diff --git a/.DS_Store b/.DS_Store new file mode 100644 index 0000000..77d0f81 Binary files /dev/null and b/.DS_Store differ diff --git a/dev/.DS_Store b/dev/.DS_Store new file mode 100644 index 0000000..a79b90f Binary files /dev/null and b/dev/.DS_Store differ diff --git a/dev/ontology/.DS_Store b/dev/ontology/.DS_Store new file mode 100644 index 0000000..cdbfda7 Binary files /dev/null and b/dev/ontology/.DS_Store differ diff --git a/dev/ontology/catalog-v001.xml b/dev/ontology/catalog-v001.xml new file mode 100644 index 0000000..84a0da0 --- /dev/null +++ b/dev/ontology/catalog-v001.xml @@ -0,0 +1,15 @@ + + + + + + + + + + + + + + + diff --git a/dev/ontology/swo_core.owl b/dev/ontology/swo_core.owl index c470fc6..e928f82 100644 --- a/dev/ontology/swo_core.owl +++ b/dev/ontology/swo_core.owl @@ -252,18 +252,6 @@ - - - - - - - The relationship between an entity and the set of legal restrictions, i.e. license, which are applied in using or otherwise interacting with that entity. Eg. relationship between a software license and the software which implements it. - is license for - - - - @@ -589,13 +577,23 @@ - + The relationship between an entity and the set of legal restrictions, i.e. license, which are applied in using or otherwise interacting with that entity. Eg. relationship between software and a software license. has license + + + + + The relationship between an entity and the set of legal restrictions, i.e. license, which are applied in using or otherwise interacting with that entity. Eg. relationship between a software license and the software which implements it. + is license for + + + + @@ -973,7 +971,6 @@ called clusters. - @@ -27481,7 +27478,7 @@ tiple samples - + @@ -28238,5 +28235,5 @@ According to the GNU project, the Apache 2.0 license is better for substantial p - + diff --git a/release/.DS_Store b/release/.DS_Store new file mode 100644 index 0000000..bcb2f3c Binary files /dev/null and b/release/.DS_Store differ diff --git a/release/swo_inferred.owl b/release/swo_inferred.owl index b17c7b5..76f3ccd 100644 --- a/release/swo_inferred.owl +++ b/release/swo_inferred.owl @@ -18,8 +18,9 @@ EDAM editors: Jon Ison, Matus Kalas, and Herve Menager. Contributors: Inge Jonassen, Dan Bolser, Hamish McWilliam, Mahmut Uludag, James Malone, Rodrigo Lopez, Steve Pettifer, and Peter Rice. Contibutions from these projects: EMBRACE, ELIXIR, and BioMedBridges (EU); EMBOSS (BBSRC, UK); eSysbio, FUGE Bioinformatics Platform, and ELIXIR.NO/Norwegian Bioinformatics Platform (Research Council of Norway). See http://edamontology.org for documentation and licence. application/rdf+xml - EDAM is an ontology of well established, familiar concepts that are prevalent within bioinformatics, including types of data and data identifiers, data formats, operations and topics. EDAM is a simple ontology - essentially a set of terms with synonyms and definitions - organised into an intuitive hierarchy for convenient use by curators, software developers and end-users. EDAM is suitable for large-scale semantic annotations and categorization of diverse bioinformatics resources. EDAM is also suitable for diverse application including for example within workbenches and workflow-management systems, software distributions, and resource registries. + 3791 EDAM + EDAM is an ontology of well established, familiar concepts that are prevalent within bioinformatics, including types of data and data identifiers, data formats, operations and topics. EDAM is a simple ontology - essentially a set of terms with synonyms and definitions - organised into an intuitive hierarchy for convenient use by curators, software developers and end-users. EDAM is suitable for large-scale semantic annotations and categorisation of diverse bioinformatics resources. EDAM is also suitable for diverse application including for example within workbenches and workflow-management systems, software distributions, and resource registries. SWO and EDAM include some terms released under CC-BY license from the OBO Foundry. We acknowledge those with the use of the OBO PURLs were appropriate. Some of the definitions have been modified from the original; for the latest original definition please visit the URI. Allyson Lister relations "EDAM relations" @@ -28,21 +29,20 @@ Andy Brown concept_properties "EDAM concept properties" The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. It contains SWO-specific classes and axioms as well as imported information from a variety of sources including OBI, IAO, BFO and EDAM. Please note that EDAM is imported as a whole and as such, some comments in the ontology header directly relate to EDAM only. - 12.05.2016 18:23 GMT - 3751 Matúš Kalaš James Malone Bioinformatics operations, data types, formats, identifiers and topics - 1.15 data "EDAM types of data" EDAM_format http://edamontology.org/format_ "EDAM data formats" + 1.16 EDAM_topic http://edamontology.org/topic_ "EDAM topics" Jon Ison, Matus Kalas, Hervé Ménager 0.4 formats "EDAM data formats" - Nandini Badarinarayan + 31.10.2016 23:58 GMT EDAM http://edamontology.org/ "EDAM relations and concept properties" + Nandini Badarinarayan 1.6 EDAM_operation http://edamontology.org/operation_ "EDAM operations" edam "EDAM" @@ -90,7 +90,7 @@ - + 1.13 true Publication reference @@ -98,141 +98,162 @@ Publication concept_properties Citation - + + + + + + + - + true Version in which a concept was created. concept_properties Created in - + - + true 'Documentation' trailing modifier (qualifier, 'documentation') of 'xref' links of 'Format' concepts. When 'true', the link is pointing to a page with explanation, description, documentation, or specification of the given data format. Specification concept_properties Documentation - + - + true 'Example' concept property ('example' metadata tag) lists examples of valid values of types of identifiers (accessions). Applicable to some other types of data, too. concept_properties - Separated by bar ('|'). + Separated by bar ('|'). For more complex data and data formats, it can be a link to a website with examples, instead. Example - + - + true 'File extension' concept property ('file_extension' metadata tag) lists examples of usual file extensions of formats. + 'Ontology used' concept property ('ontology_used' metadata tag) of format concepts links to a domain ontology that is used inside the given data format, or contains a note about ontology use within the format. concept_properties + N.B.: File extensions that are not correspondigly defined at http://filext.com are recorded in EDAM only if not in conflict with http://filext.com, and/or unique and usual within life-science computing. Separated by bar ('|'), without a dot ('.') prefix, preferrably not all capital characters. File extension - + Ontology used + - + true - When 'true', the term has been proposed or is supported within Debian Med as a tag. + When 'true', the concept has been proposed or is supported within Debian as a tag. concept_properties isdebtag - + - + true 'Media type' trailing modifier (qualifier, 'media_type') of 'xref' links of 'Format' concepts. When 'true', the link is pointing to a page specifying a media type of the given data format. MIME type concept_properties Media type - + - + - + + true + Version in which a concept was made obsolete. + concept_properties + Obsolete since + - + - + + + + + + + true - Version in which a concept was made obsolete. + 'Organisation' trailing modifier (qualifier, 'organisation') of 'xref' links of 'Format' concepts. When 'true', the link is pointing to an organisation that developed, standardised, and maintains the given data format. + Organization concept_properties - Obsolete since - + Organisation + - + true 'Regular expression' concept property ('regex' metadata tag) specifies the allowed values of types of identifiers (accessions). Applicable to some other types of data, too. concept_properties Regular expression - + - + A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not. IAO example of usage - + - + definition definition - + - + alternative term - + - + definition source definition source - + @@ -280,29 +301,35 @@ - + The version in which a class or property has been made obsolete EFO Development Team obsoleted in version - + - + The reason a class or property was made obsolete EFO Development Team reason for obsolescence - + - + SWO definition - + + + + + + + @@ -399,79 +426,57 @@ - + 'is about' relates an information entity to other entities in which the information entity holds some information which dscribes some facet of the other entity, such as the arrow direction on a sign. IAO James Malone Alan Ruttenberg is about - + - + OBO Foundry Please note that, as stated on one of the RO documentation pages (https://code.google.com/p/obo-relations/wiki/ROAndBFO), some of the relations RO makes use are either uncontroversial (non-temporalized) parts of BFO2, or will be incorporated in the future. In the case of BFO_0000063, it is not currently in BFO2, but may be in the future. The RO ontologists assume this is the transitive form. For a full definition, refer to the inverse of this property, BFO_0000060. (Allyson Lister) preceded by - + - + The assertion P 'followed by' P1 tells us something about Ps in general: that is, it tells us something about what happened later, given what we know about what happened earlier. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be preceded by some instance of P. Note that assertions using this property only are rather weak. Typically we will be interested in stronger relations, for example in the relation 'directly followed by'. Modified by Allyson Lister from the preceded_by (which is the inverse of precedes / 'followed by') definition within RO: http://www.obofoundry.org/ro/ro.owl OBO Foundry Please note that, as stated on one of the RO documentation pages (https://code.google.com/p/obo-relations/wiki/ROAndBFO), some of the relations RO makes use are either uncontroversial (non-temporalized) parts of BFO2, or will be incorporated in the future. In the case of BFO_0000060, it is not currently in BFO2, but may be in the future. The RO ontologists assume this is the transitive form. (Allyson Lister) followed by - - - - - - - - c is_manufactured_by o means that there was a process p in which c was -built in which a person, or set of people or machines did the work(bore -the "Manufacturer Role", and those people/and or machines were members -or of directed by the organization to do this. - OBI - is manufactured by - + - + Andy Brown Please see the official RO definition for the inverse of this property, 'has participant.' participates in - + - + The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. http://obo-relations.googlecode.com/svn/trunk/src/ontology/core.owl Andy Brown has participant - - - - - - - - has_role - has_role - + @@ -508,30 +513,6 @@ or of directed by the organization to do this. - - - - - - - - - - The relationship between an entity and the set of legal restrictions, i.e. license, which are applied in using or otherwise interacting with that entity. Eg. relationship between a software license and the software which implements it. - is license for - - - - - - - - The relationship between a software and software developer. - is developed by - - - - @@ -659,29 +640,6 @@ or of directed by the organization to do this. - - - - 'uses platform' should be used to link a particular piece of software to one or more operating systems which that software can run on. This is in contrast to both 'uses software' (which describes one piece of software directly executing another), and has_part, which can be used to describe related but independent software in a package, for example. - Allyson Lister - This property, together with 'uses software', is probably best modelled as a child of has_part. Its current position in the property hierarchy is based on simplicity of use. 'uses platform' was deemed an appropriate addition (rather than making use of already extant has_part or 'uses software') due to the already present definitions of those classes which restrict their use to particular situations. - uses platform - - - - - - - - Provides a method of asserting what type of interactions are possible for the class in question. The interface must be from the 'software interface' hierarchy. - Allyson Lister - Andy Brown - Andy Brown - has interface - - - - @@ -707,37 +665,14 @@ or of directed by the organization to do this. - - - - 'is published by' elucidates the relationship between a piece of software or a data format specification and its owning organization. Please note that this is not the same as authorship of the software. For instance, affy is published within Bioconductor, but has its own distinct authorship list. - Allyson Lister - James Malone - is published by - - - - - + Stores those object properties which are no longer appropriate for use within SWO. Marked as obsolete by Allyson Lister Allyson Lister obsolete object property - - - - - - - - is executed in defines the relationship between a software class and an appropriate process in the information processing hierarchy. Specifically, it allows the linking of a particular piece of software to a process of a particular purpose, - Allyson Lister - Allyson Lister - OBI - is executed in - + @@ -780,6 +715,21 @@ or of directed by the organization to do this. + + + + + + + + + + The relationship between an entity and the set of legal restrictions, i.e. license, which are applied in using or otherwise interacting with that entity. Eg. relationship between a software license and the software which implements it. + is license for + + + + @@ -803,12 +753,6 @@ or of directed by the organization to do this. - - - - - - - - - Should be used to link a particular class (e.g. a piece of software or an algorithm) with a publication(s) which act as the primary reference(s) for that class. - Allyson Lister - has documentation - - - - @@ -844,32 +778,12 @@ or of directed by the organization to do this. - + The URL of the homepage for the resource this property is associated with. Allyson Lister has website homepage has website homepage - - - - - - - - Andy Brown - The official date of release of software - has release date - - - - - - - - Andy Brown - A URL for a source of support information about software - has support URL - + @@ -901,7 +815,7 @@ or of directed by the organization to do this. - + beta12orEarlier Information, represented in an information artefact (data record) that is 'understandable' by dedicated computational tools that can use the data as input or produce it as output. Data record @@ -918,7 +832,13 @@ or of directed by the organization to do this. http://wsio.org/data_002 http://www.ifomis.org/bfo/1.1/snap#Continuant http://www.onto-med.de/ontologies/gfo.owl#Perpetuant - + + + + + Data record + EDAM does not distinguish a data record (a tool-understandable information artefact) from data or datum (its content, the tool-understandable encoding of an information). + @@ -931,12 +851,6 @@ or of directed by the organization to do this. Datum EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). - - - - Data record - EDAM does not distinguish a data record (a tool-understandable information artefact) from data or datum (its content, the tool-understandable encoding of an information). - @@ -1190,7 +1104,6 @@ or of directed by the organization to do this. beta12orEarlier 1.5 - A character used to replace (mask) other characters in a molecular sequence. Sequence mask character @@ -1393,7 +1306,6 @@ or of directed by the organization to do this. beta12orEarlier 1.5 - Some simple value controlling a sequence alignment (or similar 'match') operation. Sequence alignment parameter @@ -1886,7 +1798,6 @@ or of directed by the organization to do this. beta12orEarlier 1.8 3D structural motifs in a protein. - Protein 3D motifs Protein structural motifs and surfaces true @@ -1932,8 +1843,6 @@ or of directed by the organization to do this. 1.4 An informative report on architecture (spatial arrangement of secondary structure) of a protein structure. - Protein property (architecture) - Protein structure report (architecture) Protein architecture report true @@ -1947,7 +1856,7 @@ or of directed by the organization to do this. beta12orEarlier 1.8 - A report on an analysis or model of protein folding properties, folding pathways, residues or sites that are key to protein folding, nucleation or stabilization centers etc. + A report on an analysis or model of protein folding properties, folding pathways, residues or sites that are key to protein folding, nucleation or stabilisation centers etc. Protein folding report @@ -1964,9 +1873,6 @@ or of directed by the organization to do this. beta13 Data on the effect of (typically point) mutation on protein folding, stability, structure and function. - Protein property (mutation) - Protein report (mutation) - Protein structure report (mutation) This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. Protein features (mutation) @@ -2183,7 +2089,7 @@ or of directed by the organization to do this. beta12orEarlier 1.8 - PCR primers and hybridization oligos in a nucleic acid sequence. + PCR primers and hybridisation oligos in a nucleic acid sequence. Nucleic acid features report (primers) @@ -2282,7 +2188,7 @@ or of directed by the organization to do this. beta12orEarlier Data quantifying the level of expression of (typically) multiple genes, derived for example from microarray experiments. - Gene expression pattern + Gene expression pattern Gene expression profile @@ -2328,7 +2234,6 @@ or of directed by the organization to do this. beta12orEarlier Output from a serial analysis of gene expression (SAGE) experiment. - Serial analysis of gene expression (SAGE) experimental data SAGE experimental data true @@ -2344,7 +2249,6 @@ or of directed by the organization to do this. beta12orEarlier Massively parallel signature sequencing (MPSS) data. - Massively parallel signature sequencing (MPSS) experimental data MPSS experimental data true @@ -2360,7 +2264,6 @@ or of directed by the organization to do this. beta12orEarlier Sequencing by synthesis (SBS) data. - Sequencing by synthesis (SBS) experimental data SBS experimental data true @@ -2497,9 +2400,11 @@ or of directed by the organization to do this. + beta12orEarlier - Protein or peptide identifications with evidence supporting the identifications, typically from comparing a peptide mass fingerprint (from mass spectrometry) to a sequence database. + Protein or peptide identifications with evidence supporting the identifications, for example from comparing a peptide mass fingerprint (from mass spectrometry) to a sequence database, or the set of typical spectra one obtains when running a protein through a mass spectrometer. + 'Protein identification' Peptide identification @@ -2618,10 +2523,6 @@ or of directed by the organization to do this. Development status / maturity may be part of the version information, for example in case of tools, standards, or some data records. Version information - "http://purl.obolibrary.org/obo/IAO_0000129" - http://semanticscience.org/resource/SIO_000653 - http://usefulinc.com/ns/doap#Version - http://www.ebi.ac.uk/swo/maturity/SWO_9000061 true @@ -2701,7 +2602,6 @@ or of directed by the organization to do this. beta12orEarlier 1.5 - Moby:PDGJOB Textual metadata on a submitted or completed job. Job metadata @@ -2840,9 +2740,11 @@ or of directed by the organization to do this. - + beta12orEarlier - A document of scientific text, typically a full text article from a scientific journal. + A scientific text, typically a full text article from a scientific journal. + Article text + Scientific article Article @@ -2854,6 +2756,7 @@ or of directed by the organization to do this. + beta12orEarlier An abstract of the results of text mining. Text mining output @@ -3241,7 +3144,7 @@ or of directed by the organization to do this. beta12orEarlier - International Non-proprietary Name (INN or 'generic name') of a chemical compound, assigned by the World Health Organization (WHO). + International Non-proprietary Name (INN or 'generic name') of a chemical compound, assigned by the World Health Organisation (WHO). INN chemical name @@ -3591,6 +3494,23 @@ or of directed by the organization to do this. + + + + + + + beta12orEarlier + A name of a sequence feature, e.g. the name of a feature to be displayed to an end-user. Typically an EMBL or Swiss-Prot feature label. + Sequence feature name + + + A feature label identifies a feature of a sequence database entry. When used with the database name and the entry's primary accession number, it is a unique identifier of that feature. + Sequence feature label + + + + @@ -4854,7 +4774,6 @@ or of directed by the organization to do this. beta12orEarlier beta12orEarlier - The EMBOSS type of a molecular sequence. See the EMBOSS documentation (http://emboss.sourceforge.net/) for a definition of what this includes. @@ -5018,7 +4937,6 @@ or of directed by the organization to do this. beta12orEarlier beta12orEarlier - The type of a BLAST sequence alignment. BLAST sequence alignment type @@ -5081,7 +4999,6 @@ or of directed by the organization to do this. 1.5 A label (text token) describing the type of a comparison matrix. - Substitution matrix type For example 'blosum', 'pam', 'gonnet', 'id' etc. Comparison matrix type may be required where a series of matrices of a certain type are used. Comparison matrix type @@ -6331,7 +6248,7 @@ or of directed by the organization to do this. beta12orEarlier beta12orEarlier - A library of nucleotide sequences to avoid during hybridization events. Hybridization of the internal oligo to sequences in this library is avoided, rather than priming from them. The file is in a restricted FASTA format. + A library of nucleotide sequences to avoid during hybridisation events. Hybridisation of the internal oligo to sequences in this library is avoided, rather than priming from them. The file is in a restricted FASTA format. Primer3 internal oligo mishybridizing library true @@ -6422,7 +6339,6 @@ or of directed by the organization to do this. 1.5 Size of a sequence word. - Word length Word size is used for example in word-based sequence database search methods. Word size @@ -6504,7 +6420,7 @@ or of directed by the organization to do this. SO:0000110 - This includes annotation of positional sequence features, organized into a standard feature table, or any other report of sequence features. General feature reports are a source of sequence feature table information although internal conversion would be required. + This includes annotation of positional sequence features, organised into a standard feature table, or any other report of sequence features. General feature reports are a source of sequence feature table information although internal conversion would be required. Sequence features http://purl.bioontology.org/ontology/MSH/D058977 @@ -6718,7 +6634,7 @@ or of directed by the organization to do this. beta12orEarlier - Annotation of positional sequence features, organized into a standard feature table. + Annotation of positional sequence features, organised into a standard feature table. Sequence feature table @@ -7020,9 +6936,8 @@ or of directed by the organization to do this. 1.5 Location of short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences. - Repeat sequence map - The report might include derived data map such as classification, annotation, organization, periodicity etc. + The report might include derived data map such as classification, annotation, organisation, periodicity etc. Sequence features (repeats) true @@ -8040,7 +7955,7 @@ or of directed by the organization to do this. - + beta12orEarlier A simple floating point number defining the penalty for opening or extending a gap in an alignment. @@ -8056,7 +7971,6 @@ or of directed by the organization to do this. beta12orEarlier beta12orEarlier - Whether end gaps are scored or not. Score end gaps control @@ -8071,7 +7985,6 @@ or of directed by the organization to do this. beta12orEarlier beta12orEarlier - Controls the order of sequences in an output sequence alignment. Aligned sequence order @@ -8475,8 +8388,6 @@ or of directed by the organization to do this. 1.5 A report of data concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees. - Phylogenetic tree report - Phylogenetic tree-derived report This is a broad data type and is used for example for reports on confidence, shape or stratigraphic (age) data derived from phylogenetic tree analysis. Phylogenetic report @@ -8582,7 +8493,6 @@ or of directed by the organization to do this. beta12orEarlier Matrix of integer numbers for sequence comparison. - Substitution matrix (integers) Comparison matrix (integers) true @@ -8598,7 +8508,6 @@ or of directed by the organization to do this. beta12orEarlier Matrix of floating point numbers for sequence comparison. - Substitution matrix (floats) Comparison matrix (floats) true @@ -8676,7 +8585,6 @@ or of directed by the organization to do this. beta12orEarlier Matrix of integer numbers for amino acid comparison. - Amino acid substitution matrix (integers) Amino acid comparison matrix (integers) true @@ -8692,7 +8600,6 @@ or of directed by the organization to do this. beta12orEarlier Matrix of floating point numbers for amino acid comparison. - Amino acid substitution matrix (floats) Amino acid comparison matrix (floats) true @@ -9007,7 +8914,6 @@ or of directed by the organization to do this. Alignment (superimposition) of exactly two protein tertiary (3D) structures. - Protein pair structural alignment Structure alignment (protein pair) true @@ -9053,7 +8959,6 @@ or of directed by the organization to do this. 1.5 Alignment (superimposition) of protein tertiary (3D) structures (typically C-alpha atoms only considered). - C-alpha trace C-beta atoms from amino acid side-chains may be considered. Structure alignment (protein C-alpha atoms) @@ -9133,7 +9038,6 @@ or of directed by the organization to do this. Alignment (superimposition) of exactly two nucleic acid tertiary (3D) structures. - Nucleic acid pair structure alignment Structure alignment (nucleic acid pair) true @@ -9360,7 +9264,6 @@ or of directed by the organization to do this. 1.5 An informative report on a specific enzyme. - Protein report (enzyme) Enzyme report true @@ -9376,8 +9279,6 @@ or of directed by the organization to do this. 1.5 An informative report on a specific restriction enzyme such as enzyme reference data. - Protein report (restriction enzyme) - Restriction enzyme pattern data This might include name of enzyme, organism, isoschizomers, methylation, source, suppliers, literature references, or data on restriction enzyme patterns such as name of enzyme, recognition site, length of pattern, number of cuts made by enzyme, details of blunt or sticky end cut etc. Restriction enzyme report @@ -9583,10 +9484,10 @@ or of directed by the organization to do this. beta12orEarlier beta13 - An informative report on protein subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or destination (exported / extracellular proteins). - Protein report (subcellular localization) + An informative report on protein subcellular localisation (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or destination (exported / extracellular proteins). + Protein report (subcellular localisation) - Protein subcellular localization + Protein subcellular localisation true @@ -9684,9 +9585,6 @@ or of directed by the organization to do this. 1.4 Informative report on flexibility or motion of a protein structure. - Protein flexibility or motion - Protein property (flexibility or motion) - Protein structure report (flexibility or motion) This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. Protein flexibility or motion report @@ -9717,7 +9615,6 @@ or of directed by the organization to do this. 1.4 Data on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure. - Protein structure report (surface) This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. Protein surface report @@ -9813,7 +9710,6 @@ or of directed by the organization to do this. 1.4 Non-canonical atomic interactions in protein structures. - Protein non-canonical interactions report Protein non-canonical interactions true @@ -9829,7 +9725,6 @@ or of directed by the organization to do this. 1.5 Information on a node from the CATH database. - CATH classification node report The report (for example http://www.cathdb.info/cathnode/1.10.10.10) includes CATH code (of the node and upper levels in the hierarchy), classification text (of appropriate levels in hierarchy), list of child nodes, representative domain and other relevant data and links. CATH node @@ -9846,7 +9741,6 @@ or of directed by the organization to do this. 1.5 Information on a node from the SCOP database. - SCOP classification node SCOP node true @@ -9966,7 +9860,7 @@ or of directed by the organization to do this. beta12orEarlier beta12orEarlier - A report on known protein structural domains or folds that are recognized (identified) in protein sequence(s). + A report on known protein structural domains or folds that are recognised (identified) in protein sequence(s). Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH. Protein fold recognition report @@ -10039,7 +9933,7 @@ or of directed by the organization to do this. beta12orEarlier - Enthalpy of hybridized or double stranded nucleic acid (DNA or RNA/DNA). + Enthalpy of hybridised or double stranded nucleic acid (DNA or RNA/DNA). Nucleic acid enthalpy @@ -10052,7 +9946,7 @@ or of directed by the organization to do this. beta12orEarlier - Entropy of hybridized or double stranded nucleic acid (DNA or RNA/DNA). + Entropy of hybridised or double stranded nucleic acid (DNA or RNA/DNA). Nucleic acid entropy @@ -10067,7 +9961,7 @@ or of directed by the organization to do this. beta12orEarlier beta12orEarlier - Melting temperature of hybridized or double stranded nucleic acid (DNA or RNA/DNA). + Melting temperature of hybridised or double stranded nucleic acid (DNA or RNA/DNA). Nucleic acid melting temperature true @@ -10080,7 +9974,7 @@ or of directed by the organization to do this. beta12orEarlier - Stitch profile of hybridized or double stranded nucleic acid (DNA or RNA/DNA). + Stitch profile of hybridised or double stranded nucleic acid (DNA or RNA/DNA). A stitch profile diagram shows partly melted DNA conformations (with probabilities) at a range of temperatures. For example, a stitch profile might show possible loop openings with their location, size, probability and fluctuations at a given temperature. @@ -10134,7 +10028,6 @@ or of directed by the organization to do this. beta12orEarlier beta12orEarlier - RNA parameters used by the Vienna package. Vienna RNA parameters @@ -10149,7 +10042,6 @@ or of directed by the organization to do this. beta12orEarlier beta12orEarlier - Structure constraints used by the Vienna package. Vienna RNA structure constraints @@ -10164,7 +10056,6 @@ or of directed by the organization to do this. beta12orEarlier beta12orEarlier - RNA concentration data used by the Vienna package. Vienna RNA concentration data @@ -10256,7 +10147,6 @@ or of directed by the organization to do this. beta12orEarlier A simple measure of synonymous codon usage bias often used to predict gene expression levels. - CAI Codon adaptation index true @@ -10352,8 +10242,8 @@ or of directed by the organization to do this. - + beta12orEarlier A graphical 2D tabular representation of gene expression data, typically derived from a DNA microarray experiment. @@ -10373,7 +10263,6 @@ or of directed by the organization to do this. beta12orEarlier Affymetrix library file of information about which probes belong to which probe set. - CDF file Affymetrix probe sets library file true @@ -10598,7 +10487,6 @@ or of directed by the organization to do this. 1.5 Information on a database (or ontology) version, for example name, version number and release date. - Ontology version information Database version information true @@ -10941,7 +10829,6 @@ or of directed by the organization to do this. beta12orEarlier 1.5 - Number of iterations of an algorithm. Number of iterations @@ -10956,7 +10843,6 @@ or of directed by the organization to do this. beta12orEarlier 1.5 - Number of entities (for example database hits, sequences, alignments etc) to write to an output file. Number of output entities @@ -10971,7 +10857,6 @@ or of directed by the organization to do this. beta12orEarlier beta12orEarlier - Controls the order of hits (reported matches) in an output file from a database search. Hit sort order @@ -11126,12 +11011,7 @@ or of directed by the organization to do this. beta12orEarlier beta12orEarlier - Moby:Annotated_GO_Term - Moby:Annotated_GO_Term_With_Probability - Moby:GOTerm - Moby:GO_Term A term definition from The Gene Ontology (GO). - Gene Ontology term GO true @@ -11846,14 +11726,6 @@ or of directed by the organization to do this. http://www.geneontology.org/doc/GO.xrf_abbs: HGNC_gene Symbol of a gene approved by the HUGO Gene Nomenclature Committee. - Gene name (HUGO) - HGNC gene name - HGNC gene symbol - HGNC symbol - HUGO gene name - HUGO gene symbol - HUGO symbol - Official gene name Gene name (HGNC) true @@ -11948,7 +11820,6 @@ or of directed by the organization to do this. beta12orEarlier beta13 - http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Gmorsitans Gene identifier from Glossina morsitans GeneDB database. Gene ID (GeneDB Glossina morsitans) @@ -11964,7 +11835,6 @@ or of directed by the organization to do this. beta12orEarlier beta13 - http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Lmajor Gene identifier from Leishmania major GeneDB database. Gene ID (GeneDB Leishmania major) @@ -12094,7 +11964,6 @@ or of directed by the organization to do this. beta12orEarlier Any name (other than the recommended one) for a gene. - Gene name synonym Gene synonym true @@ -12272,7 +12141,6 @@ or of directed by the organization to do this. - Moby:MapFeature A feature which may mapped (positioned) on a genetic or other type of map. Mappable features may be based on Gramene's notion of map features; see http://www.gramene.org/db/cmap/feature_type_info. @@ -12432,7 +12300,6 @@ or of directed by the organization to do this. beta12orEarlier An alternative for a word. - Alternative name Synonym true @@ -12582,7 +12449,6 @@ or of directed by the organization to do this. Moby_namespace:MIPS_GE_Maize Identifier for genetic elements in MIPS Maize database. - MIPS genetic element identifier (Maize) Gene ID (MIPS Maize) true @@ -12599,7 +12465,6 @@ or of directed by the organization to do this. Moby_namespace:MIPS_GE_Medicago Identifier for genetic elements in MIPS Medicago database. - MIPS genetic element identifier (Medicago) Gene ID (MIPS Medicago) true @@ -12630,7 +12495,6 @@ or of directed by the organization to do this. beta12orEarlier 1.3 - Moby_namespace:ArabidopsisGeneSymbol A unique identifier for an Arabidopsis gene, which is an acronym or abbreviation of the gene name. Gene name (Arabidopsis) @@ -12663,7 +12527,6 @@ or of directed by the organization to do this. beta12orEarlier 1.3 - Moby_namespace:GENEFARM_GeneName Name of a gene from the GeneFarm database. GeneFarm gene ID @@ -12880,7 +12743,6 @@ or of directed by the organization to do this. Moby:SO_QTL A stretch of DNA that is closely linked to the genes underlying a quantitative trait (a phenotype that varies in degree and depends upon the interactions between multiple genes and their environment). - QTL A QTL sometimes but does not necessarily correspond to a gene. Quantitative trait locus @@ -13055,7 +12917,6 @@ or of directed by the organization to do this. beta12orEarlier beta12orEarlier - Data used by the Vienna RNA analysis package. Vienna RNA structural data @@ -13070,7 +12931,6 @@ or of directed by the organization to do this. beta12orEarlier 1.5 - Data used to replace (mask) characters in a molecular sequence. Sequence mask parameter @@ -13129,7 +12989,6 @@ or of directed by the organization to do this. Raw data from or annotation on laboratory experiments. - Experimental measurement data This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. Experimental data @@ -13312,7 +13171,6 @@ or of directed by the organization to do this. beta12orEarlier 1.5 - Some simple value controlling a search operation, typically a search of a database. Search parameter @@ -13374,7 +13232,6 @@ or of directed by the organization to do this. 1.8 Data concerning, extracted from, or derived from the analysis of molecular alignment of some type. - Alignment report This is a broad data type and is used a placeholder for other, more specific types. Alignment data @@ -13609,7 +13466,6 @@ or of directed by the organization to do this. Moby_namespace:GeneId Name of an entry (gene) from the KEGG GENES database. - KEGG GENES entry name Gene name (KEGG GENES) true @@ -13932,7 +13788,6 @@ or of directed by the organization to do this. beta12orEarlier beta12orEarlier - A type of point or block mutation, including insertion, deletion, change, duplication and moves. Mutation type @@ -13961,7 +13816,6 @@ or of directed by the organization to do this. beta12orEarlier 1.5 - A control of the order of data that is output, for example the order of sequences in an alignment. Possible options including sorting by score, rank, by increasing P-value (probability, i.e. most statistically significant hits given first) and so on. @@ -13977,7 +13831,6 @@ or of directed by the organization to do this. beta12orEarlier beta12orEarlier - A simple parameter that is a toggle (boolean value), typically a control for a modal tool. Toggle @@ -14019,7 +13872,7 @@ or of directed by the organization to do this. beta12orEarlier - A temperature concerning nucleic acid denaturation, typically the temperature at which the two strands of a hybridized or double stranded nucleic acid (DNA or RNA/DNA) molecule separate. + A temperature concerning nucleic acid denaturation, typically the temperature at which the two strands of a hybridised or double stranded nucleic acid (DNA or RNA/DNA) molecule separate. Melting temperature @@ -14092,7 +13945,6 @@ or of directed by the organization to do this. beta12orEarlier 1.5 - An offset for a single-point sequence position. Sequence offset @@ -14107,7 +13959,6 @@ or of directed by the organization to do this. beta12orEarlier 1.5 - A value that serves as a threshold for a tool (usually to control scoring or output). Threshold @@ -14124,7 +13975,6 @@ or of directed by the organization to do this. beta13 An informative report on a transcription factor protein. - Transcription factor binding site data This might include conformational or physicochemical properties, as well as sequence information for transcription factor(s) binding sites. Protein report (transcription factor) @@ -14169,7 +14019,6 @@ or of directed by the organization to do this. beta12orEarlier beta12orEarlier - Specification of one or more colors. Color @@ -14184,10 +14033,7 @@ or of directed by the organization to do this. beta12orEarlier 1.5 - A parameter that is used to control rendering (drawing) to a device or image. - Graphical parameter - Graphics parameter Rendering parameter true @@ -14216,7 +14062,6 @@ or of directed by the organization to do this. beta12orEarlier 1.5 - A temporal date. Date @@ -14321,7 +14166,7 @@ or of directed by the organization to do this. A plot of pK versus pH for a protein. - Protein ionization curve + Protein ionisation curve @@ -14419,7 +14264,6 @@ or of directed by the organization to do this. beta12orEarlier beta12orEarlier - The number of a certain thing. Cardinality @@ -14883,7 +14727,6 @@ or of directed by the organization to do this. 1.5 An XML Schema. - XSD XML Schema true @@ -15104,7 +14947,6 @@ or of directed by the organization to do this. 1.3 Name of an entry (gene) from the AceView genes database. - AceView gene name Gene name (AceView) true @@ -15432,10 +15274,10 @@ or of directed by the organization to do this. beta12orEarlier - A score derived from the alignment of two sequences, which is then normalized with respect to the scoring system. + A score derived from the alignment of two sequences, which is then normalised with respect to the scoring system. - Bit scores are normalized with respect to the scoring system and therefore can be used to compare alignment scores from different searches. + Bit scores are normalised with respect to the scoring system and therefore can be used to compare alignment scores from different searches. Bit score @@ -15907,7 +15749,6 @@ or of directed by the organization to do this. beta12orEarlier 1.8 An informative report on individual spot(s) from a two-dimensional (2D PAGE) gel. - 2D PAGE spot annotation 2D PAGE spot report @@ -16384,13 +16225,13 @@ or of directed by the organization to do this. beta12orEarlier - Data concerning, extracted from, or derived from the analysis of a scientific text (or texts) such as a full text article from a scientific journal. - Article report + Article data + Scientific text data This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. It includes concepts that are best described as scientific text or closely concerned with or derived from text. - Article data + Text data @@ -16398,17 +16239,13 @@ or of directed by the organization to do this. - + beta12orEarlier + 1.16 Typically a simple numerical or string value that controls the operation of a tool. - Parameters - Tool parameter - Tool-specific parameter - - + Parameter - http://semanticscience.org/resource/SIO_000144 - http://www.e-lico.eu/ontologies/dmo/DMOP/DMOP.owl#Parameter + true @@ -16421,7 +16258,6 @@ or of directed by the organization to do this. beta13 Data concerning a specific type of molecule. - Molecule-specific data This is a broad data type and is used a placeholder for other, more specific types. Molecular data @@ -16439,7 +16275,6 @@ or of directed by the organization to do this. An informative report on a specific molecule. - Molecular report Molecule report true @@ -16467,8 +16302,8 @@ or of directed by the organization to do this. beta12orEarlier Annotation on a wet lab experiment, such as experimental conditions. - Experiment annotation - Experiment metadata + Experiment annotation + Experiment metadata Experiment report @@ -16494,7 +16329,7 @@ or of directed by the organization to do this. - + beta12orEarlier An attribute of a molecular sequence, possibly in reference to some other sequence. Sequence parameter @@ -16588,7 +16423,6 @@ or of directed by the organization to do this. beta13 Data concerning an index of data. - Database index This is a broad data type and is used a placeholder for other, more specific types. Data index data @@ -16675,7 +16509,6 @@ or of directed by the organization to do this. 1.5 A simple summary of expressed genes. - Gene annotation (expressed gene list) Expressed gene list true @@ -16952,8 +16785,6 @@ or of directed by the organization to do this. beta12orEarlier An informative report on the physical, chemical or other information concerning the interaction of two or more molecules (or parts of molecules). - Molecular interaction data - Molecular interaction report Molecule interaction report @@ -17011,11 +16842,27 @@ or of directed by the organization to do this. beta12orEarlier - Image or hybridisation data for a microarray, typically a study of gene expression. + Image, hybridisation or some other data arising from a study of gene expression, typically profiling or quantification. + Gene product profile + Gene product quantification data + Gene transcription profile + Gene transcription quantification data Microarray data + Non-coding RNA profile + Non-coding RNA quantification data + RNA profile + RNA quantification data + RNA-seq data + Transcriptome profile + Transcriptome quantification data + mRNA profile + mRNA quantification data + Protein profile + Protein quantification data + Proteome profile + Proteome quantification data - This is a broad data type and is used a placeholder for other, more specific types. See also http://edamontology.org/data_0931 Gene expression data Microarray data @@ -18732,7 +18579,6 @@ or of directed by the organization to do this. 1.5 Annotation on an embryo or concerning embryological development. - Embryo annotation Embryo report true @@ -20310,7 +20156,6 @@ or of directed by the organization to do this. 1.5 An informative report on general information, properties or features of one or more molecular secondary structures. - Secondary structure-derived report Secondary structure report true @@ -20341,8 +20186,6 @@ or of directed by the organization to do this. 1.5 Features concerning RNA or regions of DNA that encode an RNA molecule. - Nucleic acid features (RNA features) - RNA features RNA features report true @@ -20798,7 +20641,7 @@ or of directed by the organization to do this. - + beta12orEarlier Metadata on sequence features. @@ -20891,7 +20734,8 @@ or of directed by the organization to do this. beta12orEarlier 1.5 - + + Data derived from the analysis of a scientific text such as a full text article from a scientific journal. Article report @@ -21007,9 +20851,6 @@ or of directed by the organization to do this. beta12orEarlier 1.8 An informative report on a two-dimensional (2D PAGE) gel. - 2D PAGE gel annotation - 2D PAGE image annotation - 2D PAGE image report 2D PAGE gel report @@ -21041,7 +20882,6 @@ or of directed by the organization to do this. 1.5 An image from a microarray experiment which (typically) allows a visualisation of probe hybridisation and gene-expression data. - Gene expression image Microarray image true @@ -21243,7 +21083,6 @@ or of directed by the organization to do this. beta12orEarlier An informative report concerning the classification of protein sequences or structures. - Protein classification data This is a broad data type and is used a placeholder for other, more specific types. Protein classification @@ -21301,7 +21140,7 @@ or of directed by the organization to do this. - + beta12orEarlier An informative report concerning or derived from the analysis of a biological pathway or network, such as a map (diagram) or annotation. @@ -21333,7 +21172,6 @@ or of directed by the organization to do this. beta12orEarlier Data concerning the classification of nucleic acid sequences or structures. - Nucleic acid classification data This is a broad data type and is used a placeholder for other, more specific types. Nucleic acid classification @@ -21348,7 +21186,6 @@ or of directed by the organization to do this. 1.5 A report on a classification of molecular sequences, structures or other entities. - Classification data This can include an entire classification, components such as classifiers, assignments of entities to a classification and so on. Classification report @@ -21551,9 +21388,9 @@ or of directed by the organization to do this. beta13 1.5 - A type of data that (typically) corresponds to entries from the primary biological databases and which is (typically) the primary input or output of a tool, i.e. the data the tool processes or generates, as distinct from metadata and identifiers which describe and identify such core data, parameters that control the behaviour of tools, reports of derivative data generated by tools and annotation. + Core data entities typically have a format and may be identified by an accession number. Core data true @@ -21698,7 +21535,6 @@ or of directed by the organization to do this. beta13 1.5 - Basic information concerning geographical location or time. Geotemporal metadata @@ -21728,6 +21564,7 @@ or of directed by the organization to do this. 1.15 A name of a sequence feature, e.g. the name of a feature to be displayed to an end-user. + Sequence feature name true @@ -22361,7 +22198,6 @@ or of directed by the organization to do this. 1.1 1.8 Report concerning genome-wide association study experiments. - Genome-wide association study GWAS report @@ -23056,11 +22892,11 @@ or of directed by the organization to do this. - 1.12 - Any free or plain text, as often specified as some search query. + Any free or plain text, typically for human consumption and in English. Can instantiate also as a textual search query. Free text - Plain text + Plain text + Textual search query Text @@ -23245,7 +23081,7 @@ or of directed by the organization to do this. 1.15 - An identifier of a lane within a flow cell of a sequencing machine, within which millions of sequences are immobilized, amplified and sequenced. + An identifier of a lane within a flow cell of a sequencing machine, within which millions of sequences are immobilised, amplified and sequenced. Lane identifier @@ -23338,6 +23174,135 @@ or of directed by the organization to do this. + + + + + 1.16 + An informative report containing a ranked list of categories (usually ontology concepts), each associated with a statistical metric of over-/under-representation within the studied data. + Enrichment report + Functional enrichment report + + + Over-representation report + + + + + + + + + 1.16 + GO-term report + An informative report containing a ranked list of Gene Ontology concepts, each associated with a p-value, concerning or derived from the analysis of e.g. a set of genes or proteins. + Gene ontology concept over-representation report + Gene ontology enrichment report + Gene ontology term enrichment report + + + GO-term enrichment report + + + + + + + + + 1.16 + Score for localization of one or more post-translational modifications in peptide sequence measured by mass spectrometry. + False localisation rate + PTM localisation + PTM score + + + Localisation score + + + + + + + + + 1.16 + Identifier of a protein modification catalogued in the Unimod database. + + + + Unimod ID + + + + + + + + + 1.16 + Identifier for mass spectrometry proteomics data in the proteomexchange.org repository. + + + + ProteomeXchange ID + + + + + + + + + 1.16 + Groupings of gene expression profiles according to a clustering algorithm. + + + Clustered gene expression profiles + + + + + + + + + 1.16 + An identifier of a concept from the BRENDA ontology. + + + + BRENDA ontology concept ID + + + + + + + + + 1.16 + A text (such as a scientific article), annotated with notes, data and metadata, such as recognised entities, concepts, and their relations. + + + Annotated text + + + + + + + + + 1.16 + A structured query, in form of a script, that defines a database search task. + + + Query script + + + + @@ -24376,7 +24341,6 @@ or of directed by the organization to do this. beta12orEarlier Entry format of PDB database in mmCIF format. - Chemical MIME (http://www.ch.ic.ac.uk/chemime): chemical/x-mmcif mmcif @@ -25127,7 +25091,7 @@ or of directed by the organization to do this. beta12orEarlier - Report format on PCR primers and hybridization oligos as generated by Whitehead primer3 program. + Report format on PCR primers and hybridisation oligos as generated by Whitehead primer3 program. Primer3 primer @@ -25720,12 +25684,14 @@ or of directed by the organization to do this. - + + beta12orEarlier - iHOP abstract format. + The format of iHOP (Information Hyperlinked over Proteins) text-mining result. - iHOP text mining abstract format + iHOP format + @@ -25733,14 +25699,16 @@ or of directed by the organization to do this. - + + + beta12orEarlier - Text mining abstract format from the Oscar 3 application. + OSCAR format of annotated chemical text. - Oscar 3 performs chemistry-specific parsing of chemical documents. It attempts to identify chemical names, ontology concepts and chemical data from a document. - Oscar3 + OSCAR (Open-Source Chemistry Analysis Routines) software performs chemistry-specific parsing of chemical documents. It attempts to identify chemical names, ontology concepts, and chemical data from a document. + OSCAR format @@ -25847,7 +25815,6 @@ or of directed by the organization to do this. beta12orEarlier beta12orEarlier - Moby:ColiCard Format of a report on Escherichia coli genes, proteins and molecules from the CyberCell Database (CCDB). ColiCard report format @@ -25916,7 +25883,7 @@ or of directed by the organization to do this. - + beta12orEarlier Data model A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere. @@ -25941,7 +25908,7 @@ or of directed by the organization to do this. http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality http://www.onto-med.de/ontologies/gfo.owl#Perpetuant http://www.onto-med.de/ontologies/gfo.owl#Symbol_structure - + @@ -26773,8 +26740,9 @@ or of directed by the organization to do this. beta12orEarlier - - + + + Generic Feature Format version 3 (GFF3) of sequence features. @@ -27297,7 +27265,7 @@ or of directed by the organization to do this. beta12orEarlier - Data format for an abstract (report) from text mining. + Data format of a report from text mining. Text mining report format @@ -27621,7 +27589,7 @@ or of directed by the organization to do this. beta12orEarlier - Format of a report on PCR primers or hybridization oligos in a nucleic acid sequence. + Format of a report on PCR primers or hybridisation oligos in a nucleic acid sequence. Nucleic acid features (primers) format @@ -28237,7 +28205,6 @@ or of directed by the organization to do this. beta12orEarlier 1.0 - Format of a report on organism strain data / cell line. Strain data format @@ -28431,7 +28398,7 @@ or of directed by the organization to do this. beta12orEarlier Textual format. - Plain text + Plain text format txt @@ -28537,11 +28504,12 @@ or of directed by the organization to do this. beta12orEarlier - A broad class of format distinguished by the scientific nature of the data that is identified. + A placeholder concept for visual navigation by dividing data formats by the content of the data that is represented. + Format (typed) This concept exists only to assist EDAM maintenance and navigation in graphical browsers. It does not add semantic information. The concept branch under 'Format (typed)' provides an alternative organisation of the concepts nested under the other top-level branches ('Binary', 'HTML', 'RDF', 'Text' and 'XML'. All concepts under here are already included under those branches. - Format (typed) + Format (by type of data) @@ -28556,14 +28524,33 @@ or of directed by the organization to do this. + beta12orEarlier + + + + + + Any ontology allowed, none mandatory. Preferrably with URIs but URIs are not mandatory. Non-ontology terms are also allowed as the last resort in case of a lack of suitable ontology. + 'BioXSD' belongs to the 'BioXSD|GTrack' ecosystem of generic formats. 'BioXSD in XML' is the XML format based on the common, unified 'BioXSD data model', a.k.a. 'BioXSD|BioJSON|BioYAML'. + BioXSD + BioXSD data model + BioXSD format + BioXSD/GTrack + BioXSD|BioJSON|BioYAML + BioXSD|GTrack - BioXSD XML format of basic bioinformatics types of data (sequence records, alignments, feature records, references to resources, and more). + + BioXSD-schema-based XML format of sequence-based data and some other common data - sequence records, alignments, feature records, references to resources, and more - optimised for integrative bioinformatics, Web services, and object-oriented programming. + BioXSD XML BioXSD XML format + BioXSD in XML + BioXSD in XML format + BioXSD+XML - BioXSD + BioXSD (XML) @@ -28661,7 +28648,7 @@ or of directed by the organization to do this. - + beta12orEarlier A sequence format resembling uniprotkb entry format. @@ -29680,13 +29667,26 @@ or of directed by the organization to do this. + 1.0 + + + + 'GTrack' belongs to the 'BioXSD|GTrack' ecosystem of generic formats, and particular to its subset, the 'GTrack ecosystem' (GTrack, GSuite, BTrack). 'GTrack' is the tabular format for representing features of sequences and genomes. + GTrack ecosystem of formats - GTrack is an optimised tabular format for genome/sequence feature tracks unifying the power of other tabular formats (e.g. GFF3, BED, WIG). + + + GTrack is a generic and optimised tabular format for genome or sequence feature tracks. GTrack unifies the power of other track formats (e.g. GFF3, BED, WIG), and while optimised in size, adds more flexibility, customisation, and automation ("machine understandability"). + BioXSD/GTrack GTrack + BioXSD|GTrack GTrack + GTrack format + GTrack|BTrack|GSuite GTrack + GTrack|GSuite|BTrack GTrack GTrack @@ -29963,7 +29963,7 @@ or of directed by the organization to do this. 1.2 - The Terse RDF Triple Language (Turtle) is a human-friendly serialization format for RDF (Resource Description Framework) graphs. + The Terse RDF Triple Language (Turtle) is a human-friendly serialisation format for RDF (Resource Description Framework) graphs. The SPARQL Query Language incorporates a very similar syntax. @@ -29992,7 +29992,7 @@ or of directed by the organization to do this. - A shorthand non-XML serialization of Resource Description Framework model, designed with human-readability in mind. + A shorthand non-XML serialisation of Resource Description Framework model, designed with human-readability in mind. N3 @@ -30010,7 +30010,7 @@ or of directed by the organization to do this. Resource Description Framework (RDF) XML format. - RDF/XML is a serialization syntax for OWL DL, but not for OWL Full. + RDF/XML is a serialisation syntax for OWL DL, but not for OWL Full. RDF/XML http://www.ebi.ac.uk/SWO/data/SWO_3000006 @@ -30365,24 +30365,17 @@ or of directed by the organization to do this. - + 1.7 tsv|tab - DSV - Delimiter-separated values - Tabular format + Tabular data represented as tab-separated values in a text file. Tab-separated values - CSV - Comma-separated values TSV - http://filext.com/file-extension/CSV - http://www.iana.org/assignments/media-types/text/csv - https://en.wikipedia.org/wiki/Delimiter-separated_values @@ -30621,7 +30614,7 @@ or of directed by the organization to do this. 1.9 - Nearly Raw Rasta Data format designed to support scientific visualization and image processing involving N-dimensional raster data. + Nearly Raw Rasta Data format designed to support scientific visualisation and image processing involving N-dimensional raster data. nrrd @@ -30662,12 +30655,28 @@ or of directed by the organization to do this. 1.9 - EMBL entry format wrapped in HTML elements. - MHTML + + mhtml|mht|eml + + MHTML is not strictly an HTML format, it is encoded as an HTML email message (although with multipart/related instead of multipart/alternative). It, however, contains the main HTML block as its core, and thus it is for practical reasons incuded in EDAM as a specialisation of 'HTML'. + + + + MIME HTML format for Web pages, which can include external resources, including images, Flash animations and so on. + HTML email format + HTML email message format + MHT + MHT format + MHTML format + MIME HTML + MIME HTML format + MIME multipart + MIME multipart format + MIME multipart message + MIME multipart message format - MHT - MIME HTML format for Web pages, which can include external resources, including images, Flash animations and so on. + MHTML @@ -30871,11 +30880,11 @@ or of directed by the organization to do this. 1.11 - Binary format used by Galaxy for hierarchical data. + HDF5 is a generic hierarchical data file format used to store and organize large amounts of data. h5 - An HDF5 file appears to the user as a directed graph. The nodes of this graph are the higher-level HDF5 objects that are exposed by the HDF5 APIs: Groups, Datasets, Named datatypes. H5py uses straightforward NumPy and Python metaphors, like dictionary and NumPy array syntax. + An HDF5 file appears to the user as a directed graph. The nodes of this graph are the higher-level HDF5 objects that are exposed by the HDF5 APIs: Groups, Datasets, Named datatypes. hdf5 @@ -31357,11 +31366,11 @@ or of directed by the organization to do this. 1.11 - https://www.sqlite.org/fileformat2.html + Data format used by the SQLite database. - SQLite + SQLite format @@ -31369,13 +31378,14 @@ or of directed by the organization to do this. - + + 1.11 - https://gemini.readthedocs.org/en/latest/content/quick_start.html + Data format used by the SQLite database conformant to the Gemini schema. - GeminiSQLite + Gemini SQLite format @@ -31504,7 +31514,7 @@ or of directed by the organization to do this. http://sashimi.sourceforge.net/schema_revision/pepXML/pepXML_v118.xsd Open data format for the storage, exchange, and processing of peptide sequence assignments of MS/MS scans, intended to provide a common data output format for many different MS/MS search engines and subsequent peptide-level analyses. - + pepXML @@ -31535,6 +31545,7 @@ or of directed by the organization to do this. oxlicg + A list of k-mers and their occurences in a dataset. Can also be used as an implicit De Bruijn graph. K-mer countgraph @@ -31985,7 +31996,7 @@ experiments employing a combination of technologies. Synthetic Biology Open Language (SBOL) is an XML format for the specification and exchange of biological design information in synthetic biology. - SBOL introduces a standardized format for the electronic exchange of information on the structural and functional aspects of biological designs. + SBOL introduces a standardised format for the electronic exchange of information on the structural and functional aspects of biological designs. SBOL @@ -32067,7 +32078,7 @@ experiments employing a combination of technologies. BIological Observation Matrix format - BIOM is a recognized standard for the Earth Microbiome Project, and is a project supported by Genomics Standards Consortium. Supported in QIIME, Mothur, MEGAN, etc. + BIOM is a recognised standard for the Earth Microbiome Project, and is a project supported by Genomics Standards Consortium. Supported in QIIME, Mothur, MEGAN, etc. BIOM format @@ -32137,7 +32148,7 @@ experiments employing a combination of technologies. yaml|yml - YAML (YAML Ain't Markup Language) is a human-readable tree-structured data serialization language. + YAML (YAML Ain't Markup Language) is a human-readable tree-structured data serialisation language. YAML Ain't Markup Language @@ -32148,9 +32159,484 @@ experiments employing a combination of technologies. + + + + + 1.16 + Tabular format + + Tabular data represented as values in a text file delimited by some character. + Delimiter-separated values + + + DSV + + + + + + + + + 1.16 + csv + + + + Tabular data represented as comma-separated values in a text file. + Comma-separated values + + + CSV + + + + + + + + + + 1.16 + "Raw" result file from SEQUEST database search. + + + SEQUEST .out file + + + + + + + + + + 1.16 + http://open-ms.sourceforge.net/schemas/ + XML file format for files containing information about peptide identifications from mass spectrometry data analysis carried out with OpenMS. + + + idXML + + + + + + + + + 1.16 + Data table formatted such that it can be passed/streamed within the KNIME platform. + + + KNIME datatable format + + + + + + + + + + + 1.16 + + UniProtKB XML sequence features format is an XML format available for downloading UniProt entries. + UniProt XML + UniProt XML format + UniProtKB XML format + + + UniProtKB XML + + + + + + + + + + 1.16 + + UniProtKB RDF sequence features format is an RDF format available for downloading UniProt entries (in RDF/XML). + UniProt RDF + UniProt RDF format + UniProtKB RDF format + UniProt RDF/XML + UniProt RDF/XML format + UniProtKB RDF/XML + UniProtKB RDF/XML format + + + UniProtKB RDF + + + + + + + + + + + + + + 1.16 + + + + Work in progress. 'BioXSD' belongs to the 'BioXSD|GTrack' ecosystem of generic formats. 'BioJSON' is the JSON format based on the common, unified 'BioXSD data model', a.k.a. 'BioXSD|BioJSON|BioYAML'. + + BioJSON is a BioXSD-schema-based JSON format of sequence-based data and some other common data - sequence records, alignments, feature records, references to resources, and more - optimised for integrative bioinformatics, web applications and APIs, and object-oriented programming. + BioJSON (BioXSD data model) + BioJSON format (BioXSD) + BioXSD BioJSON + BioXSD BioJSON format + BioXSD JSON + BioXSD JSON format + BioXSD in JSON + BioXSD in JSON format + BioXSD+JSON + BioXSD/GTrack BioJSON + BioXSD|BioJSON|BioYAML BioJSON + BioXSD|GTrack BioJSON + + + BioJSON (BioXSD) + + + + + + + + + + + + + + 1.16 + + + + Work in progress. 'BioXSD' belongs to the 'BioXSD|GTrack' ecosystem of generic formats. 'BioYAML' is the YAML format based on the common, unified 'BioXSD data model', a.k.a. 'BioXSD|BioJSON|BioYAML'. + + BioYAML is a BioXSD-schema-based YAML format of sequence-based data and some other common data - sequence records, alignments, feature records, references to resources, and more - optimised for integrative bioinformatics, web APIs, human readability and editting, and object-oriented programming. + BioXSD BioYAML + BioXSD BioYAML format + BioXSD YAML + BioXSD YAML format + BioXSD in YAML + BioXSD in YAML format + BioXSD+YAML + BioXSD/GTrack BioYAML + BioXSD|BioJSON|BioYAML BioYAML + BioXSD|GTrack BioYAML + BioYAML (BioXSD data model) + BioYAML (BioXSD) + BioYAML format + BioYAML format (BioXSD) + + + BioYAML + + + + + + + + + + + 1.16 + + + BioJSON is a JSON format of single multiple sequence alignments, with their annotations, features, and custom visualisation and application settings for the Jalview workbench. + BioJSON format (Jalview) + JSON (Jalview) + JSON format (Jalview) + Jalview BioJSON + Jalview BioJSON format + Jalview JSON + Jalview JSON format + + + BioJSON (Jalview) + + + + + + + + + + + + 1.16 + + + 'GSuite' belongs to the 'BioXSD|GTrack' ecosystem of generic formats, and particular to its subset, the 'GTrack ecosystem' (GTrack, GSuite, BTrack). 'GSuite' is the tabular format for an annotated collection of individual GTrack files. + + + GSuite is a tabular format for collections of genome or sequence feature tracks, suitable for integrative multi-track analysis. GSuite contains links to genome/sequence tracks, with additional metadata. + BioXSD/GTrack GSuite + BioXSD|GTrack GSuite + GSuite (GTrack ecosystem of formats) + GSuite format + GTrack|BTrack|GSuite GSuite + GTrack|GSuite|BTrack GSuite + + + GSuite + + + + + + + + + + + + 1.16 + 'BTrack' belongs to the 'BioXSD|GTrack' ecosystem of generic formats, and particular to its subset, the 'GTrack ecosystem' (GTrack, GSuite, BTrack). 'BTrack' is the binary, optionally compressed HDF5-based version of the GTrack and GSuite formats. + BTrack is an HDF5-based binary format for genome or sequence feature tracks and their collections, suitable for integrative multi-track analysis. BTrack is a binary, compressed alternative to the GTrack and GSuite formats. + BTrack (GTrack ecosystem of formats) + BTrack format + BioXSD/GTrack BTrack + BioXSD|GTrack BTrack + GTrack|BTrack|GSuite BTrack + GTrack|GSuite|BTrack BTrack + + + BTrack + + + + + + + + + + 1.16 + + + + + + + Multi-Crop Passport Descriptors is a format available in 2 successive versions, V.1 (FAO/IPGRI 2001) and V.2 (FAO/Bioversity 2012). + + + + + The FAO/Bioversity/IPGRI Multi-Crop Passport Descriptors (MCPD) is an international standard format for exchange of germplasm information. + Bioversity MCPD + FAO MCPD + MCPD format + Multi-Crop Passport Descriptors + Multi-Crop Passport Descriptors format + IPGRI MCPD + MCPD V.1 + MCPD V.2 + + + MCPD + + + + + + + + + + 1.16 + Data format of an annotated text, e.g. with recognised entities, concepts, and relations. + + + Annotated text format + + + + + + + + + + + 1.16 + + + JSON format of annotated scientific text used by PubAnnotations and other tools. + + + PubAnnotation format + + + + + + + + + + + 1.16 + + + BioC is a standardised XML format for sharing and integrating text data and annotations. + + + BioC + + + + + + + + + + + + 1.16 + + + Native textual export format of annotated scientific text from PubTator. + + + PubTator format + + + + + + + + + + 1.16 + + + A format of text annotation using the linked-data Open Annotation Data Model, serialised typically in RDF or JSON-LD. + + + Open Annotation format + + + + + + + + + + + 1.16 + + + + + + + + + + + + + A family of similar formats of text annotation, used by BRAT and other tools, known as BioNLP Shared Task format (BioNLP 2009 Shared Task on Event Extraction, BioNLP Shared Task 2011, BioNLP Shared Task 2013), BRAT format, BRAT standoff format, and similar. + BRAT format + BRAT standoff format + + + BioNLP Shared Task format + + + + + + + + + 1.16 + A query language (format) for structured database queries. + Query format + + + Query language + + + + + + + + + 1.16 + sql + + + + SQL (Structured Query Language) is the de-facto standard query language (format of queries) for querying and manipulating data in relational databases. + Structured Query Language + + + SQL + + + + + + + + + + 1.16 + + xq|xqy|xquery + + XQuery (XML Query) is a query language (format of queries) for querying and manipulating structured and unstructured data, usually in the form of XML, text, and with vendor-specific extensions for other data formats (JSON, binary, etc.). + XML Query + + + XQuery + + + + + + + + + + 1.16 + + + SPARQL (SPARQL Protocol and RDF Query Language) is a semantic query language for querying and manipulating data stored in Resource Description Framework (RDF) format. + SPARQL Protocol and RDF Query Language + + + SPARQL + + + + + - + beta12orEarlier Function A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs). @@ -32187,7 +32673,7 @@ experiments employing a combination of technologies. http://www.onto-med.de/ontologies/gfo.owl#Function http://www.onto-med.de/ontologies/gfo.owl#Perpetuant http://www.onto-med.de/ontologies/gfo.owl#Process - + @@ -32276,7 +32762,6 @@ experiments employing a combination of technologies. 1.6 Analyse an index of biological data. - Database index analysis Data index analysis true @@ -32442,7 +32927,6 @@ experiments employing a combination of technologies. Motif detection Motif recognition Motif search - Protein secondary database search Sequence motif detection Sequence motif search Sequence profile search @@ -33042,7 +33526,6 @@ experiments employing a combination of technologies. beta13 Retrieve information on restriction enzymes or restriction enzyme sites. - Restriction enzyme information retrieval Data retrieval (restriction enzyme annotation) true @@ -33081,7 +33564,7 @@ experiments employing a combination of technologies. Mapping involves ordering genetic loci along a chromosome and estimating the physical distance between loci. A genetic map shows the relative (not physical) position of known genes and genetic markers. - This includes mapping of the genetic architecture of dynamic complex traits (functional mapping), e.g. by characterization of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs). + This includes mapping of the genetic architecture of dynamic complex traits (functional mapping), e.g. by characterisation of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs). Genetic mapping @@ -33226,9 +33709,9 @@ experiments employing a combination of technologies. beta12orEarlier Align (identify equivalent sites within) molecular sequences. - Sequence alignment computation Sequence alignment construction Sequence alignment generation + Consensus-based sequence alignment Sequence alignment @@ -33244,8 +33727,6 @@ experiments employing a combination of technologies. beta13 Align two or more molecular sequences of different types (for example genomic DNA to EST, cDNA or mRNA). - Hybrid sequence alignment - Hybrid sequence alignment generation Hybrid sequence alignment construction true @@ -33277,10 +33758,6 @@ experiments employing a combination of technologies. beta12orEarlier Align (superimpose) molecular tertiary structures. - Multiple structure alignment construction - Multiple structure alignment generation - Structure alignment construction - Structure alignment generation Structure alignment @@ -33325,13 +33802,12 @@ experiments employing a combination of technologies. beta12orEarlier Align sequence profiles (representing sequence alignments). + Profile-to-profile alignment Sequence profile alignment - Sequence profile alignment construction - Sequence profile alignment generation - See also 'Sequence alignment comparison'. - Profile-to-profile alignment + Methods might perform one-to-one, one-to-many or many-to-many comparisons. See also 'Sequence alignment comparison'. + Profile-profile alignment @@ -33343,14 +33819,10 @@ experiments employing a combination of technologies. beta12orEarlier Align structural (3D) profiles or templates (representing structures or structure alignments). 3D profile alignment - 3D profile alignment (multiple) - Multiple 3D profile alignment construction Structural profile alignment - Structural profile alignment construction - Structural profile alignment construction (multiple) - Structural profile alignment generation + Methods might perform one-to-one, one-to-many or many-to-many comparisons. 3D profile-to-3D profile alignment @@ -33363,8 +33835,6 @@ experiments employing a combination of technologies. beta12orEarlier Align molecular sequence(s) to sequence profile(s). Sequence-profile alignment - Sequence-profile alignment construction - Sequence-profile alignment generation A sequence profile typically represents a sequence alignment. Methods might perform one-to-one, one-to-many or many-to-many comparisons. @@ -33381,8 +33851,6 @@ experiments employing a combination of technologies. beta12orEarlier Align molecular sequence(s) to structural (3D) profile(s) or template(s) (representing a structure or structure alignment). Sequence-3D profile alignment - Sequence-3D profile alignment construction - Sequence-3D profile alignment generation Methods might perform one-to-one, one-to-many or many-to-many comparisons. @@ -33447,7 +33915,7 @@ experiments employing a combination of technologies. beta12orEarlier - Query the biomedical and informatics literature. + Query scientific literature, in search for articles, article data, concepts, named entities, or for statistics. Literature search @@ -33458,13 +33926,20 @@ experiments employing a combination of technologies. + beta12orEarlier - Process and analyse text (typically the biomedical and informatics literature) to extract information from it. + Text analysis + Process and analyse text (typically scientific literature) to extract information from it. + Literature mining + Text analytics Text data mining + Article analysis + Literature analysis Text mining + @@ -33536,14 +34011,14 @@ experiments employing a combination of technologies. - - + beta12orEarlier + 1.16 Standardize or normalize microarray data. - - - This includes statistical analysis, for example of variability amongst microarrays experiments, comparison of heterogeneous microarray platforms etc. - Microarray data standardization and normalization + + + Microarray data standardisation and normalisation + true @@ -33569,7 +34044,7 @@ experiments employing a combination of technologies. beta12orEarlier - Perform cluster analysis of gene expression (microarray) data, for example clustering of similar gene expression profiles. + Perform cluster analysis of gene expression data to identify groups with similar gene-expression profiles, for example by clustering. Gene expression profile clustering @@ -33583,17 +34058,23 @@ experiments employing a combination of technologies. beta12orEarlier - The measurement of the expression of multiple genes in a cell, tissue, sample etc., in order to get an impression of biological function. - Expression profiling - Functional profiling + Gene expression quantification + The measurement of the gene expression of multiple genes in a cell, tissue, sample etc., in order to get an impression of biological function. Gene expression profile construction Gene expression profile generation + Gene transcription profiling Metagenomic inference + Non-coding RNA profiling + RNA profiling + mRNA profiling + Functional profiling + Protein profiling - Gene expression profiling generates some sort of gene expression profile or pattern, for example from microarray data. + Gene expression profiling generates some sort of gene expression profile, for example from microarray data. Metagenomic inference is the profiling of phylogenetic marker genes in order to predict metagenome function. Gene expression profiling + https://en.wikipedia.org/wiki/Gene_expression_profiling @@ -33604,7 +34085,7 @@ experiments employing a combination of technologies. beta12orEarlier - Compare gene expression profiles or patterns. + Comparison of gene expression profiles. Gene expression profile comparison @@ -33934,7 +34415,6 @@ experiments employing a combination of technologies. beta12orEarlier Visualise, plot or render (graphically) biomolecular data such as molecular sequences or structures. Rendering - Visualization Visualisation @@ -34065,7 +34545,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - + + beta12orEarlier Search a sequence database and retrieve sequences that are similar to a query sequence. @@ -34129,7 +34610,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern 1.6 Search a sequence database and retrieve sequences that are similar to a query sequence using a word-based method. - Sequence similarity search (word-based methods) Word-based methods (for example BLAST, gapped BLAST, MEGABLAST, WU-BLAST etc.) are usually quicker than alignment-based methods. They may or may not handle gaps. Sequence database search (by sequence using word-based methods) @@ -34146,7 +34626,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern 1.6 Search a sequence database and retrieve sequences that are similar to a query sequence using a sequence profile-based method, or with a supplied profile as query. - Sequence similarity search (profile-based methods) This includes tools based on PSI-BLAST. Sequence database search (by sequence using profile-based methods) @@ -34163,7 +34642,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern 1.6 Search a sequence database for sequences that are similar to a query sequence using a local alignment-based method. - Sequence similarity search (local alignment-based methods) This includes tools based on the Smith-Waterman algorithm or FASTA. Sequence database search (by sequence using local alignment-based methods) @@ -34180,7 +34658,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern 1.6 Search sequence(s) or a sequence database for sequences that are similar to a query sequence using a global alignment-based method. - Sequence similarity search (global alignment-based methods) This includes tools based on the Needleman and Wunsch algorithm. Sequence database search (by sequence using global alignment-based methods) @@ -34197,7 +34674,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern 1.6 Search a DNA database (for example a database of conserved sequence tags) for matches to Sequence-Tagged Site (STS) primer sequences. - Sequence similarity search (primer sequences) STSs are genetic markers that are easily detected by the polymerase chain reaction (PCR) using specific primers. Sequence database search (by sequence for primer sequences) @@ -34383,10 +34859,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta12orEarlier - Mutate a molecular sequence a specified amount or shuffle it to produce a randomized sequence with the same overall composition. + Mutate a molecular sequence a specified amount or shuffle it to produce a randomised sequence with the same overall composition. - Sequence mutation and randomization + Sequence mutation and randomisation @@ -34507,7 +34983,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta12orEarlier - Analyse repeat sequence organization such as periodicity. + Analyse repeat sequence organisation such as periodicity. Repeat sequence organisation analysis @@ -34918,7 +35394,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta12orEarlier - Detect or predict signal peptides (and typically predict subcellular localization) of eukaryotic proteins. + Detect or predict signal peptides (and typically predict subcellular localisation) of eukaryotic proteins. Protein signal peptide detection (eukaryotes) @@ -34931,7 +35407,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta12orEarlier - Detect or predict signal peptides (and typically predict subcellular localization) of bacterial proteins. + Detect or predict signal peptides (and typically predict subcellular localisation) of bacterial proteins. Protein signal peptide detection (bacteria) @@ -34963,7 +35439,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern 1.6 Predict, recognise and identify positional features in protein sequences such as functional sites or regions and secondary structure. - Sequence feature detection (protein) Methods typically involve scanning for known motifs, patterns and regular expressions. Protein feature prediction (from sequence) @@ -35068,7 +35543,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta12orEarlier - Predict protein sites that are key to protein folding, such as possible sites of nucleation or stabilization. + Predict protein sites that are key to protein folding, such as possible sites of nucleation or stabilisation. Protein folding site prediction @@ -35825,7 +36300,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Protein structure comparative modelling - The model might be of a whole, part or aspect of protein structure. Molecular modelling methods might use sequence-structure alignment, structural templates, molecular dynamics, energy minimization etc. + The model might be of a whole, part or aspect of protein structure. Molecular modelling methods might use sequence-structure alignment, structural templates, molecular dynamics, energy minimisation etc. Protein modelling @@ -35959,7 +36434,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Map the genetic architecture of dynamic complex traits. - This can involve characterization of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs). + This can involve characterisation of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs). Functional mapping true @@ -35978,7 +36453,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Haplotype reconstruction - Haplotype inference can help in population genetic studies and the identification of complex disease genes, , and is typically based on aligned single nucleotide polymorphism (SNP) fragments. Haplotype comparison is a useful way to characterize the genetic variation between individuals. An individual's haplotype describes which nucleotide base occurs at each position for a set of common SNPs. Tools might use combinatorial functions (for example parsimony) or a likelihood function or model with optimization such as minimum error correction (MEC) model, expectation-maximization algorithm (EM), genetic algorithm or Markov chain Monte Carlo (MCMC). + Haplotype inference can help in population genetic studies and the identification of complex disease genes, , and is typically based on aligned single nucleotide polymorphism (SNP) fragments. Haplotype comparison is a useful way to characterize the genetic variation between individuals. An individual's haplotype describes which nucleotide base occurs at each position for a set of common SNPs. Tools might use combinatorial functions (for example parsimony) or a likelihood function or model with optimisation such as minimum error correction (MEC) model, expectation-maximisation algorithm (EM), genetic algorithm or Markov chain Monte Carlo (MCMC). Haplotype mapping @@ -36030,11 +36505,10 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - + beta12orEarlier Align exactly two molecular sequences. - Pairwise sequence alignment construction - Pairwise sequence alignment generation + Pairwise alignment Methods might perform one-to-one, one-to-many or many-to-many comparisons. @@ -36048,9 +36522,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta12orEarlier - Align two or more molecular sequences. - Multiple sequence alignment construction - Multiple sequence alignment generation + Align more than two molecular sequences. + Multiple alignment This includes methods that use an existing alignment, for example to incorporate sequences into an alignment, or combine several multiple alignments into a single, improved alignment. @@ -36068,9 +36541,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Locally align exactly two molecular sequences. - Local pairwise sequence alignment construction - Pairwise sequence alignment (local) - Pairwise sequence alignment construction (local) Local alignment methods identify regions of local similarity. Pairwise sequence alignment generation (local) @@ -36088,9 +36558,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Globally align exactly two molecular sequences. - Global pairwise sequence alignment construction - Pairwise sequence alignment (global) - Pairwise sequence alignment construction (global) Global alignment methods identify similarity across the entire length of the sequences. Pairwise sequence alignment generation (global) @@ -36105,16 +36572,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta12orEarlier Locally align two or more molecular sequences. - Local multiple sequence alignment construction - Multiple sequence alignment (local) - Multiple sequence alignment construction (local) + Local sequence alignment Sequence alignment (local) - Sequence alignment generation (local) Smith-Waterman Local alignment methods identify regions of local similarity. - Local sequence alignment + Local alignment @@ -36125,15 +36589,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta12orEarlier Globally align two or more molecular sequences. - Global multiple sequence alignment construction - Multiple sequence alignment (global) - Multiple sequence alignment construction (global) + Global sequence alignment Sequence alignment (global) - Sequence alignment generation (global) Global alignment methods identify similarity across the entire length of the sequences. - Global sequence alignment + Global alignment @@ -36144,11 +36605,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta12orEarlier Align two or more molecular sequences with user-defined constraints. - Constrained multiple sequence alignment construction Multiple sequence alignment (constrained) - Multiple sequence alignment construction (constrained) Sequence alignment (constrained) - Sequence alignment generation (constrained) Constrained sequence alignment @@ -36159,17 +36617,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - + beta12orEarlier + 1.16 Align two or more molecular sequences using multiple methods to achieve higher quality. - Consensus multiple sequence alignment construction - Multiple sequence alignment (consensus) - Multiple sequence alignment construction (consensus) - Sequence alignment (consensus) - Sequence alignment generation (consensus) - - + + Consensus-based sequence alignment + true @@ -36201,8 +36656,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern 1.6 Align molecular secondary structure (represented as a 1D string). - Secondary structure alignment - Secondary structure alignment construction Secondary structure alignment generation true @@ -36250,8 +36703,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta12orEarlier Align (superimpose) exactly two molecular tertiary structures. - Pairwise structure alignment construction - Pairwise structure alignment generation + Structure alignment (pairwise) Pairwise structure alignment @@ -36262,16 +36714,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - + beta12orEarlier - 1.6 - - Align (superimpose) two or more molecular tertiary structures. - Multiple structure alignment - + Align (superimpose) more than two molecular tertiary structures. + Structure alignment (multiple) + + This includes methods that use an existing alignment. - Multiple structure alignment construction - true + Multiple structure alignment @@ -36315,9 +36765,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Locally align (superimpose) exactly two molecular tertiary structures. - Local pairwise structure alignment construction - Pairwise structure alignment (local) - Pairwise structure alignment construction (local) Local alignment methods identify regions of local similarity, common substructures etc. Pairwise structure alignment generation (local) @@ -36335,9 +36782,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Globally align (superimpose) exactly two molecular tertiary structures. - Global pairwise structure alignment construction - Pairwise structure alignment (global) - Pairwise structure alignment construction (global) Global alignment methods identify similarity across the entire structures. Pairwise structure alignment generation (global) @@ -36352,11 +36796,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta12orEarlier Locally align (superimpose) two or more molecular tertiary structures. - Local multiple structure alignment construction - Multiple structure alignment (local) - Multiple structure alignment construction (local) - Structure alignment construction (local) - Structure alignment generation (local) + Structure alignment (local) Local alignment methods identify regions of local similarity, common substructures etc. @@ -36371,11 +36811,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta12orEarlier Globally align (superimpose) two or more molecular tertiary structures. - Global multiple structure alignment construction - Multiple structure alignment (global) - Multiple structure alignment construction (global) - Structure alignment construction (global) - Structure alignment generation (global) + Structure alignment (global) Global alignment methods identify similarity across the entire structures. @@ -36387,18 +36823,15 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - + beta12orEarlier + 1.16 Align exactly two molecular profiles. - Pairwise sequence profile alignment construction - Sequence alignment generation (pairwise profile) - Sequence profile alignment (pairwise) - Sequence profile alignment construction (pairwise) - Sequence profile alignment generation (pairwise) - - + + Methods might perform one-to-one, one-to-many or many-to-many comparisons. - Profile-to-profile alignment (pairwise) + Profile-profile alignment (pairwise) + true @@ -36411,10 +36844,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern 1.6 Align two or more molecular profiles. - Multiple sequence profile alignment construction - Sequence profile alignment (multiple) - Sequence profile alignment construction (multiple) - Sequence profile alignment generation (multiple) Sequence alignment generation (multiple profile) true @@ -36425,17 +36854,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - + beta12orEarlier + 1.16 Align exactly two molecular Structural (3D) profiles. - Pairwise structural (3D) profile alignment construction - Structural (3D) profile alignment (pairwise) - Structural profile alignment construction (pairwise) - Structural profile alignment generation (pairwise) - - - Methods might perform one-to-one, one-to-many or many-to-many comparisons. + + 3D profile-to-3D profile alignment (pairwise) + true @@ -36448,9 +36874,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern 1.6 Align two or more molecular 3D profiles. - Multiple structural (3D) profile alignment construction - Structural (3D) profile alignment (multiple) - Structural profile alignment construction (multiple) Structural profile alignment generation (multiple) true @@ -36466,8 +36889,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern 1.6 Search and retrieve names of or documentation on bioinformatics tools, for example by keyword or which perform a particular function. - Data retrieval (tool annotation) - Tool information retrieval Data retrieval (tool metadata) true @@ -36483,8 +36904,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern 1.6 Search and retrieve names of or documentation on bioinformatics databases or query terms, for example by keyword. - Data retrieval (database annotation) - Database information retrieval Data retrieval (database metadata) true @@ -36647,12 +37066,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta12orEarlier - Make gene to tag assignments (tag mapping) of SAGE, MPSS and SBS data, by annotating tags with ontology concepts. + Make sequence tag to gene assignments (tag mapping) of SAGE, MPSS and SBS data. Tag to gene assignment - Tag mapping might assign experimentally obtained tags to known transcripts or annotate potential virtual tags in a genome. - Tag mapping + Sequence tag mapping assigns experimentally obtained sequence tags