN] -comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). +def: "A material entity that minimally consists of a protein." [PRO:DAN] +comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566). synonym: "protein" NARROW [PRO:DAN] synonym: "protein aggregate" NARROW [PRO:DAN] synonym: "protein complex" NARROW [PRO:DAN] @@ -7718,7 +7849,7 @@ xref: ZFA:0005647 is_a: UBERON:0007846 {source="VSAO"} ! dense regular connective tissue relationship: has_part CL:0000327 {source="AEO"} ! extracellular matrix secreting cell relationship: part_of UBERON:0002204 {source="OG"} ! musculoskeletal system -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002176 UBERON:0001474 ! connects bone element relationship: RO:0002176 UBERON:0001630 ! connects muscle organ property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg" xsd:anyURI @@ -7744,6 +7875,7 @@ xref: UMLS:C0687028 {source="ncithesaurus:Duct"} xref: Wikipedia:Duct_(anatomy) xref: XAO:0004000 xref: ZFA:0005171 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000063 ! organ subunit relationship: has_part UBERON:0034969 ! epithelial layer of duct relationship: RO:0000086 PATO:0002299 ! has quality tubular @@ -7946,7 +8078,7 @@ xref: SCTID:118966000 xref: UMLS:C1519343 {source="ncithesaurus:Skeletal_System_Part"} is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision relationship: part_of UBERON:0001434 ! skeletal system -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002473 UBERON:0004765 ! composed primarily of skeletal element [Term] @@ -8129,7 +8261,7 @@ is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000108 {source="BILS"} ! blastula stage relationship: RO:0002082 GO:0007369 ! simultaneous with gastrulation -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0000110 @@ -8145,7 +8277,7 @@ is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000109 ! gastrula stage relationship: RO:0002082 GO:0001841 ! simultaneous with neural tube formation -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: seeAlso "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/343" xsd:anyURI @@ -8165,7 +8297,7 @@ xref: Wikipedia:Organogenesis is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: RO:0002082 GO:0048513 ! simultaneous with animal organ development -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: seeAlso "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/533" xsd:anyURI @@ -8223,7 +8355,7 @@ xref: XAO:0003029 xref: ZFA:0000547 xref: ZFA:0000590 is_a: UBERON:0004921 ! subdivision of digestive tract -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002202 UBERON:0035804 ! develops from future mouth property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/661" xsd:anyURI @@ -8282,7 +8414,7 @@ is_a: UBERON:0011216 ! organ system subdivision intersection_of: UBERON:0011216 ! organ system subdivision intersection_of: RO:0002473 UBERON:0001015 ! composed primarily of musculature relationship: capable_of GO:0003012 ! muscle system process -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002473 UBERON:0001015 ! composed primarily of musculature property_value: IAO:0000116 "consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77" xsd:string property_value: RO:0002161 NCBITaxon:6040 @@ -8731,6 +8863,7 @@ xref: VHOG:0000387 xref: Wikipedia:Epithelium xref: XAO:0003045 xref: ZFA:0001486 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: RO:0002473 CL:0000066 ! composed primarily of epithelial cell @@ -8738,7 +8871,7 @@ union_of: UBERON:0000486 ! multilaminar epithelium union_of: UBERON:0000490 ! unilaminar epithelium relationship: has_part GO:0005911 ! cell-cell junction relationship: has_part UBERON:0005769 ! basement membrane of epithelium -relationship: RO:0002160 NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! in taxon Metazoa relationship: RO:0002473 CL:0000066 ! composed primarily of epithelial cell property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI @@ -8871,7 +9004,7 @@ xref: Wikipedia:Germ_layer xref: XAO:0003011 xref: ZFA:0001122 is_a: UBERON:0010316 ! germ layer / neural crest -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0000924 @@ -9025,7 +9158,7 @@ xref: ZFA:0001290 is_a: UBERON:0013522 ! subdivision of tube relationship: part_of UBERON:0000924 ! ectoderm relationship: part_of UBERON:0035804 ! future mouth -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI property_value: IAO:0000116 "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" xsd:string @@ -9070,7 +9203,7 @@ disjoint_from: UBERON:0002330 ! exocrine system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0004456 ! entire sense organ system -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002473 UBERON:0002368 ! composed primarily of endocrine gland relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage @@ -9217,7 +9350,7 @@ disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of GO:0003013 ! circulatory system process -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} @@ -9267,7 +9400,6 @@ namespace: uberon def: "The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]." [BIRNLEX:844, ISBN:0-14-051288-8, ISBN:3110148986, NLM:nervous+system, WB:rynl, Wikipedia:Nervous_system, ZFIN:curator] subset: cumbo subset: efo_slim -subset: human_reference_atlas subset: pheno_slim subset: uberon_slim subset: vertebrate_core @@ -9310,14 +9442,13 @@ disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: capable_of GO:0050877 ! nervous system process relationship: has_part CL:0000540 ! neuron -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002473 CL:0002319 ! composed primarily of neural cell relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage relationship: RO:0002495 UBERON:0016880 {source="Bgee:AN"} ! immediate transformation of future nervous system property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:6040 -property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001017 @@ -9364,7 +9495,7 @@ xref: ZFA:0000012 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0011216 {source="FBbt", source="cjm"} ! organ system subdivision relationship: part_of UBERON:0001016 ! nervous system -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria relationship: RO:0002495 UBERON:0016879 {source="Bgee:AN"} ! immediate transformation of future central nervous system property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} property_value: RO:0002175 NCBITaxon:9606 @@ -9645,7 +9776,7 @@ intersection_of: UBERON:0004765 ! skeletal element intersection_of: RO:0002473 UBERON:0002481 ! composed primarily of bone tissue disjoint_from: UBERON:0001630 ! muscle organ disjoint_from: UBERON:0005090 ! muscle structure -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002473 UBERON:0002481 {source="VSAO-modified"} ! composed primarily of bone tissue [Term] @@ -9683,7 +9814,7 @@ xref: WBbt:0005743 xref: ZFA:0000112 is_a: UBERON:0000025 ! tube relationship: part_of UBERON:0001007 ! digestive system -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002176 UBERON:0000165 ! connects mouth relationship: RO:0002495 UBERON:0007026 {source="NCBIBook:NBK10107"} ! immediate transformation of presumptive gut property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} @@ -9854,7 +9985,7 @@ xref: EMAPA:18765 xref: FMA:74562 xref: MA:0000013 is_a: UBERON:0000467 {source="MA"} ! anatomical system -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria [Term] id: UBERON:0002204 @@ -9929,7 +10060,7 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0011137 ! axial skeletal system relationship: produces PR:000014841 ! sonic hedgehog protein -relationship: RO:0002160 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! in taxon Chordata relationship: RO:0002202 UBERON:0004880 {source="ZFA"} ! develops from chordamesoderm relationship: RO:0002202 UBERON:0006267 {source="EHDAA2"} ! develops from notochordal plate relationship: RO:0002488 UBERON:0000068 ! existence starts during embryo stage @@ -9972,7 +10103,7 @@ xref: XAO:0000058 xref: ZFA:0000155 is_a: UBERON:0005423 ! developing anatomical structure is_a: UBERON:0007503 {source="EHDAA2"} ! epithelial vesicle -relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {source="GOTAX:0000352"} ! in taxon Chordata relationship: RO:0002202 UBERON:0003059 {source="ZFA"} ! develops from presomitic mesoderm property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:7712 {source="PMID:17237766"} @@ -9994,11 +10125,12 @@ xref: NCIT:C12957 xref: UMLS:C1516995 {source="ncithesaurus:Exocrine_System"} xref: Wikipedia:Exocrine_gland xref: WikipediaCategory:Exocrine_system +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000467 ! anatomical system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0004456 ! entire sense organ system -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002473 UBERON:0002365 ! composed primarily of exocrine gland relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage @@ -10036,7 +10168,7 @@ is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0010316 ! germ layer / neural crest relationship: part_of UBERON:0002346 {source="XAO", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! neurectoderm -relationship: RO:0002160 NCBITaxon:89593 ! only in taxon Craniata +relationship: RO:0002162 NCBITaxon:89593 ! in taxon Craniata relationship: RO:0002202 UBERON:0003075 {source="BTO"} ! develops from neural plate relationship: RO:0002202 UBERON:0005062 {source="PMID:11523831"} ! develops from neural fold relationship: RO:0002473 CL:0000333 ! composed primarily of migratory neural crest cell @@ -10103,6 +10235,7 @@ xref: NCIT:C12712 xref: SCTID:115976003 xref: UMLS:C0015282 {source="ncithesaurus:Exocrine_Gland"} xref: Wikipedia:Exocrine_gland +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002530 ! gland intersection_of: UBERON:0002530 ! gland intersection_of: part_of UBERON:0002330 ! exocrine system @@ -10222,7 +10355,7 @@ xref: VSAO:0000017 xref: XAO:0001017 xref: ZFA:0001632 is_a: UBERON:0000479 ! tissue -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -10254,7 +10387,7 @@ intersection_of: UBERON:0000479 ! tissue intersection_of: RO:0002473 CL:0000187 ! composed primarily of muscle cell relationship: capable_of GO:0006936 ! muscle contraction relationship: part_of UBERON:0001015 ! musculature -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002473 CL:0000187 ! composed primarily of muscle cell [Term] @@ -10300,7 +10433,7 @@ is_a: UBERON:0004120 ! mesoderm-derived structure disjoint_from: UBERON:0002405 ! immune system disjoint_from: UBERON:0004456 ! entire sense organ system relationship: part_of UBERON:0002193 {source="FMA"} ! hemolymphoid system -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002202 UBERON:0003061 ! develops from blood island property_value: RO:0002175 NCBITaxon:9606 @@ -10363,7 +10496,7 @@ xref: ZFA:0005621 is_a: UBERON:0004755 {source="VSAO"} ! skeletal tissue disjoint_from: UBERON:0005090 ! muscle structure relationship: part_of UBERON:0001474 ! bone element -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata property_value: IAO:0000116 "see https://github.com/obophenotype/uberon/issues/27" xsd:string [Term] @@ -10400,7 +10533,7 @@ xref: WikipediaCategory:Glands is_a: UBERON:0000062 ! organ relationship: capable_of GO:0046903 ! secretion relationship: produces UBERON:0000463 ! organism substance -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/a/a1/Gray1026.png" xsd:anyURI [Term] @@ -10522,7 +10655,7 @@ xref: XAO:0000205 xref: ZFA:0001204 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0000926 ! mesoderm -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002202 UBERON:0000926 ! develops from mesoderm property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI @@ -10556,7 +10689,7 @@ xref: ZFA:0000132 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0016879 ! future central nervous system -relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {source="GOTAX:0000352"} ! in taxon Chordata relationship: RO:0002256 UBERON:0002328 {source="Wikipedia"} ! developmentally induced by notochord relationship: RO:0002495 UBERON:0007284 {source="Bgee:AN"} ! immediate transformation of presumptive neural plate property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI @@ -10623,7 +10756,7 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue relationship: part_of UBERON:0000926 {source="EHDAA2", source="VHOG"} ! mesoderm -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria relationship: RO:0002221 UBERON:0003887 ! surrounds intraembryonic coelom property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI @@ -10716,7 +10849,7 @@ xref: ZFA:0000393 is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002328 GO:0032502 ! functionally related to developmental process relationship: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI @@ -10979,7 +11112,7 @@ is_a: UBERON:0034925 ! anatomical collection intersection_of: UBERON:0034925 ! anatomical collection intersection_of: RO:0002351 UBERON:0000982 ! has member skeletal joint relationship: part_of UBERON:0001434 {source="FMA"} ! skeletal system -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria relationship: RO:0002328 GO:0040011 ! functionally related to locomotion relationship: RO:0002351 UBERON:0000982 ! has member skeletal joint relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage @@ -11001,7 +11134,7 @@ xref: TAO:0000091 xref: ZFA:0000091 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0003068 ! axial mesoderm -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata [Term] id: UBERON:0004905 @@ -11044,7 +11177,7 @@ subset: upper_level xref: FMA:82485 is_a: UBERON:0000064 ! organ part relationship: part_of UBERON:0000060 ! anatomical wall -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0005061 @@ -11109,7 +11242,7 @@ synonym: "musculus" EXACT [FMA:30316] xref: FMA:30316 is_a: UBERON:0000061 ! anatomical structure relationship: has_part CL:0000187 ! muscle cell -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0005157 @@ -11221,11 +11354,12 @@ xref: NCIT:C13191 xref: SCTID:68989006 xref: UMLS:C0004799 {source="ncithesaurus:Basement_Membrane"} xref: Wikipedia:Basement_membrane +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005764 {source="FMA"} ! acellular membrane relationship: adjacent_to CL:0000066 ! epithelial cell relationship: has_part GO:0005587 ! collagen type IV trimer relationship: part_of UBERON:0000483 ! epithelium -relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa relationship: RO:0002473 GO:0005604 ! composed primarily of basement membrane property_value: RO:0002175 NCBITaxon:80999 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} @@ -11265,7 +11399,7 @@ xref: NCIT:C34232 xref: UMLS:C1518430 {source="ncithesaurus:Notochordal_Process"} xref: VHOG:0001213 is_a: UBERON:0005423 ! developing anatomical structure -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002202 UBERON:0000924 {source="EHDAA2"} ! develops from ectoderm [Term] @@ -11283,7 +11417,7 @@ intersection_of: UBERON:0006598 ! presumptive structure intersection_of: part_of UBERON:0000307 ! blastula intersection_of: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm relationship: part_of UBERON:0000307 ! blastula -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm [Term] @@ -11320,7 +11454,7 @@ intersection_of: UBERON:0006598 ! presumptive structure intersection_of: part_of UBERON:0000307 ! blastula intersection_of: RO:0002387 UBERON:0000924 ! has potential to develop into ectoderm relationship: part_of UBERON:0000307 ! blastula -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002387 UBERON:0000924 ! has potential to develop into ectoderm [Term] @@ -11338,7 +11472,7 @@ intersection_of: UBERON:0006598 ! presumptive structure intersection_of: part_of UBERON:0000307 ! blastula intersection_of: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm relationship: part_of UBERON:0000307 ! blastula -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm [Term] @@ -11502,6 +11636,7 @@ name: regular connective tissue namespace: uberon def: "Connective tissue, which consists of fibroblasts, the intercellular matrix of which contains a regular network of collagen and elastic fiber bundles. Examples: bone (tissue), cartilage (tissue), dense regular connective tissue." [FMA:20103] xref: FMA:20103 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002384 {source="FMA"} ! connective tissue disjoint_from: UBERON:0011821 ! irregular connective tissue relationship: has_part CL:0000057 ! fibroblast @@ -11695,6 +11830,7 @@ xref: AAO:0000121 xref: NCIT:C32450 xref: UMLS:C1511770 {source="ncithesaurus:Dense_Connective_Tissue"} xref: Wikipedia:Dense_connective_tissue +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002384 ! connective tissue intersection_of: UBERON:0002384 ! connective tissue intersection_of: RO:0002473 UBERON:0011860 ! composed primarily of collection of collagen fibrils @@ -11709,6 +11845,7 @@ xref: FMA:63212 xref: MESH:D024022 xref: NCIT:C32339 xref: NIF_Subcellular:sao7547390221 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000476 {source="ZFA"} ! acellular anatomical structure relationship: RO:0002473 GO:0005581 ! composed primarily of collagen trimer relationship: RO:0002473 GO:0098643 ! composed primarily of banded collagen fibril @@ -11744,7 +11881,7 @@ synonym: "schizocoelom" NARROW [] xref: EHDAA2:0004731 xref: Wikipedia:Coelom is_a: UBERON:0000481 {source="EHDAA2"} ! multi-tissue structure -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria property_value: IAO:0000116 "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." xsd:string property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} @@ -11801,7 +11938,7 @@ namespace: uberon def: "A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages." [https://orcid.org/0000-0002-6601-2165] subset: non_informative is_a: UBERON:0000475 ! organism subdivision -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0013702 @@ -11851,7 +11988,7 @@ intersection_of: RO:0002219 UBERON:0011899 ! surrounded by epimysium intersection_of: RO:0002473 UBERON:0001134 ! composed primarily of skeletal muscle tissue relationship: part_of UBERON:0018254 ! skeletal musculature relationship: RO:0002103 CL:0000100 ! synapsed by motor neuron -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002202 UBERON:0003082 ! develops from myotome relationship: RO:0002219 UBERON:0011899 ! surrounded by epimysium relationship: RO:0002473 UBERON:0001134 ! composed primarily of skeletal muscle tissue @@ -11885,7 +12022,7 @@ def: "Any structure that is placed on one side of the left-right axis of a bilat subset: grouping_class subset: non_informative is_a: UBERON:0000061 ! anatomical structure -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria [Term] id: UBERON:0015228 @@ -13456,9 +13593,7 @@ inverse_of: output_of ! output of [Typedef] id: has_part name: has part -name: has_part namespace: external -namespace: quality def: "a core relation that holds between a whole and its part" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology @@ -13663,9 +13798,7 @@ expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://p [Typedef] id: part_of name: part of -name: part_of namespace: external -namespace: quality def: "a core relation that holds between a part and its whole" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term diff --git a/subsets/general_cell_types_upper_slim.owl b/subsets/general_cell_types_upper_slim.owl index 0df0a51ec..8065f3828 100644 --- a/subsets/general_cell_types_upper_slim.owl +++ b/subsets/general_cell_types_upper_slim.owl @@ -22,8 +22,8 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - 2024-08-16 + + 2024-09-26 @@ -392,6 +392,14 @@ WHERE { + + + + + + + + @@ -1038,6 +1046,12 @@ WHERE { + + + + + + @@ -1076,17 +1090,13 @@ WHERE { - - created by - + - - creation date - + @@ -1172,9 +1182,7 @@ WHERE { - - id - + @@ -1283,7 +1291,6 @@ WHERE { A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. BFO:0000050 external - quality part_of @@ -1292,7 +1299,6 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of part of part of - part_of http://www.obofoundry.org/ro/#OBO_REL:part_of @@ -1314,7 +1320,6 @@ A continuant cannot be part of an occurrent: use 'participates in'. An A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. BFO:0000051 external - quality has_part @@ -1322,7 +1327,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part has part has part - has_part @@ -4768,7 +4772,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -4812,44 +4816,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - Any sensory receptor cell that is a(n) neuron and is capable of some detection of stimulus involved in sensory perception. - ZFA:0009001 - neuronal receptor cell (sensu Animalia) - - neuronal receptor cell - - - - - Any sensory receptor cell that is a(n) neuron and is capable of some detection of stimulus involved in sensory perception. - FBC:Autogenerated - - - - - ZFA:0009001 - - - - - @@ -4887,6 +4853,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -5189,6 +5156,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -5604,7 +5572,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -5847,6 +5815,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -5993,6 +5962,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6204,8 +6174,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different A vertebrate phagocyte with a single nucleus. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Mononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. +In addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses. +Mononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer. BTO:0001433 ZFA:0009064 + https://cellxgene.cziscience.com/cellguide/CL_0000113 mononuclear phagocyte @@ -6224,6 +6200,18 @@ Each of these 3 primitives can be composed to yield a cross-product of different GOC:tfm ISBN:0781735149 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Mononuclear phagocytes are immune cells that form a critical part of the body's innate immune system, the body's first line of defense against infections. Mononuclear phagocytes are characterized by the presence of a single, large nucleus. The ‘Mononuclear Phagocyte System’ nomenclature was introduced to distinguish mononuclear monocytes and macrophages from other cells with multiple nuclei. However, the cells within the mononuclear phagocyte system represent a highly heterogeneous group, all of which are able to perform highly efficient phagocytosis - engulfing and digesting microbes and cellular debris to fight infections and to maintain normal tissue homeostasis. +In addition to phagocytosis, mononuclear phagocytes also secrete chemical compounds to recruit other immune cells to a site of infection. These cells produce different types of signaling molecules, including cytokines, chemokines, and reactive oxygen species, triggering a cascade of responses to ensure rapid and efficient containment and neutralization of invading pathogens. These cells are also involved in antigen presentation, a process essential for stimulating an adaptive immune response. They can process and present antigens to T cells, thereby linking the innate and adaptive immune responses. +Mononuclear phagocytes play key roles in tissue repair and remodeling. After infection or injury, these cells help in the clearance of dead cells and debris, a crucial step in the initiation of tissue remodeling and the resolution of inflammation. Overall, mononuclear phagocytes are versatile cells that have tailored their functions to meet the unique challenges of different tissues within the body. They are pivotal in homeostasis, immunity, and inflammation, making them important aspects in a range of human diseases including infection, autoimmunity, and cancer. + DOI:10.1016/j.coi.2005.11.008 + DOI:10.1038/nri3087 + DOI:10.3389/fimmu.2019.01893 + @@ -6239,11 +6227,19 @@ Each of these 3 primitives can be composed to yield a cross-product of different A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Glial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons. +These different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning. +Oligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. +Microglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response. +Despite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis. BTO:0002606 CALOHA:TS-0415 FBbt:00005144 FMA:54536 ZFA:0009073 + https://cellxgene.cziscience.com/cellguide/CL_0000125 neuroglial cell neuroglia @@ -6258,6 +6254,22 @@ Each of these 3 primitives can be composed to yield a cross-product of different A non-neuronal cell of the nervous system. They not only provide physical support, but also respond to injury, regulate the ionic and chemical composition of the extracellular milieu. Guide neuronal migration during development, and exchange metabolites with neurons. MESH:D009457 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Glial cells, also known as neuroglia or simply glia, are non-neuronal cells in the central and peripheral nervous systems that provide support and protection for neurons. They constitute approximately half of the total cells in the human brain and more than half in other parts of the nervous system. Glial cells perform several key functions including, but not limited to, maintaining homeostasis, forming the myelin sheath around the neuron axons, and providing support and nutrition to neurons. +These different functions are performed by various glial cell types, including astrocytes, oligodendrocytes, microglia and other specialized types. Astrocytes, for example, are the most abundant glial cells and provide metabolic and nutrient support to neurons, help regulate the extracellular ion and neurotransmitter levels, and play a role in the formation and maintenance of the blood-brain barrier, contributing to the overall homeostasis and functioning of the nervous system. Additionally, astrocytes are involved in synaptic communication and participate in processes such as synaptogenesis and synaptic pruning. +Oligodendrocytes in the central nervous system function to insulate neurons by producing a fatty substance known as myelin. The myelin sheath enhances the speed and efficiency of nerve impulse conduction along the axons. +Microglia, the immune cells of the central nervous system, protect neurons from pathogens and clear away dead neurons through phagocytosis, a process also known as cellular eating. They also contribute to the regulation of inflammation in response to signals of tissue damage or infection in the central nervous system by releasing cytokines and other signaling molecules that modulate the immune response. +Despite their overarching function in the support and protection of neurons, glial cells have also been shown to play significant roles in the pathophysiology of many psychiatric and neurodegenerative diseases, such as Alzheimer’s, Parkinson’s Disease and multiple sclerosis. + DOI:10.1002/glia.24343 + DOI:10.1038/nn1988 + DOI:10.1101/cshperspect.a020602 + DOI:10.1126/science.aat0473 + DOI:10.3389/fncel.2017.00024 + @@ -6534,6 +6546,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6637,6 +6650,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6689,6 +6703,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6757,6 +6772,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6813,7 +6829,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -6902,45 +6918,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A cell that is capable of detection of a stimulus involved in sensory perception. - MESH:D011984 - receptor cell - sensory receptor cell - - - - @@ -6950,19 +6927,20 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + + - + - A cell specialized to detect and transduce light. + A cell specialized in detecting light stimuli that are involved in visual perception. BTO:0001060 CALOHA:TS-0868 FBbt:00004211 @@ -6972,16 +6950,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different photoreceptor cell https://www.swissbiopics.org/api/image/Photoreceptor_cell.svg - - - - - true - - A cell specialized to detect and transduce light. + A cell specialized in detecting light stimuli that are involved in visual perception. MESH:D010786 @@ -7065,6 +7037,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -7096,6 +7069,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -7129,6 +7103,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -7171,6 +7146,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -7205,6 +7181,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -7213,11 +7190,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell with more than one nucleus. - AEO:0000203 - WBbt:0008074 - syncitium - syncytial cell - syncytium + multinucleated cells + polynuclear cells multinucleate cell @@ -7225,6 +7199,19 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell with more than one nucleus. FB:ma + Wikipedia:Multinucleate + + + + + multinucleated cells + Wikipedia:Multinucleate + + + + + polynuclear cells + Wikipedia:Multinucleate @@ -7424,7 +7411,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -7433,11 +7420,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - Any cell that only exists in Eukaryota. + Any cell that in taxon some Eukaryota. MESH:D005057 eukaryotic cell @@ -7445,7 +7432,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - Any cell that only exists in Eukaryota. + Any cell that in taxon some Eukaryota. FBC:Autogenerated @@ -7530,7 +7517,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -7625,7 +7612,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -7636,7 +7623,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -7758,6 +7745,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -8046,7 +8034,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -8327,6 +8315,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -8474,6 +8463,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -8548,6 +8538,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -8805,6 +8796,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -8964,7 +8956,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -9122,6 +9114,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -9295,6 +9288,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -9417,6 +9411,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -9626,7 +9621,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + @@ -10058,7 +10055,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -10420,6 +10417,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -10464,6 +10462,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -10678,7 +10677,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -10717,7 +10716,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -10800,26 +10799,26 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - A transversely striated, synctial muscle cell, formed by the fusion of myoblasts. + A transversely striated, multinucleated syncytial muscle cell, formed by the fusion of myoblasts during muscle development. 