to known transcripts or annotate potential virtual sequence tags in a genome. + Sequence tag mapping @@ -36665,7 +37084,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta12orEarlier Process (read and / or write) serial analysis of gene expression (SAGE) data. - Serial analysis of gene expression data processing SAGE data processing true @@ -36681,7 +37099,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta12orEarlier Process (read and / or write) massively parallel signature sequencing (MPSS) data. - Massively parallel signature sequencing data processing MPSS data processing true @@ -36697,7 +37114,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta12orEarlier Process (read and / or write) sequencing by synthesis (SBS) data. - Sequencing by synthesis data processing SBS data processing true @@ -36711,7 +37127,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta12orEarlier - Generate a heat map of gene expression from microarray data. + Generate a heat map of gene expression from e.g. microarray data. Heat map construction @@ -37114,7 +37530,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta12orEarlier 1.12 Predict and optimise peptide ligands that elicit an immunological response. - Peptide immunogen prediction Immunogenicity prediction @@ -37498,7 +37913,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta12orEarlier - Analyse a known network of gene regulation. @@ -37530,7 +37944,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern 1.6 Query a sequence data resource (typically a database) and retrieve sequences and / or annotation. - Data retrieval (sequences) This includes direct retrieval methods (e.g. the dbfetch program) but not those that perform calculations on the sequence. Sequence retrieval @@ -38022,7 +38435,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta12orEarlier beta12orEarlier - WHATIF: ResidueDSSP Determine for residue the DSSP determined secondary structure in three-state (HSC). DSSP secondary structure assignment @@ -38184,7 +38596,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta13 Search and retrieve documentation on a bioinformatics ontology. - Ontology information retrieval Data retrieval (ontology annotation) true @@ -38200,7 +38611,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta13 Query an ontology and retrieve concepts or relations. - Ontology retrieval Data retrieval (ontology concept) true @@ -38260,7 +38670,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Perform a statistical data operation of some type, e.g. calibration or validation. Statistical analysis Statistical testing - Statistics Gibbs sampling @@ -38307,7 +38716,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta12orEarlier beta13 - An operation performing purely illustrative (pedagogical) purposes. Demonstration @@ -38489,7 +38897,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern 1.6 Process (read and / or write) one or more structural (3D) profile(s) or template(s) of some type. - 3D profile processing Structural profile processing true @@ -38505,7 +38912,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern 1.6 Process (read and / or write) an index of (typically a file of) biological data. - Database index processing Data index processing true @@ -38724,7 +39130,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta12orEarlier Validate some data. - Validation and standardisation Quality control @@ -38821,14 +39226,20 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern + + 1.8 beta12orEarlier - Analyse a set of genes (genes corresponding to an expression profile, or any other set) to find functional annotations (such as cellular processes or metaobolic pathways) that the sets are significantly associated with, providing biological insight into the a set of genes. - GO term enrichment + Analysis of a set of genes, corresponding e.g. to a gene expression profile, annotated with Gene Ontology (GO) concepts, where eventual over-/under-representation of certain GO concept within the studied set of genes is revealed. + Gene-set over-represenation analysis + GO-term enrichment + Gene Ontology concept enrichment + Gene Ontology term enrichment - The Gene Ontology (GO) is invariably used, the input is a set of Gene IDs and the output of the analysis is typically a ranked list of GO terms, each associated with a p-value. - Functional enrichment + The Gene Ontology (GO) is typically used, the input is a set of Gene IDs, and the output of the analysis is typically a ranked list of GO concepts, each associated with a p-value. + Gene-set enrichment analysis + @@ -38969,7 +39380,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern 1.6 Process (read and / or write) one or more molecular sequences and associated annotation. - Sequence processing (general) Sequence processing true @@ -39073,14 +39483,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + beta12orEarlier + 1.16 Classify G-protein coupled receptors (GPCRs) into families and subfamilies. - G protein-coupled receptor (GPCR) classification - - + + GPCR classification + true @@ -39228,7 +39638,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta13 Retrieve information on a protein. - Protein information retrieval Data retrieval (protein annotation) true @@ -39274,7 +39683,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta13 Retrieve information on a protein family. - Protein family information retrieval Data retrieval (protein family annotation) true @@ -39290,7 +39698,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta13 Retrieve information on an RNA family. - RNA family information retrieval Data retrieval (RNA family annotation) true @@ -39306,7 +39713,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta13 Retrieve information on a specific gene. - Gene information retrieval Data retrieval (gene annotation) true @@ -39322,7 +39728,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta13 Retrieve information on a specific genotype or phenotype. - Genotype and phenotype information retrieval Data retrieval (genotype and phenotype annotation) true @@ -39528,12 +39933,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta12orEarlier - Predict the subcellular localization of a protein sequence. + Predict the subcellular localisation of a protein sequence. Protein targeting prediction - The prediction might include subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or export (extracellular proteins) of a protein. - Protein subcellular localization prediction + The prediction might include subcellular localisation (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or export (extracellular proteins) of a protein. + Protein subcellular localisation prediction @@ -39602,15 +40007,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta12orEarlier - Gene expression profile analysis Process (read and / or write) gene expression (typically microarray) data, including analysis of one or more gene expression profiles, typically to interpret them in functional terms. - Gene expression (microarray) data processing - Gene expression analysis - Gene expression data processing - Microarray data processing + Gene expression data analysis + Microarray data analysis + RNA-seq analysis - Gene expression data analysis + Gene expression analysis @@ -39756,6 +40159,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta12orEarlier 1.6 + Process (read and / or write) text. Text processing @@ -39983,7 +40387,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern 1.6 Process (read and / or write) a DNA map of some type. - DNA map data processing Map data processing true @@ -40298,12 +40701,15 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - + beta12orEarlier + 1.16 + + Analyse a body of scientific text (typically a full text article from a scientific journal.) - - + Article analysis + true @@ -40678,7 +41084,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern 1.6 Screen a molecular sequence(s) against a database (of some type) to identify similarities between the sequence and database entries. - Sequence screening Database search (by sequence) true @@ -40766,7 +41171,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Reconstruction of a sequence assembly in a localised area. - Localized reassembly + Localised reassembly @@ -41005,6 +41410,21 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp + + + + + 1.1 + Analyse DNA sequences in order to identify a DNA 'barcode'; marker genes or any short fragment(s) of DNA that are useful to diagnose the taxa of biological organisms. + Sample barcoding + DNA barcoding + + + Community profiling + + + + @@ -41114,7 +41534,6 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Genome browsing Genome rendering Genome viewing - Genome visualization Genome visualisation @@ -41177,7 +41596,6 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp 1.1 1.12 Generate an index of a genome sequence using a suffix arrays algorithm. - Suffix arrays A suffix array consists of the lexicographically sorted list of suffixes of a genome. @@ -41362,8 +41780,8 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Identify biologically interesting variants by prioritizing individual variants, for example, homozygous variants absent in control genomes. - Variant prioritization can be used for example to produce a list of variants responsible for 'knocking out' genes in specific genomes. Methods amino acid substitution, aggregative approaches, probabilistic approach, inheritance and unified likelihood-frameworks. - Variant prioritization + Variant prioritisation can be used for example to produce a list of variants responsible for 'knocking out' genes in specific genomes. Methods amino acid substitution, aggregative approaches, probabilistic approach, inheritance and unified likelihood-frameworks. + Variant prioritisation @@ -41396,7 +41814,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Detect large regions in a genome subject to copy-number variation, or other structural variations in genome(s). - Methods might involve analysis of whole-genome array comparative genome hybridization or single-nucleotide polymorphism arrays, paired-end mapping of sequencing data, or from analysis of short reads from new sequencing technologies. + Methods might involve analysis of whole-genome array comparative genome hybridisation or single-nucleotide polymorphism arrays, paired-end mapping of sequencing data, or from analysis of short reads from new sequencing technologies. Structural variation discovery @@ -41436,9 +41854,9 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp 1.1 Combine classical quantitative trait loci (QTL) analysis with gene expression profiling, for example, to describe describe cis- and trans-controlling elements for the expression of phenotype associated genes. + Gene expression QTL profiling + Gene expression quantitative trait loci profiling eQTL profiling - expression QTL profiling - expression quantitative trait loci profiling Gene expression QTL analysis @@ -41451,7 +41869,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp 1.1 - Estimate the number of copies of loci of particular gene(s) in DNA sequences typically from gene-expression profiling technology based on microarray hybridization-based experiments. For example, estimate copy number (or marker dosage) of a dominant marker in samples from polyploid plant cells or tissues, or chromosomal gains and losses in tumors. + Estimate the number of copies of loci of particular gene(s) in DNA sequences typically from gene-expression profiling technology based on microarray hybridisation-based experiments. For example, estimate copy number (or marker dosage) of a dominant marker in samples from polyploid plant cells or tissues, or chromosomal gains and losses in tumors. Transcript copy number estimation @@ -41555,6 +41973,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Document clustering + @@ -41563,15 +41982,19 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - 1.3 - Recognise named entities (text tokens) within documents. - Entity chunking - Entity extraction - Entity identification + Recognise named entities, ontology concepts, tags, events, and dictionary terms within documents. + Concept mining + Entity chunking + Entity extraction + Entity identification + Event extraction + Named-entity recognition - Named entity recognition + Named-entity and concept recognition + + @@ -41710,8 +42133,8 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp + 1.4 - Recognition of which format the given data is in. Format identification Format inference @@ -41723,8 +42146,8 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - - + + The has_input "Data" (data_0006) may cause visualisation or other problems although ontologically correct. But on the other hand it may be useful to distinguish from nullary operations without inputs. @@ -41837,14 +42260,15 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - + 1.6 - Standardize or normalize data. - Normalization - Standardization + Standardize or normalize data by some statistical method. + Normalisation + Standardisation - Standardization and normalization + In the simplest normalisation means adjusting values measured on different scales to a common scale (often between 0.0 and 1.0), but can refer to more sophisticated adjustment whereby entire probability distributions of adjusted values are brought into alignment. Standardisation typically refers to an operation whereby a range of values are standardised to measure how many standard deviations a value is from its mean. + Standardisation and normalisation @@ -41938,7 +42362,6 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp 1.7 Image processing The analysis of a image (typically a digital image) of some type in order to extract information from it. - Image analysis @@ -42269,14 +42692,16 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - + 1.8 - Analyse a dataset with respect to concepts from an ontology. - Term enrichment + Analysis of a set of objects, such as genes, annotated with given categories, where eventual over-/under-representation of certain categories within the studied set of objects is revealed. + Enrichment + Enrichment analysis + Functional enrichment - A relevant ontology will be used. The input is typically a set of identifiers or other data, and the output of the analysis is typically a ranked list of ontology terms, each associated with a p-value. - Enrichment + Categories from a relevant ontology can be used. The input is typically a set of genes or other biological objects, possibly represented by their identifiers, and the output of the analysis is typically a ranked list of categories, each associated with a statistical metric of over-/under-representation within the studied data. + Over-representation analysis @@ -42342,7 +42767,6 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp 1.9 Visualise images resulting from various types of microscopy. - Microscopy image visualisation Microscope image visualisation @@ -42492,10 +42916,11 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp 1.12 - Identify semantic relationships within a text or between two or more texts using text mining techniques. + Identify semantic relations among entities and concepts within a text, using text mining techniques. + Relationship inference - Relationship inference + Relation inference @@ -42547,10 +42972,10 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp 1.12 Technique for determining the amount of proteins in a sample. - Quantitation + Protein quantitation - Quantification + Protein quantification @@ -43090,8 +43515,8 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp 1.15 + Differential protein analysis The analysis, using proteomics techniques, to identify proteins whose encoding genes are differentially expressed under a given experimental setup. - Differential protein analysis Differential protein expression analysis @@ -43107,7 +43532,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp The analysis, using any of diverse techniques, to identify genes that are differentially expressed under a given experimental setup. - Differential expression analysis + Differential gene expression analysis @@ -43132,7 +43557,7 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp 1.15 The extrapolation of empirical characteristics of individuals or populations, backwards in time, to their common ancestors. Character mapping - Character optimization + Character optimisation Ancestral reconstruction is often used to recover possible ancestral character states of ancient, extinct organisms. @@ -43141,6 +43566,120 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp + + + + + 1.16 + Site localisation of post-translational modifications in peptide or protein mass spectra. + PTM scoring + Site localisation + + + PTM localisation + + + + + + + + + 1.16 + Operations concerning the handling and use of other tools. + + + Service management + + + + + + + + + 1.16 + An operation supporting the browsing or discovery of other tools and services. + + + Service discovery + + + + + + + + + 1.16 + An operation supporting the aggregation of other services (at least two) into a funtional unit, for the automation of some task. + + + Service composition + + + + + + + + + 1.16 + An operation supporting the calling (invocation) of other tools and services. + + + Service invocation + + + + + + + + + 1.16 + A data mining method typically used for studying biological networks based on pairwise correlations between variables. + WGCNA + Weighted gene co-expression network analysis + + + Weighted correlation network analysis + + + + + + + + + + 1.16 + Identification of protein, for example from one or more peptide identifications by tandem mass spectrometry. + Protein inference + + + Protein identification + + + + + + + + + + 1.16 + Text annotation is the operation of adding notes, data and metadata, recognised entities and concepts, and their relations to a text (such as a scientific article). + Article annotation + Literature annotation + + + Text annotation + + + + + @@ -43360,7 +43899,6 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp beta12orEarlier 1.13 - VT 1.3.3 Information retrieval The search and query of data sources (typically databases or ontologies) in order to retrieve entries or other information. @@ -43496,7 +44034,6 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp 1.3 The study of codon usage in nucleotide sequence(s), genetic codes and so on. - Codon usage analysis Genetic codes and codon usage true @@ -43527,8 +44064,6 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp 1.3 Methods that aims to identify, predict, model or analyse genes or gene structure in DNA sequences. - Gene discovery - Gene prediction This includes the study of promoters, coding regions, splice sites, etc. Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc. Gene finding @@ -43611,12 +44146,11 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Metaproteomics Peptide identification Protein and peptide identification - Protein expression Includes metaproteomics: proteomics analysis of an environmental sample. - Proteomics includes any methods (especially high-throughput) that separate, characterize and identify expressed proteins such as mass spectrometry, two-dimensional gel electrophoresis and protein microarrays, as well as in-silico methods that perform proteolytic or mass calculations on a protein sequence and other analyses of protein expression data, for example in different cells or tissues. + Proteomics includes any methods (especially high-throughput) that separate, characterize and identify expressed proteins such as mass spectrometry, two-dimensional gel electrophoresis and protein microarrays, as well as in-silico methods that perform proteolytic or mass calculations on a protein sequence and other analyses of protein production data, for example in different cells or tissues. Proteomics http://purl.bioontology.org/ontology/MSH/D040901 @@ -43761,13 +44295,13 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp beta12orEarlier - The study of how proteins are transported within and without the cell, including signal peptides, protein subcellular localization and export. - Protein localization + The study of how proteins are transported within and without the cell, including signal peptides, protein subcellular localisation and export. + Protein localisation Protein sorting Protein targeting - Protein targeting and localization + Protein targeting and localisation @@ -43826,7 +44360,6 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp 1.3 Protein-protein interactions, individual interactions and networks, protein complexes, protein functional coupling etc. - Protein interaction networks Protein-protein interactions true @@ -43950,6 +44483,8 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp This concept excludes macromolecules such as proteins and nucleic acids. This includes the structures of drugs, drug target, their interactions and binding affinities. Also the structures of reactants or products of metabolism, for example small molecules such as including vitamins, polyols, nucleotides and amino acids. Also the physicochemical, biochemical or structural properties of amino acids or peptides. Also structural and associated data for toxic chemical substances. Small molecules + + @@ -44070,7 +44605,6 @@ long terminal repeats (LTRs); sequences (typically retroviral) directly repeated beta12orEarlier 1.7 The comparison and grouping together of molecular sequences on the basis of their similarities. - Sequence clusters This includes systems that generate, process and analyse sequence clusters. @@ -44108,7 +44642,6 @@ long terminal repeats (LTRs); sequences (typically retroviral) directly repeated 1.3 The processing, analysis or use of some type of structural (3D) profile or template; a computational entity (typically a numerical matrix) that is derived from and represents a structure or structure alignment. - Structural profiles Structural (3D) profiles true @@ -44294,7 +44827,6 @@ long terminal repeats (LTRs); sequences (typically retroviral) directly repeated beta12orEarlier 1.3 The alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment). - Sequence-structure alignment Threading @@ -44359,8 +44891,6 @@ long terminal repeats (LTRs); sequences (typically retroviral) directly repeated beta13 Simulated polymerase chain reaction (PCR). - PCR - Polymerase chain reaction Virtual PCR true @@ -44378,7 +44908,7 @@ long terminal repeats (LTRs); sequences (typically retroviral) directly repeated Assembly - Assembly has two broad types, de-novo and re-sequencing. Re-sequencing is a specialized case of assembly, where an assembled (typically de-novo assembled) reference genome is available and is about 95% identical to the re-sequenced genome. All other cases of assembly are 'de-novo'. + Assembly has two broad types, de-novo and re-sequencing. Re-sequencing is a specialised case of assembly, where an assembled (typically de-novo assembled) reference genome is available and is about 95% identical to the re-sequenced genome. All other cases of assembly are 'de-novo'. Sequence assembly @@ -44411,7 +44941,6 @@ long terminal repeats (LTRs); sequences (typically retroviral) directly repeated 1.3 Microarrays, for example, to process microarray data or design probes and experiments. - DNA microarrays Microarrays http://purl.bioontology.org/ontology/MSH/D046228 @@ -44448,7 +44977,6 @@ long terminal repeats (LTRs); sequences (typically retroviral) directly repeated The analysis of levels and patterns of synthesis of gene products (proteins and functional RNA) including interpretation in functional terms of gene expression data. Codon usage DNA microarrays - Expression profiling Gene expression profiling Transcription @@ -44457,6 +44985,7 @@ long terminal repeats (LTRs); sequences (typically retroviral) directly repeated Gene expression levels are analysed by identifying, quantifying or comparing mRNA transcripts, for example using microarrays, RNA-seq, northern blots, gene-indexed expression profiles etc. This includes the study of codon usage in nucleotide sequence(s), genetic codes and so on. Gene expression + http://purl.bioontology.org/ontology/MSH/D015870 @@ -44578,9 +45107,9 @@ long terminal repeats (LTRs); sequences (typically retroviral) directly repeated beta12orEarlier 1.3 - The processing and analysis of the bioinformatics literature and bibliographic data, such as literature search and query. + Literature analysis true @@ -44591,15 +45120,22 @@ long terminal repeats (LTRs); sequences (typically retroviral) directly repeated + beta12orEarlier - Literature analysis - The analysis of the biomedical and informatics literature. - Literature mining + The processing and analysis of natural language, such as scientific literature in English, in order to extract data and information, or to enable human-computer interaction. + NLP + BioNLP + Literature mining + Text analytics Text data mining + Text mining - Text mining + Natural language processing + + + @@ -44625,7 +45161,6 @@ long terminal repeats (LTRs); sequences (typically retroviral) directly repeated beta12orEarlier 1.13 - VT 1.3.6 Multimedia, hypermedia The management and manipulation of digital documents, including database records, files and reports. @@ -44815,9 +45350,9 @@ long terminal repeats (LTRs); sequences (typically retroviral) directly repeated beta12orEarlier 1.3 - Data resources for the biological or biomedical literature, either a primary source of literature or some derivative. + Literature data resources true @@ -44849,8 +45384,6 @@ long terminal repeats (LTRs); sequences (typically retroviral) directly repeated 1.3 General cell culture or data on a specific cell lines. - Cell culture - Tissue culture Cell and tissue culture true @@ -44940,17 +45473,6 @@ long terminal repeats (LTRs); sequences (typically retroviral) directly repeated 1.3 A specific organelle, or organelles in general, typically the genes and proteins (or genome and proteome). - Cell membrane - Centriole - Cytoplasm - Golgi apparatus - Lysosome - Mitochondria - Nucleus - Organelle genes and proteins - Ribosome - Rough endoplasmic reticulum - Smooth endoplasmic reticulum Organelles true @@ -44966,7 +45488,6 @@ long terminal repeats (LTRs); sequences (typically retroviral) directly repeated 1.3 Ribosomes, typically of ribosome-related genes and proteins. - Ribosome genes and proteins Ribosomes true @@ -45115,7 +45636,7 @@ long terminal repeats (LTRs); sequences (typically retroviral) directly repeated beta12orEarlier true - Molecular probes (e.g. a peptide probe or DNA microarray probe) or PCR primers and hybridization oligos in a nucleic acid sequence. + Molecular probes (e.g. a peptide probe or DNA microarray probe) or PCR primers and hybridisation oligos in a nucleic acid sequence. Primers Probes @@ -45762,8 +46283,6 @@ positional features such as functional sites in nucleotide sequences.1.3 Informatics resources that aim to identify, map or analyse genetic markers in DNA sequences, for example to produce a genetic (linkage) map of a chromosome or genome or to analyse genetic linkage and synteny. - Genetic linkage - Linkage mapping Genetic mapping and linkage true @@ -45873,7 +46392,7 @@ positional features such as functional sites in nucleotide sequences. beta12orEarlier 1.13 - PCR primers and hybridization oligos in a nucleic acid sequence. + PCR primers and hybridisation oligos in a nucleic acid sequence. Primers @@ -46081,7 +46600,6 @@ positional features such as functional sites in nucleotide sequences.1.3 Protein data resources. - Protein data resources Protein databases true @@ -46190,14 +46708,13 @@ positional features such as functional sites in nucleotide sequences.true The holistic modelling and analysis of complex biological systems and the interactions therein. Biological modelling - Biological models Biological system modelling This includes databases of models and methods to construct or analyse a model. Systems biology - http://en.wikipedia.org/wiki/Systems_biology + http://purl.bioontology.org/ontology/MSH/D049490 @@ -46245,8 +46762,6 @@ positional features such as functional sites in nucleotide sequences.beta12orEarlier true The construction, analysis, evaluation, refinement etc. of models of a molecules properties or behaviour, including the modelling the structure of proteins in complex with small molecules or other macromolecules (docking). - Molecular modeling - Comparative modeling Comparative modelling Homology modeling Homology modelling @@ -46419,9 +46934,9 @@ positional features such as functional sites in nucleotide sequences. beta12orEarlier beta12orEarlier - A topic concerning primarily bioinformatics software tools, typically the broad function or purpose of a tool. + Tool topic true @@ -46434,9 +46949,9 @@ positional features such as functional sites in nucleotide sequences. beta12orEarlier beta12orEarlier - A general area of bioinformatics study, typically the broad scope or category of content of a bioinformatics journal or conference proceeding. + Study topic true @@ -46512,8 +47027,6 @@ positional features such as functional sites in nucleotide sequences.1.3 Informatics resource (typically a database) primarily focussed on genes. - Gene database - Gene resource Gene resources true @@ -46704,7 +47217,7 @@ positional features such as functional sites in nucleotide sequences.beta12orEarlier beta13 - Parallelized sequencing processes that are capable of sequencing many thousands of sequences simultaneously. + Parallelised sequencing processes that are capable of sequencing many thousands of sequences simultaneously. Next-generation sequencing High-throughput sequencing @@ -46720,7 +47233,6 @@ positional features such as functional sites in nucleotide sequences.beta12orEarlier 1.7 The comparison and grouping together of molecular structures on the basis of similarity; generate, process or analyse structural clusters. - Structure classification Structural clustering @@ -46869,7 +47381,6 @@ positional features such as functional sites in nucleotide sequences.1.2 Molecular secondary or tertiary (3D) structural data resources, typically of proteins and nucleic acids. - Structure data resources Structure databases true @@ -46900,9 +47411,6 @@ positional features such as functional sites in nucleotide sequences.1.3 Molecular sequence data resources, including sequence sites, alignments, motifs and profiles. - Sequence data - Sequence data resource - Sequence data resources Sequence databases true @@ -46918,7 +47426,6 @@ positional features such as functional sites in nucleotide sequences.1.3 Nucleotide sequences and associated concepts such as sequence sites, alignments, motifs and profiles. - Nucleotide sequences Nucleic acid sequences true @@ -47010,8 +47517,6 @@ positional features such as functional sites in nucleotide sequences.1.3 The comparison, grouping together and classification of macromolecules on the basis of sequence similarity. - Sequence clusters - Sequence families This includes the results of sequence clustering, ortholog identification, assignment to families, annotation etc. Sequence clusters and classification @@ -47186,15 +47691,17 @@ positional features such as functional sites in nucleotide sequences. beta13 true - The scientific literature, reference information and documentation. + The scientific literature, language processing, reference information, and documentation. Bibliography + Citations Documentation - Literature sources + References + Scientific literature This includes the documentation of resources such as tools, services and databases, user support, how to get help etc. - Literature and reference + Literature and language http://purl.bioontology.org/ontology/MSH/D011642 @@ -47330,8 +47837,6 @@ positional features such as functional sites in nucleotide sequences.1.3 Specific genes and/or their encoded proteins or a family or other grouping of related genes and proteins. - Gene and protein families - Gene family Genes and proteins resources true @@ -47401,7 +47906,7 @@ positional features such as functional sites in nucleotide sequences. This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes), restriction enzyme recognition sites (restriction sites) etc. - This includes sites involved with DNA replication and recombination. This includes binding sites for initiation of replication (origin of replication), regions where transfer is initiated during the conjugation or mobilization (origin of transfer), starting sites for DNA duplication (origin of replication) and regions which are eliminated through any of kind of recombination. Also nucleosome exclusion regions, i.e. specific patterns or regions which exclude nucleosomes (the basic structural units of eukaryotic chromatin which play a significant role in regulating gene expression). + This includes sites involved with DNA replication and recombination. This includes binding sites for initiation of replication (origin of replication), regions where transfer is initiated during the conjugation or mobilisation (origin of transfer), starting sites for DNA duplication (origin of replication) and regions which are eliminated through any of kind of recombination. Also nucleosome exclusion regions, i.e. specific patterns or regions which exclude nucleosomes (the basic structural units of eukaryotic chromatin which play a significant role in regulating gene expression). DNA binding sites @@ -47487,7 +47992,7 @@ positional features such as functional sites in nucleotide sequences. - Amplicon sequencing is the ultra-deep sequencing of PCR products (amplicons), usually for the purpose of efficient genetic variant identification and characterization in specific genomic regions. + Amplicon sequencing is the ultra-deep sequencing of PCR products (amplicons), usually for the purpose of efficient genetic variant identification and characterisation in specific genomic regions. Sequencing http://purl.bioontology.org/ontology/MSH/D059014 @@ -47539,7 +48044,6 @@ positional features such as functional sites in nucleotide sequences. DNA methylation - http://purl.bioontology.org/ontology/MSH/D019175 true @@ -47556,6 +48060,7 @@ positional features such as functional sites in nucleotide sequences. Metabolomics + http://purl.bioontology.org/ontology/MSH/D055432 @@ -47589,7 +48094,10 @@ positional features such as functional sites in nucleotide sequences.Community genomics Ecogenomics Environmental genomics + Environmental omics The study of genetic material recovered from environmental samples, and associated environmental data. + Biome sequencing + Environmental sequencing Shotgun metagenomics @@ -47639,7 +48147,6 @@ positional features such as functional sites in nucleotide sequences.1.3 A topic concerning high-throughput sequencing of randomly fragmented genomic DNA, for example, to investigate whole-genome sequencing and resequencing, SNP discovery, identification of copy number variations and chromosomal rearrangements. - DNA-seq DNA-Seq true @@ -47655,7 +48162,6 @@ positional features such as functional sites in nucleotide sequences.1.3 The alignment of sequences of (typically millions) of short reads to a reference genome. This is a specialised topic within sequence alignment, especially because of complications arising from RNA splicing. - RNA-seq alignment RNA-Seq alignment true @@ -47683,7 +48189,7 @@ positional features such as functional sites in nucleotide sequences. 1.3 - The protection of data, such as patient health data, from damage or unwanted access from unauthorized users. + The protection of data, such as patient health data, from damage or unwanted access from unauthorised users. Data privacy @@ -47749,14 +48255,13 @@ positional features such as functional sites in nucleotide sequences. 1.3 true - Bisulfite sequencing + Topic concerning the study of heritable changes, for example in gene expression or phenotype, caused by mechanisms other than changes in the DNA sequence. DNA methylation Histone modification - Topic concerning the study of heritable changes, for example in gene expression or phenotype, caused by mechanisms other than changes in the DNA sequence. - This includes sub-topics such as histone modification and DNA methylation. DNA methylation includes bisulfite sequencing, methylation sites and analysis, for example of patterns and profiles of DNA methylation in a population, tissue etc. + This includes sub-topics such as histone modification and DNA methylation (methylation sites and analysis, for example of patterns and profiles of DNA methylation in a population, tissue etc.) Epigenetics http://purl.bioontology.org/ontology/MSH/D019175 @@ -48314,7 +48819,6 @@ positional features such as functional sites in nucleotide sequences. 1.3 - Translational medicine Collections of chemicals, typically for use in high-throughput screening experiments. Chemical library Chemical screening @@ -48334,8 +48838,8 @@ positional features such as functional sites in nucleotide sequences.1.3 true VT 3.3 Health sciences + Topic concerning biological science that is (typically) performed in the context of medicine. Health science - Topic concerning biological science that is (typically) performed in the context of medicine. @@ -48349,7 +48853,7 @@ positional features such as functional sites in nucleotide sequences. 1.3 - Topic concerning the identity of biological entities, or reports on such entities, and the mapping of entities and records in different databases. + Topic concerning the identity of biological entities, or reports on such entities, and the mapping of entities and records in different databases. @@ -48547,6 +49051,7 @@ positional features such as functional sites in nucleotide sequences. 1.4 The process of formulating abd administering a pharmaceutical compound to achieve a therapeutic effect. + Biotherapeutics Drug delivery Drug formulation @@ -48569,7 +49074,6 @@ positional features such as functional sites in nucleotide sequences.Drug absorption Drug distribution Drug excretion - Drug metabolism Pharmacodynamics Pharmacokinetics @@ -49371,6 +49875,7 @@ positional features such as functional sites in nucleotide sequences.Knowledge discovery in databases VT 1.3.2 Data mining The discovery of patterns in large data sets and the extraction and trasnsformation of those patterns into a useful format. + Pattern recognition Data mining @@ -49489,7 +49994,6 @@ positional features such as functional sites in nucleotide sequences.PolyA signal PolyA site Signal peptide coding sequence - Transcription Transit peptide coding sequence cDNA mRNA @@ -49569,7 +50073,6 @@ positional features such as functional sites in nucleotide sequences.1.8 Microarray experiments including conditions, protocol, sample:data relationships etc. Microarrays - ChIP-chip ChIP-on-chip Genotyping array Methylation array @@ -49612,9 +50115,9 @@ positional features such as functional sites in nucleotide sequences.2D PAGE experiment Mass spectrometry Northern blot experiment - This includes two-dimensional gel electrophoresis (2D PAGE) experiments, gels or spots in a gel. Also mass spectrometry - an analytical chemistry technique that measures the mass-to-charge ratio and abundance of irons in the gas phase. Also Northern blot experiments. + This includes two-dimensional gel electrophoresis (2D PAGE) experiments, gels or spots in a gel. Also mass spectrometry - an analytical chemistry technique that measures the mass-to-charge ratio and abundance of irons in the gas phase. Also Northern blot experiments. Proteomics experiment @@ -50030,15 +50533,13 @@ positional features such as functional sites in nucleotide sequences. 1.10 - The quality, integrity, cleaning up and enrichment of data. + The quality, integrity, and cleaning up of data. Data clean-up - Data enrichment Data integrity Data quality Data quality management - http://purl.bioontology.org/ontology/MSH/D030541 @@ -50121,7 +50622,7 @@ positional features such as functional sites in nucleotide sequences. - Personalized medicine + Personalised medicine @@ -50559,26 +51060,26 @@ For example, bagging of decision trees algorithm includes the specification of a - + the life of an organism, the process of sleeping, the process of cell-division A processual entity that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities. BFO process process - + - + Collection of random bacteria, a chair, dorsal surface of the body. A material entity is a real world physical object. It is an entity that exists in full during the length of time of its existence, persists through this time while maintaining its identity and has no temporal parts. For example a heart, a human, a fly, a microarray. An independent continuant [snap:IndependentContinuant] that is spatially extended whose identity is independent of that of other entities and can be maintained through time. Note: Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology. BFO James Malone material entity - + @@ -50613,13 +51114,13 @@ For example, bagging of decision trees algorithm includes the specification of a - + Examples of information content entites include journal articles, data, graphical layouts, and graphs. An information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity. IAO information content entity information content entity - + @@ -58213,7 +58714,7 @@ tiple samples - + A license is a legal instrument (usually by way of contract law, with or without printed material) governing the use or redistribution of the resource containing the license. Modified from http://en.wikipedia.org/wiki/Software_license James Malone @@ -61572,7 +62073,7 @@ A program is free software if users have all of these freedoms. Thus, you should - + @@ -63354,14 +63855,14 @@ According to the GNU project, the Apache 2.0 license is better for substantial p - + the role of a person as a surgeon, the role of a chemical compound in an experiment, the role of a patient relative as defined by a hospital administrative form, the role of a woman as a legal mother in the context of system of laws, the role of a biological grandfather as legal guardian in the context of a system of laws, the role of ingested matter in digestion, the role of a student in a university A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. A role is an entity which is borne in a material entity in some kinds of natural, social or institutional contexts, but which is not essential to the fundamental definition of that material entity (i.e. the material entity exists with or without the role). For example, the role of a person as a surgeon, the role of an artificial heart in pumping blood, the role of a chemical compound in an experiment, the role of a drug in the treatment of a disease. BFO role role - + @@ -63397,15 +63898,15 @@ According to the GNU project, the Apache 2.0 license is better for substantial p OBO_REL:is_a has format http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality" - relations false + relations false 'A has_format B' defines for the subject A, that it has the object B as its data format. - edam - false 'A has_function B' defines for the subject A, that it has the object B as its function. + false + edam false has function true @@ -63480,8 +63981,8 @@ According to the GNU project, the Apache 2.0 license is better for substantial p http://wsio.org/has_output false edam - 'A has_output B' defines for the subject A, that it has the object B as a necessary or actual output or output argument. false + 'A has_output B' defines for the subject A, that it has the object B as a necessary or actual output or output argument. false @@ -63518,11 +64019,20 @@ According to the GNU project, the Apache 2.0 license is better for substantial p true In very unusual cases. + + concept_properties + true + "Supported by the given data format" here means, that the given format enables representation of data that satisfies the information standard. + Minimum information checklist + 'Information standard' trailing modifier (qualifier, 'information_standard') of 'xref' links of 'Format' concepts. When 'true', the link is pointing to an information standard supported by the given data format. + Minimum information standard + Information standard + is format of false - false 'A is_format_of B' defines for the subject A, that it is a data format of the object B. + false false Subject A can either be a concept that is a 'Format', or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a 'Format' or is in the role of a 'Format'. Object B can be any concept or entity outside of an ontology that is (or is in a role of) 'Data', or an input, output, input or output argument of an 'Operation'. In EDAM, only 'is_format_of' is explicitly defined between EDAM concepts ('Format' 'is_format_of' 'Data'). The inverse, 'has_format', is not explicitly defined. http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in @@ -63540,8 +64050,8 @@ According to the GNU project, the Apache 2.0 license is better for substantial p http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in - is function of OBO_REL:function_of + is function of false http://wsio.org/is_function_of OBO_REL:is_a @@ -63588,8 +64098,8 @@ According to the GNU project, the Apache 2.0 license is better for substantial p relations false OBO_REL:is_a - 'A is_input_of B' defines for the subject A, that it as a necessary or actual input or input argument of the object B. edam + 'A is_input_of B' defines for the subject A, that it as a necessary or actual input or input argument of the object B. "http://purl.obolibrary.org/obo/OBI_0000295" true is input of @@ -63664,6 +64174,18 @@ According to the GNU project, the Apache 2.0 license is better for substantial p OBO_REL:quality_of Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:quality_of' might be seen narrower in the sense that it only relates subjects that are a 'quality' (snap:Quality) with objects that are an 'independent_continuant' (snap:IndependentContinuant), and is broader in the sense that it relates any qualities of the object. + + OBI + c is_manufactured_by o means that there was a process p in which c was +built in which a person, or set of people or machines did the work(bore +the "Manufacturer Role", and those people/and or machines were members +or of directed by the organization to do this. + is manufactured by + + + has_role + has_role + Affymetrix @@ -63777,6 +64299,10 @@ According to the GNU project, the Apache 2.0 license is better for substantial p SAS Institute Inc. + + The relationship between a software and software developer. + is developed by + Speed Berkeley Research Group @@ -63812,6 +64338,11 @@ According to the GNU project, the Apache 2.0 license is better for substantial p Strand Life Sciences + + Should be used to link a particular class (e.g. a piece of software or an algorithm) with a publication(s) which act as the primary reference(s) for that class. + has documentation + Allyson Lister + For further information, please see http://softwareontology.wordpress.com/2012/06/20/versioning-in-swo/ Allyson Lister @@ -63829,6 +64360,12 @@ According to the GNU project, the Apache 2.0 license is better for substantial p is implemented by is the relationship between an algorithm and a piece of software which includes an implementation of that software for use when the software is executed. is implemented by + + This property, together with 'uses software', is probably best modelled as a child of has_part. Its current position in the property hierarchy is based on simplicity of use. 'uses platform' was deemed an appropriate addition (rather than making use of already extant has_part or 'uses software') due to the already present definitions of those classes which restrict their use to particular situations. + 'uses platform' should be used to link a particular piece of software to one or more operating systems which that software can run on. This is in contrast to both 'uses software' (which describes one piece of software directly executing another), and has_part, which can be used to describe related but independent software in a package, for example. + Allyson Lister + uses platform + is software for @@ -63837,6 +64374,26 @@ According to the GNU project, the Apache 2.0 license is better for substantial p relationship between an entity and a version name or number For further information, please see http://softwareontology.wordpress.com/2012/06/20/versioning-in-swo/ + + Andy Brown + has interface + Allyson Lister + Andy Brown + Provides a method of asserting what type of interactions are possible for the class in question. The interface must be from the 'software interface' hierarchy. + + + 'is published by' elucidates the relationship between a piece of software or a data format specification and its owning organization. Please note that this is not the same as authorship of the software. For instance, affy is published within Bioconductor, but has its own distinct authorship list. + Allyson Lister + is published by + James Malone + + + Allyson Lister + Allyson Lister + is executed in + OBI + is executed in defines the relationship between a software class and an appropriate process in the information processing hierarchy. Specifically, it allows the linking of a particular piece of software to a process of a particular purpose, + The format for BioPAX Manchester OWL syntax is an alternative format of the BioPAX RDF/XML format. Allyson Lister @@ -63852,6 +64409,16 @@ According to the GNU project, the Apache 2.0 license is better for substantial p http://www.gnu.org/licenses/gpl-faq.html#WhatDoesCompatMean, accessed 12 June 2013. 'is compatible license of' provides a method of marking two software licenses as compatible and without conflicts, e.g. that the Apache License version 2 is compatible with GNU GPL version 3. If two licenses are connected with this property, it means code released under one license can be released with code from the other license in a larger program. + + has release date + Andy Brown + The official date of release of software + + + Andy Brown + has support URL + A URL for a source of support information about software + Microsoft @@ -64077,13 +64644,13 @@ According to the GNU project, the Apache 2.0 license is better for substantial p The inverse property. 'part of', contains the full official RO definition. - has part has_part + has part OBO Foundry RO - For continuants: C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.) This property can be used to describe related but independent members of a larger software package. In other cases, where parts of a larger software package are independent of one another in development but one piece of software executes another directly, please use "uses software". + For continuants: C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.) Cytoscape plugins would be linked to the Cytoscape application via uses software, while Microsoft Excel is linked to Microsoft Office via has_part. part of @@ -64092,12 +64659,12 @@ According to the GNU project, the Apache 2.0 license is better for substantial p This property can be used to describe related but independent members of a larger software package. In other cases, where parts of a larger software package are independent of one another in development but one piece of software executes another directly, please use "uses software". - + - + diff --git a/release/swo_merged.owl b/release/swo_merged.owl index 2207617..dad5fd6 100644 --- a/release/swo_merged.owl +++ b/release/swo_merged.owl @@ -1,70 +1,61 @@ - - - - - - - - - - - - - - - -]> - - - - - EDAM http://edamontology.org/ "EDAM relations and concept properties" + xmlns:doap="http://usefulinc.com/ns/doap#" + xmlns:xml="http://www.w3.org/XML/1998/namespace" + xmlns:obo="http://purl.obolibrary.org/obo/" + xmlns:foaf="http://xmlns.com/foaf/0.1/" + xmlns:dc="http://purl.org/dc/elements/1.1/"> + + EDAM editors: Jon Ison, Matus Kalas, and Herve Menager. Contributors: Inge Jonassen, Dan Bolser, Hamish McWilliam, Mahmut Uludag, James Malone, Rodrigo Lopez, Steve Pettifer, and Peter Rice. Contibutions from these projects: EMBRACE, ELIXIR, and BioMedBridges (EU); EMBOSS (BBSRC, UK); eSysbio, FUGE Bioinformatics Platform, and ELIXIR.NO/Norwegian Bioinformatics Platform (Research Council of Norway). See http://edamontology.org for documentation and licence. + application/rdf+xml + EDAM + 3791 + SWO and EDAM include some terms released under CC-BY license from the OBO Foundry. We acknowledge those with the use of the OBO PURLs were appropriate. Some of the definitions have been modified from the original; for the latest original definition please visit the URI. + EDAM is an ontology of well established, familiar concepts that are prevalent within bioinformatics, including types of data and data identifiers, data formats, operations and topics. EDAM is a simple ontology - essentially a set of terms with synonyms and definitions - organised into an intuitive hierarchy for convenient use by curators, software developers and end-users. EDAM is suitable for large-scale semantic annotations and categorisation of diverse bioinformatics resources. EDAM is also suitable for diverse application including for example within workbenches and workflow-management systems, software distributions, and resource registries. + Allyson Lister + relations "EDAM relations" Hervé Ménager - Matúš Kalaš - Robert Stevens - EDAM_data http://edamontology.org/data_ "EDAM types of data" + Duncan Hull + Andy Brown concept_properties "EDAM concept properties" - SWO and EDAM include some terms released under CC-BY license from the OBO Foundry. We acknowledge those with the use of the OBO PURLs were appropriate. Some of the definitoin have been modified from the original; for the latest original definition please visit the URI. + The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, provenance and associated data. It contains SWO-specific classes and axioms as well as imported information from a variety of sources including OBI, IAO, BFO and EDAM. Please note that EDAM is imported as a whole and as such, some comments in the ontology header directly relate to EDAM only. + Matúš Kalaš James Malone - Helen Parkinson - Jon Ison, Matus Kalas, Herve Menager - topics "EDAM topics" - application/rdf+xml - operations "EDAM operations" + Bioinformatics operations, data types, formats, identifiers and topics data "EDAM types of data" + EDAM_format http://edamontology.org/format_ "EDAM data formats" + 1.16 + EDAM_topic http://edamontology.org/topic_ "EDAM topics" + + Jon Ison, Matus Kalas, Hervé Ménager + 0.4 + formats "EDAM data formats" + 31.10.2016 23:58 GMT Nandini Badarinarayan - EDAM is an ontology of well established, familiar concepts that are prevalent within bioinformatics, including types of data and data identifiers, data formats, operations and topics. EDAM is a simple ontology - essentially a set of terms with synonyms and definitions - organised into an intuitive hierarchy for convenient use by curators, software developers and end-users. EDAM is suitable for large-scale semantic annotations and categorization of diverse bioinformatics resources. EDAM is also suitable for diverse application including for example within workbenches and workflow-management systems, software distributions, and resource registries. + EDAM http://edamontology.org/ "EDAM relations and concept properties" + 1.6 EDAM_operation http://edamontology.org/operation_ "EDAM operations" - 1.5 - identifiers "EDAM types of identifiers" - formats "EDAM data formats" edam "EDAM" - EDAM editors: Jon Ison, Matus Kalas, and Herve Menager. Contributors: Inge Jonassen, Dan Bolser, Hamish McWilliam, Mahmut Uludag, James Malone, Rodrigo Lopez, Steve Pettifer, and Peter Rice. Contibutions from these projects: EMBRACE, ELIXIR, and BioMedBridges (EU); EMBOSS (BBSRC, UK); eSysbio, FUGE Bioinformatics Platform, and ELIXIR.NO/Norwegian Bioinformatics Platform (Research Council of Norway). See http://edamontology.org for documentation and licence. - Duncan Hull - EDAM_topic http://edamontology.org/topic_ "EDAM topics" - Andy Brown - Date of release: 8th February 2015 - Allyson Lister - EDAM - relations "EDAM relations" - - + Robert Stevens + Helen Parkinson + Date of release: 12th October 2016 + operations "EDAM operations" + topics "EDAM topics" + identifiers "EDAM types of identifiers" + EDAM_data http://edamontology.org/data_ "EDAM types of data" + Jon Ison + @@ -82,112 +73,197 @@ - + - + - + - + + + + + + + + 1.13 + true + Publication reference + 'Citation' concept property ('citation' metadata tag) contains a dereferenceable URI, preferrably including a DOI, pointing to a citeable publication of the given data format. + Publication + concept_properties + Citation + + + + + + + - - Created in - Version in which a concept was created. + true + Version in which a concept was created. concept_properties + Created in - - Documentation - Specification - 'Documentation' trailing modifier (qualifier, 'documentation') of 'xref' links of 'Format' concepts. When 'true', the link is pointing to a page with explanation, description, documentation, or specification of the given data format. + true + 'Documentation' trailing modifier (qualifier, 'documentation') of 'xref' links of 'Format' concepts. When 'true', the link is pointing to a page with explanation, description, documentation, or specification of the given data format. + Specification concept_properties + Documentation - + + true + 'Example' concept property ('example' metadata tag) lists examples of valid values of types of identifiers (accessions). Applicable to some other types of data, too. + concept_properties + Separated by bar ('|'). For more complex data and data formats, it can be a link to a website with examples, instead. Example - 'Example' concept property ('example' metadat tag) lists examples of valid values of types of identifiers (accessions). Applicable to some other types of data, too. + + + + + + + + true + 'File extension' concept property ('file_extension' metadata tag) lists examples of usual file extensions of formats. + 'Ontology used' concept property ('ontology_used' metadata tag) of format concepts links to a domain ontology that is used inside the given data format, or contains a note about ontology use within the format. + concept_properties + N.B.: File extensions that are not correspondigly defined at http://filext.com are recorded in EDAM only if not in conflict with http://filext.com, and/or unique and usual within life-science computing. + Separated by bar ('|'), without a dot ('.') prefix, preferrably not all capital characters. + File extension + Ontology used + + + + + + + + true + "Supported by the given data format" here means, that the given format enables representation of data that satisfies the information standard. + 'Information standard' trailing modifier (qualifier, 'information_standard') of 'xref' links of 'Format' concepts. When 'true', the link is pointing to an information standard supported by the given data format. + Minimum information checklist + Minimum information standard + concept_properties + Information standard + + + + + + + true + When 'true', the concept has been proposed or is supported within Debian as a tag. concept_properties + isdebtag - + - + + true + 'Media type' trailing modifier (qualifier, 'media_type') of 'xref' links of 'Format' concepts. When 'true', the link is pointing to a page specifying a media type of the given data format. + MIME type + concept_properties + Media type + - + + true + Version in which a concept was made obsolete. + concept_properties Obsolete since + + + + + + + + + + + + + true + 'Organisation' trailing modifier (qualifier, 'organisation') of 'xref' links of 'Format' concepts. When 'true', the link is pointing to an organisation that developed, standardised, and maintains the given data format. + Organization concept_properties - Version in which a concept was made obsolete. + Organisation - - Regular expression + + true 'Regular expression' concept property ('regex' metadata tag) specifies the allowed values of types of identifiers (accessions). Applicable to some other types of data, too. concept_properties - true + Regular expression - - example of usage - A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not. - IAO + + A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not. + IAO + example of usage - - definition + definition + definition - + alternative term @@ -195,148 +271,148 @@ - - definition source + definition source + definition source - + - + - + - + - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - + - + - - obsoleted in version - EFO Development Team - The version in which a class or property has been made obsolete + + The version in which a class or property has been made obsolete + EFO Development Team + obsoleted in version - - reason for obsolescence - EFO Development Team - The reason a class or property was made obsolete + + The reason a class or property was made obsolete + EFO Development Team + reason for obsolescence - + SWO definition @@ -344,106 +420,118 @@ - + + + + + + + - + - + - + + + + + + + - + - + - + - + - + - + - + - + - + - + - + - + deprecated - + - + @@ -460,378 +548,378 @@ - - has format - "http://purl.obolibrary.org/obo/OBI_0000298" - Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) 'Data', or an input, output, input or output argument of an 'Operation'. Object B can either be a concept that is a 'Format', or in unexpected cases an entity outside of an ontology that is a 'Format' or is in the role of a 'Format'. In EDAM, 'has_format' is not explicitly defined between EDAM concepts, only the inverse 'is_format_of'. - false - OBO_REL:is_a - relations - http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality" + + + + + false false false - edam + OBO_REL:is_a 'A has_format B' defines for the subject A, that it has the object B as its data format. - false - - + edam + relations + false + Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) 'Data', or an input, output, input or output argument of an 'Operation'. Object B can either be a concept that is a 'Format', or in unexpected cases an entity outside of an ontology that is a 'Format' or is in the role of a 'Format'. In EDAM, 'has_format' is not explicitly defined between EDAM concepts, only the inverse 'is_format_of'. + has format + "http://purl.obolibrary.org/obo/OBI_0000298" + http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality" - - has function - http://wsio.org/has_function + + + false + false + false OBO_REL:is_a + 'A has_function B' defines for the subject A, that it has the object B as its function. OBO_REL:bearer_of edam - Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is (or is in a role of) a function, or an entity outside of an ontology that is (or is in a role of) a function specification. In the scope of EDAM, 'has_function' serves only for relating annotated entities outside of EDAM with 'Operation' concepts. - false - http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality" + relations true - 'A has_function B' defines for the subject A, that it has the object B as its function. + Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is (or is in a role of) a function, or an entity outside of an ontology that is (or is in a role of) a function specification. In the scope of EDAM, 'has_function' serves only for relating annotated entities outside of EDAM with 'Operation' concepts. + has function "http://purl.obolibrary.org/obo/OBI_0000306" - relations - false - + http://wsio.org/has_function + http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality" - In very unusual cases. - true - - - - + + OBO_REL:bearer_of Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:bearer_of' is narrower in the sense that it only relates ontological categories (concepts) that are an 'independent_continuant' (snap:IndependentContinuant) with ontological categories that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant), and broader in the sense that it relates with any borne objects not just functions of the subject. - - + + + + + true + In very unusual cases. - - has identifier - false + + + + false - relations + false + false OBO_REL:is_a - edam 'A has_identifier B' defines for the subject A, that it has the object B as its identifier. - Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is an 'Identifier', or an entity outside of an ontology that is an 'Identifier' or is in the role of an 'Identifier'. In EDAM, 'has_identifier' is not explicitly defined between EDAM concepts, only the inverse 'is_identifier_of'. + edam + relations false - false - - + Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is an 'Identifier', or an entity outside of an ontology that is an 'Identifier' or is in the role of an 'Identifier'. In EDAM, 'has_identifier' is not explicitly defined between EDAM concepts, only the inverse 'is_identifier_of'. + has identifier - - has input - OBO_REL:has_participant - "http://purl.obolibrary.org/obo/OBI_0000293" + + + + false - http://wsio.org/has_input - Subject A can either be concept that is or has an 'Operation' function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an 'Operation' function or is an 'Operation'. Object B can be any concept or entity. In EDAM, only 'has_input' is explicitly defined between EDAM concepts ('Operation' 'has_input' 'Data'). The inverse, 'is_input_of', is not explicitly defined. - relations - OBO_REL:is_a + false false + OBO_REL:is_a 'A has_input B' defines for the subject A, that it has the object B as a necessary or actual input or input argument. - false - true + OBO_REL:has_participant edam - - + relations + true + Subject A can either be concept that is or has an 'Operation' function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an 'Operation' function or is an 'Operation'. Object B can be any concept or entity. In EDAM, only 'has_input' is explicitly defined between EDAM concepts ('Operation' 'has_input' 'Data'). The inverse, 'is_input_of', is not explicitly defined. + has input + "http://purl.obolibrary.org/obo/OBI_0000293" + http://wsio.org/has_input - 'OBO_REL:has_participant' is narrower in the sense that it only relates ontological categories (concepts) that are a 'process' (span:Process) with ontological categories that are a 'continuant' (snap:Continuant), and broader in the sense that it relates with any participating objects not just inputs or input arguments of the subject. + + OBO_REL:has_participant - - + 'OBO_REL:has_participant' is narrower in the sense that it only relates ontological categories (concepts) that are a 'process' (span:Process) with ontological categories that are a 'continuant' (snap:Continuant), and broader in the sense that it relates with any participating objects not just inputs or input arguments of the subject. - In very unusual cases. + + true - - + In very unusual cases. - - has output - http://wsio.org/has_output - Subject A can either be concept that is or has an 'Operation' function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an 'Operation' function or is an 'Operation'. Object B can be any concept or entity. In EDAM, only 'has_output' is explicitly defined between EDAM concepts ('Operation' 'has_output' 'Data'). The inverse, 'is_output_of', is not explicitly defined. - edam - "http://purl.obolibrary.org/obo/OBI_0000299" + + + + + false + false + false OBO_REL:is_a - relations + 'A has_output B' defines for the subject A, that it has the object B as a necessary or actual output or output argument. OBO_REL:has_participant + edam + relations true - 'A has_output B' defines for the subject A, that it has the object B as a necessary or actual output or output argument. - false - false - false - - + Subject A can either be concept that is or has an 'Operation' function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an 'Operation' function or is an 'Operation'. Object B can be any concept or entity. In EDAM, only 'has_output' is explicitly defined between EDAM concepts ('Operation' 'has_output' 'Data'). The inverse, 'is_output_of', is not explicitly defined. + has output + "http://purl.obolibrary.org/obo/OBI_0000299" + http://wsio.org/has_output - 'OBO_REL:has_participant' is narrower in the sense that it only relates ontological categories (concepts) that are a 'process' (span:Process) with ontological categories that are a 'continuant' (snap:Continuant), and broader in the sense that it relates with any participating objects not just outputs or output arguments of the subject. It is also not clear whether an output (result) actually participates in the process that generates it. + + OBO_REL:has_participant - - + 'OBO_REL:has_participant' is narrower in the sense that it only relates ontological categories (concepts) that are a 'process' (span:Process) with ontological categories that are a 'continuant' (snap:Continuant), and broader in the sense that it relates with any participating objects not just outputs or output arguments of the subject. It is also not clear whether an output (result) actually participates in the process that generates it. + + true In very unusual cases. - - - - has topic - relations - true - Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology that is a 'Topic' or is in the role of a 'Topic'. In EDAM, only 'has_topic' is explicitly defined between EDAM concepts ('Operation' or 'Data' 'has_topic' 'Topic'). The inverse, 'is_topic_of', is not explicitly defined. - false - 'A has_topic B' defines for the subject A, that it has the object B as its topic (A is in the scope of a topic B). - edam - OBO_REL:is_a - http://annotation-ontology.googlecode.com/svn/trunk/annotation-core.owl#hasTopic - false - "http://purl.obolibrary.org/obo/IAO_0000136" - false - http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality - "http://purl.obolibrary.org/obo/OBI_0000298" - + + - - + + + + false + false + false + OBO_REL:is_a + 'A has_topic B' defines for the subject A, that it has the object B as its topic (A is in the scope of a topic B). + edam + relations + true + Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology that is a 'Topic' or is in the role of a 'Topic'. In EDAM, only 'has_topic' is explicitly defined between EDAM concepts ('Operation' or 'Data' 'has_topic' 'Topic'). The inverse, 'is_topic_of', is not explicitly defined. + has topic + "http://purl.obolibrary.org/obo/IAO_0000136" + "http://purl.obolibrary.org/obo/OBI_0000298" + http://annotation-ontology.googlecode.com/svn/trunk/annotation-core.owl#hasTopic + http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality - In very unusual cases. + + true - - + In very unusual cases. - - is format of + + + false - OBO_REL:is_a false false - false + OBO_REL:is_a 'A is_format_of B' defines for the subject A, that it is a data format of the object B. + OBO_REL:quality_of edam relations + false Subject A can either be a concept that is a 'Format', or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a 'Format' or is in the role of a 'Format'. Object B can be any concept or entity outside of an ontology that is (or is in a role of) 'Data', or an input, output, input or output argument of an 'Operation'. In EDAM, only 'is_format_of' is explicitly defined between EDAM concepts ('Format' 'is_format_of' 'Data'). The inverse, 'has_format', is not explicitly defined. - OBO_REL:quality_of + is format of http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in - - - + + OBO_REL:quality_of Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:quality_of' might be seen narrower in the sense that it only relates subjects that are a 'quality' (snap:Quality) with objects that are an 'independent_continuant' (snap:IndependentContinuant), and is broader in the sense that it relates any qualities of the object. - - - - is function of - Subject A can either be concept that is (or is in a role of) a function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) a function specification. Object B can be any concept or entity. Within EDAM itself, 'is_function_of' is not used. - OBO_REL:inheres_in - true - OBO_REL:is_a + + + false false + false + OBO_REL:is_a 'A is_function_of B' defines for the subject A, that it is a function of the object B. OBO_REL:function_of + OBO_REL:inheres_in edam - http://wsio.org/is_function_of relations + true + Subject A can either be concept that is (or is in a role of) a function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) a function specification. Object B can be any concept or entity. Within EDAM itself, 'is_function_of' is not used. + is function of + http://wsio.org/is_function_of http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in - false - false - - + + OBO_REL:function_of Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:function_of' only relates subjects that are a 'function' (snap:Function) with objects that are an 'independent_continuant' (snap:IndependentContinuant), so for example no processes. It does not define explicitly that the subject is a function of the object. - - - - - In very unusual cases. - true - - + + OBO_REL:inheres_in Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:inheres_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant) with ontological categories that are an 'independent_continuant' (snap:IndependentContinuant), and broader in the sense that it relates any borne subjects not just functions. - - + + + + + true + In very unusual cases. - - is identifier of + + + false false + false + OBO_REL:is_a + 'A is_identifier_of B' defines for the subject A, that it is an identifier of the object B. edam - false relations + false Subject A can either be a concept that is an 'Identifier', or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is an 'Identifier' or is in the role of an 'Identifier'. Object B can be any concept or entity outside of an ontology. In EDAM, only 'is_identifier_of' is explicitly defined between EDAM concepts (only 'Identifier' 'is_identifier_of' 'Data'). The inverse, 'has_identifier', is not explicitly defined. - OBO_REL:is_a - 'A is_identifier_of B' defines for the subject A, that it is an identifier of the object B. - false - - - + is identifier of - - is input of + + + false - http://wsio.org/is_input_of - relations - true false - OBO_REL:participates_in + false OBO_REL:is_a - "http://purl.obolibrary.org/obo/OBI_0000295" + 'A is_input_of B' defines for the subject A, that it as a necessary or actual input or input argument of the object B. + OBO_REL:participates_in edam + relations + true Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an 'Operation' function, or an entity outside of an ontology that has an 'Operation' function or is an 'Operation'. In EDAM, 'is_input_of' is not explicitly defined between EDAM concepts, only the inverse 'has_input'. - false - 'A is_input_of B' defines for the subject A, that it as a necessary or actual input or input argument of the object B. - - - + is input of + "http://purl.obolibrary.org/obo/OBI_0000295" + http://wsio.org/is_input_of - 'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just inputs or input arguments. + + OBO_REL:participates_in - - + 'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just inputs or input arguments. - In very unusual cases. + + true - - + In very unusual cases. - - is output of - OBO_REL:is_a + + + + false false false - Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an 'Operation' function, or an entity outside of an ontology that has an 'Operation' function or is an 'Operation'. In EDAM, 'is_output_of' is not explicitly defined between EDAM concepts, only the inverse 'has_output'. - edam - false + OBO_REL:is_a 'A is_output_of B' defines for the subject A, that it as a necessary or actual output or output argument of the object B. OBO_REL:participates_in - http://wsio.org/is_output_of - true + edam relations + true + Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an 'Operation' function, or an entity outside of an ontology that has an 'Operation' function or is an 'Operation'. In EDAM, 'is_output_of' is not explicitly defined between EDAM concepts, only the inverse 'has_output'. + is output of "http://purl.obolibrary.org/obo/OBI_0000312" - - - + http://wsio.org/is_output_of - In very unusual cases. - true - - - - + + OBO_REL:participates_in 'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just outputs or output arguments. It is also not clear whether an output (result) actually participates in the process that generates it. - - + + + + + true + In very unusual cases. - - is topic of - 'A is_topic_of B' defines for the subject A, that it is a topic of the object B (a topic A is the scope of B). - relations - OBO_REL:quality_of - false - true - false - Subject A can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a 'Topic' or is in the role of a 'Topic'. Object B can be any concept or entity outside of an ontology. In EDAM, 'is_topic_of' is not explicitly defined between EDAM concepts, only the inverse 'has_topic'. - http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in - false - OBO_REL:is_a - edam - - + + - - + + + false + false + false + OBO_REL:is_a + 'A is_topic_of B' defines for the subject A, that it is a topic of the object B (a topic A is the scope of B). + OBO_REL:quality_of + edam + relations + true + Subject A can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a 'Topic' or is in the role of a 'Topic'. Object B can be any concept or entity outside of an ontology. In EDAM, 'is_topic_of' is not explicitly defined between EDAM concepts, only the inverse 'has_topic'. + is topic of + http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in + + OBO_REL:quality_of Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:quality_of' might be seen narrower in the sense that it only relates subjects that are a 'quality' (snap:Quality) with objects that are an 'independent_continuant' (snap:IndependentContinuant), and is broader in the sense that it relates any qualities of the object. - - + + true In very unusual cases. - - @@ -839,474 +927,508 @@ - is about - 'is about' relates an information entity to other entities in which the information entity holds some information which dscribes some facet of the other entity, such as the arrow direction on a sign. - IAO - James Malone + + 'is about' relates an information entity to other entities in which the information entity holds some information which dscribes some facet of the other entity, such as the arrow direction on a sign. + IAO + James Malone Alan Ruttenberg - + is about - - - preceded by - Please note that, as stated on one of the RO documentation pages (https://code.google.com/p/obo-relations/wiki/ROAndBFO), some of the relations RO makes use are either uncontroversial (non-temporalized) parts of BFO2, or will be incorporated in the future. In the case of BFO_0000063, it is not currently in BFO2, but may be in the future. The RO ontologists assume this is the transitive form. For a full definition, refer to the inverse of this property, BFO_0000060. (Allyson Lister) + + + + OBO Foundry - + Please note that, as stated on one of the RO documentation pages (https://code.google.com/p/obo-relations/wiki/ROAndBFO), some of the relations RO makes use are either uncontroversial (non-temporalized) parts of BFO2, or will be incorporated in the future. In the case of BFO_0000063, it is not currently in BFO2, but may be in the future. The RO ontologists assume this is the transitive form. For a full definition, refer to the inverse of this property, BFO_0000060. (Allyson Lister) + preceded by - - - followed by - Modified by Allyson Lister from the preceded_by (which is the inverse of precedes / 'followed by') definition within RO: http://www.obofoundry.org/ro/ro.owl - Please note that, as stated on one of the RO documentation pages (https://code.google.com/p/obo-relations/wiki/ROAndBFO), some of the relations RO makes use are either uncontroversial (non-temporalized) parts of BFO2, or will be incorporated in the future. In the case of BFO_0000060, it is not currently in BFO2, but may be in the future. The RO ontologists assume this is the transitive form. (Allyson Lister) - The assertion P 'followed by' P1 tells us something about Ps in general: that is, it tells us something about what happened later, given what we know about what happened earlier. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be preceded by some instance of P. Note that assertions using this property only are rather weak. Typically we will be interested in stronger relations, for example in the relation 'directly followed by'. + + + + The assertion P 'followed by' P1 tells us something about Ps in general: that is, it tells us something about what happened later, given what we know about what happened earlier. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be preceded by some instance of P. Note that assertions using this property only are rather weak. Typically we will be interested in stronger relations, for example in the relation 'directly followed by'. + Modified by Allyson Lister from the preceded_by (which is the inverse of precedes / 'followed by') definition within RO: http://www.obofoundry.org/ro/ro.owl OBO Foundry - - + Please note that, as stated on one of the RO documentation pages (https://code.google.com/p/obo-relations/wiki/ROAndBFO), some of the relations RO makes use are either uncontroversial (non-temporalized) parts of BFO2, or will be incorporated in the future. In the case of BFO_0000060, it is not currently in BFO2, but may be in the future. The RO ontologists assume this is the transitive form. (Allyson Lister) + followed by - - is manufactured by - OBI - c is_manufactured_by o means that there was a process p in which c was + + + c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the "Manufacturer Role", and those people/and or machines were members or of directed by the organization to do this. - + OBI + is manufactured by - - participates in - Andy Brown - Please see the official RO definition for the inverse of this property, 'has participant.' + + + Andy Brown + Please see the official RO definition for the inverse of this property, 'has participant.' + participates in - - has participant - Andy Brown - Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. - The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. - http://obo-relations.googlecode.com/svn/trunk/src/ontology/core.owl - + + The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. + Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. + http://obo-relations.googlecode.com/svn/trunk/src/ontology/core.owl + Andy Brown + has participant - - has_role - has_role + + has_role + has_role - + + + An entity A is the 'input of' another entity B if A was put into the system, entity or software represented by B. + Allyson Lister input of - Allyson Lister - An entity A is the 'input of' another entity B if A was put into the system, entity or software represented by B. - - + + + A piece of software can be the output of a particular software company via a software publishing process; data might be the output of a particular piece of data-producing software. + An entity A is the 'output of' another entity B if it was produced as a result of the functioning of entity B. + Allyson Lister output of - A piece of software can be the output of a particular software company via a software publishing process; data might be the output of a particular piece of data-producing software. - Allyson Lister - An entity A is the 'output of' another entity B if it was produced as a result of the functioning of entity B. - - - is developed by - The relationship between a software and software developer. - + + + The relationship between a software and software developer. + is developed by - - obsolete_is_published_by - The relationship between software and a software publisher. - true + + + + The relationship between software and a software publisher. Marked as obsolete by Allyson Lister. - This class can be entirely replaced with 'is published by', SWO_0004004. Please use SWO_0004004 instead. 0.5 - - + This class can be entirely replaced with 'is published by', SWO_0004004. Please use SWO_0004004 instead. + obsolete_is_published_by + true - - has legal status - 1.4 - Marked as obsolete by Allyson Lister. - This property was not in use anywhere in the ontology. Further, it had no definition and therefore its intended usage was unclear. Until a time when this property is required and an official definition created, this property is obsolete so as not to introduce inconsistent usage. - true - + + + Marked as obsolete by Allyson Lister. + 1.4 + This property was not in use anywhere in the ontology. Further, it had no definition and therefore its intended usage was unclear. Until a time when this property is required and an official definition created, this property is obsolete so as not to introduce inconsistent usage. + has legal status + true - - implements - James Malone + + + + implements is the relationship between software and an algorithm that is defined for use within that software when executed. - - + James Malone + implements - - is encoded in - Allyson Lister - Is encoded in is an "is about" relationship which describes the type of encoding used for the referenced class. - Linking a type of software to its particular programming language. + + Linking a type of software to its particular programming language. + Is encoded in is an "is about" relationship which describes the type of encoding used for the referenced class. + Allyson Lister + is encoded in - - is version of - 'is version of' provides a link between a 'version name' and the entity with that version. - For further information, please see http://softwareontology.wordpress.com/2012/06/20/versioning-in-swo/ + + + + 'is version of' provides a link between a 'version name' and the entity with that version. Allyson Lister - + For further information, please see http://softwareontology.wordpress.com/2012/06/20/versioning-in-swo/ + is version of - - uses software - Cytoscape plugins would be linked to the Cytoscape application via uses software, while Microsoft Excel is linked to Microsoft Office via has_part. - This property allows the linkage of two different pieces of software such that one directly executes or uses the other. The has_part relationship should instead be used to describe related but independent members of a larger software package. + + + + + Cytoscape plugins would be linked to the Cytoscape application via uses software, while Microsoft Excel is linked to Microsoft Office via has_part. + This property allows the linkage of two different pieces of software such that one directly executes or uses the other. The has_part relationship should instead be used to describe related but independent members of a larger software package, and 'uses platform' relationship should be used to describe which operating system(s) a particular piece of software can use. Allyson Lister - - + uses software - - is implemented by + + + is implemented by is the relationship between an algorithm and a piece of software which includes an implementation of that software for use when the software is executed. James Malone - - - + is implemented by - - has specified data input - See also http://softwareontology.wordpress.com/2011/04/15/ins-and-outs-of-software/ - The relationship between input data which is permitted to a piece of software. + + + + + The relationship between input data which is permitted to a piece of software. James Malone - - + See also http://softwareontology.wordpress.com/2011/04/15/ins-and-outs-of-software/ + has specified data input - - has specified data output - See also http://softwareontology.wordpress.com/2011/04/15/ins-and-outs-of-software/ - James Malone + + + + The relationship between a piece of software and the data that it is possible to output. - - + James Malone + See also http://softwareontology.wordpress.com/2011/04/15/ins-and-outs-of-software/ + has specified data output - - is specified data input of + + + + The relationship between a data and the software which can possibly take this data as input. James Malone - - - - + is specified data input of - - is specified data output of - James Malone + + + + The relationship between a data and the software which can possibly produce this data as output. - - - - + James Malone + is specified data output of - - directly preceded by - Allyson Lister - Entity A is 'directly preceded by' entity B if there are no intermediate entities temporally between the two entities. WIthin SWO this property is mainly used to describe versions of entities such as software. - Microsoft version 2007 is directly preceded by Microsoft version 2003. - OBO Foundry - + + + + Microsoft version 2007 is directly preceded by Microsoft version 2003. + Entity A is 'directly preceded by' entity B if there are no intermediate entities temporally between the two entities. WIthin SWO this property is mainly used to describe versions of entities such as software. + Allyson Lister + OBO Foundry + directly preceded by - + + + 'directly followed by' is an object property which further specializes the parent 'followed by' property. In the assertion 'C directly followed by C1', says that Cs generally are immediately followed by C1s. + Allyson Lister directly followed by - 'directly followed by' is an object property which further specializes the parent 'followed by' property. In the assertion 'C directly followed by C1', says that Cs generally are immediately followed by C1s. - Allyson Lister - - + + + + + + + + + + 'uses platform' should be used to link a particular piece of software to one or more operating systems which that software can run on. This is in contrast to both 'uses software' (which describes one piece of software directly executing another), and has_part, which can be used to describe related but independent software in a package, for example. + Allyson Lister + This property, together with 'uses software', is probably best modelled as a child of has_part. Its current position in the property hierarchy is based on simplicity of use. 'uses platform' was deemed an appropriate addition (rather than making use of already extant has_part or 'uses software') due to the already present definitions of those classes which restrict their use to particular situations. + uses platform + + + + + + + + + + is software for - - has version - For further information, please see http://softwareontology.wordpress.com/2012/06/20/versioning-in-swo/ + + relationship between an entity and a version name or number - - + For further information, please see http://softwareontology.wordpress.com/2012/06/20/versioning-in-swo/ + has version - - has interface - Allyson Lister - Andy Brown - Provides a method of asserting what type of interactions are possible for the class in question. The interface must be from the 'software interface' hierarchy. + + + Provides a method of asserting what type of interactions are possible for the class in question. The interface must be from the 'software interface' hierarchy. + Allyson Lister + Andy Brown Andy Brown - + has interface - - has format specification - Allyson Lister - Has format specification is a type of "is encoded in" relationship which specifically describes the relationship between data and a data format specification. - - - + + + + + Has format specification is a type of "is encoded in" relationship which specifically describes the relationship between data and a data format specification. + Allyson Lister + has format specification - - obsolete_is developed by - James Malone - true + + + Marked as obsolete by Allyson Lister. + James Malone 0.3 is developed by and is_developed_by. The former is from the core file and originally had no identifier (though it is now identified via SWO_0004003), and the latter is from the original file (SWO_0000394). SWO_0000394 was retained and SWO_0004003 marked as obsolete as SWO_0004003 had no usages while SWO_0000394 has many usages. Finally, the underscores were removed from the label of SWO_0000394 so it would conform to our naming scheme. Please use SWO_0000394 instead. - Marked as obsolete by Allyson Lister. - + obsolete_is developed by + true - - is published by - 'is published by' elucidates the relationship between a piece of software or a data format specification and its owning organization. Please note that this is not the same as authorship of the software. For instance, affy is published within Bioconductor, but has its own distinct authorship list. - Allyson Lister - James Malone - - + + - - + + + + 'is published by' elucidates the relationship between a piece of software or a data format specification and its owning organization. Please note that this is not the same as authorship of the software. For instance, affy is published within Bioconductor, but has its own distinct authorship list. + Allyson Lister + James Malone + is published by - - obsolete object property - Marked as obsolete by Allyson Lister + Stores those object properties which are no longer appropriate for use within SWO. + Marked as obsolete by Allyson Lister Allyson Lister + obsolete object property - - is executed in - OBI + + + + is executed in defines the relationship between a software class and an appropriate process in the information processing hierarchy. Specifically, it allows the linking of a particular piece of software to a process of a particular purpose, Allyson Lister Allyson Lister - is executed in defines the relationship between a software class and an appropriate process in the information processing hierarchy. Specifically, it allows the linking of a particular piece of software to a process of a particular purpose, - - + OBI + is executed in - - obsolete_is specified output of - true - 0.3 + + Marked as obsolete by Allyson Lister. + 0.3 There is an object property duplication for is specified output of, where one is from OBI (OBI_0000312) and one is from SWO (SWO_9000058); additionally, the reasoner infers these two object properties as equivalent. Both are the inverse properties for has specified output. It makes sense to retain the OBI object property. The SWO class URI was renamed to the OBI term URI (to make the moving of the axioms across to the OBI term simple), and then an SWO class with the original URI was marked as obsolete. Please use OBI_0000312 instead. - + obsolete_is specified output of + true - - has clause - Allyson Lister - Axioms using the 'has clause' property, e.g. C 'has clause' C1, provide links from the left hand class to the instances within the 'license clause' hierarchy. This provides a way to more precisely assert the constraints of the licensing applied. + - + + Axioms using the 'has clause' property, e.g. C 'has clause' C1, provide links from the left hand class to the instances within the 'license clause' hierarchy. This provides a way to more precisely assert the constraints of the licensing applied. + Allyson Lister + has clause - - has license + + + The relationship between an entity and the set of legal restrictions, i.e. license, which are applied in using or otherwise interacting with that entity. Eg. relationship between software and a software license. + has license + + + + + + + - + The relationship between an entity and the set of legal restrictions, i.e. license, which are applied in using or otherwise interacting with that entity. Eg. relationship between a software license and the software which implements it. + is license for - - + + + + + The format for BioPAX Manchester OWL syntax is an alternative format of the BioPAX RDF/XML format. + With both a domain and range of 'data format specification', this property provides a means of stating that two different data format specifications are valid specifications for the same type of data. + Allyson Lister is alternative format of - Allyson Lister - The format for BioPAX Manchester OWL syntax is an alternative format of the BioPAX RDF/XML format. - With both a domain and range of 'data format specification', this property provides a means of stating that two different data format specifications are valid specifications for the same type of data. - - - - - is compatible license of - http://www.gnu.org/licenses/gpl-faq.html#WhatDoesCompatMean, accessed 12 June 2013. + + + + 'is compatible license of' provides a method of marking two software licenses as compatible and without conflicts, e.g. that the Apache License version 2 is compatible with GNU GPL version 3. If two licenses are connected with this property, it means code released under one license can be released with code from the other license in a larger program. + http://www.gnu.org/licenses/gpl-faq.html#WhatDoesCompatMean, accessed 12 June 2013. Allyson Lister - - + is compatible license of - - has declared status - 'has declared status' provides a way to assert the developmental status of a class, such as whether it is stable or under development. Is especially useful for software that might not be complete or stable yet, and when combined with version information. - Allyson Lister + - + + 'has declared status' provides a way to assert the developmental status of a class, such as whether it is stable or under development. Is especially useful for software that might not be complete or stable yet, and when combined with version information. + Allyson Lister + has declared status - - obsolete_has_participant - 1.4 - Exact equivalence with RO class http://purl.obolibrary.org/obo/RO_0000057, to the extent that the inverse of RO_0000057 was already present in this ontology as the inverse of this SWO class. - true - + + + 1.4 + Exact equivalence with RO class http://purl.obolibrary.org/obo/RO_0000057, to the extent that the inverse of RO_0000057 was already present in this ontology as the inverse of this SWO class. + obsolete_has_participant + true @@ -1314,10 +1436,11 @@ or of directed by the organization to do this. - - has part - has_part - The inverse property. 'part of', contains the full official RO definition. + + + The inverse property. 'part of', contains the full official RO definition. + has part + has_part @@ -1325,20 +1448,19 @@ or of directed by the organization to do this. - - part of - Cytoscape plugins would be linked to the Cytoscape application via uses software, while Microsoft Excel is linked to Microsoft Office via has_part. - For continuants: C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.) - OBO Foundry RO - This property can be used to describe related but independent members of a larger software package. In other cases, where parts of a larger software package are independent of one another in development but one piece of software executes another directly, please use "uses software". - + + Cytoscape plugins would be linked to the Cytoscape application via uses software, while Microsoft Excel is linked to Microsoft Office via has_part. + For continuants: C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.) + This property can be used to describe related but independent members of a larger software package. In other cases, where parts of a larger software package are independent of one another in development but one piece of software executes another directly, please use "uses software". + OBO Foundry RO + part of - This property can be used to describe related but independent members of a larger software package. In other cases, where parts of a larger software package are independent of one another in development but one piece of software executes another directly, please use "uses software". - + + This property can be used to describe related but independent members of a larger software package. In other cases, where parts of a larger software package are independent of one another in development but one piece of software executes another directly, please use "uses software". - + @@ -1357,57 +1479,58 @@ or of directed by the organization to do this. - - has documentation - Allyson Lister + + Should be used to link a particular class (e.g. a piece of software or an algorithm) with a publication(s) which act as the primary reference(s) for that class. - + Allyson Lister + has documentation - - has download location - Allyson Lister - The location from where the software can be downloaded. + + + + The location from where the software can be downloaded. + Allyson Lister Allyson Lister - - + has download location - + + + The URL of the homepage for the resource this property is associated with. + Allyson Lister has website homepage - Allyson Lister - The URL of the homepage for the software this property is associated with. - + has website homepage - + + + Andy Brown + The official date of release of software has release date - Andy Brown - The official date of release of software - - + + + Andy Brown + A URL for a source of support information about software has support URL - A URL for a source of support information about software - Andy Brown - @@ -1423,54719 +1546,53990 @@ or of directed by the organization to do this. - + - - Correlation - - - - - - - - Identify a correlation, i.e. a statistical relationship between two random variables or two sets of data. - 1.7 - - + + + beta12orEarlier + beta12orEarlier + + A type of computational resource used in bioinformatics. + + Resource type + true - + - - Resource type - - beta12orEarlier - beta12orEarlier - A type of computational resource used in bioinformatics. - true - + + + + + + beta12orEarlier + Information, represented in an information artefact (data record) that is 'understandable' by dedicated computational tools that can use the data as input or produce it as output. + Data record + Data set + Datum + + + Data + "http://purl.obolibrary.org/obo/IAO_0000027" + "http://purl.obolibrary.org/obo/IAO_0000030" + http://purl.org/biotop/biotop.owl#DigitalEntity + http://semanticscience.org/resource/SIO_000069 + http://semanticscience.org/resource/SIO_000088 + http://wsio.org/data_002 + http://www.ifomis.org/bfo/1.1/snap#Continuant + http://www.onto-med.de/ontologies/gfo.owl#Perpetuant + + + + Data record + EDAM does not distinguish a data record (a tool-understandable information artefact) from data or datum (its content, the tool-understandable encoding of an information). + + + + + Data set + EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). + + + + + Datum + EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). + - - Tool - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier A bioinformatics package or tool, e.g. a standalone application or web service. - beta12orEarlier + + + Tool true - - - Database - + + + beta12orEarlier + beta12orEarlier A digital data archive typically based around a relational model but sometimes using an object-oriented, tree or graph-based model. - beta12orEarlier + + + Database true - beta12orEarlier - - - Ontology - + + + - - + + - beta12orEarlier - Ontologies + beta12orEarlier An ontology of biological or bioinformatics concepts and relations, a controlled vocabulary, structured glossary etc. - - + Ontologies + + + Ontology - - Directory metadata - - 1.5 + + + beta12orEarlier + 1.5 + A directory on disk from which files are read. - beta12orEarlier + + Directory metadata true - - - + + + beta12orEarlier + beta12orEarlier + + Controlled vocabulary from National Library of Medicine. The MeSH thesaurus is used to index articles in biomedical journals for the Medline/PubMED databases. + MeSH vocabulary - - beta12orEarlier true - Controlled vocabulary from National Library of Medicine. The MeSH thesaurus is used to index articles in biomedical journals for the Medline/PubMED databases. - beta12orEarlier - - - - HGNC vocabulary - - beta12orEarlier - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + Controlled vocabulary for gene names (symbols) from HUGO Gene Nomenclature Committee. + + HGNC vocabulary true - - - - UMLS vocabulary - + + + beta12orEarlier + beta12orEarlier + Compendium of controlled vocabularies for the biomedical domain (Unified Medical Language System). - beta12orEarlier - beta12orEarlier + + UMLS vocabulary true - - - - Identifier - + + - - + + - - - http://semanticscience.org/resource/SIO_000115 - beta12orEarlier + + beta12orEarlier + A text token, number or something else which identifies an entity, but which may not be persistent (stable) or unique (the same identifier may identify multiple things). ID + + + + + Identifier "http://purl.org/dc/elements/1.1/identifier" + http://semanticscience.org/resource/SIO_000115 http://wsio.org/data_005 - A text token, number or something else which identifies an entity, but which may not be persistent (stable) or unique (the same identifier may identify multiple things). - - - - + + + Almost exact but limited to identifying resources. - - - - - Database entry - - beta12orEarlier - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + An entry (retrievable via URL) from a biological database. + + Database entry true - - - - Molecular mass - + + + beta12orEarlier Mass of a molecule. - beta12orEarlier - - + + + Molecular mass - - Molecular charge - - Net charge of a molecule. - beta12orEarlier + + + beta12orEarlier PDBML:pdbx_formal_charge - - + Net charge of a molecule. + + + Molecular charge - - Chemical formula - - Chemical structure specification + + + beta12orEarlier A specification of a chemical structure. - beta12orEarlier - - + Chemical structure specification + + + Chemical formula - - QSAR descriptor - + + + beta12orEarlier A QSAR quantitative descriptor (name-value pair) of chemical structure. + + QSAR descriptors have numeric values that quantify chemical information encoded in a symbolic representation of a molecule. They are used in quantitative structure activity relationship (QSAR) applications. Many subtypes of individual descriptors (not included in EDAM) cover various types of protein properties. - beta12orEarlier - - + QSAR descriptor - - Raw sequence - - beta12orEarlier + + + beta12orEarlier A raw molecular sequence (string of characters) which might include ambiguity, unknown positions and non-sequence characters. + + Non-sequence characters may be used for example for gaps and translation stop. - - + Raw sequence - + + + beta12orEarlier + SO:2000061 + A molecular sequence and associated metadata. + + Sequence record - http://purl.bioontology.org/ontology/MSH/D058977 - beta12orEarlier - A molecular sequence and associated metadata. - SO:2000061 - - - - Sequence set - + + + beta12orEarlier A collection of multiple molecular sequences and associated metadata that do not (typically) correspond to molecular sequence database records or entries and which (typically) are derived from some analytical method. - This concept may be used for arbitrary sequence sets and associated data arising from processing. - beta12orEarlier SO:0001260 - - + + + This concept may be used for arbitrary sequence sets and associated data arising from processing. + Sequence set - + + + beta12orEarlier + 1.5 + A character used to replace (mask) other characters in a molecular sequence. + Sequence mask character - true - beta12orEarlier - 1.5 - A character used to replace (mask) other characters in a molecular sequence. - - - - Sequence mask type - + + + beta12orEarlier + 1.5 + A label (text token) describing the type of sequence masking to perform. + Sequence masking is where specific characters or positions in a molecular sequence are masked (replaced) with an another (mask character). The mask type indicates what is masked, for example regions that are not of interest or which are information-poor including acidic protein regions, basic protein regions, proline-rich regions, low compositional complexity regions, short-periodicity internal repeats, simple repeats and low complexity regions. Masked sequences are used in database search to eliminate statistically significant but biologically uninteresting hits. - beta12orEarlier - 1.5 + Sequence mask type true - - - - DNA sense specification - + + + beta12orEarlier + The strand of a DNA sequence (forward or reverse). DNA strand specification - beta12orEarlier Strand - The strand of a DNA sequence (forward or reverse). + + The forward or 'top' strand might specify a sequence is to be used as given, the reverse or 'bottom' strand specifying the reverse complement of the sequence is to be used. - - + DNA sense specification - + + + beta12orEarlier + 1.5 + + A specification of sequence length(s). + Sequence length specification - true - A specification of sequence length(s). - beta12orEarlier - 1.5 - - - - Sequence metadata - - beta12orEarlier + + + beta12orEarlier + 1.5 + Basic or general information concerning molecular sequences. + This is used for such things as a report including the sequence identifier, type and length. - 1.5 + Sequence metadata true - - - - Sequence feature source - - This might be the name and version of a software tool, the name of a database, or 'curated' to indicate a manual annotation (made by a human). + + + beta12orEarlier How the annotation of a sequence feature (for example in EMBL or Swiss-Prot) was derived. - beta12orEarlier - - + + + This might be the name and version of a software tool, the name of a database, or 'curated' to indicate a manual annotation (made by a human). + Sequence feature source - - Sequence search results - - beta12orEarlier - Database hits (sequence) + + + beta12orEarlier + A report of sequence hits and associated data from searching a database of sequences (for example a BLAST search). This will typically include a list of scores (often with statistical evaluation) and a set of alignments for the hits. + Database hits (sequence) Sequence database hits + Sequence database search results Sequence search hits + + The score list includes the alignment score, percentage of the query sequence matched, length of the database sequence entry in this alignment, identifier of the database sequence entry, excerpt of the database sequence entry description etc. - A report of sequence hits and associated data from searching a database of sequences (for example a BLAST search). This will typically include a list of scores (often with statistical evaluation) and a set of alignments for the hits. - Sequence database search results - - + Sequence search results - - Sequence signature matches - - Sequence motif matches - Protein secondary database search results - beta12orEarlier + + + beta12orEarlier Report on the location of matches in one or more sequences to profiles, motifs (conserved or functional patterns) or other signatures. + Sequence motif matches Sequence profile matches - This ncluding reports of hits from a search of a protein secondary or domain database. + Protein secondary database search results Search results (protein secondary database) - - + + + This ncluding reports of hits from a search of a protein secondary or domain database. + Sequence signature matches - - Sequence signature model - + + + beta12orEarlier + beta12orEarlier + Data files used by motif or profile methods. - beta12orEarlier - beta12orEarlier + + Sequence signature model true - - - - Sequence signature data - + + - - + + - beta12orEarlier - This can include metadata about a motif or sequence profile such as its name, length, technical details about the profile construction, and so on. + beta12orEarlier Data concering concerning specific or conserved pattern in molecular sequences and the classifiers used for their identification, including sequence motifs, profiles or other diagnostic element. - - + + + This can include metadata about a motif or sequence profile such as its name, length, technical details about the profile construction, and so on. + Sequence signature data - + + + beta12orEarlier + 1.5 + + Alignment of exact matches between subsequences (words) within two or more molecular sequences. + Sequence word alignment + Sequence alignment (words) - - 1.5 - beta12orEarlier true - Sequence word alignment - Alignment of exact matches between subsequences (words) within two or more molecular sequences. - - - - Dotplot - + + + beta12orEarlier A dotplot of sequence similarities identified from word-matching or character comparison. - beta12orEarlier - - + + + Dotplot - - Sequence alignment - + + - - + + + beta12orEarlier + Alignment of multiple molecular sequences. + + + Sequence alignment http://en.wikipedia.org/wiki/Sequence_alignment http://purl.bioontology.org/ontology/MSH/D016415 http://semanticscience.org/resource/SIO_010066 - beta12orEarlier - Alignment of multiple molecular sequences. - - - - Sequence alignment parameter - + + + beta12orEarlier + 1.5 Some simple value controlling a sequence alignment (or similar 'match') operation. + + Sequence alignment parameter true - 1.5 - beta12orEarlier - - - - Sequence similarity score - + + + beta12orEarlier A value representing molecular sequence similarity. - beta12orEarlier - - + + + Sequence similarity score - - Sequence alignment metadata - + + + beta12orEarlier + 1.5 + Report of general information on a sequence alignment, typically include a description, sequence identifiers and alignment score. - beta12orEarlier + + Sequence alignment metadata true - 1.5 - - - - Sequence alignment report - - Use this for any computer-generated reports on sequence alignments, and for general information (metadata) on a sequence alignment, such as a description, sequence identifiers and alignment score. + + + beta12orEarlier An informative report of molecular sequence alignment-derived data or metadata. - beta12orEarlier - - + + + Use this for any computer-generated reports on sequence alignments, and for general information (metadata) on a sequence alignment, such as a description, sequence identifiers and alignment score. + Sequence alignment report - - Sequence profile alignment - - beta12orEarlier + + + beta12orEarlier A profile-profile alignment (each profile typically representing a sequence alignment). - - + Sequence profile alignment + + + Profile-profile alignment - - Sequence-profile alignment - - beta12orEarlier + + + beta12orEarlier Alignment of one or more molecular sequence(s) to one or more sequence profile(s) (each profile typically representing a sequence alignment). + + Data associated with the alignment might also be included, e.g. ranked list of best-scoring sequences and a graphical representation of scores. - - + Sequence-profile alignment - - Sequence distance matrix - - beta12orEarlier + + + beta12orEarlier Moby:phylogenetic_distance_matrix A matrix of estimated evolutionary distance between molecular sequences, such as is suitable for phylogenetic tree calculation. Phylogenetic distance matrix + + Methods might perform character compatibility analysis or identify patterns of similarity in an alignment or data matrix. - - + Sequence distance matrix - - Phylogenetic character data - + + + beta12orEarlier Basic character data from which a phylogenetic tree may be generated. + + As defined, this concept would also include molecular sequences, microsatellites, polymorphisms (RAPDs, RFLPs, or AFLPs), restriction sites and fragments + Phylogenetic character data http://www.evolutionaryontology.org/cdao.owl#Character - beta12orEarlier - - - - Phylogenetic tree - + + - - + + - Phylogeny + beta12orEarlier Moby:Tree - http://www.evolutionaryontology.org/cdao.owl#Tree - A phylogenetic tree is usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. See also 'Phylogenetic tree image'. - http://purl.bioontology.org/ontology/MSH/D010802 + Moby:myTree Moby:phylogenetic_tree The raw data (not just an image) from which a phylogenetic tree is directly generated or plotted, such as topology, lengths (in time or in expected amounts of variance) and a confidence interval for each length. - beta12orEarlier - Moby:myTree - - + Phylogeny + + + A phylogenetic tree is usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. See also 'Phylogenetic tree image'. + Phylogenetic tree + http://purl.bioontology.org/ontology/MSH/D010802 + http://www.evolutionaryontology.org/cdao.owl#Tree - - Comparison matrix - - beta12orEarlier - The comparison matrix might include matrix name, optional comment, height and width (or size) of matrix, an index row/column (of characters) and data rows/columns (of integers or floats). + + + beta12orEarlier Matrix of integer or floating point numbers for amino acid or nucleotide sequence comparison. Substitution matrix - - + + + The comparison matrix might include matrix name, optional comment, height and width (or size) of matrix, an index row/column (of characters) and data rows/columns (of integers or floats). + Comparison matrix - - Protein topology - - beta12orEarlier - beta12orEarlier + + + beta12orEarlier + beta12orEarlier Predicted or actual protein topology represented as a string of protein secondary structure elements. - true + + The location and size of the secondary structure elements and intervening loop regions is usually indicated. - - + Protein topology + true - + + + beta12orEarlier + 1.8 + Secondary structure (predicted or real) of a protein. + + Protein features report (secondary structure) - - beta12orEarlier - 1.8 true - Topic concerning secondary structure (predicted or real) of a protein. - - - - Protein features report (super-secondary) - - 1.8 + + + beta12orEarlier + 1.8 + Super-secondary structure of protein sequence(s). + + Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. + Protein features report (super-secondary) true - beta12orEarlier - Topic concerning super-secondary structure of protein sequence(s). - - - - Secondary structure alignment (protein) - - + + + + beta12orEarlier Alignment of the (1D representations of) secondary structure of two or more proteins. - beta12orEarlier - - + + + Secondary structure alignment (protein) - - Secondary structure alignment metadata (protein) - + + + beta12orEarlier + beta12orEarlier + An informative report on protein secondary structure alignment-derived data or metadata. - beta12orEarlier - beta12orEarlier + + Secondary structure alignment metadata (protein) true - - - - RNA secondary structure - + + - - + + - An informative report of secondary structure (predicted or real) of an RNA molecule. - This includes thermodynamically stable or evolutionarily conserved structures such as knots, pseudoknots etc. + beta12orEarlier Moby:RNAStructML + An informative report of secondary structure (predicted or real) of an RNA molecule. Secondary structure (RNA) - beta12orEarlier - - + + + This includes thermodynamically stable or evolutionarily conserved structures such as knots, pseudoknots etc. + RNA secondary structure - - Secondary structure alignment (RNA) - + + + beta12orEarlier Moby:RNAStructAlignmentML Alignment of the (1D representations of) secondary structure of two or more RNA molecules. - beta12orEarlier - - + + + Secondary structure alignment (RNA) - + + + beta12orEarlier + beta12orEarlier + + An informative report of RNA secondary structure alignment-derived data or metadata. + Secondary structure alignment metadata (RNA) - true - beta12orEarlier - An informative report of RNA secondary structure alignment-derived data or metadata. - beta12orEarlier - - - - Structure - + + - - + + - beta12orEarlier + beta12orEarlier + 3D coordinate and associated data for a macromolecular tertiary (3D) structure or part of a structure. Coordinate model Structure data + + The coordinate data may be predicted or real. + Structure http://purl.bioontology.org/ontology/MSH/D015394 - 3D coordinate and associated data for a macromolecular tertiary (3D) structure or part of a structure. - - - + + + beta12orEarlier + beta12orEarlier + + An entry from a molecular tertiary (3D) structure database. + Tertiary structure record - true - beta12orEarlier - beta12orEarlier - An entry from a molecular tertiary (3D) structure database. - - - - Structure database search results - - 1.8 + + + beta12orEarlier + 1.8 + Results (hits) from searching a database of tertiary structure. - beta12orEarlier + + Structure database search results true - - - - Structure alignment - + + - - + + + beta12orEarlier Alignment (superimposition) of molecular tertiary (3D) structures. + + A tertiary structure alignment will include the untransformed coordinates of one macromolecule, followed by the second (or subsequent) structure(s) with all the coordinates transformed (by rotation / translation) to give a superposition. - beta12orEarlier - - + Structure alignment - - Structure alignment report - - beta12orEarlier - This is a broad data type and is used a placeholder for other, more specific types. + + + beta12orEarlier An informative report of molecular tertiary structure alignment-derived data. - - + + + This is a broad data type and is used a placeholder for other, more specific types. + Structure alignment report - - Structure similarity score - - beta12orEarlier + + + beta12orEarlier A value representing molecular structure similarity, measured from structure alignment or some other type of structure comparison. - - + + + Structure similarity score - - Structural profile - + + - - + + - beta12orEarlier - 3D profile + beta12orEarlier Some type of structural (3D) profile or template (representing a structure or structure alignment). + 3D profile Structural (3D) profile - - + + + Structural profile - - Structural (3D) profile alignment - - beta12orEarlier - Structural profile alignment + + + beta12orEarlier A 3D profile-3D profile alignment (each profile representing structures or a structure alignment). - - + Structural profile alignment + + + Structural (3D) profile alignment - - Sequence-3D profile alignment - - Sequence-structural profile alignment - 1.5 + + + beta12orEarlier + 1.5 + An alignment of a sequence to a 3D profile (representing structures or a structure alignment). - beta12orEarlier + Sequence-structural profile alignment + + Sequence-3D profile alignment true - - - - Protein sequence-structure scoring matrix - - beta12orEarlier + + + beta12orEarlier Matrix of values used for scoring sequence-structure compatibility. - - + + + Protein sequence-structure scoring matrix - - Sequence-structure alignment - - beta12orEarlier + + + beta12orEarlier An alignment of molecular sequence to structure (from threading sequence(s) through 3D structure or representation of structure(s)). - - + + + Sequence-structure alignment - - Amino acid annotation - + + + beta12orEarlier + 1.4 + An informative report about a specific amino acid. - 1.4 + + Amino acid annotation true - beta12orEarlier - - - + + + beta12orEarlier + 1.4 + + An informative report about a specific peptide. + Peptide annotation - - 1.4 true - An informative report about a specific peptide. - beta12orEarlier - - - - Protein report - - Gene product annotation - beta12orEarlier + + + beta12orEarlier An informative human-readable report about one or more specific protein molecules or protein structural domains, derived from analysis of primary (sequence or structural) data. - - + Gene product annotation + + + Protein report - - Protein property - - Protein physicochemical property + + + beta12orEarlier A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a protein molecule or model. - beta12orEarlier - Protein sequence statistics + Protein physicochemical property Protein properties + Protein sequence statistics + + The report may be based on analysis of nucleic acid sequence or structural data. This is a broad data type and is used a placeholder for other, more specific types. - - + Protein property - + + + beta12orEarlier + 1.8 + 3D structural motifs in a protein. + Protein structural motifs and surfaces - - Topic concerning 3D structural motifs in a protein. true - 1.8 - beta12orEarlier - Protein 3D motifs - - + + + beta12orEarlier + 1.5 + + Data concerning the classification of the sequences and/or structures of protein structural domain(s). + Protein domain classification - true - Data concerning the classification of the sequences and/or structures of protein structural domain(s). - 1.5 - beta12orEarlier - - - + + + beta12orEarlier + 1.8 + structural domains or 3D folds in a protein or polypeptide chain. + + Protein features report (domains) - true - 1.8 - Topic concerning structural domains or 3D folds in a protein or polypeptide chain. - beta12orEarlier - - - - Protein architecture report - - 1.4 + + + beta12orEarlier + 1.4 + An informative report on architecture (spatial arrangement of secondary structure) of a protein structure. - Protein property (architecture) - Protein structure report (architecture) - beta12orEarlier + + Protein architecture report true - - - + + + beta12orEarlier + 1.8 + A report on an analysis or model of protein folding properties, folding pathways, residues or sites that are key to protein folding, nucleation or stabilisation centers etc. + + Protein folding report - - beta12orEarlier - A report on an analysis or model of protein folding properties, folding pathways, residues or sites that are key to protein folding, nucleation or stabilization centers etc. true - 1.8 - - - - Protein features (mutation) - - This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. + + + beta12orEarlier + beta13 + Data on the effect of (typically point) mutation on protein folding, stability, structure and function. + + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. + Protein features (mutation) true - beta12orEarlier - Protein property (mutation) - Protein structure report (mutation) - beta13 - Protein report (mutation) - - - - Protein interaction raw data - - This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. + + + beta12orEarlier Protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc. - beta12orEarlier - - + + + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. + Protein interaction raw data - - Protein interaction report - + + - - + + - beta12orEarlier - Protein report (interaction) + beta12orEarlier + An informative report on interactions (predicted or known) within or between a protein, structural domain or part of a protein. This includes intra- and inter-residue contacts and distances, as well as interactions with other proteins and non-protein entities such as nucleic acid, metal atoms, water, ions etc. + + + Protein interaction record - An informative report on the interactions (predicted or known) of a protein, protein domain or part of a protein with some other molecule(s), which might be another protein, nucleic acid or some other ligand. - - + Protein report (interaction) + Atom interaction data + Protein non-covalent interactions report + Residue interaction data + + + Protein interaction report - - Protein family report - + + - - + + - beta12orEarlier + beta12orEarlier + Protein classification data An informative report on a specific protein family or other classification or group of protein sequences or structures. Protein family annotation - Protein classification data - - + + + Protein family report - - Vmax - - beta12orEarlier + + + beta12orEarlier The maximum initial velocity or rate of a reaction. It is the limiting velocity as substrate concentrations get very large. - - + + + Vmax - - Km - + + + beta12orEarlier Km is the concentration (usually in Molar units) of substrate that leads to half-maximal velocity of an enzyme-catalysed reaction. - beta12orEarlier - - + + + Km - + + + beta12orEarlier + 1.4 + + An informative report about a specific nucleotide base. + Nucleotide base annotation - - beta12orEarlier true - An informative report about a specific nucleotide base. - 1.4 - - - - Nucleic acid property - + + + beta12orEarlier A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a nucleic acid molecule. - The report may be based on analysis of nucleic acid sequence or structural data. This is a broad data type and is used a placeholder for other, more specific types. Nucleic acid physicochemical property - beta12orEarlier - - + GC-content + + + The report may be based on analysis of nucleic acid sequence or structural data. This is a broad data type and is used a placeholder for other, more specific types. + Nucleic acid property - - Codon usage data - + + - - + + - beta12orEarlier + beta12orEarlier Data derived from analysis of codon usage (typically a codon usage table) of DNA sequences. + + This is a broad data type and is used a placeholder for other, more specific types. - - + Codon usage data - - Gene report - - Gene structure (repot) + + + beta12orEarlier + Moby:GeneInfo + Moby:gene + Moby_namespace:Human_Readable_Description A report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc. Gene and transcript structure (report) + Gene annotation Gene features report + Gene function (report) + Gene structure (repot) Nucleic acid features (gene and transcript structure) - Moby:gene + + This includes any report on a particular locus or gene. This might include the gene name, description, summary and so on. It can include details about the function of a gene, such as its encoded protein or a functional classification of the gene sequence along according to the encoded protein(s). - Gene annotation - beta12orEarlier - Moby_namespace:Human_Readable_Description - Gene function (report) - Moby:GeneInfo - - + Gene report - + + + beta12orEarlier + beta12orEarlier + + A report on the classification of nucleic acid / gene sequences according to the functional classification of their gene products. + Gene classification - - beta12orEarlier true - A report on the classification of nucleic acid / gene sequences according to the functional classification of their gene products. - beta12orEarlier - - - + + + beta12orEarlier + 1.8 + stable, naturally occuring mutations in a nucleotide sequence including alleles, naturally occurring mutations such as single base nucleotide substitutions, deletions and insertions, RFLPs and other polymorphisms. + + DNA variation - - Topic concerning stable, naturally occuring mutations in a nucleotide sequence including alleles, naturally occurring mutations such as single base nucleotide substitutions, deletions and insertions, RFLPs and other polymorphisms. true - 1.8 - beta12orEarlier - - - - Chromosome report - - - - - - - - beta12orEarlier + + + beta12orEarlier An informative report on a specific chromosome. + + This includes basic information. e.g. chromosome number, length, karyotype features, chromosome sequence etc. - - + Chromosome report - - Genotype/phenotype report - + + + beta12orEarlier An informative report on the set of genes (or allelic forms) present in an individual, organism or cell and associated with a specific physical characteristic, or a report concerning an organisms traits and phenotypes. Genotype/phenotype annotation - beta12orEarlier - - + + + Genotype/phenotype report - + + + beta12orEarlier + 1.8 + PCR primers and hybridisation oligos in a nucleic acid sequence. + + Nucleic acid features report (primers) - true - 1.8 - beta12orEarlier - Topic concerning PCR primers and hybridization oligos in a nucleic acid sequence. - - - + + + beta12orEarlier + 1.8 + PCR experiments, e.g. quantitative real-time PCR. + + PCR experiment report - true - beta12orEarlier - 1.8 - Topic concerning PCR experiments, e.g. quantitative real-time PCR. - - - - Sequence trace - - + + + + beta12orEarlier Fluorescence trace data generated by an automated DNA sequencer, which can be interprted as a molecular sequence (reads), given associated sequencing metadata such as base-call quality scores. + + This is the raw data produced by a DNA sequencing machine. - beta12orEarlier - - + Sequence trace - - Sequence assembly - - beta12orEarlier + + + beta12orEarlier An assembly of fragments of a (typically genomic) DNA sequence. - http://en.wikipedia.org/wiki/Sequence_assembly + Contigs + SO:0000353 SO:0001248 + + Typically, an assembly is a collection of contigs (for example ESTs and genomic DNA fragments) that are ordered, aligned and merged. Annotation of the assembled sequence might be included. - SO:0000353 - - + Sequence assembly + http://en.wikipedia.org/wiki/Sequence_assembly - Perhaps surprisingly, the definition of 'SO:assembly' is narrower than the 'SO:sequence_assembly'. + + SO:0001248 - - + Perhaps surprisingly, the definition of 'SO:assembly' is narrower than the 'SO:sequence_assembly'. - - Radiation Hybrid (RH) scores - - beta12orEarlier - Radiation Hybrid (RH) scores are used in Radiation Hybrid mapping. + + + beta12orEarlier Radiation hybrid scores (RH) scores for one or more markers. - - + + + Radiation Hybrid (RH) scores are used in Radiation Hybrid mapping. + Radiation Hybrid (RH) scores - - Genetic linkage report - - beta12orEarlier + + + beta12orEarlier + An informative report on the linkage of alleles. Gene annotation (linkage) Linkage disequilibrium (report) - An informative report on the linkage of alleles. + + This includes linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome). - - + Genetic linkage report - - Gene expression profile - + + + beta12orEarlier Data quantifying the level of expression of (typically) multiple genes, derived for example from microarray experiments. - beta12orEarlier - Gene expression pattern - - + Gene expression pattern + + + Gene expression profile - + + + beta12orEarlier + 1.8 + microarray experiments including conditions, protocol, sample:data relationships etc. + + Microarray experiment report - - Topic concerning microarray experiments including conditions, protocol, sample:data relationships etc. true - 1.8 - beta12orEarlier - - - + + + beta12orEarlier + beta13 + + Data on oligonucleotide probes (typically for use with DNA microarrays). + Oligonucleotide probe data - - beta12orEarlier - beta13 true - Data on oligonucleotide probes (typically for use with DNA microarrays). - - - + + + beta12orEarlier + beta12orEarlier + + Output from a serial analysis of gene expression (SAGE) experiment. + SAGE experimental data - - beta12orEarlier true - Output from a serial analysis of gene expression (SAGE) experiment. - Serial analysis of gene expression (SAGE) experimental data - beta12orEarlier - - - - MPSS experimental data - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + Massively parallel signature sequencing (MPSS) data. - beta12orEarlier - Massively parallel signature sequencing (MPSS) experimental data + + MPSS experimental data true - - - + + + beta12orEarlier + beta12orEarlier + + Sequencing by synthesis (SBS) data. + SBS experimental data - - beta12orEarlier - beta12orEarlier true - Sequencing by synthesis (SBS) experimental data - Sequencing by synthesis (SBS) data. - - - - Sequence tag profile (with gene assignment) - - beta12orEarlier + + + beta12orEarlier + 1.14 Tag to gene assignments (tag mapping) of SAGE, MPSS and SBS data. Typically this is the sequencing-based expression profile annotated with gene identifiers. - - + + + Sequence tag profile (with gene assignment) + true - - Protein X-ray crystallographic data - + + + beta12orEarlier X-ray crystallography data. - beta12orEarlier - - + + + Protein X-ray crystallographic data - - Protein NMR data - + + + beta12orEarlier Protein nuclear magnetic resonance (NMR) raw data. - beta12orEarlier - - + + + Protein NMR data - - Protein circular dichroism (CD) spectroscopic data - - beta12orEarlier + + + beta12orEarlier Protein secondary structure from protein coordinate or circular dichroism (CD) spectroscopic data. - - + + + Protein circular dichroism (CD) spectroscopic data - - Electron microscopy volume map - + + - - + + - beta12orEarlier + beta12orEarlier Volume map data from electron microscopy. EM volume map - - + + + Electron microscopy volume map - - Electron microscopy model - + + - - + + - beta12orEarlier + beta12orEarlier Annotation on a structural 3D model (volume map) from electron microscopy. + + This might include the location in the model of the known features of a particular macromolecule. - - + Electron microscopy model - - 2D PAGE image - + + - - + + - beta12orEarlier + beta12orEarlier Two-dimensional gel electrophoresis image - - + + + 2D PAGE image - - Mass spectrometry spectra - + + - - + + - beta12orEarlier + beta12orEarlier Spectra from mass spectrometry. - - + + + Mass spectrometry spectra - - Peptide mass fingerprint - - + + + - - + + + beta12orEarlier + A set of peptide masses (peptide mass fingerprint) from mass spectrometry. Peak list Protein fingerprint - A set of peptide masses (peptide mass fingerprint) from mass spectrometry. - beta12orEarlier - - + Molecular weights standard fingerprint + + + A molecular weight standard fingerprint is standard protonated molecular masses e.g. from trypsin (modified porcine trypsin, Promega) and keratin peptides. + Peptide mass fingerprint - - Peptide identification - + + + - - + + - Protein or peptide identifications with evidence supporting the identifications, typically from comparing a peptide mass fingerprint (from mass spectrometry) to a sequence database. - beta12orEarlier - - + beta12orEarlier + Protein or peptide identifications with evidence supporting the identifications, for example from comparing a peptide mass fingerprint (from mass spectrometry) to a sequence database, or the set of typical spectra one obtains when running a protein through a mass spectrometer. + 'Protein identification' + + + Peptide identification - + + + beta12orEarlier + beta12orEarlier + + An informative report about a specific biological pathway or network, typically including a map (diagram) of the pathway. + Pathway or network annotation - - beta12orEarlier true - An informative report about a specific biological pathway or network, typically including a map (diagram) of the pathway. - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + A map (typically a diagram) of a biological pathway. + Biological pathway map - - beta12orEarlier true - A map (typically a diagram) of a biological pathway. - beta12orEarlier - - - + + + beta12orEarlier + 1.5 + + A definition of a data resource serving one or more types of data, including metadata and links to the resource or data proper. + Data resource definition - - beta12orEarlier true - 1.5 - A definition of a data resource serving one or more types of data, including metadata and links to the resource or data proper. - - - - Workflow metadata - + + + beta12orEarlier Basic information, annotation or documentation concerning a workflow (but not the workflow itself). - beta12orEarlier - - + + + Workflow metadata - - Mathematical model - + + - - + + - Biological model - beta12orEarlier + beta12orEarlier A biological model represented in mathematical terms. - - + Biological model + + + Mathematical model - - Statistical estimate score - - beta12orEarlier + + + beta12orEarlier A value representing estimated statistical significance of some observed data; typically sequence database hits. - - + + + Statistical estimate score - - EMBOSS database resource definition - - beta12orEarlier + + + beta12orEarlier + 1.5 + Resource definition for an EMBOSS database. + + EMBOSS database resource definition true - 1.5 - - - - Version information - - "http://purl.obolibrary.org/obo/IAO_0000129" - 1.5 - Development status / maturity may be part of the version information, for example in case of tools, standards, or some data records. - http://www.ebi.ac.uk/swo/maturity/SWO_9000061 - beta12orEarlier + + + beta12orEarlier + 1.5 + Information on a version of software or data, for example name, version number and release date. - http://semanticscience.org/resource/SIO_000653 + + Development status / maturity may be part of the version information, for example in case of tools, standards, or some data records. + Version information true - http://usefulinc.com/ns/doap#Version - - - - Database cross-mapping - - beta12orEarlier + + + beta12orEarlier A mapping of the accession numbers (or other database identifier) of entries between (typically) two biological or biomedical databases. + + The cross-mapping is typically a table where each row is an accession number and each column is a database being cross-referenced. The cells give the accession number or identifier of the corresponding entry in a database. If a cell in the table is not filled then no mapping could be found for the database. Additional information might be given on version, date etc. - - + Database cross-mapping - - Data index - + + - - + + + beta12orEarlier An index of data of biological relevance. - beta12orEarlier - - + + + Data index - - Data index report - + + - - + + + beta12orEarlier A report of an analysis of an index of biological data. Database index annotation - beta12orEarlier - - + + + Data index report - - Database metadata - + + + beta12orEarlier Basic information on bioinformatics database(s) or other data sources such as name, type, description, URL etc. - beta12orEarlier - - + + + Database metadata - - Tool metadata - - beta12orEarlier + + + beta12orEarlier Basic information about one or more bioinformatics applications or packages, such as name, type, description, or other documentation. - - + + + Tool metadata - + + + beta12orEarlier + 1.5 + + Textual metadata on a submitted or completed job. + Job metadata - - beta12orEarlier true - 1.5 - Moby:PDGJOB - Textual metadata on a submitted or completed job. - - - - User metadata - - beta12orEarlier + + + beta12orEarlier Textual metadata on a software author or end-user, for example a person or other software. - - + + + User metadata - - Small molecule report - + + - - + + - Small molecule annotation - Small molecule report - Chemical structure report + beta12orEarlier An informative report on a specific chemical compound. - beta12orEarlier Chemical compound annotation - - + Chemical structure report + Small molecule annotation + + + Small molecule report - - Cell line report - - Organism strain data - Cell line annotation + + + beta12orEarlier Report on a particular strain of organism cell line including plants, virus, fungi and bacteria. The data typically includes strain number, organism type, growth conditions, source and so on. - beta12orEarlier - - + Cell line annotation + Organism strain data + + + Cell line report - - Scent annotation - - beta12orEarlier + + + beta12orEarlier + 1.4 + An informative report about a specific scent. - 1.4 + + Scent annotation true - - - - Ontology term - - Ontology class name - beta12orEarlier + + + beta12orEarlier A term (name) from an ontology. + Ontology class name Ontology terms - - + + + Ontology term - - Ontology concept data - - beta12orEarlier + + + beta12orEarlier + Data concerning or derived from a concept from a biological ontology. Ontology class metadata Ontology term metadata - Data concerning or derived from a concept from a biological ontology. - - + + + Ontology concept data - - Keyword - - Phrases - Keyword(s) or phrase(s) used (typically) for text-searching purposes. - Boolean operators (AND, OR and NOT) and wildcard characters may be allowed. - Moby:QueryString - beta12orEarlier + + + beta12orEarlier Moby:BooleanQueryString - Moby:Wildcard_Query Moby:Global_Keyword - Terms - Text - - + Moby:QueryString + Moby:Wildcard_Query + Keyword(s) or phrase(s) used (typically) for text-searching purposes. + Phrases + Term + + + Boolean operators (AND, OR and NOT) and wildcard characters may be allowed. + Keyword - - Citation - - Bibliographic data that uniquely identifies a scientific article, book or other published material. - A bibliographic reference might include information such as authors, title, journal name, date and (possibly) a link to the abstract or full-text of the article if available. + + + beta12orEarlier Moby:GCP_SimpleCitation - Reference - Bibliographic reference Moby:Publication - beta12orEarlier - - + Bibliographic data that uniquely identifies a scientific article, book or other published material. + Bibliographic reference + Reference + + + A bibliographic reference might include information such as authors, title, journal name, date and (possibly) a link to the abstract or full-text of the article if available. + Citation - + + + + beta12orEarlier + A scientific text, typically a full text article from a scientific journal. + Article text + Scientific article + + Article - - - - - - - - A document of scientific text, typically a full text article from a scientific journal. - beta12orEarlier - - - - Text mining report - + + + + beta12orEarlier An abstract of the results of text mining. - beta12orEarlier Text mining output + + A text mining abstract will typically include an annotated a list of words or sentences extracted from one or more scientific articles. - - + Text mining report - + + + beta12orEarlier + beta12orEarlier + + An identifier of a biological entity or phenomenon. + Entity identifier - - beta12orEarlier true - beta12orEarlier - An identifier of a biological entity or phenomenon. - - - + + + beta12orEarlier + beta12orEarlier + + An identifier of a data resource. + Data resource identifier - true - An identifier of a data resource. - beta12orEarlier - beta12orEarlier - - - - Identifier (typed) - - beta12orEarlier - This concept exists only to assist EDAM maintenance and navigation in graphical browsers. It does not add semantic information. This branch provides an alternative organisation of the concepts nested under 'Accession' and 'Name'. All concepts under here are already included under 'Accession' or 'Name'. + + + beta12orEarlier An identifier that identifies a particular type of data. - - - + + + + This concept exists only to assist EDAM maintenance and navigation in graphical browsers. It does not add semantic information. This branch provides an alternative organisation of the concepts nested under 'Accession' and 'Name'. All concepts under here are already included under 'Accession' or 'Name'. + Identifier (typed) - - Tool identifier - + + + beta12orEarlier An identifier of a bioinformatics tool, e.g. an application or web service. - beta12orEarlier - - - + + + + Tool identifier - + + + beta12orEarlier + beta12orEarlier + + Name or other identifier of a discrete entity (any biological thing with a distinct, discrete physical existence). + Discrete entity identifier - - beta12orEarlier true - beta12orEarlier - Name or other identifier of a discrete entity (any biological thing with a distinct, discrete physical existence). - - - + + + beta12orEarlier + beta12orEarlier + + Name or other identifier of an entity feature (a physical part or region of a discrete biological entity, or a feature that can be mapped to such a thing). + Entity feature identifier - true - beta12orEarlier - Name or other identifier of an entity feature (a physical part or region of a discrete biological entity, or a feature that can be mapped to such a thing). - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + Name or other identifier of a collection of discrete biological entities. + Entity collection identifier - - beta12orEarlier true - beta12orEarlier - Name or other identifier of a collection of discrete biological entities. - - - + + + beta12orEarlier + beta12orEarlier + + Name or other identifier of a physical, observable biological occurrence or event. + Phenomenon identifier - - beta12orEarlier true - beta12orEarlier - Name or other identifier of a physical, observable biological occurrence or event. - - - - Molecule identifier - + + + beta12orEarlier Name or other identifier of a molecule. - beta12orEarlier - - - + + + + Molecule identifier - - Atom ID - - Atom identifier + + + beta12orEarlier Identifier (e.g. character symbol) of a specific atom. - beta12orEarlier - - - + Atom identifier + + + + Atom ID - - Molecule name - - + + + + beta12orEarlier Name of a specific molecule. - beta12orEarlier - - - + + + + Molecule name - - Molecule type - + + + beta12orEarlier + Protein|DNA|RNA + 1.5 + + A label (text token) describing the type a molecule. + For example, 'Protein', 'DNA', 'RNA' etc. + Molecule type true - 1.5 - beta12orEarlier - A label (text token) describing the type a molecule. - Protein|DNA|RNA - - - + + + beta12orEarlier + beta12orEarlier + + Unique identifier of a chemical compound. + Chemical identifier - true - beta12orEarlier - beta12orEarlier - Unique identifier of a chemical compound. - - - - Chromosome name - - + + + - - + + - beta12orEarlier + beta12orEarlier Name of a chromosome. - - - + + + + Chromosome name - - Peptide identifier - + + + beta12orEarlier Identifier of a peptide chain. - beta12orEarlier - - - + + + + Peptide identifier - - Protein identifier - + + - - + + - beta12orEarlier + beta12orEarlier Identifier of a protein. - - - + + + + Protein identifier - - Compound name - - - Chemical name + + + + beta12orEarlier Unique name of a chemical compound. - beta12orEarlier - - - + Chemical name + + + + Compound name - - Chemical registry number - - beta12orEarlier + + + beta12orEarlier Unique registry number of a chemical compound. - - - + + + + Chemical registry number - + + + beta12orEarlier + beta12orEarlier + + Code word for a ligand, for example from a PDB file. + Ligand identifier - true - beta12orEarlier - Code word for a ligand, for example from a PDB file. - beta12orEarlier - - - - Drug identifier - + + - - + + - beta12orEarlier + beta12orEarlier Identifier of a drug. - - - + + + + Drug identifier - - Amino acid identifier - + + - - + + + beta12orEarlier Identifier of an amino acid. - beta12orEarlier Residue identifier - - - + + + + Amino acid identifier - - Nucleotide identifier - - beta12orEarlier + + + beta12orEarlier Name or other identifier of a nucleotide. - - - + + + + Nucleotide identifier - - Monosaccharide identifier - - beta12orEarlier + + + beta12orEarlier Identifier of a monosaccharide. - - - + + + + Monosaccharide identifier - - Chemical name (ChEBI) - - ChEBI chemical name + + + beta12orEarlier Unique name from Chemical Entities of Biological Interest (ChEBI) of a chemical compound. - beta12orEarlier + ChEBI chemical name + + + This is the recommended chemical name for use for example in database annotation. - - - + Chemical name (ChEBI) - - Chemical name (IUPAC) - + + + beta12orEarlier IUPAC recommended name of a chemical compound. IUPAC chemical name - beta12orEarlier - - - + + + + Chemical name (IUPAC) - - Chemical name (INN) - + + + beta12orEarlier + International Non-proprietary Name (INN or 'generic name') of a chemical compound, assigned by the World Health Organisation (WHO). INN chemical name - beta12orEarlier - International Non-proprietary Name (INN or 'generic name') of a chemical compound, assigned by the World Health Organization (WHO). - - - + + + + Chemical name (INN) - - Chemical name (brand) - + + + beta12orEarlier Brand name of a chemical compound. Brand chemical name - beta12orEarlier - - - + + + + Chemical name (brand) - - Chemical name (synonymous) - - beta12orEarlier - Synonymous chemical name + + + beta12orEarlier Synonymous name of a chemical compound. - - - + Synonymous chemical name + + + + Chemical name (synonymous) - - Chemical registry number (CAS) - - CAS chemical registry number + + + beta12orEarlier CAS registry number of a chemical compound. - beta12orEarlier - - - + CAS chemical registry number + + + + Chemical registry number (CAS) - - Chemical registry number (Beilstein) - - Beilstein chemical registry number - beta12orEarlier + + + beta12orEarlier Beilstein registry number of a chemical compound. - - - + Beilstein chemical registry number + + + + Chemical registry number (Beilstein) - - Chemical registry number (Gmelin) - - Gmelin chemical registry number - beta12orEarlier + + + beta12orEarlier Gmelin registry number of a chemical compound. - - - + Gmelin chemical registry number + + + + Chemical registry number (Gmelin) - - HET group name - + + + beta12orEarlier 3-letter code word for a ligand (HET group) from a PDB file, for example ATP. - Short ligand name Component identifier code - beta12orEarlier - - - + Short ligand name + + + + HET group name - - Amino acid name - + + + beta12orEarlier String of one or more ASCII characters representing an amino acid. - beta12orEarlier - - - + + + + Amino acid name - - Nucleotide code - - - beta12orEarlier + + + + beta12orEarlier String of one or more ASCII characters representing a nucleotide. - - - + + + + Nucleotide code - - Polypeptide chain ID - + + - - + + - beta12orEarlier + beta12orEarlier + PDBML:pdbx_PDB_strand_id WHATIF: chain - Chain identifier Identifier of a polypeptide chain from a protein. - PDBML:pdbx_PDB_strand_id - Protein chain identifier - PDB strand id + Chain identifier PDB chain identifier - This is typically a character (for the chain) appended to a PDB identifier, e.g. 1cukA + PDB strand id Polypeptide chain identifier - - - + Protein chain identifier + + + + This is typically a character (for the chain) appended to a PDB identifier, e.g. 1cukA + Polypeptide chain ID - - Protein name - - + + + + beta12orEarlier Name of a protein. - beta12orEarlier - - - + + + + Protein name - - Enzyme identifier - - beta12orEarlier + + + beta12orEarlier Name or other identifier of an enzyme or record from a database of enzymes. - - - + + + + Enzyme identifier - - EC number - - [0-9]+\.-\.-\.-|[0-9]+\.[0-9]+\.-\.-|[0-9]+\.[0-9]+\.[0-9]+\.-|[0-9]+\.[0-9]+\.[0-9]+\.[0-9]+ - EC code + + + beta12orEarlier + [0-9]+\.-\.-\.-|[0-9]+\.[0-9]+\.-\.-|[0-9]+\.[0-9]+\.[0-9]+\.-|[0-9]+\.[0-9]+\.[0-9]+\.[0-9]+ + Moby:Annotated_EC_Number Moby:EC_Number An Enzyme Commission (EC) number of an enzyme. EC - Moby:Annotated_EC_Number - beta12orEarlier + EC code Enzyme Commission number - - - + + + + EC number - - Enzyme name - - + + + + beta12orEarlier Name of an enzyme. - beta12orEarlier - - - + + + + Enzyme name - - Restriction enzyme name - + + + beta12orEarlier Name of a restriction enzyme. - beta12orEarlier - - - + + + + Restriction enzyme name - - Sequence position specification - - 1.5 + + + beta12orEarlier + 1.5 + A specification (partial or complete) of one or more positions or regions of a molecular sequence or map. - beta12orEarlier + + Sequence position specification true - - - - Sequence feature ID - - + + + + beta12orEarlier A unique identifier of molecular sequence feature, for example an ID of a feature that is unique within the scope of the GFF file. - beta12orEarlier - - - + + + + Sequence feature ID - - Sequence position - - WHATIF: number - WHATIF: PDBx_atom_site - beta12orEarlier + + + beta12orEarlier PDBML:_atom_site.id - SO:0000735 + WHATIF: PDBx_atom_site + WHATIF: number A position of one or more points (base or residue) in a sequence, or part of such a specification. - - + SO:0000735 + + + Sequence position - - Sequence range - - beta12orEarlier + + + beta12orEarlier Specification of range(s) of sequence positions. - - + + + Sequence range - - Nucleic acid feature identifier - - beta12orEarlier - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + Name or other identifier of an nucleic acid feature. + + Nucleic acid feature identifier true - - - - Protein feature identifier - + + + beta12orEarlier + beta12orEarlier + Name or other identifier of a protein feature. + + Protein feature identifier true - beta12orEarlier - beta12orEarlier - - - - Sequence feature key - - Sequence feature method + + + beta12orEarlier The type of a sequence feature, typically a term or accession from the Sequence Ontology, for example an EMBL or Swiss-Prot sequence feature key. + Sequence feature method Sequence feature type - beta12orEarlier + + A feature key indicates the biological nature of the feature or information about changes to or versions of the sequence. - - + Sequence feature key - - Sequence feature qualifier - - beta12orEarlier + + + beta12orEarlier Typically one of the EMBL or Swiss-Prot feature qualifiers. + + Feature qualifiers hold information about a feature beyond that provided by the feature key and location. - - + Sequence feature qualifier - - Sequence feature label - + + + + + beta12orEarlier + A name of a sequence feature, e.g. the name of a feature to be displayed to an end-user. Typically an EMBL or Swiss-Prot feature label. Sequence feature name - Typically an EMBL or Swiss-Prot feature label. + + A feature label identifies a feature of a sequence database entry. When used with the database name and the entry's primary accession number, it is a unique identifier of that feature. - beta12orEarlier - - + Sequence feature label - - EMBOSS Uniform Feature Object - - - beta12orEarlier - UFO + + + + beta12orEarlier The name of a sequence feature-containing entity adhering to the standard feature naming scheme used by all EMBOSS applications. - - + UFO + + + EMBOSS Uniform Feature Object - - Codon name - - beta12orEarlier - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + String of one or more ASCII characters representing a codon. + + Codon name true - - - - Gene identifier - + + - - + + + beta12orEarlier Moby:GeneAccessionList An identifier of a gene, such as a name/symbol or a unique identifier of a gene in a database. - beta12orEarlier - - - + + + + Gene identifier - - Gene symbol - - Moby_namespace:Global_GeneSymbol - beta12orEarlier + + + beta12orEarlier Moby_namespace:Global_GeneCommonName + Moby_namespace:Global_GeneSymbol The short name of a gene; a single word that does not contain white space characters. It is typically derived from the gene name. - - - + + + + Gene symbol - - Gene ID (NCBI) - - - NCBI geneid - Gene identifier (NCBI) + + + + beta12orEarlier + http://www.geneontology.org/doc/GO.xrf_abbs:LocusID http://www.geneontology.org/doc/GO.xrf_abbs:NCBI_Gene + An NCBI unique identifier of a gene. Entrez gene ID Gene identifier (Entrez) - http://www.geneontology.org/doc/GO.xrf_abbs:LocusID - An NCBI unique identifier of a gene. + Gene identifier (NCBI) NCBI gene ID - beta12orEarlier - - - + NCBI geneid + + + + Gene ID (NCBI) - + + + beta12orEarlier + beta12orEarlier + + An NCBI RefSeq unique identifier of a gene. + Gene identifier (NCBI RefSeq) - - beta12orEarlier true - beta12orEarlier - An NCBI RefSeq unique identifier of a gene. - - - - Gene identifier (NCBI UniGene) - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + An NCBI UniGene unique identifier of a gene. - beta12orEarlier + + Gene identifier (NCBI UniGene) true - - - - Gene identifier (Entrez) - + + + beta12orEarlier + beta12orEarlier + [0-9]+ + An Entrez unique identifier of a gene. - beta12orEarlier + + Gene identifier (Entrez) true - [0-9]+ - beta12orEarlier - - - - Gene ID (CGD) - - CGD ID + + + beta12orEarlier Identifier of a gene or feature from the CGD database. - beta12orEarlier - - - + CGD ID + + + + Gene ID (CGD) - - Gene ID (DictyBase) - - beta12orEarlier + + + beta12orEarlier Identifier of a gene from DictyBase. - - - + + + + Gene ID (DictyBase) - - Ensembl gene ID - - - beta12orEarlier - Gene ID (Ensembl) + + + + beta12orEarlier Unique identifier for a gene (or other feature) from the Ensembl database. - - - + Gene ID (Ensembl) + + + + Ensembl gene ID - - Gene ID (SGD) - - + + + + beta12orEarlier + S[0-9]+ Identifier of an entry from the SGD database. - S[0-9]+ SGD identifier - beta12orEarlier - - - + + + + Gene ID (SGD) - - Gene ID (GeneDB) - + + + beta12orEarlier + [a-zA-Z_0-9\.-]* Moby_namespace:GeneDB - GeneDB identifier - beta12orEarlier - [a-zA-Z_0-9\.-]* Identifier of a gene from the GeneDB database. - - - + GeneDB identifier + + + + Gene ID (GeneDB) - - TIGR identifier - - - beta12orEarlier + + + + beta12orEarlier Identifier of an entry from the TIGR database. - - - + + + + TIGR identifier - - TAIR accession (gene) - - - Gene:[0-9]{7} - beta12orEarlier + + + + beta12orEarlier + Gene:[0-9]{7} Identifier of an gene from the TAIR database. - - - + + + + TAIR accession (gene) - - Protein domain ID - - + + + - - + + - beta12orEarlier + beta12orEarlier Identifier of a protein structural domain. + + + This is typically a character or string concatenated with a PDB identifier and a chain identifier. - - - + Protein domain ID - - SCOP domain identifier - + + + beta12orEarlier Identifier of a protein domain (or other node) from the SCOP database. - beta12orEarlier - - - + + + + SCOP domain identifier - - CATH domain ID - - 1nr3A00 - beta12orEarlier - CATH domain identifier + + + beta12orEarlier + 1nr3A00 Identifier of a protein domain from CATH. - - - + CATH domain identifier + + + + CATH domain ID - - SCOP concise classification string (sccs) - + + + beta12orEarlier A SCOP concise classification string (sccs) is a compact representation of a SCOP domain classification. - beta12orEarlier + + + An scss includes the class (alphabetical), fold, superfamily and family (all numerical) to which a given domain belongs. - - - + SCOP concise classification string (sccs) - - SCOP sunid - + + + beta12orEarlier + 33229 Unique identifier (number) of an entry in the SCOP hierarchy, for example 33229. - beta12orEarlier - A sunid uniquely identifies an entry in the SCOP hierarchy, including leaves (the SCOP domains) and higher level nodes including entries corresponding to the protein level. - sunid SCOP unique identifier - 33229 - - - + sunid + + + + A sunid uniquely identifies an entry in the SCOP hierarchy, including leaves (the SCOP domains) and higher level nodes including entries corresponding to the protein level. + SCOP sunid - - CATH node ID - - 3.30.1190.10.1.1.1.1.1 - CATH code + + + beta12orEarlier + 3.30.1190.10.1.1.1.1.1 A code number identifying a node from the CATH database. + CATH code CATH node identifier - beta12orEarlier - - - + + + + CATH node ID - - Kingdom name - + + + beta12orEarlier The name of a biological kingdom (Bacteria, Archaea, or Eukaryotes). - beta12orEarlier - - - + + + + Kingdom name - - Species name - + + + beta12orEarlier The name of a species (typically a taxonomic group) of organism. Organism species - beta12orEarlier - - - + + + + Species name - - Strain name - - - beta12orEarlier + + + + beta12orEarlier The name of a strain of an organism variant, typically a plant, virus or bacterium. - - - + + + + Strain name - - URI - + + + beta12orEarlier A string of characters that name or otherwise identify a resource on the Internet. URIs - beta12orEarlier - - + + + URI - - Database ID - + + - - + + + beta12orEarlier An identifier of a biological or bioinformatics database. Database identifier - beta12orEarlier - - - + + + + Database ID - - Directory name - - beta12orEarlier + + + beta12orEarlier The name of a directory. - - - + + + + Directory name - - File name - + + + beta12orEarlier The name (or part of a name) of a file (of any type). - beta12orEarlier - - - + + + + File name - - Ontology name - - + + + - - + + - beta12orEarlier + beta12orEarlier Name of an ontology of biological or bioinformatics concepts and relations. - - - + + + + Ontology name - - URL - - A Uniform Resource Locator (URL). - Moby:URL + + + beta12orEarlier Moby:Link - beta12orEarlier - - + Moby:URL + A Uniform Resource Locator (URL). + + + URL - - URN - - beta12orEarlier + + + beta12orEarlier A Uniform Resource Name (URN). - - + + + URN - - LSID - - beta12orEarlier - LSIDs provide a standard way to locate and describe data. An LSID is represented as a Uniform Resource Name (URN) with the following format: URN:LSID:<Authority>:<Namespace>:<ObjectID>[:<Version>] - Life Science Identifier + + + beta12orEarlier A Life Science Identifier (LSID) - a unique identifier of some data. - - + Life Science Identifier + + + LSIDs provide a standard way to locate and describe data. An LSID is represented as a Uniform Resource Name (URN) with the following format: URN:LSID:<Authority>:<Namespace>:<ObjectID>[:<Version>] + LSID - - Database name - - + + + + beta12orEarlier The name of a biological or bioinformatics database. - beta12orEarlier - - - + + + + Database name - - Sequence database name - + + + beta12orEarlier + beta13 + The name of a molecular sequence database. + + Sequence database name true - beta13 - beta12orEarlier - - - - Enumerated file name - - beta12orEarlier + + + beta12orEarlier The name of a file (of any type) with restricted possible values. - - - + + + + Enumerated file name - - File name extension - + + + beta12orEarlier The extension of a file name. + + + A file extension is the characters appearing after the final '.' in the file name. - beta12orEarlier - - - + File name extension - - File base name - - beta12orEarlier + + + beta12orEarlier The base name of a file. + + + A file base name is the file name stripped of its directory specification and extension. - - - + File base name - - QSAR descriptor name - - + + + - - + + - beta12orEarlier + beta12orEarlier Name of a QSAR descriptor. - - - + + + + QSAR descriptor name - + + + beta12orEarlier + beta12orEarlier + + An identifier of an entry from a database where the same type of identifier is used for objects (data) of different semantic type. + + This concept is required for completeness. It should never have child concepts. Database entry identifier - true - This concept is required for completeness. It should never have child concepts. - beta12orEarlier - An identifier of an entry from a database where the same type of identifier is used for objects (data) of different semantic type. - beta12orEarlier - - - - Sequence identifier - + + - - + + + beta12orEarlier An identifier of molecular sequence(s) or entries from a molecular sequence database. - beta12orEarlier - - - + + + + Sequence identifier - - Sequence set ID - - + + + - - + + + beta12orEarlier An identifier of a set of molecular sequence(s). - beta12orEarlier - - - + + + + Sequence set ID - + + + beta12orEarlier + beta12orEarlier + + + Identifier of a sequence signature (motif or profile) for example from a database of sequence patterns. + Sequence signature identifier - - beta12orEarlier - beta12orEarlier true - Identifier of a sequence signature (motif or profile) for example from a database of sequence patterns. - - - - - Sequence alignment ID - - + + + - - + + + beta12orEarlier Identifier of a molecular sequence alignment, for example a record from an alignment database. - beta12orEarlier - - - + + + + Sequence alignment ID - - Phylogenetic distance matrix identifier - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + Identifier of a phylogenetic distance matrix. + + Phylogenetic distance matrix identifier true - beta12orEarlier - - - - Phylogenetic tree ID - - + + + - - + + - beta12orEarlier + beta12orEarlier Identifier of a phylogenetic tree for example from a phylogenetic tree database. - - - + + + + Phylogenetic tree ID - - Comparison matrix identifier - + + - - + + + beta12orEarlier An identifier of a comparison matrix. Substitution matrix identifier - beta12orEarlier - - - + + + + Comparison matrix identifier - - Structure ID - - - beta12orEarlier + + + + beta12orEarlier A unique and persistent identifier of a molecular tertiary structure, typically an entry from a structure database. - - - + + + + Structure ID - - Structural (3D) profile ID - - + + + - - + + - Structural profile identifier + beta12orEarlier Identifier or name of a structural (3D) profile or template (representing a structure or structure alignment). - beta12orEarlier - - - + Structural profile identifier + + + + Structural (3D) profile ID - - Structure alignment ID - - + + + - - + + - beta12orEarlier + beta12orEarlier Identifier of an entry from a database of tertiary structure alignments. - - - + + + + Structure alignment ID - - Amino acid index ID - - + + + - - + + + beta12orEarlier Identifier of an index of amino acid physicochemical and biochemical property data. - beta12orEarlier - - - + + + + Amino acid index ID - - Protein interaction ID - - + + + - - + + - beta12orEarlier + beta12orEarlier Molecular interaction ID Identifier of a report of protein interactions from a protein interaction database (typically). - - - + + + + Protein interaction ID - - Protein family identifier - + + - - + + - Protein secondary database record identifier + beta12orEarlier Identifier of a protein family. - beta12orEarlier - - - + Protein secondary database record identifier + + + + Protein family identifier - - Codon usage table name - - + + + - - + + - - + + + beta12orEarlier Unique name of a codon usage table. - beta12orEarlier - - - + + + + Codon usage table name - - Transcription factor identifier - - + + + + beta12orEarlier Identifier of a transcription factor (or a TF binding site). - beta12orEarlier - - - + + + + Transcription factor identifier - - Microarray experiment annotation ID - + + - - + + - beta12orEarlier + beta12orEarlier Identifier of an entry from a database of microarray data. - - - + + + + Experiment annotation ID - - Electron microscopy model ID - - + + + - - + + + beta12orEarlier Identifier of an entry from a database of electron microscopy data. - beta12orEarlier - - - + + + + Electron microscopy model ID - - Gene expression report ID - - + + + - - + + + beta12orEarlier Accession of a report of gene expression (e.g. a gene expression profile) from a database. - beta12orEarlier Gene expression profile identifier - - - + + + + Gene expression report ID - - Genotype and phenotype annotation ID - - + + + - - + + + beta12orEarlier Identifier of an entry from a database of genotypes and phenotypes. - beta12orEarlier - - - + + + + Genotype and phenotype annotation ID - - Pathway or network identifier - + + - - + + + beta12orEarlier Identifier of an entry from a database of biological pathways or networks. - beta12orEarlier - - - + + + + Pathway or network identifier - - Workflow ID - - - beta12orEarlier + + + + beta12orEarlier Identifier of a biological or biomedical workflow, typically from a database of workflows. - - - + + + + Workflow ID - - Data resource definition ID - - beta12orEarlier + + + beta12orEarlier Identifier of a data type definition from some provider. Data resource definition identifier - - - + + + + Data resource definition ID - - Biological model ID - + + - - + + - Biological model identifier - beta12orEarlier + beta12orEarlier Identifier of a mathematical model, typically an entry from a database. - - - + Biological model identifier + + + + Biological model ID - - Compound identifier - + + - - + + - beta12orEarlier - Chemical compound identifier + beta12orEarlier Identifier of an entry from a database of chemicals. + Chemical compound identifier Small molecule identifier - - - + + + + Compound identifier - - Ontology concept ID - - + + + + beta12orEarlier A unique (typically numerical) identifier of a concept in an ontology of biological or bioinformatics concepts and relations. - beta12orEarlier - Ontology concept ID - - - + + + + Ontology concept ID - - Article ID - - + + + - - + + - beta12orEarlier + beta12orEarlier Unique identifier of a scientific article. Article identifier - - - + + + + Article ID - - FlyBase ID - - + + + + beta12orEarlier + FB[a-zA-Z_0-9]{2}[0-9]{7} Identifier of an object from the FlyBase database. - FB[a-zA-Z_0-9]{2}[0-9]{7} - beta12orEarlier - - - + + + + FlyBase ID - - WormBase name - - + + + + beta12orEarlier Name of an object from the WormBase database, usually a human-readable name. - beta12orEarlier - - - + + + + WormBase name - - WormBase class - - beta12orEarlier + + + beta12orEarlier Class of an object from the WormBase database. + + + A WormBase class describes the type of object such as 'sequence' or 'protein'. - - - + WormBase class - - Sequence accession - - - beta12orEarlier + + + + beta12orEarlier A persistent, unique identifier of a molecular sequence database entry. Sequence accession number - - - + + + + Sequence accession - - Sequence type - - 1.5 - Sequence type might reflect the molecule (protein, nucleic acid etc) or the sequence itself (gapped, ambiguous etc). + + + beta12orEarlier + 1.5 + A label (text token) describing a type of molecular sequence. + + Sequence type might reflect the molecule (protein, nucleic acid etc) or the sequence itself (gapped, ambiguous etc). + Sequence type true - beta12orEarlier - - - - EMBOSS Uniform Sequence Address - - - EMBOSS USA - beta12orEarlier + + + + beta12orEarlier The name of a sequence-based entity adhering to the standard sequence naming scheme used by all EMBOSS applications. - - - + EMBOSS USA + + + + EMBOSS Uniform Sequence Address - - Sequence accession (protein) - + + - - + + + beta12orEarlier Accession number of a protein sequence database entry. Protein sequence accession number - beta12orEarlier - - - + + + + Sequence accession (protein) - - Sequence accession (nucleic acid) - + + - - + + + beta12orEarlier Accession number of a nucleotide sequence database entry. - beta12orEarlier Nucleotide sequence accession number - - - + + + + Sequence accession (nucleic acid) - - RefSeq accession - + + + beta12orEarlier + (NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|YP|ZP)_[0-9]+ Accession number of a RefSeq database entry. - beta12orEarlier RefSeq ID - (NC|AC|NG|NT|NW|NZ|NM|NR|XM|XR|NP|AP|XP|YP|ZP)_[0-9]+ - - - + + + + RefSeq accession - + + + beta12orEarlier + Q7M1G0|P43353-2|P01012.107 + 1.0 + [A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]|[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9].[0-9]+|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9].[0-9]+|[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]-[0-9]+|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]-[0-9]+ + + Accession number of a UniProt (protein sequence) database entry. May contain version or isoform number. + UniProt accession (extended) - true - Accession number of a UniProt (protein sequence) database entry. May contain version or isoform number. - [A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]|[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9].[0-9]+|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9].[0-9]+|[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]-[0-9]+|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]-[0-9]+ - beta12orEarlier - Q7M1G0|P43353-2|P01012.107 - 1.0 - - - - PIR identifier - + + - - + + + beta12orEarlier An identifier of PIR sequence database entry. - beta12orEarlier PIR ID PIR accession number - - - + + + + PIR identifier - - TREMBL accession - - beta12orEarlier + + + beta12orEarlier + 1.2 Identifier of a TREMBL sequence database entry. + + + TREMBL accession true - 1.2 - - - - Gramene primary identifier - - beta12orEarlier - Gramene primary ID + + + beta12orEarlier Primary identifier of a Gramene database entry. - - - + Gramene primary ID + + + + Gramene primary identifier - - EMBL/GenBank/DDBJ ID - + + + beta12orEarlier Identifier of a (nucleic acid) entry from the EMBL/GenBank/DDBJ databases. - beta12orEarlier - - - + + + + EMBL/GenBank/DDBJ ID - - Sequence cluster ID (UniGene) - - UniGene identifier - UniGene cluster id + + + beta12orEarlier + A unique identifier of an entry (gene cluster) from the NCBI UniGene database. UniGene ID UniGene cluster ID - beta12orEarlier - A unique identifier of an entry (gene cluster) from the NCBI UniGene database. - - - + UniGene cluster id + UniGene identifier + + + + Sequence cluster ID (UniGene) - - dbEST accession - - - dbEST ID + + + + beta12orEarlier Identifier of a dbEST database entry. - beta12orEarlier - - - + dbEST ID + + + + dbEST accession - - dbSNP ID - - beta12orEarlier - dbSNP identifier + + + beta12orEarlier Identifier of a dbSNP database entry. - - - + dbSNP identifier + + + + dbSNP ID - + + + beta12orEarlier + beta12orEarlier + The EMBOSS type of a molecular sequence. + + See the EMBOSS documentation (http://emboss.sourceforge.net/) for a definition of what this includes. EMBOSS sequence type - - beta12orEarlier true - See the EMBOSS documentation (http://emboss.sourceforge.net/) for a definition of what this includes. - beta12orEarlier - The EMBOSS type of a molecular sequence. - - - - EMBOSS listfile - - 1.5 + + + beta12orEarlier + 1.5 + List of EMBOSS Uniform Sequence Addresses (EMBOSS listfile). + + EMBOSS listfile true - beta12orEarlier - - - - Sequence cluster ID - + + - - + + + beta12orEarlier An identifier of a cluster of molecular sequence(s). - beta12orEarlier - - - + + + + Sequence cluster ID - - Sequence cluster ID (COG) - - COG ID - beta12orEarlier + + + beta12orEarlier Unique identifier of an entry from the COG database. - - - + COG ID + + + + Sequence cluster ID (COG) - - Sequence motif identifier - + + - - + + + beta12orEarlier Identifier of a sequence motif, for example an entry from a motif database. - beta12orEarlier - - - + + + + Sequence motif identifier - - Sequence profile ID - - + + + - - + + + beta12orEarlier Identifier of a sequence profile. - beta12orEarlier + + + A sequence profile typically represents a sequence alignment. - - - + Sequence profile ID - - ELM ID - + + + beta12orEarlier Identifier of an entry from the ELMdb database of protein functional sites. - beta12orEarlier - - - + + + + ELM ID - - Prosite accession number - - beta12orEarlier + + + beta12orEarlier + PS[0-9]{5} Accession number of an entry from the Prosite database. - PS[0-9]{5} Prosite ID - - - + + + + Prosite accession number - - HMMER hidden Markov model ID - + + - - + + + beta12orEarlier Unique identifier or name of a HMMER hidden Markov model. - beta12orEarlier - - - + + + + HMMER hidden Markov model ID - - JASPAR profile ID - - beta12orEarlier + + + beta12orEarlier Unique identifier or name of a profile from the JASPAR database. - - - + + + + JASPAR profile ID - + + + beta12orEarlier + 1.5 + + A label (text token) describing the type of a sequence alignment. + + Possible values include for example the EMBOSS alignment types, BLAST alignment types and so on. Sequence alignment type - - beta12orEarlier - 1.5 true - Possible values include for example the EMBOSS alignment types, BLAST alignment types and so on. - A label (text token) describing the type of a sequence alignment. - - - + + + beta12orEarlier + beta12orEarlier + The type of a BLAST sequence alignment. + BLAST sequence alignment type - true - beta12orEarlier - beta12orEarlier - The type of a BLAST sequence alignment. - - - - Phylogenetic tree type - + + + beta12orEarlier + nj|upgmp + 1.5 + + A label (text token) describing the type of a phylogenetic tree. + For example 'nj', 'upgmp' etc. - beta12orEarlier + Phylogenetic tree type true - A label (text token) describing the type of a phylogenetic tree. - 1.5 - nj|upgmp - - - - TreeBASE study accession number - + + + beta12orEarlier Accession number of an entry from the TreeBASE database. - beta12orEarlier - - - + + + + TreeBASE study accession number - - TreeFam accession number - - beta12orEarlier + + + beta12orEarlier Accession number of an entry from the TreeFam database. - - - + + + + TreeFam accession number - - Comparison matrix type - - 1.5 - true - beta12orEarlier - blosum|pam|gonnet|id + + + beta12orEarlier + blosum|pam|gonnet|id + 1.5 + A label (text token) describing the type of a comparison matrix. - Substitution matrix type + For example 'blosum', 'pam', 'gonnet', 'id' etc. Comparison matrix type may be required where a series of matrices of a certain type are used. - - + Comparison matrix type + true - - Comparison matrix name - - + + + - - + + - beta12orEarlier + beta12orEarlier + Unique name or identifier of a comparison matrix. Substitution matrix name + + + See for example http://www.ebi.ac.uk/Tools/webservices/help/matrix. - Unique name or identifier of a comparison matrix. - - - + Comparison matrix name - - PDB ID - + + + beta12orEarlier + [a-zA-Z_0-9]{4} An identifier of an entry from the PDB database. - [a-zA-Z_0-9]{4} - PDBID PDB identifier - beta12orEarlier - - - + PDBID + + + + PDB ID - - AAindex ID - - beta12orEarlier + + + beta12orEarlier Identifier of an entry from the AAindex database. - - - + + + + AAindex ID - - BIND accession number - + + + beta12orEarlier Accession number of an entry from the BIND database. - beta12orEarlier - - - + + + + BIND accession number - - IntAct accession number - - EBI\-[0-9]+ - beta12orEarlier + + + beta12orEarlier + EBI\-[0-9]+ Accession number of an entry from the IntAct database. - - - + + + + IntAct accession number - - Protein family name - - - beta12orEarlier + + + + beta12orEarlier Name of a protein family. - - - + + + + Protein family name - - InterPro entry name - + + - - + + - beta12orEarlier + beta12orEarlier Name of an InterPro entry, usually indicating the type of protein matches for that entry. - - - + + + + InterPro entry name - - InterPro accession - + + - - + + + beta12orEarlier + IPR015590 + IPR[0-9]{6} Primary accession number of an InterPro entry. InterPro primary accession - Every InterPro entry has a unique accession number to provide a persistent citation of database records. - beta12orEarlier InterPro primary accession number - IPR015590 - IPR[0-9]{6} - - - + + + + Every InterPro entry has a unique accession number to provide a persistent citation of database records. + InterPro accession - - InterPro secondary accession - + + - - + + + beta12orEarlier Secondary accession number of an InterPro entry. - beta12orEarlier InterPro secondary accession number - - - + + + + InterPro secondary accession - - Gene3D ID - - beta12orEarlier + + + beta12orEarlier Unique identifier of an entry from the Gene3D database. - - - + + + + Gene3D ID - - PIRSF ID - - PIRSF[0-9]{6} - beta12orEarlier + + + beta12orEarlier + PIRSF[0-9]{6} Unique identifier of an entry from the PIRSF database. - - - + + + + PIRSF ID - - PRINTS code - - beta12orEarlier - PR[0-9]{5} + + + beta12orEarlier + PR[0-9]{5} The unique identifier of an entry in the PRINTS database. - - - + + + + PRINTS code - - Pfam accession number - - PF[0-9]{5} + + + beta12orEarlier + PF[0-9]{5} Accession number of a Pfam entry. - beta12orEarlier - - - + + + + Pfam accession number - - SMART accession number - + + + beta12orEarlier + SM[0-9]{5} Accession number of an entry from the SMART database. - beta12orEarlier - SM[0-9]{5} - - - + + + + SMART accession number - - Superfamily hidden Markov model number - + + + beta12orEarlier Unique identifier (number) of a hidden Markov model from the Superfamily database. - beta12orEarlier - - - + + + + Superfamily hidden Markov model number - - TIGRFam ID - - TIGRFam accession number + + + beta12orEarlier Accession number of an entry (family) from the TIGRFam database. - beta12orEarlier - - - + TIGRFam accession number + + + + TIGRFam ID - - ProDom accession number - + + + beta12orEarlier + PD[0-9]+ A ProDom domain family accession number. - PD[0-9]+ - beta12orEarlier + + + ProDom is a protein domain family database. - - - + ProDom accession number - - TRANSFAC accession number - - beta12orEarlier + + + beta12orEarlier Identifier of an entry from the TRANSFAC database. - - - + + + + TRANSFAC accession number - - ArrayExpress accession number - + + + beta12orEarlier + [AEP]-[a-zA-Z_0-9]{4}-[0-9]+ Accession number of an entry from the ArrayExpress database. - beta12orEarlier - [AEP]-[a-zA-Z_0-9]{4}-[0-9]+ ArrayExpress experiment ID - - - + + + + ArrayExpress accession number - - PRIDE experiment accession number - - [0-9]+ - beta12orEarlier + + + beta12orEarlier + [0-9]+ PRIDE experiment accession number. - - - + + + + PRIDE experiment accession number - - EMDB ID - - beta12orEarlier + + + beta12orEarlier Identifier of an entry from the EMDB electron microscopy database. - - - + + + + EMDB ID - - GEO accession number - + + + beta12orEarlier + o^GDS[0-9]+ Accession number of an entry from the GEO database. - o^GDS[0-9]+ - beta12orEarlier - - - + + + + GEO accession number - - GermOnline ID - - beta12orEarlier + + + beta12orEarlier Identifier of an entry from the GermOnline database. - - - + + + + GermOnline ID - - EMAGE ID - + + + beta12orEarlier Identifier of an entry from the EMAGE database. - beta12orEarlier - - - + + + + EMAGE ID - + + + + beta12orEarlier + Accession number of an entry from a database of disease. + + + Disease ID - - - - - - - - - Identifier of an entry from a database of disease. - beta12orEarlier - - - - - HGVbase ID - + + + beta12orEarlier Identifier of an entry from the HGVbase database. - beta12orEarlier - - - + + + + HGVbase ID - + + + beta12orEarlier + beta12orEarlier + + Identifier of an entry from the HIVDB database. + HIVDB identifier - true - beta12orEarlier - Identifier of an entry from the HIVDB database. - beta12orEarlier - - - - OMIM ID - - beta12orEarlier - [*#+%^]?[0-9]{6} + + + beta12orEarlier + [*#+%^]?[0-9]{6} Identifier of an entry from the OMIM database. - - - + + + + OMIM ID - - KEGG object identifier - - - beta12orEarlier + + + + beta12orEarlier Unique identifier of an object from one of the KEGG databases (excluding the GENES division). - - - + + + + KEGG object identifier - - Pathway ID (reactome) - + + + beta12orEarlier + REACT_[0-9]+(\.[0-9]+)? Identifier of an entry from the Reactome database. Reactome ID - beta12orEarlier - REACT_[0-9]+(\.