2010-09-24T01:13:01Z FBbt:00005812 - myotubule - single cell sarcomere + myofiber + myofibril myotube - A transversely striated, synctial muscle cell, formed by the fusion of myoblasts. + A transversely striated, multinucleated syncytial muscle cell, formed by the fusion of myoblasts during muscle development. GOC:dos GOC:tfm ISBN:0323052908 @@ -10831,6 +10830,18 @@ Each of these 3 primitives can be composed to yield a cross-product of different FBbt:00005812 + + + + myofiber + FBbt:00005812 + + + + + myofibril + FBbt:00005812 + @@ -10848,7 +10859,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -11064,6 +11075,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -11086,6 +11098,41 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + Any neuron that is capable of part of some visual perception. + + 2017-07-09T19:12:36Z + visual system neuron + + + + + Any neuron that is capable of part of some visual perception. + FBC:Autogenerated + + + + @@ -11173,6 +11220,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. +After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. +Disorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis. + https://cellxgene.cziscience.com/cellguide/CL_0011012 neural crest cell @@ -11183,6 +11236,19 @@ Each of these 3 primitives can be composed to yield a cross-product of different https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-9900-7880 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. +After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. +Disorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis. + DOI:10.1002/dvg.23276 + DOI:10.1242/dev.193193 + DOI:10.3389/fcell.2020.00635/full + https://doi.org/10.1016/j.ydbio.2011.12.042 + @@ -11200,6 +11266,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -11376,6 +11443,61 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + + + + + A multinucleate cell formed by the fusion of multiple uninuclear cells through plasma membrane fusion. This process leads to a single large cell containing multiple nuclei within a shared cytoplasm. + + 2024-08-15T10:38:46Z + syncytium + SC + syncytial cell + + + + + A multinucleate cell formed by the fusion of multiple uninuclear cells through plasma membrane fusion. This process leads to a single large cell containing multiple nuclei within a shared cytoplasm. + PMID:20851884 + Wikipedia:Syncytium + + + + + syncytium + WBbt:0008074 + + + + + SC + PMID:9067520 + + + + + @@ -11394,10 +11516,42 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells. + cell fusion + biological_process + GO:0000768 + syncytium formation by plasma membrane fusion + + + + + The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells. + GOC:mtg_muscle + GOC:tb + + + + - + @@ -11405,6 +11559,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome. + https://github.com/geneontology/go-ontology/issues/28301 GO:0000789 GO:0000790 GO:0005717 @@ -12879,32 +13034,32 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. Wikipedia:Collagen cellular_component GO:0005581 collagen trimer - + - + - + PMID:12382326 - + PMID:12382326 @@ -13869,6 +14024,43 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + + The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane. Syncytia are normally derived from single cells that fuse or fail to complete cell division. + biological_process + GO:0006949 + + syncytium formation + + + + + The formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane. Syncytia are normally derived from single cells that fuse or fail to complete cell division. + ISBN:0198506732 + + + + @@ -13951,6 +14143,58 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + + + + + + + A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the plasma membrane. + plasma membrane organisation + biological_process + plasma membrane organization and biogenesis + GO:0007009 + + plasma membrane organization + + + + + A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the plasma membrane. + GOC:dph + GOC:jl + GOC:mah + + + + + plasma membrane organization and biogenesis + GOC:mah + + + + @@ -14926,6 +15170,51 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endomembrane system. + endomembrane organization + endomembrane system organisation + biological_process + GO:0010256 + + endomembrane system organization + + + + + A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the endomembrane system. + GOC:mah + GOC:sm + + + + + endomembrane system organisation + GOC:mah + + + + @@ -15420,6 +15709,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different The self-renewing division of a stem cell. A stem cell is an undifferentiated cell, in the embryo or adult, that can undergo unlimited division and give rise to one or several different cell types. + + + stem cell renewal biological_process GO:0017145 @@ -17052,12 +17344,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - + A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. GO:0043234 @@ -17087,33 +17374,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - A macromolecular complex containing both protein and DNA molecules. - DNA-protein complex - cellular_component - GO:0032993 - - Note that this term is intended to classify complexes that have DNA as one of the members of the complex, that is, the complex does not exist if DNA is not present. Protein complexes that interact with DNA e.g. transcription factor complexes should not be classified here. - protein-DNA complex - - - - - A macromolecular complex containing both protein and DNA molecules. - GOC:mah - - - - - DNA-protein complex - GOC:mah - - - - @@ -17829,10 +18089,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. + https://github.com/geneontology/go-ontology/issues/28153 NIF_Subcellular:sao414196390 membrane-enclosed organelle cellular_component GO:0043227 + membrane-bounded organelle @@ -17850,11 +18112,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. https://github.com/geneontology/go-ontology/issues/21881 + https://github.com/geneontology/go-ontology/issues/28153 NIF_Subcellular:sao1456184038 non-membrane-enclosed organelle cellular_component biological condensate GO:0043228 + non-membrane-bounded organelle @@ -17889,8 +18153,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. + https://github.com/geneontology/go-ontology/issues/28153 cellular_component GO:0043229 + intracellular organelle @@ -18111,10 +18377,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component. + https://github.com/geneontology/go-ontology/issues/27194 GO:0071843 cellular component biogenesis at cellular level biological_process GO:0044085 + cellular component biogenesis @@ -18264,12 +18532,55 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + + The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell. + GO:0006947 + cell fusion + cell-cell fusion + biological_process + GO:0045026 + plasma membrane fusion + + + + + The joining of the lipid bilayer membrane that surround a cell with that of another cell, producing a single cell. + GOC:elh + GOC:mtg_muscle + + + + Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens. + + + GO:0002226 Wikipedia:Innate_immune_system innate immunity @@ -19537,6 +19848,49 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + The series of events involved in visual perception in which a light stimulus is received and converted into a molecular signal. + sensory detection of light during visual perception + sensory detection of light stimulus during visual perception + sensory transduction of light during visual perception + sensory transduction of light stimulus during visual perception + visual perception, detection of light stimulus + visual perception, sensory transduction during perception of light + visual perception, sensory transduction of light stimulus + biological_process + GO:0050908 + detection of light stimulus involved in visual perception + + + + + The series of events involved in visual perception in which a light stimulus is received and converted into a molecular signal. + GOC:ai + GOC:dos + + + + @@ -20796,6 +21150,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -21486,6 +21841,35 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + A cellular process in which two or more cells combine together, their plasma membrane fusing, producing a single cell. In some cases, nuclei fuse, producing a polyploid cell, while in other cases, nuclei remain separate, producing a syncytium. + https://github.com/geneontology/go-ontology/issues/15939 + pg + 2018-08-13T18:38:18Z + cell fusion + cell cell fusion + biological_process + GO:0140253 + cell-cell fusion + + + + + A cellular process in which two or more cells combine together, their plasma membrane fusing, producing a single cell. In some cases, nuclei fuse, producing a polyploid cell, while in other cases, nuclei remain separate, producing a syncytium. + Wikipedia:Cell_fusion + + + + @@ -23417,7 +23801,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -25442,51 +25826,51 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + - A molecular entity that minimally consists of a protein. + A material entity that minimally consists of a protein. protein protein aggregate protein complex protein-containing complex protein - PR:000064867 - Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). - protein-containing molecular entity + PR:000050567 + Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566). + protein-containing material entity - + - A molecular entity that minimally consists of a protein. + A material entity that minimally consists of a protein. PRO:DAN - + protein PRO:DAN - + protein aggregate PRO:DAN - + protein complex PRO:DAN - + protein-containing complex PRO:DAN @@ -25697,11 +26081,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + - + @@ -25746,11 +26130,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different tendon http://upload.wikimedia.org/wikipedia/commons/3/3c/Achilles-tendon.jpg - + - + @@ -25763,13 +26147,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + OG - + AEO @@ -25806,6 +26190,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -26298,7 +26683,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -26674,7 +27059,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -26683,7 +27068,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -26710,14 +27095,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different gastrula stage - + - + BILS @@ -26789,7 +27174,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -26832,7 +27217,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -26866,7 +27251,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -27105,7 +27490,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -28111,6 +28496,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -28124,7 +28510,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -28166,14 +28552,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg - - + + - + http://palaeos.com/metazoa/porifera/homoscleromorpha.html @@ -28425,7 +28811,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -28516,7 +28902,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. AAO:0000137 BILA:0000036 @@ -28551,14 +28937,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png - + - + Bgee:AN @@ -28598,7 +28984,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. AAO:0000139 BILA:0000038 @@ -28633,14 +29019,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png - + - + Bgee:AN @@ -28681,7 +29067,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The middle germ layer of the embryo, between the endoderm and ectoderm. UBERON:0003263 @@ -28722,14 +29108,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png - + - + Bgee:AN @@ -28784,7 +29170,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -28891,7 +29277,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -28985,8 +29371,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + @@ -29018,24 +29404,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different eye - + - + - + PMID:21062451 - + PMID:21062451 @@ -29250,7 +29636,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -29407,7 +29793,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -29429,7 +29815,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -29438,7 +29824,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]. - AAO:0000324 BILA:0000079 BIRNLEX:844 @@ -29473,7 +29858,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0001016 - @@ -29481,14 +29865,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png - + - + Bgee:AN @@ -29550,11 +29934,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. @@ -29599,7 +29983,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different central nervous system - + @@ -29613,7 +29997,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Bgee:AN @@ -30329,11 +30713,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + Skeletal element that is composed of bone tissue. @@ -30375,14 +30759,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different bone element - + - + VSAO-modified @@ -30438,7 +30822,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -30448,7 +30832,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A tube extending from the mouth to the anus. @@ -30485,14 +30869,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different digestive tract - + - + NCBIBook:NBK10107 @@ -30899,7 +31283,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -31021,9 +31405,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - + + + @@ -31071,15 +31455,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - - + + - + - + @@ -31098,19 +31482,19 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -31150,8 +31534,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. mesodermal cluster @@ -31189,11 +31573,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - - + + - + @@ -31206,13 +31590,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + GOTAX:0000352 - + ZFA @@ -31271,10 +31655,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different + - + @@ -31337,22 +31722,22 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + - - + + - + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. AAO:0010578 BTO:0001764 @@ -31385,45 +31770,45 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - + BTO - + PMID:11523831 - + PMID:11523831 @@ -31552,6 +31937,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -31730,7 +32116,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -31786,14 +32172,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different bone marrow http://upload.wikimedia.org/wikipedia/commons/7/74/Gray72-en.svg - + - + FMA MA @@ -31841,7 +32227,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -31932,7 +32318,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -32005,10 +32391,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -32059,14 +32445,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different hematopoietic system - + - + FMA @@ -32165,7 +32551,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -32250,7 +32636,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -32476,7 +32862,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. AAO:0011086 EFO:0001982 @@ -32499,14 +32885,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different presomitic mesoderm - + - + Bgee:AN @@ -32612,7 +32998,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -32660,9 +33046,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. AAO:0011072 BTO:0001765 @@ -32691,34 +33077,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - - + + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -32758,7 +33144,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. AAO:0010568 EFO:0003515 @@ -32784,7 +33170,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -32797,7 +33183,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Bgee:AN @@ -32844,10 +33230,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -32884,7 +33270,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -32897,7 +33283,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 VHOG @@ -32947,7 +33333,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -32988,7 +33374,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different myotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - + @@ -33001,7 +33387,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2-abduced @@ -33083,7 +33469,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -33161,7 +33547,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults EHDAA:251 @@ -33176,14 +33562,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different intraembryonic coelom - + - + Wikipedia @@ -33485,7 +33871,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The bilaminar epithelium formed from the myotome and dermatome. AAO:0010572 AEO:0000214 @@ -33503,7 +33889,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0004290 dermomyotome - + @@ -33522,7 +33908,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 ZFA @@ -33853,7 +34239,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. AAO:0011129 TAO:0001890 @@ -33867,14 +34253,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different skeletal element - + - + VSAO @@ -33901,10 +34287,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -33940,14 +34326,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0004770 articular system - + - + FMA @@ -33989,7 +34375,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -34155,7 +34541,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -34316,7 +34702,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -34388,7 +34774,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -34404,14 +34790,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different trunk mesenchyme - + - + EHDAA2 @@ -34619,6 +35005,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -34634,7 +35021,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -34720,7 +35107,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB EHDAA2:0001278 @@ -34734,7 +35121,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different notochordal plate - + @@ -34747,7 +35134,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 @@ -34771,11 +35158,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -34792,14 +35179,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -34844,7 +35231,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -34953,7 +35340,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -35017,7 +35404,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -35410,7 +35797,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -35436,7 +35823,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different presumptive paraxial mesoderm - + @@ -35452,7 +35839,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + https://github.com/obophenotype/uberon/issues/1277 @@ -35501,7 +35888,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -35509,7 +35896,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0007524 dense mesenchyme tissue - + @@ -35522,7 +35909,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + AEO @@ -35537,6 +35924,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -35680,7 +36068,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -35697,14 +36085,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -35726,7 +36114,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -35734,14 +36122,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -36150,6 +36538,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -36185,6 +36574,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -36221,7 +36611,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -36245,7 +36635,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0011899 epimysium - + @@ -36258,7 +36648,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + FMA @@ -36295,7 +36685,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -36364,7 +36754,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -36385,7 +36775,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0012429 hematopoietic tissue - + @@ -36398,7 +36788,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + defitional @@ -36531,7 +36921,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -36639,7 +37029,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -36768,7 +37158,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -36953,7 +37343,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -36976,7 +37366,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0016887 entire extraembryonic component - + @@ -36989,7 +37379,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + AEO @@ -37075,7 +37465,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -37092,14 +37482,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different skeletal musculature - + - + MA @@ -37576,48 +37966,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different /////////////////////////////////////////////////////////////////////////////////////// --> - - - - - - - - - - - - - - - 1 - - - - - - - - - - - - - - - - - - - - - 2 - - - - - - @@ -37648,6 +37996,454 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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+_:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid783 +_:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid791 +_:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid798 +_:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid808 +_:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid821 +_:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid837 +_:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid845 +_:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid852 +_:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid862 +_:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid889 +_:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid906 +_:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid915 +_:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid965 +_:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid973 +_:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid981 +_:B0be79aadX2D3b9dX2D4de8X2D9b61X2Dad49ee9a54c2genid993 "cell" - "neuronal receptor cell" "early embryonic cell (metazoa)" "stem cell" "hematopoietic stem cell" @@ -313,7 +346,6 @@ _:B993c35aeX2D65c9X2D47bfX2Dbc91X2D1922643fd86cgenid993 "muscle cell" "cell of skeletal muscle" "smooth muscle cell" - "sensory receptor cell" "photoreceptor cell" "electrically active cell" "motile cell" @@ -394,6 +426,7 @@ _:B993c35aeX2D65c9X2D47bfX2Dbc91X2D1922643fd86cgenid993 "skeletal muscle fiber" "visceral muscle cell" "mesenchymal cell" + "visual system neuron" "retinal cell" "zygote" "cardiac myoblast" @@ -403,7 +436,9 @@ _:B993c35aeX2D65c9X2D47bfX2Dbc91X2D1922643fd86cgenid993 "neutrophillic cytoplasm" "basophilic cytoplasm" "bone marrow hematopoietic cell" + "syncytial cell" "lytic vacuole" + "syncytium formation by plasma membrane fusion" "chromatin" "euchromatin" "heterochromatin" @@ -474,8 +509,10 @@ _:B993c35aeX2D65c9X2D47bfX2Dbc91X2D1922643fd86cgenid993 "vesicle fusion" "phagocytosis" "muscle contraction" + "syncytium formation" "immune response" "organelle organization" + "plasma membrane organization" "cell communication" "cell-cell signaling" "chemical synaptic transmission" @@ -509,6 +546,7 @@ _:B993c35aeX2D65c9X2D47bfX2Dbc91X2D1922643fd86cgenid993 "tissue development" "hormone transport" "cellular process" + "endomembrane system organization" "membrane invagination" "gene expression" "regulation of hormone levels" @@ -567,7 +605,6 @@ _:B993c35aeX2D65c9X2D47bfX2Dbc91X2D1922643fd86cgenid993 "secretion by cell" "protein-containing complex disassembly" "protein-containing complex" - "protein-DNA complex" "V(D)J recombination" "immunoglobulin V(D)J recombination" "monoatomic ion transmembrane transport" @@ -603,6 +640,7 @@ _:B993c35aeX2D65c9X2D47bfX2Dbc91X2D1922643fd86cgenid993 "primary metabolic process" "cellular biosynthetic process" "biological process involved in interspecies interaction between organisms" + "plasma membrane fusion" "innate immune response" "synapse" "leukocyte activation" @@ -639,6 +677,7 @@ _:B993c35aeX2D65c9X2D47bfX2Dbc91X2D1922643fd86cgenid993 "nervous system process" "response to stimulus" "detection of stimulus involved in sensory perception" + "detection of light stimulus involved in visual perception" "sensory perception of light stimulus" "detection of light stimulus involved in sensory perception" "localization" @@ -694,6 +733,7 @@ _:B993c35aeX2D65c9X2D47bfX2Dbc91X2D1922643fd86cgenid993 "plasma membrane bounded cell projection" "plasma membrane bounded cell projection organization" "exocytic process" + "cell-cell fusion" "export from cell" "defense response to symbiont" "regulation of leukocyte differentiation" @@ -831,7 +871,7 @@ _:B993c35aeX2D65c9X2D47bfX2Dbc91X2D1922643fd86cgenid993 "eukaryotic protein" "cathepsin-like protease" "receptor-type tyrosine-protein phosphatase C isoform CD45R" - "protein-containing molecular entity" + "protein-containing material entity" "processual entity" "sense organ" "tube" diff --git a/subsets/kidney_upper_slim.json b/subsets/kidney_upper_slim.json index 5bc36508b..ddee7b988 100644 --- a/subsets/kidney_upper_slim.json +++ b/subsets/kidney_upper_slim.json @@ -4,9 +4,9 @@ "meta" : { "basicPropertyValues" : [ { "pred" : "http://www.w3.org/2002/07/owl#versionInfo", - "val" : "2024-08-16" + "val" : "2024-09-26" } ], - "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-08-16/subsets/kidney_upper_slim.owl" + "version" : "http://purl.obolibrary.org/obo/cl/releases/2024-09-26/subsets/kidney_upper_slim.owl" }, "nodes" : [ { "id" : "http://purl.obolibrary.org/obo/CL_0000000", @@ -491,6 +491,10 @@ "lbl" : "squamous epithelial cell", "type" : "CLASS", "meta" : { + "definition" : { + "val" : "Any epithelial cell that is part of some squamous epithelium.", + "xrefs" : [ "FBC:Autogenerated" ] + }, "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], "xrefs" : [ { "val" : "CALOHA:TS-1249" @@ -899,7 +903,7 @@ "type" : "CLASS", "meta" : { "definition" : { - "val" : "Any cell that only exists in Eukaryota.", + "val" : "Any cell that in taxon some Eukaryota.", "xrefs" : [ "FBC:Autogenerated" ] }, "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], @@ -1441,6 +1445,12 @@ } ], "xrefs" : [ { "val" : "ZFA:0009286" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0000666" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nFenestrated cells are specialized epithelial cells that are characterized by a distinctive structural feature, fenestrations or tiny pores, which allow an exchange of substances such as fluids, nutrients, and waste between blood vessels and the surrounding tissue environments. These cells are present in various types of epithelial tissues in the human body, including the intestinal tract, endocrine glands, and certain parts of the renal system. \nThere are multiple types of endothelial cell fenestrations. The most common type is found in systemic capillaries of the endocrine tissue (e.g., pancreatic islets), gastrointestinal mucosa, and renal peritubular capillaries. Here, the fenestrated cells have fenestrations in their peripheral cytoplasm with a unique thin and permeable diaphragm that provides a high degree of selectivity, blocking the passage of larger molecules while allowing the free movement of smaller ones. In contrast, other types of fenestrations, such as the discontinuous epithelium of the liver sinusoidal endothelial cells, do not have diaphragms. \nCharacteristically, fenestrated cells play a vital role in the filtering process of body systems. They are a key part of the glomeruli in the kidneys where blood is filtered under high pressure. The fenestrations present in the endothelial cells lining the capillaries of the glomerulus allow the free passage of water and small solute molecules towards the Bowman's capsule, leaving behind larger proteins and cells in the blood, thereby aiding in the filtration and waste removal process. \nIn the endocrine system, fenestrated cells in glandular capillaries allow the prompt release of hormones into the bloodstream. These cells have tightly clustered fenestrations which increase the surface area available for passive diffusion, improving the efficiency of hormone secretion. In villi of the small intestine, these cells increase absorption efficiency, permitting the exchange of water, electrolytes, and nutrients.