[0-9]+)? - - - + + + + Pathway ID (reactome) - - Pathway ID (aMAZE) - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + + Identifier of an entry from the aMAZE database. aMAZE ID + + Pathway ID (aMAZE) true - beta12orEarlier - Identifier of an entry from the aMAZE database. - - - - Pathway ID (BioCyc) - - - BioCyc pathway ID - beta12orEarlier + + + + beta12orEarlier Identifier of an pathway from the BioCyc biological pathways database. - - - + BioCyc pathway ID + + + + Pathway ID (BioCyc) - - Pathway ID (INOH) - - beta12orEarlier - INOH identifier + + + beta12orEarlier Identifier of an entry from the INOH database. - - - + INOH identifier + + + + Pathway ID (INOH) - - Pathway ID (PATIKA) - + + + beta12orEarlier Identifier of an entry from the PATIKA database. PATIKA ID - beta12orEarlier - - - + + + + Pathway ID (PATIKA) - - Pathway ID (CPDB) - - This concept refers to identifiers used by the databases collated in CPDB; CPDB identifiers are not independently defined. - CPDB ID + + + beta12orEarlier Identifier of an entry from the CPDB (ConsensusPathDB) biological pathways database, which is an identifier from an external database integrated into CPDB. - beta12orEarlier - - - + CPDB ID + + + + This concept refers to identifiers used by the databases collated in CPDB; CPDB identifiers are not independently defined. + Pathway ID (CPDB) - - Pathway ID (Panther) - + + + beta12orEarlier + PTHR[0-9]{5} Identifier of a biological pathway from the Panther Pathways database. - beta12orEarlier - PTHR[0-9]{5} Panther Pathways ID - - - + + + + Pathway ID (Panther) - - MIRIAM identifier - + + - - + + + beta12orEarlier + MIR:00100005 + MIR:[0-9]{8} Unique identifier of a MIRIAM data resource. - MIR:00100005 - MIR:[0-9]{8} - beta12orEarlier + + + This is the identifier used internally by MIRIAM for a data type. - - - + MIRIAM identifier - - MIRIAM data type name - + + - - + + - beta12orEarlier + beta12orEarlier The name of a data type from the MIRIAM database. - - - + + + + MIRIAM data type name - - MIRIAM URI - - + + + - - + + - beta12orEarlier + beta12orEarlier + urn:miriam:pubmed:16333295|urn:miriam:obo.go:GO%3A0045202 The URI (URL or URN) of a data entity from the MIRIAM database. identifiers.org synonym - urn:miriam:pubmed:16333295|urn:miriam:obo.go:GO%3A0045202 + + + A MIRIAM URI consists of the URI of the MIRIAM data type (PubMed, UniProt etc) followed by the identifier of an element of that data type, for example PMID for a publication or an accession number for a GO term. - - - + MIRIAM URI - - MIRIAM data type primary name - - beta12orEarlier - The primary name of a MIRIAM data type is taken from a controlled vocabulary. - UniProt|Enzyme Nomenclature + + + beta12orEarlier + UniProt|Enzyme Nomenclature The primary name of a data type from the MIRIAM database. - - - + + + + The primary name of a MIRIAM data type is taken from a controlled vocabulary. + MIRIAM data type primary name + + UniProt|Enzyme Nomenclature A protein entity has the MIRIAM data type 'UniProt', and an enzyme has the MIRIAM data type 'Enzyme Nomenclature'. - - - - MIRIAM data type synonymous name - + + + beta12orEarlier A synonymous name of a data type from the MIRIAM database. + + + A synonymous name for a MIRIAM data type taken from a controlled vocabulary. - beta12orEarlier - - - + MIRIAM data type synonymous name - - Taverna workflow ID - - beta12orEarlier + + + beta12orEarlier Unique identifier of a Taverna workflow. - - - + + + + Taverna workflow ID - - Biological model name - - - beta12orEarlier + + + + beta12orEarlier Name of a biological (mathematical) model. - - - + + + + Biological model name - - BioModel ID - + + + beta12orEarlier + (BIOMD|MODEL)[0-9]{10} Unique identifier of an entry from the BioModel database. - beta12orEarlier - (BIOMD|MODEL)[0-9]{10} - - - + + + + BioModel ID - - PubChem CID - - - [0-9]+ - PubChem compound accession identifier + + + + beta12orEarlier + [0-9]+ Chemical structure specified in PubChem Compound Identification (CID), a non-zero integer identifier for a unique chemical structure. - beta12orEarlier - - - + PubChem compound accession identifier + + + + PubChem CID - - ChemSpider ID - + + + beta12orEarlier + [0-9]+ Identifier of an entry from the ChemSpider database. - beta12orEarlier - [0-9]+ - - - + + + + ChemSpider ID - - ChEBI ID - + + + beta12orEarlier + CHEBI:[0-9]+ Identifier of an entry from the ChEBI database. ChEBI IDs ChEBI identifier - CHEBI:[0-9]+ - beta12orEarlier - - - + + + + ChEBI ID - - BioPax concept ID - - beta12orEarlier + + + beta12orEarlier An identifier of a concept from the BioPax ontology. - - - + + + + BioPax concept ID - - GO concept ID - - GO concept identifier - [0-9]{7}|GO:[0-9]{7} - beta12orEarlier + + + beta12orEarlier + [0-9]{7}|GO:[0-9]{7} An identifier of a concept from The Gene Ontology. - - - + GO concept identifier + + + + GO concept ID - - MeSH concept ID - - beta12orEarlier + + + beta12orEarlier An identifier of a concept from the MeSH vocabulary. - - - + + + + MeSH concept ID - - HGNC concept ID - - beta12orEarlier + + + beta12orEarlier An identifier of a concept from the HGNC controlled vocabulary. - - - + + + + HGNC concept ID - - NCBI taxonomy ID - - - NCBI taxonomy identifier - [1-9][0-9]{0,8} - NCBI tax ID + + + + beta12orEarlier + 9662|3483|182682 + [1-9][0-9]{0,8} A stable unique identifier for each taxon (for a species, a family, an order, or any other group in the NCBI taxonomy database. - 9662|3483|182682 - beta12orEarlier - - - + NCBI tax ID + NCBI taxonomy identifier + + + + NCBI taxonomy ID - - Plant Ontology concept ID - + + + beta12orEarlier An identifier of a concept from the Plant Ontology (PO). - beta12orEarlier - - - + + + + Plant Ontology concept ID - - UMLS concept ID - + + + beta12orEarlier An identifier of a concept from the UMLS vocabulary. - beta12orEarlier - - - + + + + UMLS concept ID - - FMA concept ID - + + + beta12orEarlier + FMA:[0-9]+ An identifier of a concept from Foundational Model of Anatomy. - FMA:[0-9]+ + + + Classifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented. - beta12orEarlier - - - + FMA concept ID - - EMAP concept ID - - beta12orEarlier + + + beta12orEarlier An identifier of a concept from the EMAP mouse ontology. - - - + + + + EMAP concept ID - - ChEBI concept ID - - beta12orEarlier + + + beta12orEarlier An identifier of a concept from the ChEBI ontology. - - - + + + + ChEBI concept ID - - MGED concept ID - - beta12orEarlier + + + beta12orEarlier An identifier of a concept from the MGED ontology. - - - + + + + MGED concept ID - - myGrid concept ID - - beta12orEarlier - The ontology is provided as two components, the service ontology and the domain ontology. The domain ontology acts provides concepts for core bioinformatics data types and their relations. The service ontology describes the physical and operational features of web services. + + + beta12orEarlier An identifier of a concept from the myGrid ontology. - - - + + + + The ontology is provided as two components, the service ontology and the domain ontology. The domain ontology acts provides concepts for core bioinformatics data types and their relations. The service ontology describes the physical and operational features of web services. + myGrid concept ID - - PubMed ID - - PMID - [1-9][0-9]{0,8} + + + beta12orEarlier + 4963447 + [1-9][0-9]{0,8} PubMed unique identifier of an article. - beta12orEarlier - 4963447 - - - + PMID + + + + PubMed ID - - DOI - - beta12orEarlier - (doi\:)?[0-9]{2}\.[0-9]{4}/.* - Digital Object Identifier + + + beta12orEarlier + (doi\:)?[0-9]{2}\.[0-9]{4}/.* Digital Object Identifier (DOI) of a published article. - - - + Digital Object Identifier + + + + DOI - - Medline UI - - beta12orEarlier + + + beta12orEarlier Medline UI (unique identifier) of an article. - The use of Medline UI has been replaced by the PubMed unique identifier. Medline unique identifier - - - + + + + The use of Medline UI has been replaced by the PubMed unique identifier. + Medline UI - - Tool name - + + + beta12orEarlier The name of a computer package, application, method or function. - beta12orEarlier - - - + + + + Tool name - - Tool name (signature) - - beta12orEarlier + + + beta12orEarlier The unique name of a signature (sequence classifier) method. + + + Signature methods from http://www.ebi.ac.uk/Tools/InterProScan/help.html#results include BlastProDom, FPrintScan, HMMPIR, HMMPfam, HMMSmart, HMMTigr, ProfileScan, ScanRegExp, SuperFamily and HAMAP. - - - + Tool name (signature) - - Tool name (BLAST) - - This include 'blastn', 'blastp', 'blastx', 'tblastn' and 'tblastx'. + + + beta12orEarlier The name of a BLAST tool. - beta12orEarlier BLAST name - - - + + + + This include 'blastn', 'blastp', 'blastx', 'tblastn' and 'tblastx'. + Tool name (BLAST) - - Tool name (FASTA) - - beta12orEarlier + + + beta12orEarlier The name of a FASTA tool. + + + This includes 'fasta3', 'fastx3', 'fasty3', 'fastf3', 'fasts3' and 'ssearch'. - - - + Tool name (FASTA) - - Tool name (EMBOSS) - + + + beta12orEarlier The name of an EMBOSS application. - beta12orEarlier - - - + + + + Tool name (EMBOSS) - - Tool name (EMBASSY package) - + + + beta12orEarlier The name of an EMBASSY package. - beta12orEarlier - - - + + + + Tool name (EMBASSY package) - - QSAR descriptor (constitutional) - + + + beta12orEarlier A QSAR constitutional descriptor. - beta12orEarlier QSAR constitutional descriptor - - + + + QSAR descriptor (constitutional) - - QSAR descriptor (electronic) - - beta12orEarlier + + + beta12orEarlier A QSAR electronic descriptor. QSAR electronic descriptor - - + + + QSAR descriptor (electronic) - - QSAR descriptor (geometrical) - - QSAR geometrical descriptor + + + beta12orEarlier A QSAR geometrical descriptor. - beta12orEarlier - - + QSAR geometrical descriptor + + + QSAR descriptor (geometrical) - - QSAR descriptor (topological) - - beta12orEarlier - QSAR topological descriptor + + + beta12orEarlier A QSAR topological descriptor. - - + QSAR topological descriptor + + + QSAR descriptor (topological) - - QSAR descriptor (molecular) - + + + beta12orEarlier A QSAR molecular descriptor. QSAR molecular descriptor - beta12orEarlier - - + + + QSAR descriptor (molecular) - - Sequence set (protein) - + + + beta12orEarlier Any collection of multiple protein sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries. - beta12orEarlier - - + + + Sequence set (protein) - - Sequence set (nucleic acid) - - beta12orEarlier + + + beta12orEarlier Any collection of multiple nucleotide sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries. - - + + + Sequence set (nucleic acid) - - Sequence cluster - + + - - - - - - - - + + + beta12orEarlier A set of sequences that have been clustered or otherwise classified as belonging to a group including (typically) sequence cluster information. + + The cluster might include sequences identifiers, short descriptions, alignment and summary information. - beta12orEarlier - - + Sequence cluster - - Psiblast checkpoint file - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + + A file of intermediate results from a PSIBLAST search that is used for priming the search in the next PSIBLAST iteration. + A Psiblast checkpoint file uses ASN.1 Binary Format and usually has the extension '.asn'. - beta12orEarlier + Psiblast checkpoint file true - A file of intermediate results from a PSIBLAST search that is used for priming the search in the next PSIBLAST iteration. - - - - HMMER synthetic sequences set - + + + beta12orEarlier + beta12orEarlier + Sequences generated by HMMER package in FASTA-style format. - beta12orEarlier - beta12orEarlier + + HMMER synthetic sequences set true - - - - Proteolytic digest - + + - - + + - beta12orEarlier + beta12orEarlier A protein sequence cleaved into peptide fragments (by enzymatic or chemical cleavage) with fragment masses. - - + + + Proteolytic digest - - Restriction digest - - Restriction digest fragments from digesting a nucleotide sequence with restriction sites using a restriction endonuclease. + + + beta12orEarlier SO:0000412 - beta12orEarlier - - + Restriction digest fragments from digesting a nucleotide sequence with restriction sites using a restriction endonuclease. + + + Restriction digest - - PCR primers - - beta12orEarlier + + + beta12orEarlier Oligonucleotide primer(s) for PCR and DNA amplification, for example a minimal primer set. - - + + + PCR primers - + + + beta12orEarlier + beta12orEarlier + + File of sequence vectors used by EMBOSS vectorstrip application, or any file in same format. + vectorstrip cloning vector definition file - - beta12orEarlier true - File of sequence vectors used by EMBOSS vectorstrip application, or any file in same format. - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + A library of nucleotide sequences to avoid during hybridisation events. Hybridisation of the internal oligo to sequences in this library is avoided, rather than priming from them. The file is in a restricted FASTA format. + Primer3 internal oligo mishybridizing library - true - beta12orEarlier - A library of nucleotide sequences to avoid during hybridization events. Hybridization of the internal oligo to sequences in this library is avoided, rather than priming from them. The file is in a restricted FASTA format. - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + A nucleotide sequence library of sequences to avoid during amplification (for example repetitive sequences, or possibly the sequences of genes in a gene family that should not be amplified. The file must is in a restricted FASTA format. + Primer3 mispriming library file - true - A nucleotide sequence library of sequences to avoid during amplification (for example repetitive sequences, or possibly the sequences of genes in a gene family that should not be amplified. The file must is in a restricted FASTA format. - beta12orEarlier - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + File of one or more pairs of primer sequences, as used by EMBOSS primersearch application. + primersearch primer pairs sequence record - true - beta12orEarlier - beta12orEarlier - File of one or more pairs of primer sequences, as used by EMBOSS primersearch application. - - - - Sequence cluster (protein) - - + + + + beta12orEarlier + A cluster of protein sequences. Protein sequence cluster + + The sequences are typically related, for example a family of sequences. - beta12orEarlier - A cluster of protein sequences. - - + Sequence cluster (protein) - - Sequence cluster (nucleic acid) - - + + + + beta12orEarlier A cluster of nucleotide sequences. Nucleotide sequence cluster - beta12orEarlier + + The sequences are typically related, for example a family of sequences. - - + Sequence cluster (nucleic acid) - - Sequence length - - beta12orEarlier + + + beta12orEarlier The size (length) of a sequence, subsequence or region in a sequence, or range(s) of lengths. - - + + + Sequence length - - Word size - - Word size is used for example in word-based sequence database search methods. - Word length - 1.5 + + + beta12orEarlier + 1.5 + Size of a sequence word. + + Word size is used for example in word-based sequence database search methods. + Word size true - beta12orEarlier - - - + + + beta12orEarlier + 1.5 + + Size of a sequence window. + + A window is a region of fixed size but not fixed position over a molecular sequence. It is typically moved (computationally) over a sequence during scoring. Window size - - 1.5 true - A window is a region of fixed size but not fixed position over a molecular sequence. It is typically moved (computationally) over a sequence during scoring. - beta12orEarlier - Size of a sequence window. - - - + + + beta12orEarlier + 1.5 + + Specification of range(s) of length of sequences. + Sequence length range - true - Specification of range(s) of length of sequences. - beta12orEarlier - 1.5 - - - - Sequence information report - + + + beta12orEarlier + beta12orEarlier Report on basic information about a molecular sequence such as name, accession number, type (nucleic or protein), length, description etc. - beta12orEarlier - beta12orEarlier + + + Sequence information report true - - - - Sequence property - - beta12orEarlier + + + beta12orEarlier An informative report about non-positional sequence features, typically a report on general molecular sequence properties derived from sequence analysis. Sequence properties report - - + + + Sequence property - - Sequence features - - Sequence features report - beta12orEarlier - http://purl.bioontology.org/ontology/MSH/D058977 - SO:0000110 - This includes annotation of positional sequence features, organized into a standard feature table, or any other report of sequence features. General feature reports are a source of sequence feature table information although internal conversion would be required. - General sequence features + + + beta12orEarlier Annotation of positional features of molecular sequence(s), i.e. that can be mapped to position(s) in the sequence. - Features Feature record - - + Features + General sequence features + Sequence features report + SO:0000110 + + + This includes annotation of positional sequence features, organised into a standard feature table, or any other report of sequence features. General feature reports are a source of sequence feature table information although internal conversion would be required. + Sequence features + http://purl.bioontology.org/ontology/MSH/D058977 - - Sequence features (comparative) - + + + beta12orEarlier + beta13 + Comparative data on sequence features such as statistics, intersections (and data on intersections), differences etc. - beta13 + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. + Sequence features (comparative) true - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + A report of general sequence properties derived from protein sequence data. + Sequence property (protein) - true - A report of general sequence properties derived from protein sequence data. - beta12orEarlier - beta12orEarlier - - - - Sequence property (nucleic acid) - + + + beta12orEarlier + beta12orEarlier + A report of general sequence properties derived from nucleotide sequence data. - beta12orEarlier + + Sequence property (nucleic acid) true - beta12orEarlier - - - - Sequence complexity report - + + + beta12orEarlier A report on sequence complexity, for example low-complexity or repeat regions in sequences. - beta12orEarlier Sequence property (complexity) - - + + + Sequence complexity report - - Sequence ambiguity report - + + + beta12orEarlier A report on ambiguity in molecular sequence(s). Sequence property (ambiguity) - beta12orEarlier - - + + + Sequence ambiguity report - - Sequence composition report - - beta12orEarlier + + + beta12orEarlier A report (typically a table) on character or word composition / frequency of a molecular sequence(s). Sequence property (composition) - - + + + Sequence composition report - - Peptide molecular weight hits - + + + beta12orEarlier A report on peptide fragments of certain molecular weight(s) in one or more protein sequences. - beta12orEarlier - - + + + Peptide molecular weight hits - - Base position variability plot - - beta12orEarlier + + + beta12orEarlier A plot of third base position variability in a nucleotide sequence. - - + + + Base position variability plot - - Sequence composition table - + + + beta12orEarlier + beta12orEarlier + A table of character or word composition / frequency of a molecular sequence. - beta12orEarlier + + Sequence composition table true - beta12orEarlier - - - - Base frequencies table - - - beta12orEarlier + + + + beta12orEarlier A table of base frequencies of a nucleotide sequence. - - + + + Base frequencies table - - Base word frequencies table - - + + + + beta12orEarlier A table of word composition of a nucleotide sequence. - beta12orEarlier - - + + + Base word frequencies table - - Amino acid frequencies table - - - Sequence composition (amino acid frequencies) + + + + beta12orEarlier A table of amino acid frequencies of a protein sequence. - beta12orEarlier - - + Sequence composition (amino acid frequencies) + + + Amino acid frequencies table - - Amino acid word frequencies table - - + + + + beta12orEarlier A table of amino acid word composition of a protein sequence. Sequence composition (amino acid words) - beta12orEarlier - - + + + Amino acid word frequencies table - - DAS sequence feature annotation - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + Annotation of a molecular sequence in DAS format. - beta12orEarlier + + DAS sequence feature annotation true - - - - Feature table - + + + beta12orEarlier + Annotation of positional sequence features, organised into a standard feature table. Sequence feature table - beta12orEarlier - Annotation of positional sequence features, organized into a standard feature table. - - + + + Feature table - - Map - + + - - + + - DNA map - beta12orEarlier + beta12orEarlier A map of (typically one) DNA sequence annotated with positional or non-positional features. - - + DNA map + + + Map - - Nucleic acid features - - + + + + beta12orEarlier An informative report on intrinsic positional features of a nucleotide sequence. - beta12orEarlier + Feature table (nucleic acid) + Nucleic acid feature table Genome features - This includes nucleotide sequence feature annotation in any known sequence feature table format and any other report of nucleic acid features. Genomic features - Nucleic acid feature table - Feature table (nucleic acid) - - + + + This includes nucleotide sequence feature annotation in any known sequence feature table format and any other report of nucleic acid features. + Nucleic acid features - - Protein features - - + + + + beta12orEarlier An informative report on intrinsic positional features of a protein sequence. - beta12orEarlier - This includes protein sequence feature annotation in any known sequence feature table format and any other report of protein features. Feature table (protein) Protein feature table - - + + + This includes protein sequence feature annotation in any known sequence feature table format and any other report of protein features. + Protein features - - Genetic map - + + + beta12orEarlier + Moby:GeneticMap A map showing the relative positions of genetic markers in a nucleic acid sequence, based on estimation of non-physical distance such as recombination frequencies. - beta12orEarlier - A genetic (linkage) map indicates the proximity of two genes on a chromosome, whether two genes are linked and the frequency they are transmitted together to an offspring. They are limited to genetic markers of traits observable only in whole organisms. Linkage map - Moby:GeneticMap - - + + + A genetic (linkage) map indicates the proximity of two genes on a chromosome, whether two genes are linked and the frequency they are transmitted together to an offspring. They are limited to genetic markers of traits observable only in whole organisms. + Genetic map - - Sequence map - - A sequence map typically includes annotation on significant subsequences such as contigs, haplotypes and genes. The contigs shown will (typically) be a set of small overlapping clones representing a complete chromosomal segment. - beta12orEarlier + + + beta12orEarlier A map of genetic markers in a contiguous, assembled genomic sequence, with the sizes and separation of markers measured in base pairs. - - + + + A sequence map typically includes annotation on significant subsequences such as contigs, haplotypes and genes. The contigs shown will (typically) be a set of small overlapping clones representing a complete chromosomal segment. + Sequence map - - Physical map - + + + beta12orEarlier A map of DNA (linear or circular) annotated with physical features or landmarks such as restriction sites, cloned DNA fragments, genes or genetic markers, along with the physical distances between them. + + Distance in a physical map is measured in base pairs. A physical map might be ordered relative to a reference map (typically a genetic map) in the process of genome sequencing. - beta12orEarlier - - + Physical map - + + + beta12orEarlier + beta12orEarlier + Image of a sequence with matches to signatures, motifs or profiles. + + Sequence signature map - true - Image of a sequence with matches to signatures, motifs or profiles. - beta12orEarlier - beta12orEarlier - - - - Cytogenetic map - - beta12orEarlier + + + beta12orEarlier A map showing banding patterns derived from direct observation of a stained chromosome. - Cytologic map Chromosome map Cytogenic map + Cytologic map + + This is the lowest-resolution physical map and can provide only rough estimates of physical (base pair) distances. Like a genetic map, they are limited to genetic markers of traits observable only in whole organisms. - - + Cytogenetic map - - DNA transduction map - - beta12orEarlier + + + beta12orEarlier A gene map showing distances between loci based on relative cotransduction frequencies. - - + + + DNA transduction map - - Gene map - + + + beta12orEarlier Sequence map of a single gene annotated with genetic features such as introns, exons, untranslated regions, polyA signals, promoters, enhancers and (possibly) mutations defining alleles of a gene. - beta12orEarlier - - + + + Gene map - - Plasmid map - + + + beta12orEarlier Sequence map of a plasmid (circular DNA). - beta12orEarlier - - + + + Plasmid map - - Genome map - - beta12orEarlier + + + beta12orEarlier Sequence map of a whole genome. - - + + + Genome map - - Restriction map - - + + + + beta12orEarlier Image of the restriction enzyme cleavage sites (restriction sites) in a nucleic acid sequence. - beta12orEarlier - - + + + Restriction map - - InterPro compact match image - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier Image showing matches between protein sequence(s) and InterPro Entries. + + The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Each protein is represented as a scaled horizontal line with colored bars indicating the position of the matches. - beta12orEarlier + InterPro compact match image true - - - - InterPro detailed match image - - beta12orEarlier - beta12orEarlier + + + beta12orEarlier + beta12orEarlier Image showing detailed information on matches between protein sequence(s) and InterPro Entries. + + The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. + InterPro detailed match image true - - - + + + beta12orEarlier + beta12orEarlier + Image showing the architecture of InterPro domains in a protein sequence. + + + The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Domain architecture is shown as a series of non-overlapping domains in the protein. InterPro architecture image - - beta12orEarlier - beta12orEarlier true - The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Domain architecture is shown as a series of non-overlapping domains in the protein. - Image showing the architecture of InterPro domains in a protein sequence. - - - + + + beta12orEarlier + beta12orEarlier + + SMART protein schematic in PNG format. + SMART protein schematic - true - beta12orEarlier - beta12orEarlier - SMART protein schematic in PNG format. - - - + + + beta12orEarlier + beta12orEarlier + Images based on GlobPlot prediction of intrinsic disordered regions and globular domains in protein sequences. + + GlobPlot domain image - - beta12orEarlier - beta12orEarlier true - Images based on GlobPlot prediction of intrinsic disordered regions and globular domains in protein sequences. - - - - Sequence motif matches - - beta12orEarlier + + + beta12orEarlier + 1.8 Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more sequences. - 1.8 + + + Sequence motif matches true - - - + + + beta12orEarlier + 1.5 + + Location of short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences. + + The report might include derived data map such as classification, annotation, organisation, periodicity etc. Sequence features (repeats) - - beta12orEarlier true - 1.5 - Repeat sequence map - The report might include derived data map such as classification, annotation, organization, periodicity etc. - Location of short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences. - - - - - Gene and transcript structure (report) - - 1.5 - beta12orEarlier + + + beta12orEarlier + 1.5 + A report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc. + + Gene and transcript structure (report) true - - - + + + beta12orEarlier + 1.8 + regions of a nucleic acid sequence containing mobile genetic elements. + + Mobile genetic elements - true - beta12orEarlier - 1.8 - Topic concerning regions of a nucleic acid sequence containing mobile genetic elements. - - - + + + beta12orEarlier + 1.8 + regions or sites in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript. + + Nucleic acid features report (PolyA signal or site) - - Topic concerning regions or sites in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript. true - 1.8 - beta12orEarlier - - - + + + beta12orEarlier + 1.5 + + A report on quadruplex-forming motifs in a nucleotide sequence. + Nucleic acid features (quadruplexes) - true - 1.5 - A report on quadruplex-forming motifs in a nucleotide sequence. - beta12orEarlier - - - + + + beta12orEarlier + 1.8 + CpG rich regions (isochores) in a nucleotide sequence. + + Nucleic acid features report (CpG island and isochore) - - 1.8 - beta12orEarlier - Topic concerning CpG rich regions (isochores) in a nucleotide sequence. true - - - + + + beta12orEarlier + 1.8 + restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence. + + Nucleic acid features report (restriction sites) - - beta12orEarlier true - 1.8 - Topic concerning restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence. - - - + + + beta12orEarlier + 1.8 + Report on nucleosome formation potential or exclusion sequence(s). + + Nucleosome exclusion sequences - - beta12orEarlier true - Report on nucleosome formation potential or exclusion sequence(s). - 1.8 - - - + + + beta12orEarlier + 1.8 + splice sites in a nucleotide sequence or alternative RNA splicing events. + + Nucleic acid features report (splice sites) - - beta12orEarlier - Topic concerning splice sites in a nucleotide sequence or alternative RNA splicing events. true - 1.8 - - - + + + beta12orEarlier + 1.8 + matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence. + + Nucleic acid features report (matrix/scaffold attachment sites) - - 1.8 true - beta12orEarlier - Topic concerning matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence. - - - + + + beta12orEarlier + beta13 + A report on exonic splicing enhancers (ESE) in an exon. + + Gene features (exonic splicing enhancer) - - beta12orEarlier - beta13 true - A report on exonic splicing enhancers (ESE) in an exon. - - - + + + beta12orEarlier + 1.5 + + A report on microRNA sequence (miRNA) or precursor, microRNA targets, miRNA binding sites in an RNA sequence etc. + Nucleic acid features (microRNA) - true - beta12orEarlier - A report on microRNA sequence (miRNA) or precursor, microRNA targets, miRNA binding sites in an RNA sequence etc. - 1.5 - - - + + + beta12orEarlier + 1.8 + operons (operators, promoters and genes) from a bacterial genome. + + Gene features report (operon) - true - 1.8 - Topic concerning operons (operators, promoters and genes) from a bacterial genome. - beta12orEarlier - - - + + + beta12orEarlier + 1.8 + whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in a DNA sequence. + + Nucleic acid features report (promoters) - - 1.8 - Topic concerning whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in a DNA sequence. true - beta12orEarlier - - - + + + beta12orEarlier + 1.8 + protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames. + + Coding region - - beta12orEarlier - Topic concerning protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames. - 1.8 true - - - - Gene features (SECIS element) - - beta12orEarlier - beta13 + + + beta12orEarlier + beta13 + A report on selenocysteine insertion sequence (SECIS) element in a DNA sequence. + + Gene features (SECIS element) true - - - + + + beta12orEarlier + 1.8 + transcription factor binding sites (TFBS) in a DNA sequence. + + Transcription factor binding sites - - beta12orEarlier - Topic concerning transcription factor binding sites (TFBS) in a DNA sequence. true - 1.8 - - - + + + beta12orEarlier + beta12orEarlier + + A report on predicted or known key residue positions (sites) in a protein sequence, such as binding or functional sites. + + Use this concept for collections of specific sites which are not necessarily contiguous, rather than contiguous stretches of amino acids. Protein features (sites) - true - beta12orEarlier - Use this concept for collections of specific sites which are not necessarily contiguous, rather than contiguous stretches of amino acids. - beta12orEarlier - A report on predicted or known key residue positions (sites) in a protein sequence, such as binding or functional sites. - - - + + + beta12orEarlier + 1.8 + signal peptides or signal peptide cleavage sites in protein sequences. + + Protein features report (signal peptides) - - Topic concerning signal peptides or signal peptide cleavage sites in protein sequences. true - 1.8 - beta12orEarlier - - - + + + beta12orEarlier + 1.8 + cleavage sites (for a proteolytic enzyme or agent) in a protein sequence. + + Protein features report (cleavage sites) - true - Topic concerning cleavage sites (for a proteolytic enzyme or agent) in a protein sequence. - 1.8 - beta12orEarlier - - - + + + beta12orEarlier + 1.8 + post-translation modifications in a protein sequence, typically describing the specific sites involved. + + Protein features (post-translation modifications) - true - beta12orEarlier - Topic concerning post-translation modifications in a protein sequence, typically describing the specific sites involved. - 1.8 - - - + + + beta12orEarlier + 1.8 + catalytic residues (active site) of an enzyme. + + Protein features report (active sites) - - Topic concerning catalytic residues (active site) of an enzyme. - 1.8 true - beta12orEarlier - - - + + + beta12orEarlier + 1.8 + ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids. + + Protein features report (binding sites) - - Topic concerning ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids. - beta12orEarlier true - 1.8 - - - - Protein features (epitopes) - + + + beta12orEarlier + beta13 A report on antigenic determinant sites (epitopes) in proteins, from sequence and / or structural data. - beta13 - beta12orEarlier + + Epitope mapping is commonly done during vaccine design. + Protein features (epitopes) true - - - + + + beta12orEarlier + 1.8 + RNA and DNA-binding proteins and binding sites in protein sequences. + + Protein features report (nucleic acid binding sites) - true - beta12orEarlier - Topic concerning RNA and DNA-binding proteins and binding sites in protein sequences. - 1.8 - - - + + + beta12orEarlier + beta12orEarlier + + A report on epitopes that bind to MHC class I molecules. + MHC Class I epitopes report - - beta12orEarlier - beta12orEarlier true - A report on epitopes that bind to MHC class I molecules. - - - + + + beta12orEarlier + beta12orEarlier + + A report on predicted epitopes that bind to MHC class II molecules. + MHC Class II epitopes report - - beta12orEarlier - beta12orEarlier true - A report on predicted epitopes that bind to MHC class II molecules. - - - - Protein features (PEST sites) - - beta12orEarlier + + + beta12orEarlier + beta13 A report or plot of PEST sites in a protein sequence. - true - beta13 + + 'PEST' motifs target proteins for proteolytic degradation and reduce the half-lives of proteins dramatically. - - + Protein features (PEST sites) + true - - Sequence database hits scores list - + + + beta12orEarlier + beta12orEarlier + Scores from a sequence database search (for example a BLAST search). - beta12orEarlier + + Sequence database hits scores list true - beta12orEarlier - - - - Sequence database hits alignments list - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + Alignments from a sequence database search (for example a BLAST search). - beta12orEarlier + + Sequence database hits alignments list true - - - - Sequence database hits evaluation data - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + A report on the evaluation of the significance of sequence similarity scores from a sequence database search (for example a BLAST search). - beta12orEarlier + + Sequence database hits evaluation data true - - - - MEME motif alphabet - + + + beta12orEarlier + beta12orEarlier + Alphabet for the motifs (patterns) that MEME will search for. - beta12orEarlier - beta12orEarlier + + MEME motif alphabet true - - - - MEME background frequencies file - + + + beta12orEarlier + beta12orEarlier + MEME background frequencies file. + + MEME background frequencies file true - beta12orEarlier - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + File of directives for ordering and spacing of MEME motifs. + MEME motifs directive file - - beta12orEarlier true - File of directives for ordering and spacing of MEME motifs. - beta12orEarlier - - - - Dirichlet distribution - + + + beta12orEarlier Dirichlet distribution used by hidden Markov model analysis programs. - beta12orEarlier - - + + + Dirichlet distribution - - HMM emission and transition counts - + + + beta12orEarlier + 1.4 + + Emission and transition counts of a hidden Markov model, generated once HMM has been determined, for example after residues/gaps have been assigned to match, delete and insert states. + + HMM emission and transition counts true - 1.4 - beta12orEarlier - - - - - Regular expression - + + + beta12orEarlier Regular expression pattern. - beta12orEarlier - - + + + Regular expression - - Sequence motif - + + - - + + - beta12orEarlier + beta12orEarlier Any specific or conserved pattern (typically expressed as a regular expression) in a molecular sequence. - - + + + Sequence motif - - Sequence profile - + + - - + + + beta12orEarlier Some type of statistical model representing a (typically multiple) sequence alignment. + + + Sequence profile http://semanticscience.org/resource/SIO_010531 - beta12orEarlier - - - - Protein signature - + + + beta12orEarlier An informative report about a specific or conserved protein sequence pattern. InterPro entry - Protein repeat signature + Protein domain signature + Protein family signature Protein region signature + Protein repeat signature Protein site signature - beta12orEarlier - Protein family signature - Protein domain signature - - + + + Protein signature - - Prosite nucleotide pattern - + + + beta12orEarlier + beta12orEarlier + A nucleotide regular expression pattern from the Prosite database. - beta12orEarlier + + Prosite nucleotide pattern true - beta12orEarlier - - - - Prosite protein pattern - + + + beta12orEarlier + beta12orEarlier + A protein regular expression pattern from the Prosite database. - beta12orEarlier - beta12orEarlier + + Prosite protein pattern true - - - - Position frequency matrix - - beta12orEarlier - PFM + + + beta12orEarlier A profile (typically representing a sequence alignment) that is a simple matrix of nucleotide (or amino acid) counts per position. - - + PFM + + + Position frequency matrix - - Position weight matrix - - PWM - beta12orEarlier + + + beta12orEarlier A profile (typically representing a sequence alignment) that is weighted matrix of nucleotide (or amino acid) counts per position. + PWM + + Contributions of individual sequences to the matrix might be uneven (weighted). - - + Position weight matrix - - Information content matrix - - beta12orEarlier - ICM + + + beta12orEarlier A profile (typically representing a sequence alignment) derived from a matrix of nucleotide (or amino acid) counts per position that reflects information content at each position. - - + ICM + + + Information content matrix - - Hidden Markov model - + + + + beta12orEarlier + A statistical Markov model of a system which is assumed to be a Markov process with unobserved (hidden) states. For example, a hidden Markov model representation of a set or alignment of sequences. HMM - beta12orEarlier - A hidden Markov model representation of a set or alignment of sequences. - - + + + Hidden Markov model - - Fingerprint - - beta12orEarlier + + + beta12orEarlier One or more fingerprints (sequence classifiers) as used in the PRINTS database. - - + + + Fingerprint - - Domainatrix signature - + + + beta12orEarlier + beta12orEarlier + A protein signature of the type used in the EMBASSY Signature package. + + Domainatrix signature true - beta12orEarlier - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + NULL hidden Markov model representation used by the HMMER package. + HMMER NULL hidden Markov model - - beta12orEarlier - beta12orEarlier true - NULL hidden Markov model representation used by the HMMER package. - - - - Protein family signature - + + + beta12orEarlier + 1.5 + + A protein family signature (sequence classifier) from the InterPro database. + Protein family signatures cover all domains in the matching proteins and span >80% of the protein length and with no adjacent protein domain signatures or protein region signatures. - beta12orEarlier + Protein family signature true - 1.5 - A protein family signature (sequence classifier) from the InterPro database. - - - - Protein domain signature - - beta12orEarlier - 1.5 - true + + + beta12orEarlier + 1.5 + A protein domain signature (sequence classifier) from the InterPro database. + Protein domain signatures identify structural or functional domains or other units with defined boundaries. - - + Protein domain signature + true - - Protein region signature - + + + beta12orEarlier + 1.5 + A protein region signature (sequence classifier) from the InterPro database. - true - beta12orEarlier - 1.5 + A protein region signature defines a region which cannot be described as a protein family or domain signature. - - + Protein region signature + true - + + + beta12orEarlier + 1.5 + + A protein repeat signature (sequence classifier) from the InterPro database. + + A protein repeat signature is a repeated protein motif, that is not in single copy expected to independently fold into a globular domain. Protein repeat signature - true - 1.5 - A protein repeat signature is a repeated protein motif, that is not in single copy expected to independently fold into a globular domain. - beta12orEarlier - A protein repeat signature (sequence classifier) from the InterPro database. - - - - Protein site signature - - A protein site signature is a classifier for a specific site in a protein. - beta12orEarlier + + + beta12orEarlier + 1.5 + A protein site signature (sequence classifier) from the InterPro database. + + A protein site signature is a classifier for a specific site in a protein. + Protein site signature true - 1.5 - - - + + + beta12orEarlier + 1.4 + + A protein conserved site signature (sequence classifier) from the InterPro database. + + A protein conserved site signature is any short sequence pattern that may contain one or more unique residues and is cannot be described as a active site, binding site or post-translational modification. Protein conserved site signature - - 1.4 true - A protein conserved site signature is any short sequence pattern that may contain one or more unique residues and is cannot be described as a active site, binding site or post-translational modification. - A protein conserved site signature (sequence classifier) from the InterPro database. - beta12orEarlier - - - - Protein active site signature - + + + beta12orEarlier + 1.4 + A protein active site signature (sequence classifier) from the InterPro database. + A protein active site signature corresponds to an enzyme catalytic pocket. An active site typically includes non-contiguous residues, therefore multiple signatures may be required to describe an active site. ; residues involved in enzymatic reactions for which mutational data is typically available. + Protein active site signature true - 1.4 - beta12orEarlier - - - - Protein binding site signature - - 1.4 + + + beta12orEarlier + 1.4 + A protein binding site signature (sequence classifier) from the InterPro database. - true + A protein binding site signature corresponds to a site that reversibly binds chemical compounds, which are not themselves substrates of the enzymatic reaction. This includes enzyme cofactors and residues involved in electron transport or protein structure modification. - beta12orEarlier - - + Protein binding site signature + true - - Protein post-translational modification signature - + + + beta12orEarlier + 1.4 + A protein post-translational modification signature (sequence classifier) from the InterPro database. + A protein post-translational modification signature corresponds to sites that undergo modification of the primary structure, typically to activate or de-activate a function. For example, methylation, sumoylation, glycosylation etc. The modification might be permanent or reversible. - 1.4 - beta12orEarlier + Protein post-translational modification signature true - - - + + + beta12orEarlier + Alignment of exactly two molecular sequences. + + Sequence alignment (pair) - http://semanticscience.org/resource/SIO_010068 - beta12orEarlier - Alignment of exactly two molecular sequences. - - - - Sequence alignment (multiple) - - beta12orEarlier - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + Alignment of more than two molecular sequences. + + Sequence alignment (multiple) true - - - - Sequence alignment (nucleic acid) - - beta12orEarlier + + + beta12orEarlier Alignment of multiple nucleotide sequences. - - + + + Sequence alignment (nucleic acid) - - Sequence alignment (protein) - - + + + + beta12orEarlier Alignment of multiple protein sequences. - beta12orEarlier - - + + + Sequence alignment (protein) - - Sequence alignment (hybrid) - + + + beta12orEarlier Alignment of multiple molecular sequences of different types. + + Hybrid sequence alignments include for example genomic DNA to EST, cDNA or mRNA. - beta12orEarlier - - + Sequence alignment (hybrid) - - Sequence alignment (nucleic acid pair) - - - beta12orEarlier + + + beta12orEarlier + 1.12 + + Alignment of exactly two nucleotide sequences. - - + + Sequence alignment (nucleic acid pair) + true - - Sequence alignment (protein pair) - - + + + beta12orEarlier + 1.12 + + Alignment of exactly two protein sequences. - beta12orEarlier - - + + Sequence alignment (protein pair) + true - + + + beta12orEarlier + beta12orEarlier + + Alignment of exactly two molecular sequences of different types. + Hybrid sequence alignment (pair) - true - beta12orEarlier - beta12orEarlier - Alignment of exactly two molecular sequences of different types. - - - - Multiple nucleotide sequence alignment - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + Alignment of more than two nucleotide sequences. + + Multiple nucleotide sequence alignment true - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + Alignment of more than two protein sequences. + Multiple protein sequence alignment - true - beta12orEarlier - beta12orEarlier - Alignment of more than two protein sequences. - - - - Alignment score or penalty - - beta12orEarlier + + + beta12orEarlier A simple floating point number defining the penalty for opening or extending a gap in an alignment. - - + + + Alignment score or penalty - - Score end gaps control - - beta12orEarlier - beta12orEarlier + + + beta12orEarlier + beta12orEarlier Whether end gaps are scored or not. + + Score end gaps control true - - - + + + beta12orEarlier + beta12orEarlier + Controls the order of sequences in an output sequence alignment. + Aligned sequence order - - beta12orEarlier - beta12orEarlier true - Controls the order of sequences in an output sequence alignment. - - - - Gap opening penalty - + + + beta12orEarlier A penalty for opening a gap in an alignment. - beta12orEarlier - - + + + Gap opening penalty - - Gap extension penalty - + + + beta12orEarlier A penalty for extending a gap in an alignment. - beta12orEarlier - - + + + Gap extension penalty - - Gap separation penalty - - beta12orEarlier + + + beta12orEarlier A penalty for gaps that are close together in an alignment. - - + + + Gap separation penalty - - Terminal gap penalty - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + + A penalty for gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences. + + Terminal gap penalty true - beta12orEarlier - - - - - Match reward score - - beta12orEarlier + + + beta12orEarlier The score for a 'match' used in various sequence database search applications with simple scoring schemes. - - + + + Match reward score - - Mismatch penalty score - - beta12orEarlier + + + beta12orEarlier The score (penalty) for a 'mismatch' used in various alignment and sequence database search applications with simple scoring schemes. - - + + + Mismatch penalty score - - Drop off score - + + + beta12orEarlier This is the threshold drop in score at which extension of word alignment is halted. - beta12orEarlier - - + + + Drop off score - + + + beta12orEarlier + beta12orEarlier + + A simple floating point number defining the penalty for opening a gap in an alignment. + Gap opening penalty (integer) - - beta12orEarlier true - A simple floating point number defining the penalty for opening a gap in an alignment. - beta12orEarlier - - - - Gap opening penalty (float) - - beta12orEarlier - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + A simple floating point number defining the penalty for opening a gap in an alignment. + + Gap opening penalty (float) true - - - + + + beta12orEarlier + beta12orEarlier + + A simple floating point number defining the penalty for extending a gap in an alignment. + Gap extension penalty (integer) - true - A simple floating point number defining the penalty for extending a gap in an alignment. - beta12orEarlier - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + A simple floating point number defining the penalty for extending a gap in an alignment. + Gap extension penalty (float) - - beta12orEarlier true - A simple floating point number defining the penalty for extending a gap in an alignment. - beta12orEarlier - - - - Gap separation penalty (integer) - + + + beta12orEarlier + beta12orEarlier + A simple floating point number defining the penalty for gaps that are close together in an alignment. - beta12orEarlier + + Gap separation penalty (integer) true - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + A simple floating point number defining the penalty for gaps that are close together in an alignment. + Gap separation penalty (float) - - beta12orEarlier true - beta12orEarlier - A simple floating point number defining the penalty for gaps that are close together in an alignment. - - - - Terminal gap opening penalty - - beta12orEarlier + + + beta12orEarlier A number defining the penalty for opening gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences. - - + + + Terminal gap opening penalty - - Terminal gap extension penalty - + + + beta12orEarlier A number defining the penalty for extending gaps at the termini of an alignment, either from the N/C terminal of protein or 5'/3' terminal of nucleotide sequences. - beta12orEarlier - - + + + Terminal gap extension penalty - - Sequence identity - + + + beta12orEarlier Sequence identity is the number (%) of matches (identical characters) in positions from an alignment of two molecular sequences. - beta12orEarlier - - + + + Sequence identity - - Sequence similarity - - beta12orEarlier + + + beta12orEarlier Sequence similarity is the similarity (expressed as a percentage) of two molecular sequences calculated from their alignment, a scoring matrix for scoring characters substitutions and penalties for gap insertion and extension. + + Data Type is float probably. - - + Sequence similarity - + + + beta12orEarlier + beta12orEarlier + + Data on molecular sequence alignment quality (estimated accuracy). + Sequence alignment metadata (quality report) - - beta12orEarlier true - beta12orEarlier - Data on molecular sequence alignment quality (estimated accuracy). - - - - Sequence alignment report (site conservation) - - beta12orEarlier + + + beta12orEarlier + 1.4 + Data on character conservation in a molecular sequence alignment. - 1.4 + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. Use this concept for calculated substitution rates, relative site variability, data on sites with biased properties, highly conserved or very poorly conserved sites, regions, blocks etc. + Sequence alignment report (site conservation) true - - - - Sequence alignment report (site correlation) - - 1.4 - beta12orEarlier + + + beta12orEarlier + 1.4 + Data on correlations between sites in a molecular sequence alignment, typically to identify possible covarying positions and predict contacts or structural constraints in protein structures. + + Sequence alignment report (site correlation) true - - - - Sequence-profile alignment (Domainatrix signature) - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + Alignment of molecular sequences to a Domainatrix signature (representing a sequence alignment). - beta12orEarlier + + Sequence-profile alignment (Domainatrix signature) true - - - + + + beta12orEarlier + 1.5 + + Alignment of molecular sequence(s) to a hidden Markov model(s). + Sequence-profile alignment (HMM) - - beta12orEarlier - 1.5 true - Alignment of molecular sequence(s) to a hidden Markov model(s). - - - - Sequence-profile alignment (fingerprint) - + + + beta12orEarlier + 1.5 + Alignment of molecular sequences to a protein fingerprint from the PRINTS database. - 1.5 - beta12orEarlier + + Sequence-profile alignment (fingerprint) true - - - - Phylogenetic continuous quantitative data - - beta12orEarlier + + + beta12orEarlier + Continuous quantitative data that may be read during phylogenetic tree calculation. Phylogenetic continuous quantitative characters Quantitative traits - Continuous quantitative data that may be read during phylogenetic tree calculation. - - + + + Phylogenetic continuous quantitative data - - Phylogenetic discrete data - - Discrete characters + + + beta12orEarlier Character data with discrete states that may be read during phylogenetic tree calculation. - Phylogenetic discrete states - beta12orEarlier + Discrete characters Discretely coded characters - - + Phylogenetic discrete states + + + Phylogenetic discrete data - - Phylogenetic character cliques - + + + beta12orEarlier One or more cliques of mutually compatible characters that are generated, for example from analysis of discrete character data, and are used to generate a phylogeny. Phylogenetic report (cliques) - beta12orEarlier - - + + + Phylogenetic character cliques - - Phylogenetic invariants - + + - - + + + beta12orEarlier Phylogenetic invariants data for testing alternative tree topologies. - beta12orEarlier Phylogenetic report (invariants) - - + + + Phylogenetic invariants - - Phylogenetic report - - beta12orEarlier + + + beta12orEarlier + 1.5 + A report of data concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees. - Phylogenetic tree report - 1.5 - Phylogenetic report - Phylogenetic tree-derived report + This is a broad data type and is used for example for reports on confidence, shape or stratigraphic (age) data derived from phylogenetic tree analysis. + Phylogenetic report true - - - - DNA substitution model - - Substitution model + + + beta12orEarlier + A model of DNA substitution that explains a DNA sequence alignment, derived from phylogenetic tree analysis. Phylogenetic tree report (DNA substitution model) Sequence alignment report (DNA substitution model) - beta12orEarlier - A model of DNA substitution that explains a DNA sequence alignment, derived from phylogenetic tree analysis. - - + Substitution model + + + DNA substitution model - + + + beta12orEarlier + 1.4 + + Data about the shape of a phylogenetic tree. + Phylogenetic tree report (tree shape) - - beta12orEarlier true - 1.4 - Data about the shape of a phylogenetic tree. - - - + + + beta12orEarlier + 1.4 + + Data on the confidence of a phylogenetic tree. + Phylogenetic tree report (tree evaluation) - - beta12orEarlier true - 1.4 - Data on the confidence of a phylogenetic tree. - - - - Phylogenetic tree distances - - beta12orEarlier - Phylogenetic tree report (tree distances) + + + beta12orEarlier Distances, such as Branch Score distance, between two or more phylogenetic trees. - - + Phylogenetic tree report (tree distances) + + + Phylogenetic tree distances - + + + beta12orEarlier + 1.4 + + Molecular clock and stratigraphic (age) data derived from phylogenetic tree analysis. + Phylogenetic tree report (tree stratigraphic) - - beta12orEarlier - 1.4 true - Molecular clock and stratigraphic (age) data derived from phylogenetic tree analysis. - - - - Phylogenetic character contrasts - - Phylogenetic report (character contrasts) + + + beta12orEarlier Independent contrasts for characters used in a phylogenetic tree, or covariances, regressions and correlations between characters for those contrasts. - beta12orEarlier - - + Phylogenetic report (character contrasts) + + + Phylogenetic character contrasts - - Comparison matrix (integers) - - beta12orEarlier - Substitution matrix (integers) - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + Matrix of integer numbers for sequence comparison. + + Comparison matrix (integers) true - - - + + + beta12orEarlier + beta12orEarlier + + Matrix of floating point numbers for sequence comparison. + Comparison matrix (floats) - - beta12orEarlier - beta12orEarlier true - Matrix of floating point numbers for sequence comparison. - Substitution matrix (floats) - - - - Comparison matrix (nucleotide) - + + + beta12orEarlier Matrix of integer or floating point numbers for nucleotide comparison. - beta12orEarlier Nucleotide substitution matrix - - + + + Comparison matrix (nucleotide) - - Comparison matrix (amino acid) - - - Amino acid comparison matrix - beta12orEarlier + + + + beta12orEarlier Matrix of integer or floating point numbers for amino acid comparison. + Amino acid comparison matrix Amino acid substitution matrix - - + + + Comparison matrix (amino acid) - - Nucleotide comparison matrix (integers) - - Nucleotide substitution matrix (integers) - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + Matrix of integer numbers for nucleotide comparison. + Nucleotide substitution matrix (integers) + + Nucleotide comparison matrix (integers) true - beta12orEarlier - - - - Nucleotide comparison matrix (floats) - - beta12orEarlier - true + + + beta12orEarlier + beta12orEarlier + Matrix of floating point numbers for nucleotide comparison. - beta12orEarlier Nucleotide substitution matrix (floats) - - + + Nucleotide comparison matrix (floats) + true - - Amino acid comparison matrix (integers) - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + Matrix of integer numbers for amino acid comparison. - Amino acid substitution matrix (integers) + + Amino acid comparison matrix (integers) true - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + Matrix of floating point numbers for amino acid comparison. + Amino acid comparison matrix (floats) - - beta12orEarlier - Amino acid substitution matrix (floats) - beta12orEarlier true - Matrix of floating point numbers for amino acid comparison. - - - + + + beta12orEarlier + 1.8 + trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements. + + Protein features report (membrane regions) - true - beta12orEarlier - 1.8 - Topic concerning trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements. - - - - Nucleic acid structure - + + - - + + + beta12orEarlier 3D coordinate and associated data for a nucleic acid tertiary (3D) structure. - beta12orEarlier - - + + + Nucleic acid structure - - Protein structure - + + - - + + - Protein structures + beta12orEarlier 3D coordinate and associated data for a protein tertiary (3D) structure. - beta12orEarlier - - + Protein structures + + + Protein structure - - Protein-ligand complex - + + + beta12orEarlier The structure of a protein in complex with a ligand, typically a small molecule such as an enzyme substrate or cofactor, but possibly another macromolecule. - beta12orEarlier + + This includes interactions of proteins with atoms, ions and small molecules or macromolecules such as nucleic acids or other polypeptides. For stable inter-polypeptide interactions use 'Protein complex' instead. - - + Protein-ligand complex - - Carbohydrate structure - + + - - + + - - + + - beta12orEarlier + beta12orEarlier 3D coordinate and associated data for a carbohydrate (3D) structure. - - + + + Carbohydrate structure - - Small molecule structure - + + - - + + + beta12orEarlier 3D coordinate and associated data for the (3D) structure of a small molecule, such as any common chemical compound. CHEBI:23367 - beta12orEarlier - - + + + Small molecule structure - - DNA structure - - beta12orEarlier + + + beta12orEarlier 3D coordinate and associated data for a DNA tertiary (3D) structure. - - + + + DNA structure - - RNA structure - + + - - + + - beta12orEarlier + beta12orEarlier 3D coordinate and associated data for an RNA tertiary (3D) structure. - - + + + RNA structure - - tRNA structure - + + + beta12orEarlier 3D coordinate and associated data for a tRNA tertiary (3D) structure, including tmRNA, snoRNAs etc. - beta12orEarlier - - + + + tRNA structure - - Protein chain - - beta12orEarlier + + + beta12orEarlier 3D coordinate and associated data for the tertiary (3D) structure of a polypeptide chain. - - + + + Protein chain - - Protein domain - + + - - + + + beta12orEarlier 3D coordinate and associated data for the tertiary (3D) structure of a protein domain. - beta12orEarlier - - + + + Protein domain - + + + beta12orEarlier + 1.5 + + 3D coordinate and associated data for a protein tertiary (3D) structure (all atoms). + Protein structure (all atoms) - - beta12orEarlier - 1.5 true - 3D coordinate and associated data for a protein tertiary (3D) structure (all atoms). - - - - C-alpha trace - + + + beta12orEarlier 3D coordinate and associated data for a protein tertiary (3D) structure (typically C-alpha atoms only). - C-beta atoms from amino acid side-chains may be included. Protein structure (C-alpha atoms) - beta12orEarlier - - + + + C-beta atoms from amino acid side-chains may be included. + C-alpha trace - - Protein chain (all atoms) - + + + beta12orEarlier + beta12orEarlier + 3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (all atoms). - beta12orEarlier - beta12orEarlier + + Protein chain (all atoms) true - - - - Protein chain (C-alpha atoms) - - true + + + beta12orEarlier + beta12orEarlier + 3D coordinate and associated data for a polypeptide chain tertiary (3D) structure (typically C-alpha atoms only). - beta12orEarlier - beta12orEarlier + C-beta atoms from amino acid side-chains may be included. - - + Protein chain (C-alpha atoms) + true - - Protein domain (all atoms) - + + + beta12orEarlier + beta12orEarlier + 3D coordinate and associated data for a protein domain tertiary (3D) structure (all atoms). - beta12orEarlier + + Protein domain (all atoms) true - beta12orEarlier - - - - Protein domain (C-alpha atoms) - + + + beta12orEarlier + beta12orEarlier + + 3D coordinate and associated data for a protein domain tertiary (3D) structure (typically C-alpha atoms only). + C-beta atoms from amino acid side-chains may be included. + Protein domain (C-alpha atoms) true - 3D coordinate and associated data for a protein domain tertiary (3D) structure (typically C-alpha atoms only). - beta12orEarlier - beta12orEarlier - - - - Structure alignment (pair) - + + + beta12orEarlier Alignment (superimposition) of exactly two molecular tertiary (3D) structures. - beta12orEarlier Pair structure alignment - - + + + Structure alignment (pair) - + + + beta12orEarlier + beta12orEarlier + + Alignment (superimposition) of more than two molecular tertiary (3D) structures. + Structure alignment (multiple) - - beta12orEarlier - beta12orEarlier true - Alignment (superimposition) of more than two molecular tertiary (3D) structures. - - - - Structure alignment (protein) - - - Protein structure alignment - beta12orEarlier + + + + beta12orEarlier Alignment (superimposition) of protein tertiary (3D) structures. - - + Protein structure alignment + + + Structure alignment (protein) - - Structure alignment (nucleic acid) - - beta12orEarlier + + + beta12orEarlier Alignment (superimposition) of nucleic acid tertiary (3D) structures. Nucleic acid structure alignment - - + + + Structure alignment (nucleic acid) - - Structure alignment (protein pair) - - - Protein pair structural alignment - beta12orEarlier + + + beta12orEarlier + 1.12 + + Alignment (superimposition) of exactly two protein tertiary (3D) structures. - - + + Structure alignment (protein pair) + true - - Multiple protein tertiary structure alignment - + + + beta12orEarlier + beta12orEarlier + Alignment (superimposition) of more than two protein tertiary (3D) structures. - beta12orEarlier + + Multiple protein tertiary structure alignment true - beta12orEarlier - - - - Structure alignment (protein all atoms) - - 1.5 + + + beta12orEarlier + 1.5 + Alignment (superimposition) of protein tertiary (3D) structures (all atoms considered). - beta12orEarlier + + Structure alignment (protein all atoms) true - - - - Structure alignment (protein C-alpha atoms) - + + + beta12orEarlier + 1.5 + Alignment (superimposition) of protein tertiary (3D) structures (typically C-alpha atoms only considered). + C-beta atoms from amino acid side-chains may be considered. - 1.5 - C-alpha trace + Structure alignment (protein C-alpha atoms) true - beta12orEarlier - - - - Pairwise protein tertiary structure alignment (all atoms) - + + + beta12orEarlier + beta12orEarlier + Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered). + + Pairwise protein tertiary structure alignment (all atoms) true - beta12orEarlier - beta12orEarlier - - - - Pairwise protein tertiary structure alignment (C-alpha atoms) - + + + beta12orEarlier + beta12orEarlier + + Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered). + C-beta atoms from amino acid side-chains may be included. + Pairwise protein tertiary structure alignment (C-alpha atoms) true - beta12orEarlier - Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered). - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered). + Multiple protein tertiary structure alignment (all atoms) - - beta12orEarlier true - Alignment (superimposition) of exactly two protein tertiary (3D) structures (all atoms considered). - beta12orEarlier - - - - Multiple protein tertiary structure alignment (C-alpha atoms) - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + Alignment (superimposition) of exactly two protein tertiary (3D) structures (typically C-alpha atoms only considered). - true - beta12orEarlier + C-beta atoms from amino acid side-chains may be included. - - + Multiple protein tertiary structure alignment (C-alpha atoms) + true - - Structure alignment (nucleic acid pair) - - - beta12orEarlier - Nucleic acid pair structure alignment + + + beta12orEarlier + 1.12 + + Alignment (superimposition) of exactly two nucleic acid tertiary (3D) structures. - - + + Structure alignment (nucleic acid pair) + true - - Multiple nucleic acid tertiary structure alignment - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + Alignment (superimposition) of more than two nucleic acid tertiary (3D) structures. + + Multiple nucleic acid tertiary structure alignment true - beta12orEarlier - - - - Structure alignment (RNA) - - RNA structure alignment + + + beta12orEarlier Alignment (superimposition) of RNA tertiary (3D) structures. - beta12orEarlier - - + RNA structure alignment + + Structure alignment (RNA) - - Structural transformation matrix - + + + beta12orEarlier Matrix to transform (rotate/translate) 3D coordinates, typically the transformation necessary to superimpose two molecular structures. - beta12orEarlier - - + + + Structural transformation matrix - - DaliLite hit table - + + + beta12orEarlier + beta12orEarlier + DaliLite hit table of protein chain tertiary structure alignment data. + The significant and top-scoring hits for regions of the compared structures is shown. Data such as Z-Scores, number of aligned residues, root-mean-square deviation (RMSD) of atoms and sequence identity are given. - beta12orEarlier + DaliLite hit table true - beta12orEarlier - - - - Molecular similarity score - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + A score reflecting structural similarities of two molecules. + + Molecular similarity score true - beta12orEarlier - - - - Root-mean-square deviation - - RMSD - beta12orEarlier + + + beta12orEarlier Root-mean-square deviation (RMSD) is calculated to measure the average distance between superimposed macromolecular coordinates. - - + RMSD + + + Root-mean-square deviation - - Tanimoto similarity score - - beta12orEarlier + + + beta12orEarlier A measure of the similarity between two ligand fingerprints. + + A ligand fingerprint is derived from ligand structural data from a Protein DataBank file. It reflects the elements or groups present or absent, covalent bonds and bond orders and the bonded environment in terms of SATIS codes and BLEEP atom types. - - + Tanimoto similarity score - - 3D-1D scoring matrix - + + + beta12orEarlier A matrix of 3D-1D scores reflecting the probability of amino acids to occur in different tertiary structural environments. - beta12orEarlier - - + + + 3D-1D scoring matrix - - Amino acid index - - - beta12orEarlier + + + + beta12orEarlier A table of 20 numerical values which quantify a property (e.g. physicochemical or biochemical) of the common amino acids. - - + + + Amino acid index - - Amino acid index (chemical classes) - - Chemical classes (amino acids) + + + beta12orEarlier Chemical classification (small, aliphatic, aromatic, polar, charged etc) of amino acids. - beta12orEarlier - - + Chemical classes (amino acids) + + + Amino acid index (chemical classes) - - Amino acid pair-wise contact potentials - - Contact potentials (amino acid pair-wise) + + + beta12orEarlier Statistical protein contact potentials. - beta12orEarlier - - + Contact potentials (amino acid pair-wise) + + + Amino acid pair-wise contact potentials - - Amino acid index (molecular weight) - + + + beta12orEarlier Molecular weights of amino acids. Molecular weight (amino acids) - beta12orEarlier - - + + + Amino acid index (molecular weight) - - Amino acid index (hydropathy) - + + + beta12orEarlier Hydrophobic, hydrophilic or charge properties of amino acids. - beta12orEarlier Hydropathy (amino acids) - - + + + Amino acid index (hydropathy) - - Amino acid index (White-Wimley data) - - beta12orEarlier - White-Wimley data (amino acids) + + + beta12orEarlier Experimental free energy values for the water-interface and water-octanol transitions for the amino acids. - - + White-Wimley data (amino acids) + + + Amino acid index (White-Wimley data) - - Amino acid index (van der Waals radii) - - van der Waals radii (amino acids) + + + beta12orEarlier Van der Waals radii of atoms for different amino acid residues. - beta12orEarlier - - + van der Waals radii (amino acids) + + + Amino acid index (van der Waals radii) - + + + beta12orEarlier + 1.5 + + An informative report on a specific enzyme. + Enzyme report - true - 1.5 - Protein report (enzyme) - beta12orEarlier - Enzyme report - An informative report on a specific enzyme. - - - - Restriction enzyme report - + + + beta12orEarlier + 1.5 + An informative report on a specific restriction enzyme such as enzyme reference data. - Restriction enzyme pattern data - beta12orEarlier - 1.5 + This might include name of enzyme, organism, isoschizomers, methylation, source, suppliers, literature references, or data on restriction enzyme patterns such as name of enzyme, recognition site, length of pattern, number of cuts made by enzyme, details of blunt or sticky end cut etc. - Protein report (restriction enzyme) - Restriction enzyme report + Restriction enzyme report true - - - - Peptide molecular weights - - beta12orEarlier + + + beta12orEarlier List of molecular weight(s) of one or more proteins or peptides, for example cut by proteolytic enzymes or reagents. + + The report might include associated data such as frequency of peptide fragment molecular weights. - - + Peptide molecular weights - - Peptide hydrophobic moment - - beta12orEarlier + + + beta12orEarlier Report on the hydrophobic moment of a polypeptide sequence. + + Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. - - + Peptide hydrophobic moment - - Protein aliphatic index - + + + beta12orEarlier The aliphatic index of a protein. - beta12orEarlier + + The aliphatic index is the relative protein volume occupied by aliphatic side chains. - - + Protein aliphatic index - - Protein sequence hydropathy plot - - Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. + + + beta12orEarlier A protein sequence with annotation on hydrophobic or hydrophilic / charged regions, hydrophobicity plot etc. - beta12orEarlier - - + + + Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. + Protein sequence hydropathy plot - - Protein charge plot - - beta12orEarlier + + + beta12orEarlier A plot of the mean charge of the amino acids within a window of specified length as the window is moved along a protein sequence. - - + + + Protein charge plot - - Protein solubility - - beta12orEarlier + + + beta12orEarlier The solubility or atomic solvation energy of a protein sequence or structure. Protein solubility data - - + + + Protein solubility - - Protein crystallizability - - beta12orEarlier - Protein crystallizability data + + + beta12orEarlier Data on the crystallizability of a protein sequence. - - + Protein crystallizability data + + + Protein crystallizability - - Protein globularity - - Protein globularity data - beta12orEarlier + + + beta12orEarlier Data on the stability, intrinsic disorder or globularity of a protein sequence. - - + Protein globularity data + + + Protein globularity - - Protein titration curve - - + + + + beta12orEarlier The titration curve of a protein. - beta12orEarlier - - + + + Protein titration curve - - Protein isoelectric point - - beta12orEarlier + + + beta12orEarlier The isoelectric point of one proteins. - - + + + Protein isoelectric point - - Protein pKa value - + + + beta12orEarlier The pKa value of a protein. - beta12orEarlier - - + + + Protein pKa value - - Protein hydrogen exchange rate - - beta12orEarlier + + + beta12orEarlier The hydrogen exchange rate of a protein. - - + + + Protein hydrogen exchange rate - - Protein extinction coefficient - + + + beta12orEarlier The extinction coefficient of a protein. - beta12orEarlier - - + + + Protein extinction coefficient - - Protein optical density - + + + beta12orEarlier The optical density of a protein. - beta12orEarlier - - + + + Protein optical density - - Protein subcellular localization - - Protein report (subcellular localization) - An informative report on protein subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or destination (exported / extracellular proteins). - beta12orEarlier + + + beta12orEarlier + beta13 + + An informative report on protein subcellular localisation (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or destination (exported / extracellular proteins). + Protein report (subcellular localisation) + + Protein subcellular localisation true - beta13 - - - - Peptide immunogenicity data - + + + beta12orEarlier An report on allergenicity / immunogenicity of peptides and proteins. - Peptide immunogenicity report - beta12orEarlier Peptide immunogenicity + Peptide immunogenicity report + + This includes data on peptide ligands that elicit an immune response (immunogens), allergic cross-reactivity, predicted antigenicity (Hopp and Woods plot) etc. These data are useful in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data. - - + Peptide immunogenicity data - - MHC peptide immunogenicity report - + + + beta12orEarlier + beta13 + A report on the immunogenicity of MHC class I or class II binding peptides. - beta13 + + MHC peptide immunogenicity report true - beta12orEarlier - - - - Protein structure report - - - Protein structural property - Protein structure-derived report - This includes for example reports on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure, protein flexibility or motion, and protein architecture (spatial arrangement of secondary structure). + + + + beta12orEarlier + Annotation about, or structural information derived from, one or more specific protein 3D structure(s) or structural domains. Protein property (structural) - Annotation on or structural information derived from one or more specific protein 3D structure(s) or structural domains. - beta12orEarlier Protein report (structure) + Protein structural property Protein structure report (domain) - - + Protein structure-derived report + + + This includes for example reports on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure, protein flexibility or motion, and protein architecture (spatial arrangement of secondary structure). + Protein structure report - - Protein structural quality report - + + + beta12orEarlier Report on the quality of a protein three-dimensional model. + Protein property (structural quality) + Protein report (structural quality) Protein structure report (quality evaluation) Protein structure validation report - Protein property (structural quality) + + Model validation might involve checks for atomic packing, steric clashes, agreement with electron density maps etc. - Protein report (structural quality) - beta12orEarlier - - + Protein structural quality report - - Protein residue interactions - - - - - - - - Residue interaction data + + + beta12orEarlier + 1.12 Data on inter-atomic or inter-residue contacts, distances and interactions in protein structure(s) or on the interactions of protein atoms or residues with non-protein groups. - beta12orEarlier - Atom interaction data - - + + + Protein non-covalent interactions report + true - - Protein flexibility or motion report - - This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. - Protein property (flexibility or motion) + + + beta12orEarlier + 1.4 + Informative report on flexibility or motion of a protein structure. - Protein flexibility or motion - beta12orEarlier + + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. + Protein flexibility or motion report true - 1.4 - Protein structure report (flexibility or motion) - - - - Protein solvent accessibility - - This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. This concept covers definitions of the protein surface, interior and interfaces, accessible and buried residues, surface accessible pockets, interior inaccessible cavities etc. - beta12orEarlier + + + beta12orEarlier Data on the solvent accessible or buried surface area of a protein structure. - - + + + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. This concept covers definitions of the protein surface, interior and interfaces, accessible and buried residues, surface accessible pockets, interior inaccessible cavities etc. + Protein solvent accessibility report - - Protein surface report - - This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. - Protein structure report (surface) - 1.4 + + + beta12orEarlier + 1.4 + Data on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure. - beta12orEarlier + + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. + Protein surface report true - - - - Ramachandran plot - - beta12orEarlier + + + beta12orEarlier Phi/psi angle data or a Ramachandran plot of a protein structure. - - + + + Ramachandran plot - - Protein dipole moment - + + + beta12orEarlier Data on the net charge distribution (dipole moment) of a protein structure. - beta12orEarlier - - + + + Protein dipole moment - - Protein distance matrix - - beta12orEarlier + + + + beta12orEarlier A matrix of distances between amino acid residues (for example the C-alpha atoms) in a protein structure. - - + + + Protein distance matrix - - Protein contact map - + + + beta12orEarlier An amino acid residue contact map for a protein structure. - beta12orEarlier - - + + + Protein contact map - - Protein residue 3D cluster - - beta12orEarlier + + + beta12orEarlier Report on clusters of contacting residues in protein structures such as a key structural residue network. - - + + + Protein residue 3D cluster - - Protein hydrogen bonds - + + + beta12orEarlier Patterns of hydrogen bonding in protein structures. - beta12orEarlier - - + + + Protein hydrogen bonds - + + + beta12orEarlier + 1.4 + + Non-canonical atomic interactions in protein structures. + Protein non-canonical interactions - - Protein non-canonical interactions report true - Non-canonical atomic interactions in protein structures. - 1.4 - beta12orEarlier - - - - CATH node - + + + beta12orEarlier + 1.5 + Information on a node from the CATH database. + The report (for example http://www.cathdb.info/cathnode/1.10.10.10) includes CATH code (of the node and upper levels in the hierarchy), classification text (of appropriate levels in hierarchy), list of child nodes, representative domain and other relevant data and links. - 1.5 - beta12orEarlier + CATH node true - CATH classification node report - - - + + + beta12orEarlier + 1.5 + + Information on a node from the SCOP database. + SCOP node - true - SCOP classification node - Information on a node from the SCOP database. - 1.5 - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + An EMBASSY domain classification file (DCF) of classification and other data for domains from SCOP or CATH, in EMBL-like format. + + EMBASSY domain classification - - beta12orEarlier - beta12orEarlier true - An EMBASSY domain classification file (DCF) of classification and other data for domains from SCOP or CATH, in EMBL-like format. - - - CATH class - - beta12orEarlier - 1.5 + + + beta12orEarlier + 1.5 + Information on a protein 'class' node from the CATH database. + + CATH class true - - - - CATH architecture - - beta12orEarlier - 1.5 + + + beta12orEarlier + 1.5 + Information on a protein 'architecture' node from the CATH database. + + CATH architecture true - - - + + + beta12orEarlier + 1.5 + + Information on a protein 'topology' node from the CATH database. + CATH topology - true - 1.5 - Information on a protein 'topology' node from the CATH database. - beta12orEarlier - - - + + + beta12orEarlier + 1.5 + + Information on a protein 'homologous superfamily' node from the CATH database. + CATH homologous superfamily - - 1.5 true - beta12orEarlier - Information on a protein 'homologous superfamily' node from the CATH database. - - - + + + beta12orEarlier + 1.5 + + Information on a protein 'structurally similar group' node from the CATH database. + CATH structurally similar group - - 1.5 true - beta12orEarlier - Information on a protein 'structurally similar group' node from the CATH database. - - - - CATH functional category - + + + beta12orEarlier + 1.5 + Information on a protein 'functional category' node from the CATH database. + + CATH functional category true - 1.5 - beta12orEarlier - - - - Protein fold recognition report - + + + beta12orEarlier + beta12orEarlier + + A report on known protein structural domains or folds that are recognised (identified) in protein sequence(s). + Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH. - beta12orEarlier - A report on known protein structural domains or folds that are recognized (identified) in protein sequence(s). + Protein fold recognition report true - beta12orEarlier - - - + + + beta12orEarlier + 1.8 + protein-protein interaction(s), including interactions between protein domains. + + Protein-protein interaction report - - beta12orEarlier true - Topic concerning protein-protein interaction(s), including interactions between protein domains. - 1.8 - - - - Protein-ligand interaction report - - beta12orEarlier + + + beta12orEarlier An informative report on protein-ligand (small molecule) interaction(s). - - + Protein-drug interaction report + + + Protein-ligand interaction report - + + + beta12orEarlier + 1.8 + protein-DNA/RNA interaction(s). + + Protein-nucleic acid interactions report - true - Topic concerning protein-DNA/RNA interaction(s). - beta12orEarlier - 1.8 - - - - Nucleic acid melting profile - + + + beta12orEarlier + Data on the dissociation characteristics of a double-stranded nucleic acid molecule (DNA or a DNA/RNA hybrid) during heating. Nucleic acid stability profile + + A melting (stability) profile calculated the free energy required to unwind and separate the nucleic acid strands, plotted for sliding windows over a sequence. - Data on the dissociation characteristics of a double-stranded nucleic acid molecule (DNA or a DNA/RNA hybrid) during heating. - beta12orEarlier - - + Nucleic acid melting profile - + + + beta12orEarlier + Enthalpy of hybridised or double stranded nucleic acid (DNA or RNA/DNA). + + Nucleic acid enthalpy - - beta12orEarlier - Enthalpy of hybridized or double stranded nucleic acid (DNA or RNA/DNA). - - - + + + beta12orEarlier + Entropy of hybridised or double stranded nucleic acid (DNA or RNA/DNA). + + Nucleic acid entropy - - Entropy of hybridized or double stranded nucleic acid (DNA or RNA/DNA). - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + Melting temperature of hybridised or double stranded nucleic acid (DNA or RNA/DNA). + Nucleic acid melting temperature - - Melting temperature of hybridized or double stranded nucleic acid (DNA or RNA/DNA). - beta12orEarlier - beta12orEarlier true - - - - Nucleic acid stitch profile - - beta12orEarlier - Stitch profile of hybridized or double stranded nucleic acid (DNA or RNA/DNA). + + + beta12orEarlier + Stitch profile of hybridised or double stranded nucleic acid (DNA or RNA/DNA). + + A stitch profile diagram shows partly melted DNA conformations (with probabilities) at a range of temperatures. For example, a stitch profile might show possible loop openings with their location, size, probability and fluctuations at a given temperature. - - + Nucleic acid stitch profile - - DNA base pair stacking energies data - + + + beta12orEarlier DNA base pair stacking energies data. - beta12orEarlier - - + + + DNA base pair stacking energies data - - DNA base pair twist angle data - - beta12orEarlier + + + beta12orEarlier DNA base pair twist angle data. - - + + + DNA base pair twist angle data - - DNA base trimer roll angles data - - beta12orEarlier + + + beta12orEarlier DNA base trimer roll angles data. - - + + + DNA base trimer roll angles data - - Vienna RNA parameters - + + + beta12orEarlier + beta12orEarlier RNA parameters used by the Vienna package. + + Vienna RNA parameters true - beta12orEarlier - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + Structure constraints used by the Vienna package. + Vienna RNA structure constraints - true - Structure constraints used by the Vienna package. - beta12orEarlier - beta12orEarlier - - - - Vienna RNA concentration data - + + + beta12orEarlier + beta12orEarlier RNA concentration data used by the Vienna package. - beta12orEarlier + + Vienna RNA concentration data true - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + RNA calculated energy data generated by the Vienna package. + Vienna RNA calculated energy - - beta12orEarlier - beta12orEarlier true - RNA calculated energy data generated by the Vienna package. - - - - Base pairing probability matrix dotplot - - - beta12orEarlier - Such as generated by the Vienna package. + + + + beta12orEarlier Dotplot of RNA base pairing probability matrix. - - + + + Such as generated by the Vienna package. + Base pairing probability matrix dotplot - - Nucleic acid folding report - - Nucleic acid report (folding) - beta12orEarlier - Nucleic acid report (folding model) - RNA secondary structure folding probablities + + + beta12orEarlier A report on an analysis of RNA/DNA folding, minimum folding energies for DNA or RNA sequences, energy landscape of RNA mutants etc. - This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. + Nucleic acid report (folding model) + Nucleic acid report (folding) RNA secondary structure folding classification - - + RNA secondary structure folding probablities + + + Nucleic acid folding report - - Codon usage table - + + - - + + + beta12orEarlier Table of codon usage data calculated from one or more nucleic acid sequences. + + A codon usage table might include the codon usage table name, optional comments and a table with columns for codons and corresponding codon usage data. A genetic code can be extracted from or represented by a codon usage table. - beta12orEarlier - - + Codon usage table - - Genetic code - - beta12orEarlier + + + beta12orEarlier A genetic code for an organism. + + A genetic code need not include detailed codon usage information. - - + Genetic code - + + + beta12orEarlier + beta12orEarlier + + A simple measure of synonymous codon usage bias often used to predict gene expression levels. + Codon adaptation index - true - A simple measure of synonymous codon usage bias often used to predict gene expression levels. - CAI - beta12orEarlier - beta12orEarlier - - - - Codon usage bias plot - - Synonymous codon usage statistic plot - beta12orEarlier + + + beta12orEarlier A plot of the synonymous codon usage calculated for windows over a nucleotide sequence. - - + Synonymous codon usage statistic plot + + + Codon usage bias plot - + + + beta12orEarlier + beta12orEarlier + + The effective number of codons used in a gene sequence. This reflects how far codon usage of a gene departs from equal usage of synonymous codons. + Nc statistic - true - beta12orEarlier - The effective number of codons used in a gene sequence. This reflects how far codon usage of a gene departs from equal usage of synonymous codons. - beta12orEarlier - - - - Codon usage fraction difference - + + + beta12orEarlier The differences in codon usage fractions between two codon usage tables. - beta12orEarlier - - + + + Codon usage fraction difference - - Pharmacogenomic test report - - beta12orEarlier - The report might correlate gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity. + + + beta12orEarlier Data on the influence of genotype on drug response. - - + + + The report might correlate gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity. + Pharmacogenomic test report - - Disease report - + + - - + + + beta12orEarlier An informative report on a specific disease. + + For example, an informative report on a specific tumor including nature and origin of the sample, anatomic site, organ or tissue, tumor type, including morphology and/or histologic type, and so on. - beta12orEarlier - Disease report - - + Disease report - + + + beta12orEarlier + 1.8 + A report on linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome). + + Linkage disequilibrium (report) - true - A report on linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome). - 1.8 - beta12orEarlier - - - - Heatmap - Heat map - - - + + + + + beta12orEarlier A graphical 2D tabular representation of gene expression data, typically derived from a DNA microarray experiment. - beta12orEarlier + + A heat map is a table where rows and columns correspond to different genes and contexts (for example, cells or samples) and the cell color represents the level of expression of a gene that context. - - + Heat map + Heatmap - + + + beta12orEarlier + beta12orEarlier + + Affymetrix library file of information about which probes belong to which probe set. + Affymetrix probe sets library file - true - Affymetrix library file of information about which probes belong to which probe set. - CDF file - beta12orEarlier - beta12orEarlier - - - - Affymetrix probe sets information library file - - true + + + beta12orEarlier + beta12orEarlier + Affymetrix library file of information about the probe sets such as the gene name with which the probe set is associated. GIN file - beta12orEarlier - beta12orEarlier - - + + Affymetrix probe sets information library file + true - - Molecular weights standard fingerprint - - beta12orEarlier + + + beta12orEarlier + 1.12 Standard protonated molecular masses from trypsin (modified porcine trypsin, Promega) and keratin peptides, used in EMBOSS. - - + + + Molecular weights standard fingerprint + true - - Metabolic pathway report - - This includes carbohydrate, energy, lipid, nucleotide, amino acid, glycan, PK/NRP, cofactor/vitamin, secondary metabolite, xenobiotics etc. - beta12orEarlier + + + beta12orEarlier + 1.8 A report typically including a map (diagram) of a metabolic pathway. - 1.8 + + + This includes carbohydrate, energy, lipid, nucleotide, amino acid, glycan, PK/NRP, cofactor/vitamin, secondary metabolite, xenobiotics etc. + Metabolic pathway report true - - - + + + beta12orEarlier + 1.8 + genetic information processing pathways. + + Genetic information processing pathway report - - beta12orEarlier - Topic concerning genetic information processing pathways. - 1.8 true - - - + + + beta12orEarlier + 1.8 + environmental information processing pathways. + + Environmental information processing pathway report - - Topic concerning environmental information processing pathways. true - beta12orEarlier - 1.8 - - - - Signal transduction pathway report - + + + beta12orEarlier + 1.8 A report typically including a map (diagram) of a signal transduction pathway. - 1.8 + + + Signal transduction pathway report true - beta12orEarlier - - - - Cellular process pathways report - - 1.8 + + + beta12orEarlier + 1.8 Topic concernning cellular process pathways. + + + Cellular process pathways report true - beta12orEarlier - - - + + + beta12orEarlier + 1.8 + disease pathways, typically of human disease. + + Disease pathway or network report - true - beta12orEarlier - 1.8 - Topic concerning disease pathways, typically of human disease. - - - - Drug structure relationship map - + + + beta12orEarlier A report typically including a map (diagram) of drug structure relationships. - beta12orEarlier - - + + + Drug structure relationship map - + + + beta12orEarlier + 1.8 + + networks of protein interactions. + Protein interaction networks - - Topic concerning networks of protein interactions. - 1.8 true - beta12orEarlier - - - - MIRIAM datatype - - A MIRIAM entry describes a MIRIAM data type including the official name, synonyms, root URI, identifier pattern (regular expression applied to a unique identifier of the data type) and documentation. Each data type can be associated with several resources. Each resource is a physical location of a service (typically a database) providing information on the elements of a data type. Several resources may exist for each data type, provided the same (mirrors) or different information. MIRIAM provides a stable and persistent reference to its data types. + + + beta12orEarlier + 1.5 + An entry (data type) from the Minimal Information Requested in the Annotation of Biochemical Models (MIRIAM) database of data resources. - beta12orEarlier + + A MIRIAM entry describes a MIRIAM data type including the official name, synonyms, root URI, identifier pattern (regular expression applied to a unique identifier of the data type) and documentation. Each data type can be associated with several resources. Each resource is a physical location of a service (typically a database) providing information on the elements of a data type. Several resources may exist for each data type, provided the same (mirrors) or different information. MIRIAM provides a stable and persistent reference to its data types. + MIRIAM datatype true - 1.5 - - - - E-value - - An expectation value (E-Value) is the expected number of observations which are at least as extreme as observations expected to occur by random chance. The E-value describes the number of hits with a given score or better that are expected to occur at random when searching a database of a particular size. It decreases exponentially with the score (S) of a hit. A low E value indicates a more significant score. - beta12orEarlier + + + beta12orEarlier A simple floating point number defining the lower or upper limit of an expectation value (E-value). Expectation value - - + + + An expectation value (E-Value) is the expected number of observations which are at least as extreme as observations expected to occur by random chance. The E-value describes the number of hits with a given score or better that are expected to occur at random when searching a database of a particular size. It decreases exponentially with the score (S) of a hit. A low E value indicates a more significant score. + E-value - - Z-value - - beta12orEarlier + + + beta12orEarlier The z-value is the number of standard deviations a data value is above or below a mean value. + + A z-value might be specified as a threshold for reporting hits from database searches. - - + Z-value - - P-value - - beta12orEarlier - A z-value might be specified as a threshold for reporting hits from database searches. + + + beta12orEarlier The P-value is the probability of obtaining by random chance a result that is at least as extreme as an observed result, assuming a NULL hypothesis is true. - - + + + A z-value might be specified as a threshold for reporting hits from database searches. + P-value - + + + beta12orEarlier + 1.5 + + Information on a database (or ontology) version, for example name, version number and release date. + Database version information - true - Ontology version information - 1.5 - Information on a database (or ontology) version, for example name, version number and release date. - beta12orEarlier - - - - Tool version information - - beta12orEarlier + + + beta12orEarlier + 1.5 + Information on an application version, for example name, version number and release date. + + Tool version information true - 1.5 - - - + + + beta12orEarlier + beta12orEarlier + + Information on a version of the CATH database. + CATH version information - - beta12orEarlier - beta12orEarlier true - Information on a version of the CATH database. - - - - Swiss-Prot to PDB mapping - + + + beta12orEarlier + beta12orEarlier + Cross-mapping of Swiss-Prot codes to PDB identifiers. - beta12orEarlier + + Swiss-Prot to PDB mapping true - beta12orEarlier - - - - Sequence database cross-references - + + + beta12orEarlier + beta12orEarlier + Cross-references from a sequence record to other databases. - beta12orEarlier + + Sequence database cross-references true - beta12orEarlier - - - - Job status - + + + beta12orEarlier + 1.5 + Metadata on the status of a submitted job. - beta12orEarlier - 1.5 - true + Values for EBI services are 'DONE' (job has finished and the results can then be retrieved), 'ERROR' (the job failed or no results where found), 'NOT_FOUND' (the job id is no longer available; job results might be deleted, 'PENDING' (the job is in a queue waiting processing), 'RUNNING' (the job is currently being processed). - - + Job status + true - - Job ID - - 1.0 + + + beta12orEarlier + 1.0 + The (typically numeric) unique identifier of a submitted job. - beta12orEarlier + + Job ID true - - + + + beta12orEarlier + 1.5 + + A label (text token) describing the type of job, for example interactive or non-interactive. + Job type - - 1.5 true - beta12orEarlier - A label (text token) describing the type of job, for example interactive or non-interactive. - - - - Tool log - - 1.5 + + + beta12orEarlier + 1.5 + A report of tool-specific metadata on some analysis or process performed, for example a log of diagnostic or error messages. + + Tool log true - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + DaliLite log file describing all the steps taken by a DaliLite alignment of two protein structures. + DaliLite log file - true - beta12orEarlier - DaliLite log file describing all the steps taken by a DaliLite alignment of two protein structures. - beta12orEarlier - - - - STRIDE log file - + + + beta12orEarlier + beta12orEarlier + STRIDE log file. + + STRIDE log file true - beta12orEarlier - beta12orEarlier - - - - + + + beta12orEarlier + beta12orEarlier + + NACCESS log file. + NACCESS log file - - beta12orEarlier - beta12orEarlier true - NACCESS log file. - - - - - EMBOSS wordfinder log file - + + + beta12orEarlier + beta12orEarlier + EMBOSS wordfinder log file. - beta12orEarlier - beta12orEarlier + + EMBOSS wordfinder log file true - - - - EMBOSS domainatrix log file - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + EMBOSS (EMBASSY) domainatrix application log file. - beta12orEarlier + + EMBOSS domainatrix log file true - - - + + + beta12orEarlier + beta12orEarlier + + EMBOSS (EMBASSY) sites application log file. + EMBOSS sites log file - true - beta12orEarlier - beta12orEarlier - EMBOSS (EMBASSY) sites application log file. - - - - EMBOSS supermatcher error file - + + + beta12orEarlier + beta12orEarlier + EMBOSS (EMBASSY) supermatcher error file. - beta12orEarlier - beta12orEarlier + + EMBOSS supermatcher error file true - - - - EMBOSS megamerger log file - - beta12orEarlier - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + EMBOSS megamerger log file. + + EMBOSS megamerger log file true - - - + + + beta12orEarlier + beta12orEarlier + + EMBOSS megamerger log file. + EMBOSS whichdb log file - - beta12orEarlier true - EMBOSS megamerger log file. - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + EMBOSS vectorstrip log file. + EMBOSS vectorstrip log file - true - beta12orEarlier - beta12orEarlier - EMBOSS vectorstrip log file. - - - - Username - + + + beta12orEarlier A username on a computer system. - beta12orEarlier - - - + + + + Username - - Password - - beta12orEarlier + + + beta12orEarlier A password on a computer system. - - - + + + + Password - - Email address - - beta12orEarlier + + + beta12orEarlier Moby:Email - A valid email address of an end-user. Moby:EmailAddress - - - + A valid email address of an end-user. + + + + Email address - - Person name - - beta12orEarlier + + + beta12orEarlier The name of a person. - - - + + + + Person name - - Number of iterations - - 1.5 + + + beta12orEarlier + 1.5 Number of iterations of an algorithm. + + Number of iterations true - beta12orEarlier - - - - Number of output entities - + + + beta12orEarlier + 1.5 Number of entities (for example database hits, sequences, alignments etc) to write to an output file. - 1.5 - beta12orEarlier + + Number of output entities true - - - - Hit sort order - + + + beta12orEarlier + beta12orEarlier Controls the order of hits (reported matches) in an output file from a database search. - beta12orEarlier - beta12orEarlier + + Hit sort order true - - - - - Drug report - + + - - + + + beta12orEarlier + An informative report on a specific drug. - beta12orEarlier Drug annotation - - - + + + Drug report - - Phylogenetic tree image - - beta12orEarlier + + + beta12orEarlier An image (for viewing or printing) of a phylogenetic tree including (typically) a plot of rooted or unrooted phylogenies, cladograms, circular trees or phenograms and associated information. + + See also 'Phylogenetic tree' - - + Phylogenetic tree image - - RNA secondary structure image - - beta12orEarlier + + + beta12orEarlier Image of RNA secondary structure, knots, pseudoknots etc. - - + + + RNA secondary structure image - - Protein secondary structure image - + + + beta12orEarlier Image of protein secondary structure. - beta12orEarlier - - + + + Protein secondary structure image - - Structure image - - beta12orEarlier + + + beta12orEarlier Image of one or more molecular tertiary (3D) structures. - - + + + Structure image - - Sequence alignment image - - beta12orEarlier + + + beta12orEarlier Image of two or more aligned molecular sequences possibly annotated with alignment features. - - + + + Sequence alignment image - - Chemical structure image - + + + beta12orEarlier An image of the structure of a small chemical compound. - The molecular identifier and formula are typically included. Small molecule structure image - beta12orEarlier - - + + + The molecular identifier and formula are typically included. + Chemical structure image - - Fate map - - + + + - - + + - beta12orEarlier + beta12orEarlier A fate map is a plan of early stage of an embryo such as a blastula, showing areas that are significance to development. - - + + + Fate map - - Microarray spots image - - - beta12orEarlier + + + + beta12orEarlier An image of spots from a microarray experiment. - - + + + Microarray spots image - - BioPax term - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + A term from the BioPax ontology. - beta12orEarlier + + BioPax term true - - - + + + beta12orEarlier + beta12orEarlier + + A term definition from The Gene Ontology (GO). + GO - - beta12orEarlier - Gene Ontology term - Moby:Annotated_GO_Term - Moby:Annotated_GO_Term_With_Probability true - A term definition from The Gene Ontology (GO). - beta12orEarlier - Moby:GO_Term - Moby:GOTerm - - - + + + beta12orEarlier + beta12orEarlier + + A term from the MeSH vocabulary. + MeSH - true - A term from the MeSH vocabulary. - beta12orEarlier - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + A term from the HGNC controlled vocabulary. + HGNC - - beta12orEarlier true - A term from the HGNC controlled vocabulary. - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + A term from the NCBI taxonomy vocabulary. + NCBI taxonomy vocabulary - - beta12orEarlier - beta12orEarlier true - A term from the NCBI taxonomy vocabulary. - - - + + + beta12orEarlier + beta12orEarlier + + A term from the Plant Ontology (PO). + Plant ontology term - - beta12orEarlier true - beta12orEarlier - A term from the Plant Ontology (PO). - - - - UMLS - - beta12orEarlier - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + A term from the UMLS vocabulary. + + UMLS true - - - - FMA - - beta12orEarlier - Classifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented. - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + A term from Foundational Model of Anatomy. + + Classifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented. + FMA true - - - - EMAP - + + + beta12orEarlier + beta12orEarlier + A term from the EMAP mouse ontology. + + EMAP true - beta12orEarlier - beta12orEarlier - - - - ChEBI - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + A term from the ChEBI ontology. + + ChEBI true - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + A term from the MGED ontology. + MGED - - beta12orEarlier true - A term from the MGED ontology. - beta12orEarlier - - - - myGrid - + + + beta12orEarlier + beta12orEarlier + + A term from the myGrid ontology. + The ontology is provided as two components, the service ontology and the domain ontology. The domain ontology acts provides concepts for core bioinformatics data types and their relations. The service ontology describes the physical and operational features of web services. - beta12orEarlier + myGrid true - A term from the myGrid ontology. - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + A term definition for a biological process from the Gene Ontology (GO). + + Data Type is an enumerated string. GO (biological process) - - beta12orEarlier true - beta12orEarlier - Data Type is an enumerated string. - A term definition for a biological process from the Gene Ontology (GO). - - - - GO (molecular function) - + + + beta12orEarlier + beta12orEarlier + A term definition for a molecular function from the Gene Ontology (GO). - beta12orEarlier + Data Type is an enumerated string. + GO (molecular function) true - beta12orEarlier - - - - GO (cellular component) - - beta12orEarlier - true + + + beta12orEarlier + beta12orEarlier + A term definition for a cellular component from the Gene Ontology (GO). - beta12orEarlier + Data Type is an enumerated string. - - + GO (cellular component) + true - + + + beta12orEarlier + 1.5 + + A relation type defined in an ontology. + Ontology relation type - - 1.5 - beta12orEarlier true - A relation type defined in an ontology. - - - - Ontology concept definition - - beta12orEarlier - Ontology class definition + + + beta12orEarlier The definition of a concept from an ontology. - - + Ontology class definition + + + Ontology concept definition - + + + beta12orEarlier + 1.4 + + A comment on a concept from an ontology. + Ontology concept comment - - beta12orEarlier - 1.4 true - A comment on a concept from an ontology. - - - + + + beta12orEarlier + beta12orEarlier + + Reference for a concept from an ontology. + Ontology concept reference - - beta12orEarlier true - Reference for a concept from an ontology. - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + Information on a published article provided by the doc2loc program. + + The doc2loc output includes the url, format, type and availability code of a document for every service provider. doc2loc document information - - beta12orEarlier true - The doc2loc output includes the url, format, type and availability code of a document for every service provider. - beta12orEarlier - Information on a published article provided by the doc2loc program. - - - - PDB residue number - - WHATIF: pdb_number + + + beta12orEarlier PDBML:PDB_residue_no - beta12orEarlier + WHATIF: pdb_number A residue identifier (a string) from a PDB file. - - + + + PDB residue number - - Atomic coordinate - + + + beta12orEarlier Cartesian coordinate of an atom (in a molecular structure). - beta12orEarlier Cartesian coordinate - - + + + Atomic coordinate - - Atomic x coordinate - - WHATIF: PDBx_Cartn_x - Cartesian x coordinate - beta12orEarlier + + + beta12orEarlier PDBML:_atom_site.Cartn_x in PDBML + WHATIF: PDBx_Cartn_x Cartesian x coordinate of an atom (in a molecular structure). - - + Cartesian x coordinate + + + Atomic x coordinate - - Atomic y coordinate - - WHATIF: PDBx_Cartn_y - Cartesian y coordinate - beta12orEarlier + + + beta12orEarlier PDBML:_atom_site.Cartn_y in PDBML + WHATIF: PDBx_Cartn_y Cartesian y coordinate of an atom (in a molecular structure). - - + Cartesian y coordinate + + + Atomic y coordinate - - Atomic z coordinate - + + + beta12orEarlier PDBML:_atom_site.Cartn_z WHATIF: PDBx_Cartn_z Cartesian z coordinate of an atom (in a molecular structure). - beta12orEarlier Cartesian z coordinate - - + + + Atomic z coordinate - - PDB atom name - - WHATIF: PDBx_type_symbol - beta12orEarlier + + + beta12orEarlier + PDBML:pdbx_PDB_atom_name WHATIF: PDBx_auth_atom_id + WHATIF: PDBx_type_symbol WHATIF: alternate_atom - PDBML:pdbx_PDB_atom_name WHATIF: atom_type Identifier (a string) of a specific atom from a PDB file for a molecular structure. - - - + + + + PDB atom name - - Protein atom - + + + beta12orEarlier + Data on a single atom from a protein structure. Atom data CHEBI:33250 + + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. - Data on a single atom from a protein structure. - beta12orEarlier - - + Protein atom - - Protein residue - - beta12orEarlier + + + beta12orEarlier Data on a single amino acid residue position in a protein structure. - This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. Residue - - + + + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. + Protein residue - - Atom name - - + + + + beta12orEarlier Name of an atom. - beta12orEarlier - - - + + + + Atom name - - PDB residue name - - Three-letter amino acid residue names as used in PDB files. + + + beta12orEarlier WHATIF: type - beta12orEarlier - - - + Three-letter amino acid residue names as used in PDB files. + + + + PDB residue name - - PDB model number - - Identifier of a model structure from a PDB file. - beta12orEarlier + + + beta12orEarlier PDBML:pdbx_PDB_model_num - Model number WHATIF: model_number - - - + Identifier of a model structure from a PDB file. + Model number + + + + PDB model number - + + + beta12orEarlier + beta13 + + Summary of domain classification information for a CATH domain. + + The report (for example http://www.cathdb.info/domain/1cukA01) includes CATH codes for levels in the hierarchy for the domain, level descriptions and relevant data and links. CATH domain report - - beta12orEarlier true - beta13 - The report (for example http://www.cathdb.info/domain/1cukA01) includes CATH codes for levels in the hierarchy for the domain, level descriptions and relevant data and links. - Summary of domain classification information for a CATH domain. - - - - CATH representative domain sequences (ATOM) - - beta12orEarlier - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + FASTA sequence database (based on ATOM records in PDB) for CATH domains (clustered at different levels of sequence identity). + + CATH representative domain sequences (ATOM) true - - - + + + beta12orEarlier + beta12orEarlier + + FASTA sequence database (based on COMBS sequence data) for CATH domains (clustered at different levels of sequence identity). + CATH representative domain sequences (COMBS) - true - FASTA sequence database (based on COMBS sequence data) for CATH domains (clustered at different levels of sequence identity). - beta12orEarlier - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + FASTA sequence database for all CATH domains (based on PDB ATOM records). + CATH domain sequences (ATOM) - true - FASTA sequence database for all CATH domains (based on PDB ATOM records). - beta12orEarlier - beta12orEarlier - - - - CATH domain sequences (COMBS) - + + + beta12orEarlier + beta12orEarlier + FASTA sequence database for all CATH domains (based on COMBS sequence data). - beta12orEarlier + + CATH domain sequences (COMBS) true - beta12orEarlier - - - - Sequence version - - beta12orEarlier + + + beta12orEarlier Information on an molecular sequence version. Sequence version information - - + + + Sequence version - - Score - + + + beta12orEarlier A numerical value, that is some type of scored value arising for example from a prediction method. - beta12orEarlier - - + + + Score - + + + beta12orEarlier + beta13 + + Report on general functional properties of specific protein(s). + + For properties that can be mapped to a sequence, use 'Sequence report' instead. Protein report (function) - true - For properties that can be mapped to a sequence, use 'Sequence report' instead. - beta13 - Report on general functional properties of specific protein(s). - beta12orEarlier - - - + + + beta12orEarlier + 1.3 + + http://www.geneontology.org/doc/GO.xrf_abbs:ASPGD_LOCUS + Name of a gene from Aspergillus Genome Database. + Gene name (ASPGD) - - 1.3 - beta12orEarlier true - Name of a gene from Aspergillus Genome Database. - http://www.geneontology.org/doc/GO.xrf_abbs:ASPGD_LOCUS - - - - Gene name (CGD) - + + + beta12orEarlier + 1.3 + + http://www.geneontology.org/doc/GO.xrf_abbs:CGD_LOCUS Name of a gene from Candida Genome Database. + + Gene name (CGD) true - http://www.geneontology.org/doc/GO.xrf_abbs:CGD_LOCUS - beta12orEarlier - 1.3 - - - - Gene name (dictyBase) - + + + beta12orEarlier + 1.3 + http://www.geneontology.org/doc/GO.xrf_abbs:dictyBase - beta12orEarlier - 1.3 - true Name of a gene from dictyBase database. - - + + Gene name (dictyBase) + true - - Gene name (EcoGene primary) - + + + beta12orEarlier + 1.3 + http://www.geneontology.org/doc/GO.xrf_abbs:ECOGENE_G Primary name of a gene from EcoGene Database. EcoGene primary gene name - 1.3 + + Gene name (EcoGene primary) true - beta12orEarlier - - - - Gene name (MaizeGDB) - + + + beta12orEarlier + 1.3 + http://www.geneontology.org/doc/GO.xrf_abbs:MaizeGDB_Locus - 1.3 Name of a gene from MaizeGDB (maize genes) database. + + Gene name (MaizeGDB) true - beta12orEarlier - - - - Gene name (SGD) - - true - 1.3 - beta12orEarlier + + + beta12orEarlier + 1.3 + http://www.geneontology.org/doc/GO.xrf_abbs:SGD_LOCUS Name of a gene from Saccharomyces Genome Database. - - + + Gene name (SGD) + true - - Gene name (TGD) - - beta12orEarlier - 1.3 + + + beta12orEarlier + 1.3 + + http://www.geneontology.org/doc/GO.xrf_abbs:TGD_LOCUS Name of a gene from Tetrahymena Genome Database. + + Gene name (TGD) true - http://www.geneontology.org/doc/GO.xrf_abbs:TGD_LOCUS - - - - Gene name (CGSC) - - beta12orEarlier - 1.3 - true + + + beta12orEarlier + 1.3 + http://www.geneontology.org/doc/GO.xrf_abbs: CGSC Symbol of a gene from E.coli Genetic Stock Center. - - + + Gene name (CGSC) + true - - Gene name (HGNC) - - beta12orEarlier - HUGO symbol - 1.3 - true - HGNC symbol - Official gene name - HUGO gene name + + + beta12orEarlier + 1.3 + HGNC:[0-9]{1,5} + http://www.geneontology.org/doc/GO.xrf_abbs: HGNC_gene - HGNC gene name - HUGO gene symbol - HGNC:[0-9]{1,5} - Gene name (HUGO) - HGNC gene symbol Symbol of a gene approved by the HUGO Gene Nomenclature Committee. - - + + Gene name (HGNC) + true - - Gene name (MGD) - - MGI:[0-9]+ - Symbol of a gene from the Mouse Genome Database. + + + beta12orEarlier + 1.3 + MGI:[0-9]+ + http://www.geneontology.org/doc/GO.xrf_abbs: MGD - 1.3 + Symbol of a gene from the Mouse Genome Database. + + Gene name (MGD) true - beta12orEarlier - - - - Gene name (Bacillus subtilis) - + + + beta12orEarlier + 1.3 + http://www.geneontology.org/doc/GO.xrf_abbs: SUBTILISTG Symbol of a gene from Bacillus subtilis Genome Sequence Project. - beta12orEarlier - 1.3 + + Gene name (Bacillus subtilis) true - - - - Gene ID (PlasmoDB) - - Identifier of a gene from PlasmoDB Plasmodium Genome Resource. - beta12orEarlier + + + beta12orEarlier http://www.geneontology.org/doc/GO.xrf_abbs: ApiDB_PlasmoDB - - - + Identifier of a gene from PlasmoDB Plasmodium Genome Resource. + + + + Gene ID (PlasmoDB) - - Gene ID (EcoGene) - + + + beta12orEarlier Identifier of a gene from EcoGene Database. EcoGene Accession EcoGene ID - beta12orEarlier - - - + + + + Gene ID (EcoGene) - - Gene ID (FlyBase) - - beta12orEarlier - Gene identifier from FlyBase database. + + + beta12orEarlier http://www.geneontology.org/doc/GO.xrf_abbs: FB http://www.geneontology.org/doc/GO.xrf_abbs: FlyBase - - - + Gene identifier from FlyBase database. + + + + Gene ID (FlyBase) - + + + beta12orEarlier + beta13 + + Gene identifier from Glossina morsitans GeneDB database. + Gene ID (GeneDB Glossina morsitans) - true - http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Gmorsitans - beta13 - Gene identifier from Glossina morsitans GeneDB database. - beta12orEarlier - - - - Gene ID (GeneDB Leishmania major) - + + + beta12orEarlier + beta13 + Gene identifier from Leishmania major GeneDB database. + + Gene ID (GeneDB Leishmania major) true - http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Lmajor - beta12orEarlier - beta13 - - - - Gene ID (GeneDB Plasmodium falciparum) - + + + beta12orEarlier + beta13 + + http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Pfalciparum Gene identifier from Plasmodium falciparum GeneDB database. + + Gene ID (GeneDB Plasmodium falciparum) true - http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Pfalciparum - beta13 - beta12orEarlier - - - - Gene ID (GeneDB Schizosaccharomyces pombe) - + + + beta12orEarlier + beta13 + http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Spombe - beta12orEarlier - true - beta13 Gene identifier from Schizosaccharomyces pombe GeneDB database. - - + + Gene ID (GeneDB Schizosaccharomyces pombe) + true - - Gene ID (GeneDB Trypanosoma brucei) - + + + beta12orEarlier + beta13 + + http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Tbrucei Gene identifier from Trypanosoma brucei GeneDB database. + + Gene ID (GeneDB Trypanosoma brucei) true - beta13 - beta12orEarlier - http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Tbrucei - - - - Gene ID (Gramene) - - http://www.geneontology.org/doc/GO.xrf_abbs: GR_gene - beta12orEarlier + + + beta12orEarlier http://www.geneontology.org/doc/GO.xrf_abbs: GR_GENE + http://www.geneontology.org/doc/GO.xrf_abbs: GR_gene Gene identifier from Gramene database. - - - + + + + Gene ID (Gramene) - - Gene ID (Virginia microbial) - - beta12orEarlier + + + beta12orEarlier http://www.geneontology.org/doc/GO.xrf_abbs: PAMGO_VMD - Gene identifier from Virginia Bioinformatics Institute microbial database. http://www.geneontology.org/doc/GO.xrf_abbs: VMD - - - + Gene identifier from Virginia Bioinformatics Institute microbial database. + + + + Gene ID (Virginia microbial) - - Gene ID (SGN) - + + + beta12orEarlier http://www.geneontology.org/doc/GO.xrf_abbs: SGN Gene identifier from Sol Genomics Network. - beta12orEarlier - - - + + + + Gene ID (SGN) - - Gene ID (WormBase) - - - Gene identifier used by WormBase database. - WBGene[0-9]{8} + + + + beta12orEarlier + WBGene[0-9]{8} http://www.geneontology.org/doc/GO.xrf_abbs: WB http://www.geneontology.org/doc/GO.xrf_abbs: WormBase - beta12orEarlier - - - + Gene identifier used by WormBase database. + + + + Gene ID (WormBase) - + + + beta12orEarlier + beta12orEarlier + + Any name (other than the recommended one) for a gene. + Gene synonym - - Gene name synonym true - Any name (other than the recommended one) for a gene. - beta12orEarlier - beta12orEarlier - - - - ORF name - - - beta12orEarlier + + + + beta12orEarlier The name of an open reading frame attributed by a sequencing project. - - - + + + + ORF name - - Sequence assembly component - + + + beta12orEarlier + beta12orEarlier + A component of a larger sequence assembly. + + Sequence assembly component true - beta12orEarlier - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + A report on a chromosome aberration such as abnormalities in chromosome structure. + Chromosome annotation (aberration) - - beta12orEarlier - beta12orEarlier true - A report on a chromosome aberration such as abnormalities in chromosome structure. - - - - Clone ID - - beta12orEarlier + + + beta12orEarlier An identifier of a clone (cloned molecular sequence) from a database. - - - + + + + Clone ID - - PDB insertion code - - beta12orEarlier - WHATIF: insertion_code + + + beta12orEarlier PDBML:pdbx_PDB_ins_code + WHATIF: insertion_code An insertion code (part of the residue number) for an amino acid residue from a PDB file. - - + + + PDB insertion code - - Atomic occupancy - + + + beta12orEarlier WHATIF: PDBx_occupancy The fraction of an atom type present at a site in a molecular structure. - beta12orEarlier + + The sum of the occupancies of all the atom types at a site should not normally significantly exceed 1.0. - - + Atomic occupancy - - Isotropic B factor - - Isotropic B factor (atomic displacement parameter) for an atom from a PDB file. + + + beta12orEarlier WHATIF: PDBx_B_iso_or_equiv - beta12orEarlier - - + Isotropic B factor (atomic displacement parameter) for an atom from a PDB file. + + + Isotropic B factor - - Deletion map - - A cytogenetic map is built from a set of mutant cell lines with sub-chromosomal deletions and a reference wild-type line ('genome deletion panel'). The panel is used to map markers onto the genome by comparing mutant to wild-type banding patterns. Markers are linked (occur in the same deleted region) if they share the same banding pattern (presence or absence) as the deletion panel. - beta12orEarlier + + + beta12orEarlier A cytogenetic map showing chromosome banding patterns in mutant cell lines relative to the wild type. Deletion-based cytogenetic map - - + + + A cytogenetic map is built from a set of mutant cell lines with sub-chromosomal deletions and a reference wild-type line ('genome deletion panel'). The panel is used to map markers onto the genome by comparing mutant to wild-type banding patterns. Markers are linked (occur in the same deleted region) if they share the same banding pattern (presence or absence) as the deletion panel. + Deletion map - - QTL map - + + + beta12orEarlier A genetic map which shows the approximate location of quantitative trait loci (QTL) between two or more markers. - beta12orEarlier Quantitative trait locus map - - + + + QTL map - - Haplotype map - - beta12orEarlier + + + beta12orEarlier Moby:Haplotyping_Study_obj A map of haplotypes in a genome or other sequence, describing common patterns of genetic variation. - - + + + Haplotype map - - Map set data - - beta12orEarlier - Data describing a set of multiple genetic or physical maps, typically sharing a common set of features which are mapped. + + + beta12orEarlier Moby:GCP_CorrelatedLinkageMapSet Moby:GCP_CorrelatedMapSet - - + Data describing a set of multiple genetic or physical maps, typically sharing a common set of features which are mapped. + + + Map set data - - Map feature - - beta12orEarlier - true + + + beta12orEarlier + beta12orEarlier + + + A feature which may mapped (positioned) on a genetic or other type of map. - Moby:MapFeature - beta12orEarlier + Mappable features may be based on Gramene's notion of map features; see http://www.gramene.org/db/cmap/feature_type_info. - - - - + Map feature + true - - Map type - + + + beta12orEarlier + 1.5 + A designation of the type of map (genetic map, physical map, sequence map etc) or map set. + Map types may be based on Gramene's notion of a map type; see http://www.gramene.org/db/cmap/map_type_info. - 1.5 + Map type true - beta12orEarlier - - - - Protein fold name - + + + beta12orEarlier The name of a protein fold. - beta12orEarlier - - - + + + + Protein fold name - - Taxon - + + + beta12orEarlier + Moby:BriefTaxonConcept Moby:PotentialTaxon - Taxonomy rank - beta12orEarlier + The name of a group of organisms belonging to the same taxonomic rank. Taxonomic rank + Taxonomy rank + + + For a complete list of taxonomic ranks see https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary. - The name of a group of organisms belonging to the same taxonomic rank. - Moby:BriefTaxonConcept - - - + Taxon - - Organism identifier - + + - - + + - beta12orEarlier + beta12orEarlier A unique identifier of a (group of) organisms. - - - + + + + Organism identifier - - Genus name - - beta12orEarlier + + + beta12orEarlier The name of a genus of organism. - - - + + + + Genus name - - Taxonomic classification - - Moby:TaxonName + + + beta12orEarlier Moby:GCP_Taxon - beta12orEarlier - The full name for a group of organisms, reflecting their biological classification and (usually) conforming to a standard nomenclature. + Moby:TaxonName + Moby:TaxonScientificName + Moby:TaxonTCS Moby:iANT_organism-xml + The full name for a group of organisms, reflecting their biological classification and (usually) conforming to a standard nomenclature. + Taxonomic information Taxonomic name + + + Name components correspond to levels in a taxonomic hierarchy (e.g. 'Genus', 'Species', etc.) Meta information such as a reference where the name was defined and a date might be included. - Taxonomic information - Moby:TaxonScientificName - Moby:TaxonTCS - - - + Taxonomic classification - - iHOP organism ID - - beta12orEarlier + + + beta12orEarlier Moby_namespace:iHOPorganism A unique identifier for an organism used in the iHOP database. - - - + + + + iHOP organism ID - - Genbank common name - + + + beta12orEarlier Common name for an organism as used in the GenBank database. - beta12orEarlier - - - + + + + Genbank common name - - NCBI taxon - + + + beta12orEarlier The name of a taxon from the NCBI taxonomy database. - beta12orEarlier - - - + + + + NCBI taxon - + + + beta12orEarlier + beta12orEarlier + + An alternative for a word. + Synonym - - beta12orEarlier - Alternative name - beta12orEarlier true - An alternative for a word. - - - - Misspelling - + + + beta12orEarlier + beta12orEarlier + A common misspelling of a word. - beta12orEarlier + + Misspelling true - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + An abbreviation of a phrase or word. + Acronym - true - An abbreviation of a phrase or word. - beta12orEarlier - beta12orEarlier - - - - Misnomer - + + + beta12orEarlier + beta12orEarlier + A term which is likely to be misleading of its meaning. - beta12orEarlier - beta12orEarlier + + Misnomer true - - - - Author ID - - Information on the authors of a published work. + + + beta12orEarlier Moby:Author - beta12orEarlier - - - + Information on the authors of a published work. + + + + Author ID - - DragonDB author identifier - + + + beta12orEarlier An identifier representing an author in the DragonDB database. - beta12orEarlier - - - + + + + DragonDB author identifier - - Annotated URI - - beta12orEarlier - A URI along with annotation describing the data found at the address. + + + beta12orEarlier Moby:DescribedLink - - + A URI along with annotation describing the data found at the address. + + + Annotated URI - + + + beta12orEarlier + beta12orEarlier + + A controlled vocabulary for words and phrases that can appear in the keywords field (KW line) of entries from the UniProt database. + UniProt keywords - true - beta12orEarlier - beta12orEarlier - A controlled vocabulary for words and phrases that can appear in the keywords field (KW line) of entries from the UniProt database. - - - - Gene ID (GeneFarm) - + + + beta12orEarlier Moby_namespace:GENEFARM_GeneID Identifier of a gene from the GeneFarm database. - beta12orEarlier - - - + + + + Gene ID (GeneFarm) - - Blattner number - - beta12orEarlier + + + beta12orEarlier Moby_namespace:Blattner_number The blattner identifier for a gene. - - - + + + + Blattner number - - Gene ID (MIPS Maize) - - MIPS genetic element identifier (Maize) - Identifier for genetic elements in MIPS Maize database. - beta12orEarlier + + + beta12orEarlier + beta13 + Moby_namespace:MIPS_GE_Maize - beta13 + Identifier for genetic elements in MIPS Maize database. + + Gene ID (MIPS Maize) true - - - - Gene ID (MIPS Medicago) - - MIPS genetic element identifier (Medicago) - beta12orEarlier - beta13 - true + + + beta12orEarlier + beta13 + Moby_namespace:MIPS_GE_Medicago Identifier for genetic elements in MIPS Medicago database. - - + + Gene ID (MIPS Medicago) + true - + + + beta12orEarlier + 1.3 + + Moby_namespace:DragonDB_Gene + The name of an Antirrhinum Gene from the DragonDB database. + Gene name (DragonDB) - true - The name of an Antirrhinum Gene from the DragonDB database. - beta12orEarlier - Moby_namespace:DragonDB_Gene - 1.3 - - - + + + beta12orEarlier + 1.3 + + A unique identifier for an Arabidopsis gene, which is an acronym or abbreviation of the gene name. + Gene name (Arabidopsis) - - Moby_namespace:ArabidopsisGeneSymbol true - A unique identifier for an Arabidopsis gene, which is an acronym or abbreviation of the gene name. - beta12orEarlier - 1.3 - - - - iHOP symbol - - - - A unique identifier of a protein or gene used in the iHOP database. + + + + + beta12orEarlier Moby_namespace:iHOPsymbol - beta12orEarlier - - - + A unique identifier of a protein or gene used in the iHOP database. + + + + iHOP symbol - - Gene name (GeneFarm) - - 1.3 - true + + + beta12orEarlier + 1.3 + Name of a gene from the GeneFarm database. - Moby_namespace:GENEFARM_GeneName GeneFarm gene ID - beta12orEarlier - - + + Gene name (GeneFarm) + true - - Locus ID - - + + + - - + + + beta12orEarlier A unique name or other identifier of a genetic locus, typically conforming to a scheme that names loci (such as predicted genes) depending on their position in a molecular sequence, for example a completely sequenced genome or chromosome. - Locus name - beta12orEarlier Locus identifier - - - + Locus name + + + + Locus ID - - Locus ID (AGI) - - AT[1-5]G[0-9]{5} - AGI ID - Locus identifier for Arabidopsis Genome Initiative (TAIR, TIGR and MIPS databases) + + + beta12orEarlier + AT[1-5]G[0-9]{5} http://www.geneontology.org/doc/GO.xrf_abbs:AGI_LocusCode - Arabidopsis gene loci number - AGI locus code - beta12orEarlier + Locus identifier for Arabidopsis Genome Initiative (TAIR, TIGR and MIPS databases) + AGI ID AGI identifier - - - + AGI locus code + Arabidopsis gene loci number + + + + Locus ID (AGI) - - Locus ID (ASPGD) - - beta12orEarlier + + + beta12orEarlier http://www.geneontology.org/doc/GO.xrf_abbs: ASPGD http://www.geneontology.org/doc/GO.xrf_abbs: ASPGDID Identifier for loci from ASPGD (Aspergillus Genome Database). - - - + + + + Locus ID (ASPGD) - - Locus ID (MGG) - - Identifier for loci from Magnaporthe grisea Database at the Broad Institute. + + + beta12orEarlier http://www.geneontology.org/doc/GO.xrf_abbs: Broad_MGG - beta12orEarlier - - - + Identifier for loci from Magnaporthe grisea Database at the Broad Institute. + + + + Locus ID (MGG) - - Locus ID (CGD) - - Identifier for loci from CGD (Candida Genome Database). + + + beta12orEarlier + http://www.geneontology.org/doc/GO.xrf_abbs: CGD http://www.geneontology.org/doc/GO.xrf_abbs: CGDID - beta12orEarlier - CGDID + Identifier for loci from CGD (Candida Genome Database). CGD locus identifier - http://www.geneontology.org/doc/GO.xrf_abbs: CGD - - - + CGDID + + + + Locus ID (CGD) - - Locus ID (CMR) - + + + beta12orEarlier + http://www.geneontology.org/doc/GO.xrf_abbs: JCVI_CMR http://www.geneontology.org/doc/GO.xrf_abbs: TIGR_CMR Locus identifier for Comprehensive Microbial Resource at the J. Craig Venter Institute. - http://www.geneontology.org/doc/GO.xrf_abbs: JCVI_CMR - beta12orEarlier - - - + + + + Locus ID (CMR) - - NCBI locus tag - - beta12orEarlier + + + beta12orEarlier Moby_namespace:LocusID - Locus ID (NCBI) http://www.geneontology.org/doc/GO.xrf_abbs: NCBI_locus_tag Identifier for loci from NCBI database. - - - + Locus ID (NCBI) + + + + NCBI locus tag - - Locus ID (SGD) - - - Identifier for loci from SGD (Saccharomyces Genome Database). - http://www.geneontology.org/doc/GO.xrf_abbs: SGDID - beta12orEarlier + + + + beta12orEarlier http://www.geneontology.org/doc/GO.xrf_abbs: SGD + http://www.geneontology.org/doc/GO.xrf_abbs: SGDID + Identifier for loci from SGD (Saccharomyces Genome Database). SGDID - - - + + + + Locus ID (SGD) - - Locus ID (MMP) - - Identifier of loci from Maize Mapping Project. + + + beta12orEarlier Moby_namespace:MMP_Locus - beta12orEarlier - - - + Identifier of loci from Maize Mapping Project. + + + + Locus ID (MMP) - - Locus ID (DictyBase) - + + + beta12orEarlier Moby_namespace:DDB_gene Identifier of locus from DictyBase (Dictyostelium discoideum). - beta12orEarlier - - - + + + + Locus ID (DictyBase) - - Locus ID (EntrezGene) - - Identifier of a locus from EntrezGene database. - beta12orEarlier - Moby_namespace:EntrezGene_ID + + + beta12orEarlier Moby_namespace:EntrezGene_EntrezGeneID - - - + Moby_namespace:EntrezGene_ID + Identifier of a locus from EntrezGene database. + + + + Locus ID (EntrezGene) - - Locus ID (MaizeGDB) - - Identifier of locus from MaizeGDB (Maize genome database). + + + beta12orEarlier Moby_namespace:MaizeGDB_Locus - beta12orEarlier - - - + Identifier of locus from MaizeGDB (Maize genome database). + + + + Locus ID (MaizeGDB) - - Quantitative trait locus - - QTL + + + beta12orEarlier + beta12orEarlier + + Moby:SO_QTL + A stretch of DNA that is closely linked to the genes underlying a quantitative trait (a phenotype that varies in degree and depends upon the interactions between multiple genes and their environment). + A QTL sometimes but does not necessarily correspond to a gene. + Quantitative trait locus true - beta12orEarlier - beta12orEarlier - A stretch of DNA that is closely linked to the genes underlying a quantitative trait (a phenotype that varies in degree and depends upon the interactions between multiple genes and their environment). - Moby:SO_QTL - - - - Gene ID (KOME) - - Identifier of a gene from the KOME database. - beta12orEarlier + + + beta12orEarlier Moby_namespace:GeneId - - - + Identifier of a gene from the KOME database. + + + + Gene ID (KOME) - - Locus ID (Tropgene) - - Identifier of a locus from the Tropgene database. + + + beta12orEarlier Moby:Tropgene_locus - beta12orEarlier - - - + Identifier of a locus from the Tropgene database. + + + + Locus ID (Tropgene) - - Alignment - + + + beta12orEarlier An alignment of molecular sequences, structures or profiles derived from them. - beta12orEarlier - - + + + Alignment - - Atomic property - - General atomic property + + + beta12orEarlier Data for an atom (in a molecular structure). - beta12orEarlier - - + General atomic property + + + Atomic property - - UniProt keyword - - beta12orEarlier - A word or phrase that can appear in the keywords field (KW line) of entries from the UniProt database. + + + beta12orEarlier Moby_namespace:SP_KW http://www.geneontology.org/doc/GO.xrf_abbs: SP_KW - - + A word or phrase that can appear in the keywords field (KW line) of entries from the UniProt database. + + + UniProt keyword - + + + beta12orEarlier + beta12orEarlier + + A name for a genetic locus conforming to a scheme that names loci (such as predicted genes) depending on their position in a molecular sequence, for example a completely sequenced genome or chromosome. + Ordered locus name - - beta12orEarlier true - A name for a genetic locus conforming to a scheme that names loci (such as predicted genes) depending on their position in a molecular sequence, for example a completely sequenced genome or chromosome. - beta12orEarlier - - - - Sequence coordinates - - - - Map position - Moby:Position - Locus - Sequence co-ordinates - A position in a map (for example a genetic map), either a single position (point) or a region / interval. + + + + + beta12orEarlier + Moby:GCP_MapInterval + Moby:GCP_MapPoint + Moby:GCP_MapPosition Moby:GenePosition - This includes positions in genomes based on a reference sequence. A position may be specified for any mappable object, i.e. anything that may have positional information such as a physical position in a chromosome. Data might include sequence region name, strand, coordinate system name, assembly name, start position and end position. Moby:HitPosition - beta12orEarlier - Moby:MapPosition Moby:Locus - Moby:GCP_MapInterval - Moby:GCP_MapPosition - Moby:GCP_MapPoint + Moby:MapPosition + Moby:Position PDBML:_atom_site.id - - + A position in a map (for example a genetic map), either a single position (point) or a region / interval. + Locus + Map position + Sequence co-ordinates + + + This includes positions in genomes based on a reference sequence. A position may be specified for any mappable object, i.e. anything that may have positional information such as a physical position in a chromosome. Data might include sequence region name, strand, coordinate system name, assembly name, start position and end position. + Sequence coordinates - - Amino acid property - + + + beta12orEarlier Data concerning the intrinsic physical (e.g. structural) or chemical properties of one, more or all amino acids. Amino acid data - beta12orEarlier - - + + + Amino acid property - + + + beta12orEarlier + beta13 + + A human-readable collection of information which (typically) is generated or collated by hand and which describes a biological entity, phenomena or associated primary (e.g. sequence or structural) data, as distinct from the primary data itself and computer-generated reports derived from it. + + This is a broad data type and is used a placeholder for other, more specific types. Annotation - - beta12orEarlier true - beta13 - This is a broad data type and is used a placeholder for other, more specific types. - A human-readable collection of information which (typically) is generated or collated by hand and which describes a biological entity, phenomena or associated primary (e.g. sequence or structural) data, as distinct from the primary data itself and computer-generated reports derived from it. - - - - Map data - + + - - + + + beta12orEarlier + A molecular map (genetic or physical), an attribute of such a map, or data extracted from or derived from the analysis of such a map. Map attribute - beta12orEarlier - An attribute of a molecular map (genetic or physical), or data extracted from or derived from the analysis of such a map. - - + + + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. It includes concepts that are best described as scientific text or closely concerned with or derived from text. + Map data - + + + beta12orEarlier + beta12orEarlier + Data used by the Vienna RNA analysis package. + Vienna RNA structural data - true - Data used by the Vienna RNA analysis package. - beta12orEarlier - beta12orEarlier - - - + + + beta12orEarlier + 1.5 + Data used to replace (mask) characters in a molecular sequence. + Sequence mask parameter - - beta12orEarlier - 1.5 true - Data used to replace (mask) characters in a molecular sequence. - - - - Enzyme kinetics data - - + + + + beta12orEarlier Data concerning chemical reaction(s) catalysed by enzyme(s). - beta12orEarlier + + This is a broad data type and is used a placeholder for other, more specific types. - - + Enzyme kinetics data - - Michaelis Menten plot - + + + beta12orEarlier A plot giving an approximation of the kinetics of an enzyme-catalysed reaction, assuming simple kinetics (i.e. no intermediate or product inhibition, allostericity or cooperativity). It plots initial reaction rate to the substrate concentration (S) from which the maximum rate (vmax) is apparent. - beta12orEarlier - - + + + Michaelis Menten plot - - Hanes Woolf plot - - beta12orEarlier + + + beta12orEarlier A plot based on the Michaelis Menten equation of enzyme kinetics plotting the ratio of the initial substrate concentration (S) against the reaction velocity (v). - - + + + Hanes Woolf plot - - Experimental data - + + + beta12orEarlier + beta13 + + + Raw data from or annotation on laboratory experiments. + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. + Experimental data true - Raw data from or annotation on laboratory experiments. - beta12orEarlier - Experimental measurement data - beta13 - - - - + + + beta12orEarlier + 1.5 + + Information on a genome version. + Genome version information - - beta12orEarlier true - Information on a genome version. - 1.5 - - - - Evidence - + + + beta12orEarlier Typically a statement about some data or results, including evidence or the source of a statement, which may include computational prediction, laboratory experiment, literature reference etc. - beta12orEarlier - - + + + Evidence - - Sequence record lite - - beta12orEarlier + + + beta12orEarlier + 1.8 A molecular sequence and minimal metadata, typically an identifier of the sequence and/or a comment. + + + Sequence record lite true - 1.8 - - - - Sequence - + + - - + + - http://purl.bioontology.org/ontology/MSH/D008969 + beta12orEarlier + One or more molecular sequences, possibly with associated annotation. Sequences - http://purl.org/biotop/biotop.owl#BioMolecularSequenceInformation + + This concept is a placeholder of concepts for primary sequence data including raw sequences and sequence records. It should not normally be used for derivatives such as sequence alignments, motifs or profiles. - beta12orEarlier - One or more molecular sequences, possibly with associated annotation. - - + Sequence + http://purl.bioontology.org/ontology/MSH/D008969 + http://purl.org/biotop/biotop.owl#BioMolecularSequenceInformation - + + + beta12orEarlier + 1.8 + A nucleic acid sequence and minimal metadata, typically an identifier of the sequence and/or a comment. + + Nucleic acid sequence record (lite) - - beta12orEarlier - 1.8 true - A nucleic acid sequence and minimal metadata, typically an identifier of the sequence and/or a comment. - - - - Protein sequence record (lite) - - 1.8 - Sequence record lite (protein) - beta12orEarlier + + + beta12orEarlier + 1.8 A protein sequence and minimal metadata, typically an identifier of the sequence and/or a comment. + Sequence record lite (protein) + + + Protein sequence record (lite) true - - - - Report - + + + beta12orEarlier + A human-readable collection of information including annotation on a biological entity or phenomena, computer-generated reports of analysis of primary data (e.g. sequence or structural), and metadata (data about primary data) or any other free (essentially unformatted) text, as distinct from the primary data itself. + Document + + You can use this term by default for any textual report, in case you can't find another, more specific term. Reports may be generated automatically or collated by hand and can include metadata on the origin, source, history, ownership or location of some thing. + Report http://semanticscience.org/resource/SIO_000148 - Document - A human-readable collection of information including annotation on a biological entity or phenomena, computer-generated reports of analysis of primary data (e.g. sequence or structural), and metadata (data about primary data) or any other free (essentially unformatted) text, as distinct from the primary data itself. - beta12orEarlier - - - - Molecular property (general) - - General molecular property + + + beta12orEarlier General data for a molecule. - beta12orEarlier - - + General molecular property + + + Molecular property (general) - - Structural data - + + + beta12orEarlier + beta13 + + + Data concerning molecular structural data. + This is a broad data type and is used a placeholder for other, more specific types. - beta12orEarlier + Structural data true - Data concerning molecular structural data. - beta13 - - - - - Sequence motif (nucleic acid) - + + + beta12orEarlier + A nucleotide sequence motif. Nucleic acid sequence motif DNA sequence motif - A nucleotide sequence motif. - beta12orEarlier RNA sequence motif - - + + + Sequence motif (nucleic acid) - - Sequence motif (protein) - - beta12orEarlier + + + beta12orEarlier An amino acid sequence motif. Protein sequence motif - - + + + Sequence motif (protein) - + + + beta12orEarlier + 1.5 + Some simple value controlling a search operation, typically a search of a database. + Search parameter - - beta12orEarlier - 1.5 true - Some simple value controlling a search operation, typically a search of a database. - - - - Database search results - - beta12orEarlier + + + beta12orEarlier A report of hits from searching a database of some type. - Search results Database hits - - + Search results + + + Database search results - + + + beta12orEarlier + 1.5 + + The secondary structure assignment (predicted or real) of a nucleic acid or protein. + Secondary structure - - 1.5 true - beta12orEarlier - The secondary structure assignment (predicted or real) of a nucleic acid or protein. - - - - Matrix - - beta12orEarlier + + + beta12orEarlier + An array of numerical values. Array + + This is a broad data type and is used a placeholder for other, more specific types. - An array of numerical values. - - + Matrix - - Alignment data - - beta12orEarlier - 1.8 - true + + + beta12orEarlier + 1.8 + Data concerning, extracted from, or derived from the analysis of molecular alignment of some type. + This is a broad data type and is used a placeholder for other, more specific types. - Alignment report - - + Alignment data + true - - Nucleic acid report - + + + beta12orEarlier An informative human-readable report about one or more specific nucleic acid molecules, derived from analysis of primary (sequence or structural) data. - beta12orEarlier - - + + + Nucleic acid report - - Structure report - + + + beta12orEarlier An informative report on general information, properties or features of one or more molecular tertiary (3D) structures. - beta12orEarlier Structure-derived report - - + + + Structure report - - Nucleic acid structure data - + + + beta12orEarlier + A report on nucleic acid structure-derived data, describing structural properties of a DNA molecule, or any other annotation or information about specific nucleic acid 3D structure(s). Nucleic acid property (structural) - This includes reports on the stiffness, curvature, twist/roll data or other conformational parameters or properties. Nucleic acid structural property - beta12orEarlier - A report on nucleic acid structure-derived data, describing structural properties of a DNA molecule, or any other annotation or information about specific nucleic acid 3D structure(s). - - + + + This includes reports on the stiffness, curvature, twist/roll data or other conformational parameters or properties. + Nucleic acid structure data - - Molecular property - - beta12orEarlier - SO:0000400 + + + beta12orEarlier A report on the physical (e.g. structural) or chemical properties of molecules, or parts of a molecule. Physicochemical property - - + SO:0000400 + + + Molecular property - - DNA base structural data - + + + beta12orEarlier Structural data for DNA base pairs or runs of bases, such as energy or angle data. - beta12orEarlier - - + + + DNA base structural data - + + + beta12orEarlier + 1.5 + + Information on a database (or ontology) entry version, such as name (or other identifier) or parent database, unique identifier of entry, data, author and so on. + Database entry version information - true - beta12orEarlier - 1.5 - Information on a database (or ontology) entry version, such as name (or other identifier) or parent database, unique identifier of entry, data, author and so on. - - - - Accession - - beta12orEarlier - http://semanticscience.org/resource/SIO_000731 + + + beta12orEarlier A persistent (stable) and unique identifier, typically identifying an object (entry) from a database. + + + + Accession http://semanticscience.org/resource/SIO_000675 - - - + http://semanticscience.org/resource/SIO_000731 - + + + beta12orEarlier + 1.8 + single nucleotide polymorphism (SNP) in a DNA sequence. + + SNP - true - Topic concerning single nucleotide polymorphism (SNP) in a DNA sequence. - beta12orEarlier - 1.8 - - - - Data reference - - A list of database accessions or identifiers are usually included. + + + beta12orEarlier Reference to a dataset (or a cross-reference between two datasets), typically one or more entries in a biological database or ontology. - beta12orEarlier - - + + + A list of database accessions or identifiers are usually included. + Data reference - + + + beta12orEarlier + An identifier of a submitted job. + + + Job identifier - http://wsio.org/data_009 - An identifier of a submitted job. - beta12orEarlier - - - - + + + beta12orEarlier + + A name of a thing, which need not necessarily uniquely identify it. + Symbolic name + + + Name - + "http://www.w3.org/2000/01/rdf-schema#label http://semanticscience.org/resource/SIO_000116 http://usefulinc.com/ns/doap#name - "http://www.w3.org/2000/01/rdf-schema#label - beta12orEarlier - A name of a thing, which need not necessarily uniquely identify it. - Symbolic name - - - - + + + Closely related, but focusing on labeling and human readability but not on identification. - - - - - Type - + + + beta12orEarlier + 1.5 + A label (text token) describing the type of a thing, typically an enumerated string (a string with one of a limited set of values). + + Type http://purl.org/dc/elements/1.1/type - 1.5 - beta12orEarlier true - - - - User ID - + + + beta12orEarlier An identifier of a software end-user (typically a person). - beta12orEarlier - - - + + + + User ID - - KEGG organism code - - + + + + beta12orEarlier A three-letter code used in the KEGG databases to uniquely identify organisms. - beta12orEarlier - - - + + + + KEGG organism code - - Gene name (KEGG GENES) - - beta12orEarlier - KEGG GENES entry name - [a-zA-Z_0-9]+:[a-zA-Z_0-9\.-]* - Name of an entry (gene) from the KEGG GENES database. + + + beta12orEarlier + 1.3 + [a-zA-Z_0-9]+:[a-zA-Z_0-9\.-]* + Moby_namespace:GeneId + Name of an entry (gene) from the KEGG GENES database. + + Gene name (KEGG GENES) true - 1.3 - - - - BioCyc ID - - + + + + beta12orEarlier Identifier of an object from one of the BioCyc databases. - beta12orEarlier - - - + + + + BioCyc ID - - Compound ID (BioCyc) - - - BioCyc compound identifier + + + + beta12orEarlier Identifier of a compound from the BioCyc chemical compounds database. BioCyc compound ID - beta12orEarlier - - - + BioCyc compound identifier + + + + Compound ID (BioCyc) - - Reaction ID (BioCyc) - - + + + - - + + - beta12orEarlier + beta12orEarlier Identifier of a biological reaction from the BioCyc reactions database. - - - + + + + Reaction ID (BioCyc) - - Enzyme ID (BioCyc) - - - BioCyc enzyme ID - beta12orEarlier + + + + beta12orEarlier Identifier of an enzyme from the BioCyc enzymes database. - - - + BioCyc enzyme ID + + + + Enzyme ID (BioCyc) - - Reaction ID - - + + + - - + + - beta12orEarlier + beta12orEarlier Identifier of a biological reaction from a database. - - - + + + + Reaction ID - - Identifier (hybrid) - + + + beta12orEarlier An identifier that is re-used for data objects of fundamentally different types (typically served from a single database). - beta12orEarlier + + + This branch provides an alternative organisation of the concepts nested under 'Accession' and 'Name'. All concepts under here are already included under 'Accession' or 'Name'. - - - + Identifier (hybrid) - - Molecular property identifier - + + - - + + - beta12orEarlier + beta12orEarlier Identifier of a molecular property. - - - + + + + Molecular property identifier - - Codon usage table ID - + + - - + + - - + + + beta12orEarlier Identifier of a codon usage table, for example a genetic code. Codon usage table identifier - beta12orEarlier - - - + + + + Codon usage table ID - - FlyBase primary identifier - - beta12orEarlier + + + beta12orEarlier Primary identifier of an object from the FlyBase database. - - - + + + + FlyBase primary identifier - - WormBase identifier - - beta12orEarlier + + + beta12orEarlier Identifier of an object from the WormBase database. - - - + + + + WormBase identifier - - WormBase wormpep ID - - + + + + beta12orEarlier + CE[0-9]{5} Protein identifier used by WormBase database. - CE[0-9]{5} - beta12orEarlier - - - + + + + WormBase wormpep ID - + + + beta12orEarlier + beta12orEarlier + + An informative report on a trinucleotide sequence that encodes an amino acid including the triplet sequence, the encoded amino acid or whether it is a start or stop codon. + Nucleic acid features (codon) - - beta12orEarlier true - An informative report on a trinucleotide sequence that encodes an amino acid including the triplet sequence, the encoded amino acid or whether it is a start or stop codon. - beta12orEarlier - - - - Map identifier - + + - - + + + beta12orEarlier An identifier of a map of a molecular sequence. - beta12orEarlier - - - + + + + Map identifier - - Person identifier - + + + beta12orEarlier An identifier of a software end-user (typically a person). - beta12orEarlier - - - + + + + Person identifier - - Nucleic acid identifier - + + - - + + + beta12orEarlier Name or other identifier of a nucleic acid molecule. - beta12orEarlier - - - + + + + Nucleic acid identifier - - Translation frame specification - - beta12orEarlier + + + beta12orEarlier Frame for translation of DNA (3 forward and 3 reverse frames relative to a chromosome). - - + + + Translation frame specification - - Genetic code identifier - + + - - + + + beta12orEarlier An identifier of a genetic code. - beta12orEarlier - - - + + + + Genetic code identifier - - Genetic code name - - + + + + beta12orEarlier Informal name for a genetic code, typically an organism name. - beta12orEarlier - - - + + + + Genetic code name - - File format name - - + + + + beta12orEarlier Name of a file format such as HTML, PNG, PDF, EMBL, GenBank and so on. - beta12orEarlier - - - + + + + File format name - + + + beta12orEarlier + 1.5 + + A label (text token) describing a type of sequence profile such as frequency matrix, Gribskov profile, hidden Markov model etc. + Sequence profile type - true - 1.5 - A label (text token) describing a type of sequence profile such as frequency matrix, Gribskov profile, hidden Markov model etc. - beta12orEarlier - - - - Operating system name - - beta12orEarlier + + + beta12orEarlier Name of a computer operating system such as Linux, PC or Mac. - - - + + + + Operating system name - + + + beta12orEarlier + beta12orEarlier + A type of point or block mutation, including insertion, deletion, change, duplication and moves. + Mutation type - - beta12orEarlier true - beta12orEarlier - A type of point or block mutation, including insertion, deletion, change, duplication and moves. - - - - Logical operator - - beta12orEarlier + + + beta12orEarlier A logical operator such as OR, AND, XOR, and NOT. - - - + + + + Logical operator - - Results sort order - + + + beta12orEarlier + 1.5 + A control of the order of data that is output, for example the order of sequences in an alignment. + Possible options including sorting by score, rank, by increasing P-value (probability, i.e. most statistically significant hits given first) and so on. - beta12orEarlier + Results sort order true - 1.5 - A control of the order of data that is output, for example the order of sequences in an alignment. - - - - Toggle - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier A simple parameter that is a toggle (boolean value), typically a control for a modal tool. + + Toggle true - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + The width of an output sequence or alignment. + Sequence width - true - beta12orEarlier - beta12orEarlier - The width of an output sequence or alignment. - - - - Gap penalty - - beta12orEarlier + + + beta12orEarlier A penalty for introducing or extending a gap in an alignment. - - + + + Gap penalty - - Nucleic acid melting temperature - - beta12orEarlier - A temperature concerning nucleic acid denaturation, typically the temperature at which the two strands of a hybridized or double stranded nucleic acid (DNA or RNA/DNA) molecule separate. + + + beta12orEarlier + A temperature concerning nucleic acid denaturation, typically the temperature at which the two strands of a hybridised or double stranded nucleic acid (DNA or RNA/DNA) molecule separate. Melting temperature - - + + + Nucleic acid melting temperature - - Concentration - - beta12orEarlier + + + beta12orEarlier The concentration of a chemical compound. - - + + + Concentration - + + + beta12orEarlier + 1.5 + + Size of the incremental 'step' a sequence window is moved over a sequence. + Window step size - - 1.5 - beta12orEarlier true - Size of the incremental 'step' a sequence window is moved over a sequence. - - - + + + beta12orEarlier + beta12orEarlier + + An image of a graph generated by the EMBOSS suite. + EMBOSS graph - - beta12orEarlier true - beta12orEarlier - An image of a graph generated by the EMBOSS suite. - - - - EMBOSS report - + + + beta12orEarlier + beta12orEarlier + An application report generated by the EMBOSS suite. - beta12orEarlier - beta12orEarlier + + EMBOSS report true - - - + + + beta12orEarlier + 1.5 + An offset for a single-point sequence position. + Sequence offset - true - beta12orEarlier - 1.5 - An offset for a single-point sequence position. - - - + + + beta12orEarlier + 1.5 + A value that serves as a threshold for a tool (usually to control scoring or output). + Threshold - - 1.5 - beta12orEarlier true - A value that serves as a threshold for a tool (usually to control scoring or output). - - - + + + beta12orEarlier + beta13 + + An informative report on a transcription factor protein. + + This might include conformational or physicochemical properties, as well as sequence information for transcription factor(s) binding sites. Protein report (transcription factor) - - beta13 true - This might include conformational or physicochemical properties, as well as sequence information for transcription factor(s) binding sites. - An informative report on a transcription factor protein. - Transcription factor binding site data - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + The name of a category of biological or bioinformatics database. + Database category name - true - The name of a category of biological or bioinformatics database. - beta12orEarlier - beta12orEarlier - - - - Sequence profile name - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + Name of a sequence profile. + + Sequence profile name true - beta12orEarlier - - - - Color - + + + beta12orEarlier + beta12orEarlier Specification of one or more colors. - beta12orEarlier + + Color true - beta12orEarlier - - - + + + beta12orEarlier + 1.5 + A parameter that is used to control rendering (drawing) to a device or image. + Rendering parameter - true - beta12orEarlier - 1.5 - A parameter that is used to control rendering (drawing) to a device or image. - Graphics parameter - Graphical parameter - - - - Sequence name - - + + + + beta12orEarlier Any arbitrary name of a molecular sequence. - beta12orEarlier - - - + + + + Sequence name - - Date - - 1.5 + + + beta12orEarlier + 1.5 A temporal date. - beta12orEarlier + + Date true - - - - Word composition - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + + Word composition data for a molecular sequence. + + Word composition true - beta12orEarlier - - - - - Fickett testcode plot - + + + beta12orEarlier A plot of Fickett testcode statistic (identifying protein coding regions) in a nucleotide sequences. - beta12orEarlier - - + + + Fickett testcode plot - - Sequence similarity plot - - - Use this concept for calculated substitution rates, relative site variability, data on sites with biased properties, highly conserved or very poorly conserved sites, regions, blocks etc. - beta12orEarlier - Sequence conservation report - Sequence similarity plot + + + + beta12orEarlier A plot of sequence similarities identified from word-matching or character comparison. - - + Sequence conservation report + + + Use this concept for calculated substitution rates, relative site variability, data on sites with biased properties, highly conserved or very poorly conserved sites, regions, blocks etc. + Sequence similarity plot - - Helical wheel - - beta12orEarlier + + + beta12orEarlier An image of peptide sequence sequence looking down the axis of the helix for highlighting amphipathicity and other properties. - - + + + Helical wheel - - Helical net - - beta12orEarlier - Useful for highlighting amphipathicity and other properties. + + + beta12orEarlier An image of peptide sequence sequence in a simple 3,4,3,4 repeating pattern that emulates at a simple level the arrangement of residues around an alpha helix. - - + + + Useful for highlighting amphipathicity and other properties. + Helical net - + + + beta12orEarlier + beta12orEarlier + + A plot of general physicochemical properties of a protein sequence. + Protein sequence properties plot - true - beta12orEarlier - beta12orEarlier - A plot of general physicochemical properties of a protein sequence. - - - - Protein ionization curve - - - beta12orEarlier + + + + beta12orEarlier A plot of pK versus pH for a protein. - - + + + Protein ionisation curve - - Sequence composition plot - - - beta12orEarlier + + + + beta12orEarlier A plot of character or word composition / frequency of a molecular sequence. - - + + + Sequence composition plot - - Nucleic acid density plot - - - beta12orEarlier + + + + beta12orEarlier Density plot (of base composition) for a nucleotide sequence. - - + + + Nucleic acid density plot - - Sequence trace image - + + + beta12orEarlier Image of a sequence trace (nucleotide sequence versus probabilities of each of the 4 bases). - beta12orEarlier - - + + + Sequence trace image - + + + beta12orEarlier + 1.5 + + A report on siRNA duplexes in mRNA. + Nucleic acid features (siRNA) - true - 1.5 - beta12orEarlier - A report on siRNA duplexes in mRNA. - - - + + + beta12orEarlier + beta12orEarlier + + A collection of multiple molecular sequences and (typically) associated metadata that is intended for sequential processing. + + This concept may be used for sequence sets that are expected to be read and processed a single sequence at a time. Sequence set (stream) - - beta12orEarlier true - This concept may be used for sequence sets that are expected to be read and processed a single sequence at a time. - A collection of multiple molecular sequences and (typically) associated metadata that is intended for sequential processing. - beta12orEarlier - - - - FlyBase secondary identifier - + + + beta12orEarlier Secondary identifier of an object from the FlyBase database. + + + Secondary identifier are used to handle entries that were merged with or split from other entries in the database. - beta12orEarlier - - - + FlyBase secondary identifier - - Cardinality - + + + beta12orEarlier + beta12orEarlier The number of a certain thing. - beta12orEarlier + + Cardinality true - beta12orEarlier - - - - Exactly 1 - - beta12orEarlier - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + A single thing. + + Exactly 1 true - - - 1 or more - + + + beta12orEarlier + beta12orEarlier + One or more things. - beta12orEarlier + + 1 or more true - beta12orEarlier - - - Exactly 2 - + + + beta12orEarlier + beta12orEarlier + Exactly two things. - beta12orEarlier + + Exactly 2 true - beta12orEarlier - - - 2 or more - + + + beta12orEarlier + beta12orEarlier + Two or more things. - beta12orEarlier - beta12orEarlier + + 2 or more true - - - Sequence checksum - + + + beta12orEarlier A fixed-size datum calculated (by using a hash function) for a molecular sequence, typically for purposes of error detection or indexing. - beta12orEarlier + Hash Hash code Hash sum - Hash Hash value - - + + + Sequence checksum - + + + beta12orEarlier + 1.8 + chemical modification of a protein. + + Protein features report (chemical modifications) - - 1.8 - beta12orEarlier - Topic concerning chemical modification of a protein. true - - - - Error - - beta12orEarlier + + + beta12orEarlier + 1.5 + Data on an error generated by computer system or tool. - 1.5 + + Error true - - - - Database entry metadata - - beta12orEarlier + + + beta12orEarlier Basic information on any arbitrary database entry. - - + + + Database entry metadata - + + + beta12orEarlier + beta13 + + A cluster of similar genes. + Gene cluster - - beta13 true - beta12orEarlier - A cluster of similar genes. - - - + + + beta12orEarlier + 1.8 + A molecular sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database. + + Sequence record full - true - beta12orEarlier - A molecular sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database. - 1.8 - - - - Plasmid identifier - + + + beta12orEarlier An identifier of a plasmid in a database. - beta12orEarlier - - - + + + + Plasmid identifier - - Mutation ID - - - beta12orEarlier + + + + beta12orEarlier A unique identifier of a specific mutation catalogued in a database. - - - + + + + Mutation ID - - Mutation annotation (basic) - + + + beta12orEarlier + beta12orEarlier + Information describing the mutation itself, the organ site, tissue and type of lesion where the mutation has been identified, description of the patient origin and life-style. - beta12orEarlier + + Mutation annotation (basic) true - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + An informative report on the prevalence of mutation(s), including data on samples and mutation prevalence (e.g. by tumour type).. + Mutation annotation (prevalence) - - beta12orEarlier true - An informative report on the prevalence of mutation(s), including data on samples and mutation prevalence (e.g. by tumour type).. - beta12orEarlier - - - - Mutation annotation (prognostic) - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + An informative report on mutation prognostic data, such as information on patient cohort, the study settings and the results of the study. - beta12orEarlier + + Mutation annotation (prognostic) true - - - - Mutation annotation (functional) - + + + beta12orEarlier + beta12orEarlier + An informative report on the functional properties of mutant proteins including transcriptional activities, promotion of cell growth and tumorigenicity, dominant negative effects, capacity to induce apoptosis, cell-cycle arrest or checkpoints in human cells and so on. + + Mutation annotation (functional) true - beta12orEarlier - beta12orEarlier - - - - Codon number - - beta12orEarlier + + + beta12orEarlier The number of a codon, for instance, at which a mutation is located. - - + + + Codon number - + + + beta12orEarlier + 1.4 + + An informative report on a specific tumor including nature and origin of the sample, anatomic site, organ or tissue, tumor type, including morphology and/or histologic type, and so on. + Tumor annotation - true - 1.4 - An informative report on a specific tumor including nature and origin of the sample, anatomic site, organ or tissue, tumor type, including morphology and/or histologic type, and so on. - beta12orEarlier - - - - Server metadata - + + + beta12orEarlier + 1.5 + Basic information about a server on the web, such as an SRS server. - beta12orEarlier - 1.5 + + Server metadata true - - - - Database field name - + + + beta12orEarlier The name of a field in a database. - beta12orEarlier - - - + + + + Database field name - - Sequence cluster ID (SYSTERS) - - SYSTERS cluster ID + + + beta12orEarlier Unique identifier of a sequence cluster from the SYSTERS database. - beta12orEarlier - - - + SYSTERS cluster ID + + + + Sequence cluster ID (SYSTERS) - - Ontology metadata - + + - - + + - beta12orEarlier + beta12orEarlier Data concerning a biological ontology. - - + + + Ontology metadata - - Raw SCOP domain classification - - true - beta12orEarlier + + + beta12orEarlier + beta13 + Raw SCOP domain classification data files. - beta13 + These are the parsable data files provided by SCOP. - - + Raw SCOP domain classification + true - - Raw CATH domain classification - + + + beta12orEarlier + beta13 + Raw CATH domain classification data files. + These are the parsable data files provided by CATH. + Raw CATH domain classification true - beta13 - beta12orEarlier - - - + + + beta12orEarlier + 1.4 + + An informative report on the types of small molecules or 'heterogens' (non-protein groups) that are represented in PDB files. + Heterogen annotation - - 1.4 true - beta12orEarlier - An informative report on the types of small molecules or 'heterogens' (non-protein groups) that are represented in PDB files. - - - - Phylogenetic property values - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + Phylogenetic property values data. + + Phylogenetic property values true - beta12orEarlier - - - - Sequence set (bootstrapped) - - 1.5 - beta12orEarlier + + + beta12orEarlier + 1.5 + + A collection of sequences output from a bootstrapping (resampling) procedure. + Bootstrapping is often performed in phylogenetic analysis. + Sequence set (bootstrapped) true - A collection of sequences output from a bootstrapping (resampling) procedure. - - - + + + beta12orEarlier + beta12orEarlier + + A consensus phylogenetic tree derived from comparison of multiple trees. + Phylogenetic consensus tree - true - A consensus phylogenetic tree derived from comparison of multiple trees. - beta12orEarlier - beta12orEarlier - - - + + + beta12orEarlier + 1.5 + + A data schema for organising or transforming data of some type. + Schema - - beta12orEarlier true - A data schema for organising or transforming data of some type. - 1.5 - - - - DTD - + + + beta12orEarlier + 1.5 + A DTD (document type definition). + + DTD true - beta12orEarlier - 1.5 - - - - XML Schema - - beta12orEarlier - XSD + + + beta12orEarlier + 1.5 + An XML Schema. + + XML Schema true - 1.5 - - - - Relax-NG schema - - beta12orEarlier - 1.5 + + + beta12orEarlier + 1.5 + A relax-NG schema. + + Relax-NG schema true - - - - XSLT stylesheet - - 1.5 - beta12orEarlier + + + beta12orEarlier + 1.5 + An XSLT stylesheet. + + XSLT stylesheet true - - - Data resource definition name - - - beta12orEarlier + + + + beta12orEarlier The name of a data type. - - - + + + + Data resource definition name - - OBO file format name - + + + beta12orEarlier Name of an OBO file format such as OBO-XML, plain and so on. - beta12orEarlier - - - + + + + OBO file format name - - Gene ID (MIPS) - + + + beta12orEarlier Identifier for genetic elements in MIPS database. - beta12orEarlier MIPS genetic element identifier - - - + + + + Gene ID (MIPS) - - Sequence identifier (protein) - + + + beta12orEarlier + beta12orEarlier + An identifier of protein sequence(s) or protein sequence database entries. - beta12orEarlier - beta12orEarlier + + Sequence identifier (protein) true - - - - Sequence identifier (nucleic acid) - + + + beta12orEarlier + beta12orEarlier + An identifier of nucleotide sequence(s) or nucleotide sequence database entries. - beta12orEarlier + + Sequence identifier (nucleic acid) true - beta12orEarlier - - - - EMBL accession - + + + beta12orEarlier + An accession number of an entry from the EMBL sequence database. EMBL ID - beta12orEarlier EMBL accession number EMBL identifier - An accession number of an entry from the EMBL sequence database. - - - + + + + EMBL accession - - UniProt ID - + + - - + + - UniProtKB identifier + beta12orEarlier An identifier of a polypeptide in the UniProt database. - UniProtKB entry name - beta12orEarlier - UniProt identifier UniProt entry name - - - + UniProt identifier + UniProtKB entry name + UniProtKB identifier + + + + UniProt ID - - GenBank accession - - GenBank ID - GenBank identifier + + + beta12orEarlier Accession number of an entry from the GenBank sequence database. - beta12orEarlier + GenBank ID GenBank accession number - - - + GenBank identifier + + + + GenBank accession - - Gramene secondary identifier - - beta12orEarlier - Gramene internal identifier - Gramene internal ID + + + beta12orEarlier Secondary (internal) identifier of a Gramene database entry. + Gramene internal ID + Gramene internal identifier Gramene secondary ID - - - + + + + Gramene secondary identifier - - Sequence variation ID - - + + + + beta12orEarlier An identifier of an entry from a database of molecular sequence variation. - beta12orEarlier - - - + + + + Sequence variation ID - - Gene ID - - - Gene accession - beta12orEarlier + + + + beta12orEarlier A unique (and typically persistent) identifier of a gene in a database, that is (typically) different to the gene name/symbol. + Gene accession Gene code - - - + + + + Gene ID - + + + beta12orEarlier + 1.3 + + Name of an entry (gene) from the AceView genes database. + Gene name (AceView) - - AceView gene name - 1.3 true - Name of an entry (gene) from the AceView genes database. - beta12orEarlier - - - - Gene ID (ECK) - - ECK accession - beta12orEarlier - E. coli K-12 gene identifier - Identifier of an E. coli K-12 gene from EcoGene Database. + + + beta12orEarlier http://www.geneontology.org/doc/GO.xrf_abbs: ECK - - - + Identifier of an E. coli K-12 gene from EcoGene Database. + E. coli K-12 gene identifier + ECK accession + + + + Gene ID (ECK) - - Gene ID (HGNC) - - HGNC ID - beta12orEarlier + + + beta12orEarlier Identifier for a gene approved by the HUGO Gene Nomenclature Committee. - - - + HGNC ID + + + + Gene ID (HGNC) - - Gene name - - + + + + beta12orEarlier The name of a gene, (typically) assigned by a person and/or according to a naming scheme. It may contain white space characters and is typically more intuitive and readable than a gene symbol. It (typically) may be used to identify similar genes in different species and to derive a gene symbol. Allele name - beta12orEarlier - - - + + + + Gene name - - Gene name (NCBI) - - beta12orEarlier - 1.3 - NCBI gene name + + + beta12orEarlier + 1.3 + Name of an entry (gene) from the NCBI genes database. + NCBI gene name + + Gene name (NCBI) true - - - - SMILES string - + + + beta12orEarlier A specification of a chemical structure in SMILES format. - beta12orEarlier - - + + + SMILES string - - STRING ID - + + + beta12orEarlier Unique identifier of an entry from the STRING database of protein-protein interactions. - beta12orEarlier - - - + + + + STRING ID - - Virus annotation - + + + beta12orEarlier + 1.4 + An informative report on a specific virus. + + Virus annotation true - 1.4 - beta12orEarlier - - - - Virus annotation (taxonomy) - + + + beta12orEarlier + 1.4 + An informative report on the taxonomy of a specific virus. - beta12orEarlier + + Virus annotation (taxonomy) true - 1.4 - - - - Reaction ID (SABIO-RK) - + + + beta12orEarlier + [0-9]+ Identifier of a biological reaction from the SABIO-RK reactions database. - beta12orEarlier - [0-9]+ - - - + + + + Reaction ID (SABIO-RK) - - Carbohydrate report - + + + beta12orEarlier Annotation on or information derived from one or more specific carbohydrate 3D structure(s). - beta12orEarlier - - + + + Carbohydrate report - - GI number - - beta12orEarlier + + + beta12orEarlier + A series of digits that are assigned consecutively to each sequence record processed by NCBI. The GI number bears no resemblance to the Accession number of the sequence record. NCBI GI number gi number - A series of digits that are assigned consecutively to each sequence record processed by NCBI. The GI number bears no resemblance to the Accession number of the sequence record. + + + Nucleotide sequence GI number is shown in the VERSION field of the database record. Protein sequence GI number is shown in the CDS/db_xref field of a nucleotide database record, and the VERSION field of a protein database record. - - - + GI number - - NCBI version - - beta12orEarlier - NCBI accession.version - Nucleotide sequence version contains two letters followed by six digits, a dot, and a version number (or for older nucleotide sequence records, the format is one letter followed by five digits, a dot, and a version number). Protein sequence version contains three letters followed by five digits, a dot, and a version number. + + + beta12orEarlier An identifier assigned to sequence records processed by NCBI, made of the accession number of the database record followed by a dot and a version number. + NCBI accession.version accession.version - - - + + + + Nucleotide sequence version contains two letters followed by six digits, a dot, and a version number (or for older nucleotide sequence records, the format is one letter followed by five digits, a dot, and a version number). Protein sequence version contains three letters followed by five digits, a dot, and a version number. + NCBI version - - Cell line name - - beta12orEarlier + + + beta12orEarlier The name of a cell line. - - - + + + + Cell line name - - Cell line name (exact) - - beta12orEarlier + + + beta12orEarlier The name of a cell line. - - - + + + + Cell line name (exact) - - Cell line name (truncated) - + + + beta12orEarlier The name of a cell line. - beta12orEarlier - - - + + + + Cell line name (truncated) - - Cell line name (no punctuation) - + + + beta12orEarlier The name of a cell line. - beta12orEarlier - - - + + + + Cell line name (no punctuation) - - Cell line name (assonant) - + + + beta12orEarlier The name of a cell line. - beta12orEarlier - - - + + + + Cell line name (assonant) - - Enzyme ID - - - beta12orEarlier + + + + beta12orEarlier A unique, persistent identifier of an enzyme. Enzyme accession - - - + + + + Enzyme ID - - REBASE enzyme number - + + + beta12orEarlier Identifier of an enzyme from the REBASE enzymes database. - beta12orEarlier - - - + + + + REBASE enzyme number - - DrugBank ID - - beta12orEarlier - DB[0-9]{5} + + + beta12orEarlier + DB[0-9]{5} Unique identifier of a drug from the DrugBank database. - - - + + + + DrugBank ID - - GI number (protein) - - beta12orEarlier - protein gi number + + + beta12orEarlier A unique identifier assigned to NCBI protein sequence records. - Nucleotide sequence GI number is shown in the VERSION field of the database record. Protein sequence GI number is shown in the CDS/db_xref field of a nucleotide database record, and the VERSION field of a protein database record. protein gi - - - + protein gi number + + + + Nucleotide sequence GI number is shown in the VERSION field of the database record. Protein sequence GI number is shown in the CDS/db_xref field of a nucleotide database record, and the VERSION field of a protein database record. + GI number (protein) - + + + beta12orEarlier + A score derived from the alignment of two sequences, which is then normalised with respect to the scoring system. + + + Bit scores are normalised with respect to the scoring system and therefore can be used to compare alignment scores from different searches. Bit score - - A score derived from the alignment of two sequences, which is then normalized with respect to the scoring system. - Bit scores are normalized with respect to the scoring system and therefore can be used to compare alignment scores from different searches. - beta12orEarlier - - - - Translation phase specification - - beta12orEarlier + + + beta12orEarlier Phase for translation of DNA (0, 1 or 2) relative to a fragment of the coding sequence. Phase - - + + + Translation phase specification - - Resource metadata - + + + beta12orEarlier Data concerning or describing some core computational resource, as distinct from primary data. This includes metadata on the origin, source, history, ownership or location of some thing. - This is a broad data type and is used a placeholder for other, more specific types. Provenance metadata - beta12orEarlier - - + + + This is a broad data type and is used a placeholder for other, more specific types. + Resource metadata - - Ontology identifier - + + - - + + - beta12orEarlier + beta12orEarlier Any arbitrary identifier of an ontology. - - - + + + + Ontology identifier - - Ontology concept name - - + + + + beta12orEarlier The name of a concept in an ontology. - beta12orEarlier - - - + + + + Ontology concept name - - Genome build identifier - - beta12orEarlier + + + beta12orEarlier An identifier of a build of a particular genome. - - - + + + + Genome build identifier - - Pathway or network name - + + + beta12orEarlier The name of a biological pathway or network. - beta12orEarlier - - - + + + + Pathway or network name - - Pathway ID (KEGG) - - + + + + beta12orEarlier + [a-zA-Z_0-9]{2,3}[0-9]{5} Identifier of a pathway from the KEGG pathway database. - beta12orEarlier - [a-zA-Z_0-9]{2,3}[0-9]{5} KEGG pathway ID - - - + + + + Pathway ID (KEGG) - - Pathway ID (NCI-Nature) - - beta12orEarlier - [a-zA-Z_0-9]+ + + + beta12orEarlier + [a-zA-Z_0-9]+ Identifier of a pathway from the NCI-Nature pathway database. - - - + + + + Pathway ID (NCI-Nature) - - Pathway ID (ConsensusPathDB) - - - beta12orEarlier + + + + beta12orEarlier Identifier of a pathway from the ConsensusPathDB pathway database. - - - + + + + Pathway ID (ConsensusPathDB) - - Sequence cluster ID (UniRef) - + + + beta12orEarlier Unique identifier of an entry from the UniRef database. UniRef cluster id UniRef entry accession - beta12orEarlier - - - + + + + Sequence cluster ID (UniRef) - - Sequence cluster ID (UniRef100) - + + + beta12orEarlier + Unique identifier of an entry from the UniRef100 database. UniRef100 cluster id - beta12orEarlier UniRef100 entry accession - Unique identifier of an entry from the UniRef100 database. - - - + + + + Sequence cluster ID (UniRef100) - - Sequence cluster ID (UniRef90) - - UniRef90 entry accession - beta12orEarlier - UniRef90 cluster id + + + beta12orEarlier Unique identifier of an entry from the UniRef90 database. - - - + UniRef90 cluster id + UniRef90 entry accession + + + + Sequence cluster ID (UniRef90) - - Sequence cluster ID (UniRef50) - - beta12orEarlier + + + beta12orEarlier + Unique identifier of an entry from the UniRef50 database. UniRef50 cluster id UniRef50 entry accession - Unique identifier of an entry from the UniRef50 database. - - - + + + + Sequence cluster ID (UniRef50) - - Ontology data - + + - - + + + beta12orEarlier Data concerning or derived from an ontology. Ontological data - beta12orEarlier + + This is a broad data type and is used a placeholder for other, more specific types. - - + Ontology data - - RNA family report - - beta12orEarlier + + + beta12orEarlier An informative report on a specific RNA family or other group of classified RNA sequences. RNA family annotation - - + + + RNA family report - - RNA family identifier - + + - - + + - beta12orEarlier + beta12orEarlier Identifier of an RNA family, typically an entry from a RNA sequence classification database. - - - + + + + RNA family identifier - - RFAM accession - - + + + + beta12orEarlier Stable accession number of an entry (RNA family) from the RFAM database. - beta12orEarlier - - - + + + + RFAM accession - + + + beta12orEarlier + 1.5 + + A label (text token) describing a type of protein family signature (sequence classifier) from the InterPro database. + Protein signature type - - beta12orEarlier true - A label (text token) describing a type of protein family signature (sequence classifier) from the InterPro database. - 1.5 - - - + + + beta12orEarlier + 1.5 + + An informative report on protein domain-DNA/RNA interaction(s). + Domain-nucleic acid interaction report - - 1.5 true - An informative report on protein domain-DNA/RNA interaction(s). - beta12orEarlier - - - - Domain-domain interactions - - 1.8 + + + beta12orEarlier + 1.8 + An informative report on protein domain-protein domain interaction(s). - beta12orEarlier + + Domain-domain interactions true - - - + + + beta12orEarlier + beta12orEarlier + + Data on indirect protein domain-protein domain interaction(s). + Domain-domain interaction (indirect) - true - beta12orEarlier - beta12orEarlier - Data on indirect protein domain-protein domain interaction(s). - - - - Sequence accession (hybrid) - + + - - + + + beta12orEarlier Accession number of a nucleotide or protein sequence database entry. - beta12orEarlier - - - + + + + Sequence accession (hybrid) - - 2D PAGE data - + + + beta12orEarlier + beta13 + Data concerning two-dimensional polygel electrophoresis. + + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. - beta13 - beta12orEarlier + 2D PAGE data true - Data concerning two-dimensional polygel electrophoresis. - - - - + + + beta12orEarlier + 1.8 + two-dimensional gel electrophoresis experiments, gels or spots in a gel. + + 2D PAGE report - - Topic concerning two-dimensional gel electrophoresis experiments, gels or spots in a gel. - beta12orEarlier - 1.8 true - - - - Pathway or network accession - - + + + + beta12orEarlier A persistent, unique identifier of a biological pathway or network (typically a database entry). - beta12orEarlier - - - + + + + Pathway or network accession - - Secondary structure alignment - + + + beta12orEarlier Alignment of the (1D representations of) secondary structure of two or more