\nOverall, fenestrated cells contribute immensely to important physiological processes of filtration, absorption, and secretion, primarily connecting our body's circulation system with the surrounding tissues and organs." } ] } }, { @@ -2080,27 +2090,6 @@ "val" : "2011-02-08T10:46:34Z" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/CL_0002546", - "lbl" : "embryonic blood vessel endothelial progenitor cell", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "An endothelial progenitor cell that participates in angiogenesis during development.", - "xrefs" : [ "GOC:tfm" ] - }, - "comments" : [ "See CL:0002619." ], - "xrefs" : [ { - "val" : "ZFA:0005773" - } ], - "basicPropertyValues" : [ { - "pred" : "http://purl.org/dc/terms/contributor", - "val" : "https://orcid.org/0000-0003-1980-3228" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "val" : "2011-02-28T04:20:39Z" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/CL_0002584", "lbl" : "renal cortical epithelial cell", @@ -2159,6 +2148,12 @@ "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], "xrefs" : [ { "val" : "ZFA:0005322" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0005009" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nRenal principal cells are the major cell type in the initial collecting tubule and the cortical and outer medullary collecting ducts, as well as the connecting tubule, in the nephrons of the kidneys.\nA key function of renal principal cells is the regulation of water balance in the body. These cells express aquaporin-2 (AQP2) water channels, which facilitate the reabsorption of water from the fluid within the renal tubule lumen back into the blood. The translocation of AQP2 to the cell membrane is controlled by the hormone vasopressin: In response to high vasopressin levels, AQP2 moves to the cell membrane, allowing water to pass through effectively and be reabsorbed, therefore concentrating the urine. Conversely, in low vasopressin conditions, AQP2 is removed from the membrane, reducing water reabsorption and diluting the urine. \nRenal principal cells are also involved in the regulation of sodium and potassium levels in the body. They have sodium channels (ENaC) in their luminal membranes which permit the reabsorption of sodium ions from the tubule fluid back into the blood, resulting in a net reabsorption of sodium ions into the systemic circulation. This process is controlled, in part, by the hormone aldosterone. Additionally, renal principal cells contain potassium channels that facilitate the secretion of potassium ions into the urine. The activities of these channels, in coordination with other cell types in the nephron, are critical for maintaining electrolyte balance and overall body homeostasis." } ] } }, { @@ -2282,7 +2277,14 @@ "val" : "A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells.", "xrefs" : [ "https://orcid.org/0000-0001-5208-3432", "https://orcid.org/0000-0002-9900-7880" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ] + "subsets" : [ "http://purl.obolibrary.org/obo/cl#cellxgene_subset" ], + "xrefs" : [ { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_0011012" + } ], + "basicPropertyValues" : [ { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." + } ] } }, { "id" : "http://purl.obolibrary.org/obo/CL_0011026", @@ -2423,10 +2425,15 @@ "val" : "FMA:70982" }, { "val" : "KUPO:0001059" + }, { + "val" : "https://cellxgene.cziscience.com/cellguide/CL_1000454" } ], "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002175", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" + }, { + "pred" : "http://purl.org/dc/terms/description", + "val" : "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nKidney collecting duct epithelial cells are a specialized type of cells that form an integral part of the renal system. Located in the collecting duct system of the kidneys, these cells are responsible for one of the final steps in the process of urine formation, and they are instrumental in the fine tuning of the volume and composition of urine by reabsorbing water and certain solutes back into the bloodstream.\nThese cells express specific channels and carriers that actively and passively transport ions and water. They also have channels on their membranes, such as sodium channels and potassium channels, involved in reabsorbing or secreting these electrolytes depending upon the body's needs. The function of renal collecting duct epithelial cells can be regulated by a variety of hormones, including vasopressin (antidiuretic hormone), which can modulate the ion channels and carriers and hence indirectly influence body fluid homeostasis.\nAside from their function in ion and water balance, kidney collecting duct epithelial cells also aid in maintaining the body's acid-base balance. They have specialized functionality to secret hydrogen ions into the tubular lumen, which contributes to acid excretion. Any dysfunction may have serious implications and lead to various renal or systemic diseases, exemplifying the importance of these cells in maintaining overall body homeostasis." } ] } }, { @@ -2921,6 +2928,9 @@ "val" : "NIF_Subcellular:sao1615953555" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28301" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "GO:0000789" }, { @@ -3139,7 +3149,7 @@ "val" : "A slow mechanism of blood pressure regulation that responds to changes in pressure resulting from fluid and salt intake by modulating the quantity of blood in the circulatory system.", "xrefs" : [ "GOC:dph", "GOC:tb", "ISBN:0721643949" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_obsoletion_candidate" ], "synonyms" : [ { "pred" : "hasRelatedSynonym", "val" : "renal blood volume control of blood pressure" @@ -4533,6 +4543,15 @@ "val" : "gametogenesis" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_2" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_2157" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "GO:0009552" }, { @@ -5503,6 +5522,15 @@ "val" : "stem cell renewal" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_2" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_2157" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "biological_process" } ] @@ -6448,27 +6476,6 @@ "val" : "cellular_component" } ] } - }, { - "id" : "http://purl.obolibrary.org/obo/GO_0032993", - "lbl" : "protein-DNA complex", - "type" : "CLASS", - "meta" : { - "definition" : { - "val" : "A macromolecular complex containing both protein and DNA molecules.", - "xrefs" : [ "GOC:mah" ] - }, - "comments" : [ "Note that this term is intended to classify complexes that have DNA as one of the members of the complex, that is, the complex does not exist if DNA is not present. Protein complexes that interact with DNA e.g. transcription factor complexes should not be classified here." ], - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], - "synonyms" : [ { - "pred" : "hasExactSynonym", - "val" : "DNA-protein complex", - "xrefs" : [ "GOC:mah" ] - } ], - "basicPropertyValues" : [ { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "cellular_component" - } ] - } }, { "id" : "http://purl.obolibrary.org/obo/GO_0033036", "lbl" : "macromolecule localization", @@ -6642,6 +6649,15 @@ "xrefs" : [ "PMID:19129259" ] } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_2" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_2157" + }, { + "pred" : "http://purl.obolibrary.org/obo/RO_0002161", + "val" : "http://purl.obolibrary.org/obo/NCBITaxon_4751" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#created_by", "val" : "bf" }, { @@ -6883,6 +6899,7 @@ "val" : "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.", "xrefs" : [ "GOC:go_curators" ] }, + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "membrane-enclosed organelle" @@ -6891,6 +6908,9 @@ "val" : "NIF_Subcellular:sao414196390" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28153" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -6904,7 +6924,7 @@ "val" : "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes.", "xrefs" : [ "GOC:go_curators" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_mouse" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_mouse" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "non-membrane-enclosed organelle" @@ -6918,6 +6938,9 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", "val" : "https://github.com/geneontology/go-ontology/issues/21881" + }, { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28153" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" @@ -6932,8 +6955,11 @@ "val" : "Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane.", "xrefs" : [ "GOC:go_curators" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_pir" ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/28153" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "cellular_component" } ] @@ -7090,12 +7116,15 @@ "val" : "A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component.", "xrefs" : [ "GOC:jl", "GOC:mah" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/go#goslim_pir" ], + "subsets" : [ "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "http://purl.obolibrary.org/obo/go#goslim_pir" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "cellular component biogenesis at cellular level" } ], "basicPropertyValues" : [ { + "pred" : "http://purl.obolibrary.org/obo/IAO_0000233", + "val" : "https://github.com/geneontology/go-ontology/issues/27194" + }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId", "val" : "GO:0071843" }, { @@ -11928,15 +11957,15 @@ } ] } }, { - "id" : "http://purl.obolibrary.org/obo/PR_000064867", - "lbl" : "protein-containing molecular entity", + "id" : "http://purl.obolibrary.org/obo/PR_000050567", + "lbl" : "protein-containing material entity", "type" : "CLASS", "meta" : { "definition" : { - "val" : "A molecular entity that minimally consists of a protein.", + "val" : "A material entity that minimally consists of a protein.", "xrefs" : [ "PRO:DAN" ] }, - "comments" : [ "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565)." ], + "comments" : [ "Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566)." ], "synonyms" : [ { "pred" : "hasNarrowSynonym", "val" : "protein", @@ -16773,7 +16802,7 @@ "val" : "The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO].", "xrefs" : [ "BIRNLEX:844", "ISBN:0-14-051288-8", "ISBN:3110148986", "NLM:nervous+system", "WB:rynl", "Wikipedia:Nervous_system", "ZFIN:curator" ] }, - "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#cumbo", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#human_reference_atlas", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], + "subsets" : [ "http://purl.obolibrary.org/obo/uberon/core#cumbo", "http://purl.obolibrary.org/obo/uberon/core#efo_slim", "http://purl.obolibrary.org/obo/uberon/core#pheno_slim", "http://purl.obolibrary.org/obo/uberon/core#uberon_slim", "http://purl.obolibrary.org/obo/uberon/core#vertebrate_core" ], "synonyms" : [ { "pred" : "hasExactSynonym", "val" : "neurological system", @@ -16846,9 +16875,6 @@ "basicPropertyValues" : [ { "pred" : "http://purl.obolibrary.org/obo/RO_0002161", "val" : "http://purl.obolibrary.org/obo/NCBITaxon_6040" - }, { - "pred" : "http://purl.obolibrary.org/obo/RO_0002175", - "val" : "http://purl.obolibrary.org/obo/NCBITaxon_9606" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "uberon" @@ -29093,7 +29119,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000050", - "lbl" : "part_of", + "lbl" : "part of", "type" : "PROPERTY", "propertyType" : "OBJECT", "meta" : { @@ -29116,9 +29142,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "part_of" @@ -29138,7 +29161,7 @@ } }, { "id" : "http://purl.obolibrary.org/obo/BFO_0000051", - "lbl" : "has_part", + "lbl" : "has part", "type" : "PROPERTY", "propertyType" : "OBJECT", "meta" : { @@ -29161,9 +29184,6 @@ }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", "val" : "external" - }, { - "pred" : "http://www.geneontology.org/formats/oboInOwl#hasOBONamespace", - "val" : "quality" }, { "pred" : "http://www.geneontology.org/formats/oboInOwl#shorthand", "val" : "has_part" @@ -33028,6 +33048,10 @@ "id" : "http://purl.obolibrary.org/obo/go#gocheck_do_not_annotate", "type" : "PROPERTY", "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.obolibrary.org/obo/go#gocheck_obsoletion_candidate", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.obolibrary.org/obo/go#goslim_agr", "type" : "PROPERTY", @@ -33366,6 +33390,10 @@ "id" : "http://purl.org/dc/terms/date", "type" : "PROPERTY", "propertyType" : "ANNOTATION" + }, { + "id" : "http://purl.org/dc/terms/description", + "type" : "PROPERTY", + "propertyType" : "ANNOTATION" }, { "id" : "http://purl.org/dc/terms/license", "type" : "PROPERTY", @@ -33391,12 +33419,10 @@ "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#created_by", - "lbl" : "created by", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#creation_date", - "lbl" : "creation date", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { @@ -33489,7 +33515,6 @@ "propertyType" : "ANNOTATION" }, { "id" : "http://www.geneontology.org/formats/oboInOwl#id", - "lbl" : "id", "type" : "PROPERTY", "propertyType" : "ANNOTATION" }, { @@ -33559,12 +33584,16 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000000", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_131567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000007", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0002321" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000034", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000034", "pred" : "is_a", @@ -33738,7 +33767,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000066", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000066", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -33759,10 +33788,6 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000071", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0004638" - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0000071", - "pred" : "http://purl.obolibrary.org/obo/RO_0002202", - "obj" : "http://purl.obolibrary.org/obo/CL_0002546" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000072", "pred" : "is_a", @@ -33779,6 +33804,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000076", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000066" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000076", + "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", + "obj" : "http://purl.obolibrary.org/obo/UBERON_0006914" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000081", "pred" : "is_a", @@ -33797,6 +33826,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000115", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000213" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000115", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000115", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -33843,6 +33876,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000187", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000183" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000187", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000187", "pred" : "is_a", @@ -33883,6 +33920,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000219", "pred" : "http://purl.obolibrary.org/obo/RO_0002215", "obj" : "http://purl.obolibrary.org/obo/GO_0048870" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000221", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000221", "pred" : "is_a", @@ -33891,6 +33932,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000221", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000924" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000222", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000222", "pred" : "is_a", @@ -33899,6 +33944,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000222", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000926" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000223", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000223", "pred" : "is_a", @@ -33947,7 +33996,7 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0000000" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000255", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000329", @@ -33995,7 +34044,7 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0010017" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000365", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000393", @@ -34043,6 +34092,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000547", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0002242" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000547", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000547", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -34117,6 +34170,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000549", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000549", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -34139,6 +34196,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000550", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000550", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", @@ -34279,6 +34340,10 @@ "val" : "true" } ] } + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000558", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000558", "pred" : "http://purl.obolibrary.org/obo/CL_4030046", @@ -34349,6 +34414,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000566", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0011026" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000566", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000566", "pred" : "http://purl.obolibrary.org/obo/RO_0002104", @@ -34435,6 +34504,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000680", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000055" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000680", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000680", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", @@ -34451,6 +34524,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000723", "pred" : "http://purl.obolibrary.org/obo/RO_0002215", "obj" : "http://purl.obolibrary.org/obo/GO_0048103" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000763", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000763", "pred" : "is_a", @@ -34543,10 +34620,18 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000765", "pred" : "http://purl.obolibrary.org/obo/RO_0002215", "obj" : "http://purl.obolibrary.org/obo/GO_0030218" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000837", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000837", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0008001" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0000837", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0000837", "pred" : "http://purl.obolibrary.org/obo/CL_4030046", @@ -34633,6 +34718,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0000988", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0002031", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002031", "pred" : "is_a", @@ -34645,6 +34734,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0002031", "pred" : "http://purl.obolibrary.org/obo/RO_0002202", "obj" : "http://purl.obolibrary.org/obo/CL_0002032" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0002032", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002032", "pred" : "is_a", @@ -34719,6 +34812,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0002188", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0002681" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0002188", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002188", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -34782,7 +34879,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002319", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002319", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -34790,7 +34887,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002320", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002320", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -34802,7 +34899,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002494", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002494", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -34821,10 +34918,6 @@ "val" : "true" } ] } - }, { - "sub" : "http://purl.obolibrary.org/obo/CL_0002546", - "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000222" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0002584", "pred" : "is_a", @@ -34897,6 +34990,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0008019", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0000219" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0008019", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0008019", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -34921,6 +35018,10 @@ "sub" : "http://purl.obolibrary.org/obo/CL_0011012", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/CL_0002321" + }, { + "sub" : "http://purl.obolibrary.org/obo/CL_0011026", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_0011026", "pred" : "is_a", @@ -35016,7 +35117,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_1000497", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_1000497", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -35318,7 +35419,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/CL_4030031", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/CL_0000000" + "obj" : "http://purl.obolibrary.org/obo/CL_0000255" }, { "sub" : "http://purl.obolibrary.org/obo/CL_4030031", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -35354,7 +35455,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/GO_0000785", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0032993" + "obj" : "http://purl.obolibrary.org/obo/GO_0110165" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0000785", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -35707,8 +35808,8 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0043232" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0005840", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", - "obj" : "http://purl.obolibrary.org/obo/PR_000000001" + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0005840", "pred" : "http://purl.obolibrary.org/obo/RO_0002216", @@ -36427,12 +36528,8 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0005575" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0032991", - "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", - "obj" : "http://purl.obolibrary.org/obo/PR_000000001" - }, { - "sub" : "http://purl.obolibrary.org/obo/GO_0032993", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/GO_0032991" + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0033036", "pred" : "is_a", @@ -37149,6 +37246,10 @@ "sub" : "http://purl.obolibrary.org/obo/GO_0098644", "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/GO_0099080" + }, { + "sub" : "http://purl.obolibrary.org/obo/GO_0098644", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/GO_0098644", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", @@ -37680,7 +37781,7 @@ }, { "sub" : "http://purl.obolibrary.org/obo/PR_000000001", "pred" : "is_a", - "obj" : "http://purl.obolibrary.org/obo/PR_000064867" + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/PR_000000001", "pred" : "http://purl.obolibrary.org/obo/RO_0002353", @@ -37818,7 +37919,7 @@ "pred" : "is_a", "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { - "sub" : "http://purl.obolibrary.org/obo/PR_000064867", + "sub" : "http://purl.obolibrary.org/obo/PR_000050567", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/PR_000000001" }, { @@ -37839,7 +37940,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000475" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000026", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000055", @@ -37937,6 +38038,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000057", "pred" : "http://purl.obolibrary.org/obo/uberon/core#channels_from", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001255" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0000058", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000058", "pred" : "is_a", @@ -38086,7 +38191,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0001434" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000075", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000075", @@ -38294,7 +38399,7 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0007369" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000109", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000110", @@ -38314,7 +38419,7 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0001841" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000110", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000111", @@ -38330,7 +38435,7 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0048513" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000111", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000119", @@ -38342,7 +38447,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000475" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000154", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000158", @@ -38382,7 +38487,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000162", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000163", @@ -38432,7 +38537,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000164", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000164", @@ -38448,7 +38553,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0004921" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000165", @@ -38462,6 +38567,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000174", "pred" : "http://purl.obolibrary.org/obo/RO_0002353", "obj" : "http://purl.obolibrary.org/obo/GO_0007588" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0000178", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000178", "pred" : "is_a", @@ -38514,7 +38623,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0002193" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000179", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000307", @@ -38534,7 +38643,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000064" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000353", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000353", @@ -38566,7 +38675,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0011216" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000383", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000383", @@ -38682,6 +38791,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0000481", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000479" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0000483", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000483", "pred" : "is_a", @@ -38696,7 +38809,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0005769" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000483", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208", "meta" : { "basicPropertyValues" : [ { @@ -38770,7 +38883,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000916", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000922", @@ -38790,7 +38903,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0010316" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000923", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000924", @@ -38860,7 +38973,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0035804" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000930", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000931", @@ -38888,7 +39001,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000931", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000931", @@ -38930,7 +39043,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0004151" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000948", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000948", @@ -38954,7 +39067,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000471" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000958", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0000958", @@ -39022,7 +39135,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_8450002" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001008", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001008", @@ -39038,7 +39151,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000467" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001009", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001009", @@ -39070,7 +39183,7 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0000540" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001016", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001016", @@ -39117,7 +39230,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0001016" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001017", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001017", @@ -39758,7 +39871,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0001007" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001555", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001555", @@ -39842,6 +39955,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001915", "pred" : "http://purl.obolibrary.org/obo/BFO_0000050", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001982" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001969", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001969", "pred" : "is_a", @@ -39900,6 +40017,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0001980", "pred" : "http://purl.obolibrary.org/obo/RO_0002433", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001637" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001981", "pred" : "is_a", @@ -39989,7 +40110,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0012275" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001986", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0001986", @@ -40087,7 +40208,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000026" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002091", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7776" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002091", @@ -40125,7 +40246,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002113", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002113", @@ -40193,7 +40314,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002193", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002201", @@ -40239,6 +40360,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0002224", "pred" : "http://purl.obolibrary.org/obo/RO_0002572", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000915" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0002303", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002303", "pred" : "is_a", @@ -40381,7 +40506,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0011137" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002328", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711", "meta" : { "basicPropertyValues" : [ { @@ -40433,7 +40558,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002329", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711", "meta" : { "basicPropertyValues" : [ { @@ -40502,7 +40627,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_89593" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002342", @@ -40568,7 +40693,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000479" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002384", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002385", @@ -40584,7 +40709,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0001015" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002385", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002385", @@ -40614,7 +40739,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002390", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0002390", @@ -40774,7 +40899,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000926" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003068", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003068", @@ -40822,7 +40947,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0016879" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003075", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711", "meta" : { "basicPropertyValues" : [ { @@ -40919,7 +41044,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003081", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003081", @@ -40991,7 +41116,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003089", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742", "meta" : { "basicPropertyValues" : [ { @@ -41019,7 +41144,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000479" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003104", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003104", @@ -41191,7 +41316,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000064" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003891", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0003891", @@ -41603,6 +41728,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004341", "pred" : "http://purl.obolibrary.org/obo/RO_0002387", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000926" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004535", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004535", "pred" : "is_a", @@ -41619,6 +41748,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004535", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001981" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004537", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004537", "pred" : "is_a", @@ -41627,6 +41760,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004537", "pred" : "http://purl.obolibrary.org/obo/RO_0002473", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001981" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004572", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004572", "pred" : "is_a", @@ -41641,6 +41778,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0004572", "pred" : "http://purl.obolibrary.org/obo/RO_0002351", "obj" : "http://purl.obolibrary.org/obo/UBERON_0001637" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0004582", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004582", "pred" : "is_a", @@ -41775,7 +41916,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004770", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004770", @@ -41907,7 +42048,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0003068" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004880", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004905", @@ -41939,7 +42080,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000060" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0004923", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005061", @@ -42007,7 +42148,7 @@ "obj" : "http://purl.obolibrary.org/obo/CL_0000187" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005090", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005095", @@ -42353,6 +42494,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0005764", "pred" : "http://purl.obolibrary.org/obo/RO_0002007", "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", "pred" : "is_a", @@ -42373,7 +42518,7 @@ "obj" : "http://purl.obolibrary.org/obo/GO_0005587" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0005769", @@ -42534,7 +42679,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0005423" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006268", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7711" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006268", @@ -42604,7 +42749,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000307" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006595", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006595", @@ -42636,7 +42781,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000307" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006601", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006601", @@ -42652,7 +42797,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000307" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006603", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006603", @@ -42700,6 +42845,10 @@ "sub" : "http://purl.obolibrary.org/obo/UBERON_0006914", "pred" : "http://purl.obolibrary.org/obo/BFO_0000051", "obj" : "http://purl.obolibrary.org/obo/CL_0000076" + }, { + "sub" : "http://purl.obolibrary.org/obo/UBERON_0006965", + "pred" : "is_a", + "obj" : "http://purl.obolibrary.org/obo/PR_000050567" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0006965", "pred" : "is_a", @@ -43001,7 +43150,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0010707" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007823", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0007823", @@ -43163,7 +43312,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0006555" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0009773", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0009856", @@ -43409,7 +43558,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0015212" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0010707", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_7742" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0010707", @@ -43601,7 +43750,7 @@ } }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0011997", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0012274", @@ -43745,7 +43894,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000475" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0013701", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_6072" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0013702", @@ -43803,7 +43952,7 @@ "obj" : "http://purl.obolibrary.org/obo/UBERON_0000061" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0015212", - "pred" : "http://purl.obolibrary.org/obo/RO_0002160", + "pred" : "http://purl.obolibrary.org/obo/RO_0002162", "obj" : "http://purl.obolibrary.org/obo/NCBITaxon_33213" }, { "sub" : "http://purl.obolibrary.org/obo/UBERON_0015228", @@ -45237,6 +45386,13 @@ "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0001981" } ] + }, { + "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000076", + "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000066" ], + "restrictions" : [ { + "propertyId" : "http://purl.obolibrary.org/obo/BFO_0000050", + "fillerId" : "http://purl.obolibrary.org/obo/UBERON_0006914" + } ] }, { "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000081", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000988" ], @@ -45288,7 +45444,7 @@ "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000255", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0000000" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002160", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002162", "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_2759" } ] }, { @@ -45302,7 +45458,7 @@ "definedClassId" : "http://purl.obolibrary.org/obo/CL_0000365", "genusIds" : [ "http://purl.obolibrary.org/obo/CL_0010017" ], "restrictions" : [ { - "propertyId" : "http://purl.obolibrary.org/obo/RO_0002160", + "propertyId" : "http://purl.obolibrary.org/obo/RO_0002162", "fillerId" : "http://purl.obolibrary.org/obo/NCBITaxon_33208" } ] }, { diff --git a/subsets/kidney_upper_slim.obo b/subsets/kidney_upper_slim.obo index 467009d20..abc4ba250 100644 --- a/subsets/kidney_upper_slim.obo +++ b/subsets/kidney_upper_slim.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: cl/releases/2024-08-16/subsets/kidney_upper_slim.owl +data-version: cl/releases/2024-09-26/subsets/kidney_upper_slim.owl subsetdef: abnormal_slim "" subsetdef: added_for_HCA "" subsetdef: attribute_slim "" @@ -19,6 +19,7 @@ subsetdef: eye_upper_slim "a subset of general classes related to specific cell subsetdef: functional_classification "" subsetdef: general_cell_types_upper_slim "a subset of general classes of cell types in the cell ontology." subsetdef: gocheck_do_not_annotate "" +subsetdef: gocheck_obsoletion_candidate "" subsetdef: goslim_agr "" subsetdef: goslim_candida "" subsetdef: goslim_chembl "" @@ -95,7 +96,7 @@ idspace: oboInOwl http://www.geneontology.org/formats/oboInOwl# idspace: sssom https://w3id.org/sssom/ idspace: terms http://purl.org/dc/terms/ ontology: cl/subsets/kidney_upper_slim -property_value: owl:versionInfo "2024-08-16" xsd:string +property_value: owl:versionInfo "2024-09-26" xsd:string [Term] id: CL:0000000 @@ -118,7 +119,7 @@ is_a: UBERON:0000061 ! anatomical structure disjoint_from: GO:0031012 ! extracellular matrix disjoint_from: GO:0032991 ! protein-containing complex disjoint_from: GO:0043226 ! organelle -relationship: RO:0002160 NCBITaxon:131567 ! only in taxon cellular organisms +relationship: RO:0002162 NCBITaxon:131567 ! in taxon cellular organisms [Term] id: CL:0000007 @@ -139,6 +140,7 @@ synonym: "animal stem cell" EXACT [] xref: CALOHA:TS-2086 xref: FMA:63368 xref: ZFA:0005957 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0011115 ! precursor cell intersection_of: CL:0000000 ! cell intersection_of: capable_of GO:0017145 ! stem cell division @@ -355,7 +357,7 @@ xref: FBbt:00000124 {sssom:mapping_justification="https://w3id.org/semapv/vocab/ xref: FMA:66768 xref: WBbt:0003672 xref: ZFA:0009034 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell relationship: part_of UBERON:0000483 ! epithelium property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Epithelial_cells.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 @@ -382,7 +384,6 @@ is_a: CL:0002139 ! endothelial cell of vascular tree intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0001981 ! blood vessel relationship: part_of UBERON:0004638 ! blood vessel endothelium -relationship: RO:0002202 CL:0002546 ! develops from embryonic blood vessel endothelial progenitor cell property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -404,10 +405,14 @@ property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000076 name: squamous epithelial cell +def: "Any epithelial cell that is part of some squamous epithelium." [FBC:Autogenerated] subset: cellxgene_subset xref: CALOHA:TS-1249 xref: ZFA:0009039 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000066 ! epithelial cell +intersection_of: CL:0000066 ! epithelial cell +intersection_of: part_of UBERON:0006914 ! squamous epithelium +relationship: part_of UBERON:0006914 ! squamous epithelium [Term] id: CL:0000081 @@ -436,6 +441,7 @@ xref: CALOHA:TS-0278 xref: FMA:66772 xref: ZFA:0009065 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000213 ! lining cell +is_a: CL:0000255 ! eukaryotic cell relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell property_value: RO:0002175 NCBITaxon:9606 @@ -516,6 +522,7 @@ xref: FMA:67328 xref: WBbt:0003675 xref: ZFA:0009114 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000183 ! contractile cell +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000393 ! electrically responsive cell relationship: RO:0002202 CL:0000056 ! develops from myoblast property_value: foaf:depiction "https://www.swissbiopics.org/api/image/Muscle_cells.svg" xsd:anyURI @@ -579,6 +586,7 @@ def: "A cell of the outer of the three germ layers of the embryo." [MESH:D004475 synonym: "ectoderm cell" EXACT [] xref: FMA:72549 xref: ZFA:0009137 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000924 ! ectoderm @@ -591,6 +599,7 @@ synonym: "mesoblast" EXACT [] synonym: "mesoderm cell" EXACT [] xref: FMA:72554 xref: ZFA:0009138 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000926 ! mesoderm @@ -601,6 +610,7 @@ def: "A cell of the inner of the three germ layers of the embryo." [MESH:D004707 synonym: "endoderm cell" EXACT [] xref: FMA:72555 xref: ZFA:0009139 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0002321 ! embryonic cell (metazoa) relationship: part_of UBERON:0000925 ! endoderm @@ -634,13 +644,13 @@ property_value: RO:0002175 NCBITaxon:9606 [Term] id: CL:0000255 name: eukaryotic cell -def: "Any cell that only exists in Eukaryota." [FBC:Autogenerated] +def: "Any cell that in taxon some Eukaryota." [FBC:Autogenerated] subset: cellxgene_subset xref: MESH:D005057 is_a: CL:0000000 ! cell intersection_of: CL:0000000 ! cell -intersection_of: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota -relationship: RO:0002160 NCBITaxon:2759 ! only in taxon Eukaryota +intersection_of: RO:0002162 NCBITaxon:2759 ! in taxon Eukaryota +relationship: RO:0002162 NCBITaxon:2759 ! in taxon Eukaryota [Term] id: CL:0000329 @@ -688,8 +698,8 @@ is_a: CL:0000007 ! early embryonic cell (metazoa) is_a: CL:0000255 ! eukaryotic cell is_a: CL:0010017 ! zygote intersection_of: CL:0010017 ! zygote -intersection_of: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa -relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +intersection_of: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa [Term] id: CL:0000393 @@ -753,6 +763,7 @@ synonym: "rubriblast" EXACT [ISBN:0721601464] xref: FMA:83518 is_a: CL:0000764 {is_inferred="true"} ! erythroid lineage cell is_a: CL:0002242 ! nucleate cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000764 ! erythroid lineage cell intersection_of: bearer_of PATO:0002505 ! nucleated intersection_of: bearer_of PATO:0040072 ! high nuclear/cytoplasmic ratio @@ -798,6 +809,7 @@ synonym: "prorubricyte" EXACT [ISBN:0721601464] xref: FMA:83505 xref: ZFA:0005236 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000765 {is_inferred="true"} ! erythroblast +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017503 ! basophilic cytoplasm intersection_of: has_part GO:0000792 ! heterochromatin @@ -819,6 +831,7 @@ synonym: "rubricyte" EXACT [ISBN:0721601464] xref: FMA:83506 xref: ZFA:0005241 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000765 {is_inferred="true"} ! erythroblast +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000765 ! erythroblast intersection_of: has_part CL:0017504 ! polychromatophilic cytoplasm intersection_of: has_part GO:0000792 ! heterochromatin @@ -932,6 +945,7 @@ xref: CALOHA:TS-0864 xref: MESH:D012156 xref: ZFA:0009252 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000764 {is_inferred="true"} ! erythroid lineage cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000764 ! erythroid lineage cell intersection_of: capable_of GO:0071971 ! extracellular exosome assembly intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -971,6 +985,7 @@ synonym: "chondroplast" EXACT [] xref: ZFA:0009258 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000134 {is_inferred="true"} ! mesenchymal stem cell is_a: CL:0011026 ! progenitor cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000134 ! mesenchymal stem cell intersection_of: RO:0002104 PR:000001444 ! has plasma membrane part cadherin-5 intersection_of: RO:0002104 PR:000002112 ! has plasma membrane part vascular endothelial growth factor receptor 2 @@ -1042,11 +1057,13 @@ name: fenestrated endothelial cell def: "An endothelial cell that has small pores, or fenestrations, which allow for the efficient exchange of substances between the blood and surrounding tissues." [DOI:10.1007/978-3-211-99390-3_133] subset: cellxgene_subset synonym: "window cell" EXACT [] +xref: https://cellxgene.cziscience.com/cellguide/CL_0000666 xref: ZFA:0009286 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000115 ! endothelial cell intersection_of: CL:0000115 ! endothelial cell intersection_of: bearer_of PATO:0002064 ! fenestrated relationship: bearer_of PATO:0002064 ! fenestrated +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nFenestrated cells are specialized epithelial cells that are characterized by a distinctive structural feature, fenestrations or tiny pores, which allow an exchange of substances such as fluids, nutrients, and waste between blood vessels and the surrounding tissue environments. These cells are present in various types of epithelial tissues in the human body, including the intestinal tract, endocrine glands, and certain parts of the renal system. \nThere are multiple types of endothelial cell fenestrations. The most common type is found in systemic capillaries of the endocrine tissue (e.g., pancreatic islets), gastrointestinal mucosa, and renal peritubular capillaries. Here, the fenestrated cells have fenestrations in their peripheral cytoplasm with a unique thin and permeable diaphragm that provides a high degree of selectivity, blocking the passage of larger molecules while allowing the free movement of smaller ones. In contrast, other types of fenestrations, such as the discontinuous epithelium of the liver sinusoidal endothelial cells, do not have diaphragms. \nCharacteristically, fenestrated cells play a vital role in the filtering process of body systems. They are a key part of the glomeruli in the kidneys where blood is filtered under high pressure. The fenestrations present in the endothelial cells lining the capillaries of the glomerulus allow the free passage of water and small solute molecules towards the Bowman's capsule, leaving behind larger proteins and cells in the blood, thereby aiding in the filtration and waste removal process. \nIn the endocrine system, fenestrated cells in glandular capillaries allow the prompt release of hormones into the bloodstream. These cells have tightly clustered fenestrations which increase the surface area available for passive diffusion, improving the efficiency of hormone secretion. In villi of the small intestine, these cells increase absorption efficiency, permitting the exchange of water, electrolytes, and nutrients.