molecules. - beta12orEarlier - - + + + Secondary structure alignment - - ASTD ID - - - beta12orEarlier + + + + beta12orEarlier Identifier of an object from the ASTD database. - - - + + + + ASTD ID - - ASTD ID (exon) - - beta12orEarlier + + + beta12orEarlier Identifier of an exon from the ASTD database. - - - + + + + ASTD ID (exon) - - ASTD ID (intron) - - beta12orEarlier + + + beta12orEarlier Identifier of an intron from the ASTD database. - - - + + + + ASTD ID (intron) - - ASTD ID (polya) - + + + beta12orEarlier Identifier of a polyA signal from the ASTD database. - beta12orEarlier - - - + + + + ASTD ID (polya) - - ASTD ID (tss) - + + + beta12orEarlier Identifier of a transcription start site from the ASTD database. - beta12orEarlier - - - + + + + ASTD ID (tss) - - 2D PAGE spot report - - 2D PAGE spot annotation - beta12orEarlier + + + beta12orEarlier + 1.8 An informative report on individual spot(s) from a two-dimensional (2D PAGE) gel. - 1.8 + + + 2D PAGE spot report true - - - - Spot ID - - - beta12orEarlier + + + + beta12orEarlier Unique identifier of a spot from a two-dimensional (protein) gel. - - - + + + + Spot ID - - Spot serial number - + + + beta12orEarlier Unique identifier of a spot from a two-dimensional (protein) gel in the SWISS-2DPAGE database. - beta12orEarlier - - - + + + + Spot serial number - - Spot ID (HSC-2DPAGE) - + + + beta12orEarlier Unique identifier of a spot from a two-dimensional (protein) gel from a HSC-2DPAGE database. - beta12orEarlier - - - + + + + Spot ID (HSC-2DPAGE) - + + + beta12orEarlier + beta13 + + Data on the interaction of a protein (or protein domain) with specific structural (3D) and/or sequence motifs. + Protein-motif interaction - - beta13 true - Data on the interaction of a protein (or protein domain) with specific structural (3D) and/or sequence motifs. - beta12orEarlier - - - - Strain identifier - + + + beta12orEarlier Identifier of a strain of an organism variant, typically a plant, virus or bacterium. - beta12orEarlier - - - + + + + Strain identifier - - CABRI accession - - + + + + beta12orEarlier A unique identifier of an item from the CABRI database. - beta12orEarlier - - - + + + + CABRI accession - + + + beta12orEarlier + 1.8 + Report of genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods. + + Experiment report (genotyping) - true - Report of genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods. - 1.8 - beta12orEarlier - - - - Genotype experiment ID - - + + + - - + + - beta12orEarlier + beta12orEarlier Identifier of an entry from a database of genotype experiment metadata. - - - + + + + Genotype experiment ID - - EGA accession - - beta12orEarlier + + + beta12orEarlier Identifier of an entry from the EGA database. - - - + + + + EGA accession - - IPI protein ID - + + + beta12orEarlier + IPI[0-9]{8} Identifier of a protein entry catalogued in the International Protein Index (IPI) database. - IPI[0-9]{8} - beta12orEarlier - - - + + + + IPI protein ID - - RefSeq accession (protein) - - RefSeq protein ID + + + beta12orEarlier Accession number of a protein from the RefSeq database. - beta12orEarlier - - - + RefSeq protein ID + + + + RefSeq accession (protein) - - EPD ID - - beta12orEarlier + + + beta12orEarlier Identifier of an entry (promoter) from the EPD database. EPD identifier - - - + + + + EPD ID - - TAIR accession - - - beta12orEarlier + + + + beta12orEarlier Identifier of an entry from the TAIR database. - - - + + + + TAIR accession - - TAIR accession (At gene) - - beta12orEarlier + + + beta12orEarlier Identifier of an Arabidopsis thaliana gene from the TAIR database. - - - + + + + TAIR accession (At gene) - - UniSTS accession - - beta12orEarlier + + + beta12orEarlier Identifier of an entry from the UniSTS database. - - - + + + + UniSTS accession - - UNITE accession - - beta12orEarlier + + + beta12orEarlier Identifier of an entry from the UNITE database. - - - + + + + UNITE accession - - UTR accession - - beta12orEarlier + + + beta12orEarlier Identifier of an entry from the UTR database. - - - + + + + UTR accession - - UniParc accession - - beta12orEarlier - UPI[A-F0-9]{10} + + + beta12orEarlier + UPI[A-F0-9]{10} Accession number of a UniParc (protein sequence) database entry. - UniParc ID UPI - - - + UniParc ID + + + + UniParc accession - - mFLJ/mKIAA number - - beta12orEarlier + + + beta12orEarlier Identifier of an entry from the Rouge or HUGE databases. - - - + + + + mFLJ/mKIAA number - + + + beta12orEarlier + 1.4 + + An informative report on a specific fungus. + Fungi annotation - true - beta12orEarlier - 1.4 - An informative report on a specific fungus. - - - - Fungi annotation (anamorph) - - beta12orEarlier + + + beta12orEarlier + 1.4 + An informative report on a specific fungus anamorph. - 1.4 + + Fungi annotation (anamorph) true - - - + + + beta12orEarlier + 1.8 + exons in a nucleotide sequences. + + Gene features report (exon) - true - Topic concerning exons in a nucleotide sequences. - 1.8 - beta12orEarlier - - - - Ensembl protein ID - - + + + + beta12orEarlier + Unique identifier for a protein from the Ensembl database. Ensembl ID (protein) - beta12orEarlier Protein ID (Ensembl) - Unique identifier for a protein from the Ensembl database. - - - + + + + Ensembl protein ID - + + + beta12orEarlier + 1.8 + transcription of DNA into RNA including the regulation of transcription. + + Gene transcriptional features report - - 1.8 - beta12orEarlier true - Topic concerning transcription of DNA into RNA including the regulation of transcription. - - - - Toxin annotation - - beta12orEarlier + + + beta12orEarlier + 1.4 + An informative report on a specific toxin. - 1.4 + + Toxin annotation true - - - + + + beta12orEarlier + beta12orEarlier + + An informative report on a membrane protein. + Protein report (membrane protein) - - beta12orEarlier true - An informative report on a membrane protein. - beta12orEarlier - - - - Protein-drug interaction report - - - + + + beta12orEarlier + 1.12 An informative report on tentative or known protein-drug interaction(s). - beta12orEarlier - - + + + Protein-drug interaction report + true - - Map data - - beta12orEarlier + + + beta12orEarlier + beta13 + + + Data concerning a map of molecular sequence(s). + This is a broad data type and is used a placeholder for other, more specific types. + Map data true - beta13 - Data concerning a map of molecular sequence(s). - - - - - Phylogenetic data - + + + beta12orEarlier Data concerning phylogeny, typically of molecular sequences, including reports of information concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees. - Phylogenetic data + + This is a broad data type and is used a placeholder for other, more specific types. - beta12orEarlier - - + Phylogenetic data - - Protein data - - This is a broad data type and is used a placeholder for other, more specific types. - beta13 + + + beta12orEarlier + beta13 + Data concerning one or more protein molecules. + + This is a broad data type and is used a placeholder for other, more specific types. + Protein data true - beta12orEarlier - - - - Nucleic acid data - - true + + + beta12orEarlier + beta13 + Data concerning one or more nucleic acid molecules. - beta13 - beta12orEarlier + This is a broad data type and is used a placeholder for other, more specific types. - - + Nucleic acid data + true - - Article data - - beta12orEarlier - This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. It includes concepts that are best described as scientific text or closely concerned with or derived from text. - Article report + + + + + + + + + beta12orEarlier Data concerning, extracted from, or derived from the analysis of a scientific text (or texts) such as a full text article from a scientific journal. - - - + Article data + Scientific text data + + + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. It includes concepts that are best described as scientific text or closely concerned with or derived from text. + Text data - - Parameter - - http://semanticscience.org/resource/SIO_000144 - Tool-specific parameter - beta12orEarlier - http://www.e-lico.eu/ontologies/dmo/DMOP/DMOP.owl#Parameter + + + beta12orEarlier + 1.16 Typically a simple numerical or string value that controls the operation of a tool. - Parameters - Tool parameter - - + + Parameter + true - - Molecular data - - Molecule-specific data - true + + + beta12orEarlier + beta13 + Data concerning a specific type of molecule. - beta13 - beta12orEarlier + This is a broad data type and is used a placeholder for other, more specific types. - - + Molecular data + true - - Molecule report - + + + beta12orEarlier + 1.5 + + An informative report on a specific molecule. - beta12orEarlier - Molecular report - 1.5 + + Molecule report true - - - - - Organism report - + + + beta12orEarlier An informative report on a specific organism. - beta12orEarlier Organism annotation - - + + + Organism report - - Experiment report - - Experiment metadata - beta12orEarlier - Experiment annotation + + + beta12orEarlier Annotation on a wet lab experiment, such as experimental conditions. - - + Experiment annotation + Experiment metadata + + + Experiment report - + + + beta12orEarlier + 1.8 + DNA mutation. + + Nucleic acid features report (mutation) - - Topic concerning DNA mutation. - 1.8 true - beta12orEarlier - - - - Sequence attribute - + + + beta12orEarlier An attribute of a molecular sequence, possibly in reference to some other sequence. Sequence parameter - beta12orEarlier - - + + + Sequence attribute - - Sequence tag profile - - SAGE, MPSS and SBS experiments are usually performed to study gene expression. The sequence tags are typically subsequently annotated (after a database search) with the mRNA (and therefore gene) the tag was extracted from. - beta12orEarlier - Sequencing-based expression profile + + + beta12orEarlier Output from a serial analysis of gene expression (SAGE), massively parallel signature sequencing (MPSS) or sequencing by synthesis (SBS) experiment. In all cases this is a list of short sequence tags and the number of times it is observed. - - + Sequencing-based expression profile + Sequence tag profile (with gene assignment) + + + SAGE, MPSS and SBS experiments are usually performed to study gene expression. The sequence tags are typically subsequently annotated (after a database search) with the mRNA (and therefore gene) the tag was extracted from. + This includes tag to gene assignments (tag mapping) of SAGE, MPSS and SBS data. Typically this is the sequencing-based expression profile annotated with gene identifiers. + Sequence tag profile - - Mass spectrometry data - - beta12orEarlier + + + beta12orEarlier Data concerning a mass spectrometry measurement. - - + + + Mass spectrometry data - - Protein structure raw data - - beta12orEarlier + + + beta12orEarlier Raw data from experimental methods for determining protein structure. + + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. - - + Protein structure raw data - - Mutation identifier - + + + beta12orEarlier An identifier of a mutation. - beta12orEarlier - - - + + + + Mutation identifier - - Alignment data - + + + beta12orEarlier + beta13 + + + Data concerning an alignment of two or more molecular sequences, structures or derived data. + This is a broad data type and is used a placeholder for other, more specific types. This includes entities derived from sequences and structures such as motifs and profiles. + Alignment data true - beta13 - Data concerning an alignment of two or more molecular sequences, structures or derived data. - beta12orEarlier - - - - - Data index data - - true + + + beta12orEarlier + beta13 + Data concerning an index of data. - beta12orEarlier - beta13 - Database index + This is a broad data type and is used a placeholder for other, more specific types. - - + Data index data + true - - Amino acid name (single letter) - - beta12orEarlier + + + beta12orEarlier Single letter amino acid identifier, e.g. G. - - - + + + + Amino acid name (single letter) - - Amino acid name (three letter) - - beta12orEarlier + + + beta12orEarlier Three letter amino acid identifier, e.g. GLY. - - - + + + + Amino acid name (three letter) - - Amino acid name (full name) - - beta12orEarlier + + + beta12orEarlier Full name of an amino acid, e.g. Glycine. - - - + + + + Amino acid name (full name) - - Toxin identifier - + + - - + + - beta12orEarlier + beta12orEarlier Identifier of a toxin. - - - + + + + Toxin identifier - - ArachnoServer ID - + + + beta12orEarlier Unique identifier of a toxin from the ArachnoServer database. - beta12orEarlier - - - + + + + ArachnoServer ID - + + + beta12orEarlier + 1.5 + + A simple summary of expressed genes. + Expressed gene list - - beta12orEarlier true - 1.5 - Gene annotation (expressed gene list) - A simple summary of expressed genes. - - - - BindingDB Monomer ID - + + + beta12orEarlier Unique identifier of a monomer from the BindingDB database. - beta12orEarlier - - - + + + + BindingDB Monomer ID - + + + beta12orEarlier + beta12orEarlier + + The name of a concept from the GO ontology. + GO concept name - true - beta12orEarlier - beta12orEarlier - The name of a concept from the GO ontology. - - - - GO concept ID (biological process) - - [0-9]{7}|GO:[0-9]{7} - beta12orEarlier + + + beta12orEarlier + [0-9]{7}|GO:[0-9]{7} An identifier of a 'biological process' concept from the the Gene Ontology. - - - + + + + GO concept ID (biological process) - - GO concept ID (molecular function) - - beta12orEarlier - [0-9]{7}|GO:[0-9]{7} + + + beta12orEarlier + [0-9]{7}|GO:[0-9]{7} An identifier of a 'molecular function' concept from the the Gene Ontology. - - - + + + + GO concept ID (molecular function) - - GO concept name (cellular component) - + + + beta12orEarlier + beta12orEarlier + The name of a concept for a cellular component from the GO ontology. + + GO concept name (cellular component) true - beta12orEarlier - beta12orEarlier - - - - Northern blot image - - beta12orEarlier + + + beta12orEarlier An image arising from a Northern Blot experiment. - - + + + Northern blot image - - Blot ID - - + + + + beta12orEarlier Unique identifier of a blot from a Northern Blot. - beta12orEarlier - - - + + + + Blot ID - - BlotBase blot ID - - beta12orEarlier + + + beta12orEarlier Unique identifier of a blot from a Northern Blot from the BlotBase database. - - - + + + + BlotBase blot ID - - Hierarchy - - beta12orEarlier + + + beta12orEarlier Raw data on a biological hierarchy, describing the hierarchy proper, hierarchy components and possibly associated annotation. Hierarchy annotation - - + + + Hierarchy - - Hierarchy identifier - + + + beta12orEarlier + beta12orEarlier + Identifier of an entry from a database of biological hierarchies. - beta12orEarlier - beta12orEarlier + + Hierarchy identifier true - - - - Brite hierarchy ID - - beta12orEarlier + + + beta12orEarlier Identifier of an entry from the Brite database of biological hierarchies. - - - + + + + Brite hierarchy ID - + + + beta12orEarlier + beta12orEarlier + + A type (represented as a string) of cancer. + Cancer type - true - A type (represented as a string) of cancer. - beta12orEarlier - beta12orEarlier - - - - BRENDA organism ID - + + + beta12orEarlier A unique identifier for an organism used in the BRENDA database. - beta12orEarlier - - - + + + + BRENDA organism ID - - UniGene taxon - + + + beta12orEarlier The name of a taxon using the controlled vocabulary of the UniGene database. UniGene organism abbreviation - beta12orEarlier - - - + + + + UniGene taxon - - UTRdb taxon - - beta12orEarlier + + + beta12orEarlier The name of a taxon using the controlled vocabulary of the UTRdb database. - - - + + + + UTRdb taxon - - Catalogue ID - - beta12orEarlier + + + beta12orEarlier An identifier of a catalogue of biological resources. Catalogue identifier - - - + + + + Catalogue ID - - CABRI catalogue name - - + + + + beta12orEarlier The name of a catalogue of biological resources from the CABRI database. - beta12orEarlier - - - + + + + CABRI catalogue name - - Secondary structure alignment metadata - + + + beta12orEarlier + beta12orEarlier + An informative report on protein secondary structure alignment-derived data or metadata. - beta12orEarlier - beta12orEarlier + + Secondary structure alignment metadata true - - - - Molecule interaction report - + + + beta12orEarlier + An informative report on the physical, chemical or other information concerning the interaction of two or more molecules (or parts of molecules). - beta12orEarlier - Molecular interaction report - Molecular interaction data - + Molecule interaction report - - Pathway or network - + + - - + + + beta12orEarlier + Primary data about a specific biological pathway or network (the nodes and connections within the pathway or network). Network - beta12orEarlier Pathway - Primary data about a specific biological pathway or network (the nodes and connections within the pathway or network). - - + + + Pathway or network - + + + beta12orEarlier + beta13 + + Data concerning one or more small molecules. + + This is a broad data type and is used a placeholder for other, more specific types. Small molecule data - true - This is a broad data type and is used a placeholder for other, more specific types. - beta12orEarlier - beta13 - Data concerning one or more small molecules. - - - + + + beta12orEarlier + beta13 + + Data concerning a particular genotype, phenotype or a genotype / phenotype relation. + Genotype and phenotype data - - beta12orEarlier true - beta13 - Data concerning a particular genotype, phenotype or a genotype / phenotype relation. - - - - Microarray data - Gene expression data - + + + - - + + - beta12orEarlier - Image or hybridisation data for a microarray, typically a study of gene expression. + beta12orEarlier + Image, hybridisation or some other data arising from a study of gene expression, typically profiling or quantification. + Gene product profile + Gene product quantification data + Gene transcription profile + Gene transcription quantification data Microarray data - This is a broad data type and is used a placeholder for other, more specific types. See also http://edamontology.org/data_0931 - - + Non-coding RNA profile + Non-coding RNA quantification data + RNA profile + RNA quantification data + RNA-seq data + Transcriptome profile + Transcriptome quantification data + mRNA profile + mRNA quantification data + Protein profile + Protein quantification data + Proteome profile + Proteome quantification data + + + Gene expression data + Microarray data - - Compound ID (KEGG) - - - C[0-9]+ + + + + beta12orEarlier + C[0-9]+ Unique identifier of a chemical compound from the KEGG database. - beta12orEarlier KEGG compound ID KEGG compound identifier - - - + + + + Compound ID (KEGG) - - RFAM name - - + + + + beta12orEarlier Name (not necessarily stable) an entry (RNA family) from the RFAM database. - beta12orEarlier - - - + + + + RFAM name - - Reaction ID (KEGG) - - + + + + beta12orEarlier + R[0-9]+ Identifier of a biological reaction from the KEGG reactions database. - R[0-9]+ - beta12orEarlier - - - + + + + Reaction ID (KEGG) - - Drug ID (KEGG) - - - beta12orEarlier + + + + beta12orEarlier + D[0-9]+ Unique identifier of a drug from the KEGG Drug database. - D[0-9]+ - - - + + + + Drug ID (KEGG) - - Ensembl ID - - - beta12orEarlier - ENS[A-Z]*[FPTG][0-9]{11} + + + + beta12orEarlier + ENS[A-Z]*[FPTG][0-9]{11} Identifier of an entry (exon, gene, transcript or protein) from the Ensembl database. Ensembl IDs - - - + + + + Ensembl ID - - ICD identifier - + + - - + + + beta12orEarlier + [A-Z][0-9]+(\.[-[0-9]+])? An identifier of a disease from the International Classification of Diseases (ICD) database. - beta12orEarlier - [A-Z][0-9]+(\.[-[0-9]+])? - - - + + + + ICD identifier - - Sequence cluster ID (CluSTr) - + + + beta12orEarlier + [0-9A-Za-z]+:[0-9]+:[0-9]{1,5}(\.[0-9])? Unique identifier of a sequence cluster from the CluSTr database. - [0-9A-Za-z]+:[0-9]+:[0-9]{1,5}(\.[0-9])? CluSTr ID - beta12orEarlier CluSTr cluster ID - - - + + + + Sequence cluster ID (CluSTr) - - KEGG Glycan ID - - - G[0-9]+ + + + + beta12orEarlier + G[0-9]+ Unique identifier of a glycan ligand from the KEGG GLYCAN database (a subset of KEGG LIGAND). - beta12orEarlier - - - + + + + KEGG Glycan ID - - TCDB ID - - beta12orEarlier - OBO file for regular expression. - TC number - [0-9]+\.[A-Z]\.[0-9]+\.[0-9]+\.[0-9]+ + + + beta12orEarlier + [0-9]+\.[A-Z]\.[0-9]+\.[0-9]+\.[0-9]+ A unique identifier of a family from the transport classification database (TCDB) of membrane transport proteins. - - - + TC number + + + + OBO file for regular expression. + TCDB ID - - MINT ID - - MINT\-[0-9]{1,5} + + + beta12orEarlier + MINT\-[0-9]{1,5} Unique identifier of an entry from the MINT database of protein-protein interactions. - beta12orEarlier - - - + + + + MINT ID - - DIP ID - + + + beta12orEarlier + DIP[\:\-][0-9]{3}[EN] Unique identifier of an entry from the DIP database of protein-protein interactions. - beta12orEarlier - DIP[\:\-][0-9]{3}[EN] - - - + + + + DIP ID - - Signaling Gateway protein ID - - beta12orEarlier + + + beta12orEarlier + A[0-9]{6} Unique identifier of a protein listed in the UCSD-Nature Signaling Gateway Molecule Pages database. - A[0-9]{6} - - - + + + + Signaling Gateway protein ID - - Protein modification ID - - - beta12orEarlier + + + + beta12orEarlier Identifier of a protein modification catalogued in a database. - - - + + + + Protein modification ID - - RESID ID - + + + beta12orEarlier + AA[0-9]{4} Identifier of a protein modification catalogued in the RESID database. - AA[0-9]{4} - beta12orEarlier - - - + + + + RESID ID - - RGD ID - - - [0-9]{4,7} - beta12orEarlier + + + + beta12orEarlier + [0-9]{4,7} Identifier of an entry from the RGD database. - - - + + + + RGD ID - - TAIR accession (protein) - - + + + - - + + - AASequence:[0-9]{10} + beta12orEarlier + AASequence:[0-9]{10} Identifier of a protein sequence from the TAIR database. - beta12orEarlier - - - + + + + TAIR accession (protein) - - Compound ID (HMDB) - - HMDB[0-9]{5} - beta12orEarlier - HMDB ID + + + beta12orEarlier + HMDB[0-9]{5} Identifier of a small molecule metabolite from the Human Metabolome Database (HMDB). - - - + HMDB ID + + + + Compound ID (HMDB) - - LIPID MAPS ID - - beta12orEarlier - LM ID + + + beta12orEarlier + LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4})? Identifier of an entry from the LIPID MAPS database. - LM(FA|GL|GP|SP|ST|PR|SL|PK)[0-9]{4}([0-9a-zA-Z]{4})? - - - + LM ID + + + + LIPID MAPS ID - - PeptideAtlas ID - - Identifier of a peptide from the PeptideAtlas peptide databases. + + + beta12orEarlier + PAp[0-9]{8} PDBML:pdbx_PDB_strand_id - beta12orEarlier - PAp[0-9]{8} - - - + Identifier of a peptide from the PeptideAtlas peptide databases. + + + + PeptideAtlas ID - - Molecular interaction ID - + + + beta12orEarlier + 1.7 Identifier of a report of molecular interactions from a database (typically). + + + Molecular interaction ID true - beta12orEarlier - 1.7 - - - - BioGRID interaction ID - - [0-9]+ - beta12orEarlier + + + beta12orEarlier + [0-9]+ A unique identifier of an interaction from the BioGRID database. - - - + + + + BioGRID interaction ID - - Enzyme ID (MEROPS) - - MEROPS ID + + + beta12orEarlier + S[0-9]{2}\.[0-9]{3} Unique identifier of a peptidase enzyme from the MEROPS database. - beta12orEarlier - S[0-9]{2}\.[0-9]{3} - - - + MEROPS ID + + + + Enzyme ID (MEROPS) - - Mobile genetic element ID - - + + + + beta12orEarlier An identifier of a mobile genetic element. - beta12orEarlier - - - + + + + Mobile genetic element ID - - ACLAME ID - - beta12orEarlier - mge:[0-9]+ + + + beta12orEarlier + mge:[0-9]+ An identifier of a mobile genetic element from the Aclame database. - - - + + + + ACLAME ID - - SGD ID - - - PWY[a-zA-Z_0-9]{2}\-[0-9]{3} - beta12orEarlier + + + + beta12orEarlier + PWY[a-zA-Z_0-9]{2}\-[0-9]{3} Identifier of an entry from the Saccharomyces genome database (SGD). - - - + + + + SGD ID - - Book ID - - - beta12orEarlier + + + + beta12orEarlier Unique identifier of a book. - - - + + + + Book ID - - ISBN - - beta12orEarlier - (ISBN)?(-13|-10)?[:]?[ ]?([0-9]{2,3}[ -]?)?[0-9]{1,5}[ -]?[0-9]{1,7}[ -]?[0-9]{1,6}[ -]?([0-9]|X) + + + beta12orEarlier + (ISBN)?(-13|-10)?[:]?[ ]?([0-9]{2,3}[ -]?)?[0-9]{1,5}[ -]?[0-9]{1,7}[ -]?[0-9]{1,6}[ -]?([0-9]|X) The International Standard Book Number (ISBN) is for identifying printed books. - - - + + + + ISBN - - Compound ID (3DMET) - - B[0-9]{5} - 3DMET ID - beta12orEarlier + + + beta12orEarlier + B[0-9]{5} Identifier of a metabolite from the 3DMET database. - - - + 3DMET ID + + + + Compound ID (3DMET) - - MatrixDB interaction ID - - ([A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9])_.*|([OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*) + + + beta12orEarlier + ([A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9])_.*|([OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]_.*)|(GAG_.*)|(MULT_.*)|(PFRAG_.*)|(LIP_.*)|(CAT_.*) A unique identifier of an interaction from the MatrixDB database. - beta12orEarlier - - - + + + + MatrixDB interaction ID - - cPath ID - - - [0-9]+ - These identifiers are unique within the cPath database, however, they are not stable between releases. - beta12orEarlier + + + + beta12orEarlier + [0-9]+ A unique identifier for pathways, reactions, complexes and small molecules from the cPath (Pathway Commons) database. - - - + + + + These identifiers are unique within the cPath database, however, they are not stable between releases. + cPath ID - - PubChem bioassay ID - - + + + + beta12orEarlier + [0-9]+ Identifier of an assay from the PubChem database. - [0-9]+ - beta12orEarlier - - - + + + + PubChem bioassay ID - - PubChem ID - - - PubChem identifier - beta12orEarlier + + + + beta12orEarlier Identifier of an entry from the PubChem database. - - - + PubChem identifier + + + + PubChem ID - - Reaction ID (MACie) - - beta12orEarlier - M[0-9]{4} - MACie entry number + + + beta12orEarlier + M[0-9]{4} Identifier of an enzyme reaction mechanism from the MACie database. - - - + MACie entry number + + + + Reaction ID (MACie) - - Gene ID (miRBase) - - beta12orEarlier - miRNA name - miRNA ID + + + beta12orEarlier + MI[0-9]{7} Identifier for a gene from the miRBase database. - MI[0-9]{7} + miRNA ID miRNA identifier - - - + miRNA name + + + + Gene ID (miRBase) - - Gene ID (ZFIN) - + + + beta12orEarlier + ZDB\-GENE\-[0-9]+\-[0-9]+ Identifier for a gene from the Zebrafish information network genome (ZFIN) database. - beta12orEarlier - ZDB\-GENE\-[0-9]+\-[0-9]+ - - - + + + + Gene ID (ZFIN) - - Reaction ID (Rhea) - - [0-9]{5} + + + beta12orEarlier + [0-9]{5} Identifier of an enzyme-catalysed reaction from the Rhea database. - beta12orEarlier - - - + + + + Reaction ID (Rhea) - - Pathway ID (Unipathway) - - UPA[0-9]{5} - upaid - beta12orEarlier + + + beta12orEarlier + UPA[0-9]{5} Identifier of a biological pathway from the Unipathway database. - - - + upaid + + + + Pathway ID (Unipathway) - - Compound ID (ChEMBL) - + + + beta12orEarlier + [0-9]+ Identifier of a small molecular from the ChEMBL database. ChEMBL ID - beta12orEarlier - [0-9]+ - - - + + + + Compound ID (ChEMBL) - - LGICdb identifier - + + + beta12orEarlier + [a-zA-Z_0-9]+ Unique identifier of an entry from the Ligand-gated ion channel (LGICdb) database. - beta12orEarlier - [a-zA-Z_0-9]+ - - - + + + + LGICdb identifier - - Reaction kinetics ID (SABIO-RK) - + + + beta12orEarlier + [0-9]+ Identifier of a biological reaction (kinetics entry) from the SABIO-RK reactions database. - [0-9]+ - beta12orEarlier - - - + + + + Reaction kinetics ID (SABIO-RK) - - PharmGKB ID - - - beta12orEarlier + + + + beta12orEarlier + PA[0-9]+ Identifier of an entry from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). - PA[0-9]+ - - - + + + + PharmGKB ID - - Pathway ID (PharmGKB) - - - PA[0-9]+ + + + + beta12orEarlier + PA[0-9]+ Identifier of a pathway from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). - beta12orEarlier - - - + + + + Pathway ID (PharmGKB) - - Disease ID (PharmGKB) - - + + + + beta12orEarlier + PA[0-9]+ Identifier of a disease from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). - beta12orEarlier - PA[0-9]+ - - - + + + + Disease ID (PharmGKB) - - Drug ID (PharmGKB) - - - beta12orEarlier + + + + beta12orEarlier + PA[0-9]+ Identifier of a drug from the pharmacogenetics and pharmacogenomics knowledge base (PharmGKB). - PA[0-9]+ - - - + + + + Drug ID (PharmGKB) - - Drug ID (TTD) - - DAP[0-9]+ + + + beta12orEarlier + DAP[0-9]+ Identifier of a drug from the Therapeutic Target Database (TTD). - beta12orEarlier - - - + + + + Drug ID (TTD) - - Target ID (TTD) - - TTDS[0-9]+ + + + beta12orEarlier + TTDS[0-9]+ Identifier of a target protein from the Therapeutic Target Database (TTD). - beta12orEarlier - - - + + + + Target ID (TTD) - - Cell type identifier - - beta12orEarlier - Cell type ID + + + beta12orEarlier A unique identifier of a type or group of cells. - - - + + + + Cell type identifier - - NeuronDB ID - - [0-9]+ - beta12orEarlier + + + beta12orEarlier + [0-9]+ A unique identifier of a neuron from the NeuronDB database. - - - + + + + NeuronDB ID - - NeuroMorpho ID - - beta12orEarlier + + + beta12orEarlier + [a-zA-Z_0-9]+ A unique identifier of a neuron from the NeuroMorpho database. - [a-zA-Z_0-9]+ - - - + + + + NeuroMorpho ID - - Compound ID (ChemIDplus) - + + + beta12orEarlier + [0-9]+ Identifier of a chemical from the ChemIDplus database. ChemIDplus ID - [0-9]+ - beta12orEarlier - - - + + + + Compound ID (ChemIDplus) - - Pathway ID (SMPDB) - - beta12orEarlier + + + beta12orEarlier + SMP[0-9]{5} Identifier of a pathway from the Small Molecule Pathway Database (SMPDB). - SMP[0-9]{5} - - - + + + + Pathway ID (SMPDB) - - BioNumbers ID - + + + beta12orEarlier + [0-9]+ Identifier of an entry from the BioNumbers database of key numbers and associated data in molecular biology. - [0-9]+ - beta12orEarlier - - - + + + + BioNumbers ID - - T3DB ID - - beta12orEarlier - T3D[0-9]+ + + + beta12orEarlier + T3D[0-9]+ Unique identifier of a toxin from the Toxin and Toxin Target Database (T3DB) database. - - - + + + + T3DB ID - - Carbohydrate identifier - + + - - + + - - + + - beta12orEarlier + beta12orEarlier Identifier of a carbohydrate. - - - + + + + Carbohydrate identifier - - GlycomeDB ID - + + + beta12orEarlier + [0-9]+ Identifier of an entry from the GlycomeDB database. - beta12orEarlier - [0-9]+ - - - + + + + GlycomeDB ID - - LipidBank ID - - beta12orEarlier - [a-zA-Z_0-9]+[0-9]+ + + + beta12orEarlier + [a-zA-Z_0-9]+[0-9]+ Identifier of an entry from the LipidBank database. - - - + + + + LipidBank ID - - CDD ID - - beta12orEarlier - cd[0-9]{5} + + + beta12orEarlier + cd[0-9]{5} Identifier of a conserved domain from the Conserved Domain Database. - - - + + + + CDD ID - - MMDB ID - - [0-9]{1,5} - beta12orEarlier + + + beta12orEarlier + [0-9]{1,5} An identifier of an entry from the MMDB database. MMDB accession - - - + + + + MMDB ID - - iRefIndex ID - + + + beta12orEarlier + [0-9]+ Unique identifier of an entry from the iRefIndex database of protein-protein interactions. - beta12orEarlier - [0-9]+ - - - + + + + iRefIndex ID - - ModelDB ID - + + + beta12orEarlier + [0-9]+ Unique identifier of an entry from the ModelDB database. - [0-9]+ - beta12orEarlier - - - + + + + ModelDB ID - - Pathway ID (DQCS) - - [0-9]+ + + + beta12orEarlier + [0-9]+ Identifier of a signaling pathway from the Database of Quantitative Cellular Signaling (DQCS). - beta12orEarlier - - - + + + + Pathway ID (DQCS) - + + + beta12orEarlier + beta12orEarlier + ENS([EGTP])[0-9]{11} + + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database (Homo sapiens division). + Ensembl ID (Homo sapiens) - - beta12orEarlier true - beta12orEarlier - ENS([EGTP])[0-9]{11} - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database (Homo sapiens division). - - - - Ensembl ID ('Bos taurus') - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + ENSBTA([EGTP])[0-9]{11} + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Bos taurus' division). + + Ensembl ID ('Bos taurus') true - beta12orEarlier - ENSBTA([EGTP])[0-9]{11} - - - - Ensembl ID ('Canis familiaris') - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + ENSCAF([EGTP])[0-9]{11} + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Canis familiaris' division). + + Ensembl ID ('Canis familiaris') true - ENSCAF([EGTP])[0-9]{11} - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + ENSCPO([EGTP])[0-9]{11} + + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Cavia porcellus' division). + Ensembl ID ('Cavia porcellus') - - ENSCPO([EGTP])[0-9]{11} true - beta12orEarlier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Cavia porcellus' division). - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + ENSCIN([EGTP])[0-9]{11} + + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona intestinalis' division). + Ensembl ID ('Ciona intestinalis') - true - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona intestinalis' division). - beta12orEarlier - beta12orEarlier - ENSCIN([EGTP])[0-9]{11} - - - - Ensembl ID ('Ciona savignyi') - + + + beta12orEarlier + beta12orEarlier + ENSCSAV([EGTP])[0-9]{11} + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona savignyi' division). - ENSCSAV([EGTP])[0-9]{11} - beta12orEarlier - beta12orEarlier + + Ensembl ID ('Ciona savignyi') true - - - - Ensembl ID ('Danio rerio') - + + + beta12orEarlier + beta12orEarlier + ENSDAR([EGTP])[0-9]{11} + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Danio rerio' division). + + Ensembl ID ('Danio rerio') true - beta12orEarlier - beta12orEarlier - ENSDAR([EGTP])[0-9]{11} - - - - Ensembl ID ('Dasypus novemcinctus') - + + + beta12orEarlier + beta12orEarlier + ENSDNO([EGTP])[0-9]{11} + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Dasypus novemcinctus' division). - beta12orEarlier - beta12orEarlier - ENSDNO([EGTP])[0-9]{11} + + Ensembl ID ('Dasypus novemcinctus') true - - - + + + beta12orEarlier + beta12orEarlier + ENSETE([EGTP])[0-9]{11} + + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Echinops telfairi' division). + Ensembl ID ('Echinops telfairi') - - ENSETE([EGTP])[0-9]{11} true - beta12orEarlier - beta12orEarlier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Echinops telfairi' division). - - - + + + beta12orEarlier + beta12orEarlier + ENSEEU([EGTP])[0-9]{11} + + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Erinaceus europaeus' division). + Ensembl ID ('Erinaceus europaeus') - true - ENSEEU([EGTP])[0-9]{11} - beta12orEarlier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Erinaceus europaeus' division). - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + ENSFCA([EGTP])[0-9]{11} + + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Felis catus' division). + Ensembl ID ('Felis catus') - - beta12orEarlier true - ENSFCA([EGTP])[0-9]{11} - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Felis catus' division). - beta12orEarlier - - - - Ensembl ID ('Gallus gallus') - - ENSGAL([EGTP])[0-9]{11} + + + beta12orEarlier + beta12orEarlier + ENSGAL([EGTP])[0-9]{11} + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gallus gallus' division). - beta12orEarlier + + Ensembl ID ('Gallus gallus') true - beta12orEarlier - - - - Ensembl ID ('Gasterosteus aculeatus') - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + ENSGAC([EGTP])[0-9]{11} + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gasterosteus aculeatus' division). + + Ensembl ID ('Gasterosteus aculeatus') true - ENSGAC([EGTP])[0-9]{11} - beta12orEarlier - - - - Ensembl ID ('Homo sapiens') - - ENSHUM([EGTP])[0-9]{11} - beta12orEarlier - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + ENSHUM([EGTP])[0-9]{11} + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Homo sapiens' division). + + Ensembl ID ('Homo sapiens') true - - - + + + beta12orEarlier + beta12orEarlier + ENSLAF([EGTP])[0-9]{11} + + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Loxodonta africana' division). + Ensembl ID ('Loxodonta africana') - - beta12orEarlier true - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Loxodonta africana' division). - ENSLAF([EGTP])[0-9]{11} - beta12orEarlier - - - - Ensembl ID ('Macaca mulatta') - + + + beta12orEarlier + beta12orEarlier + ENSMMU([EGTP])[0-9]{11} + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Macaca mulatta' division). - beta12orEarlier - ENSMMU([EGTP])[0-9]{11} + + Ensembl ID ('Macaca mulatta') true - beta12orEarlier - - - - Ensembl ID ('Monodelphis domestica') - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + ENSMOD([EGTP])[0-9]{11} + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Monodelphis domestica' division). + + Ensembl ID ('Monodelphis domestica') true - ENSMOD([EGTP])[0-9]{11} - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + ENSMUS([EGTP])[0-9]{11} + + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Mus musculus' division). + Ensembl ID ('Mus musculus') - - ENSMUS([EGTP])[0-9]{11} true - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Mus musculus' division). - beta12orEarlier - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + ENSMLU([EGTP])[0-9]{11} + + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Myotis lucifugus' division). + Ensembl ID ('Myotis lucifugus') - - beta12orEarlier - ENSMLU([EGTP])[0-9]{11} true - beta12orEarlier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Myotis lucifugus' division). - - - + + + beta12orEarlier + beta12orEarlier + ENSOAN([EGTP])[0-9]{11} + + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ornithorhynchus anatinus' division). + Ensembl ID ("Ornithorhynchus anatinus") - - beta12orEarlier true - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ornithorhynchus anatinus' division). - ENSOAN([EGTP])[0-9]{11} - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + ENSOCU([EGTP])[0-9]{11} + + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryctolagus cuniculus' division). + Ensembl ID ('Oryctolagus cuniculus') - - beta12orEarlier - ENSOCU([EGTP])[0-9]{11} true - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryctolagus cuniculus' division). - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + ENSORL([EGTP])[0-9]{11} + + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryzias latipes' division). + Ensembl ID ('Oryzias latipes') - - ENSORL([EGTP])[0-9]{11} true - beta12orEarlier - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryzias latipes' division). - beta12orEarlier - - - - Ensembl ID ('Otolemur garnettii') - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + ENSSAR([EGTP])[0-9]{11} + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Otolemur garnettii' division). + + Ensembl ID ('Otolemur garnettii') true - beta12orEarlier - ENSSAR([EGTP])[0-9]{11} - - - - Ensembl ID ('Pan troglodytes') - - beta12orEarlier - beta12orEarlier - ENSPTR([EGTP])[0-9]{11} + + + beta12orEarlier + beta12orEarlier + ENSPTR([EGTP])[0-9]{11} + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Pan troglodytes' division). + + Ensembl ID ('Pan troglodytes') true - - - + + + beta12orEarlier + beta12orEarlier + ENSRNO([EGTP])[0-9]{11} + + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Rattus norvegicus' division). + Ensembl ID ('Rattus norvegicus') - - beta12orEarlier true - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Rattus norvegicus' division). - ENSRNO([EGTP])[0-9]{11} - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + ENSSTO([EGTP])[0-9]{11} + + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Spermophilus tridecemlineatus' division). + Ensembl ID ('Spermophilus tridecemlineatus') - true - beta12orEarlier - ENSSTO([EGTP])[0-9]{11} - Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Spermophilus tridecemlineatus' division). - beta12orEarlier - - - - Ensembl ID ('Takifugu rubripes') - - beta12orEarlier - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + ENSFRU([EGTP])[0-9]{11} + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Takifugu rubripes' division). - ENSFRU([EGTP])[0-9]{11} + + Ensembl ID ('Takifugu rubripes') true - - - - Ensembl ID ('Tupaia belangeri') - - beta12orEarlier - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + ENSTBE([EGTP])[0-9]{11} + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Tupaia belangeri' division). + + Ensembl ID ('Tupaia belangeri') true - ENSTBE([EGTP])[0-9]{11} - - - - Ensembl ID ('Xenopus tropicalis') - + + + beta12orEarlier + beta12orEarlier + ENSXET([EGTP])[0-9]{11} + Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Xenopus tropicalis' division). - beta12orEarlier - beta12orEarlier + + Ensembl ID ('Xenopus tropicalis') true - ENSXET([EGTP])[0-9]{11} - - - - CATH identifier - - beta12orEarlier + + + beta12orEarlier Identifier of a protein domain (or other node) from the CATH database. - - - + + + + CATH identifier - - CATH node ID (family) - - beta12orEarlier + + + beta12orEarlier + 2.10.10.10 A code number identifying a family from the CATH database. - 2.10.10.10 - - - + + + + CATH node ID (family) - - Enzyme ID (CAZy) - + + + beta12orEarlier Identifier of an enzyme from the CAZy enzymes database. - beta12orEarlier CAZy ID - - - + + + + Enzyme ID (CAZy) - - Clone ID (IMAGE) - + + + beta12orEarlier + A unique identifier assigned by the I.M.A.G.E. consortium to a clone (cloned molecular sequence). I.M.A.G.E. cloneID IMAGE cloneID - A unique identifier assigned by the I.M.A.G.E. consortium to a clone (cloned molecular sequence). - beta12orEarlier - - - + + + + Clone ID (IMAGE) - - GO concept ID (cellular compartment) - - An identifier of a 'cellular compartment' concept from the Gene Ontology. - [0-9]{7}|GO:[0-9]{7} - beta12orEarlier + + + beta12orEarlier + [0-9]{7}|GO:[0-9]{7} + An identifier of a 'cellular component' concept from the Gene Ontology. GO concept identifier (cellular compartment) - - - + + + + GO concept ID (cellular component) - - Chromosome name (BioCyc) - + + + beta12orEarlier Name of a chromosome as used in the BioCyc database. - beta12orEarlier - - - + + + + Chromosome name (BioCyc) - - CleanEx entry name - - beta12orEarlier + + + beta12orEarlier An identifier of a gene expression profile from the CleanEx database. - - - + + + + CleanEx entry name - - CleanEx dataset code - - beta12orEarlier + + + beta12orEarlier An identifier of (typically a list of) gene expression experiments catalogued in the CleanEx database. - - - + + + + CleanEx dataset code - - Genome report - + + + beta12orEarlier An informative report of general information concerning a genome as a whole. - beta12orEarlier - - + + + Genome report - - Protein ID (CORUM) - - beta12orEarlier - CORUM complex ID + + + beta12orEarlier Unique identifier for a protein complex from the CORUM database. - - - + CORUM complex ID + + + + Protein ID (CORUM) - - CDD PSSM-ID - - beta12orEarlier + + + beta12orEarlier Unique identifier of a position-specific scoring matrix from the CDD database. - - - + + + + CDD PSSM-ID - - Protein ID (CuticleDB) - - CuticleDB ID - beta12orEarlier + + + beta12orEarlier Unique identifier for a protein from the CuticleDB database. - - - + CuticleDB ID + + + + Protein ID (CuticleDB) - - DBD ID - + + + beta12orEarlier Identifier of a predicted transcription factor from the DBD database. - beta12orEarlier - - - + + + + DBD ID - - Oligonucleotide probe annotation - + + - - + + - beta12orEarlier - General annotation on an oligonucleotide probe. - - + beta12orEarlier + General annotation on an oligonucleotide probe, or a set of probes. + Oligonucleotide probe sets annotation + + + Oligonucleotide probe annotation - - Oligonucleotide ID - - + + + + beta12orEarlier Identifier of an oligonucleotide from a database. - beta12orEarlier - - - + + + + Oligonucleotide ID - - dbProbe ID - + + + beta12orEarlier Identifier of an oligonucleotide probe from the dbProbe database. - beta12orEarlier - - - + + + + dbProbe ID - - Dinucleotide property - - beta12orEarlier + + + beta12orEarlier Physicochemical property data for one or more dinucleotides. - - + + + Dinucleotide property - - DiProDB ID - - beta12orEarlier + + + beta12orEarlier Identifier of an dinucleotide property from the DiProDB database. - - - + + + + DiProDB ID - + + + beta12orEarlier + 1.8 + disordered structure in a protein. + + Protein features report (disordered structure) - - 1.8 true - beta12orEarlier - Topic concerning disordered structure in a protein. - - - - Protein ID (DisProt) - - DisProt ID - beta12orEarlier + + + beta12orEarlier Unique identifier for a protein from the DisProt database. - - - + DisProt ID + + + + Protein ID (DisProt) - - Embryo report - + + + beta12orEarlier + 1.5 + Annotation on an embryo or concerning embryological development. + + Embryo report true - Embryo annotation - beta12orEarlier - 1.5 - - - - Ensembl transcript ID - - - beta12orEarlier - Transcript ID (Ensembl) + + + + beta12orEarlier Unique identifier for a gene transcript from the Ensembl database. - - - + Transcript ID (Ensembl) + + + + Ensembl transcript ID - - Inhibitor annotation - - 1.4 - beta12orEarlier + + + beta12orEarlier + 1.4 + An informative report on one or more small molecules that are enzyme inhibitors. + + Inhibitor annotation true - - - - Promoter ID - - - beta12orEarlier - An identifier of a promoter of a gene that is catalogued in a database. + + + + beta12orEarlier Moby:GeneAccessionList - - - + An identifier of a promoter of a gene that is catalogued in a database. + + + + Promoter ID - - EST accession - + + + beta12orEarlier Identifier of an EST sequence. - beta12orEarlier - - - + + + + EST accession - - COGEME EST ID - - beta12orEarlier + + + beta12orEarlier Identifier of an EST sequence from the COGEME database. - - - + + + + COGEME EST ID - - COGEME unisequence ID - + + + beta12orEarlier Identifier of a unisequence from the COGEME database. + + + A unisequence is a single sequence assembled from ESTs. - beta12orEarlier - - - + COGEME unisequence ID - - Protein family ID (GeneFarm) - - GeneFarm family ID - beta12orEarlier + + + beta12orEarlier Accession number of an entry (family) from the TIGRFam database. - - - + GeneFarm family ID + + + + Protein family ID (GeneFarm) - - Family name - - beta12orEarlier + + + beta12orEarlier The name of a family of organism. - - - + + + + Family name - + + + beta12orEarlier + beta13 + + The name of a genus of viruses. + Genus name (virus) - true - The name of a genus of viruses. - beta13 - beta12orEarlier - - - - Family name (virus) - - beta13 + + + beta12orEarlier + beta13 + The name of a family of viruses. + + Family name (virus) true - beta12orEarlier - - - + + + beta12orEarlier + beta13 + + The name of a SwissRegulon database. + Database name (SwissRegulon) - true - beta13 - The name of a SwissRegulon database. - beta12orEarlier - - - - Sequence feature ID (SwissRegulon) - - beta12orEarlier + + + beta12orEarlier A feature identifier as used in the SwissRegulon database. + + + This can be name of a gene, the ID of a TFBS, or genomic coordinates in form "chr:start..end". - - - + Sequence feature ID (SwissRegulon) - - FIG ID - - A FIG ID consists of four parts: a prefix, genome id, locus type and id number. + + + beta12orEarlier A unique identifier of gene in the NMPDR database. - beta12orEarlier - - - + + + + A FIG ID consists of four parts: a prefix, genome id, locus type and id number. + FIG ID - - Gene ID (Xenbase) - + + + beta12orEarlier A unique identifier of gene in the Xenbase database. - beta12orEarlier - - - + + + + Gene ID (Xenbase) - - Gene ID (Genolist) - - beta12orEarlier + + + beta12orEarlier A unique identifier of gene in the Genolist database. - - - + + + + Gene ID (Genolist) - + + + beta12orEarlier + 1.3 + + Name of an entry (gene) from the Genolist genes database. + Genolist gene name + Gene name (Genolist) - - beta12orEarlier true - Genolist gene name - 1.3 - Name of an entry (gene) from the Genolist genes database. - - - - ABS ID - - ABS identifier - beta12orEarlier + + + beta12orEarlier Identifier of an entry (promoter) from the ABS database. - - - + ABS identifier + + + + ABS ID - - AraC-XylS ID - + + + beta12orEarlier Identifier of a transcription factor from the AraC-XylS database. - beta12orEarlier - - - + + + + AraC-XylS ID - + + + beta12orEarlier + beta12orEarlier + + Name of an entry (gene) from the HUGO database. + Gene name (HUGO) - - beta12orEarlier - beta12orEarlier true - Name of an entry (gene) from the HUGO database. - - - - Locus ID (PseudoCAP) - - beta12orEarlier + + + beta12orEarlier Identifier of a locus from the PseudoCAP database. - - - + + + + Locus ID (PseudoCAP) - - Locus ID (UTR) - - beta12orEarlier + + + beta12orEarlier Identifier of a locus from the UTR database. - - - + + + + Locus ID (UTR) - - MonosaccharideDB ID - + + + beta12orEarlier Unique identifier of a monosaccharide from the MonosaccharideDB database. - beta12orEarlier - - - + + + + MonosaccharideDB ID - + + + beta12orEarlier + beta13 + + The name of a subdivision of the Collagen Mutation Database (CMD) database. + Database name (CMD) - - beta12orEarlier true - The name of a subdivision of the Collagen Mutation Database (CMD) database. - beta13 - - - + + + beta12orEarlier + beta13 + + The name of a subdivision of the Osteogenesis database. + Database name (Osteogenesis) - - beta12orEarlier true - beta13 - The name of a subdivision of the Osteogenesis database. - - - - Genome identifier - + + + beta12orEarlier An identifier of a particular genome. - beta12orEarlier - - - + + + + Genome identifier - - GenomeReviews ID - - beta12orEarlier + + + beta12orEarlier An identifier of a particular genome. - - - + + + + GenomeReviews ID - - GlycoMap ID - - [0-9]+ - beta12orEarlier + + + beta12orEarlier + [0-9]+ Identifier of an entry from the GlycosciencesDB database. - - - + + + + GlycoMap ID - - Carbohydrate conformational map - - beta12orEarlier + + + beta12orEarlier A conformational energy map of the glycosidic linkages in a carbohydrate molecule. - - + + + Carbohydrate conformational map - + + + beta12orEarlier + 1.8 + introns in a nucleotide sequences. + + Gene features report (intron) - - Topic concerning introns in a nucleotide sequences. true - beta12orEarlier - 1.8 - - - - Transcription factor name - - + + + + beta12orEarlier The name of a transcription factor. - beta12orEarlier - - - + + + + Transcription factor name - - TCID - + + + beta12orEarlier Identifier of a membrane transport proteins from the transport classification database (TCDB). - beta12orEarlier - - - + + + + TCID - - Pfam domain name - - beta12orEarlier + + + beta12orEarlier + PF[0-9]{5} Name of a domain from the Pfam database. - PF[0-9]{5} - - - + + + + Pfam domain name - - Pfam clan ID - - beta12orEarlier - CL[0-9]{4} + + + beta12orEarlier + CL[0-9]{4} Accession number of a Pfam clan. - - - + + + + Pfam clan ID - - Gene ID (VectorBase) - - VectorBase ID - beta12orEarlier + + + beta12orEarlier Identifier for a gene from the VectorBase database. - - - + VectorBase ID + + + + Gene ID (VectorBase) - - UTRSite ID - + + + beta12orEarlier Identifier of an entry from the UTRSite database of regulatory motifs in eukaryotic UTRs. - beta12orEarlier - - - + + + + UTRSite ID - - Sequence signature report - + + - - + + + beta12orEarlier + An informative report about a specific or conserved pattern in a molecular sequence, such as its context in genes or proteins, its role, origin or method of construction, etc. Sequence motif report Sequence profile report - An informative report about a specific or conserved pattern in a molecular sequence, such as its context in genes or proteins, its role, origin or method of construction, etc. - beta12orEarlier - - + + + Sequence signature report - - Locus annotation - + + + beta12orEarlier + beta12orEarlier + + An informative report on a particular locus. Locus report + + Locus annotation true - beta12orEarlier - An informative report on a particular locus. - beta12orEarlier - - - - Protein name (UniProt) - + + + beta12orEarlier Official name of a protein as used in the UniProt database. - beta12orEarlier - - - + + + + Protein name (UniProt) - - Term ID list - + + + beta12orEarlier + 1.5 + One or more terms from one or more controlled vocabularies which are annotations on an entity. - beta12orEarlier - true + The concepts are typically provided as a persistent identifier or some other link the source ontologies. Evidence of the validity of the annotation might be included. - 1.5 - - + Term ID list + true - - HAMAP ID - + + + beta12orEarlier Name of a protein family from the HAMAP database. - beta12orEarlier - - - + + + + HAMAP ID - - Identifier with metadata - + + + beta12orEarlier + 1.12 + Basic information concerning an identifier of data (typically including the identifier itself). For example, a gene symbol with information concerning its provenance. - beta12orEarlier - - + + Identifier with metadata + true - + + + beta12orEarlier + beta12orEarlier + + Annotation about a gene symbol. + Gene symbol annotation - true - beta12orEarlier - Annotation about a gene symbol. - beta12orEarlier - - - - Transcript ID - - + + + - - + + + beta12orEarlier Identifier of a RNA transcript. - beta12orEarlier - - - + + + + Transcript ID - - HIT ID - + + + beta12orEarlier Identifier of an RNA transcript from the H-InvDB database. - beta12orEarlier - - - + + + + HIT ID - - HIX ID - + + + beta12orEarlier A unique identifier of gene cluster in the H-InvDB database. - beta12orEarlier - - - + + + + HIX ID - - HPA antibody id - - beta12orEarlier + + + beta12orEarlier Identifier of a antibody from the HPA database. - - - + + + + HPA antibody id - - IMGT/HLA ID - + + + beta12orEarlier Identifier of a human major histocompatibility complex (HLA) or other protein from the IMGT/HLA database. - beta12orEarlier - - - + + + + IMGT/HLA ID - - Gene ID (JCVI) - + + + beta12orEarlier A unique identifier of gene assigned by the J. Craig Venter Institute (JCVI). - beta12orEarlier - - - + + + + Gene ID (JCVI) - - Kinase name - - beta12orEarlier + + + beta12orEarlier The name of a kinase protein. - - - + + + + Kinase name - - ConsensusPathDB entity ID - - + + + + beta12orEarlier Identifier of a physical entity from the ConsensusPathDB database. - beta12orEarlier - - - + + + + ConsensusPathDB entity ID - - ConsensusPathDB entity name - - - beta12orEarlier + + + + beta12orEarlier Name of a physical entity from the ConsensusPathDB database. - - - + + + + ConsensusPathDB entity name - - CCAP strain number - + + + beta12orEarlier The number of a strain of algae and protozoa from the CCAP database. - beta12orEarlier - - - + + + + CCAP strain number - - Stock number - - - beta12orEarlier + + + + beta12orEarlier An identifier of stock from a catalogue of biological resources. - - - + + + + Stock number - - Stock number (TAIR) - - beta12orEarlier + + + beta12orEarlier A stock number from The Arabidopsis information resource (TAIR). - - - + + + + Stock number (TAIR) - - REDIdb ID - - beta12orEarlier + + + beta12orEarlier Identifier of an entry from the RNA editing database (REDIdb). - - - + + + + REDIdb ID - - SMART domain name - + + + beta12orEarlier Name of a domain from the SMART database. - beta12orEarlier - - - + + + + SMART domain name - - Protein family ID (PANTHER) - - beta12orEarlier - Panther family ID + + + beta12orEarlier Accession number of an entry (family) from the PANTHER database. - - - + Panther family ID + + + + Protein family ID (PANTHER) - - RNAVirusDB ID - - beta12orEarlier - Could list (or reference) other taxa here from https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary. + + + beta12orEarlier A unique identifier for a virus from the RNAVirusDB database. - - - + + + + Could list (or reference) other taxa here from https://www.phenoscape.org/wiki/Taxonomic_Rank_Vocabulary. + RNAVirusDB ID - - Virus ID - - - beta12orEarlier + + + + beta12orEarlier An accession of annotation on a (group of) viruses (catalogued in a database). - - - + + + + Virus ID - - NCBI Genome Project ID - + + + beta12orEarlier An identifier of a genome project assigned by NCBI. - beta12orEarlier - - - + + + + NCBI Genome Project ID - - NCBI genome accession - + + + beta12orEarlier A unique identifier of a whole genome assigned by the NCBI. - beta12orEarlier - - - + + + + NCBI genome accession - - Sequence profile data - - 1.8 + + + beta12orEarlier + 1.8 Data concerning, extracted from, or derived from the analysis of a sequence profile, such as its name, length, technical details about the profile or it's construction, the biological role or annotation, and so on. + + + Sequence profile data true - beta12orEarlier - - - - Protein ID (TopDB) - - beta12orEarlier - TopDB ID + + + beta12orEarlier Unique identifier for a membrane protein from the TopDB database. - - - + TopDB ID + + + + Protein ID (TopDB) - - Gel ID - - Gel identifier + + + beta12orEarlier Identifier of a two-dimensional (protein) gel. - beta12orEarlier - - - + Gel identifier + + + + Gel ID - - Reference map name (SWISS-2DPAGE) - - - beta12orEarlier + + + + beta12orEarlier Name of a reference map gel from the SWISS-2DPAGE database. - - - + + + + Reference map name (SWISS-2DPAGE) - - Protein ID (PeroxiBase) - - PeroxiBase ID - beta12orEarlier + + + beta12orEarlier Unique identifier for a peroxidase protein from the PeroxiBase database. - - - + PeroxiBase ID + + + + Protein ID (PeroxiBase) - - SISYPHUS ID - - beta12orEarlier + + + beta12orEarlier Identifier of an entry from the SISYPHUS database of tertiary structure alignments. - - - + + + + SISYPHUS ID - - ORF ID - - - beta12orEarlier + + + + beta12orEarlier Accession of an open reading frame (catalogued in a database). - - - + + + + ORF ID - - ORF identifier - + + + beta12orEarlier An identifier of an open reading frame. - beta12orEarlier - - - + + + + ORF identifier - - Linucs ID - + + + beta12orEarlier Identifier of an entry from the GlycosciencesDB database. - beta12orEarlier - - - + + + + Linucs ID - - Protein ID (LGICdb) - - beta12orEarlier - LGICdb ID + + + beta12orEarlier Unique identifier for a ligand-gated ion channel protein from the LGICdb database. - - - + LGICdb ID + + + + Protein ID (LGICdb) - - MaizeDB ID - - beta12orEarlier + + + beta12orEarlier Identifier of an EST sequence from the MaizeDB database. - - - + + + + MaizeDB ID - - Gene ID (MfunGD) - - beta12orEarlier + + + beta12orEarlier A unique identifier of gene in the MfunGD database. - - - + + + + Gene ID (MfunGD) - - Orpha number - + + - - + + - beta12orEarlier + beta12orEarlier An identifier of a disease from the Orpha database. - - - + + + + Orpha number - - Protein ID (EcID) - - beta12orEarlier + + + beta12orEarlier Unique identifier for a protein from the EcID database. - - - + + + + Protein ID (EcID) - - Clone ID (RefSeq) - - + + + + beta12orEarlier A unique identifier of a cDNA molecule catalogued in the RefSeq database. - beta12orEarlier - - - + + + + Clone ID (RefSeq) - - Protein ID (ConoServer) - - beta12orEarlier + + + beta12orEarlier Unique identifier for a cone snail toxin protein from the ConoServer database. - - - + + + + Protein ID (ConoServer) - - GeneSNP ID - + + + beta12orEarlier Identifier of a GeneSNP database entry. - beta12orEarlier - - - + + + + GeneSNP ID - - Lipid identifier - + + - - + + - - + + + beta12orEarlier Identifier of a lipid. - beta12orEarlier - - - + + + + Lipid identifier - + + + beta12orEarlier + beta12orEarlier + A flat-file (textual) data archive. + + Databank - true - beta12orEarlier - A flat-file (textual) data archive. - beta12orEarlier - - - Web portal - + + + beta12orEarlier + beta12orEarlier A web site providing data (web pages) on a common theme to a HTTP client. - beta12orEarlier + + + Web portal true - beta12orEarlier - - - Gene ID (VBASE2) - + + + beta12orEarlier Identifier for a gene from the VBASE2 database. - beta12orEarlier VBASE2 ID - - - + + + + Gene ID (VBASE2) - - DPVweb ID - - DPVweb virus ID - beta12orEarlier + + + beta12orEarlier A unique identifier for a virus from the DPVweb database. - - - + DPVweb virus ID + + + + DPVweb ID - - Pathway ID (BioSystems) - - beta12orEarlier + + + beta12orEarlier + [0-9]+ Identifier of a pathway from the BioSystems pathway database. - [0-9]+ - - - + + + + Pathway ID (BioSystems) - + + + beta12orEarlier + beta12orEarlier + + Data concerning a proteomics experiment. + Experimental data (proteomics) - true - Data concerning a proteomics experiment. - beta12orEarlier - beta12orEarlier - - - - Abstract - - beta12orEarlier + + + beta12orEarlier An abstract of a scientific article. - - + + + Abstract - - Lipid structure - - beta12orEarlier + + + beta12orEarlier 3D coordinate and associated data for a lipid structure. - - + + + Lipid structure - - Drug structure - - beta12orEarlier + + + beta12orEarlier 3D coordinate and associated data for the (3D) structure of a drug. - - + + + Drug structure - - Toxin structure - + + + beta12orEarlier 3D coordinate and associated data for the (3D) structure of a toxin. - beta12orEarlier - - + + + Toxin structure - - Position-specific scoring matrix - - - beta12orEarlier - PSSM + + + + beta12orEarlier A simple matrix of numbers, where each value (or column of values) is derived derived from analysis of the corresponding position in a sequence alignment. - - + PSSM + + + Position-specific scoring matrix - - Distance matrix - + + + beta12orEarlier A matrix of distances between molecular entities, where a value (distance) is (typically) derived from comparison of two entities and reflects their similarity. - beta12orEarlier - - + + + Distance matrix - - Structural distance matrix - + + + beta12orEarlier Distances (values representing similarity) between a group of molecular structures. - beta12orEarlier - - + + + Structural distance matrix - + + + beta12orEarlier + 1.5 + + Bibliographic data concerning scientific article(s). + Article metadata - true - beta12orEarlier - Bibliographic data concerning scientific article(s). - 1.5 - - - - Ontology concept - - beta12orEarlier - This includes any fields from the concept definition such as concept name, definition, comments and so on. + + + beta12orEarlier A concept from a biological ontology. - - + + + This includes any fields from the concept definition such as concept name, definition, comments and so on. + Ontology concept - - Codon usage bias - + + + beta12orEarlier A numerical measure of differences in the frequency of occurrence of synonymous codons in DNA sequences. - beta12orEarlier - - + + + Codon usage bias - + + + beta12orEarlier + 1.8 + Northern Blot experiments. + + Northern blot report - - Topic concerning Northern Blot experiments. true - beta12orEarlier - 1.8 - - - + + + beta12orEarlier + 1.8 + variable number of tandem repeat (VNTR) polymorphism in a DNA sequence. + + Nucleic acid features report (VNTR) - - 1.8 - beta12orEarlier true - Topic concerning variable number of tandem repeat (VNTR) polymorphism in a DNA sequence. - - - + + + beta12orEarlier + 1.8 + + microsatellite polymorphism in a DNA sequence. + + Nucleic acid features report (microsatellite) - true - Topic concerning microsatellite polymorphism in a DNA sequence. - 1.8 - beta12orEarlier - - - - + + + beta12orEarlier + 1.8 + restriction fragment length polymorphisms (RFLP) in a DNA sequence. + + Nucleic acid features report (RFLP) - - beta12orEarlier true - 1.8 - Topic concerning restriction fragment length polymorphisms (RFLP) in a DNA sequence. - - - - Radiation hybrid map - - The radiation method can break very closely linked markers providing a more detailed map. Most genetic markers and subsequences may be located to a defined map position and with a more precise estimates of distance than a linkage map. + + + beta12orEarlier A map showing distance between genetic markers estimated by radiation-induced breaks in a chromosome. - beta12orEarlier RH map - - + + + The radiation method can break very closely linked markers providing a more detailed map. Most genetic markers and subsequences may be located to a defined map position and with a more precise estimates of distance than a linkage map. + Radiation hybrid map - - ID list - + + + beta12orEarlier A simple list of data identifiers (such as database accessions), possibly with additional basic information on the addressed data. - beta12orEarlier - - + + + ID list - - Phylogenetic gene frequencies data - - beta12orEarlier + + + beta12orEarlier Gene frequencies data that may be read during phylogenetic tree calculation. - - + + + Phylogenetic gene frequencies data - + + + beta12orEarlier + beta13 + + A set of sub-sequences displaying some type of polymorphism, typically indicating the sequence in which they occur, their position and other metadata. + Sequence set (polymorphic) - - beta13 - beta12orEarlier true - A set of sub-sequences displaying some type of polymorphism, typically indicating the sequence in which they occur, their position and other metadata. - - - - DRCAT resource - - 1.5 + + + beta12orEarlier + 1.5 + An entry (resource) from the DRCAT bioinformatics resource catalogue. - beta12orEarlier + + DRCAT resource true - - - - Protein complex - - beta12orEarlier + + + beta12orEarlier 3D coordinate and associated data for a multi-protein complex; two or more polypeptides chains in a stable, functional association with one another. - - + + + Protein complex - - Protein structural motif - - beta12orEarlier + + + beta12orEarlier 3D coordinate and associated data for a protein (3D) structural motif; any group of contiguous or non-contiguous amino acid residues but typically those forming a feature with a structural or functional role. - - + + + Protein structural motif - - Lipid report - - beta12orEarlier + + + beta12orEarlier Annotation on or information derived from one or more specific lipid 3D structure(s). - - + + + Lipid report - - Secondary structure image - - 1.4 - beta12orEarlier + + + beta12orEarlier + 1.4 + Image of one or more molecular secondary structures. + + Secondary structure image true - - - + + + beta12orEarlier + 1.5 + + An informative report on general information, properties or features of one or more molecular secondary structures. + Secondary structure report - - Secondary structure-derived report - beta12orEarlier true - An informative report on general information, properties or features of one or more molecular secondary structures. - 1.5 - - - - DNA features - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + DNA sequence-specific feature annotation (not in a feature table). + + DNA features true - beta12orEarlier - - - + + + beta12orEarlier + 1.5 + + Features concerning RNA or regions of DNA that encode an RNA molecule. + RNA features report - true - beta12orEarlier - 1.5 - Features concerning RNA or regions of DNA that encode an RNA molecule. - RNA features - Nucleic acid features (RNA features) - - - - Plot - - beta12orEarlier - true - beta12orEarlier + + + beta12orEarlier Biological data that has been plotted as a graph of some type. - - + + + Plot - + + + beta12orEarlier + DNA polymorphism. + + Nucleic acid features report (polymorphism) - true - Topic concerning DNA polymorphism. - beta12orEarlier - - - - Protein sequence record - - + + + + beta12orEarlier A protein sequence and associated metadata. - beta12orEarlier - Protein sequence record Sequence record (protein) - - + + + Protein sequence record - - Nucleic acid sequence record - - - RNA sequence record - Nucleotide sequence record + + + + beta12orEarlier A nucleic acid sequence and associated metadata. - beta12orEarlier - DNA sequence record + Nucleotide sequence record Sequence record (nucleic acid) - - + DNA sequence record + RNA sequence record + + + Nucleic acid sequence record - - Protein sequence record (full) - + + + beta12orEarlier + 1.8 A protein sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database. - 1.8 - beta12orEarlier + + + Protein sequence record (full) true - - - + + + beta12orEarlier + 1.8 + A nucleic acid sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database. + + Nucleic acid sequence record (full) - true - A nucleic acid sequence and comprehensive metadata (such as a feature table), typically corresponding to a full entry from a molecular sequence database. - beta12orEarlier - 1.8 - - - - Biological model accession - - - beta12orEarlier + + + + beta12orEarlier Accession of a mathematical model, typically an entry from a database. - - - + + + + Biological model accession - - Cell type name - - + + + + beta12orEarlier The name of a type or group of cells. - beta12orEarlier - - - + + + + Cell type name - - Cell type accession - - - beta12orEarlier + + + + beta12orEarlier Accession of a type or group of cells (catalogued in a database). - - - + Cell type ID + + + + Cell type accession - - Compound accession - - - Small molecule accession + + + + beta12orEarlier Accession of an entry from a database of chemicals. - beta12orEarlier Chemical compound accession - - - + Small molecule accession + + + + Compound accession - - Drug accession - - + + + + beta12orEarlier Accession of a drug. - beta12orEarlier - - - + + + + Drug accession - - Toxin name - - + + + + beta12orEarlier Name of a toxin. - beta12orEarlier - - - + + + + Toxin name - - Toxin accession - - - beta12orEarlier + + + + beta12orEarlier Accession of a toxin (catalogued in a database). - - - + + + + Toxin accession - - Monosaccharide accession - - + + + + beta12orEarlier Accession of a monosaccharide (catalogued in a database). - beta12orEarlier - - - + + + + Monosaccharide accession - - Drug name - - - beta12orEarlier + + + + beta12orEarlier Common name of a drug. - - - + + + + Drug name - - Carbohydrate accession - - + + + + beta12orEarlier Accession of an entry from a database of carbohydrates. - beta12orEarlier - - - + + + + Carbohydrate accession - - Molecule accession - - + + + + beta12orEarlier Accession of a specific molecule (catalogued in a database). - beta12orEarlier - - - + + + + Molecule accession - - Data resource definition accession - - - beta12orEarlier + + + + beta12orEarlier Accession of a data definition (catalogued in a database). - - - + + + + Data resource definition accession - - Genome accession - - + + + + beta12orEarlier An accession of a particular genome (in a database). - beta12orEarlier - - - + + + + Genome accession - - Map accession - - + + + + beta12orEarlier An accession of a map of a molecular sequence (deposited in a database). - beta12orEarlier - - - + + + + Map accession - - Lipid accession - - - beta12orEarlier + + + + beta12orEarlier Accession of an entry from a database of lipids. - - - + + + + Lipid accession - - Peptide ID - - - beta12orEarlier + + + + beta12orEarlier Accession of a peptide deposited in a database. - - - + + + + Peptide ID - - Protein accession - - - Protein accessions - beta12orEarlier + + + + beta12orEarlier Accession of a protein deposited in a database. - - - + Protein accessions + + + + Protein accession - - Organism accession - - + + + + beta12orEarlier An accession of annotation on a (group of) organisms (catalogued in a database). - beta12orEarlier - - - + + + + Organism accession - - Organism name - - - Moby:Organism_Name - Moby:OrganismsShortName - Moby:OccurrenceRecord + + + + beta12orEarlier Moby:BriefOccurrenceRecord Moby:FirstEpithet Moby:InfraspecificEpithet - beta12orEarlier + Moby:OccurrenceRecord + Moby:Organism_Name Moby:OrganismsLongName + Moby:OrganismsShortName The name of an organism (or group of organisms). - - - + + + + Organism name - - Protein family accession - - - beta12orEarlier + + + + beta12orEarlier Accession of a protein family (that is deposited in a database). - - - + + + + Protein family accession - - Transcription factor accession - - - - beta12orEarlier + + + + + beta12orEarlier Accession of an entry from a database of transcription factors or binding sites. - - - + + + + Transcription factor accession - - Strain accession - - + + + - - + + - beta12orEarlier + beta12orEarlier Identifier of a strain of an organism variant, typically a plant, virus or bacterium. - - - + + + + Strain accession - - Virus identifier - + + + beta12orEarlier An accession of annotation on a (group of) viruses (catalogued in a database). - beta12orEarlier - - - + + + + Virus identifier - - Sequence features metadata - - beta12orEarlier + + + beta12orEarlier Metadata on sequence features. - - + + + Sequence features metadata - - Gramene identifier - - beta12orEarlier + + + beta12orEarlier Identifier of a Gramene database entry. - - - + + + + Gramene identifier - - DDBJ accession - - beta12orEarlier + + + beta12orEarlier + An identifier of an entry from the DDBJ sequence database. + DDBJ ID DDBJ accession number DDBJ identifier - DDBJ ID - An identifier of an entry from the DDBJ sequence database. - - - + + + + DDBJ accession - - ConsensusPathDB identifier - - beta12orEarlier + + + beta12orEarlier An identifier of an entity from the ConsensusPathDB database. - - - + + + + ConsensusPathDB identifier - - Sequence data - + + + beta12orEarlier + 1.8 + + Data concerning, extracted from, or derived from the analysis of molecular sequence(s). + This is a broad data type and is used a placeholder for other, more specific types. - 1.8 - beta12orEarlier + Sequence data true - Data concerning, extracted from, or derived from the analysis of molecular sequence(s). - - - - Codon usage - - beta12orEarlier - true - beta13 + + + beta12orEarlier + beta13 + Data concerning codon usage. + This is a broad data type and is used a placeholder for other, more specific types. - - + Codon usage + true - - Article report - - beta12orEarlier - 1.5 + + + beta12orEarlier + 1.5 + + Data derived from the analysis of a scientific text such as a full text article from a scientific journal. + + Article report true - - - - Sequence report - + + + beta12orEarlier An informative report of information about molecular sequence(s), including basic information (metadata), and reports generated from molecular sequence analysis, including positional features and non-positional properties. - beta12orEarlier Sequence-derived report - - + + + Sequence report - - Protein secondary structure report - + + + beta12orEarlier An informative report about the properties or features of one or more protein secondary structures. - beta12orEarlier - - + + + Protein secondary structure report - - Hopp and Woods plot - - + + + + beta12orEarlier A Hopp and Woods plot of predicted antigenicity of a peptide or protein. - beta12orEarlier - - + + + Hopp and Woods plot - - Nucleic acid melting curve - - - Shows the proportion of nucleic acid which are double-stranded versus temperature. + + + + beta12orEarlier A melting curve of a double-stranded nucleic acid molecule (DNA or DNA/RNA). - beta12orEarlier - - + + + Shows the proportion of nucleic acid which are double-stranded versus temperature. + Nucleic acid melting curve - - Nucleic acid probability profile - + + + beta12orEarlier A probability profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA). - beta12orEarlier + + Shows the probability of a base pair not being melted (i.e. remaining as double-stranded DNA) at a specified temperature - - + Nucleic acid probability profile - - Nucleic acid temperature profile - + + + beta12orEarlier A temperature profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA). - Plots melting temperature versus base position. - beta12orEarlier Melting map - - + + + Plots melting temperature versus base position. + Nucleic acid temperature profile - - Gene regulatory network report - - 1.8 + + + beta12orEarlier + 1.8 A report typically including a map (diagram) of a gene regulatory network. + + + Gene regulatory network report true - beta12orEarlier - - - - 2D PAGE gel report - + + + beta12orEarlier + 1.8 An informative report on a two-dimensional (2D PAGE) gel. - 2D PAGE image report - 1.8 + + + 2D PAGE gel report true - 2D PAGE gel annotation - beta12orEarlier - 2D PAGE image annotation - - - - Oligonucleotide probe sets annotation - - beta12orEarlier + + + beta12orEarlier + 1.14 General annotation on a set of oligonucleotide probes, such as the gene name with which the probe set is associated and which probes belong to the set. - - + + + Oligonucleotide probe sets annotation + true - - Microarray image - - 1.5 - beta12orEarlier - Gene expression image + + + beta12orEarlier + 1.5 + An image from a microarray experiment which (typically) allows a visualisation of probe hybridisation and gene-expression data. + + Microarray image true - - - - Image + + + + beta12orEarlier + Biological or biomedical data has been rendered into an image, typically for display on screen. + Image data + + Image - - http://semanticscience.org/resource/SIO_000081 + Image http://semanticscience.org/resource/SIO_000079 - Image data - beta12orEarlier - Biological or biomedical data that may be rendered, for example displayed on screen or plotted on a graph of some type. - - + http://semanticscience.org/resource/SIO_000081 - - Sequence image - - + + + + beta12orEarlier Image of a molecular sequence, possibly with sequence features or properties shown. - beta12orEarlier - - + + + Sequence image - - Protein hydropathy data - - Protein hydropathy report + + + beta12orEarlier A report on protein properties concerning hydropathy. - beta12orEarlier - - + Protein hydropathy report + + + Protein hydropathy data - - Workflow data - - beta12orEarlier - beta13 + + + beta12orEarlier + beta13 + Data concerning a computational workflow. + + Workflow data true - - - + + + beta12orEarlier + 1.5 + + A computational workflow. + Workflow - true - beta12orEarlier - 1.5 - A computational workflow. - - - + + + beta12orEarlier + beta13 + + Data concerning molecular secondary structure data. + Secondary structure data - - beta13 true - beta12orEarlier - Data concerning molecular secondary structure data. - - - - Protein sequence (raw) - - + + + + beta12orEarlier + A raw protein sequence (string of characters). Raw protein sequence - beta12orEarlier Raw sequence (protein) - A raw protein sequence (string of characters). - - + + + Protein sequence (raw) - - Nucleic acid sequence (raw) - - + + + + beta12orEarlier + A raw nucleic acid sequence. Nucleic acid raw sequence - beta12orEarlier Nucleotide sequence (raw) Raw sequence (nucleic acid) - A raw nucleic acid sequence. - - + + + Nucleic acid sequence (raw) - - Protein sequence - + + + beta12orEarlier One or more protein sequences, possibly with associated annotation. Protein sequences - beta12orEarlier + + + Protein sequence http://purl.org/biotop/biotop.owl#AminoAcidSequenceInformation - - - - Nucleic acid sequence - + + + beta12orEarlier One or more nucleic acid sequences, possibly with associated annotation. - beta12orEarlier - DNA sequence + Nucleic acid sequences Nucleotide sequence Nucleotide sequences - Nucleic acid sequences + DNA sequence + + + Nucleic acid sequence http://purl.org/biotop/biotop.owl#NucleotideSequenceInformation - - - - Reaction data - + + + beta12orEarlier + Data concerning a biochemical reaction, typically data and more general annotation on the kinetics of enzyme-catalysed reaction. Enzyme kinetics annotation - This is a broad data type and is used a placeholder for other, more specific types. - beta12orEarlier Reaction annotation - Data concerning a biochemical reaction, typically data and more general annotation on the kinetics of enzyme-catalysed reaction. - - + + + This is a broad data type and is used a placeholder for other, more specific types. + Reaction data - - Peptide property - - beta12orEarlier - Peptide data + + + beta12orEarlier Data concerning small peptides. - - + Peptide data + + + Peptide property - - Protein classification - - This is a broad data type and is used a placeholder for other, more specific types. - Protein classification data + + + beta12orEarlier + An informative report concerning the classification of protein sequences or structures. - beta12orEarlier - + This is a broad data type and is used a placeholder for other, more specific types. + Protein classification - - Sequence motif data - - true - 1.8 + + + beta12orEarlier + 1.8 Data concerning specific or conserved pattern in molecular sequences. - beta12orEarlier + + This is a broad data type and is used a placeholder for other, more specific types. - - + Sequence motif data + true - + + + beta12orEarlier + beta13 + + Data concerning models representing a (typically multiple) sequence alignment. + + This is a broad data type and is used a placeholder for other, more specific types. Sequence profile data - - beta12orEarlier true - This is a broad data type and is used a placeholder for other, more specific types. - beta13 - Data concerning models representing a (typically multiple) sequence alignment. - - - - Pathway or network data - + + + beta12orEarlier + beta13 + + Data concerning a specific biological pathway or network. - beta13 + + Pathway or network data true - beta12orEarlier - - - - - Pathway or network report - + + - - + + - beta12orEarlier + beta12orEarlier An informative report concerning or derived from the analysis of a biological pathway or network, such as a map (diagram) or annotation. - - + + + Pathway or network report - - Nucleic acid thermodynamic data - - Nucleic acid property (thermodynamic or kinetic) + + + beta12orEarlier A thermodynamic or kinetic property of a nucleic acid molecule. + Nucleic acid property (thermodynamic or kinetic) Nucleic acid thermodynamic property - beta12orEarlier - - + + + Nucleic acid thermodynamic data - - Nucleic acid classification - - This is a broad data type and is used a placeholder for other, more specific types. - beta12orEarlier + + + beta12orEarlier + Data concerning the classification of nucleic acid sequences or structures. - Nucleic acid classification data - + This is a broad data type and is used a placeholder for other, more specific types. + Nucleic acid classification - - Classification report - + + + beta12orEarlier + 1.5 + + A report on a classification of molecular sequences, structures or other entities. + This can include an entire classification, components such as classifiers, assignments of entities to a classification and so on. - beta12orEarlier + Classification report true - Classification data - A report on a classification of molecular sequences, structures or other entities. - 1.5 - - - + + + beta12orEarlier + 1.8 + key residues involved in protein folding. + + Protein features report (key folding sites) - - Topic concerning key residues involved in protein folding. - beta12orEarlier - 1.8 true - - - - Protein torsion angle data - + + + beta12orEarlier + Geometry data for a protein structure, for example bond lengths, bond angles, torsion angles, chiralities, planaraties etc. Torsion angle data - Torsion angle data for a protein structure. - beta12orEarlier - - + + + Protein geometry report - - Protein structure image - - + + + + beta12orEarlier An image of protein structure. - beta12orEarlier Structure image (protein) - - + + + Protein structure image - - Phylogenetic character weights - + + + beta12orEarlier Weights for sequence positions or characters in phylogenetic analysis where zero is defined as unweighted. - beta12orEarlier - - + + + Phylogenetic character weights - - Annotation track - - beta12orEarlier - Genomic track + + + beta12orEarlier Annotation of one particular positional feature on a biomolecular (typically genome) sequence, suitable for import and display in a genome browser. Genome annotation track - Genome-browser track Genome track + Genome-browser track + Genomic track Sequence annotation track - - + + + Annotation track - - UniProt accession - + + - - + + - UniProtKB accession number - beta12orEarlier - P43353|Q7M1G0|Q9C199|A5A6J6 + beta12orEarlier + P43353|Q7M1G0|Q9C199|A5A6J6 + [OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2} + Accession number of a UniProt (protein sequence) database entry. + UniProt accession number UniProt entry accession - [OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2} + UniProtKB accession + UniProtKB accession number Swiss-Prot entry accession TrEMBL entry accession - Accession number of a UniProt (protein sequence) database entry. - UniProtKB accession - UniProt accession number - - - + + + + UniProt accession - - NCBI genetic code ID - - + + + + beta12orEarlier + 16 + [1-9][0-9]? Identifier of a genetic code in the NCBI list of genetic codes. - [1-9][0-9]? - 16 - beta12orEarlier - - - + + + + NCBI genetic code ID - - Ontology concept identifier - + + - - + + + beta12orEarlier Identifier of a concept in an ontology of biological or bioinformatics concepts and relations. - beta12orEarlier - - - + + + + Ontology concept identifier - + + + beta12orEarlier + beta12orEarlier + + The name of a concept for a biological process from the GO ontology. + GO concept name (biological process) - true - The name of a concept for a biological process from the GO ontology. - beta12orEarlier - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + The name of a concept for a molecular function from the GO ontology. + GO concept name (molecular function) - true - beta12orEarlier - The name of a concept for a molecular function from the GO ontology. - beta12orEarlier - - - - Taxonomy - + + - - + + - This is a broad data type and is used a placeholder for other, more specific types. - beta12orEarlier + beta12orEarlier Data concerning the classification, identification and naming of organisms. Taxonomic data - - + + + This is a broad data type and is used a placeholder for other, more specific types. + Taxonomy - - Protein ID (EMBL/GenBank/DDBJ) - - beta13 + + + beta13 EMBL/GENBANK/DDBJ coding feature protein identifier, issued by International collaborators. + + + This qualifier consists of a stable ID portion (3+5 format with 3 position letters and 5 numbers) plus a version number after the decimal point. When the protein sequence encoded by the CDS changes, only the version number of the /protein_id value is incremented; the stable part of the /protein_id remains unchanged and as a result will permanently be associated with a given protein; this qualifier is valid only on CDS features which translate into a valid protein. - - - + Protein ID (EMBL/GenBank/DDBJ) - - Core data - - Core data entities typically have a format and may be identified by an accession number. + + + beta13 + 1.5 A type of data that (typically) corresponds to entries from the primary biological databases and which is (typically) the primary input or output of a tool, i.e. the data the tool processes or generates, as distinct from metadata and identifiers which describe and identify such core data, parameters that control the behaviour of tools, reports of derivative data generated by tools and annotation. - 1.5 + + + Core data entities typically have a format and may be identified by an accession number. + Core data true - beta13 - - - - Sequence feature identifier - + + - - + + - beta13 + beta13 Name or other identifier of molecular sequence feature(s). - - - + + + + Sequence feature identifier - - Structure identifier - + + - - + + - beta13 + beta13 An identifier of a molecular tertiary structure, typically an entry from a structure database. - - - + + + + Structure identifier - - Matrix identifier - + + - - + + + beta13 An identifier of an array of numerical values, such as a comparison matrix. - beta13 - - - + + + + Matrix identifier - + + + beta13 + 1.8 + A report (typically a table) on character or word composition / frequency of protein sequence(s). + + Protein sequence composition - - beta13 - 1.8 true - A report (typically a table) on character or word composition / frequency of protein sequence(s). - - - - Nucleic acid sequence composition (report) - - 1.8 + + + beta13 + 1.8 A report (typically a table) on character or word composition / frequency of nucleic acid sequence(s). + + + Nucleic acid sequence composition (report) true - beta13 - - - - Protein domain classification node - - beta13 + + + beta13 + 1.5 + A node from a classification of protein structural domain(s). + + Protein domain classification node true - 1.5 - - - - CAS number - - beta13 - CAS registry number + + + beta13 Unique numerical identifier of chemicals in the scientific literature, as assigned by the Chemical Abstracts Service. - - - + CAS registry number + + + + CAS number - - ATC code - + + + beta13 Unique identifier of a drug conforming to the Anatomical Therapeutic Chemical (ATC) Classification System, a drug classification system controlled by the WHO Collaborating Centre for Drug Statistics Methodology (WHOCC). - beta13 - - - + + + + ATC code - - UNII - - beta13 + + + beta13 A unique, unambiguous, alphanumeric identifier of a chemical substance as catalogued by the Substance Registration System of the Food and Drug Administration (FDA). Unique Ingredient Identifier - - - + + + + UNII - + + + beta13 + 1.5 + Basic information concerning geographical location or time. + Geotemporal metadata - - 1.5 - beta13 true - Basic information concerning geographical location or time. - - - - System metadata - + + + beta13 Metadata concerning the software, hardware or other aspects of a computer system. - beta13 - - + + + System metadata - - Sequence feature name - - + + + beta13 + 1.15 A name of a sequence feature, e.g. the name of a feature to be displayed to an end-user. - beta13 - - - + + + Sequence feature name + true - - Experimental measurement - - beta13 + + + beta13 Raw data such as measurements or other results from laboratory experiments, as generated from laboratory hardware. Experimental measurement data - Measurement - This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. - Measured data Experimentally measured data - Measurement metadata + Measured data + Measurement Measurement data + Measurement metadata Raw experimental data - - + + + This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. + Experimental measurement - - Raw microarray data - - - beta13 + + + + beta13 Raw data (typically MIAME-compliant) for hybridisations from a microarray experiment. + + Such data as found in Affymetrix CEL or GPR files. - - + Raw microarray data - - Processed microarray data - + + - - + + + beta13 Data generated from processing and analysis of probe set data from a microarray experiment. Gene annotation (expression) - Microarray probe set data - beta13 Gene expression report + Microarray probe set data + + Such data as found in Affymetrix .CHP files or data from other software such as RMA or dChip. - - + Processed microarray data - - Gene expression matrix - - - This combines data from all hybridisations. - beta13 - Normalised microarray data + + + + beta13 The final processed (normalised) data for a set of hybridisations in a microarray experiment. Gene expression data matrix - - + Normalised microarray data + + + This combines data from all hybridisations. + Gene expression matrix - - Sample annotation - + + + beta13 Annotation on a biological sample, for example experimental factors and their values. + + This might include compound and dose in a dose response experiment. - beta13 - - + Sample annotation - - Microarray metadata - - This might include gene identifiers, genomic coordinates, probe oligonucleotide sequences etc. + + + beta13 Annotation on the array itself used in a microarray experiment. - beta13 - - + + + This might include gene identifiers, genomic coordinates, probe oligonucleotide sequences etc. + Microarray metadata - + + + beta13 + 1.8 + Annotation on laboratory and/or data processing protocols used in an microarray experiment. + + + This might describe e.g. the normalisation methods used to process the raw data. Microarray protocol annotation - true - This might describe e.g. the normalisation methods used to process the raw data. - beta13 - 1.8 - Annotation on laboratory and/or data processing protocols used in an microarray experiment. - - - - Microarray hybridisation data - + + + beta13 Data concerning the hybridisations measured during a microarray experiment. - beta13 - - + + + Microarray hybridisation data - + + + beta13 + 1.8 + topological domains such as cytoplasmic regions in a protein. + + Protein features report (topological domains) - - 1.8 - beta13 - Topic concerning topological domains such as cytoplasmic regions in a protein. true - - - + + + beta13 + 1.5 + + A report of regions in a molecular sequence that are biased to certain characters. + Sequence features (compositionally-biased regions) - - 1.5 - beta13 true - A report of regions in a molecular sequence that are biased to certain characters. - - - - Nucleic acid features (difference and change) - - beta13 + + + beta13 + 1.5 A report on features in a nucleic acid sequence that indicate changes to or differences between sequences. - 1.5 + + + Nucleic acid features (difference and change) true - - - + + + beta13 + 1.8 + regions within a nucleic acid sequence containing a signal that alters a biological function. + + Nucleic acid features report (expression signal) - true - beta13 - Topic concerning regions within a nucleic acid sequence containing a signal that alters a biological function. - 1.8 - - - + + + beta13 + 1.8 + nucleic acids binding to some other molecule. + + + This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes). Nucleic acid features report (binding) - - 1.8 - Topic concerning nucleic acids binding to some other molecule. true - beta13 - This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes). - - - + + + beta13 + 1.8 + repetitive elements within a nucleic acid sequence. + + Nucleic acid repeats (report) - true - 1.8 - beta13 - Topic concerning repetitive elements within a nucleic acid sequence. - - - + + + beta13 + 1.8 + DNA replication or recombination. + + Nucleic acid features report (replication and recombination) - - beta13 - Topic concerning DNA replication or recombination. true - 1.8 - - - - Nucleic acid structure report - - + + + + beta13 A report on regions within a nucleic acid sequence which form secondary or tertiary (3D) structures. - Stem loop (report) - d-loop (report) Nucleic acid features (structure) Quadruplexes (report) - beta13 - - + Stem loop (report) + d-loop (report) + + + Nucleic acid structure report - + + + beta13 + 1.8 + short repetitive subsequences (repeat sequences) in a protein sequence. + + Protein features report (repeats) - - 1.8 - beta13 - Topic concerning short repetitive subsequences (repeat sequences) in a protein sequence. true - - - - Sequence motif matches (protein) - + + + beta13 + 1.8 Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more protein sequences. - 1.8 - beta13 + + + Sequence motif matches (protein) true - - - - Sequence motif matches (nucleic acid) - + + + beta13 + 1.8 Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more nucleic acid sequences. - beta13 + + + Sequence motif matches (nucleic acid) true - 1.8 - - - - Nucleic acid features (d-loop) - - beta13 - true - 1.5 + + + beta13 + 1.5 + A report on displacement loops in a mitochondrial DNA sequence. + A displacement loop is a region of mitochondrial DNA in which one of the strands is displaced by an RNA molecule. - - + Nucleic acid features (d-loop) + true - - Nucleic acid features (stem loop) - - beta13 - true + + + beta13 + 1.5 + A report on stem loops in a DNA sequence. - 1.5 + A stem loop is a hairpin structure; a double-helical structure formed when two complementary regions of a single strand of RNA or DNA molecule form base-pairs. - - + Nucleic acid features (stem loop) + true - - Gene transcript report - - This includes 5'untranslated region (5'UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3'untranslated regions (3'UTR). + + + beta13 + An informative report on features of a messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules. This includes reports on a specific gene transcript, clone or EST. + + Clone or EST (report) + Gene transcript annotation Nucleic acid features (mRNA features) - beta13 Transcript (report) - mRNA features - Gene transcript annotation - Clone or EST (report) mRNA (report) - An informative report on features of a messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules. This includes reports on a specific gene transcript, clone or EST. - - - + mRNA features + + + This includes 5'untranslated region (5'UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3'untranslated regions (3'UTR). + Gene transcript report - + + + beta13 + 1.8 + coding sequences for a signal or transit peptide. + + Nucleic acid features report (signal or transit peptide) - true - 1.8 - Topic concerning coding sequences for a signal or transit peptide. - beta13 - - - + + + beta13 + 1.8 + features of non-coding or functional RNA molecules, including tRNA and rRNA. + + Non-coding RNA - - Topic concerning features of non-coding or functional RNA molecules, including tRNA and rRNA. - beta13 true - 1.8 - - - + + + beta13 + 1.5 + + Features concerning transcription of DNA into RNA including the regulation of transcription. + + This includes promoters, CAAT signals, TATA signals, -35 signals, -10 signals, GC signals, primer binding sites for initiation of transcription or reverse transcription, enhancer, attenuator, terminators and ribosome binding sites. Transcriptional features (report) - - 1.5 true - This includes promoters, CAAT signals, TATA signals, -35 signals, -10 signals, GC signals, primer binding sites for initiation of transcription or reverse transcription, enhancer, attenuator, terminators and ribosome binding sites. - Features concerning transcription of DNA into RNA including the regulation of transcription. - beta13 - - - + + + beta13 + 1.8 + sequence tagged sites (STS) in nucleic acid sequences. + + Nucleic acid features report (STS) - - Topic concerning sequence tagged sites (STS) in nucleic acid sequences. - 1.8 true - beta13 - - - + + + beta13 + 1.5 + + A report on predicted or actual immunoglobulin gene structure including constant, switch and variable regions and diversity, joining and variable segments. + Nucleic acid features (immunoglobulin gene structure) - true - beta13 - 1.5 - A report on predicted or actual immunoglobulin gene structure including constant, switch and variable regions and diversity, joining and variable segments. - - - + + + beta13 + 1.5 + + Information on a 'class' node from the SCOP database. + SCOP class - - 1.5 - beta13 true - Information on a 'class' node from the SCOP database. - - - - SCOP fold - - beta13 + + + beta13 + 1.5 + Information on a 'fold' node from the SCOP database. - 1.5 + + SCOP fold true - - - - SCOP superfamily - - beta13 + + + beta13 + 1.5 + Information on a 'superfamily' node from the SCOP database. - 1.5 + + SCOP superfamily true - - - + + + beta13 + 1.5 + + Information on a 'family' node from the SCOP database. + SCOP family - - 1.5 true - Information on a 'family' node from the SCOP database. - beta13 - - - - SCOP protein - + + + beta13 + 1.5 + Information on a 'protein' node from the SCOP database. + + SCOP protein true - beta13 - 1.5 - - - + + + beta13 + 1.5 + + Information on a 'species' node from the SCOP database. + SCOP species - - 1.5 true - beta13 - Information on a 'species' node from the SCOP database. - - - + + + beta13 + 1.8 + mass spectrometry experiments. + + Mass spectrometry experiment - - 1.8 - Topic concerning mass spectrometry experiments. true - beta13 - - - - Gene family report - + + + beta13 + Nucleic acid classification An informative report on a particular family of genes, typically a set of genes with similar sequence that originate from duplication of a common ancestor gene, or any other classification of nucleic acid sequences or structures that reflects gene structure. - This includes reports on on gene homologues between species. - beta13 Gene annotation (homology information) - Homology information Gene annotation (homology) - Nucleic acid classification Gene family annotation Gene homology (report) - - + Homology information + + + This includes reports on on gene homologues between species. + Gene family report - - Protein image - - beta13 + + + beta13 An image of a protein. - - + + + Protein image - - Protein alignment - + + + beta13 An alignment of protein sequences and/or structures. - beta13 - - + + + Protein alignment - + + + 1.0 + 1.8 + sequencing experiment, including samples, sampling, preparation, sequencing, and analysis. + + NGS experiment - - 1.8 - 1.0 - Topic concerning sequencing experiment, including samples, sampling, preparation, sequencing, and analysis. true - - - - Sequence assembly report - + + + 1.1 An informative report about a DNA sequence assembly. - 1.1 - This might include an overall quality assement of the assembly and summary statistics including counts, average length and number of bases for reads, matches and non-matches, contigs, reads in pairs etc. Assembly report - - + + + This might include an overall quality assement of the assembly and summary statistics including counts, average length and number of bases for reads, matches and non-matches, contigs, reads in pairs etc. + Sequence assembly report - - Genome index - - 1.1 - Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment. + + + 1.1 An index of a genome sequence. - - + + + Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment. + Genome index - - GWAS report - - 1.8 - 1.1 + + + 1.1 + 1.8 Report concerning genome-wide association study experiments. + + + GWAS report true - Genome-wide association study - - - - Cytoband position - - 1.2 + + + 1.2 The position of a cytogenetic band in a genome. + + Information might include start and end position in a chromosome sequence, chromosome identifier, name of band and so on. - - + Cytoband position - - Cell type ontology ID - - - CL ID + + + + 1.2 + beta12orEarlier + CL_[0-9]{7} Cell type ontology concept ID. - CL_[0-9]{7} - 1.2 - beta12orEarlier - - - + CL ID + + + + Cell type ontology ID - - Kinetic model - - 1.2 + + + 1.2 Mathematical model of a network, that contains biochemical kinetics. - - + + + Kinetic model - - COSMIC ID - + + + 1.3 + Identifier of a COSMIC database entry. COSMIC identifier cosmic ID - Identifier of a COSMIC database entry. - cosmic identifier cosmic id - 1.3 - - - + cosmic identifier + + + + COSMIC ID - - HGMD ID - + + + beta12orEarlier Identifier of a HGMD database entry. + HGMD identifier hgmd ID - hgmd identifier - beta12orEarlier hgmd id - HGMD identifier - - - + hgmd identifier + + + + HGMD ID - - Sequence assembly ID - - Sequence assembly version + + + 1.3 Unique identifier of sequence assembly. - 1.3 - - - + Sequence assembly version + + + + Sequence assembly ID - + + + 1.3 + 1.5 + + A label (text token) describing a type of sequence feature such as gene, transcript, cds, exon, repeat, simple, misc, variation, somatic variation, structural variation, somatic structural variation, constrained or regulatory. + Sequence feature type - true - A label (text token) describing a type of sequence feature such as gene, transcript, cds, exon, repeat, simple, misc, variation, somatic variation, structural variation, somatic structural variation, constrained or regulatory. - 1.3 - 1.5 - - - + + + beta12orEarlier + 1.5 + + An informative report on gene homologues between species. + Gene homology (report) - - beta12orEarlier true - An informative report on gene homologues between species. - 1.5 - - - - Ensembl gene tree ID - - - ENSGT00390000003602 - Ensembl ID (gene tree) + + + + 1.3 + ENSGT00390000003602 Unique identifier for a gene tree from the Ensembl database. - 1.3 - - - + Ensembl ID (gene tree) + + + + Ensembl gene tree ID - - Gene tree - - 1.3 + + + 1.3 A phylogenetic tree that is an estimate of the character's phylogeny. - - + + + Gene tree - - Species tree - + + + 1.3 A phylogenetic tree that reflects phylogeny of the taxa from which the characters (used in calculating the tree) were sampled. - 1.3 - - + + + Species tree - - Sample ID - - + + + - - + + - 1.3 - Sample accession + 1.3 Name or other identifier of an entry from a biosample database. - - - + Sample accession + + + + Sample ID - - MGI accession - - + + + + 1.3 Identifier of an object from the MGI database. - 1.3 - - - + + + + MGI accession - - Phenotype name - - - 1.3 + + + + 1.3 Name of a phenotype. - Phenotypes Phenotype - - - + Phenotypes + + + + Phenotype name - - Transition matrix - + + + 1.4 A HMM transition matrix contains the probabilities of switching from one HMM state to another. - Consider for example an HMM with two states (AT-rich and GC-rich). The transition matrix will hold the probabilities of switching from the AT-rich to the GC-rich state, and vica versa. HMM transition matrix - 1.4 - + + Consider for example an HMM with two states (AT-rich and GC-rich). The transition matrix will hold the probabilities of switching from the AT-rich to the GC-rich state, and vica versa. + Transition matrix - - Emission matrix - + + + 1.4 A HMM emission matrix holds the probabilities of choosing the four nucleotides (A, C, G and T) in each of the states of a HMM. - 1.4 - Consider for example an HMM with two states (AT-rich and GC-rich). The emission matrix holds the probabilities of choosing each of the four nucleotides (A, C, G and T) in the AT-rich state and in the GC-rich state. HMM emission matrix - + + Consider for example an HMM with two states (AT-rich and GC-rich). The emission matrix holds the probabilities of choosing each of the four nucleotides (A, C, G and T) in the AT-rich state and in the GC-rich state. + Emission matrix - - Hidden Markov model - + + + 1.4 + 1.15 A statistical Markov model of a system which is assumed to be a Markov process with unobserved (hidden) states. - 1.4 - + + + Hidden Markov model + true - - Format identifier - + + + 1.4 An identifier of a data format. - 1.4 - + + Format identifier - + + + 1.5 + beta12orEarlier + Raw biological or biomedical image generated by some experimental technique. + + Raw image - - 1.5 - Amino acid data http://semanticscience.org/resource/SIO_000081 - beta12orEarlier - Image data - Raw biological or biomedical image generated by some experimental technique. - - - - Carbohydrate property - - Carbohydrate data + + + 1.5 Data concerning the intrinsic physical (e.g. structural) or chemical properties of one, more or all carbohydrates. - 1.5 - - + Carbohydrate data + + + Carbohydrate property - + + + 1.5 + 1.8 + Report concerning proteomics experiments. + + Proteomics experiment report - true - 1.8 - Report concerning proteomics experiments. - 1.5 - - - + + + 1.5 + 1.8 + RNAi experiments. + + RNAi report - - Topic concerning RNAi experiments. - 1.5 true - 1.8 - - - + + + 1.5 + 1.8 + biological computational model experiments (simulation), for example the minimum information required in order to permit its correct interpretation and reproduction. + + Simulation experiment report - - 1.5 true - 1.8 - Topic concerning biological computational model experiments (simulation), for example the minimum information required in order to permit its correct interpretation and reproduction. - - - - MRI image - + + - - + + + 1.7 + An imaging technique that uses magnetic fields and radiowaves to form images, typically to investigate the anatomy and physiology of the human body. MRT image - 1.7 - Magnetic resonance tomography image - Nuclear magnetic resonance imaging image - Magnetic resonance imaging image + Magnetic resonance tomography image NMRI image - An imaging technique that uses magnetic fields and radiowaves to form images, typically to investigate the anatomy and physiology of the human body. - - + Nuclear magnetic resonance imaging image + + + + MRI image - - Cell migration track image - + + - - + + - 1.7 + 1.7 An image from a cell migration track assay. - - + + + Cell migration track image - - Rate of association - - kon - 1.7 + + + 1.7 Rate of association of a protein with another protein or some other molecule. - - + kon + + + Rate of association - - Gene order - - Such data are often used for genome rearrangement tools and phylogenetic tree labeling. + + + 1.7 Multiple gene identifiers in a specific order. - 1.7 - - + + + Such data are often used for genome rearrangement tools and phylogenetic tree labeling. + Gene order - - Spectrum - - 1.7 + + + 1.7 The spectrum of frequencies of electromagnetic radiation emitted from a molecule as a result of some spectroscopy experiment. Spectra - - + + + Spectrum - - NMR spectrum - + + - - + + + 1.7 Spectral information for a molecule from a nuclear magnetic resonance experiment. - 1.7 NMR spectra - - + + + NMR spectrum - - Chemical structure sketch - - Chemical structure sketches are used for presentational purposes but also as inputs to various analysis software. - 1.8 - Small molecule sketch + + + 1.8 A sketch of a small molecule made with some specialised drawing package. - - + Small molecule sketch + + + Chemical structure sketches are used for presentational purposes but also as inputs to various analysis software. + Chemical structure sketch - - Nucleic acid signature - - 1.8 + + + 1.8 An informative report about a specific or conserved nucleic acid sequence pattern. - - + + + Nucleic acid signature - - DNA sequence - - DNA sequences - 1.8 + + + 1.8 A DNA sequence. - - + DNA sequences + + + DNA sequence - - RNA sequence - - A DNA sequence. - DNA sequences + + + 1.8 RNA sequences - 1.8 - - + + + RNA sequence - - RNA sequence (raw) - - - Raw sequence (RNA) - 1.8 + + + + 1.8 A raw RNA sequence. RNA raw sequence - - + Raw sequence (RNA) + + + RNA sequence (raw) - - DNA sequence (raw) - - - Raw sequence (DNA) + + + + 1.8 A raw DNA sequence. - 1.8 DNA raw sequence - - + Raw sequence (DNA) + + + DNA sequence (raw) - - Sequence variations - + + - - + + - 1.8 + 1.8 Data on gene sequence variations resulting large-scale genotyping and DNA sequencing projects. Gene sequence variations + + Variations are stored along with a reference genome. - - + Sequence variations - - Bibliography - - 1.8 + + + 1.8 A list of publications such as scientic papers or books. - - + + + Bibliography - - Ontology mapping - + + + beta12orEarlier A mapping of supplied textual terms or phrases to ontology concepts (URIs). - beta12orEarlier - - + + + Ontology mapping - + - - SMILES - - - Chemical structure specified in Simplified Molecular Input Line Entry System (SMILES) line notation. - beta12orEarlier - - - - - - + + + 1.9 + Any data concerning a specific biological or biomedical image. + Image-associated data + Image-related data + + + This can include basic provenance and technical information about the image, scientific annotation and so on. + Image metadata - + - - InChI - - - Chemical structure specified in IUPAC International Chemical Identifier (InChI) line notation. - beta12orEarlier - - + + + 1.9 + A report concerning a clinical trial. + Clinical trial information + + + Clinical trial report - + - - mf - - - Chemical structure specified by Molecular Formula (MF), including a count of each element in a compound. - beta12orEarlier - The general MF query format consists of a series of valid atomic symbols, with an optional number or range. - - + + + 1.10 + A report about a biosample. + Biosample report + + + Reference sample report - + - - inchikey - - - The InChIKey (hashed InChI) is a fixed length (25 character) condensed digital representation of an InChI chemical structure specification. It uniquely identifies a chemical compound. - beta12orEarlier - An InChI identifier is not human-readable but is more suitable for web searches than an InChI chemical structure specification. - - + + + 1.10 + Accession number of an entry from the Gene Expression Atlas. + + + + Gene Expression Atlas Experiment ID - + - - smarts - - SMILES ARbitrary Target Specification (SMARTS) format for chemical structure specification, which is a subset of the SMILES line notation. - beta12orEarlier - - + + + + + + + + + + beta12orEarlier + Identifier of an entry from a database of disease. + + + + Disease identifier - + - - unambiguous pure - - - beta12orEarlier - Alphabet for a molecular sequence with possible unknown positions but without ambiguity or non-sequence characters. - - + + + + 1.12 + The name of some disease. + + + + Disease name - + - - nucleotide - - - Non-sequence characters may be used for example for gaps. - http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Nucleotide_sequence - beta12orEarlier - Alphabet for a nucleotide sequence with possible ambiguity, unknown positions and non-sequence characters. - - + + + 1.12 + Some material that is used for educational (training) purposes. + OER + Open educational resource + + + Training material - + - - protein - - - Alphabet for a protein sequence with possible ambiguity, unknown positions and non-sequence characters. - beta12orEarlier - Non-sequence characters may be used for gaps and translation stop. - http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Amino_acid_sequence - - + + + 1.12 + A training course available for use on the Web. + On-line course + MOOC + Massive open online course + + + Online course - + - - consensus - - - beta12orEarlier - Alphabet for the consensus of two or more molecular sequences. - - + + + 1.12 + Any free or plain text, typically for human consumption and in English. Can instantiate also as a textual search query. + Free text + Plain text + Textual search query + + + Text - + - - pure nucleotide - - - beta12orEarlier - Alphabet for a nucleotide sequence with possible ambiguity and unknown positions but without non-sequence characters. - - + + + + 1.9 + A report about biodiversity data. + Biodiversity information + OTU table + + + Biodiversity report - + - - unambiguous pure nucleotide - - - beta12orEarlier - Alphabet for a nucleotide sequence (characters ACGTU only) with possible unknown positions but without ambiguity or non-sequence characters . - - + + + 1.14 + A report about biosafety data. + Biosafety information + + + Biosafety report - + - - dna - - beta12orEarlier - http://onto.eva.mpg.de/ontologies/gfo-bio.owl#DNA_sequence - Alphabet for a DNA sequence with possible ambiguity, unknown positions and non-sequence characters. - - + + + 1.14 + A report about any kind of isolation of biological material. + Geographic location + Isolation source + + + Isolation report - + - - rna - - Alphabet for an RNA sequence with possible ambiguity, unknown positions and non-sequence characters. - http://onto.eva.mpg.de/ontologies/gfo-bio.owl#RNA_sequence - beta12orEarlier - - + + + 1.14 + Information about the ability of an organism to cause disease in a corresponding host. + Pathogenicity + + + Pathogenicity report - + - - unambiguous pure dna - - - Alphabet for a DNA sequence (characters ACGT only) with possible unknown positions but without ambiguity or non-sequence characters. - beta12orEarlier - - + + + 1.14 + Information about the biosafety classification of an organism according to corresponding law. + Biosafety level + + + Biosafety classification - + - - pure dna - - - Alphabet for a DNA sequence with possible ambiguity and unknown positions but without non-sequence characters. - beta12orEarlier - - + + + 1.14 + A report about localisation of the isolaton of biological material e.g. country or coordinates. + + + Geographic location - + - - unambiguous pure rna sequence - - - Alphabet for an RNA sequence (characters ACGU only) with possible unknown positions but without ambiguity or non-sequence characters. - beta12orEarlier - - + + + 1.14 + A report about any kind of isolation source of biological material e.g. blood, water, soil. + + + Isolation source - + - - pure rna - - - Alphabet for an RNA sequence with possible ambiguity and unknown positions but without non-sequence characters. - beta12orEarlier - - + + + 1.14 + Experimentally determined parameter of the physiology of an organism, e.g. substrate spectrum. + + + Physiology parameter - + - - unambiguous pure protein - - - beta12orEarlier - Alphabet for any protein sequence with possible unknown positions but without ambiguity or non-sequence characters. - - + + + 1.14 + Experimentally determined parameter of the morphology of an organism, e.g. size & shape. + + + Morphology parameter - + - - pure protein - - - beta12orEarlier - Alphabet for any protein sequence with possible ambiguity and unknown positions but without non-sequence characters. - - + + + 1.14 + Experimental determined parameter for the cultivation of an organism. + Cultivation conditions + Carbon source + Culture media composition + Nitrogen source + Salinity + Temperature + pH value + + + Cultivation parameter - + - - UniGene entry format - - beta12orEarlier - Format of an entry from UniGene. - A UniGene entry includes a set of transcript sequences assigned to the same transcription locus (gene or expressed pseudogene), with information on protein similarities, gene expression, cDNA clone reagents, and genomic location. - beta12orEarlier - true - - + + + 1.15 + Data concerning a sequencing experiment, that may be specified as an input to some tool. + + + Sequencing metadata name - + - - COG sequence cluster format - - beta12orEarlier - true - beta12orEarlier - Format of an entry from the COG database of clusters of (related) protein sequences. - - + + + 1.15 + An identifier of a flow cell of a sequencing machine. + + + A flow cell is used to immobilise, amplify and sequence millions of molecules at once. In Illumina machines, a flowcell is composed of 8 "lanes" which allows 8 experiments in a single analysis. + Flow cell identifier - + - - EMBL feature location - - - beta12orEarlier - Feature location - Format for sequence positions (feature location) as used in DDBJ/EMBL/GenBank database. - - + + + 1.15 + An identifier of a lane within a flow cell of a sequencing machine, within which millions of sequences are immobilised, amplified and sequenced. + + + Lane identifier - + - - quicktandem - - - Report format for tandem repeats in a nucleotide sequence (format generated by the Sanger Centre quicktandem program). - beta12orEarlier - - + + + 1.15 + A number corresponding to the number of an analysis performed by a sequencing machine. For example, if it's the 13th analysis, the run is 13. + + + + Run number - + - - Sanger inverted repeats - - - beta12orEarlier - Report format for inverted repeats in a nucleotide sequence (format generated by the Sanger Centre inverted program). - - + + + 1.15 + Data concerning ecology; for example measurements and reports from the study of interactions among organisms and their environment. + + + This is a broad data type and is used a placeholder for other, more specific types. + Ecological data - + - - EMBOSS repeat - - - Report format for tandem repeats in a sequence (an EMBOSS report format). - beta12orEarlier - - + + + 1.15 + The mean species diversity in sites or habitats at a local scale. + α-diversity + + + Alpha diversity data - + - - est2genome format - - - beta12orEarlier - Format of a report on exon-intron structure generated by EMBOSS est2genome. - - + + + 1.15 + The ratio between regional and local species diversity. + True beta diversity + β-diversity + + + Beta diversity data - + - - restrict format - - - Report format for restriction enzyme recognition sites used by EMBOSS restrict program. - beta12orEarlier - - + + + 1.15 + The total species diversity in a landscape. + γ-diversity + + + Gamma diversity data - + - - restover format - - - beta12orEarlier - Report format for restriction enzyme recognition sites used by EMBOSS restover program. - - + + + + 1.15 + A plot in which community data (e.g. species abundance data) is summarised. Similar species and samples are plotted close together, and dissimilar species and samples are plotted placed far apart. + + + Ordination plot - + - - REBASE restriction sites - - - beta12orEarlier - Report format for restriction enzyme recognition sites used by REBASE database. - - + + + 1.16 + An informative report containing a ranked list of categories (usually ontology concepts), each associated with a statistical metric of over-/under-representation within the studied data. + Enrichment report + Functional enrichment report + + + Over-representation report - + - - FASTA search results format - - - Format of results of a sequence database search using FASTA. - beta12orEarlier - This includes (typically) score data, alignment data and a histogram (of observed and expected distribution of E values.) - - + + + + + + + + + 1.16 + GO-term report + An informative report containing a ranked list of Gene Ontology concepts, each associated with a p-value, concerning or derived from the analysis of e.g. a set of genes or proteins. + Gene ontology concept over-representation report + Gene ontology enrichment report + Gene ontology term enrichment report + + + GO-term enrichment report - + - - BLAST results - - - Format of results of a sequence database search using some variant of BLAST. - beta12orEarlier - This includes score data, alignment data and summary table. - - + + + 1.16 + Score for localization of one or more post-translational modifications in peptide sequence measured by mass spectrometry. + False localisation rate + PTM localisation + PTM score + + + Localisation score - + - - mspcrunch - - - beta12orEarlier - Format of results of a sequence database search using some variant of MSPCrunch. - - + + + 1.16 + Identifier of a protein modification catalogued in the Unimod database. + + + + Unimod ID - + - - Smith-Waterman format - - - beta12orEarlier - Format of results of a sequence database search using some variant of Smith Waterman. - - + + + 1.16 + Identifier for mass spectrometry proteomics data in the proteomexchange.org repository. + + + + ProteomeXchange ID - + - - dhf - - - The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database. - beta12orEarlier - Format of EMBASSY domain hits file (DHF) of hits (sequences) with domain classification information. - - + + + 1.16 + Groupings of gene expression profiles according to a clustering algorithm. + + + Clustered gene expression profiles - + - - lhf - - - beta12orEarlier - Format of EMBASSY ligand hits file (LHF) of database hits (sequences) with ligand classification information. - The hits are putative ligand-binding sequences and are found from a search of a sequence database. - - + + + 1.16 + An identifier of a concept from the BRENDA ontology. + + + + BRENDA ontology concept ID - + - - InterPro hits format - - - Results format for searches of the InterPro database. - beta12orEarlier - - + + + + 1.16 + A text (such as a scientific article), annotated with notes, data and metadata, such as recognised entities, concepts, and their relations. + + + Annotated text - + - - InterPro protein view report format - - Format of results of a search of the InterPro database showing matches of query protein sequence(s) to InterPro entries. - The report includes a classification of regions in a query protein sequence which are assigned to a known InterPro protein family or group. - beta12orEarlier - - + + + 1.16 + A structured query, in form of a script, that defines a database search task. + + + Query script - + - - InterPro match table format - - Format of results of a search of the InterPro database showing matches between protein sequence(s) and signatures for an InterPro entry. - beta12orEarlier - The table presents matches between query proteins (rows) and signature methods (columns) for this entry. Alternatively the sequence(s) might be from from the InterPro entry itself. The match position in the protein sequence and match status (true positive, false positive etc) are indicated. - - + + + + beta12orEarlier + + + + + Chemical structure specified in Simplified Molecular Input Line Entry System (SMILES) line notation. + + + SMILES - + - - HMMER Dirichlet prior - - - beta12orEarlier - Dirichlet distribution HMMER format. - - + + + + beta12orEarlier + Chemical structure specified in IUPAC International Chemical Identifier (InChI) line notation. + + + InChI - + - - MEME Dirichlet prior - - - beta12orEarlier - Dirichlet distribution MEME format. - - + + + + beta12orEarlier + Chemical structure specified by Molecular Formula (MF), including a count of each element in a compound. + + + The general MF query format consists of a series of valid atomic symbols, with an optional number or range. + mf - + - - HMMER emission and transition - - - Format of a report from the HMMER package on the emission and transition counts of a hidden Markov model. - beta12orEarlier - - + + + + beta12orEarlier + The InChIKey (hashed InChI) is a fixed length (25 character) condensed digital representation of an InChI chemical structure specification. It uniquely identifies a chemical compound. + + + An InChIKey identifier is not human- nor machine-readable but is more suitable for web searches than an InChI chemical structure specification. + InChIKey - + - - prosite-pattern - - - Format of a regular expression pattern from the Prosite database. - beta12orEarlier - - + + + beta12orEarlier + SMILES ARbitrary Target Specification (SMARTS) format for chemical structure specification, which is a subset of the SMILES line notation. + + + smarts - + - - EMBOSS sequence pattern - - - Format of an EMBOSS sequence pattern. - beta12orEarlier - - + + + + beta12orEarlier + Alphabet for a molecular sequence with possible unknown positions but without ambiguity or non-sequence characters. + + + unambiguous pure - + - - meme-motif - - - A motif in the format generated by the MEME program. - beta12orEarlier - - + + + + beta12orEarlier + Alphabet for a nucleotide sequence with possible ambiguity, unknown positions and non-sequence characters. + + + Non-sequence characters may be used for example for gaps. + nucleotide + http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Nucleotide_sequence - + - - prosite-profile - - - Sequence profile (sequence classifier) format used in the PROSITE database. - beta12orEarlier - - + + + + beta12orEarlier + Alphabet for a protein sequence with possible ambiguity, unknown positions and non-sequence characters. + + + Non-sequence characters may be used for gaps and translation stop. + protein + http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Amino_acid_sequence - + - - JASPAR format - - - beta12orEarlier - A profile (sequence classifier) in the format used in the JASPAR database. - - + + + + beta12orEarlier + Alphabet for the consensus of two or more molecular sequences. + + + consensus - + - - MEME background Markov model - - - Format of the model of random sequences used by MEME. - beta12orEarlier - - + + + + beta12orEarlier + Alphabet for a nucleotide sequence with possible ambiguity and unknown positions but without non-sequence characters. + + + pure nucleotide - + - - HMMER format - - - Format of a hidden Markov model representation used by the HMMER package. - beta12orEarlier - - + + + + beta12orEarlier + Alphabet for a nucleotide sequence (characters ACGTU only) with possible unknown positions but without ambiguity or non-sequence characters . + + + unambiguous pure nucleotide + + + + + + + + + beta12orEarlier + Alphabet for a DNA sequence with possible ambiguity, unknown positions and non-sequence characters. + + + dna + http://onto.eva.mpg.de/ontologies/gfo-bio.owl#DNA_sequence + + + + + + + + + beta12orEarlier + Alphabet for an RNA sequence with possible ambiguity, unknown positions and non-sequence characters. + + + rna + http://onto.eva.mpg.de/ontologies/gfo-bio.owl#RNA_sequence + + + + + + + + + + beta12orEarlier + Alphabet for a DNA sequence (characters ACGT only) with possible unknown positions but without ambiguity or non-sequence characters. + + + unambiguous pure dna + + + + + + + + + + beta12orEarlier + Alphabet for a DNA sequence with possible ambiguity and unknown positions but without non-sequence characters. + + + pure dna + + + + + + + + + + beta12orEarlier + Alphabet for an RNA sequence (characters ACGU only) with possible unknown positions but without ambiguity or non-sequence characters. + + + unambiguous pure rna sequence + + + + + + + + + + beta12orEarlier + Alphabet for an RNA sequence with possible ambiguity and unknown positions but without non-sequence characters. + + + pure rna + + + + + + + + + + beta12orEarlier + Alphabet for any protein sequence with possible unknown positions but without ambiguity or non-sequence characters. + + + unambiguous pure protein + + + + + + + + + + beta12orEarlier + Alphabet for any protein sequence with possible ambiguity and unknown positions but without non-sequence characters. + + + pure protein + + + + + + + + + beta12orEarlier + beta12orEarlier + + Format of an entry from UniGene. + + A UniGene entry includes a set of transcript sequences assigned to the same transcription locus (gene or expressed pseudogene), with information on protein similarities, gene expression, cDNA clone reagents, and genomic location. + UniGene entry format + true + + + + + + + + + beta12orEarlier + beta12orEarlier + + Format of an entry from the COG database of clusters of (related) protein sequences. + + COG sequence cluster format + true + + + + + + + + + + beta12orEarlier + Format for sequence positions (feature location) as used in DDBJ/EMBL/GenBank database. + Feature location + + + EMBL feature location + + + + + + + + + + beta12orEarlier + Report format for tandem repeats in a nucleotide sequence (format generated by the Sanger Centre quicktandem program). + + + quicktandem + + + + + + + + + + beta12orEarlier + Report format for inverted repeats in a nucleotide sequence (format generated by the Sanger Centre inverted program). + + + Sanger inverted repeats + + + + + + + + + + beta12orEarlier + Report format for tandem repeats in a sequence (an EMBOSS report format). + + + EMBOSS repeat + + + + + + + + + + beta12orEarlier + Format of a report on exon-intron structure generated by EMBOSS est2genome. + + + est2genome format + + + + + + + + + + beta12orEarlier + Report format for restriction enzyme recognition sites used by EMBOSS restrict program. + + + restrict format + + + + + + + + + + beta12orEarlier + Report format for restriction enzyme recognition sites used by EMBOSS restover program. + + + restover format + + + + + + + + + + beta12orEarlier + Report format for restriction enzyme recognition sites used by REBASE database. + + + REBASE restriction sites + + + + + + + + + + beta12orEarlier + Format of results of a sequence database search using FASTA. + + + This includes (typically) score data, alignment data and a histogram (of observed and expected distribution of E values.) + FASTA search results format + + + + + + + + + + beta12orEarlier + Format of results of a sequence database search using some variant of BLAST. + + + This includes score data, alignment data and summary table. + BLAST results + + + + + + + + + + beta12orEarlier + Format of results of a sequence database search using some variant of MSPCrunch. + + + mspcrunch + + + + + + + + + + beta12orEarlier + Format of results of a sequence database search using some variant of Smith Waterman. + + + Smith-Waterman format + + + + + + + + + + beta12orEarlier + Format of EMBASSY domain hits file (DHF) of hits (sequences) with domain classification information. + + + The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database. + dhf + + + + + + + + + + beta12orEarlier + Format of EMBASSY ligand hits file (LHF) of database hits (sequences) with ligand classification information. + + + The hits are putative ligand-binding sequences and are found from a search of a sequence database. + lhf + + + + + + + + + + beta12orEarlier + Results format for searches of the InterPro database. + + + InterPro hits format + + + + + + + + + beta12orEarlier + Format of results of a search of the InterPro database showing matches of query protein sequence(s) to InterPro entries. + + + The report includes a classification of regions in a query protein sequence which are assigned to a known InterPro protein family or group. + InterPro protein view report format + + + + + + + + + beta12orEarlier + Format of results of a search of the InterPro database showing matches between protein sequence(s) and signatures for an InterPro entry. + + + The table presents matches between query proteins (rows) and signature methods (columns) for this entry. Alternatively the sequence(s) might be from from the InterPro entry itself. The match position in the protein sequence and match status (true positive, false positive etc) are indicated. + InterPro match table format + + + + + + + + + + beta12orEarlier + Dirichlet distribution HMMER format. + + + HMMER Dirichlet prior + + + + + + + + + + beta12orEarlier + Dirichlet distribution MEME format. + + + MEME Dirichlet prior + + + + + + + + + + beta12orEarlier + Format of a report from the HMMER package on the emission and transition counts of a hidden Markov model. + + + HMMER emission and transition + + + + + + + + + + beta12orEarlier + Format of a regular expression pattern from the Prosite database. + + + prosite-pattern + + + + + + + + + + beta12orEarlier + Format of an EMBOSS sequence pattern. + + + EMBOSS sequence pattern + + + + + + + + + + beta12orEarlier + A motif in the format generated by the MEME program. + + + meme-motif + + + + + + + + + + beta12orEarlier + Sequence profile (sequence classifier) format used in the PROSITE database. + + + prosite-profile + + + + + + + + + + beta12orEarlier + A profile (sequence classifier) in the format used in the JASPAR database. + + + JASPAR format + + + + + + + + + + beta12orEarlier + Format of the model of random sequences used by MEME. + + + MEME background Markov model + + + + + + + + + + beta12orEarlier + Format of a hidden Markov model representation used by the HMMER package. + + + HMMER format - - HMMER-aln - - - - beta12orEarlier + + + + + beta12orEarlier FASTA-style format for multiple sequences aligned by HMMER package to an HMM. - - + + + HMMER-aln - - DIALIGN format - - + + + + beta12orEarlier Format of multiple sequences aligned by DIALIGN package. - beta12orEarlier - - + + + DIALIGN format - - daf - - - The format is clustal-like and includes annotation of domain family classification information. + + + + beta12orEarlier EMBASSY 'domain alignment file' (DAF) format, containing a sequence alignment of protein domains belonging to the same SCOP or CATH family. - beta12orEarlier - - + + + The format is clustal-like and includes annotation of domain family classification information. + daf - - Sequence-MEME profile alignment - - - beta12orEarlier + + + + beta12orEarlier Format for alignment of molecular sequences to MEME profiles (position-dependent scoring matrices) as generated by the MAST tool from the MEME package. - - + + + Sequence-MEME profile alignment - - HMMER profile alignment (sequences versus HMMs) - - + + + + beta12orEarlier Format used by the HMMER package for an alignment of a sequence against a hidden Markov model database. - beta12orEarlier - - + + + HMMER profile alignment (sequences versus HMMs) - - HMMER profile alignment (HMM versus sequences) - - + + + + beta12orEarlier Format used by the HMMER package for of an alignment of a hidden Markov model against a sequence database. - beta12orEarlier - - + + + HMMER profile alignment (HMM versus sequences) - - Phylip distance matrix - - - Data Type must include the distance matrix, probably as pairs of sequence identifiers with a distance (integer or float). - beta12orEarlier + + + + beta12orEarlier Format of PHYLIP phylogenetic distance matrix data. - - + + + Data Type must include the distance matrix, probably as pairs of sequence identifiers with a distance (integer or float). + Phylip distance matrix - - ClustalW dendrogram - - - beta12orEarlier + + + + beta12orEarlier Dendrogram (tree file) format generated by ClustalW. - - + + + ClustalW dendrogram - - Phylip tree raw - - + + + + beta12orEarlier Raw data file format used by Phylip from which a phylogenetic tree is directly generated or plotted. - beta12orEarlier - - + + + Phylip tree raw - - Phylip continuous quantitative characters - - - beta12orEarlier + + + + beta12orEarlier PHYLIP file format for continuous quantitative character data. - - + + + Phylip continuous quantitative characters - - Phylogenetic property values format - + + + beta12orEarlier + beta12orEarlier + Format of phylogenetic property data. - beta12orEarlier - beta12orEarlier + + Phylogenetic property values format true - - - - Phylip character frequencies format - - - beta12orEarlier + + + + beta12orEarlier PHYLIP file format for phylogenetics character frequency data. - - + + + Phylip character frequencies format - - Phylip discrete states format - - + + + + beta12orEarlier Format of PHYLIP discrete states data. - beta12orEarlier - - + + + Phylip discrete states format - - Phylip cliques format - - - beta12orEarlier + + + + beta12orEarlier Format of PHYLIP cliques data. - - + + + Phylip cliques format - - Phylip tree format - - + + + + beta12orEarlier Phylogenetic tree data format used by the PHYLIP program. - beta12orEarlier - - + + + Phylip tree format - - TreeBASE format - - - beta12orEarlier + + + + beta12orEarlier The format of an entry from the TreeBASE database of phylogenetic data. - - + + + TreeBASE format - - TreeFam format - - - beta12orEarlier + + + + beta12orEarlier The format of an entry from the TreeFam database of phylogenetic data. - - + + + TreeFam format - - Phylip tree distance format - - + + + + beta12orEarlier Format for distances, such as Branch Score distance, between two or more phylogenetic trees as used by the Phylip package. - beta12orEarlier - - + + + Phylip tree distance format - - dssp - - - beta12orEarlier - The DSSP database is built using the DSSP application which defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in PDB format. + + + + beta12orEarlier Format of an entry from the DSSP database (Dictionary of Secondary Structure in Proteins). - - + + + The DSSP database is built using the DSSP application which defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in PDB format. + dssp - - hssp - - + + + + beta12orEarlier Entry format of the HSSP database (Homology-derived Secondary Structure in Proteins). - beta12orEarlier - - + + + hssp - - Dot-bracket format - - - beta12orEarlier + + + + beta12orEarlier Format of RNA secondary structure in dot-bracket notation, originally generated by the Vienna RNA package/server. - Vienna RNA secondary structure format Vienna RNA format - - + Vienna RNA secondary structure format + + + Dot-bracket format - - Vienna local RNA secondary structure format - - + + + + beta12orEarlier Format of local RNA secondary structure components with free energy values, generated by the Vienna RNA package/server. - beta12orEarlier - - + + + Vienna local RNA secondary structure format - - PDB database entry format - + + - - + + - beta12orEarlier - PDB entry format + beta12orEarlier Format of an entry (or part of an entry) from the PDB database. - - + PDB entry format + + + PDB database entry format - - PDB - - - PDB format - beta12orEarlier + + + + beta12orEarlier Entry format of PDB database in PDB format. - - + PDB format + + + PDB - - mmCIF - - - Chemical MIME (http://www.ch.ic.ac.uk/chemime): chemical/x-mmcif + + + + beta12orEarlier Entry format of PDB database in mmCIF format. - beta12orEarlier mmcif - - + + + mmCIF - - PDBML - - + + + + beta12orEarlier Entry format of PDB database in PDBML (XML) format. - beta12orEarlier - - + + + PDBML - + + + beta12orEarlier + beta12orEarlier + Format of a matrix of 3D-1D scores used by the EMBOSS Domainatrix applications. + + Domainatrix 3D-1D scoring matrix format - - beta12orEarlier true - beta12orEarlier - Format of a matrix of 3D-1D scores used by the EMBOSS Domainatrix applications. - - - aaindex - - + + + + beta12orEarlier Amino acid index format used by the AAindex database. - beta12orEarlier - - + + + aaindex - - IntEnz enzyme report format - - beta12orEarlier - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + Format of an entry from IntEnz (The Integrated Relational Enzyme Database). + IntEnz is the master copy of the Enzyme Nomenclature, the recommendations of the NC-IUBMB on the Nomenclature and Classification of Enzyme-Catalysed Reactions. + IntEnz enzyme report format true - - - + + + beta12orEarlier + beta12orEarlier + + Format of an entry from the BRENDA enzyme database. + BRENDA enzyme report format - true - Format of an entry from the BRENDA enzyme database. - beta12orEarlier - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + Format of an entry from the KEGG REACTION database of biochemical reactions. + KEGG REACTION enzyme report format - true - beta12orEarlier - Format of an entry from the KEGG REACTION database of biochemical reactions. - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + Format of an entry from the KEGG ENZYME database. + KEGG ENZYME enzyme report format - - beta12orEarlier true - Format of an entry from the KEGG ENZYME database. - beta12orEarlier - - - - REBASE proto enzyme report format - + + + beta12orEarlier + beta12orEarlier + Format of an entry from the proto section of the REBASE enzyme database. + + REBASE proto enzyme report format true - beta12orEarlier - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + Format of an entry from the withrefm section of the REBASE enzyme database. + REBASE withrefm enzyme report format - - beta12orEarlier true - beta12orEarlier - Format of an entry from the withrefm section of the REBASE enzyme database. - - - - Pcons report format - - + + + + beta12orEarlier Format of output of the Pcons Model Quality Assessment Program (MQAP). - beta12orEarlier + + Pcons ranks protein models by assessing their quality based on the occurrence of recurring common three-dimensional structural patterns. Pcons returns a score reflecting the overall global quality and a score for each individual residue in the protein reflecting the local residue quality. - - + Pcons report format - - ProQ report format - - - beta12orEarlier - ProQ is a neural network-based predictor that predicts the quality of a protein model based on the number of structural features. + + + + beta12orEarlier Format of output of the ProQ protein model quality predictor. - - + + + ProQ is a neural network-based predictor that predicts the quality of a protein model based on the number of structural features. + ProQ report format - - SMART domain assignment report format - - beta12orEarlier - true + + + beta12orEarlier + beta12orEarlier + Format of SMART domain assignment data. + The SMART output file includes data on genetically mobile domains / analysis of domain architectures, including phyletic distributions, functional class, tertiary structures and functionally important residues. - beta12orEarlier - - + SMART domain assignment report format + true - - BIND entry format - + + + beta12orEarlier + beta12orEarlier + Entry format for the BIND database of protein interaction. - beta12orEarlier + + BIND entry format true - beta12orEarlier - - - - IntAct entry format - - beta12orEarlier - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + Entry format for the IntAct database of protein interaction. + + IntAct entry format true - - - - InterPro entry format - + + + beta12orEarlier + beta12orEarlier + Entry format for the InterPro database of protein signatures (sequence classifiers) and classified sequences. - true - beta12orEarlier + This includes signature metadata, sequence references and a reference to the signature itself. There is normally a header (entry accession numbers and name), abstract, taxonomy information, example proteins etc. Each entry also includes a match list which give a number of different views of the signature matches for the sequences in each InterPro entry. - beta12orEarlier - - + InterPro entry format + true - + + + beta12orEarlier + beta12orEarlier + + Entry format for the textual abstract of signatures in an InterPro entry and its protein matches. + + References are included and a functional inference is made where possible. InterPro entry abstract format - true - beta12orEarlier - References are included and a functional inference is made where possible. - beta12orEarlier - Entry format for the textual abstract of signatures in an InterPro entry and its protein matches. - - - - Gene3D entry format - + + + beta12orEarlier + beta12orEarlier + Entry format for the Gene3D protein secondary database. + + Gene3D entry format true - beta12orEarlier - beta12orEarlier - - - - PIRSF entry format - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + Entry format for the PIRSF protein secondary database. + + PIRSF entry format true - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + Entry format for the PRINTS protein secondary database. + PRINTS entry format - - beta12orEarlier - beta12orEarlier true - Entry format for the PRINTS protein secondary database. - - - - Panther Families and HMMs entry format - - beta12orEarlier - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + Entry format for the Panther library of protein families and subfamilies. + + Panther Families and HMMs entry format true - - - - Pfam entry format - + + + beta12orEarlier + beta12orEarlier + Entry format for the Pfam protein secondary database. + + Pfam entry format true - beta12orEarlier - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + Entry format for the SMART protein secondary database. + SMART entry format - true - beta12orEarlier - Entry format for the SMART protein secondary database. - beta12orEarlier - - - - Superfamily entry format - + + + beta12orEarlier + beta12orEarlier + Entry format for the Superfamily protein secondary database. - beta12orEarlier - beta12orEarlier + + Superfamily entry format true - - - + + + beta12orEarlier + beta12orEarlier + + Entry format for the TIGRFam protein secondary database. + TIGRFam entry format - - beta12orEarlier true - Entry format for the TIGRFam protein secondary database. - beta12orEarlier - - - - ProDom entry format - + + + beta12orEarlier + beta12orEarlier + Entry format for the ProDom protein domain classification database. - beta12orEarlier - beta12orEarlier + + ProDom entry format true - - - - FSSP entry format - + + + beta12orEarlier + beta12orEarlier + Entry format for the FSSP database. - beta12orEarlier + + FSSP entry format true - beta12orEarlier - - - - findkm - - - beta12orEarlier + + + + beta12orEarlier A report format for the kinetics of enzyme-catalysed reaction(s) in a format generated by EMBOSS findkm. This includes Michaelis Menten plot, Hanes Woolf plot, Michaelis Menten constant (Km) and maximum velocity (Vmax). - - + + + findkm - - Ensembl gene report format - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + Entry format of Ensembl genome database. - beta12orEarlier + + Ensembl gene report format true - - - + + + beta12orEarlier + beta12orEarlier + + Entry format of DictyBase genome database. + DictyBase gene report format - true - beta12orEarlier - Entry format of DictyBase genome database. - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + Entry format of Candida Genome database. + CGD gene report format - - beta12orEarlier true - beta12orEarlier - Entry format of Candida Genome database. - - - - DragonDB gene report format - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + Entry format of DragonDB genome database. - beta12orEarlier + + DragonDB gene report format true - - - - EcoCyc gene report format - + + + beta12orEarlier + beta12orEarlier + Entry format of EcoCyc genome database. - beta12orEarlier - beta12orEarlier + + EcoCyc gene report format true - - - + + + beta12orEarlier + beta12orEarlier + + Entry format of FlyBase genome database. + FlyBase gene report format - true - beta12orEarlier - beta12orEarlier - Entry format of FlyBase genome database. - - - - Gramene gene report format - - beta12orEarlier - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + Entry format of Gramene genome database. + + Gramene gene report format true - - - + + + beta12orEarlier + beta12orEarlier + + Entry format of KEGG GENES genome database. + KEGG GENES gene report format - true - beta12orEarlier - Entry format of KEGG GENES genome database. - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + Entry format of the Maize genetics and genomics database (MaizeGDB). + MaizeGDB gene report format - - beta12orEarlier - beta12orEarlier true - Entry format of the Maize genetics and genomics database (MaizeGDB). - - - - MGD gene report format - + + + beta12orEarlier + beta12orEarlier + Entry format of the Mouse Genome Database (MGD). - beta12orEarlier - beta12orEarlier + + MGD gene report format true - - - + + + beta12orEarlier + beta12orEarlier + + Entry format of the Rat Genome Database (RGD). + RGD gene report format - true - beta12orEarlier - Entry format of the Rat Genome Database (RGD). - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + Entry format of the Saccharomyces Genome Database (SGD). + SGD gene report format - true - beta12orEarlier - beta12orEarlier - Entry format of the Saccharomyces Genome Database (SGD). - - - - GeneDB gene report format - + + + beta12orEarlier + beta12orEarlier + Entry format of the Sanger GeneDB genome database. + + GeneDB gene report format true - beta12orEarlier - beta12orEarlier - - - - TAIR gene report format - - beta12orEarlier - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + Entry format of The Arabidopsis Information Resource (TAIR) genome database. + + TAIR gene report format true - - - - WormBase gene report format - + + + beta12orEarlier + beta12orEarlier + Entry format of the WormBase genomes database. - beta12orEarlier - beta12orEarlier + + WormBase gene report format true - - - + + + beta12orEarlier + beta12orEarlier + + Entry format of the Zebrafish Information Network (ZFIN) genome database. + ZFIN gene report format - - beta12orEarlier - beta12orEarlier true - Entry format of the Zebrafish Information Network (ZFIN) genome database. - - - + + + beta12orEarlier + beta12orEarlier + + Entry format of the TIGR genome database. + TIGR gene report format - true - Entry format of the TIGR genome database. - beta12orEarlier - beta12orEarlier - - - - dbSNP polymorphism report format - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + Entry format for the dbSNP database. + + dbSNP polymorphism report format true - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + Format of an entry from the OMIM database of genotypes and phenotypes. + OMIM entry format - - beta12orEarlier true - beta12orEarlier - Format of an entry from the OMIM database of genotypes and phenotypes. - - - + + + beta12orEarlier + beta12orEarlier + + Format of a record from the HGVbase database of genotypes and phenotypes. + HGVbase entry format - true - Format of a record from the HGVbase database of genotypes and phenotypes. - beta12orEarlier - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + Format of a record from the HIVDB database of genotypes and phenotypes. + HIVDB entry format - - beta12orEarlier - beta12orEarlier true - Format of a record from the HIVDB database of genotypes and phenotypes. - - - - KEGG DISEASE entry format - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + Format of an entry from the KEGG DISEASE database. + + KEGG DISEASE entry format true - beta12orEarlier - - - + + + + beta12orEarlier + Report format on PCR primers and hybridisation oligos as generated by Whitehead primer3 program. + + Primer3 primer - - - Report format on PCR primers and hybridization oligos as generated by Whitehead primer3 program. - beta12orEarlier - - - - ABI - - + + + + beta12orEarlier A format of raw sequence read data from an Applied Biosystems sequencing machine. - beta12orEarlier - - + + + ABI - - mira - - + + + + beta12orEarlier Format of MIRA sequence trace information file. - beta12orEarlier - - + + + mira - - CAF - - - Common Assembly Format (CAF). A sequence assembly format including contigs, base-call qualities, and other metadata. - beta12orEarlier - - - + + + + beta12orEarlier + + Common Assembly Format (CAF). A sequence assembly format including contigs, base-call qualities, and other metadata. + + + CAF - - exp - - + + + + beta12orEarlier Sequence assembly project file EXP format. - beta12orEarlier - - + + + exp - - SCF - - - Staden Chromatogram Files format (SCF) of base-called sequence reads, qualities, and other metadata. - beta12orEarlier - - - + + + + beta12orEarlier + + Staden Chromatogram Files format (SCF) of base-called sequence reads, qualities, and other metadata. + + + SCF - - PHD - - - beta12orEarlier - PHD sequence trace format to store serialised chromatogram data (reads). - - - + + + + beta12orEarlier + + PHD sequence trace format to store serialised chromatogram data (reads). + + + PHD - - dat - - + + + - - + + - beta12orEarlier + beta12orEarlier Format of Affymetrix data file of raw image data. Affymetrix image data file format - - + + + dat - - cel - - + + + - - + + - beta12orEarlier - Affymetrix probe raw data format + beta12orEarlier Format of Affymetrix data file of information about (raw) expression levels of the individual probes. - - + Affymetrix probe raw data format + + + cel - - affymetrix - - + + + + beta12orEarlier Format of affymetrix gene cluster files (hc-genes.txt, hc-chips.txt) from hierarchical clustering. - beta12orEarlier - - + + + affymetrix - + + + beta12orEarlier + beta12orEarlier + + Entry format for the ArrayExpress microarrays database. + ArrayExpress entry format - - beta12orEarlier true - Entry format for the ArrayExpress microarrays database. - beta12orEarlier - - - - affymetrix-exp - - + + + + beta12orEarlier Affymetrix data file format for information about experimental conditions and protocols. Affymetrix experimental conditions data file format - beta12orEarlier - - + + + affymetrix-exp - - CHP - - + + + - - + + - Affymetrix probe normalised data format - beta12orEarlier + beta12orEarlier Format of Affymetrix data file of information about (normalised) expression levels of the individual probes. - - + Affymetrix probe normalised data format + + + CHP - - EMDB entry format - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + Format of an entry from the Electron Microscopy DataBase (EMDB). + + EMDB entry format true - beta12orEarlier - - - - KEGG PATHWAY entry format - - beta12orEarlier - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + The format of an entry from the KEGG PATHWAY database of pathway maps for molecular interactions and reaction networks. + + KEGG PATHWAY entry format true - - - + + + beta12orEarlier + beta12orEarlier + + The format of an entry from the MetaCyc metabolic pathways database. + MetaCyc entry format - true - beta12orEarlier - The format of an entry from the MetaCyc metabolic pathways database. - beta12orEarlier - - - - HumanCyc entry format - + + + beta12orEarlier + beta12orEarlier + The format of a report from the HumanCyc metabolic pathways database. + + HumanCyc entry format true - beta12orEarlier - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + The format of an entry from the INOH signal transduction pathways database. + INOH entry format - - beta12orEarlier true - The format of an entry from the INOH signal transduction pathways database. - beta12orEarlier - - - - PATIKA entry format - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + The format of an entry from the PATIKA biological pathways database. - beta12orEarlier + + PATIKA entry format true - - - - Reactome entry format - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + The format of an entry from the reactome biological pathways database. + + Reactome entry format true - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + The format of an entry from the aMAZE biological pathways and molecular interactions database. + aMAZE entry format - - beta12orEarlier true - The format of an entry from the aMAZE biological pathways and molecular interactions database. - beta12orEarlier - - - - CPDB entry format - + + + beta12orEarlier + beta12orEarlier + The format of an entry from the CPDB database. - beta12orEarlier + + CPDB entry format true - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + The format of an entry from the Panther Pathways database. + Panther Pathways entry format - - beta12orEarlier true - beta12orEarlier - The format of an entry from the Panther Pathways database. - - - - Taverna workflow format - - - Format of Taverna workflows. + + + + beta12orEarlier Format of Taverna workflows. - beta12orEarlier - - + Format of Taverna workflows. + + + Taverna workflow format - - BioModel mathematical model format - - beta12orEarlier - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + Format of mathematical models from the BioModel database. - true + Models are annotated and linked to relevant data resources, such as publications, databases of compounds and pathways, controlled vocabularies, etc. - - + BioModel mathematical model format + true - - KEGG LIGAND entry format - + + + beta12orEarlier + beta12orEarlier + The format of an entry from the KEGG LIGAND chemical database. - beta12orEarlier - beta12orEarlier + + KEGG LIGAND entry format true - - - - KEGG COMPOUND entry format - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + The format of an entry from the KEGG COMPOUND database. + + KEGG COMPOUND entry format true - beta12orEarlier - - - - KEGG PLANT entry format - - beta12orEarlier - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + The format of an entry from the KEGG PLANT database. + + KEGG PLANT entry format true - - - + + + beta12orEarlier + beta12orEarlier + + The format of an entry from the KEGG GLYCAN database. + KEGG GLYCAN entry format - true - beta12orEarlier - The format of an entry from the KEGG GLYCAN database. - beta12orEarlier - - - - PubChem entry format - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + The format of an entry from PubChem. + + PubChem entry format true - beta12orEarlier - - - - ChemSpider entry format - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + The format of an entry from a database of chemical structures and property predictions. - beta12orEarlier + + ChemSpider entry format true - - - - ChEBI entry format - - beta12orEarlier - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + The format of an entry from Chemical Entities of Biological Interest (ChEBI). - true + ChEBI includes an ontological classification defining relations between entities or classes of entities. - - + ChEBI entry format + true - - MSDchem ligand dictionary entry format - + + + beta12orEarlier + beta12orEarlier + The format of an entry from the MSDchem ligand dictionary. - beta12orEarlier + + MSDchem ligand dictionary entry format true - beta12orEarlier - - - - HET group dictionary entry format - - + + + + beta12orEarlier The format of an entry from the HET group dictionary (HET groups from PDB files). - beta12orEarlier - - + + + HET group dictionary entry format - - KEGG DRUG entry format - + + + beta12orEarlier + beta12orEarlier + The format of an entry from the KEGG DRUG database. + + KEGG DRUG entry format true - beta12orEarlier - beta12orEarlier - - - - PubMed citation - - - beta12orEarlier + + + + beta12orEarlier Format of bibliographic reference as used by the PubMed database. - - + + + PubMed citation - - Medline Display Format - - - beta12orEarlier + + + + beta12orEarlier Format for abstracts of scientific articles from the Medline database. + + Bibliographic reference information including citation information is included - - + Medline Display Format - - CiteXplore-core - - - beta12orEarlier + + + + beta12orEarlier CiteXplore 'core' citation format including title, journal, authors and abstract. - - + + + CiteXplore-core - - CiteXplore-all - - + + + + beta12orEarlier CiteXplore 'all' citation format includes all known details such as Mesh terms and cross-references. - beta12orEarlier - - + + + CiteXplore-all - - pmc - - - beta12orEarlier + + + + beta12orEarlier Article format of the PubMed Central database. - - + + + pmc - - iHOP text mining abstract format - - - beta12orEarlier - iHOP abstract format. - - + + + + + beta12orEarlier + The format of iHOP (Information Hyperlinked over Proteins) text-mining result. + + + iHOP format + - - Oscar3 - - - Oscar 3 performs chemistry-specific parsing of chemical documents. It attempts to identify chemical names, ontology concepts and chemical data from a document. - Text mining abstract format from the Oscar 3 application. - beta12orEarlier - - + + + + + + beta12orEarlier + OSCAR format of annotated chemical text. + + + OSCAR (Open-Source Chemistry Analysis Routines) software performs chemistry-specific parsing of chemical documents. It attempts to identify chemical names, ontology concepts, and chemical data from a document. + OSCAR format - + + + beta12orEarlier + beta13 + + Format of an ATOM record (describing data for an individual atom) from a PDB file. + PDB atom record format - true - beta13 - beta12orEarlier - Format of an ATOM record (describing data for an individual atom) from a PDB file. - - - - CATH chain report format - - The report (for example http://www.cathdb.info/chain/1cukA) includes chain identifiers, domain identifiers and CATH codes for domains in a given protein chain. - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + Format of CATH domain classification information for a polypeptide chain. - beta12orEarlier + + The report (for example http://www.cathdb.info/chain/1cukA) includes chain identifiers, domain identifiers and CATH codes for domains in a given protein chain. + CATH chain report format true - - - - CATH PDB report format - - beta12orEarlier - beta12orEarlier - true + + + beta12orEarlier + beta12orEarlier + Format of CATH domain classification information for a protein PDB file. + The report (for example http://www.cathdb.info/pdb/1cuk) includes chain identifiers, domain identifiers and CATH codes for domains in a given PDB file. - - + CATH PDB report format + true - + + + beta12orEarlier + beta12orEarlier + + Entry (gene) format of the NCBI database. + NCBI gene report format - true - Entry (gene) format of the NCBI database. - beta12orEarlier - beta12orEarlier - - - - GeneIlluminator gene report format - + + + beta12orEarlier + beta12orEarlier + + Moby:GI_Gene Report format for biological functions associated with a gene name and its alternative names (synonyms, homonyms), as generated by the GeneIlluminator service. + This includes a gene name and abbreviation of the name which may be in a name space indicating the gene status and relevant organisation. - beta12orEarlier - beta12orEarlier - Moby:GI_Gene + GeneIlluminator gene report format true - - - - BacMap gene card format - + + + beta12orEarlier + beta12orEarlier + + Moby:BacMapGeneCard Format of a report on the DNA and protein sequences for a given gene label from a bacterial chromosome maps from the BacMap database. + + BacMap gene card format true - beta12orEarlier - beta12orEarlier - Moby:BacMapGeneCard - - - - ColiCard report format - + + + beta12orEarlier + beta12orEarlier + Format of a report on Escherichia coli genes, proteins and molecules from the CyberCell Database (CCDB). + + ColiCard report format true - beta12orEarlier - Moby:ColiCard - beta12orEarlier - - - - PlasMapper TextMap - - - beta12orEarlier + + + + beta12orEarlier Map of a plasmid (circular DNA) in PlasMapper TextMap format. - - + + + PlasMapper TextMap - - newick - newick - - - nh - beta12orEarlier + + + + beta12orEarlier Phylogenetic tree Newick (text) format. - - + nh + + + newick + newick - - TreeCon format - - - beta12orEarlier + + + + beta12orEarlier Phylogenetic tree TreeCon (text) format. - - + + + TreeCon format - - Nexus format - - + + + + beta12orEarlier Phylogenetic tree Nexus (text) format. - beta12orEarlier - - + + + Nexus format + + + + + + + + + + + beta12orEarlier + Data model + A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere. + Data format + Exchange format + File format + + + The main focus in EDAM lies on formats as means of structuring data exchanged between different tools or resources. The serialisation, compression, or encoding of concrete data formats/models is not in scope of EDAM. Format 'is format of' Data. + Format + "http://purl.obolibrary.org/obo/IAO_0000098" + "http://purl.org/dc/elements/1.1/format" + http://en.wikipedia.org/wiki/File_format + http://en.wikipedia.org/wiki/List_of_file_formats + http://purl.org/biotop/biotop.owl#MachineLanguage + http://purl.org/biotop/biotop.owl#Quality + http://semanticscience.org/resource/SIO_000612 + http://semanticscience.org/resource/SIO_000618 + http://wsio.org/compression_004 + http://www.ifomis.org/bfo/1.1/snap#Continuant + http://www.ifomis.org/bfo/1.1/snap#Quality + http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality + http://www.onto-med.de/ontologies/gfo.owl#Perpetuant + http://www.onto-med.de/ontologies/gfo.owl#Symbol_structure + + + + Data model + A defined data format has its implicit or explicit data model, and EDAM does not distinguish the two. Some data models however do not have any standard way of serialisation into an exchange format, and those are thus not considered formats in EDAM. (Remark: even broader - or closely related - term to 'Data model' would be an 'Information model'.) + + + + + File format + File format denotes only formats of a computer file, but the same formats apply also to data blobs or exchanged messages. + - - Atomic data format - - beta12orEarlier - beta13 + + + beta12orEarlier + beta13 + Data format for an individual atom. + + Atomic data format true - - - - Sequence record format - + + - - + + + beta12orEarlier Data format for a molecular sequence record. - beta12orEarlier - - + + + Sequence record format - - Sequence feature annotation format - + + - - + + - beta12orEarlier + beta12orEarlier Data format for molecular sequence feature information. - - + + + Sequence feature annotation format - - Alignment format - + + - - + + + beta12orEarlier Data format for molecular sequence alignment information. - beta12orEarlier - - + + + Alignment format - - acedb - - beta12orEarlier + + + beta12orEarlier ACEDB sequence format. - - + + + acedb - + + + beta12orEarlier + beta12orEarlier + + Clustalw output format. + clustal sequence format - true - beta12orEarlier - Clustalw output format. - beta12orEarlier - - - - codata - - + + + + beta12orEarlier Codata entry format. - beta12orEarlier - - + + + codata - - dbid - - beta12orEarlier + + + beta12orEarlier Fasta format variant with database name before ID. - - + + + dbid - - EMBL format - - + + + + beta12orEarlier EMBL entry format. - EMBL sequence format EMBL - beta12orEarlier - - + EMBL sequence format + + + EMBL format - - Staden experiment format - - + + + + beta12orEarlier Staden experiment file format. - beta12orEarlier - - + + + Staden experiment format - - FASTA format - FASTA - - - - beta12orEarlier + + + + + beta12orEarlier + FASTA format including NCBI-style IDs. FASTA format FASTA sequence format - FASTA format including NCBI-style IDs. - - + + + FASTA + FASTA format - - FASTQ - + + + beta12orEarlier + .fq FASTQ short read format ignoring quality scores. - beta12orEarlier FASTAQ - - + fq + + + FASTQ - - FASTQ-illumina - + + + beta12orEarlier FASTQ Illumina 1.3 short read format. - beta12orEarlier - - + + + FASTQ-illumina - - FASTQ-sanger - + + + beta12orEarlier FASTQ short read format with phred quality. - beta12orEarlier - - + + + FASTQ-sanger - - FASTQ-solexa - + + + beta12orEarlier FASTQ Solexa/Illumina 1.0 short read format. - beta12orEarlier - - + + + FASTQ-solexa - - fitch program - - + + + + beta12orEarlier Fitch program format. - beta12orEarlier - - + + + fitch program - - GCG - - + + + + beta12orEarlier + GCG sequence file format. GCG SSF - beta12orEarlier + + GCG SSF (single sequence file) file format. - GCG sequence file format. - - + GCG - - GenBank format - - - beta12orEarlier + + + + beta12orEarlier Genbank entry format. - - + GenBank + + + GenBank format - - genpept - - beta12orEarlier + + + beta12orEarlier Genpept protein entry format. + + Currently identical to refseqp format - - + genpept - - GFF2-seq - - + + + + beta12orEarlier GFF feature file format with sequence in the header. - beta12orEarlier - - + + + GFF2-seq - - GFF3-seq - - + + + + beta12orEarlier GFF3 feature file format with sequence. - beta12orEarlier - - + + + GFF3-seq - - giFASTA format - + + + beta12orEarlier FASTA sequence format including NCBI-style GIs. - beta12orEarlier - - + + + giFASTA format - - hennig86 - - - beta12orEarlier + + + + beta12orEarlier Hennig86 output sequence format. - - + + + hennig86 - - ig - - + + + + beta12orEarlier Intelligenetics sequence format. - beta12orEarlier - - + + + ig - - igstrict - - - beta12orEarlier + + + + beta12orEarlier Intelligenetics sequence format (strict version). - - + + + igstrict - - jackknifer - - + + + + beta12orEarlier Jackknifer interleaved and non-interleaved sequence format. - beta12orEarlier - - + + + jackknifer - - mase format - - - beta12orEarlier + + + + beta12orEarlier Mase program sequence format. - - + + + mase format - - mega-seq - - - beta12orEarlier + + + + beta12orEarlier Mega interleaved and non-interleaved sequence format. - - + + + mega-seq - - MSF - - GCG MSF - beta12orEarlier + + + beta12orEarlier GCG MSF (multiple sequence file) file format. - - + MSF + + + GCG MSF - - nbrf/pir - + + + beta12orEarlier NBRF/PIR entry sequence format. nbrf - beta12orEarlier pir - - + + + nbrf/pir - - nexus-seq - - - - beta12orEarlier + + + + + beta12orEarlier Nexus/paup interleaved sequence format. - - + + + nexus-seq - - pdbatom - - - - pdb format in EMBOSS. - beta12orEarlier + + + + + beta12orEarlier PDB sequence format (ATOM lines). - - + + + pdb format in EMBOSS. + pdbatom - - pdbatomnuc - - - - beta12orEarlier - pdbnuc format in EMBOSS. + + + + + beta12orEarlier PDB nucleotide sequence format (ATOM lines). - - + + + pdbnuc format in EMBOSS. + pdbatomnuc - - pdbseqresnuc - - - - pdbnucseq format in EMBOSS. + + + + + beta12orEarlier PDB nucleotide sequence format (SEQRES lines). - beta12orEarlier - - + + + pdbnucseq format in EMBOSS. + pdbseqresnuc - - pdbseqres - - - + + + + + beta12orEarlier PDB sequence format (SEQRES lines). - beta12orEarlier + + pdbseq format in EMBOSS. - - + pdbseqres - - Pearson format - - beta12orEarlier + + + beta12orEarlier Plain old FASTA sequence format (unspecified format for IDs). - - + + + Pearson format - - phylip sequence format - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + Phylip interleaved sequence format. + + phylip sequence format true - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + Phylip non-interleaved sequence format. + phylipnon sequence format - true - Phylip non-interleaved sequence format. - beta12orEarlier - beta12orEarlier - - - - raw - - - beta12orEarlier + + + + beta12orEarlier Raw sequence format with no non-sequence characters. - - + + + raw - - refseqp - - - beta12orEarlier + + + + beta12orEarlier Refseq protein entry sequence format. + + Currently identical to genpept format - - + refseqp - + + + beta12orEarlier + beta12orEarlier + + Selex sequence format. + selex sequence format - - beta12orEarlier true - beta12orEarlier - Selex sequence format. - - - - Staden format - - - beta12orEarlier - Staden suite sequence format. - - - + + + + beta12orEarlier + + - + Staden suite sequence format. + + + Staden format - - Stockholm format - - - Stockholm multiple sequence alignment format (used by Pfam and Rfam). - beta12orEarlier - + + + + beta12orEarlier + - - + Stockholm multiple sequence alignment format (used by Pfam and Rfam). + + + Stockholm format - - strider format - - + + + + beta12orEarlier DNA strider output sequence format. - beta12orEarlier - - + + + strider format - - UniProtKB format - - UniProt format - SwissProt format - beta12orEarlier + + + beta12orEarlier UniProtKB entry sequence format. - - + SwissProt format + UniProt format + + + UniProtKB format - - plain text format (unformatted) - - - beta12orEarlier + + + beta12orEarlier Plain text sequence format (essentially unformatted). - - + + + plain text format (unformatted) - + + + beta12orEarlier + beta12orEarlier + + Treecon output sequence format. + treecon sequence format - true - beta12orEarlier - beta12orEarlier - Treecon output sequence format. - - - - ASN.1 sequence format - - + + + + beta12orEarlier NCBI ASN.1-based sequence format. - beta12orEarlier - - + + + ASN.1 sequence format - - DAS format - - - das sequence format + + + + beta12orEarlier DAS sequence (XML) format (any type). - beta12orEarlier - - + das sequence format + + + DAS format - - dasdna - - - beta12orEarlier + + + + beta12orEarlier DAS sequence (XML) format (nucleotide-only). + + The use of this format is deprecated. - - + dasdna - - debug-seq - - + + + + beta12orEarlier EMBOSS debugging trace sequence format of full internal data content. - beta12orEarlier - - + + + debug-seq - - jackknifernon - - - beta12orEarlier + + + + beta12orEarlier Jackknifer output sequence non-interleaved format. - - + + + jackknifernon - - meganon sequence format - - beta12orEarlier - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + Mega non-interleaved output sequence format. + + meganon sequence format true - - - - NCBI format - + + + beta12orEarlier NCBI FASTA sequence format with NCBI-style IDs. - beta12orEarlier + + There are several variants of this. - - + NCBI format - - nexusnon - - - + + + + + beta12orEarlier Nexus/paup non-interleaved sequence format. - beta12orEarlier - - + + + nexusnon - - GFF2 - - beta12orEarlier - General Feature Format (GFF) of sequence features. - - - + + + beta12orEarlier + + General Feature Format (GFF) of sequence features. + + + GFF2 - - GFF3 - - beta12orEarlier + + + beta12orEarlier + + + Generic Feature Format version 3 (GFF3) of sequence features. - - - - + + + GFF3 - + + + beta12orEarlier + 1.7 + PIR feature format. + + pir - true - 1.7 - PIR feature format. - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + Swiss-Prot feature format. + swiss feature - true - Swiss-Prot feature format. - beta12orEarlier - beta12orEarlier - - - - DASGFF - - + + + + beta12orEarlier DAS GFF (XML) feature format. - das feature DASGFF feature - beta12orEarlier - - + das feature + + + DASGFF - - debug-feat - - + + + + beta12orEarlier EMBOSS debugging trace feature format of full internal data content. - beta12orEarlier - - + + + debug-feat - - EMBL feature - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + EMBL feature format. + + EMBL feature true - beta12orEarlier - - - - GenBank feature - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + Genbank feature format. - beta12orEarlier + + GenBank feature true - - - - ClustalW format - - - clustal - beta12orEarlier + + + + beta12orEarlier ClustalW format for (aligned) sequences. - - + clustal + + + ClustalW format - - debug - - + + + + beta12orEarlier EMBOSS alignment format for debugging trace of full internal data content. - beta12orEarlier - - + + + debug - - FASTA-aln - - - beta12orEarlier + + + + beta12orEarlier Fasta format for (aligned) sequences. - - + + + FASTA-aln - - markx0 - - beta12orEarlier + + + beta12orEarlier Pearson MARKX0 alignment format. - - + + + markx0 - - markx1 - + + + beta12orEarlier Pearson MARKX1 alignment format. - beta12orEarlier - - + + + markx1 - - markx10 - - beta12orEarlier + + + beta12orEarlier Pearson MARKX10 alignment format. - - + + + markx10 - - markx2 - - beta12orEarlier + + + beta12orEarlier Pearson MARKX2 alignment format. - - + + + markx2 - - markx3 - - beta12orEarlier + + + beta12orEarlier Pearson MARKX3 alignment format. - - + + + markx3 - - match - - + + + + beta12orEarlier Alignment format for start and end of matches between sequence pairs. - beta12orEarlier - - + + + match - - mega - + + + beta12orEarlier Mega format for (typically aligned) sequences. - beta12orEarlier - - + + + mega - - meganon - + + + beta12orEarlier Mega non-interleaved format for (typically aligned) sequences. - beta12orEarlier - - + + + meganon - + + + beta12orEarlier + beta12orEarlier + + MSF format for (aligned) sequences. + msf alignment format - true - beta12orEarlier - beta12orEarlier - MSF format for (aligned) sequences. - - - - nexus alignment format - + + + beta12orEarlier + beta12orEarlier + Nexus/paup format for (aligned) sequences. - beta12orEarlier - beta12orEarlier + + nexus alignment format true - - - + + + beta12orEarlier + beta12orEarlier + + Nexus/paup non-interleaved format for (aligned) sequences. + nexusnon alignment format - - beta12orEarlier true - Nexus/paup non-interleaved format for (aligned) sequences. - beta12orEarlier - - - - pair - + + + beta12orEarlier EMBOSS simple sequence pair alignment format. - beta12orEarlier - - + + + pair - - PHYLIP format - - phy - beta12orEarlier - ph - http://www.bioperl.org/wiki/PHYLIP_multiple_alignment_format - PHYLIP interleaved format + + + beta12orEarlier + http://www.bioperl.org/wiki/PHYLIP_multiple_alignment_format Phylip format for (aligned) sequences. - - + PHYLIP interleaved format + ph + phy + + + PHYLIP format - - phylipnon - - http://www.bioperl.org/wiki/PHYLIP_multiple_alignment_format - beta12orEarlier - PHYLIP sequential format + + + beta12orEarlier + http://www.bioperl.org/wiki/PHYLIP_multiple_alignment_format Phylip non-interleaved format for (aligned) sequences. - - + PHYLIP sequential format + + + phylipnon - - scores format - - + + + + beta12orEarlier Alignment format for score values for pairs of sequences. - beta12orEarlier - - + + + scores format - - selex - - - - beta12orEarlier + + + + + beta12orEarlier SELEX format for (aligned) sequences. - - + + + selex - - EMBOSS simple format - - + + + + beta12orEarlier EMBOSS simple multiple alignment format. - beta12orEarlier - - + + + EMBOSS simple format - - srs format - - - beta12orEarlier + + + + beta12orEarlier Simple multiple sequence (alignment) format for SRS. - - + + + srs format - - srspair - - - beta12orEarlier + + + + beta12orEarlier Simple sequence pair (alignment) format for SRS. - - + + + srspair - - T-Coffee format - - + + + + beta12orEarlier T-Coffee program alignment format. - beta12orEarlier - - + + + T-Coffee format - - TreeCon-seq - - - + + + + + beta12orEarlier Treecon format for (aligned) sequences. - beta12orEarlier - - + + + TreeCon-seq - - Phylogenetic tree format - + + - - + + + beta12orEarlier Data format for a phylogenetic tree. - beta12orEarlier - - + + + Phylogenetic tree format - - Biological pathway or network format - + + - - + + - beta12orEarlier + beta12orEarlier Data format for a biological pathway or network. - - + + + Biological pathway or network format - - Sequence-profile alignment format - + + - - + + - beta12orEarlier + beta12orEarlier Data format for a sequence-profile alignment. - - + + + Sequence-profile alignment format - + + + beta12orEarlier + beta12orEarlier + + Data format for a sequence-HMM profile alignment. + Sequence-profile alignment (HMM) format - - beta12orEarlier - beta12orEarlier true - Data format for a sequence-HMM profile alignment. - - - - Amino acid index format - + + - - + + + beta12orEarlier Data format for an amino acid index. - beta12orEarlier - - + + + Amino acid index format - - Article format - + + - - + + - beta12orEarlier - Literature format + beta12orEarlier Data format for a full-text scientific article. - - + Literature format + + + Article format - - Text mining report format - + + - - + + - beta12orEarlier - Data format for an abstract (report) from text mining. - - + beta12orEarlier + Data format of a report from text mining. + + + Text mining report format - - Enzyme kinetics report format - + + - - + + + beta12orEarlier Data format for reports on enzyme kinetics. - beta12orEarlier - - + + + Enzyme kinetics report format - - Small molecule report format - + + - - + + - beta12orEarlier - Chemical compound annotation format + beta12orEarlier Format of a report on a chemical compound. - - + Chemical compound annotation format + + + Small molecule report format - - Gene annotation format - + + - - + + + beta12orEarlier Format of a report on a particular locus, gene, gene system or groups of genes. - beta12orEarlier - - + Gene features format + + + Gene annotation format - - Workflow format - - beta12orEarlier + + + beta12orEarlier Format of a workflow. - - + + + Workflow format - - Tertiary structure format - - beta12orEarlier + + + beta12orEarlier Data format for a molecular tertiary structure. - - + + + Tertiary structure format - - Biological model format - + + + beta12orEarlier + 1.2 + Data format for a biological model. - beta12orEarlier - 1.2 + + Biological model format true - - - - Chemical formula format - + + - - + + - beta12orEarlier + beta12orEarlier Text format of a chemical formula. - - + + + Chemical formula format - - Phylogenetic character data format - + + - - + + - beta12orEarlier + beta12orEarlier Format of raw (unplotted) phylogenetic data. - - + + + Phylogenetic character data format - - Phylogenetic continuous quantitative character format - + + - - + + + beta12orEarlier Format of phylogenetic continuous quantitative character data. - beta12orEarlier - - + + + Phylogenetic continuous quantitative character format - - Phylogenetic discrete states format - + + - - + + + beta12orEarlier Format of phylogenetic discrete states data. - beta12orEarlier - - + + + Phylogenetic discrete states format - - Phylogenetic tree report (cliques) format - + + - - + + + beta12orEarlier Format of phylogenetic cliques data. - beta12orEarlier - - + + + Phylogenetic tree report (cliques) format - - Phylogenetic tree report (invariants) format - + + - - + + - beta12orEarlier + beta12orEarlier Format of phylogenetic invariants data. - - + + + Phylogenetic tree report (invariants) format - + + + beta12orEarlier + beta12orEarlier + + Annotation format for electron microscopy models. + Electron microscopy model format - - beta12orEarlier true - beta12orEarlier - Annotation format for electron microscopy models. - - - - Phylogenetic tree report (tree distances) format - + + - - + + + beta12orEarlier Format for phylogenetic tree distance data. - beta12orEarlier - - + + + Phylogenetic tree report (tree distances) format - + + + beta12orEarlier + 1.0 + + Format for sequence polymorphism data. + Polymorphism report format - - beta12orEarlier true - 1.0 - Format for sequence polymorphism data. - - - Protein family report format - + + - - + + - beta12orEarlier + beta12orEarlier Format for reports on a protein family. - - + + + Protein family report format - - Protein interaction format - + + - - + + - beta12orEarlier - Format for molecular interaction data. + beta12orEarlier Molecular interaction format - - + Format for molecular interaction data. + + + Protein interaction format - - Sequence assembly format - + + - - + + - beta12orEarlier + beta12orEarlier Format for sequence assembly data. - - + + + Sequence assembly format - + + + beta12orEarlier + Format for information about a microarray experimental per se (not the data generated from that experiment). + + Microarray experiment data format - - beta12orEarlier - Format for microarray experimental data. - - - - Sequence trace format - + + - - + + + beta12orEarlier Format for sequence trace data (i.e. including base call information). - beta12orEarlier - - + + + Sequence trace format - - Gene expression report format - + + - - + + - Format for a report on gene expression. - beta12orEarlier - - + beta12orEarlier + Format of a file of gene expression data, e.g. a gene expression matrix or profile. + Gene expression data format + + + Gene expression report format - + + + beta12orEarlier + beta12orEarlier + + Format of a report on genotype / phenotype information. + Genotype and phenotype annotation format - - beta12orEarlier true - Format of a report on genotype / phenotype information. - beta12orEarlier - - - - Map format - + + - - + + + beta12orEarlier Format of a map of (typically one) molecular sequence annotated with features. - beta12orEarlier - - + + + Map format - + + + beta12orEarlier + Format of a report on PCR primers or hybridisation oligos in a nucleic acid sequence. + + Nucleic acid features (primers) format - - beta12orEarlier - Format of a report on PCR primers or hybridization oligos in a nucleic acid sequence. - - - - Protein report format - + + - - + + + beta12orEarlier Format of a report of general information about a specific protein. - beta12orEarlier - - + + + Protein report format - - Protein report (enzyme) format - + + + beta12orEarlier + beta12orEarlier + Format of a report of general information about a specific enzyme. - beta12orEarlier + + Protein report (enzyme) format true - beta12orEarlier - - - - 3D-1D scoring matrix format - + + - - + + - beta12orEarlier + beta12orEarlier Format of a matrix of 3D-1D scores (amino acid environment probabilities). - - + + + 3D-1D scoring matrix format - - Protein structure report (quality evaluation) format - + + - - + + + beta12orEarlier Format of a report on the quality of a protein three-dimensional model. - beta12orEarlier - - + + + Protein structure report (quality evaluation) format - - Database hits (sequence) format - + + - - + + + beta12orEarlier Format of a report on sequence hits and associated data from searching a sequence database. - beta12orEarlier - - + + + Database hits (sequence) format - - Sequence distance matrix format - + + - - + + - beta12orEarlier + beta12orEarlier Format of a matrix of genetic distances between molecular sequences. - - + + + Sequence distance matrix format - - Sequence motif format - + + - - + + + beta12orEarlier Format of a sequence motif. - beta12orEarlier - - + + + Sequence motif format - - Sequence profile format - + + - - + + + beta12orEarlier Format of a sequence profile. - beta12orEarlier - - + + + Sequence profile format - - Hidden Markov model format - + + - - + + - beta12orEarlier + beta12orEarlier Format of a hidden Markov model. - - + + + Hidden Markov model format - - Dirichlet distribution format - + + - - + + + beta12orEarlier Data format of a dirichlet distribution. - beta12orEarlier - - + + + Dirichlet distribution format - - HMM emission and transition counts format - + + - - + + - - + + + beta12orEarlier Data format for the emission and transition counts of a hidden Markov model. - beta12orEarlier - - + + + HMM emission and transition counts format - - RNA secondary structure format - + + - - + + - beta12orEarlier + beta12orEarlier Format for secondary structure (predicted or real) of an RNA molecule. - - + + + RNA secondary structure format - - Protein secondary structure format - + + + beta12orEarlier Format for secondary structure (predicted or real) of a protein molecule. - beta12orEarlier - - + + + Protein secondary structure format - - Sequence range format - + + - - + + - beta12orEarlier + beta12orEarlier Format used to specify range(s) of sequence positions. - - + + + Sequence range format - - pure - - + + + + beta12orEarlier Alphabet for molecular sequence with possible unknown positions but without non-sequence characters. - beta12orEarlier - - + + + pure - - unpure - - + + + + beta12orEarlier Alphabet for a molecular sequence with possible unknown positions but possibly with non-sequence characters. - beta12orEarlier - - + + + unpure - - unambiguous sequence - - + + + + beta12orEarlier Alphabet for a molecular sequence with possible unknown positions but without ambiguity characters. - beta12orEarlier - - + + + unambiguous sequence - - ambiguous - - - beta12orEarlier + + + + beta12orEarlier Alphabet for a molecular sequence with possible unknown positions and possible ambiguity characters. - - + + + ambiguous - - Sequence features (repeats) format - - beta12orEarlier + + + beta12orEarlier Format used for map of repeats in molecular (typically nucleotide) sequences. - - + + + Sequence features (repeats) format - - Nucleic acid features (restriction sites) format - - beta12orEarlier + + + beta12orEarlier Format used for report on restriction enzyme recognition sites in nucleotide sequences. - - + + + Nucleic acid features (restriction sites) format - - Gene features (coding region) format - - beta12orEarlier + + + beta12orEarlier + 1.10 Format used for report on coding regions in nucleotide sequences. - - + + + Gene features (coding region) format + true - - Sequence cluster format - + + - - + + - beta12orEarlier + beta12orEarlier Format used for clusters of molecular sequences. - - + + + Sequence cluster format - - Sequence cluster format (protein) - + + + beta12orEarlier Format used for clusters of protein sequences. - beta12orEarlier - - + + + Sequence cluster format (protein) - - Sequence cluster format (nucleic acid) - + + + beta12orEarlier Format used for clusters of nucleotide sequences. - beta12orEarlier - - + + + Sequence cluster format (nucleic acid) - + + + beta12orEarlier + beta13 + + Format used for clusters of genes. + Gene cluster format - true - beta13 - beta12orEarlier - Format used for clusters of genes. - - - - EMBL-like (text) - - - This concept may be used for the many non-standard EMBL-like text formats. - beta12orEarlier + + + + beta12orEarlier A text format resembling EMBL entry format. - - + + + This concept may be used for the many non-standard EMBL-like text formats. + EMBL-like (text) - - FASTQ-like format (text) - - + + + + beta12orEarlier A text format resembling FASTQ short read format. + + This concept may be used for non-standard FASTQ short read-like formats. - beta12orEarlier - - + FASTQ-like format (text) - - EMBLXML - + + + beta12orEarlier XML format for EMBL entries. - beta12orEarlier - - + + + EMBLXML - - cdsxml - + + + beta12orEarlier XML format for EMBL entries. - beta12orEarlier - - + + + cdsxml - - insdxml - - beta12orEarlier + + + beta12orEarlier XML format for EMBL entries. - - + + + insdxml - - geneseq - + + + beta12orEarlier Geneseq sequence format. - beta12orEarlier - - + + + geneseq - - UniProt-like (text) - - + + + + beta12orEarlier A text sequence format resembling uniprotkb entry format. - beta12orEarlier - - + + + UniProt-like (text) - + + + beta12orEarlier + 1.8 + UniProt entry sequence format. + + UniProt format - - beta12orEarlier true - UniProt entry sequence format. - 1.8 - - - - ipi - - 1.8 - beta12orEarlier + + + beta12orEarlier + 1.8 + ipi sequence format. + + ipi true - - - - medline - - + + + + beta12orEarlier Abstract format used by MedLine database. - beta12orEarlier - - + + + medline - - Ontology format - + + - - + + + beta12orEarlier Format used for ontologies. - beta12orEarlier - - + + + Ontology format - - OBO format - - beta12orEarlier + + + beta12orEarlier A serialisation format conforming to the Open Biomedical Ontologies (OBO) model. - - + + + OBO format - - OWL format - - + + + + beta12orEarlier A serialisation format conforming to the Web Ontology Language (OWL) model. - beta12orEarlier - - + + + OWL format - - FASTA-like (text) - - + + + + beta12orEarlier + A text format resembling FASTA format. + + This concept may also be used for the many non-standard FASTA-like formats. + FASTA-like (text) http://filext.com/file-extension/FASTA - beta12orEarlier - A text format resembling FASTA format. - - - - Sequence record full format - - 1.8 - beta12orEarlier + + + beta12orEarlier + 1.8 Data format for a molecular sequence record, typically corresponding to a full entry from a molecular sequence database. + + + Sequence record full format true - - - + + + beta12orEarlier + 1.8 + Data format for a molecular sequence record 'lite', typically molecular sequence and minimal metadata, such as an identifier of the sequence and/or a comment. + + Sequence record lite format - true - 1.8 - beta12orEarlier - Data format for a molecular sequence record 'lite', typically molecular sequence and minimal metadata, such as an identifier of the sequence and/or a comment. - - - - EMBL format (XML) - - beta12orEarlier + + + beta12orEarlier An XML format for EMBL entries. + + This is a placeholder for other more specific concepts. It should not normally be used for annotation. - - + EMBL format (XML) - - GenBank-like format (text) - - + + + + beta12orEarlier A text format resembling GenBank entry (plain text) format. + + This concept may be used for the non-standard GenBank-like text formats. - beta12orEarlier - - + GenBank-like format (text) - - Sequence feature table format (text) - + + + beta12orEarlier Text format for a sequence feature table. - beta12orEarlier - - + + + Sequence feature table format (text) - - Strain data format - + + + beta12orEarlier + 1.0 Format of a report on organism strain data / cell line. - beta12orEarlier + + Strain data format true - 1.0 - - - CIP strain data format - + + + beta12orEarlier + beta12orEarlier + Format for a report of strain data as used for CIP database entries. + + CIP strain data format true - beta12orEarlier - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + PHYLIP file format for phylogenetic property data. + phylip property values - true - PHYLIP file format for phylogenetic property data. - beta12orEarlier - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + Entry format (HTML) for the STRING database of protein interaction. + STRING entry format (HTML) - - beta12orEarlier true - beta12orEarlier - Entry format (HTML) for the STRING database of protein interaction. - - - - STRING entry format (XML) - - + + + + beta12orEarlier Entry format (XML) for the STRING database of protein interaction. - beta12orEarlier - - + + + STRING entry format (XML) - - GFF - GFF - - + + + + beta12orEarlier GFF feature format (of indeterminate version). - beta12orEarlier - - + + + GFF + GFF - - GTF - - Gene Transfer Format (GTF), a restricted version of GFF. - beta12orEarlier + + + beta12orEarlier + - - - + Gene Transfer Format (GTF), a restricted version of GFF. + + + GTF - - FASTA-HTML - - + + + + beta12orEarlier FASTA format wrapped in HTML elements. - beta12orEarlier - - + + + FASTA-HTML - - EMBL-HTML - - + + + + beta12orEarlier EMBL entry format wrapped in HTML elements. - beta12orEarlier - - + + + EMBL-HTML - + + + beta12orEarlier + beta12orEarlier + + Format of an entry from the BioCyc enzyme database. + BioCyc enzyme report format - true - beta12orEarlier - beta12orEarlier - Format of an entry from the BioCyc enzyme database. - - - - ENZYME enzyme report format - + + + beta12orEarlier + beta12orEarlier + Format of an entry from the Enzyme nomenclature database (ENZYME). - beta12orEarlier - beta12orEarlier + + ENZYME enzyme report format true - - - + + + beta12orEarlier + beta12orEarlier + + Format of a report on a gene from the PseudoCAP database. + PseudoCAP gene report format - true - beta12orEarlier - beta12orEarlier - Format of a report on a gene from the PseudoCAP database. - - - - GeneCards gene report format - + + + beta12orEarlier + beta12orEarlier + Format of a report on a gene from the GeneCards database. - beta12orEarlier - beta12orEarlier + + GeneCards gene report format true - - - - Textual format - - Tabular format - http://filext.com/file-extension/TSV - http://www.iana.org/assignments/media-types/text/plain + + + + beta12orEarlier Textual format. + Plain text format + txt + + Data in text format can be compressed into binary format, or can be a value of an XML element or attribute. Markup formats are not considered textual (or more precisely, not plain-textual). + Textual format http://filext.com/file-extension/TXT - Plain text http://www.iana.org/assignments/media-types/media-types.xhtml#text - beta12orEarlier - - + http://www.iana.org/assignments/media-types/text/plain - - Many textual formats used in bioinformatics are tabular (tab-separated values, TSV). Typically with an additional header in their own format. - Tabular format - - - - - HTML - - + + + - - + + - James Malone - html, or HyperText Markup Language in full, is a data format specification is a markup language for web pages and is the publishing language of the World Wide Web. - http://www.w3.org/TR/html401/ + beta12orEarlier + html, or HyperText Markup Language in full, is a data format specification is a markup language for web pages and is the publishing language of the World Wide Web. + http://www.w3.org/TR/html401/ + James Malone HTML format. Hypertext Markup Language - beta12orEarlier + + + HTML http://filext.com/file-extension/HTML - - - - XML - XML - - Data in XML format can be serialised into text, or binary format. - beta12orEarlier - eXtensible Markup Language (XML) format. + + + + beta12orEarlier + xml + Extensible Markup Language (XML) is a standard set of rules for encoding documents in a machine-readable form defined by the W3C. James Malone - http://filext.com/file-extension/XML - Extensible Markup Language - - + + + eXtensible Markup Language (XML) format. + eXtensible Markup Language + + + Data in XML format can be serialised into text, or binary format. + XML + XML - - binary format - Binary format - - Only specific native binary formats are listed under 'Binary format' in EDAM. Generic binary formats - such as any data being zipped, or any XML data being serialised into the Efficient XML Interchange (EXI) format - are not modelled in EDAM. Refer to http://wsio.org/compression_004. - beta12orEarlier + + + + beta12orEarlier Binary format. - - + + + Only specific native binary formats are listed under 'Binary format' in EDAM. Generic binary formats - such as any data being zipped, or any XML data being serialised into the Efficient XML Interchange (EXI) format - are not modelled in EDAM. Refer to http://wsio.org/compression_004. + Binary format + binary format - + + + beta12orEarlier + beta13 + + Typical textual representation of a URI. + URI format - - beta13 true - Typical textual representation of a URI. - beta12orEarlier - - - + + + beta12orEarlier + beta12orEarlier + + The format of an entry from the NCI-Nature pathways database. + NCI-Nature pathway entry format - - beta12orEarlier true - The format of an entry from the NCI-Nature pathways database. - beta12orEarlier - - - - Format (typed) - + + + beta12orEarlier + A placeholder concept for visual navigation by dividing data formats by the content of the data that is represented. + Format (typed) + + This concept exists only to assist EDAM maintenance and navigation in graphical browsers. It does not add semantic information. The concept branch under 'Format (typed)' provides an alternative organisation of the concepts nested under the other top-level branches ('Binary', 'HTML', 'RDF', 'Text' and 'XML'. All concepts under here are already included under those branches. - beta12orEarlier - A broad class of format distinguished by the scientific nature of the data that is identified. - - + Format (by type of data) - - BioXSD - - - - - + + + + + + - - + + - - + + - - + + - BioXSD XML format - beta12orEarlier - BioXSD XML format of basic bioinformatics types of data (sequence records, alignments, feature records, references to resources, and more). - + + + + + + + + + + + + + + + + beta12orEarlier + + + + + + + Any ontology allowed, none mandatory. Preferrably with URIs but URIs are not mandatory. Non-ontology terms are also allowed as the last resort in case of a lack of suitable ontology. + 'BioXSD' belongs to the 'BioXSD|GTrack' ecosystem of generic formats. 