\nOverall, fenestrated cells contribute immensely to important physiological processes of filtration, absorption, and secretion, primarily connecting our body's circulation system with the surrounding tissues and organs." xsd:string {xref="DOI:10.1002/ar.1092200109", xref="DOI:10.1016/0306-4522(86)90162-4", xref="DOI:10.1016/j.devcel.2012.11.003", xref="DOI:10.1038/s41467-022-31571-2", xref="DOI:10.1152/ajprenal.90601.2008"} [Term] id: CL:0000669 @@ -1077,6 +1094,7 @@ def: "A non-terminally differentiated cell that is capable of developing into a subset: cellxgene_subset xref: ZFA:0009291 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000055 ! non-terminally differentiated cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0011115 ! precursor cell intersection_of: RO:0002203 CL:0000187 ! develops into muscle cell relationship: RO:0002202 CL:0000222 ! develops from mesodermal cell @@ -1103,6 +1121,7 @@ xref: BTO:0001441 xref: CALOHA:TS-0647 xref: MESH:D022423 xref: ZFA:0009324 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0000988 {is_inferred="true"} ! hematopoietic cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: RO:0002202 CL:0000049 ! develops from common myeloid progenitor @@ -1181,7 +1200,9 @@ synonym: "MPP" EXACT [] xref: BTO:0000725 xref: CALOHA:TS-0448 xref: ZFA:0009354 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001402 ! multipotent intersection_of: CL:4030046 PR:000001002 ! lacks_plasma_membrane_part CD19 molecule @@ -1256,6 +1277,7 @@ id: CL:0002031 name: hematopoietic lineage restricted progenitor cell def: "A hematopoietic progenitor cell that is capable of developing into only one lineage of hematopoietic cells." [GOC:tfm, PMID:19022770] subset: blood_and_immune_upper_slim +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001400 ! unipotent @@ -1271,6 +1293,7 @@ name: hematopoietic oligopotent progenitor cell def: "A hematopoietic oligopotent progenitor cell that has the ability to differentiate into limited cell types but lacks lineage cell markers and self renewal capabilities." [GOC:tfm, https://orcid.org/0000-0001-5208-3432, PMID:19022770] comment: This cell type is intended to be compatible with any vertebrate hematopoietic oligopotent progenitor cell. For mammalian hematopoietic oligopotent progenitor cells known to be lineage-negative, please use the term 'hematopoietic oligopotent progenitor cell' (CL_0001060). subset: blood_and_immune_upper_slim +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0008001 ! hematopoietic precursor cell intersection_of: CL:0000988 ! hematopoietic cell intersection_of: bearer_of PATO:0001401 ! oligopotent @@ -1368,6 +1391,7 @@ xref: BTO:0004632 xref: FMA:70970 is_a: CL:0000666 ! fenestrated endothelial cell is_a: CL:0002681 ! kidney cortical cell +is_a: PR:000050567 ! protein-containing material entity intersection_of: CL:0000115 ! endothelial cell intersection_of: part_of UBERON:0000074 ! renal glomerulus relationship: has_part GO:0036053 ! glomerular endothelium fenestra @@ -1428,7 +1452,7 @@ def: "A cell that is part of the nervous system." [GOC:tfm, ISBN:0618947256] subset: cellxgene_subset xref: CALOHA:TS-2040 xref: FMA:70333 -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0001016 ! nervous system relationship: part_of UBERON:0001016 ! nervous system @@ -1444,7 +1468,7 @@ xref: CALOHA:TS-2096 xref: FMA:63875 xref: MESH:D003239 xref: ZFA:0009392 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0002384 ! connective tissue relationship: part_of UBERON:0002384 ! connective tissue @@ -1473,7 +1497,7 @@ xref: BTO:0001539 xref: CALOHA:TS-0115 xref: FMA:83808 xref: FMA:84791 -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0007100 ! primary circulatory organ relationship: part_of UBERON:0007100 ! primary circulatory organ @@ -1494,16 +1518,6 @@ intersection_of: part_of UBERON:0002113 ! kidney property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 creation_date: 2011-02-08T10:46:34Z -[Term] -id: CL:0002546 -name: embryonic blood vessel endothelial progenitor cell -def: "An endothelial progenitor cell that participates in angiogenesis during development." [GOC:tfm] -comment: See CL:0002619. -xref: ZFA:0005773 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000222 ! mesodermal cell -property_value: terms:contributor https://orcid.org/0000-0003-1980-3228 -creation_date: 2011-02-28T04:20:39Z - [Term] id: CL:0002584 name: renal cortical epithelial cell @@ -1538,9 +1552,11 @@ id: CL:0005009 name: renal principal cell def: "A cuboidal epithelial cell of the kidney which regulates sodium and potassium balance. The activity of sodium and potassium channels on the apical membrane of the cell is regulated by aldosterone and vasopressin. In mammals this cell type is located in the renal collecting duct system." [CL:CVS] subset: cellxgene_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_0005009 xref: ZFA:0005322 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} is_a: CL:0000075 ! columnar/cuboidal epithelial cell is_a: CL:0002518 ! kidney epithelial cell +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nRenal principal cells are the major cell type in the initial collecting tubule and the cortical and outer medullary collecting ducts, as well as the connecting tubule, in the nephrons of the kidneys.\nA key function of renal principal cells is the regulation of water balance in the body. These cells express aquaporin-2 (AQP2) water channels, which facilitate the reabsorption of water from the fluid within the renal tubule lumen back into the blood. The translocation of AQP2 to the cell membrane is controlled by the hormone vasopressin: In response to high vasopressin levels, AQP2 moves to the cell membrane, allowing water to pass through effectively and be reabsorbed, therefore concentrating the urine. Conversely, in low vasopressin conditions, AQP2 is removed from the membrane, reducing water reabsorption and diluting the urine. \nRenal principal cells are also involved in the regulation of sodium and potassium levels in the body. They have sodium channels (ENaC) in their luminal membranes which permit the reabsorption of sodium ions from the tubule fluid back into the blood, resulting in a net reabsorption of sodium ions into the systemic circulation. This process is controlled, in part, by the hormone aldosterone. Additionally, renal principal cells contain potassium channels that facilitate the secretion of potassium ions into the urine. The activities of these channels, in coordination with other cell types in the nephron, are critical for maintaining electrolyte balance and overall body homeostasis." xsd:string {xref="DOI:10.1016/j.krcp.2013.07.005", xref="DOI:10.2215/CJN.05760513", xref="DOI:10.2215/CJN.08580813"} [Term] id: CL:0007004 @@ -1584,6 +1600,7 @@ subset: cellxgene_subset subset: human_reference_atlas synonym: "mesenchyme cell" EXACT [] is_a: CL:0000219 ! motile cell +is_a: CL:0000255 ! eukaryotic cell relationship: capable_of GO:0016477 ! cell migration relationship: part_of UBERON:0003104 ! mesenchyme property_value: RO:0002175 NCBITaxon:9606 @@ -1614,14 +1631,17 @@ id: CL:0011012 name: neural crest cell def: "A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells." [https://orcid.org/0000-0001-5208-3432, https://orcid.org/0000-0002-9900-7880] subset: cellxgene_subset +xref: https://cellxgene.cziscience.com/cellguide/CL_0011012 is_a: CL:0000048 ! multi fate stem cell is_a: CL:0002321 ! embryonic cell (metazoa) +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nNeural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. \nAfter the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull.\nDisorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis." xsd:string {xref="DOI:10.1002/dvg.23276", xref="DOI:10.1242/dev.193193", xref="DOI:10.3389/fcell.2020.00635/full", xref="https://doi.org/10.1016/j.ydbio.2011.12.042"} [Term] id: CL:0011026 name: progenitor cell def: "A precursor cell that has a tendency to differentiate into a specific type of cell. They are descendants of stem cells, only they are more constrained in their differentiation potential or capacity for self-renewal, and are often more limited in both senses." [https://doi.org/10.1016/B978-0-12-409503-8.00002-0, ISBN:978-1-62808-994-3] subset: cellxgene_subset +is_a: CL:0000255 ! eukaryotic cell is_a: CL:0011115 ! precursor cell intersection_of: CL:0011115 ! precursor cell intersection_of: RO:0002202 CL:0000034 ! develops from stem cell @@ -1708,6 +1728,7 @@ subset: human_reference_atlas subset: kidney_upper_slim synonym: "epithelial cell of renal collecting tubule" EXACT [FMA:70982] xref: FMA:70982 +xref: https://cellxgene.cziscience.com/cellguide/CL_1000454 xref: KUPO:0001059 is_a: CL:0000072 {is_inferred="true"} ! non-branched duct epithelial cell is_a: CL:1000449 ! epithelial cell of nephron @@ -1715,6 +1736,7 @@ is_a: CL:1001225 {is_inferred="true"} ! kidney collecting duct cell intersection_of: CL:0000066 ! epithelial cell intersection_of: part_of UBERON:0001232 ! collecting duct of renal tubule property_value: RO:0002175 NCBITaxon:9606 +property_value: terms:description "This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional.\n\nKidney collecting duct epithelial cells are a specialized type of cells that form an integral part of the renal system. Located in the collecting duct system of the kidneys, these cells are responsible for one of the final steps in the process of urine formation, and they are instrumental in the fine tuning of the volume and composition of urine by reabsorbing water and certain solutes back into the bloodstream.\nThese cells express specific channels and carriers that actively and passively transport ions and water. They also have channels on their membranes, such as sodium channels and potassium channels, involved in reabsorbing or secreting these electrolytes depending upon the body's needs. The function of renal collecting duct epithelial cells can be regulated by a variety of hormones, including vasopressin (antidiuretic hormone), which can modulate the ion channels and carriers and hence indirectly influence body fluid homeostasis.\nAside from their function in ion and water balance, kidney collecting duct epithelial cells also aid in maintaining the body's acid-base balance. They have specialized functionality to secret hydrogen ions into the tubular lumen, which contributes to acid excretion. Any dysfunction may have serious implications and lead to various renal or systemic diseases, exemplifying the importance of these cells in maintaining overall body homeostasis." xsd:string {xref="DOI:10.1016/j.ajpath.2014.01.014", xref="DOI:10.1016/j.semnephrol.2019.04.005", xref="DOI:10.2215/CJN.05760513", xref="DOI:10.2215/CJN.08880914"} [Term] id: CL:1000494 @@ -1738,7 +1760,7 @@ def: "A cell that is part of a kidney." [] subset: cellxgene_subset xref: KUPO:0001010 xref: ZFA:0009389 {sssom:mapping_justification="https://w3id.org/semapv/vocab/UnspecifiedMatching"} -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0002113 ! kidney relationship: part_of UBERON:0002113 ! kidney @@ -2034,7 +2056,7 @@ creation_date: 2014-06-04T15:07:42Z id: CL:4030031 name: interstitial cell def: "Any cell that is located within the interstitium between the cells most prominent in defining a given tissue. \"Interstitial cell\" is a morphological term and refers to a variety of cells with differing origins and phenotypes." [PMID:24987007] -is_a: CL:0000000 ! cell +is_a: CL:0000255 ! eukaryotic cell intersection_of: CL:0000000 ! cell intersection_of: part_of UBERON:0005169 ! interstitial tissue relationship: part_of UBERON:0005169 ! interstitial tissue @@ -2096,8 +2118,9 @@ synonym: "chromosome scaffold" RELATED [] synonym: "cytoplasmic chromatin" NARROW [] synonym: "nuclear chromatin" NARROW [] xref: NIF_Subcellular:sao1615953555 -is_a: GO:0032993 ! protein-DNA complex +is_a: GO:0110165 ! cellular anatomical entity relationship: part_of GO:0005694 ! chromosome +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28301" xsd:anyURI [Term] id: GO:0000792 @@ -2217,7 +2240,7 @@ id: GO:0001977 name: renal system process involved in regulation of blood volume namespace: biological_process def: "A slow mechanism of blood pressure regulation that responds to changes in pressure resulting from fluid and salt intake by modulating the quantity of blood in the circulatory system." [GOC:dph, GOC:tb, ISBN:0721643949] -subset: gocheck_do_not_annotate +subset: gocheck_obsoletion_candidate synonym: "renal blood volume control of blood pressure" RELATED [] synonym: "renal regulation of blood volume" RELATED [GOC:dph, GOC:tb] is_a: GO:0003071 ! renal system process involved in regulation of systemic arterial blood pressure @@ -2667,8 +2690,8 @@ synonym: "ribosomal RNA" RELATED [] xref: NIF_Subcellular:sao1429207766 xref: Wikipedia:Ribosome is_a: GO:0043232 ! intracellular non-membrane-bounded organelle +is_a: PR:000050567 ! protein-containing material entity relationship: capable_of_part_of GO:0006412 ! translation -relationship: has_part PR:000000001 ! protein [Term] id: GO:0005886 @@ -3022,6 +3045,9 @@ def: "The generation and maintenance of gametes in a multicellular organism. A g synonym: "gametogenesis" RELATED [] is_a: GO:0048609 ! multicellular organismal reproductive process relationship: part_of GO:0019953 ! sexual reproduction +property_value: RO:0002161 NCBITaxon:2 +property_value: RO:0002161 NCBITaxon:2157 +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0007369 @@ -3535,6 +3561,9 @@ is_a: GO:0051301 ! cell division intersection_of: GO:0051301 ! cell division intersection_of: has_primary_input CL:0000034 ! stem cell relationship: has_primary_input CL:0000034 ! stem cell +property_value: RO:0002161 NCBITaxon:2 +property_value: RO:0002161 NCBITaxon:2157 +property_value: RO:0002161 NCBITaxon:4751 [Term] id: GO:0019226 @@ -4060,18 +4089,8 @@ synonym: "protein complex" NARROW [] synonym: "protein containing complex" EXACT [] synonym: "protein-protein complex" NARROW [] is_a: GO:0005575 ! cellular_component +is_a: PR:000050567 ! protein-containing material entity disjoint_from: GO:0110165 ! cellular anatomical entity -relationship: has_part PR:000000001 ! protein - -[Term] -id: GO:0032993 -name: protein-DNA complex -namespace: cellular_component -def: "A macromolecular complex containing both protein and DNA molecules." [GOC:mah] -comment: Note that this term is intended to classify complexes that have DNA as one of the members of the complex, that is, the complex does not exist if DNA is not present. Protein complexes that interact with DNA e.g. transcription factor complexes should not be classified here. -subset: goslim_pir -synonym: "DNA-protein complex" EXACT [GOC:mah] -is_a: GO:0032991 ! protein-containing complex [Term] id: GO:0033036 @@ -4165,6 +4184,9 @@ def: "A large plasma membrane-lined circular pore that perforates the flattened synonym: "GEnC fenestration" EXACT [PMID:19129259] synonym: "glomerular endothelial cell fenestration" EXACT [PMID:19129259] is_a: GO:0046930 ! pore complex +property_value: RO:0002161 NCBITaxon:2 +property_value: RO:0002161 NCBITaxon:2157 +property_value: RO:0002161 NCBITaxon:4751 created_by: bf creation_date: 2011-12-12T10:53:24Z @@ -4294,6 +4316,7 @@ id: GO:0043227 name: membrane-bounded organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane." [GOC:go_curators] +subset: gocheck_do_not_annotate synonym: "membrane-enclosed organelle" EXACT [] xref: NIF_Subcellular:sao414196390 is_a: GO:0043226 ! organelle @@ -4301,30 +4324,35 @@ intersection_of: GO:0043226 ! organelle intersection_of: has_part GO:0016020 ! membrane disjoint_from: GO:0043228 ! non-membrane-bounded organelle relationship: has_part GO:0016020 ! membrane +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI [Term] id: GO:0043228 name: non-membrane-bounded organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes." [GOC:go_curators] +subset: gocheck_do_not_annotate subset: goslim_mouse synonym: "biological condensate" RELATED [] synonym: "non-membrane-enclosed organelle" EXACT [] xref: NIF_Subcellular:sao1456184038 is_a: GO:0043226 ! organelle property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/21881" xsd:anyURI +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI [Term] id: GO:0043229 name: intracellular organelle namespace: cellular_component def: "Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane." [GOC:go_curators] +subset: gocheck_do_not_annotate subset: goslim_pir is_a: GO:0043226 ! organelle intersection_of: GO:0043226 ! organelle intersection_of: part_of GO:0005622 ! intracellular anatomical structure disjoint_from: GO:0043230 ! extracellular organelle relationship: part_of GO:0005622 ! intracellular anatomical structure +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/28153" xsd:anyURI [Term] id: GO:0043230 @@ -4413,9 +4441,11 @@ name: cellular component biogenesis namespace: biological_process alt_id: GO:0071843 def: "A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component." [GOC:jl, GOC:mah] +subset: gocheck_do_not_annotate subset: goslim_pir synonym: "cellular component biogenesis at cellular level" EXACT [] is_a: GO:0071840 ! cellular component organization or biogenesis +property_value: term_tracker_item "https://github.com/geneontology/go-ontology/issues/27194" xsd:anyURI [Term] id: GO:0044207 @@ -5312,6 +5342,7 @@ def: "A complex of collagen trimers such as a fibril or collagen network." [GOC: synonym: "Supramolecular aggregate of collagen" EXACT [PMID:19693541] synonym: "Supramolecular collagen assembly" EXACT [PMID:21421911] is_a: GO:0099080 ! supramolecular complex +is_a: PR:000050567 ! protein-containing material entity relationship: has_part GO:0005581 ! collagen trimer relationship: part_of GO:0062023 ! collagen-containing extracellular matrix @@ -6378,7 +6409,7 @@ comment: The definition above excludes protein complexes, which some also consid synonym: "native protein" NARROW [IEDB:BP] synonym: "natural protein" EXACT [PRO:DAN] is_a: PR:000018263 ! amino acid chain -is_a: PR:000064867 ! protein-containing molecular entity +is_a: PR:000050567 ! protein-containing material entity relationship: output_of GO:0006412 ! translation [Term] @@ -6789,11 +6820,11 @@ synonym: "fam:angiotensinogenase" EXACT PRO-short-label [PRO:DAN] is_a: PR:000000001 ! protein [Term] -id: PR:000064867 -name: protein-containing molecular entity +id: PR:000050567 +name: protein-containing material entity namespace: protein -def: "A molecular entity that minimally consists of a protein." [PRO:DAN] -comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). +def: "A material entity that minimally consists of a protein." [PRO:DAN] +comment: Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566). synonym: "protein" NARROW [PRO:DAN] synonym: "protein aggregate" NARROW [PRO:DAN] synonym: "protein complex" NARROW [PRO:DAN] @@ -6858,7 +6889,7 @@ xref: VSAO:0000075 xref: Wikipedia:Appendage xref: XAO:0000218 is_a: UBERON:0000475 ! organism subdivision -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0000055 @@ -6978,6 +7009,7 @@ xref: UMLS:C0687028 {source="ncithesaurus:Duct"} xref: Wikipedia:Duct_(anatomy) xref: XAO:0004000 xref: ZFA:0005171 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000063 ! organ subunit relationship: has_part UBERON:0034969 ! epithelial layer of duct relationship: RO:0000086 PATO:0002299 ! has quality tubular @@ -7223,7 +7255,7 @@ xref: SCTID:118966000 xref: UMLS:C1519343 {source="ncithesaurus:Skeletal_System_Part"} is_a: UBERON:0011216 {source="cjm"} ! organ system subdivision relationship: part_of UBERON:0001434 ! skeletal system -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002473 UBERON:0004765 ! composed primarily of skeletal element [Term] @@ -7531,7 +7563,7 @@ is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000108 {source="BILS"} ! blastula stage relationship: RO:0002082 GO:0007369 ! simultaneous with gastrulation -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0000110 @@ -7547,7 +7579,7 @@ is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: preceded_by UBERON:0000109 ! gastrula stage relationship: RO:0002082 GO:0001841 ! simultaneous with neural tube formation -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: seeAlso "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/343" xsd:anyURI @@ -7567,7 +7599,7 @@ xref: Wikipedia:Organogenesis is_a: UBERON:0000105 ! life cycle stage relationship: part_of UBERON:0000068 ! embryo stage relationship: RO:0002082 GO:0048513 ! simultaneous with animal organ development -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: seeAlso "https://github.com/obophenotype/developmental-stage-ontologies/issues/84" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/533" xsd:anyURI @@ -7590,7 +7622,7 @@ id: UBERON:0000154 name: posterior region of body namespace: uberon is_a: UBERON:0000475 ! organism subdivision -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria [Term] id: UBERON:0000158 @@ -7639,7 +7671,7 @@ xref: ZFA:0005781 is_a: UBERON:0013522 ! subdivision of tube relationship: part_of UBERON:0001555 {source="ZFA"} ! digestive tract relationship: part_of UBERON:0004122 {source="AAO"} ! genitourinary system -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata property_value: IAO:0000116 "adding df link to embryonic cloaca leads to a cycle in uberon-simple, as cloaca is a suberclass of embryonic cloaca" xsd:string [Term] @@ -7680,7 +7712,7 @@ xref: VHOG:0000414 xref: Wikipedia:Definitive_urogenital_sinus is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0000163 {source="MP-def"} ! embryonic cloaca -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002202 UBERON:0003064 ! develops from intermediate mesoderm relationship: RO:0002433 UBERON:0000163 ! contributes to morphology of embryonic cloaca property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png" xsd:anyURI @@ -7739,7 +7771,7 @@ xref: XAO:0003029 xref: ZFA:0000547 xref: ZFA:0000590 is_a: UBERON:0004921 ! subdivision of digestive tract -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002202 UBERON:0035804 ! develops from future mouth property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/0/06/Mouth_illustration-Otis_Archives.jpg" xsd:anyURI property_value: seeAlso "https://github.com/obophenotype/uberon/issues/661" xsd:anyURI @@ -7801,6 +7833,7 @@ xref: VHOG:0000224 xref: Wikipedia:Blood xref: XAO:0000124 xref: ZFA:0000007 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000179 ! haemolymphatic fluid relationship: has_part CL:0000232 {source="CL:tm"} ! erythrocyte relationship: has_part UBERON:0001969 ! blood plasma @@ -7821,7 +7854,7 @@ is_a: UBERON:0006314 ! bodily fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: part_of UBERON:0002193 ! hemolymphoid system relationship: part_of UBERON:0002193 ! hemolymphoid system -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: terms:contributor https://orcid.org/0000-0002-6601-2165 creation_date: 2009-04-08T04:38:19Z @@ -7872,7 +7905,7 @@ xref: Wikipedia:Parenchyma is_a: UBERON:0000064 ! organ part disjoint_from: UBERON:0003891 ! stroma relationship: capable_of GO:0032501 ! multicellular organismal process -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0000362 @@ -7948,7 +7981,7 @@ is_a: UBERON:0011216 ! organ system subdivision intersection_of: UBERON:0011216 ! organ system subdivision intersection_of: RO:0002473 UBERON:0001015 ! composed primarily of musculature relationship: capable_of GO:0003012 ! muscle system process -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002473 UBERON:0001015 ! composed primarily of musculature property_value: IAO:0000116 "consider whether this should be restricted to skeletal musculature. See https://github.com/obophenotype/uberon/issues/77" xsd:string property_value: RO:0002161 NCBITaxon:6040 @@ -8382,12 +8415,13 @@ xref: VHOG:0000387 xref: Wikipedia:Epithelium xref: XAO:0003045 xref: ZFA:0001486 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: RO:0002473 CL:0000066 ! composed primarily of epithelial cell relationship: has_part GO:0005911 ! cell-cell junction relationship: has_part UBERON:0005769 ! basement membrane of epithelium -relationship: RO:0002160 NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} ! in taxon Metazoa relationship: RO:0002473 CL:0000066 ! composed primarily of epithelial cell property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg" xsd:anyURI @@ -8552,7 +8586,7 @@ xref: SCTID:302553009 xref: Wikipedia:Abdomen is_a: UBERON:0009569 ! subdivision of trunk relationship: part_of UBERON:0002417 {source="MA"} ! abdominal segment of trunk -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata property_value: IAO:0000116 "Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class" xsd:string [Term] @@ -8633,7 +8667,7 @@ xref: Wikipedia:Germ_layer xref: XAO:0003011 xref: ZFA:0001122 is_a: UBERON:0010316 ! germ layer / neural crest -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0000924 @@ -8787,7 +8821,7 @@ xref: ZFA:0001290 is_a: UBERON:0013522 ! subdivision of tube relationship: part_of UBERON:0000924 ! ectoderm relationship: part_of UBERON:0035804 ! future mouth -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/93/Gray977.png" xsd:anyURI property_value: IAO:0000116 "consider indicating location. e.g. anterior. Note some AOs place this as part of oral opening, but it's not clear when this structure comes into existence" xsd:string @@ -8816,7 +8850,7 @@ xref: ZFA:0000066 is_a: UBERON:0016566 {source="EHDAA2"} ! pit relationship: part_of UBERON:0007026 ! presumptive gut relationship: RO:0001025 UBERON:0012469 {source="EHDAA2"} ! located in external anal region -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002202 UBERON:0000924 ! develops from ectoderm relationship: RO:0002387 UBERON:0001353 ! has potential to develop into anal region property_value: IAO:0000116 "removed WBbt:0006795 'proctodeum' - junction between the alimentary and genital tracts in the male." xsd:string @@ -8871,7 +8905,7 @@ intersection_of: UBERON:0007100 ! primary circulatory organ intersection_of: has_part UBERON:0004151 ! cardiac chamber relationship: has_part UBERON:0004151 ! cardiac chamber relationship: part_of UBERON:0015410 {source="MA"} ! heart plus pericardium -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002202 UBERON:0004141 ! develops from heart tube relationship: RO:0002433 UBERON:0004535 ! contributes to morphology of cardiovascular system property_value: foaf:depiction "https://cdn.humanatlas.io/digital-objects/ref-organ/heart-female/v1.3/assets/3d-vh-f-heart.glb" xsd:anyURI @@ -8907,7 +8941,7 @@ synonym: "medulla" EXACT [FMA:61108] xref: FMA:61108 xref: galen:Medulla is_a: UBERON:0000471 ! compound organ component -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002219 UBERON:0001851 ! surrounded by cortex [Term] @@ -9149,7 +9183,7 @@ is_a: UBERON:8450002 ! excretory system intersection_of: UBERON:8450002 ! excretory system intersection_of: capable_of GO:0097254 ! renal tubular secretion relationship: capable_of GO:0097254 ! renal tubular secretion -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage property_value: RO:0002161 NCBITaxon:110815 {source="Wikipedia"} property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} @@ -9174,7 +9208,7 @@ disjoint_from: UBERON:0002204 ! musculoskeletal system disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:8450002 ! excretory system relationship: capable_of GO:0003013 ! circulatory system process -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg" xsd:anyURI property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} @@ -9224,7 +9258,6 @@ namespace: uberon def: "The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]." [BIRNLEX:844, ISBN:0-14-051288-8, ISBN:3110148986, NLM:nervous+system, WB:rynl, Wikipedia:Nervous_system, ZFIN:curator] subset: cumbo subset: efo_slim -subset: human_reference_atlas subset: pheno_slim subset: uberon_slim subset: vertebrate_core @@ -9265,14 +9298,13 @@ disjoint_from: UBERON:0002390 ! hematopoietic system disjoint_from: UBERON:8450002 ! excretory system relationship: capable_of GO:0050877 ! nervous system process relationship: has_part CL:0000540 ! neuron -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002473 CL:0002319 ! composed primarily of neural cell relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage relationship: RO:0002495 UBERON:0016880 {source="Bgee:AN"} ! immediate transformation of future nervous system property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg" xsd:anyURI property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:6040 -property_value: RO:0002175 NCBITaxon:9606 [Term] id: UBERON:0001017 @@ -9319,7 +9351,7 @@ xref: ZFA:0000012 is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0011216 {source="FBbt", source="cjm"} ! organ system subdivision relationship: part_of UBERON:0001016 ! nervous system -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria relationship: RO:0002495 UBERON:0016879 {source="Bgee:AN"} ! immediate transformation of future central nervous system property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} property_value: RO:0002175 NCBITaxon:9606 @@ -10286,7 +10318,7 @@ xref: WBbt:0005743 xref: ZFA:0000112 is_a: UBERON:0000025 ! tube relationship: part_of UBERON:0001007 ! digestive system -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002176 UBERON:0000165 ! connects mouth relationship: RO:0002495 UBERON:0007026 {source="NCBIBook:NBK10107"} ! immediate transformation of presumptive gut property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} @@ -10491,6 +10523,7 @@ xref: MIAA:0000052 xref: NCIT:C13356 xref: UMLS:C0032105 {source="ncithesaurus:Plasma"} xref: Wikipedia:Blood_plasma +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000179 ! haemolymphatic fluid intersection_of: UBERON:0000463 ! organism substance intersection_of: has_part GO:0005577 ! fibrinogen complex @@ -10600,6 +10633,7 @@ xref: VHOG:0001250 xref: Wikipedia:Blood_vessel xref: XAO:0001011 xref: ZFA:0005314 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000055 ! vessel is_a: UBERON:0004120 ! mesoderm-derived structure relationship: capable_of_part_of GO:0008015 ! blood circulation @@ -10677,7 +10711,7 @@ is_a: UBERON:0000487 {source="FMA-text-def", source="https://github.com/obopheno is_a: UBERON:0012275 ! meso-epithelium intersection_of: UBERON:0000483 ! epithelium intersection_of: RO:0002473 CL:0000115 ! composed primarily of endothelial cell -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002473 CL:0000115 ! composed primarily of endothelial cell property_value: RO:0002175 NCBITaxon:9606 @@ -10907,7 +10941,7 @@ xref: XAO:0003166 is_a: UBERON:0010912 ! subdivision of skeleton relationship: overlaps UBERON:0000026 ! appendage relationship: part_of UBERON:0011249 ! appendicular skeletal system -relationship: RO:0002160 NCBITaxon:7776 ! only in taxon Gnathostomata +relationship: RO:0002162 NCBITaxon:7776 ! in taxon Gnathostomata relationship: RO:0002433 UBERON:0001434 ! contributes to morphology of skeletal system property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/7/7c/Appendicular_skeleton_diagram.svg" xsd:anyURI property_value: RO:0002175 NCBITaxon:9606 @@ -10976,7 +11010,7 @@ is_a: UBERON:0000489 ! cavitated compound organ is_a: UBERON:0005172 ! abdomen element is_a: UBERON:0015212 ! lateral structure relationship: part_of UBERON:0011143 {source="FMA"} ! upper urinary tract -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002202 UBERON:0003918 ! develops from kidney mesenchyme relationship: RO:0002202 UBERON:0005095 ! develops from kidney rudiment relationship: RO:0002433 UBERON:0001008 ! contributes to morphology of renal system @@ -11036,7 +11070,7 @@ xref: EMAPA:18765 xref: FMA:74562 xref: MA:0000013 is_a: UBERON:0000467 {source="MA"} ! anatomical system -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria [Term] id: UBERON:0002201 @@ -11142,6 +11176,7 @@ xref: NCIT:C32891 xref: SCTID:362219002 xref: UMLS:C0022445 {source="ncithesaurus:Juxtaglomerular_Apparatus"} xref: Wikipedia:Juxtaglomerular_apparatus +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000061 ! anatomical structure relationship: capable_of GO:0003093 {source="GO"} ! regulation of glomerular filtration relationship: has_part CL:0000648 ! kidney granular cell @@ -11268,7 +11303,7 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0004121 ! ectoderm-derived structure relationship: part_of UBERON:0011137 ! axial skeletal system relationship: produces PR:000014841 ! sonic hedgehog protein -relationship: RO:0002160 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {source="http://tolweb.org/Chordata/2499"} ! in taxon Chordata relationship: RO:0002202 UBERON:0004880 {source="ZFA"} ! develops from chordamesoderm relationship: RO:0002202 UBERON:0006267 {source="EHDAA2"} ! develops from notochordal plate relationship: RO:0002488 UBERON:0000068 ! existence starts during embryo stage @@ -11311,7 +11346,7 @@ xref: XAO:0000058 xref: ZFA:0000155 is_a: UBERON:0005423 ! developing anatomical structure is_a: UBERON:0007503 {source="EHDAA2"} ! epithelial vesicle -relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {source="GOTAX:0000352"} ! in taxon Chordata relationship: RO:0002202 UBERON:0003059 {source="ZFA"} ! develops from presomitic mesoderm property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI property_value: RO:0002161 NCBITaxon:7712 {source="PMID:17237766"} @@ -11371,7 +11406,7 @@ is_a: UBERON:0004121 ! ectoderm-derived structure is_a: UBERON:0010314 ! structure with developmental contribution from neural crest is_a: UBERON:0010316 ! germ layer / neural crest relationship: part_of UBERON:0002346 {source="XAO", source="https://github.com/obophenotype/uberon/wiki/The-neural-crest"} ! neurectoderm -relationship: RO:0002160 NCBITaxon:89593 ! only in taxon Craniata +relationship: RO:0002162 NCBITaxon:89593 ! in taxon Craniata relationship: RO:0002202 UBERON:0003075 {source="BTO"} ! develops from neural plate relationship: RO:0002202 UBERON:0005062 {source="PMID:11523831"} ! develops from neural fold relationship: RO:0002473 CL:0000333 ! composed primarily of migratory neural crest cell @@ -11478,7 +11513,7 @@ xref: VSAO:0000017 xref: XAO:0001017 xref: ZFA:0001632 is_a: UBERON:0000479 ! tissue -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa property_value: RO:0002175 NCBITaxon:9606 [Term] @@ -11510,7 +11545,7 @@ intersection_of: UBERON:0000479 ! tissue intersection_of: RO:0002473 CL:0000187 ! composed primarily of muscle cell relationship: capable_of GO:0006936 ! muscle contraction relationship: part_of UBERON:0001015 ! musculature -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002473 CL:0000187 ! composed primarily of muscle cell [Term] @@ -11555,7 +11590,7 @@ is_a: UBERON:0000467 ! anatomical system is_a: UBERON:0004120 ! mesoderm-derived structure disjoint_from: UBERON:8450002 ! excretory system relationship: part_of UBERON:0002193 {source="FMA"} ! hemolymphoid system -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002202 UBERON:0003061 ! develops from blood island property_value: RO:0002175 NCBITaxon:9606 @@ -11752,7 +11787,7 @@ xref: XAO:0000205 xref: ZFA:0001204 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0000926 ! mesoderm -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002202 UBERON:0000926 ! develops from mesoderm property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI @@ -11819,7 +11854,7 @@ xref: ZFA:0000132 is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0010371 ! ecto-epithelium is_a: UBERON:0016879 ! future central nervous system -relationship: RO:0002160 NCBITaxon:7711 {source="GOTAX:0000352"} ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 {source="GOTAX:0000352"} ! in taxon Chordata relationship: RO:0002256 UBERON:0002328 {source="Wikipedia"} ! developmentally induced by notochord relationship: RO:0002495 UBERON:0007284 {source="Bgee:AN"} ! immediate transformation of presumptive neural plate property_value: foaf:depiction "https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png" xsd:anyURI @@ -11886,7 +11921,7 @@ is_a: UBERON:0004120 ! mesoderm-derived structure is_a: UBERON:0005291 ! embryonic tissue is_a: UBERON:0007524 {source="EHDAA2"} ! dense mesenchyme tissue relationship: part_of UBERON:0000926 {source="EHDAA2", source="VHOG"} ! mesoderm -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria relationship: RO:0002221 UBERON:0003887 ! surrounds intraembryonic coelom property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png" xsd:anyURI @@ -11936,7 +11971,7 @@ xref: XAO:0000397 xref: ZFA:0001080 is_a: UBERON:0005856 {source="EHDAA2"} ! developing mesenchymal condensation is_a: UBERON:0007530 {source="EHDAA2"} ! migrating mesenchyme population -relationship: RO:0002160 NCBITaxon:7742 {source="VHOG:0000680"} ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 {source="VHOG:0000680"} ! in taxon Vertebrata relationship: RO:0002202 UBERON:0002329 {source="ZFA"} ! develops from somite property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png" xsd:anyURI @@ -11991,7 +12026,7 @@ xref: ZFA:0000393 is_a: UBERON:0000479 ! tissue intersection_of: UBERON:0000479 ! tissue intersection_of: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002328 GO:0032502 ! functionally related to developmental process relationship: RO:0002473 CL:0008019 ! composed primarily of mesenchymal cell property_value: foaf:depiction "http://upload.wikimedia.org/wikipedia/commons/f/f4/Mesenchymal_Stem_Cell.jpg" xsd:anyURI @@ -12250,7 +12285,7 @@ xref: FMA:81494 xref: NCIT:C67387 xref: UMLS:C0927195 {source="ncithesaurus:Stroma_Connective_Tissue"} is_a: UBERON:0000064 ! organ part -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002473 UBERON:0002384 ! composed primarily of connective tissue [Term] @@ -12865,6 +12900,7 @@ xref: WikipediaCategory:Cardiovascular_system xref: XAO:0000100 xref: XAO:0001010 xref: ZFA:0000010 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0000467 ! anatomical system intersection_of: UBERON:0000467 ! anatomical system intersection_of: has_part UBERON:0000948 ! heart @@ -12888,6 +12924,7 @@ synonym: "blood vessels" RELATED [TAO:0001079] synonym: "set of blood vessels" EXACT [] xref: TAO:0001079 xref: ZFA:0001079 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0002049 ! vasculature intersection_of: UBERON:0002049 ! vasculature intersection_of: RO:0002473 UBERON:0001981 ! composed primarily of blood vessel @@ -12911,6 +12948,7 @@ xref: EMAPA:16371 xref: MA:0002719 xref: SCTID:362030008 xref: VHOG:0000273 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0007798 {source="MA"} ! vascular system relationship: RO:0002351 UBERON:0001637 ! has member artery property_value: RO:0002175 NCBITaxon:9606 @@ -12931,6 +12969,7 @@ xref: NCIT:C33858 xref: SCTID:362060003 xref: UMLS:C1267406 {source="ncithesaurus:Venous_System"} xref: VHOG:0000277 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0007798 {source="MA"} ! vascular system relationship: RO:0002473 UBERON:0001638 ! composed primarily of vein property_value: RO:0002175 NCBITaxon:9606 @@ -13108,7 +13147,7 @@ is_a: UBERON:0034925 ! anatomical collection intersection_of: UBERON:0034925 ! anatomical collection intersection_of: RO:0002351 UBERON:0000982 ! has member skeletal joint relationship: part_of UBERON:0001434 {source="FMA"} ! skeletal system -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria relationship: RO:0002328 GO:0040011 ! functionally related to locomotion relationship: RO:0002351 UBERON:0000982 ! has member skeletal joint relationship: RO:0002492 UBERON:0000066 ! existence ends during fully formed stage @@ -13265,7 +13304,7 @@ xref: TAO:0000091 xref: ZFA:0000091 is_a: UBERON:0002050 ! embryonic structure relationship: part_of UBERON:0003068 ! axial mesoderm -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata [Term] id: UBERON:0004905 @@ -13308,7 +13347,7 @@ subset: upper_level xref: FMA:82485 is_a: UBERON:0000064 ! organ part relationship: part_of UBERON:0000060 ! anatomical wall -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0005061 @@ -13393,7 +13432,7 @@ synonym: "musculus" EXACT [FMA:30316] xref: FMA:30316 is_a: UBERON:0000061 ! anatomical structure relationship: has_part CL:0000187 ! muscle cell -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0005095 @@ -13873,11 +13912,12 @@ xref: NCIT:C13191 xref: SCTID:68989006 xref: UMLS:C0004799 {source="ncithesaurus:Basement_Membrane"} xref: Wikipedia:Basement_membrane +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005764 {source="FMA"} ! acellular membrane relationship: adjacent_to CL:0000066 ! epithelial cell relationship: has_part GO:0005587 ! collagen type IV trimer relationship: part_of UBERON:0000483 ! epithelium -relationship: RO:0002160 NCBITaxon:33208 ! only in taxon Metazoa +relationship: RO:0002162 NCBITaxon:33208 ! in taxon Metazoa relationship: RO:0002473 GO:0005604 ! composed primarily of basement membrane property_value: RO:0002175 NCBITaxon:80999 {source="http://palaeos.com/metazoa/porifera/homoscleromorpha.html"} @@ -14026,7 +14066,7 @@ xref: NCIT:C34232 xref: UMLS:C1518430 {source="ncithesaurus:Notochordal_Process"} xref: VHOG:0001213 is_a: UBERON:0005423 ! developing anatomical structure -relationship: RO:0002160 NCBITaxon:7711 ! only in taxon Chordata +relationship: RO:0002162 NCBITaxon:7711 ! in taxon Chordata relationship: RO:0002202 UBERON:0000924 {source="EHDAA2"} ! develops from ectoderm [Term] @@ -14131,7 +14171,7 @@ intersection_of: UBERON:0006598 ! presumptive structure intersection_of: part_of UBERON:0000307 ! blastula intersection_of: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm relationship: part_of UBERON:0000307 ! blastula -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002387 UBERON:0000925 ! has potential to develop into endoderm [Term] @@ -14183,7 +14223,7 @@ intersection_of: UBERON:0006598 ! presumptive structure intersection_of: part_of UBERON:0000307 ! blastula intersection_of: RO:0002387 UBERON:0000924 ! has potential to develop into ectoderm relationship: part_of UBERON:0000307 ! blastula -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002387 UBERON:0000924 ! has potential to develop into ectoderm [Term] @@ -14201,7 +14241,7 @@ intersection_of: UBERON:0006598 ! presumptive structure intersection_of: part_of UBERON:0000307 ! blastula intersection_of: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm relationship: part_of UBERON:0000307 ! blastula -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa relationship: RO:0002387 UBERON:0000926 ! has potential to develop into mesoderm [Term] @@ -14270,6 +14310,7 @@ subset: efo_slim xref: EFO:0003709 xref: TAO:0005077 xref: ZFA:0005077 +is_a: PR:000050567 ! protein-containing material entity is_a: UBERON:0005423 ! developing anatomical structure relationship: has_part CL:0000115 ! endothelial cell relationship: has_part CL:0000566 ! angioblastic mesenchymal cell @@ -14601,7 +14642,7 @@ is_a: UBERON:0000475 ! organism subdivision intersection_of: UBERON:0000475 ! organism subdivision intersection_of: RO:0002551 UBERON:0010719 ! has skeleton girdle skeleton relationship: part_of UBERON:0010707 ! appendage girdle complex -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002551 UBERON:0010719 ! has skeleton girdle skeleton [Term] @@ -14757,7 +14798,7 @@ synonym: "renal tubule (generic)" EXACT [https://orcid.org/0000-0002-6601-2165] synonym: "tubule of excretory system" EXACT [https://orcid.org/0000-0002-6601-2165, OBOL:automatic] is_a: UBERON:0003914 ! epithelial tube is_a: UBERON:0006555 ! excretory tube -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria [Term] id: UBERON:0009856 @@ -14987,7 +15028,7 @@ xref: FMA:7182 xref: VSAO:0000214 is_a: UBERON:0000475 ! organism subdivision is_a: UBERON:0015212 ! lateral structure -relationship: RO:0002160 NCBITaxon:7742 ! only in taxon Vertebrata +relationship: RO:0002162 NCBITaxon:7742 ! in taxon Vertebrata relationship: RO:0002328 GO:0040011 ! functionally related to locomotion property_value: IAO:0000116 "It is still called a complex when one of the two parts is missing (?) There are fossil fishes with only an outgrowth (no record of a girdle), including thelodonts (which have a suprabranchial fin) as well as some anaspids which have a distinctive 'paired fin' (with differing published assertions on whether it's homologous to a pec fin or pelvic fin or both or neither). There are many fishes and other vertebrates with only a girdle and no outgrowth.[VSAO]" xsd:string property_value: terms:contributor https://orcid.org/0000-0001-9114-8737 @@ -15168,7 +15209,7 @@ synonym: "schizocoelom" NARROW [] xref: EHDAA2:0004731 xref: Wikipedia:Coelom is_a: UBERON:0000481 {source="EHDAA2"} ! multi-tissue structure -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria property_value: IAO:0000116 "EHDAA2 distingsuishes between the lumen, the lining, and the 'coelomic cavity', which despire it's name, is not a space - it is the aggregate of space plus lining." xsd:string property_value: RO:0002161 NCBITaxon:147099 {source="Wikipedia:Acoelomorpha"} @@ -15288,7 +15329,7 @@ namespace: uberon def: "A principle subdivision of an organism that includes all structures along the primary axis, typically the anterior-posterior axis, from head to tail, including structures of the body proper where present (for example, ribs), but excluding appendages." [https://orcid.org/0000-0002-6601-2165] subset: non_informative is_a: UBERON:0000475 ! organism subdivision -relationship: RO:0002160 NCBITaxon:6072 ! only in taxon Eumetazoa +relationship: RO:0002162 NCBITaxon:6072 ! in taxon Eumetazoa [Term] id: UBERON:0013702 @@ -15372,7 +15413,7 @@ def: "Any structure that is placed on one side of the left-right axis of a bilat subset: grouping_class subset: non_informative is_a: UBERON:0000061 ! anatomical structure -relationship: RO:0002160 NCBITaxon:33213 ! only in taxon Bilateria +relationship: RO:0002162 NCBITaxon:33213 ! in taxon Bilateria [Term] id: UBERON:0015228 @@ -17011,9 +17052,7 @@ inverse_of: output_of ! output of [Typedef] id: has_part name: has part -name: has_part namespace: external -namespace: quality def: "a core relation that holds between a whole and its part" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_ontology @@ -17218,9 +17257,7 @@ expand_expression_to: "http://purl.obolibrary.org/obo/BFO_0000051 some (http://p [Typedef] id: part_of name: part of -name: part_of namespace: external -namespace: quality def: "a core relation that holds between a part and its whole" [] subset: http://purl.obolibrary.org/obo/valid_for_go_annotation_extension subset: http://purl.obolibrary.org/obo/valid_for_go_gp2term diff --git a/subsets/kidney_upper_slim.owl b/subsets/kidney_upper_slim.owl index 68c9d4c93..ae3211d54 100644 --- a/subsets/kidney_upper_slim.owl +++ b/subsets/kidney_upper_slim.owl @@ -22,8 +22,8 @@ xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#" xmlns:ncbitaxon="http://purl.obolibrary.org/obo/ncbitaxon#"> - - 2024-08-16 + + 2024-09-26 @@ -392,6 +392,14 @@ WHERE { + + + + + + + + @@ -1038,6 +1046,12 @@ WHERE { + + + + + + @@ -1076,17 +1090,13 @@ WHERE { - - created by - + - - creation date - + @@ -1172,9 +1182,7 @@ WHERE { - - id - + @@ -1283,7 +1291,6 @@ WHERE { A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. BFO:0000050 external - quality part_of @@ -1292,7 +1299,6 @@ A continuant cannot be part of an occurrent: use 'participates in'. An part_of part of part of - part_of http://www.obofoundry.org/ro/#OBO_REL:part_of @@ -1314,7 +1320,6 @@ A continuant cannot be part of an occurrent: use 'participates in'. An A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. BFO:0000051 external - quality has_part @@ -1322,7 +1327,6 @@ A continuant cannot have an occurrent as part: use 'participates in'. has_part has part has part - has_part @@ -4773,7 +4777,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -4854,6 +4858,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -5523,7 +5528,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -5631,12 +5636,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - An endothelial cell that lines the vasculature. ZFA:0009036 @@ -5699,12 +5698,36 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + Any epithelial cell that is part of some squamous epithelium. CALOHA:TS-1249 ZFA:0009039 squamous epithelial cell + + + + Any epithelial cell that is part of some squamous epithelium. + FBC:Autogenerated + @@ -5769,6 +5792,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6023,6 +6047,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6233,6 +6258,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6264,6 +6290,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6297,6 +6324,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6418,7 +6446,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -6427,11 +6455,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - Any cell that only exists in Eukaryota. + Any cell that in taxon some Eukaryota. MESH:D005057 eukaryotic cell @@ -6439,7 +6467,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - Any cell that only exists in Eukaryota. + Any cell that in taxon some Eukaryota. FBC:Autogenerated @@ -6566,7 +6594,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -6577,7 +6605,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -6821,6 +6849,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -6970,6 +6999,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -7066,6 +7096,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -7576,6 +7607,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -7717,6 +7749,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -7944,7 +7977,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different An endothelial cell that has small pores, or fenestrations, which allow for the efficient exchange of substances between the blood and surrounding tissues. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Fenestrated cells are specialized epithelial cells that are characterized by a distinctive structural feature, fenestrations or tiny pores, which allow an exchange of substances such as fluids, nutrients, and waste between blood vessels and the surrounding tissue environments. These cells are present in various types of epithelial tissues in the human body, including the intestinal tract, endocrine glands, and certain parts of the renal system. +There are multiple types of endothelial cell fenestrations. The most common type is found in systemic capillaries of the endocrine tissue (e.g., pancreatic islets), gastrointestinal mucosa, and renal peritubular capillaries. Here, the fenestrated cells have fenestrations in their peripheral cytoplasm with a unique thin and permeable diaphragm that provides a high degree of selectivity, blocking the passage of larger molecules while allowing the free movement of smaller ones. In contrast, other types of fenestrations, such as the discontinuous epithelium of the liver sinusoidal endothelial cells, do not have diaphragms. +Characteristically, fenestrated cells play a vital role in the filtering process of body systems. They are a key part of the glomeruli in the kidneys where blood is filtered under high pressure. The fenestrations present in the endothelial cells lining the capillaries of the glomerulus allow the free passage of water and small solute molecules towards the Bowman's capsule, leaving behind larger proteins and cells in the blood, thereby aiding in the filtration and waste removal process. +In the endocrine system, fenestrated cells in glandular capillaries allow the prompt release of hormones into the bloodstream. These cells have tightly clustered fenestrations which increase the surface area available for passive diffusion, improving the efficiency of hormone secretion. In villi of the small intestine, these cells increase absorption efficiency, permitting the exchange of water, electrolytes, and nutrients. +Overall, fenestrated cells contribute immensely to important physiological processes of filtration, absorption, and secretion, primarily connecting our body's circulation system with the surrounding tissues and organs. ZFA:0009286 + https://cellxgene.cziscience.com/cellguide/CL_0000666 window cell fenestrated endothelial cell @@ -7955,6 +7996,22 @@ Each of these 3 primitives can be composed to yield a cross-product of different An endothelial cell that has small pores, or fenestrations, which allow for the efficient exchange of substances between the blood and surrounding tissues. DOI:10.1007/978-3-211-99390-3_133 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Fenestrated cells are specialized epithelial cells that are characterized by a distinctive structural feature, fenestrations or tiny pores, which allow an exchange of substances such as fluids, nutrients, and waste between blood vessels and the surrounding tissue environments. These cells are present in various types of epithelial tissues in the human body, including the intestinal tract, endocrine glands, and certain parts of the renal system. +There are multiple types of endothelial cell fenestrations. The most common type is found in systemic capillaries of the endocrine tissue (e.g., pancreatic islets), gastrointestinal mucosa, and renal peritubular capillaries. Here, the fenestrated cells have fenestrations in their peripheral cytoplasm with a unique thin and permeable diaphragm that provides a high degree of selectivity, blocking the passage of larger molecules while allowing the free movement of smaller ones. In contrast, other types of fenestrations, such as the discontinuous epithelium of the liver sinusoidal endothelial cells, do not have diaphragms. +Characteristically, fenestrated cells play a vital role in the filtering process of body systems. They are a key part of the glomeruli in the kidneys where blood is filtered under high pressure. The fenestrations present in the endothelial cells lining the capillaries of the glomerulus allow the free passage of water and small solute molecules towards the Bowman's capsule, leaving behind larger proteins and cells in the blood, thereby aiding in the filtration and waste removal process. +In the endocrine system, fenestrated cells in glandular capillaries allow the prompt release of hormones into the bloodstream. These cells have tightly clustered fenestrations which increase the surface area available for passive diffusion, improving the efficiency of hormone secretion. In villi of the small intestine, these cells increase absorption efficiency, permitting the exchange of water, electrolytes, and nutrients. +Overall, fenestrated cells contribute immensely to important physiological processes of filtration, absorption, and secretion, primarily connecting our body's circulation system with the surrounding tissues and organs. + DOI:10.1002/ar.1092200109 + DOI:10.1016/0306-4522(86)90162-4 + DOI:10.1016/j.devcel.2012.11.003 + DOI:10.1038/s41467-022-31571-2 + DOI:10.1152/ajprenal.90601.2008 + @@ -8029,6 +8086,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -8117,6 +8175,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -8447,7 +8506,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + @@ -8678,6 +8739,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -8722,6 +8784,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -8977,6 +9040,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -9163,7 +9227,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -9202,7 +9266,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -9277,7 +9341,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -9350,32 +9414,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - An endothelial progenitor cell that participates in angiogenesis during development. - - 2011-02-28T04:20:39Z - ZFA:0005773 - See CL:0002619. - embryonic blood vessel endothelial progenitor cell - - - - - An endothelial progenitor cell that participates in angiogenesis during development. - GOC:tfm - - - - - ZFA:0005773 - - - - - @@ -9470,7 +9508,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cuboidal epithelial cell of the kidney which regulates sodium and potassium balance. The activity of sodium and potassium channels on the apical membrane of the cell is regulated by aldosterone and vasopressin. In mammals this cell type is located in the renal collecting duct system. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Renal principal cells are the major cell type in the initial collecting tubule and the cortical and outer medullary collecting ducts, as well as the connecting tubule, in the nephrons of the kidneys. +A key function of renal principal cells is the regulation of water balance in the body. These cells express aquaporin-2 (AQP2) water channels, which facilitate the reabsorption of water from the fluid within the renal tubule lumen back into the blood. The translocation of AQP2 to the cell membrane is controlled by the hormone vasopressin: In response to high vasopressin levels, AQP2 moves to the cell membrane, allowing water to pass through effectively and be reabsorbed, therefore concentrating the urine. Conversely, in low vasopressin conditions, AQP2 is removed from the membrane, reducing water reabsorption and diluting the urine. +Renal principal cells are also involved in the regulation of sodium and potassium levels in the body. They have sodium channels (ENaC) in their luminal membranes which permit the reabsorption of sodium ions from the tubule fluid back into the blood, resulting in a net reabsorption of sodium ions into the systemic circulation. This process is controlled, in part, by the hormone aldosterone. Additionally, renal principal cells contain potassium channels that facilitate the secretion of potassium ions into the urine. The activities of these channels, in coordination with other cell types in the nephron, are critical for maintaining electrolyte balance and overall body homeostasis. ZFA:0005322 + https://cellxgene.cziscience.com/cellguide/CL_0005009 renal principal cell @@ -9480,6 +9524,18 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cuboidal epithelial cell of the kidney which regulates sodium and potassium balance. The activity of sodium and potassium channels on the apical membrane of the cell is regulated by aldosterone and vasopressin. In mammals this cell type is located in the renal collecting duct system. CL:CVS + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Renal principal cells are the major cell type in the initial collecting tubule and the cortical and outer medullary collecting ducts, as well as the connecting tubule, in the nephrons of the kidneys. +A key function of renal principal cells is the regulation of water balance in the body. These cells express aquaporin-2 (AQP2) water channels, which facilitate the reabsorption of water from the fluid within the renal tubule lumen back into the blood. The translocation of AQP2 to the cell membrane is controlled by the hormone vasopressin: In response to high vasopressin levels, AQP2 moves to the cell membrane, allowing water to pass through effectively and be reabsorbed, therefore concentrating the urine. Conversely, in low vasopressin conditions, AQP2 is removed from the membrane, reducing water reabsorption and diluting the urine. +Renal principal cells are also involved in the regulation of sodium and potassium levels in the body. They have sodium channels (ENaC) in their luminal membranes which permit the reabsorption of sodium ions from the tubule fluid back into the blood, resulting in a net reabsorption of sodium ions into the systemic circulation. This process is controlled, in part, by the hormone aldosterone. Additionally, renal principal cells contain potassium channels that facilitate the secretion of potassium ions into the urine. The activities of these channels, in coordination with other cell types in the nephron, are critical for maintaining electrolyte balance and overall body homeostasis. + DOI:10.1016/j.krcp.2013.07.005 + DOI:10.2215/CJN.05760513 + DOI:10.2215/CJN.08580813 + @@ -9603,6 +9659,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -9672,6 +9729,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different A cell of the neural crest. Neural crest cells are multipotent. Premigratory neural crest cells are found at the neural plate boarder, some of which will undergo ectomesynchymal transition and delamination to form migratory neural crest cells. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. +After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. +Disorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis. + https://cellxgene.cziscience.com/cellguide/CL_0011012 neural crest cell @@ -9682,6 +9745,19 @@ Each of these 3 primitives can be composed to yield a cross-product of different https://orcid.org/0000-0001-5208-3432 https://orcid.org/0000-0002-9900-7880 + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Neural crest cells are a group of transient and highly migratory cells that originate from the neuroectoderm during the early stages of embryonic development. They are multipotent cells with an exceptional degree of plasticity, capable of differentiating into various somatic cell types and therefore play a fundamental role in the formation of various organs and tissues, making them critical contributors to the developing embryo. +After the initiation of neurulation (the formation of the neural tube) neural crest cells start to undergo epithelial-to-mesenchymal transition and delaminate and migrate from the dorsal neural tube to several regions throughout the embryo. They differentiate into a range of diverse cell types, such as neurons and glial cells of the peripheral nervous system, including sensory and autonomic neurons. They also contribute to the formation of adrenal glands, pigment cells in the skin (melanocytes), cardiac structures, including parts of the heart septum and major arteries, as well as bones and cartilage of the face and skull. +Disorders or aberrations in the development or migration of the neural crest cells can lead to serious congenital malformations, such as neurocristopathies, including Hirschsprung disease, neuroblastoma, and neurofibromatosis. + DOI:10.1002/dvg.23276 + DOI:10.1242/dev.193193 + DOI:10.3389/fcell.2020.00635/full + https://doi.org/10.1016/j.ydbio.2011.12.042 + @@ -9699,6 +9775,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -9961,20 +10038,20 @@ Each of these 3 primitives can be composed to yield a cross-product of different An epithelial cell that is part of the collecting duct of renal tubule. + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Kidney collecting duct epithelial cells are a specialized type of cells that form an integral part of the renal system. Located in the collecting duct system of the kidneys, these cells are responsible for one of the final steps in the process of urine formation, and they are instrumental in the fine tuning of the volume and composition of urine by reabsorbing water and certain solutes back into the bloodstream. +These cells express specific channels and carriers that actively and passively transport ions and water. They also have channels on their membranes, such as sodium channels and potassium channels, involved in reabsorbing or secreting these electrolytes depending upon the body's needs. The function of renal collecting duct epithelial cells can be regulated by a variety of hormones, including vasopressin (antidiuretic hormone), which can modulate the ion channels and carriers and hence indirectly influence body fluid homeostasis. +Aside from their function in ion and water balance, kidney collecting duct epithelial cells also aid in maintaining the body's acid-base balance. They have specialized functionality to secret hydrogen ions into the tubular lumen, which contributes to acid excretion. Any dysfunction may have serious implications and lead to various renal or systemic diseases, exemplifying the importance of these cells in maintaining overall body homeostasis. FMA:70982 KUPO:0001059 + https://cellxgene.cziscience.com/cellguide/CL_1000454 epithelial cell of renal collecting tubule kidney collecting duct epithelial cell - - - - - true - @@ -9987,12 +10064,31 @@ Each of these 3 primitives can be composed to yield a cross-product of different An epithelial cell that is part of the collecting duct of renal tubule. GOC:tfm + + + + This extended description was generated by ChatGPT and reviewed by the CellGuide team, who added references, and by the CL editors, who approved it for inclusion in CL. It may contain information that applies to only to some subtypes and species, and so should not be considered definitional. + +Kidney collecting duct epithelial cells are a specialized type of cells that form an integral part of the renal system. Located in the collecting duct system of the kidneys, these cells are responsible for one of the final steps in the process of urine formation, and they are instrumental in the fine tuning of the volume and composition of urine by reabsorbing water and certain solutes back into the bloodstream. +These cells express specific channels and carriers that actively and passively transport ions and water. They also have channels on their membranes, such as sodium channels and potassium channels, involved in reabsorbing or secreting these electrolytes depending upon the body's needs. The function of renal collecting duct epithelial cells can be regulated by a variety of hormones, including vasopressin (antidiuretic hormone), which can modulate the ion channels and carriers and hence indirectly influence body fluid homeostasis. +Aside from their function in ion and water balance, kidney collecting duct epithelial cells also aid in maintaining the body's acid-base balance. They have specialized functionality to secret hydrogen ions into the tubular lumen, which contributes to acid excretion. Any dysfunction may have serious implications and lead to various renal or systemic diseases, exemplifying the importance of these cells in maintaining overall body homeostasis. + DOI:10.1016/j.ajpath.2014.01.014 + DOI:10.1016/j.semnephrol.2019.04.005 + DOI:10.2215/CJN.05760513 + DOI:10.2215/CJN.08880914 + epithelial cell of renal collecting tubule FMA:70982 + + + + + true + @@ -10049,7 +10145,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -10986,7 +11082,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -11138,7 +11234,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -11146,6 +11242,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome. + https://github.com/geneontology/go-ontology/issues/28301 GO:0000789 GO:0000790 GO:0005717 @@ -11550,7 +11647,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different renal blood volume control of blood pressure renal regulation of blood volume GO:0001977 - + renal system process involved in regulation of blood volume @@ -12267,32 +12364,32 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures. Wikipedia:Collagen cellular_component GO:0005581 collagen trimer - + - + - + PMID:12382326 - + PMID:12382326 @@ -12602,12 +12699,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - + @@ -13445,6 +13537,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different The generation and maintenance of gametes in a multicellular organism. A gamete is a haploid reproductive cell. + + + GO:0009552 biological_process gametogenesis @@ -14673,6 +14768,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different The self-renewing division of a stem cell. A stem cell is an undifferentiated cell, in the embryo or adult, that can undergo unlimited division and give rise to one or several different cell types. + + + stem cell renewal biological_process GO:0017145 @@ -16054,12 +16152,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - - + A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together. GO:0043234 @@ -16089,33 +16182,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - - - A macromolecular complex containing both protein and DNA molecules. - DNA-protein complex - cellular_component - GO:0032993 - - Note that this term is intended to classify complexes that have DNA as one of the members of the complex, that is, the complex does not exist if DNA is not present. Protein complexes that interact with DNA e.g. transcription factor complexes should not be classified here. - protein-DNA complex - - - - - A macromolecular complex containing both protein and DNA molecules. - GOC:mah - - - - - DNA-protein complex - GOC:mah - - - - @@ -16411,6 +16477,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different A large plasma membrane-lined circular pore that perforates the flattened glomerular endothelium and, unlike those of other fenestrated capillaries, is not spanned by diaphragms; the density and size of glomerular fenestrae account, at least in part, for the high permeability of the glomerular capillary wall to water and small solutes. + + + bf 2011-12-12T10:53:24Z GEnC fenestration @@ -16748,10 +16817,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane. + https://github.com/geneontology/go-ontology/issues/28153 NIF_Subcellular:sao414196390 membrane-enclosed organelle cellular_component GO:0043227 + membrane-bounded organelle @@ -16769,11 +16840,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different Organized structure of distinctive morphology and function, not bounded by a lipid bilayer membrane. Includes ribosomes, the cytoskeleton and chromosomes. https://github.com/geneontology/go-ontology/issues/21881 + https://github.com/geneontology/go-ontology/issues/28153 NIF_Subcellular:sao1456184038 non-membrane-enclosed organelle cellular_component biological condensate GO:0043228 + non-membrane-bounded organelle @@ -16809,8 +16882,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different Organized structure of distinctive morphology and function, occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, vesicles, ribosomes and the cytoskeleton. Excludes the plasma membrane. + https://github.com/geneontology/go-ontology/issues/28153 cellular_component GO:0043229 + intracellular organelle @@ -17057,10 +17132,12 @@ Each of these 3 primitives can be composed to yield a cross-product of different A process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a cellular component. Includes biosynthesis of constituent macromolecules, and those macromolecular modifications that are involved in synthesis or assembly of the cellular component. + https://github.com/geneontology/go-ontology/issues/27194 GO:0071843 cellular component biogenesis at cellular level biological_process GO:0044085 + cellular component biogenesis @@ -19432,6 +19509,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -22011,7 +22089,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -23133,51 +23211,51 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + - A molecular entity that minimally consists of a protein. + A material entity that minimally consists of a protein. protein protein aggregate protein complex protein-containing complex protein - PR:000064867 - Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050565). - protein-containing molecular entity + PR:000050567 + Note: This includes single proteins and derivatives thereof (PR:000000001), protein-containing complexes (GO:0032991), and protein aggregates (PR:000050566). + protein-containing material entity - + - A molecular entity that minimally consists of a protein. + A material entity that minimally consists of a protein. PRO:DAN - + protein PRO:DAN - + protein aggregate PRO:DAN - + protein complex PRO:DAN - + protein-containing complex PRO:DAN @@ -23259,7 +23337,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -23380,7 +23458,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -23434,14 +23512,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different ureter https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg - + - + GO @@ -23491,7 +23569,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -23539,14 +23617,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different urethra https://upload.wikimedia.org/wikipedia/commons/c/cb/Female_anatomy.png - + - + Wikipedia @@ -23568,6 +23646,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -24053,7 +24132,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -24103,14 +24182,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg - + - + FMA MA @@ -24192,7 +24271,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -24373,14 +24452,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -24412,24 +24491,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different metanephros - + - + - + GO - + ISBN:9780878932504 @@ -24544,8 +24623,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + An epithelial swelling on the Wolffian duct that elongates to invade the adjacent metanephric mesenchyme[MP]. BTO:0001646 EHDAA2:0002140 @@ -24569,11 +24648,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different ureteric bud - + - + @@ -24586,13 +24665,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 - + ISBN:9780878932504 @@ -24973,7 +25052,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -24982,7 +25061,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -25009,14 +25088,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different gastrula stage - + - + BILS @@ -25088,7 +25167,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -25131,7 +25210,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -25196,7 +25275,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -25276,11 +25355,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + - + @@ -25303,24 +25382,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0000162 cloaca - + - + - + ZFA - + AAO @@ -25361,8 +25440,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + @@ -25380,24 +25459,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different embryonic cloaca - + - + - + EHDAA2 - + EHDAA2 @@ -25420,10 +25499,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -25459,14 +25538,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different primitive urogenital sinus http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png - + - + MP-def @@ -25515,7 +25594,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -25741,6 +25820,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -25748,15 +25828,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - - + + A fluid that is composed of blood plasma and erythrocytes. AAO:0000046 @@ -25793,34 +25873,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different blood - + - + - + - + CL:tm - + https://github.com/obophenotype/uberon/issues/1330 - + Bgee:AN @@ -25870,7 +25950,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -25964,7 +26044,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -26188,7 +26268,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -27149,6 +27229,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -27162,7 +27243,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -27204,14 +27285,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different epithelium https://upload.wikimedia.org/wikipedia/commons/8/8f/Illu_epithelium.jpg - - + + - + http://palaeos.com/metazoa/porifera/homoscleromorpha.html @@ -27569,10 +27650,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -27604,14 +27685,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different abdomen - + - + MA @@ -27749,7 +27830,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -27840,7 +27921,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Primary germ layer that is the outer of the embryo's three germ layers and gives rise to epidermis and neural tissue. AAO:0000137 BILA:0000036 @@ -27875,14 +27956,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different ectoderm http://upload.wikimedia.org/wikipedia/commons/1/19/Gray32.png - + - + Bgee:AN @@ -27922,7 +28003,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Primary germ layer that lies remote from the surface of the embryo and gives rise to internal tissues such as gut. AAO:0000139 BILA:0000038 @@ -27957,14 +28038,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/c/c0/Endoderm2.png http://upload.wikimedia.org/wikipedia/commons/d/df/Gray10.png - + - + Bgee:AN @@ -28005,7 +28086,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The middle germ layer of the embryo, between the endoderm and ectoderm. UBERON:0003263 @@ -28046,14 +28127,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different mesoderm http://upload.wikimedia.org/wikipedia/commons/e/e8/Mesoderm.png - + - + Bgee:AN @@ -28108,7 +28189,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -28219,10 +28300,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -28262,7 +28343,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different proctodeum https://github.com/obophenotype/uberon/issues/685 - + @@ -28275,7 +28356,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 @@ -28337,7 +28418,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -28346,7 +28427,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -28408,14 +28489,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different https://cdn.humanatlas.io/digital-objects/ref-organ/heart-female/v1.3/assets/3d-vh-f-heart.glb https://cdn.humanatlas.io/digital-objects/ref-organ/heart-male/v1.3/assets/3d-vh-m-heart.glb - + - + MA @@ -28500,7 +28581,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -28969,7 +29050,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -29092,7 +29173,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -29247,7 +29328,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -29269,14 +29350,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]. - AAO:0000324 BILA:0000079 BIRNLEX:844 @@ -29311,7 +29391,6 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0001016 - @@ -29319,14 +29398,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/b/b2/TE-Nervous_system_diagram.svg http://upload.wikimedia.org/wikipedia/commons/b/ba/Nervous_system_diagram.png - + - + Bgee:AN @@ -29388,11 +29467,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the neural tube derivatives: the brain and spinal cord. In invertebrates it includes central ganglia plus nerve cord. @@ -29437,7 +29516,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different central nervous system - + @@ -29451,7 +29530,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Bgee:AN @@ -29648,7 +29727,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -29682,14 +29761,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different hindgut http://upload.wikimedia.org/wikipedia/commons/f/f7/Gray472.png - + - + Wikipedia @@ -30180,14 +30259,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -30239,24 +30318,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different renal pelvis https://upload.wikimedia.org/wikipedia/commons/c/c0/Illu_kidney2.jpg - + - + - + MA - + FMA @@ -30302,7 +30381,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -30338,14 +30417,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different https://cdn.humanatlas.io/digital-objects/ref-organ/kidney-male-right/v1.3/assets/3d-vh-m-kidney-r.glb https://upload.wikimedia.org/wikipedia/commons/6/69/Illu_kidney.jpg - + - + FMA @@ -30381,7 +30460,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -30426,14 +30505,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different renal corpuscle https://upload.wikimedia.org/wikipedia/commons/2/22/Renal_corpuscle.svg - + - + MA ZFA @@ -30507,7 +30586,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -30549,14 +30628,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different glomerular capsule http://upload.wikimedia.org/wikipedia/commons/3/30/Gray1130.svg - + - + Wikipedia @@ -30646,10 +30725,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -30693,7 +30772,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different nephron tubule - + @@ -30702,14 +30781,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + GO MA ZFA @@ -30723,7 +30802,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + ZFA @@ -30937,7 +31016,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -30984,7 +31063,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different https://cdn.humanatlas.io/digital-objects/ref-organ/urinary-bladder-male/v1.2/assets/3d-vh-m-urinary-bladder.glb https://upload.wikimedia.org/wikipedia/commons/3/30/Urinary_system.svg - + @@ -30997,7 +31076,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + FMA @@ -31127,7 +31206,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -31140,7 +31219,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The basic functional unit of the kidney. its chief function is to regulate the concentration of water and soluble substances like sodium salts by filtering the blood, reabsorbing what is needed and excreting the rest as urine. A nephron eliminates wastes from the body, regulates blood volume and blood pressure, controls levels of electrolytes and metabolites, and regulates blood pH. Its functions are vital to life and are regulated by the endocrine system by hormones such as antidiuretic hormone, aldosterone, and parathyroid hormone.[WP]. kidney terms require review for cross-vertebrate compatibility and developmental relationships. @@ -31171,24 +31250,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different nephron http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + - + - + FMA - + Bgee:AN @@ -31239,14 +31318,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -31282,11 +31361,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different proximal convoluted tubule http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + - + @@ -31299,13 +31378,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + GO - + Wikipedia @@ -31437,7 +31516,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -31464,7 +31543,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different descending limb of loop of Henle http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + @@ -31477,7 +31556,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + FMA @@ -31501,14 +31580,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -31553,11 +31632,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different proximal straight tubule - + - + @@ -31570,13 +31649,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + MA - + MA @@ -31618,7 +31697,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -31654,7 +31733,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different distal convoluted tubule https://upload.wikimedia.org/wikipedia/commons/2/21/Kidney_nephron.png - + @@ -31667,7 +31746,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EMAPA GO MA-modified-from-isa @@ -31942,7 +32021,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -31965,14 +32044,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different kidney arcuate artery https://upload.wikimedia.org/wikipedia/commons/8/87/2610_The_Kidney.jpg - + - + MA @@ -32003,7 +32082,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -32013,7 +32092,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A tube extending from the mouth to the anus. @@ -32050,14 +32129,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different digestive tract - + - + NCBIBook:NBK10107 @@ -32535,6 +32614,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -32762,6 +32842,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -32770,8 +32851,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + @@ -32784,7 +32865,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -32838,34 +32919,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different blood vessel http://upload.wikimedia.org/wikipedia/commons/2/29/Circulatory_System_en.svg - + - + - + - + AEO - + EHDAA2 - + GO:0072360 @@ -33008,7 +33089,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -33569,7 +33650,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -33722,10 +33803,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -33774,14 +33855,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different kidney - + - + FMA @@ -33816,8 +33897,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + @@ -33855,11 +33936,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different Once the more complex mesonephros forms the pronephros undergoes apoptosis in amphibians. In fishes the nephron degenerates but the organ remains and becomes a component of the immune system[Wikipedia:Pronephros]. // TODO - check developmental relationships. Note that we previously include the ZFA/XAO terms under the more specific 'pronephric kidney', but these are now merged. TODO GCI: relationship: capable_of GO:0030104 pronephros - + - + @@ -33872,13 +33953,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + OG - + ZFA @@ -33927,7 +34008,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -34204,8 +34285,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different + - + @@ -34224,7 +34306,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + An anatomical structure which consists of juxtaglomerular cells, extraglomerular mesangial cells and the macula densa. The juxtaglomerular apparatus lies adjacent to the glomerulus and regulates kidney function by maintaining the blood flow to the kidney and the filtration rate[GO]. a microscopic structure in the kidney, which regulates the function of each nephron. The juxtaglomerular apparatus is named for its proximity to the glomerulus: it is found between the vascular pole of the renal corpuscle and the returning distal convoluted tubule of the same nephron. This location is critical to its function in regulating renal blood flow and glomerular filtration rate. The three cellular components of the apparatus are the macula densa, extraglomerular mesangial cells, and juxtaglomerular cells (also known as granular cells)[WP]. BTO:0005157 @@ -34246,24 +34328,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different juxtaglomerular apparatus - + - + - + MA - + GO @@ -34387,8 +34469,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + @@ -34405,24 +34487,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different EDITOR_NOTE check MA part_ofs - should be spatially disjoint from renal glomerulus? extraglomerular mesangium - + - + - + MA - + MA @@ -34564,9 +34646,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - + + + @@ -34614,15 +34696,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different notochord http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - - + + - + - + @@ -34641,19 +34723,19 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + http://tolweb.org/Chordata/2499 - + ZFA - + EHDAA2 @@ -34693,8 +34775,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + Somites are spheres of epithelial cells that form sequentially along the anterior-posterior axis of the embryo through mesenchymal to epithelial transition of the presomitic mesoderm. mesodermal cluster @@ -34732,11 +34814,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different somite http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - - + + - + @@ -34749,13 +34831,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + GOTAX:0000352 - + ZFA @@ -34815,8 +34897,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + The macula densa is an area of specialized cells in the distal tubule that makes contact with the vascular pole of the glomerulus[GO]. BTO:0003940 @@ -34834,24 +34916,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different macula densa - + - + - + MA - + GO @@ -34876,22 +34958,22 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + - - + + - + A specialized region of ectoderm found between the neural ectoderm (neural plate) and non-neural ectoderm and composed of highly migratory pluripotent cells that delaminate in early embryonic development from the dorsal neural tube and give rise to an astounding variety of differentiated cell types[MP]. AAO:0010578 BTO:0001764 @@ -34924,45 +35006,45 @@ Each of these 3 primitives can be composed to yield a cross-product of different http://upload.wikimedia.org/wikipedia/commons/5/5f/Gray644.png https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - + - + - + - + - + XAO https://github.com/obophenotype/uberon/wiki/The-neural-crest - + BTO - + PMID:11523831 - + PMID:11523831 @@ -35162,7 +35244,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -35253,7 +35335,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -35326,10 +35408,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -35379,14 +35461,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different hematopoietic system - + - + FMA @@ -35604,7 +35686,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Unsegmented field of paraxial mesoderm present posterior to the most recently formed somite pair, from which somites will form. AAO:0011086 EFO:0001982 @@ -35627,14 +35709,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different presomitic mesoderm - + - + Bgee:AN @@ -35675,8 +35757,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + In mammals, the pronephric duct is the predecessor of the Wolffian duct[WP]. AAO:0011088 NCIT:C34279 @@ -35695,11 +35777,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different The pronephric duct collects the filtrate from the pronephric tubules and opens to the exterior of the pronephric kidney[GOC:mtg_kidney_jan10, PMID:15647339, XAO:0000063, ZFA:0000150] pronephric duct - + - + @@ -35712,13 +35794,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Wikipedia - + XAO @@ -35824,9 +35906,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - + + + @@ -35865,34 +35947,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different intermediate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + - + - + - + AAO - + EMAPA - + XAO @@ -35948,7 +36030,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -36001,7 +36083,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Paired organ that connects the primitive kidney Wolffian body (or mesonephros) to the cloaca and serves as the anlage for certain male reproductive organs. the Wolffian duct is what remains of the pronephric duct after the atrophy of the pronephros[WP]. In Zebrafish: Duct of the adult kidney (mesonephros), present bilaterally ventral to the somites and leading to the cloacal chamber[ZFA]. Consider adding subclasses for male and female specific variants TODO - mesonephric portion of the nephric duct @@ -36030,7 +36112,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different mesonephric duct http://upload.wikimedia.org/wikipedia/commons/6/6d/Gray1109.png - + @@ -36043,7 +36125,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 @@ -36097,9 +36179,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - + + + A region of embryonic ectodermal cells that lie directly above the notochord. During neurulation, they change shape and produce an infolding of the neural plate (the neural fold) that then seals to form the neural tube[XAO]. The earliest recognizable dorsal ectodermal primordium of the central nervous system present near the end of gastrulation before infolding to form the neural keel; consists of a thickened pseudostratified epithelium[ZFA]. AAO:0011072 BTO:0001765 @@ -36128,34 +36210,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different neural plate https://upload.wikimedia.org/wikipedia/commons/8/8f/Neural_Crest.png - - + + - + - + - + GOTAX:0000352 - + Wikipedia - + Bgee:AN @@ -36195,7 +36277,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The paraxial mesoderm is the mesoderm located bilaterally adjacent to the notochord and neural tube[GO]. AAO:0010568 EFO:0003515 @@ -36221,7 +36303,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different paraxial mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -36234,7 +36316,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Bgee:AN @@ -36281,10 +36363,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -36321,7 +36403,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different lateral plate mesoderm http://upload.wikimedia.org/wikipedia/commons/6/64/Gray19_with_color.png - + @@ -36334,7 +36416,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 VHOG @@ -36384,15 +36466,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + - + Bilateral groups of cells consisting of three rows: one row of endocardial precursors medially and two rows of myocardical precursors laterally. The two populations fuse at the midline to form the heart rudiment or cone. should probably be merged with heart rudiment. AAO:0011044 @@ -36409,15 +36491,15 @@ Each of these 3 primitives can be composed to yield a cross-product of different heart primordium - + - + - + @@ -36430,19 +36512,19 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + ZFA - + ZFA - + XAO @@ -36471,8 +36553,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + Ventral somitic compartment that is a precursor of the axial skeleton[XAO]. Sclerotomes eventually differentiate into the vertebrae and most of the skull. The caudal (posterior) half of one sclerotome fuses with the rostral (anterior) half of the adjacent one to form each vertebra. From their initial location within the somite, the sclerotome cells migrate medially towards the notochord. These cells meet the sclerotome cells from the other side to form the vertebral body. From this vertebral body, sclerotome cells move dorsally and surround the developing spinal cord, forming the vertebral arch[WP]. AAO:0010571 AEO:0000212 @@ -36496,11 +36578,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different sclerotome http://upload.wikimedia.org/wikipedia/commons/9/96/Gray65.png - - + + - + @@ -36519,13 +36601,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + VHOG:0000680 - + ZFA @@ -36609,7 +36691,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -36770,7 +36852,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -36796,14 +36878,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different Genes: The positional specification of the metanephrogenic mesenchyme is negatively regulated by Foxc1 and Foxc2. Next the permanent kidney forming metanephrogenic mesenchyme is specified by Hox11 genes. The competence to respond to ureteric bud inducers is regulated by WT1. GDNF secretion restricted to posterior region by Robo2 and Sprouty1. The receptors for GDNF are synthesized in the nephric ducts and later in ureteric buds [ISBN:9780878932504 "Developmental Biology"] metanephric mesenchyme - + - + ISBN:9780878932504 @@ -37491,7 +37573,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The part of the coelom in the embryo between the somatopleuric and splanchnopleuric mesoderm; the principal body cavities of the trunk (thoracic, abdominal, and pelvic) arise from this embryonic part of the coelom. consider merging with coelom. TODO - add spatial relationships to halves of LPM. Note the OG places XAO and ZFA coelem terms here. editor note: TODO check ZFA, which appears to be a structure present in adults EHDAA:251 @@ -37506,14 +37588,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different intraembryonic coelom - + - + Wikipedia @@ -37544,7 +37626,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -38093,8 +38175,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + In mammals, the proximal tubule is a nephron tubule that connects Bowman's capsule to the loop of Henle. It has a brush border epithelial morphology[GO]. TODO - ensure definition works across species. @@ -38111,24 +38193,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different proximal tubule - + - + - + GO - + GO @@ -38187,7 +38269,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The intermediate tubule is a nephron tubule that lies between the proximal and distal tubules. TODO - check for applicability across species FMA:17718 @@ -38197,14 +38279,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0004136 intermediate tubule - + - + FMA @@ -38280,8 +38362,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + A specific region of the lateral mesoderm that will form the primary beating heart tube. In mammals the primary heart field gives rise to the left ventricle. XAO:0004185 first heart field @@ -38293,24 +38375,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0004140 primary heart field - + - + - + GO:0003128 - + https://orcid.org/0000-0003-3308-6245 @@ -38363,7 +38445,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + An epithelial tube that will give rise to the mature heart. AAO:0010411 EFO:0003526 @@ -38382,14 +38464,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different heart tube - + - + ZFA-modified @@ -38611,8 +38693,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + The comma-shaped body is the precursor structure to the S-shaped body that contributes to the morphogenesis of the nephron. EMAPA:27681 ZFA:0005588 @@ -38622,24 +38704,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different comma-shaped body - + - + - + cjm - + ZFA @@ -38661,8 +38743,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + The S-shaped body is the successor of the comma-shaped body that contributes to the morphogenesis of the nephron. TODO EMAPA:27756 @@ -38674,24 +38756,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different S-shaped body - + - + - + cjm - + GO @@ -39103,7 +39185,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -39141,14 +39223,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different glomerular capillary - + - + https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -39394,6 +39476,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -39490,6 +39573,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -39531,6 +39615,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -39572,6 +39657,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -39688,7 +39774,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -39725,14 +39811,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different renal afferent arteriole http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + - + Wikipedia @@ -40092,7 +40178,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. AAO:0011129 TAO:0001890 @@ -40106,14 +40192,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different skeletal element - + - + VSAO @@ -40140,10 +40226,10 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + @@ -40179,14 +40265,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0004770 articular system - + - + FMA @@ -40484,7 +40570,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -40505,14 +40591,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different somatopleure http://upload.wikimedia.org/wikipedia/commons/2/28/Gray16.png - + - + EHDAA2 @@ -40578,9 +40664,9 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - - + + + @@ -40600,34 +40686,34 @@ Each of these 3 primitives can be composed to yield a cross-product of different urogenital fold - + - + - + - + EHDAA2 - + Wikipedia - + EHDAA2 @@ -40673,7 +40759,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -40839,7 +40925,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -41070,7 +41156,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -41102,7 +41188,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Missing definition for term UBERON:0005095. Please replace it using linked reference. class added for consistency with GO - consider merging with kidney mesenchyme. uberon @@ -41110,14 +41196,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0005095 kidney rudiment - + - + GO @@ -41233,7 +41319,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The connecting tubule is a tubular segment of the nephron; it connects the distal convoluted tubule to the collecting duct[GO]. BTO:0004539 @@ -41251,14 +41337,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different renal connecting tubule http://upload.wikimedia.org/wikipedia/commons/0/02/Gray1128.png - + - + Wikipedia @@ -41989,7 +42075,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Mesenchyme that is part of a developing trunk. EFO:0003485 EHDAA2:0002092 @@ -42005,14 +42091,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different trunk mesenchyme - + - + EHDAA2 @@ -42129,7 +42215,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Multi-tissue structure that arises from the heart rudiment and will become the heart tube. EHDAA2:0001512 EHDAA:424 @@ -42147,14 +42233,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different primitive heart tube - + - + ZFA @@ -42182,7 +42268,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -42209,7 +42295,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different gonad primordium - + @@ -42222,7 +42308,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + ZFA @@ -42281,14 +42367,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + A mesoderm that has the potential to develop into a pronephros. AAO:0011090 EFO:0003479 @@ -42306,24 +42392,24 @@ Each of these 3 primitives can be composed to yield a cross-product of different the intermediate mesoderm of the chick embryo acquires its ability to form kidneys through its interactions with the paraxial mesoderm [ISBN:9780878932504 "Developmental Biology", PMID:10720431 "Signals from trunk paraxial mesoderm induce pronephros formation in chick intermediate mesoderm"]. These interactions induce the expression of TFs including Lim1, Pax2 and Pax6 that cause the intermediate mesoderm to form the kidney pronephric mesoderm - + - + - + ZFA - + Bgee:AN @@ -42370,7 +42456,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -42387,14 +42473,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different glomerular tuft - + - + Wikipedia @@ -42534,6 +42620,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -42549,7 +42636,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -42644,7 +42731,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -42672,14 +42759,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different glomerular basement membrane http://upload.wikimedia.org/wikipedia/commons/d/de/PhysiologieGlom%C3%A9rulaire.png - + - + true https://github.com/obophenotype/uberon/wiki/Inferring-part-of-relationships @@ -42764,7 +42851,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A delimited region of dense mesenchyme within looser mesenchyme. AEO:0000148 EHDAA2_RETIRED:0003148 @@ -42774,7 +42861,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0005856 developing mesenchymal condensation - + @@ -42793,7 +42880,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + AEO-modified-relation @@ -42890,7 +42977,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -42929,14 +43016,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different cloacal membrane http://upload.wikimedia.org/wikipedia/commons/d/d2/Gray991.png - + - + Wikipedia @@ -42970,7 +43057,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The notochordal plate is the dorsal part of the notochordal process when the ventral portion breaks down. It is continuous laterally with the endoderm that composes the roof of the primitive foregut and is in contact dorsally with the neural tube. The folding off of the notochordal plate gives rise to the notochord. TODO - check ordering; awaiting confirmation from JB EHDAA2:0001278 @@ -42984,7 +43071,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different notochordal plate - + @@ -42997,7 +43084,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 @@ -43021,11 +43108,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + - + A midline cellular cord formed from the migration of mesenchymal cells from the primitive knot. EHDAA2:0001279 EHDAA:224 @@ -43042,14 +43129,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different The notochordal process grows cranially until it reaches the prechordal plate, the future site of the mouth. In this area the ectoderm is attached directly to the endoderm without intervening mesoderm. This area is known as the oropharyngeal membrane, and it will break down to become the mouth. At the other end of the primitive streak the ectoderm is also fused directly to the endoderm; this is known as the cloacal membrane (proctodeum), or primordial anus. notochordal process - + - + EHDAA2 @@ -43342,7 +43429,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -43485,7 +43572,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -43549,7 +43636,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -43593,7 +43680,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A region of nephron tubule that is part of a cortex of kidney. EMAPA:18976 MA:0002609 @@ -43603,14 +43690,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0006853 renal cortex tubule - + - + MA @@ -43781,6 +43868,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different + @@ -44282,7 +44370,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -44308,7 +44396,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different presumptive paraxial mesoderm - + @@ -44324,7 +44412,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + https://github.com/obophenotype/uberon/issues/1277 @@ -44485,7 +44573,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Mesenchyme with little extracellular matrix. AEO:0000146 EHDAA2:0003146 @@ -44493,7 +44581,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0007524 dense mesenchyme tissue - + @@ -44506,7 +44594,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + AEO @@ -44720,7 +44808,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Anatomical system that consists of all blood and lymph vessels. consider merging with vasculature @@ -44737,14 +44825,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different vascular system - + - + MA @@ -44785,7 +44873,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -44882,7 +44970,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -44920,14 +45008,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different pelvic girdle skeleton http://upload.wikimedia.org/wikipedia/commons/f/fe/Gray242.png - + - + PMID:21455939 @@ -45010,7 +45098,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The functional tissue of the kidney, consisting of the nephrons. BTO:0003604 FMA:15574 @@ -45021,7 +45109,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0008987 renal parenchyma - + @@ -45034,7 +45122,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + FMA @@ -45104,7 +45192,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -45121,14 +45209,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0009142 entire embryonic mesenchyme - + - + EHDAA2 @@ -45247,7 +45335,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2:0002094 trunk and cervical paraxial mesenchyme uberon @@ -45255,14 +45343,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0009618 trunk paraxial mesoderm - + - + EHDAA2 @@ -45287,7 +45375,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -45361,7 +45449,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EFO:0003704 TAO:0005041 ZFA:0005041 @@ -45371,14 +45459,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different anterior lateral plate mesoderm - + - + ZFA @@ -45699,7 +45787,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -45717,14 +45805,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0010227 future cardiac atrium - + - + ZFA @@ -45867,7 +45955,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -45881,7 +45969,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0010377 mesenchyme from somatopleure - + @@ -45894,7 +45982,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 @@ -45910,7 +45998,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + A vessel of the microcirculature, lying between the arterioles and venules; includes capillaries (blood and lymphatic), metarterioles and arteriovenous anastomoses. MESH:D055806 TAO:0005251 @@ -45920,14 +46008,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0010523 microcirculatory vessel - + - + ZFA @@ -45960,7 +46048,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -45976,7 +46064,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0010532 primitive nephron - + @@ -45989,7 +46077,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2 @@ -46005,7 +46093,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -46016,7 +46104,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0010536 nephron progenitor - + @@ -46029,7 +46117,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + cjm @@ -46042,7 +46130,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -46272,8 +46360,8 @@ Each of these 3 primitives can be composed to yield a cross-product of different - - + + Anatomical cluster consisting of the skeletal elements (i.e. bone elements, cartilage elements, cartilage condensations) that are part of an individual subdivision of the organism. Excludes joints. FMA:23879 SCTID:129140006 @@ -46285,11 +46373,11 @@ Each of these 3 primitives can be composed to yield a cross-product of different subdivision of skeleton - + - + @@ -46302,13 +46390,13 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + UBERONREF:0000003 - + VSAO @@ -46369,7 +46457,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + Subdivision of the skeletal system which consists of the postcranial axial skeleton plus associated joints. axial skeletal system FMA:302077 @@ -46379,7 +46467,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different postcranial axial skeletal system http://purl.obolibrary.org/obo/uberon/docs/The-axial-skeleton - + @@ -46392,7 +46480,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + cjm @@ -46416,7 +46504,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -46441,14 +46529,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different upper urinary tract - + - + FMA @@ -46645,7 +46733,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -46766,7 +46854,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -46781,14 +46869,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different We presume this is distinct from AAO:0001003, an external integumentary structure - check with amphibian anatomy ontology developers. AO notes: the text def states mesenchymal swelling, EHDAA2 splits into mesenchymal and epithelial parts embryonic cloacal fold - + - + EHDAA2 @@ -46811,20 +46899,20 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2:0004588 uberon UBERON:0012361 internal anal region - + - + EHDAA2 @@ -46834,20 +46922,20 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + EHDAA2:0004589 uberon UBERON:0012469 external anal region - + - + EHDAA2 @@ -46874,7 +46962,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -46894,14 +46982,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different skeleton of pelvic complex - + - + FMA @@ -46953,7 +47041,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The precursor of the urethra. SCTID:361531004 Wikipedia:Urethral_groove @@ -46964,14 +47052,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0013241 embryonic urethral groove - + - + Wikipedia @@ -47075,7 +47163,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -47321,7 +47409,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -47542,7 +47630,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + @@ -47565,7 +47653,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different UBERON:0016887 entire extraembryonic component - + @@ -47578,7 +47666,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + AEO @@ -47989,7 +48077,7 @@ Each of these 3 primitives can be composed to yield a cross-product of different - + The upper tract of the renal system. The renal pelvis is the large cavity in the middle of each kidney. Urine drains from each kidney through a long tube called the ureter, into the bladder, where it is stored until it is passed from the body through the urethra. NCIT:C54419 @@ -48000,14 +48088,14 @@ Each of these 3 primitives can be composed to yield a cross-product of different renal pelvis/ureter - + - + NCIT @@ -48348,6 +48436,454 @@ Each of these 3 primitives can be composed to yield a cross-product of different + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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+_:B869127b4X2D9725X2D463eX2Dbe79X2D2d475f23f3cfgenid939 +_:B869127b4X2D9725X2D463eX2Dbe79X2D2d475f23f3cfgenid952 +_:B869127b4X2D9725X2D463eX2Dbe79X2D2d475f23f3cfgenid958 +_:B869127b4X2D9725X2D463eX2Dbe79X2D2d475f23f3cfgenid964 +_:B869127b4X2D9725X2D463eX2Dbe79X2D2d475f23f3cfgenid970 +_:B869127b4X2D9725X2D463eX2Dbe79X2D2d475f23f3cfgenid976 +_:B869127b4X2D9725X2D463eX2Dbe79X2D2d475f23f3cfgenid982 +_:B869127b4X2D9725X2D463eX2Dbe79X2D2d475f23f3cfgenid988 +_:B869127b4X2D9725X2D463eX2Dbe79X2D2d475f23f3cfgenid995 "cell" "early embryonic cell (metazoa)" "stem cell" @@ -416,7 +449,6 @@ _:B37f46b34X2Dd719X2D4ca1X2D82faX2Db899d54442eagenid997 "embryonic cell (metazoa)" "cardiocyte" "kidney epithelial cell" - "embryonic blood vessel endothelial progenitor cell" "renal cortical epithelial cell" "squamous endothelial cell" "kidney cortical cell" @@ -603,7 +635,6 @@ _:B37f46b34X2Dd719X2D4ca1X2D82faX2Db899d54442eagenid997 "secretion by cell" "protein-containing complex disassembly" "protein-containing complex" - "protein-DNA complex" "macromolecule localization" "erythrocyte homeostasis" "monoatomic ion transmembrane transport" @@ -838,7 +869,7 @@ _:B37f46b34X2Dd719X2D4ca1X2D82faX2Db899d54442eagenid997 "Mus musculus protein" "eukaryotic protein" "angiotensinogenase" - "protein-containing molecular entity" + "protein-containing material entity" "processual entity" "tube" "appendage"