'BioXSD in XML' is the XML format based on the common, unified 'BioXSD data model', a.k.a. 'BioXSD|BioJSON|BioYAML'. + BioXSD + BioXSD data model + BioXSD format + BioXSD/GTrack + BioXSD|BioJSON|BioYAML + BioXSD|GTrack - - + + BioXSD-schema-based XML format of sequence-based data and some other common data - sequence records, alignments, feature records, references to resources, and more - optimised for integrative bioinformatics, Web services, and object-oriented programming. + BioXSD XML + BioXSD XML format + BioXSD in XML + BioXSD in XML format + BioXSD+XML + + + BioXSD (XML) - - RDF format - - - beta12orEarlier + + + + + beta12orEarlier + A serialisation format conforming to the Resource Description Framework (RDF) model. - - + Resource Description Framework format + RDF + Resource Description Framework + + + RDF format - - GenBank-HTML - - - beta12orEarlier + + + + beta12orEarlier Genbank entry format wrapped in HTML elements. - - + + + GenBank-HTML - + + + beta12orEarlier + beta12orEarlier + + Format of a report on protein features (domain composition). + Protein features (domains) format - - beta12orEarlier true - beta12orEarlier - Format of a report on protein features (domain composition). - - - - EMBL-like format - - beta12orEarlier + + + beta12orEarlier A format resembling EMBL entry (plain text) format. + + This concept may be used for the many non-standard EMBL-like formats. - - + EMBL-like format - - FASTQ-like format - + + + beta12orEarlier A format resembling FASTQ short read format. + + This concept may be used for non-standard FASTQ short read-like formats. - beta12orEarlier - - + FASTQ-like format - - FASTA-like - - This concept may be used for the many non-standard FASTA-like formats. - beta12orEarlier + + + beta12orEarlier A format resembling FASTA format. - - + + + This concept may be used for the many non-standard FASTA-like formats. + FASTA-like - - uniprotkb-like format - - - beta12orEarlier + + + + beta12orEarlier A sequence format resembling uniprotkb entry format. - - + + + uniprotkb-like format - - Sequence feature table format - + + - - + + + beta12orEarlier Format for a sequence feature table. - beta12orEarlier - - + + + Sequence feature table format - - OBO Flat File Format - OBO - - - beta12orEarlier + + + + beta12orEarlier OBO format is the text file format used by OBO-Edit, the open source, platform-independent application for viewing and editing ontologies. OBO flat file format OBO ontology text format. - - + + + OBO + OBO Flat File Format - - OBO-XML - - - beta12orEarlier + + + + beta12orEarlier OBO ontology XML format. - - + + + OBO-XML - - Sequence record format (text) - + + + beta12orEarlier Data format for a molecular sequence record. - beta12orEarlier - - + + + Sequence record format (text) - - Sequence record format (XML) - - beta12orEarlier + + + beta12orEarlier Data format for a molecular sequence record. - - + + + Sequence record format (XML) - - Sequence feature table format (XML) - + + + beta12orEarlier XML format for a sequence feature table. - beta12orEarlier - - + + + Sequence feature table format (XML) - - Alignment format (text) - + + + beta12orEarlier Text format for molecular sequence alignment information. - beta12orEarlier - - + + + Alignment format (text) - - Alignment format (XML) - + + + beta12orEarlier XML format for molecular sequence alignment information. - beta12orEarlier - - + + + Alignment format (XML) - - Phylogenetic tree format (text) - - beta12orEarlier + + + beta12orEarlier Text format for a phylogenetic tree. - - + + + Phylogenetic tree format (text) - - Phylogenetic tree format (XML) - - beta12orEarlier + + + beta12orEarlier XML format for a phylogenetic tree. - - + + + Phylogenetic tree format (XML) - - EMBL-like (XML) - - + + + + beta12orEarlier An XML format resembling EMBL entry format. + + This concept may be used for the any non-standard EMBL-like XML formats. - beta12orEarlier - - + EMBL-like (XML) - - GenBank-like format - + + + beta12orEarlier A format resembling GenBank entry (plain text) format. - beta12orEarlier + + This concept may be used for the non-standard GenBank-like formats. - - + GenBank-like format - - STRING entry format - - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + Entry format for the STRING database of protein interaction. - beta12orEarlier + + STRING entry format true - - - - Sequence assembly format (text) - - beta12orEarlier + + + beta12orEarlier Text format for sequence assembly data. - - + + + Sequence assembly format (text) - - Amino acid identifier format - - beta13 + + + beta12orEarlier + beta13 + Text format (representation) of amino acid residues. + + Amino acid identifier format true - beta12orEarlier - - - - completely unambiguous - - - beta12orEarlier + + + + beta12orEarlier Alphabet for a molecular sequence without any unknown positions or ambiguity characters. - - + + + completely unambiguous - - completely unambiguous pure - - - beta12orEarlier + + + + beta12orEarlier Alphabet for a molecular sequence without unknown positions, ambiguity or non-sequence characters. - - + + + completely unambiguous pure - - completely unambiguous pure nucleotide - - + + + + beta12orEarlier Alphabet for a nucleotide sequence (characters ACGTU only) without unknown positions, ambiguity or non-sequence characters . - beta12orEarlier - - + + + completely unambiguous pure nucleotide - - completely unambiguous pure dna - - - beta12orEarlier + + + + beta12orEarlier Alphabet for a DNA sequence (characters ACGT only) without unknown positions, ambiguity or non-sequence characters. - - + + + completely unambiguous pure dna - - completely unambiguous pure rna sequence - - + + + + beta12orEarlier Alphabet for an RNA sequence (characters ACGU only) without unknown positions, ambiguity or non-sequence characters. - beta12orEarlier - - + + + completely unambiguous pure rna sequence - - Raw sequence format - + + - - + + - http://www.onto-med.de/ontologies/gfo.owl#Symbol_sequence - beta12orEarlier + beta12orEarlier Format of a raw molecular sequence (i.e. the alphabet used). - - + + + Raw sequence format + http://www.onto-med.de/ontologies/gfo.owl#Symbol_sequence - - BAM - - - - beta12orEarlier - BAM format, the binary, BGZF-formatted compressed version of SAM format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data. - - - + + + + + beta12orEarlier + + BAM format, the binary, BGZF-formatted compressed version of SAM format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data. + + + BAM - - SAM - - - - The format supports short and long reads (up to 128Mbp) produced by different sequencing platforms and is used to hold mapped data within the GATK and across the Broad Institute, the Sanger Centre, and throughout the 1000 Genomes project. - beta12orEarlier - Sequence Alignment/Map (SAM) format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data. - - - + + + + + beta12orEarlier + + .sam + Sequence Alignment/Map format + Sequence Alignment/Map (SAM) format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data. + + + The format supports short and long reads (up to 128Mbp) produced by different sequencing platforms and is used to hold mapped data within the GATK and across the Broad Institute, the Sanger Centre, and throughout the 1000 Genomes project. + SAM - - SBML - - - Systems Biology Markup Language - Systems Biology Markup Language (SBML), the standard XML format for models of biological processes such as for example metabolism, cell signaling, and gene regulation. + + + + beta12orEarlier + Systems Biology Markup Language (SBML) is a machine-readable format for representing models. It's oriented towards describing systems where biological entities are involved in, and modified by, processes that occur over time. + Systems Biology Markup Language http://sbml.org - beta12orEarlier - - - + Systems Biology Markup Language (SBML), the standard XML format for models of biological processes such as for example metabolism, cell signaling, and gene regulation. + + + SBML - - completely unambiguous pure protein - - - beta12orEarlier + + + + beta12orEarlier Alphabet for any protein sequence without unknown positions, ambiguity or non-sequence characters. - - + + + completely unambiguous pure protein - - Bibliographic reference format - + + - - + + - - + + + beta12orEarlier Format of a bibliographic reference. - beta12orEarlier - - + + + Bibliographic reference format - - Sequence annotation track format - + + - - + + + beta12orEarlier Format of a sequence annotation track. - beta12orEarlier - - + + + Sequence annotation track format - - Alignment format (pair only) - + + - - + + - beta12orEarlier + beta12orEarlier Data format for molecular sequence alignment information that can hold sequence alignment(s) of only 2 sequences. - - + + + Alignment format (pair only) - - Sequence variation annotation format - + + - - + + + beta12orEarlier Format of sequence variation annotation. - beta12orEarlier - - + + + Sequence variation annotation format - - markx0 variant - - + + + + beta12orEarlier Some variant of Pearson MARKX alignment format. - beta12orEarlier - - + + + markx0 variant - - mega variant - - - + + + + + beta12orEarlier Some variant of Mega format for (typically aligned) sequences. - beta12orEarlier - - + + + mega variant - - Phylip format variant - - - - beta12orEarlier + + + + + beta12orEarlier Some variant of Phylip format for (aligned) sequences. - - + + + Phylip format variant - - AB1 - - - beta12orEarlier + + + + beta12orEarlier AB1 binary format of raw DNA sequence reads (output of Applied Biosystems' sequencing analysis software). Contains an electropherogram and the DNA base sequence. + + AB1 uses the generic binary Applied Biosystems, Inc. Format (ABIF). - - + AB1 - - ACE - - - ACE sequence assembly format including contigs, base-call qualities, and other metadata (version Aug 1998 and onwards). - beta12orEarlier - + + + + beta12orEarlier + - - + ACE sequence assembly format including contigs, base-call qualities, and other metadata (version Aug 1998 and onwards). + + + ACE - - BED format - BED - - - beta12orEarlier - BED detail format includes 2 additional columns (http://genome.ucsc.edu/FAQ/FAQformat#format1.7) and BED 15 includes 3 additional columns for experiment scores (http://genomewiki.ucsc.edu/index.php/Microarray_track). - Browser Extensible Data (BED) format of sequence annotation track, typically to be displayed in a genome browser. - + + + + beta12orEarlier + - - + Browser Extensible Data (BED) format of sequence annotation track, typically to be displayed in a genome browser. + + + BED detail format includes 2 additional columns (http://genome.ucsc.edu/FAQ/FAQformat#format1.7) and BED 15 includes 3 additional columns for experiment scores (http://genomewiki.ucsc.edu/index.php/Microarray_track). + BED + BED format - - bigBed - - - beta12orEarlier - bigBed format for large sequence annotation tracks, similar to textual BED format. - + + + + beta12orEarlier + - - + bigBed format for large sequence annotation tracks, similar to textual BED format. + + + bigBed - - WIG - - - Wiggle format (WIG) of a sequence annotation track that consists of a value for each sequence position. Typically to be displayed in a genome browser. - beta12orEarlier - + + + + beta12orEarlier + + Wiggle format - - + Wiggle format (WIG) of a sequence annotation track that consists of a value for each sequence position. Typically to be displayed in a genome browser. + + + WIG - - bigWig - - - beta12orEarlier - bigWig format for large sequence annotation tracks that consist of a value for each sequence position. Similar to textual WIG format. + + + + beta12orEarlier + - - - + bigWig format for large sequence annotation tracks that consist of a value for each sequence position. Similar to textual WIG format. + + + bigWig - - PSL - - - - PSL format of alignments, typically generated by BLAT or psLayout. Can be displayed in a genome browser like a sequence annotation track. - beta12orEarlier - + + + + + beta12orEarlier + - - + PSL format of alignments, typically generated by BLAT or psLayout. Can be displayed in a genome browser like a sequence annotation track. + + + PSL - - MAF - - - + + + + + beta12orEarlier + + .maf + Multiple Alignment Format (MAF) supporting alignments of whole genomes with rearrangements, directions, multiple pieces to the alignment, and so forth. + + Typically generated by Multiz and TBA aligners; can be displayed in a genome browser like a sequence annotation track. This should not be confused with MIRA Assembly Format or Mutation Annotation Format. - beta12orEarlier - - - - + MAF - - 2bit - - - beta12orEarlier - 2bit binary format of nucleotide sequences using 2 bits per nucleotide. In addition encodes unknown nucleotides and lower-case 'masking'. + + + + beta12orEarlier + - - - + 2bit binary format of nucleotide sequences using 2 bits per nucleotide. In addition encodes unknown nucleotides and lower-case 'masking'. + + + 2bit - - .nib - - - beta12orEarlier - .nib (nibble) binary format of a nucleotide sequence using 4 bits per nucleotide (including unknown) and its lower-case 'masking'. + + + + beta12orEarlier + - - - + .nib (nibble) binary format of a nucleotide sequence using 4 bits per nucleotide (including unknown) and its lower-case 'masking'. + + + .nib - - genePred - - + + + + beta12orEarlier + + genePred table format for gene prediction tracks. + + genePred format has 3 main variations (http://genome.ucsc.edu/FAQ/FAQformat#format9 http://www.broadinstitute.org/software/igv/genePred). They reflect UCSC Browser DB tables. - beta12orEarlier - - - - + genePred - - pgSnp - - - Personal Genome SNP (pgSnp) format for sequence variation tracks (indels and polymorphisms), supported by the UCSC Genome Browser. - beta12orEarlier - + + + + beta12orEarlier + - - + Personal Genome SNP (pgSnp) format for sequence variation tracks (indels and polymorphisms), supported by the UCSC Genome Browser. + + + pgSnp - - axt - - - beta12orEarlier - axt format of alignments, typically produced from BLASTZ. + + + + beta12orEarlier + - - - + axt format of alignments, typically produced from BLASTZ. + + + axt - - LAV - - - beta12orEarlier - LAV format of alignments generated by BLASTZ and LASTZ. - - - + + + + beta12orEarlier + + LAV format of alignments generated by BLASTZ and LASTZ. + + + LAV - - Pileup - - - beta12orEarlier - Pileup format of alignment of sequences (e.g. sequencing reads) to (a) reference sequence(s). Contains aligned bases per base of the reference sequence(s). - - + + + + beta12orEarlier + - + Pileup format of alignment of sequences (e.g. sequencing reads) to (a) reference sequence(s). Contains aligned bases per base of the reference sequence(s). + + + Pileup - - VCF - - - beta12orEarlier - Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation). - - + + + + beta12orEarlier + - + Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation). + + + VCF - - SRF - - - Sequence Read Format (SRF) of sequence trace data. Supports submission to the NCBI Short Read Archive. - beta12orEarlier - - - + + + + beta12orEarlier + + Sequence Read Format (SRF) of sequence trace data. Supports submission to the NCBI Short Read Archive. + + + SRF - - ZTR - - - ZTR format for storing chromatogram data from DNA sequencing instruments. - beta12orEarlier - - + + + + beta12orEarlier + - + ZTR format for storing chromatogram data from DNA sequencing instruments. + + + ZTR - - GVF - - - Genome Variation Format (GVF). A GFF3-compatible format with defined header and attribute tags for sequence variation. - beta12orEarlier - - + + + + beta12orEarlier + - + Genome Variation Format (GVF). A GFF3-compatible format with defined header and attribute tags for sequence variation. + + + GVF - - BCF - - - beta12orEarlier - BCF, the binary version of Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation). - - + + + + beta12orEarlier + BCF, the binary version of Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation). + + + BCF - - Matrix format - + + - - + + + beta13 Format of a matrix (array) of numerical values. - beta13 - - + + + Matrix format - - Protein domain classification format - + + - - + + + beta13 Format of data concerning the classification of the sequences and/or structures of protein structural domain(s). - beta13 - - + + + Protein domain classification format - - Raw SCOP domain classification format - + + + beta13 Format of raw SCOP domain classification data files. + + These are the parsable data files provided by SCOP. - beta13 - - + Raw SCOP domain classification format - - Raw CATH domain classification format - - These are the parsable data files provided by CATH. - beta13 + + + beta13 Format of raw CATH domain classification data files. - - + + + These are the parsable data files provided by CATH. + Raw CATH domain classification format - - CATH domain report format - + + + beta13 Format of summary of domain classification information for a CATH domain. - beta13 + + The report (for example http://www.cathdb.info/domain/1cukA01) includes CATH codes for levels in the hierarchy for the domain, level descriptions and relevant data and links. - - + CATH domain report format - - SBRML - - - 1.0 - Systems Biology Result Markup Language (SBRML), the standard XML format for simulated or calculated results (e.g. trajectories) of systems biology models. - - - + + + + 1.0 + + Systems Biology Result Markup Language (SBRML), the standard XML format for simulated or calculated results (e.g. trajectories) of systems biology models. + + + SBRML - - BioPAX - - BioPAX is an exchange format for pathway data, with its data model defined in OWL. - 1.0 + + + 1.0 + - - - + BioPAX is an exchange format for pathway data, with its data model defined in OWL. + + + BioPAX - - EBI Application Result XML - - - - EBI Application Result XML is a format returned by sequence similarity search Web services at EBI. - 1.0 - - + + + + + 1.0 + - + EBI Application Result XML is a format returned by sequence similarity search Web services at EBI. + + + EBI Application Result XML - - PSI MI XML (MIF) - - - Allyson Lister - 1.0 - Modified from http://wiki.cytoscape.org/GettingStarted, accessed 20 June 2012. - MIF + + + + 1.0 + + The PSI-MI format is an acronym for the Proteomics Standards Initiative - Molecular Interaction format. It provides an XML standard for molecular interactions and is supported by many molecular interaction databases and tools. PSI-MI format PSI-MIF - XML Molecular Interaction Format (MIF), standardised by HUPO PSI MI. - The PSI-MI format is an acronym for the Proteomics Standards Initiative - Molecular Interaction format. It provides an XML standard for molecular interactions and is supported by many molecular interaction databases and tools. - - + Modified from http://wiki.cytoscape.org/GettingStarted, accessed 20 June 2012. + Allyson Lister - + XML Molecular Interaction Format (MIF), standardised by HUPO PSI MI. + MIF + + + PSI MI XML (MIF) - - phyloXML - - - phyloXML is a standardised XML format for phylogenetic trees, networks, and associated data. - 1.0 + + + + 1.0 + - - - + phyloXML is a standardised XML format for phylogenetic trees, networks, and associated data. + + + phyloXML - - NeXML - - - 1.0 - NeXML is a standardised XML format for rich phyloinformatic data. - + + + + 1.0 + - - + NeXML is a standardised XML format for rich phyloinformatic data. + + + NeXML - - MAGE-ML - MAGE-ML - - - - 1.0 - MAGE-ML XML format for microarray expression data, standardised by MGED (now FGED). - - - + + + + + + + + + + 1.0 + + MAGE-ML XML format for microarray expression data, standardised by MGED (now FGED). + + + MAGE-ML + MAGE-ML - - MAGE-TAB - - - - - MAGE-TAB is a tab delimited data format comprimising of ADF file for array design, IDFfor experimental design, SDRF for sample data relationships and associated data files. - 1.0 + + + + + + + + + + + 1.0 + + MAGE-TAB is a tab delimited data format comprimising of ADF file for array design, IDFfor experimental design, SDRF for sample data relationships and associated data files. http://www.mged.org/mage-tab/ - A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. - MAGE-TAB textual format for microarray expression data, standardised by MGED (now FGED). - - - + MAGE-TAB textual format for microarray expression data, standardised by MGED (now FGED). + + + A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. + MAGE-TAB - - GCDML - - - GCDML XML format for genome and metagenome metadata according to MIGS/MIMS/MIMARKS information standards, standardised by the Genomic Standards Consortium (GSC). - 1.0 - + + + + 1.0 + - - + GCDML XML format for genome and metagenome metadata according to MIGS/MIMS/MIMARKS information standards, standardised by the Genomic Standards Consortium (GSC). + + + GCDML - - GTrack - - - 1.0 - GTrack is an optimised tabular format for genome/sequence feature tracks unifying the power of other tabular formats (e.g. GFF3, BED, WIG). - + + + + + + 1.0 + + + + + 'GTrack' belongs to the 'BioXSD|GTrack' ecosystem of generic formats, and particular to its subset, the 'GTrack ecosystem' (GTrack, GSuite, BTrack). 'GTrack' is the tabular format for representing features of sequences and genomes. + GTrack ecosystem of formats - - + + + GTrack is a generic and optimised tabular format for genome or sequence feature tracks. GTrack unifies the power of other track formats (e.g. GFF3, BED, WIG), and while optimised in size, adds more flexibility, customisation, and automation ("machine understandability"). + BioXSD/GTrack GTrack + BioXSD|GTrack GTrack + GTrack format + GTrack|BTrack|GSuite GTrack + GTrack|GSuite|BTrack GTrack + + + GTrack - - Biological pathway or network report format - + + - - + + + beta12orEarlier Data format for a report of information derived from a biological pathway or network. - beta12orEarlier - - + + + Biological pathway or network report format - - Experiment annotation format - + + - - + + - beta12orEarlier + beta12orEarlier Data format for annotation on a laboratory experiment. - - + + + Experiment annotation format - - Cytoband format - - + + + - - + + - 1.2 + 1.2 + + Cytoband format for chromosome cytobands. + + Reflects a UCSC Browser DB table. - - - - + Cytoband format - - CopasiML - - - - 1.2 - CopasiML, the native format of COPASI. - - + + + + + 1.2 + - + CopasiML, the native format of COPASI. + + + CopasiML - - CellML - - - CellML, the format for mathematical models of biological and other networks. - 1.2 - + + + + 1.2 + + - - + + CellML, the format for mathematical models of biological and other networks. + + + CellML - - PSI MI TAB (MITAB) - - - 1.2 - Tabular Molecular Interaction format (MITAB), standardised by HUPO PSI MI. + + + + 1.2 + - - - + Tabular Molecular Interaction format (MITAB), standardised by HUPO PSI MI. + + + PSI MI TAB (MITAB) - - PSI-PAR - - Protein affinity format (PSI-PAR), standardised by HUPO PSI MI. It is compatible with PSI MI XML (MIF) and uses the same XML Schema. - 1.2 - - + + + 1.2 + - + Protein affinity format (PSI-PAR), standardised by HUPO PSI MI. It is compatible with PSI MI XML (MIF) and uses the same XML Schema. + + + PSI-PAR - - mzML - - - mzML is the successor and unifier of the mzData format developed by PSI and mzXML developed at the Seattle Proteome Center. - 1.2 - mzML format for raw spectrometer output data, standardised by HUPO PSI MSS. - + + + + 1.2 + - - + mzML format for raw spectrometer output data, standardised by HUPO PSI MSS. + + + mzML is the successor and unifier of the mzData format developed by PSI and mzXML developed at the Seattle Proteome Center. + mzML - - Mass spectrometry data format - + + - - + + - 1.2 - Format for mass spectrometry data. - - + 1.2 + Format for mass pectra and derived data, include peptide sequences etc. + + + Mass spectrometry data format - - TraML - - - TraML (Transition Markup Language) is the format for mass spectrometry transitions, standardised by HUPO PSI MSS. - 1.2 - + + + + 1.2 + - - + TraML (Transition Markup Language) is the format for mass spectrometry transitions, standardised by HUPO PSI MSS. + + + TraML - - mzIdentML - - - mzIdentML is the exchange format for peptides and proteins identified from mass spectra, standardised by HUPO PSI PI. It can be used for outputs of proteomics search engines. - 1.2 + + + + 1.2 + - - - + mzIdentML is the exchange format for peptides and proteins identified from mass spectra, standardised by HUPO PSI PI. It can be used for outputs of proteomics search engines. + + + mzIdentML - - mzQuantML - - - mzQuantML is the format for quantitation values associated with peptides, proteins and small molecules from mass spectra, standardised by HUPO PSI PI. It can be used for outputs of quantitation software for proteomics. - 1.2 - + + + + 1.2 + - - + mzQuantML is the format for quantitation values associated with peptides, proteins and small molecules from mass spectra, standardised by HUPO PSI PI. It can be used for outputs of quantitation software for proteomics. + + + mzQuantML - - GelML - - - 1.2 - GelML is the format for describing the process of gel electrophoresis, standardised by HUPO PSI PS. + + + + 1.2 + - - - + GelML is the format for describing the process of gel electrophoresis, standardised by HUPO PSI PS. + + + GelML - - spML - - - 1.2 - spML is the format for describing proteomics sample processing, other than using gels, prior to mass spectrometric protein identification, standardised by HUPO PSI PS. It may also be applicable for metabolomics. + + + + 1.2 + - - - + spML is the format for describing proteomics sample processing, other than using gels, prior to mass spectrometric protein identification, standardised by HUPO PSI PS. It may also be applicable for metabolomics. + + + spML - - OWL Functional Syntax - - + + + + 1.2 A human-readable encoding for the Web Ontology Language (OWL). - 1.2 - - + + + OWL Functional Syntax - - Manchester OWL Syntax - - + + + + 1.2 A syntax for writing OWL class expressions. - 1.2 + + This format was influenced by the OWL Abstract Syntax and the DL style syntax. - - + Manchester OWL Syntax - - KRSS2 Syntax - - - This format is used in Protege 4. + + + + 1.2 A superset of the "Description-Logic Knowledge Representation System Specification from the KRSS Group of the ARPA Knowledge Sharing Effort". - 1.2 - - + + + This format is used in Protege 4. + KRSS2 Syntax - - Turtle - - + + + + 1.2 + The Terse RDF Triple Language (Turtle) is a human-friendly serialisation format for RDF (Resource Description Framework) graphs. + + The SPARQL Query Language incorporates a very similar syntax. - 1.2 - The Terse RDF Triple Language (Turtle) is a human-friendly serialization format for RDF (Resource Description Framework) graphs. - - + Turtle - - N-Triples - - - N-Triples should not be confused with Notation 3 which is a superset of Turtle. - 1.2 + + + + 1.2 A plain text serialisation format for RDF (Resource Description Framework) graphs, and a subset of the Turtle (Terse RDF Triple Language) format. - - + + + N-Triples should not be confused with Notation 3 which is a superset of Turtle. + N-Triples - - Notation3 - - + + + + A shorthand non-XML serialisation of Resource Description Framework model, designed with human-readability in mind. N3 - A shorthand non-XML serialization of Resource Description Framework model, designed with human-readability in mind. - - + + + Notation3 - - RDF/XML - - - - RDF + + + + 1.2 Resource Description Framework (RDF) XML format. - 1.2 + + + RDF/XML is a serialisation syntax for OWL DL, but not for OWL Full. + RDF/XML http://www.ebi.ac.uk/SWO/data/SWO_3000006 - RDF/XML is a serialization syntax for OWL DL, but not for OWL Full. - - - - OWL/XML - - + + + + 1.2 OWL ontology XML serialisation format. - 1.2 OWL - - + + + OWL/XML - - A2M - - - The A2M format is used as the primary format for multiple alignments of protein or nucleic-acid sequences in the SAM suite of tools. It is a small modification of FASTA format for sequences and is compatible with most tools that read FASTA. - 1.3 + + + + 1.3 + - - - + The A2M format is used as the primary format for multiple alignments of protein or nucleic-acid sequences in the SAM suite of tools. It is a small modification of FASTA format for sequences and is compatible with most tools that read FASTA. + + + A2M - - SFF - - - Standard flowgram format - Standard flowgram format (SFF) is a binary file format used to encode results of pyrosequencing from the 454 Life Sciences platform for high-throughput sequencing. - 1.3 - - + + + + 1.3 + - + Standard flowgram format (SFF) is a binary file format used to encode results of pyrosequencing from the 454 Life Sciences platform for high-throughput sequencing. + Standard flowgram format + + + SFF - - MAP - + + + 1.3 + The MAP file describes SNPs and is used by the Plink package. - 1.3 Plink MAP - - - + + + MAP - - PED - - Plink PED - 1.3 + + + 1.3 + The PED file describes individuals and genetic data and is used by the Plink package. - - - + Plink PED + + + PED - - Individual genetic data format - + + + 1.3 Data format for a metadata on an individual and their genetic data. - 1.3 - - + + + Individual genetic data format - - PED/MAP - - + + + + 1.3 + The PED/MAP file describes data used by the Plink package. Plink PED/MAP - 1.3 - - - + + + PED/MAP - - CT - - + + + + beta12orEarlier + + File format of a CT (Connectivity Table) file from the RNAstructure package. - beta12orEarlier Connect format Connectivity Table file format - - - - + + + CT - - SS - - - beta12orEarlier + + + + beta12orEarlier + XRNA old input style format. - - - + + + SS - - RNAML - - - + + + + + beta12orEarlier + RNA Markup Language. - beta12orEarlier - - - + + + RNAML - - GDE - - + + + + beta12orEarlier + Format for the Genetic Data Environment (GDE). - beta12orEarlier - - - + + + GDE - - BLC - - 1.3 - Block file format + + + 1.3 + A multiple alignment in vertical format, as used in the AMPS (Alignment of Multiple Protein Sequences) pacakge. - - - + Block file format + + + BLC - - Data index format - - + + + - - + + - 1.3 - - + 1.3 + + + Data index format - - BAI - + + - - + + - 1.3 + 1.3 + BAM indexing format - - - + + + BAI - - HMMER2 - + + + 1.3 + HMMER profile HMM file for HMMER versions 2.x - 1.3 - - - + + + HMMER2 - - HMMER3 - - 1.3 + + + 1.3 + HMMER profile HMM file for HMMER versions 3.x - - - + + + HMMER3 - - PO - + + + 1.3 + EMBOSS simple sequence pair alignment format. - 1.3 - - - + + + PO - - BLAST XML results format - - + + + + 1.3 XML format as produced by the NCBI Blast package - 1.3 - - + + + BLAST XML results format - - CRAM - - - Reference-based compression of alignment format - http://www.ebi.ac.uk/ena/software/cram-usage#format_specification http://samtools.github.io/hts-specs/CRAMv2.1.pdf + + + + 1.7 + http://www.ebi.ac.uk/ena/software/cram-usage#format_specification http://samtools.github.io/hts-specs/CRAMv2.1.pdf http://www.ebi.ac.uk/ena/software/cram-usage#format_specification http://samtools.github.io/hts-specs/CRAMv2.1.pdf - 1.7 - - + Reference-based compression of alignment format + + + CRAM - + + + + 1.7 + json + + + + + JavaScript Object Notation format; a lightweight, text-based format to represent tree-structured data using key-value pairs. + JavaScript Object Notation + + JSON - - 1.7 - Javascript Object Notation format; a lightweight, text-based format to represent structured data using key-value pairs. - - - - EPS - + + + 1.7 Encapsulated PostScript format - 1.7 - - + + + EPS - - GIF - - 1.7 + + + 1.7 Graphics Interchange Format. - - + + + GIF - - xls - - + + + + 1.7 Microsoft Excel spreadsheet format. Microsoft Excel format - 1.7 - - + + + xls - - TSV - - http://filext.com/file-extension/CSV - http://www.iana.org/assignments/media-types/text/csv + + + 1.7 + tsv|tab + + + Tabular data represented as tab-separated values in a text file. - 1.7 - http://filext.com/file-extension/TSV - CSV - - + Tab-separated values + + + TSV - - Gene expression data format - - - - - - - - 1.7 + + + 1.7 + 1.10 Format of a file of gene expression data, e.g. a gene expression matrix or profile. - - + + + Gene expression data format + true - - Cytoscape input file format - - + + + + 1.7 Format of the cytoscape input file of gene expression ratios or values are specified over one or more experiments. - 1.7 - - + + + Cytoscape input file format - - ebwt - + + - - + + - https://github.com/BenLangmead/bowtie/blob/master/MANUAL - Bowtie index format - 1.7 + 1.7 + https://github.com/BenLangmead/bowtie/blob/master/MANUAL Bowtie format for indexed reference genome for "small" genomes. - - + Bowtie index format + + + ebwt - - RSF - - http://www.molbiol.ox.ac.uk/tutorials/Seqlab_GCG.pdf - RSF-format files contain one or more sequences that may or may not be related. In addition to the sequence data, each sequence can be annotated with descriptive sequence information (from the GCG manual). + + + 1.7 + http://www.molbiol.ox.ac.uk/tutorials/Seqlab_GCG.pdf Rich sequence format. - 1.7 GCG RSF - - + + + RSF-format files contain one or more sequences that may or may not be related. In addition to the sequence data, each sequence can be annotated with descriptive sequence information (from the GCG manual). + RSF - - GCG format variant - - - - 1.7 + + + + + 1.7 Some format based on the GCG format. - - + + + GCG format variant - - BSML - - - http://rothlab.ucdavis.edu/genhelp/chapter_2_using_sequences.html#_Creating_and_Editing_Single_Sequenc + + + + 1.7 + http://rothlab.ucdavis.edu/genhelp/chapter_2_using_sequences.html#_Creating_and_Editing_Single_Sequenc Bioinformatics Sequence Markup Language format. - 1.7 - - + + + BSML - - ebwtl - + + - - + + - 1.7 - https://github.com/BenLangmead/bowtie/blob/master/MANUAL - Bowtie long index format + 1.7 + https://github.com/BenLangmead/bowtie/blob/master/MANUAL Bowtie format for indexed reference genome for "large" genomes. - - + Bowtie long index format + + + ebwtl - - Ensembl variation file format - - - Ensembl standard format for variation data. - 1.8 - - + + + + 1.8 + Ensembl standard format for variation data. + + + Ensembl variation file format - - docx - - - 1.8 + + + + 1.8 + Microsoft Word format. Microsoft Word format doc - Microsoft Word format. - - + + + docx - - Document format - - Portable Document Format - Microsoft Word format + + + 1.8 Format of documents including word processor, spreadsheet and presentation. - 1.8 - doc - - + + + Document format - - PDF - - - 1.8 + + + + 1.8 Portable Document Format - - + + + PDF - + - - Query and retrieval - - - - - - - + + - - + + - beta12orEarlier - Query - Retrieval - Search or query a data resource and retrieve entries and / or annotation. - Database retrieval - Search - - + 1.9 + Format used for images and image metadata. + + + Image format - + - - Data retrieval (database cross-reference) - - beta12orEarlier - Search database to retrieve all relevant references to a particular entity or entry. - true - beta13 - - + + + + 1.9 + + Medical image format corresponding to the Digital Imaging and Communications in Medicine (DICOM) standard. + + + + + DICOM format - + - - Annotation - - - - - - - - - - - - - - Annotate an entity (typically a biological or biomedical database entity) with terms from a controlled vocabulary. - beta12orEarlier - This is a broad concept and is used a placeholder for other, more specific concepts. - - + + + + 1.9 + + Medical image and metadata format of the Neuroimaging Informatics Technology Initiative. + + + NIfTI-1 format + + + nii - + - - Indexing - - - - - - - - Data indexing - beta12orEarlier - Generate an index of (typically a file of) biological data. - Database indexing - - + + + + 1.9 + + Text-based tagged file format for medical images generated using the MetaImage software package. + Metalmage format + + + mhd - + - - Data index analysis - - Database index analysis - Analyse an index of biological data. - beta12orEarlier - true - 1.6 - - + + + + 1.9 + + Nearly Raw Rasta Data format designed to support scientific visualisation and image processing involving N-dimensional raster data. + + + nrrd - + - - Annotation retrieval (sequence) - - true - beta12orEarlier - Retrieve basic information about a molecular sequence. - beta12orEarlier - - + + + 1.9 + File format used for scripts written in the R programming language for execution within the R software environment, typically for statistical computation and graphics. + + + + R file format - + - - Sequence generation - - - beta12orEarlier - Generate a molecular sequence by some means. - - + + + 1.9 + File format used for scripts for the Statistical Package for the Social Sciences. + + + + SPSS - + - - Sequence editing - - - Edit or change a molecular sequence, either randomly or specifically. - beta12orEarlier - - + + + 1.9 + + mhtml|mht|eml + + MHTML is not strictly an HTML format, it is encoded as an HTML email message (although with multipart/related instead of multipart/alternative). It, however, contains the main HTML block as its core, and thus it is for practical reasons incuded in EDAM as a specialisation of 'HTML'. + + + + MIME HTML format for Web pages, which can include external resources, including images, Flash animations and so on. + HTML email format + HTML email message format + MHT + MHT format + MHTML format + MIME HTML + MIME HTML format + MIME multipart + MIME multipart format + MIME multipart message + MIME multipart message format + + + MHTML - + - - Sequence merging - - beta12orEarlier - Merge two or more (typically overlapping) molecular sequences. - Sequence splicing - - + + + + + + + + + + 1.10 + Proprietary file format for (raw) BeadArray data used by genomewide profiling platforms from Illumina Inc. This format is output directly from the scanner and stores summary intensities for each probe-type on an array. + + + IDAT - + - - Sequence conversion - - - Convert a molecular sequence from one type to another. - beta12orEarlier - - + + + + 1.10 + + Joint Picture Group file format for lossy graphics file. + + + + Sequence of segments with markers. Begins with byte of 0xFF and follows by marker type. + JPG - + - - Sequence complexity calculation - - - - - - - - - - - - - - beta12orEarlier - Calculate sequence complexity, for example to find low-complexity regions in sequences. - - + + + + 1.10 + Reporter Code Count-A data file (.csv) output by the Nanostring nCounter Digital Analyzer, which contains gene sample information, probe information and probe counts. + + + rcc - + - - Sequence ambiguity calculation - - - - - - - - - - - - - - Calculate sequence ambiguity, for example identity regions in protein or nucleotide sequences with many ambiguity codes. - beta12orEarlier - - + + + 1.11 + + + ARFF (Attribute-Relation File Format) is an ASCII text file format that describes a list of instances sharing a set of attributes. + + + This file format is for machine learning. + arff - + - - Sequence composition calculation - - - - - - - - - - - - - - - beta12orEarlier - Calculate character or word composition or frequency of a molecular sequence. - - + + + + 1.11 + + + AFG is a single text-based file assembly format that holds read and consensus information together + + + afg - + - - Repeat sequence analysis - - - - - - - - Find and/or analyse repeat sequences in (typically nucleotide) sequences. - beta12orEarlier - Repeat sequences include tandem repeats, inverted or palindromic repeats, DNA microsatellites (Simple Sequence Repeats or SSRs), interspersed repeats, maximal duplications and reverse, complemented and reverse complemented repeats etc. Repeat units can be exact or imperfect, in tandem or dispersed, of specified or unspecified length. - - + + + + 1.11 + + + The bedGraph format allows display of continuous-valued data in track format. This display type is useful for probability scores and transcriptome data + + + Holds a tab-delimited chromosome /start /end / datavalue dataset. + bedgraph - + - - Sequence motif discovery - - - - - - - - - - - - - - Motifs and patterns might be conserved or over-represented (occur with improbable frequency). - beta12orEarlier - Discover new motifs or conserved patterns in sequences or sequence alignments (de-novo discovery). - Motif discovery - - + + + 1.11 + + + Browser Extensible Data (BED) format of sequence annotation track that strictly does not contain non-standard fields beyond the first 3 columns. + + + Galaxy allows BED files to contain non-standard fields beyond the first 3 columns, some other implementations do not. + bedstrict - + - - Sequence signature recognition - - - - - - - - - - - - - - beta12orEarlier - Motif search - Sequence motif search - Protein secondary database search - Motif detection - Sequence motif recognition - Sequence signature detection - Sequence profile search - Find (scan for) known motifs, patterns and regular expressions in molecular sequence(s). - Sequence motif detection - Motif recognition - - + + + 1.11 + + + BED file format where each feature is described by chromosome, start, end, name, score, and strand. + + + Tab delimited data in strict BED format - no non-standard columns allowed; column count forced to 6 + bed6 - + - - Sequence motif comparison - - - - - - - - - - - - - - beta12orEarlier - Find motifs shared by molecular sequences. - - + + + 1.11 + + + A BED file where each feature is described by all twelve columns. + + + Tab delimited data in strict BED format - no non-standard columns allowed; column count forced to 12 + bed12 - + - - Transcription regulatory sequence analysis - - beta12orEarlier - beta13 - Analyse the sequence, conformational or physicochemical properties of transcription regulatory elements in DNA sequences. - For example transcription factor binding sites (TFBS) analysis to predict accessibility of DNA to binding factors. - true - - + + + + 1.11 + + + Tabular format of chromosome names and sizes used by Galaxy. + + + Galaxy allows BED files to contain non-standard fields beyond the first 3 columns, some other implementations do not. + chrominfo - + - - Conserved transcription regulatory sequence identification - - - For example cross-species comparison of transcription factor binding sites (TFBS). Methods might analyse co-regulated or co-expressed genes, or sets of oppositely expressed genes. - beta12orEarlier - Identify common, conserved (homologous) or synonymous transcriptional regulatory motifs (transcription factor binding sites). - - + + + + 1.11 + + + Custom Sequence annotation track format used by Galaxy. + + + Used for tracks/track views within galaxy. + customtrack - + - - Protein property calculation (from structure) - - - - - - - - - - - - - - - This might be a residue-level search for properties such as solvent accessibility, hydropathy, secondary structure, ligand-binding etc. - Extract, calculate or predict non-positional (physical or chemical) properties of a protein from processing a protein (3D) structure. - beta12orEarlier - Protein structural property calculation - - + + + + 1.3 + + + Color space FASTA format sequence variant. + + + FASTA format extended for color space information. + csfasta - + - - Protein flexibility and motion analysis - - - beta12orEarlier - Analyse flexibility and motion in protein structure. - Use this concept for analysis of flexible and rigid residues, local chain deformability, regions undergoing conformational change, molecular vibrations or fluctuational dynamics, domain motions or other large-scale structural transitions in a protein structure. - - + + + 1.11 + + + HDF5 is a generic hierarchical data file format used to store and organize large amounts of data. + h5 + + + An HDF5 file appears to the user as a directed graph. The nodes of this graph are the higher-level HDF5 objects that are exposed by the HDF5 APIs: Groups, Datasets, Named datatypes. + hdf5 - + - - Protein structural motif recognition - - - - - - - - - Identify or screen for 3D structural motifs in protein structure(s). - This includes conserved substructures and conserved geometry, such as spatial arrangement of secondary structure or protein backbone. Methods might use structure alignment, structural templates, searches for similar electrostatic potential and molecular surface shape, surface-mapping of phylogenetic information etc. - beta12orEarlier - Protein structural feature identification - - + + + + 1.11 + + A versatile bitmap format. + + + The TIFF format is perhaps the most versatile and diverse bitmap format in existence. Its extensible nature and support for numerous data compression schemes allow developers to customize the TIFF format to fit any peculiar data storage needs. + + tiff - + - - Protein domain recognition - - - - - - - - - beta12orEarlier - Identify structural domains in a protein structure from first principles (for example calculations on structural compactness). - - + + + + 1.11 + + Standard bitmap storage format in the Microsoft Windows environment. + + + Although it is based on Windows internal bitmap data structures, it is supported by many non-Windows and non-PC applications. + bmp - + - - Protein architecture analysis - - beta12orEarlier - Analyse the architecture (spatial arrangement of secondary structure) of protein structure(s). - - + + + + 1.11 + + IM is a format used by LabEye and other applications based on the IFUNC image processing library. + + + IFUNC library reads and writes most uncompressed interchange versions of this format. + + im - + - - Residue interaction calculation - - - - - - - - - - - - - - WHATIF: SymShellTenXML - WHATIF:ListContactsRelaxed - WHATIF: SymShellTwoXML - WHATIF:ListSideChainContactsRelaxed - beta12orEarlier - WHATIF:ListSideChainContactsNormal - WHATIF:ListContactsNormal - Calculate or extract inter-atomic, inter-residue or residue-atom contacts, distances and interactions in protein structure(s). - WHATIF: SymShellFiveXML - WHATIF: SymShellOneXML - - + + + + 1.11 + + Photo CD format, which is the highest resolution format for images on a CD. + + + PCD was developed by Kodak. A PCD file contains five different resolution (ranging from low to high) of a slide or film negative. Due to it PCD is often used by many photographers and graphics professionals for high-end printed applications. + pcd - + - - Torsion angle calculation - - - - - - - - beta12orEarlier - Calculate, visualise or analyse phi/psi angles of a protein structure. - - + + + + 1.11 + + PCX is an image file format that uses a simple form of run-length encoding. It is lossless. + + + + pcx - + - - Protein property calculation - - - - - - - - - - - - - - - - Calculate (or predict) physical or chemical properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence. - This includes methods to render and visualise the properties of a protein sequence. - beta12orEarlier - Protein property rendering - - + + + + 1.11 + + The PPM format is a lowest common denominator color image file format. + + + + ppm - + - - Peptide immunogenicity prediction - - - - - - - - - - - - - - - beta12orEarlier - This is usually done in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data. - Predict antigenicity, allergenicity / immunogenicity, allergic cross-reactivity etc of peptides and proteins. - - + + + + 1.11 + + PSD (Photoshop Document) is a proprietary file that allows the user to work with the images’ individual layers even after the file has been saved. + + + psd - + - - Sequence feature detection - - - - - - - - - - - - - - - Sequence feature prediction - Predict, recognise and identify positional features in molecular sequences such as key functional sites or regions. - Sequence feature recognition - beta12orEarlier - Motif database search - SO:0000110 - - + + + + 1.11 + + X BitMap is a plain text binary image format used by the X Window System used for storing cursor and icon bitmaps used in the X GUI. + + + The XBM format was replaced by XPM for X11 in 1989. + xbm - + - - Data retrieval (feature table) - - beta13 - Extract a sequence feature table from a sequence database entry. - true - beta12orEarlier - - + + + + 1.11 + + X PixMap (XPM) is an image file format used by the X Window System, it is intended primarily for creating icon pixmaps, and supports transparent pixels. + + + + Sequence of segments with markers. Begins with byte of 0xFF and follows by marker type. + xpm - + - - Feature table query - - 1.6 - beta12orEarlier - true - Query the features (in a feature table) of molecular sequence(s). - - + + + + 1.11 + + RGB file format is the native raster graphics file format for Silicon Graphics workstations. + + + + rgb - + - - Sequence feature comparison - - - - - - - - - - - - - - - - - - - - - beta12orEarlier - Compare the feature tables of two or more molecular sequences. - Feature comparison - Feature table comparison - - + + + + 1.11 + + The PBM format is a lowest common denominator monochrome file format. It serves as the common language of a large family of bitmap image conversion filters. + + + + pbm - + - - Data retrieval (sequence alignment) - - beta12orEarlier - true - beta13 - Display basic information about a sequence alignment. - - + + + + 1.11 + + The PGM format is a lowest common denominator grayscale file format. + + + + It is designed to be extremely easy to learn and write programs for. + pgm - + - - Sequence alignment analysis - + + + + 1.11 + + PNG is a file format for image compression. + + png + + + It iis expected to replace the Graphics Interchange Format (GIF). + PNG + + + + + + + + + + 1.11 + + Scalable Vector Graphics (SVG) is an XML-based vector image format for two-dimensional graphics with support for interactivity and animation. + Scalable Vector Graphics + svg + + + The SVG specification is an open standard developed by the World Wide Web Consortium (W3C) since 1999. + SVG + + + + + + + + + + 1.11 + + Sun Raster is a raster graphics file format used on SunOS by Sun Microsystems + + + The SVG specification is an open standard developed by the World Wide Web Consortium (W3C) since 1999. + rast + + + + + + + + + - - + + - Analyse a molecular sequence alignment. - beta12orEarlier - - + 1.11 + Textual report format for sequence quality for reports from sequencing machines. + + + Sequence quality report format (text) - + - - Sequence alignment comparison - - - Compare (typically by aligning) two molecular sequence alignments. - beta12orEarlier - See also 'Sequence profile alignment'. - - + + + + 1.11 + http://en.wikipedia.org/wiki/Phred_quality_score + FASTQ format subset for Phred sequencing quality score data only (no sequences). + + + Phred quality scores are defined as a property which is logarithmically related to the base-calling error probabilities. + qual - + - - Sequence alignment conversion - - - beta12orEarlier - Convert a molecular sequence alignment from one type to another (for example amino acid to coding nucleotide sequence). - - + + + + 1.11 + FASTQ format subset for Phred sequencing quality score data only (no sequences) for Solexa/Illumina 1.0 format. + + + Solexa/Illumina 1.0 format can encode a Solexa/Illumina quality score from -5 to 62 using ASCII 59 to 126 (although in raw read data Solexa scores from -5 to 40 only are expected) + qualsolexa - + - - Nucleic acid property processing - - beta12orEarlier - true - Process (read and / or write) physicochemical property data of nucleic acids. - beta13 - - + + + + 1.11 + http://en.wikipedia.org/wiki/Phred_quality_score + FASTQ format subset for Phred sequencing quality score data only (no sequences) from Illumina 1.5 and before Illumina 1.8. + + + Starting in Illumina 1.5 and before Illumina 1.8, the Phred scores 0 to 2 have a slightly different meaning. The values 0 and 1 are no longer used and the value 2, encoded by ASCII 66 "B", is used also at the end of reads as a Read Segment Quality Control Indicator. + qualillumina - + - - Nucleic acid property calculation - - - - - - - - - beta12orEarlier - Calculate or predict physical or chemical properties of nucleic acid molecules, including any non-positional properties of the molecular sequence. - - + + + 1.11 + http://en.wikipedia.org/wiki/Phred_quality_score + FASTQ format subset for Phred sequencing quality score data only (no sequences) for SOLiD data. + + + For SOLiD data, the sequence is in color space, except the first position. The quality values are those of the Sanger format. + qualsolid - + - - Splice transcript prediction - - - - - - - - beta12orEarlier - Predict splicing alternatives or transcript isoforms from analysis of sequence data. - - + + + 1.11 + http://en.wikipedia.org/wiki/Phred_quality_score + FASTQ format subset for Phred sequencing quality score data only (no sequences) from 454 sequencers. + + + qual454 - + - - Frameshift detection - - - - - - - - - Detect frameshifts in DNA sequences, including frameshift sites and signals, and frameshift errors from sequencing projects. - Frameshift error detection - beta12orEarlier - Methods include sequence alignment (if related sequences are available) and word-based sequence comparison. - - + + + 1.11 + + + Human ENCODE peak format. + + + Format that covers both the broad peak format and narrow peak format from ENCODE. + ENCODE peak format - + - - Vector sequence detection - - - beta12orEarlier - Detect vector sequences in nucleotide sequence, typically by comparison to a set of known vector sequences. - - + + + 1.11 + + + Human ENCODE narrow peak format. + + + Format that covers both the broad peak format and narrow peak format from ENCODE. + ENCODE narrow peak format - + - - Protein secondary structure prediction - - - - - - - - - - Methods might use amino acid composition, local sequence information, multiple sequence alignments, physicochemical features, estimated energy content, statistical algorithms, hidden Markov models, support vector machines, kernel machines, neural networks etc. - Predict secondary structure of protein sequences. - Secondary structure prediction (protein) - beta12orEarlier - - + + + 1.11 + + + Human ENCODE broad peak format. + + + ENCODE broad peak format - + - - Protein super-secondary structure prediction - - - - - - - - beta12orEarlier - Predict super-secondary structure of protein sequence(s). - Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. - - + + + + 1.11 + + Blocked GNU Zip format. + + + BAM files are compressed using a variant of GZIP (GNU ZIP), into a format called BGZF (Blocked GNU Zip Format). + bgzip - + - - Transmembrane protein prediction - - - Predict and/or classify transmembrane proteins or transmembrane (helical) domains or regions in protein sequences. - beta12orEarlier - - + + + + 1.11 + + + TAB-delimited genome position file index format. + + + tabix - + - - Transmembrane protein analysis - - - - - - - - beta12orEarlier - Analyse transmembrane protein(s), typically by processing sequence and / or structural data, and write an informative report for example about the protein and its transmembrane domains / regions. - Use this (or child) concept for analysis of transmembrane domains (buried and exposed faces), transmembrane helices, helix topology, orientation, inter-helical contacts, membrane dipping (re-entrant) loops and other secondary structure etc. Methods might use pattern discovery, hidden Markov models, sequence alignment, structural profiles, amino acid property analysis, comparison to known domains or some combination (hybrid methods). - - + + + 1.11 + Data format for graph data. + + + Graph format - + - - Structure prediction - - - - - - - - - - - - - - - Predict tertiary structure of a molecular (biopolymer) sequence. - beta12orEarlier - - + + + 1.11 + + XML-based format used to store graph descriptions within Galaxy. + + + xgmml - + - - Residue interaction prediction - - - - - - - - - Methods usually involve multiple sequence alignment analysis. - Predict contacts, non-covalent interactions and distance (constraints) between amino acids in protein sequences. - beta12orEarlier - - + + + 1.11 + + SIF (simple interaction file) Format - a network/pathway format used for instance in cytoscape. + + + sif - + - - Protein interaction raw data analysis - - - - - - - - - - - - - - Analyse experimental protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc. - beta12orEarlier - - + + + + 1.11 + MS Excel spreadsheet format consisting of a set of XML documents stored in a ZIP-compressed file. + + + xlsx - + - - Protein-protein interaction prediction (from protein sequence) - - - beta12orEarlier - Identify or predict protein-protein interactions, interfaces, binding sites etc in protein sequences. - - + + + 1.11 + + Data format used by the SQLite database. + + + SQLite format - + - - Protein-protein interaction prediction (from protein structure) - - - - beta12orEarlier - Identify or predict protein-protein interactions, interfaces, binding sites etc in protein structures. - - + + + + 1.11 + + Data format used by the SQLite database conformant to the Gemini schema. + + + Gemini SQLite format - + - - Protein interaction network analysis - - - - - - - - + + + - - + + - beta12orEarlier - Analyse a network of protein interactions. - - + 1.11 + Format of a data index of some type. + + + Index format - + - - Protein interaction network comparison - - - beta12orEarlier - Compare two or more networks of protein interactions. - - + + + 1.11 + An index of a genome database, indexed for use by the snpeff tool. + + + snpeffdb - + - - RNA secondary structure prediction - - - + + - - + + - - - - - - - Predict RNA secondary structure (for example knots, pseudoknots, alternative structures etc). - beta12orEarlier - Methods might use RNA motifs, predicted intermolecular contacts, or RNA sequence-structure compatibility (inverse RNA folding). - - + 1.12 + + Binary format used by MATLAB files to store workspace variables. + .mat file format + MAT file format + MATLAB file format + + + MAT - + - - Nucleic acid folding prediction - - - - - - - - - - - - - - - - beta12orEarlier - Analyse some aspect of RNA/DNA folding, typically by processing sequence and/or structural data. - Nucleic acid folding modelling - Nucleic acid folding - - + + + 1.12 + + Format used by netCDF software library for writing and reading chromatography-MS data files. + ANDI-MS + + + netCDF - + - - Data retrieval (restriction enzyme annotation) - - beta13 - Restriction enzyme information retrieval - true - Retrieve information on restriction enzymes or restriction enzyme sites. - beta12orEarlier - - + + + 1.12 + Mascot Generic Format. Encodes multiple MS/MS spectra in a single file. + + + Files includes *m*/*z*, intensity pairs separated by headers; headers can contain a bit more information, including search engine instructions. + MGF - + - - Genetic marker identification - - true - beta12orEarlier - beta13 - Identify genetic markers in DNA sequences. - A genetic marker is any DNA sequence of known chromosomal location that is associated with and specific to a particular gene or trait. This includes short sequences surrounding a SNP, Sequence-Tagged Sites (STS) which are well suited for PCR amplification, a longer minisatellites sequence etc. - - + + + 1.12 + Spectral data format file where each spectrum is written to a separate file. + + + Each file contains one header line for the known or assumed charge and the mass of the precursor peptide ion, calculated from the measured *m*/*z* and the charge. This one line was then followed by all the *m*/*z*, intensity pairs that represent the spectrum. + dta - + - - Genetic mapping - - - - - - - - - beta12orEarlier - This includes mapping of the genetic architecture of dynamic complex traits (functional mapping), e.g. by characterization of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs). - Linkage mapping - Genetic map generation - Mapping involves ordering genetic loci along a chromosome and estimating the physical distance between loci. A genetic map shows the relative (not physical) position of known genes and genetic markers. - Generate a genetic (linkage) map of a DNA sequence (typically a chromosome) showing the relative positions of genetic markers based on estimation of non-physical distances. - Genetic map construction - Functional mapping - - + + + 1.12 + Spectral data file similar to dta. + + + Differ from .dta only in subtleties of the header line format and content and support the added feature of being able to. + pkl - + - - Linkage analysis - - - - - - - - - - - - - - beta12orEarlier - For example, estimate how close two genes are on a chromosome by calculating how often they are transmitted together to an offspring, ascertain whether two genes are linked and parental linkage, calculate linkage map distance etc. - Analyse genetic linkage. - - + + + 1.12 + https://dx.doi.org/10.1038%2Fnbt1031 + Common file format for proteomics mass spectrometric data developed at the Seattle Proteome Center/Institute for Systems Biology. + + + mzXML - + - - Codon usage table generation - - - - - - - - - Calculate codon usage statistics and create a codon usage table. - beta12orEarlier - Codon usage table construction - - + + + + 1.12 + http://sashimi.sourceforge.net/schema_revision/pepXML/pepXML_v118.xsd + Open data format for the storage, exchange, and processing of peptide sequence assignments of MS/MS scans, intended to provide a common data output format for many different MS/MS search engines and subsequent peptide-level analyses. + + + pepXML - + - - Codon usage table comparison - - - beta12orEarlier - Compare two or more codon usage tables. - - + + + + 1.12 + + Graphical Pathway Markup Language (GPML) is an XML format used + for exchanging biological pathways. + + + GPML - + - - Codon usage analysis - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - beta12orEarlier - synon: Codon usage data analysis - Process (read and / or write) codon usage data, e.g. analyse codon usage tables or codon usage in molecular sequences. - synon: Codon usage table analysis - - + + + + 1.12 + + oxlicg + + + + A list of k-mers and their occurences in a dataset. Can also be used as an implicit De Bruijn graph. + K-mer countgraph - + - - Base position variability plotting - - - - - - - - - - - - - - - Identify and plot third base position variability in a nucleotide sequence. - beta12orEarlier - - + + + + + 1.13 + + + mzTab is a tab-delimited format for mass spectrometry-based proteomics and metabolomics results. + + + mzTab - + - - Sequence word comparison - - Find exact character or word matches between molecular sequences without full sequence alignment. - beta12orEarlier - - + + + + + + 1.13 + + imzML|ibd + + imzML is a data format for mass spectrometry imaging data. NB.: See comment. + + + Data is recorded in 2 files: '.imzXML' is a metadata XML file based on mzML by HUPO-PSI, and '.ibd' is a binary file containing the mass spectra. + imzML - + - - Sequence distance matrix generation - - - - - - - - - - - - - - - Sequence distance matrix construction - Phylogenetic distance matrix generation - beta12orEarlier - Calculate a sequence distance matrix or otherwise estimate genetic distances between molecular sequences. - - + + + + + 1.13 + + + qcML is an XML format for quality-related data of mass spectrometry and other high-throughput measurements. + + + The focus of qcML is towards mass spectrometry based proteomics, but the format is suitable for metabolomics and sequencing as well. + qcML - + - - Sequence redundancy removal - - - - - - - - beta12orEarlier - Compare two or more molecular sequences, identify and remove redundant sequences based on some criteria. - - + + + + + 1.13 + + + PRIDE XML is an XML format for mass spectra, peptide and protein identifications, and metadata about a corresponding measurement, sample, experiment. + + + PRIDE XML - + - - Sequence clustering - - - - - - - - - - - - - - - - The clusters may be output or used internally for some other purpose. - Sequence cluster construction - beta12orEarlier - Build clusters of similar sequences, typically using scores from pair-wise alignment or other comparison of the sequences. - Sequence cluster generation - - + + + + + + 1.13 + + + Simulation Experiment Description Markup Language (SED-ML) is an XML format for encoding simulation setups, according to the MIASE (Minimum Information About a Simulation Experiment) requirements. + + + SED-ML - + - - Sequence alignment generation - - - - - - - - - - Sequence alignment construction - beta12orEarlier - Align (identify equivalent sites within) molecular sequences. - Sequence alignment - Sequence alignment computation - - + + + + + + 1.13 + + + Open Modeling EXchange format (OMEX) is a ZIPped format for encapsulating all information necessary for a modeling and simulation project in systems biology. + + + An OMEX file is a ZIP container that includes a manifest file, listing the content of the archive, an optional metadata file adding information about the archive and its content, and the files describing the model. OMEX is one of the standardised formats within COMBINE (Computational Modeling in Biology Network). + COMBINE OMEX - + - - Hybrid sequence alignment construction - - Hybrid sequence alignment - true - beta13 - beta12orEarlier - Align two or more molecular sequences of different types (for example genomic DNA to EST, cDNA or mRNA). - Hybrid sequence alignment generation - - + + + + + 1.13 + + + The Investigation / Study / Assay (ISA) tab-delimited (TAB) format incorporates metadata from +experiments employing a combination of technologies. + ISA-Tab + + + ISA-TAB is based on MAGE-TAB. Other than tabular, the ISA model can also be represented in RDF, and in JSON (compliable with a set of defined JSON Schemata). + ISA-TAB - + - - Structure-based sequence alignment - - Structure-based sequence alignment - Sequence alignment generation (structure-based) - Structure-based sequence alignment construction - beta12orEarlier - Sequence alignment (structure-based) - Structure-based sequence alignment generation - Align molecular sequences using sequence and structural information. - - + + + + + 1.13 + + + SBtab is a tabular format for biochemical network models. + + + SBtab - + - - Structure alignment - - - - - - - - - - Align (superimpose) molecular tertiary structures. - Structure alignment generation - Structure alignment construction - beta12orEarlier - Multiple structure alignment construction - Multiple structure alignment generation - - + + + + 1.13 + + + Biological Connection Markup Language (BCML) is an XML format for biological pathways. + + + BCML - + - - Sequence profile generation - - - - - - - - - - - - - - - - - - - - - Sequence profile construction - beta12orEarlier - Generate some type of sequence profile (for example a hidden Markov model) from a sequence alignment. - - + + + + 1.13 + + + Biological Dynamics Markup Language (BDML) is an XML format for quantitative data describing biological dynamics. + + + BDML - + - - 3D profile generation - - - - - - - - - - - - - - - - - - - - - Structural profile generation - Generate some type of structural (3D) profile or template from a structure or structure alignment. - Structural profile construction - beta12orEarlier - - + + + 1.13 + + + Biological Expression Language (BEL) is a textual format for representing scientific findings in life sciences in a computable form. + + + BEL - + - - Profile-to-profile alignment - - - - - - - - - - - - - - - - - - - - Sequence profile alignment - beta12orEarlier - See also 'Sequence alignment comparison'. - Sequence profile alignment construction - Align sequence profiles (representing sequence alignments). - Sequence profile alignment generation - - + + + + 1.13 + + + SBGN-ML is an XML format for Systems Biology Graphical Notation (SBGN) diagrams of biological pathways or networks. + + + SBGN-ML - + - - 3D profile-to-3D profile alignment - - - - - - - - - - - - - - - beta12orEarlier - 3D profile alignment (multiple) - 3D profile alignment - Multiple 3D profile alignment construction - Structural profile alignment construction (multiple) - Structural profile alignment - Structural profile alignment generation - Structural profile alignment construction - Align structural (3D) profiles or templates (representing structures or structure alignments). - - + + + + 1.13 + + + AGP is a tabular format for a sequence assembly (a contig, a scaffold/supercontig, or a chromosome). + + + AGP - + - - Sequence-to-profile alignment - - - - - - - - - - - - - - - - - - - - Sequence-profile alignment construction - Sequence-profile alignment generation - beta12orEarlier - Align molecular sequence(s) to sequence profile(s). - Sequence-profile alignment - A sequence profile typically represents a sequence alignment. Methods might perform one-to-one, one-to-many or many-to-many comparisons. - - + + + 1.13 + PostScript format + PostScript + + + PS - + - - Sequence-to-3D-profile alignment - - - - - - - - - - - - - - - beta12orEarlier - Sequence-3D profile alignment construction - Align molecular sequence(s) to structural (3D) profile(s) or template(s) (representing a structure or structure alignment). - Sequence-3D profile alignment generation - Methods might perform one-to-one, one-to-many or many-to-many comparisons. - Sequence-3D profile alignment - - + + + 1.13 + + SRA archive format (SRA) is the archive format used for input to the NCBI Sequence Read Archive. + SRA archive format + SRA + + + SRA format - + - - Protein threading - - - - - - - - - - - - - - - beta12orEarlier - Align molecular sequence to structure in 3D space (threading). - Use this concept for methods that evaluate sequence-structure compatibility by assessing residue interactions in 3D. Methods might perform one-to-one, one-to-many or many-to-many comparisons. - Sequence-structure alignment - - + + + 1.13 + + VDB ('vertical database') is the native format used for export from the NCBI Sequence Read Archive. + SRA native format + + + VDB - + - - Protein fold recognition - - - - + + - - + + - beta12orEarlier - Protein domain prediction - Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH. - Recognize (predict and identify) known protein structural domains or folds in protein sequence(s). - Protein fold prediction - - + 1.3 + + Index file format used by the samtools package to index TAB-delimited genome position files. + + + Tabix index file format - + - - Metadata retrieval - - - - - - - - Data retrieval (documentation) - Search for and retrieve data concerning or describing some core data, as distinct from the primary data that is being described. - Data retrieval (metadata) - beta12orEarlier - This includes documentation, general information and other metadata on entities such as databases, database entries and tools. - - + + + 1.13 + A five-column, tab-delimited table of feature locations and qualifiers for importing annotation into an existing Sequin submission (an NCBI tool for submitting and updating GenBank entries). + + + Sequin format - + - - Literature search - - - - - - - - - - - - - - beta12orEarlier - Query the biomedical and informatics literature. - - + + + 1.14 + Proprietary mass-spectrometry format of Thermo Scientific's ProteomeDiscoverer software. + Magellan storage file format + + + This format corresponds to an SQLite database, and you can look into the files with e.g. SQLiteStudio3. There are also some readers (http://doi.org/10.1021/pr2005154) and converters (http://doi.org/10.1016/j.jprot.2015.06.015) for this format available, which re-engineered the database schema, but there is no official DB schema specification of Thermo Scientific for the format. + MSF - + - - Text mining - - - - - - - - - - - - - + + - - + + - Text data mining - beta12orEarlier - Process and analyse text (typically the biomedical and informatics literature) to extract information from it. - - + 1.14 + Data format for biodiversity data. + + + Biodiversity data format - + - - Virtual PCR - + + - - + + - beta12orEarlier - Perform in-silico (virtual) PCR. - - + 1.14 + + Exchange format of the Access to Biological Collections Data (ABCD) Schema; a standard for the access to and exchange of data about specimens and observations (primary biodiversity data). + ABCD + + + ABCD format - + - - PCR primer design - - - - - - - - - - - - - - - - - - - - PCR primer prediction - Primer design involves predicting or selecting primers that are specific to a provided PCR template. Primers can be designed with certain properties such as size of product desired, primer size etc. The output might be a minimal or overlapping primer set. - Design or predict oligonucleotide primers for PCR and DNA amplification etc. - beta12orEarlier - - + + + + 1.14 + Tab-delimited text files of GenePattern that contain a column for each sample, a row for each gene, and an expression value for each gene in each sample. + GCT format + Res format + + + GCT/Res format - + - - Microarray probe design - - - - - - - - - - - - - - - - - - - - - - - - - - - Predict and/or optimize oligonucleotide probes for DNA microarrays, for example for transcription profiling of genes, or for genomes and gene families. - beta12orEarlier - Microarray probe prediction - - + + + + 1.14 + wiff + Mass spectrum file format from QSTAR and QTRAP instruments (ABI/Sciex). + wiff + + + WIFF format - + - - Sequence assembly - - - - - - - - - - - - - - - beta12orEarlier - For example, assemble overlapping reads from paired-end sequencers into contigs (a contiguous sequence corresponding to read overlaps). Or assemble contigs, for example ESTs and genomic DNA fragments, depending on the detected fragment overlaps. - Combine (align and merge) overlapping fragments of a DNA sequence to reconstruct the original sequence. - - + + + + + 1.14 + + Output format used by X! series search engines that is based on the XML language BIOML. + + + X!Tandem XML - + - - Microarray data standardization and normalization - - - - - - - - - - - - - - - beta12orEarlier - Standardize or normalize microarray data. - This includes statistical analysis, for example of variability amongst microarrays experiments, comparison of heterogeneous microarray platforms etc. - - + + + + 1.14 + Proprietary file format for mass spectrometry data from Thermo Scientific. + + + Proprietary format for which documentation is not available. + Thermo RAW - + - - Sequencing-based expression profile data processing - - Process (read and / or write) SAGE, MPSS or SBS experimental data. - true - beta12orEarlier - beta12orEarlier - - + + + + 1.14 + + "Raw" result file from Mascot database search. + + + Mascot .dat file - + - - Gene expression profile clustering - - - - - - - - - beta12orEarlier - Perform cluster analysis of gene expression (microarray) data, for example clustering of similar gene expression profiles. - - + + + + 1.14 + + Format of peak list files from Andromeda search engine (MaxQuant) that consist of arbitrarily many spectra. + MaxQuant APL + + + MaxQuant APL peaklist format - + - - Gene expression profiling - - - - - - - - - Expression profiling - Gene expression profile construction - Functional profiling - Generate a gene expression profile or pattern, for example from microarray data. - beta12orEarlier - Gene expression profile generation - - + + + 1.14 + + Synthetic Biology Open Language (SBOL) is an XML format for the specification and exchange of biological design information in synthetic biology. + + + SBOL introduces a standardised format for the electronic exchange of information on the structural and functional aspects of biological designs. + SBOL - + - - Gene expression profile comparison - - - - - - - - - beta12orEarlier - Compare gene expression profiles or patterns. - - + + + 1.14 + + PMML uses XML to represent mining models. The structure of the models is described by an XML Schema. + + + One or more mining models can be contained in a PMML document. + PMML - + - - Functional profiling - - true - beta12orEarlier - Interpret (in functional terms) and annotate gene expression data. - beta12orEarlier - - + + + + 1.14 + + Image file format used by the Open Microscopy Environment (OME). + + + + An OME-TIFF dataset consists of one or more files in standard TIFF or BigTIFF format, with the file extension .ome.tif or .ome.tiff, and an identical (or in the case of multiple files, nearly identical) string of OME-XML metadata embedded in the ImageDescription tag of each file’s first IFD (Image File Directory). BigTIFF file extensions are also permitted, with the file extension .ome.tf2, .ome.tf8 or .ome.btf, but note these file extensions are an addition to the original specification, and software using an older version of the specification may not be able to handle these file extensions. + OME develops open-source software and data format standards for the storage and manipulation of biological microscopy data. It is a joint project between universities, research establishments, industry and the software development community. + OME-TIFF - + - - EST and cDNA sequence analysis - - Analyse EST or cDNA sequences. - For example, identify full-length cDNAs from EST sequences or detect potential EST antisense transcripts. - beta12orEarlier - beta12orEarlier - true - - + + + 1.14 + + The LocARNA PP format combines sequence or alignment information and (respectively, single or consensus) ensemble probabilities into an PP 2.0 record. + + + Format for multiple aligned or single sequences together with the probabilistic description of the (consensus) RNA secondary structure ensemble by probabilities of base pairs, base pair stackings, and base pairs and unpaired bases in the loop of base pairs. + LocARNA PP - + - - Structural genomics target selection - - beta12orEarlier - Identify and select targets for protein structural determination. - beta12orEarlier - Methods will typically navigate a graph of protein families of known structure. - true - - + + + 1.14 + + Input format used by the Database of Genotypes and Phenotypes (dbGaP). + + + The Database of Genotypes and Phenotypes (dbGaP) is a National Institutes of Health (NIH) sponsored repository charged to archive, curate and distribute information produced by studies investigating the interaction of genotype and phenotype. + dbGaP format - + - - Protein secondary structure assignment - - - - - - - - - - - - - - beta12orEarlier - Assign secondary structure from protein coordinate or experimental data. - - + + + + + 1.15 + + biom + The BIological Observation Matrix (BIOM) is a format for representing biological sample by observation contingency tables in broad areas of comparative omics. The primary use of this format is to represent OTU tables and metagenome tables. + BIological Observation Matrix format + + + BIOM is a recognised standard for the Earth Microbiome Project, and is a project supported by Genomics Standards Consortium. Supported in QIIME, Mothur, MEGAN, etc. + BIOM format - + - - Protein structure assignment - - - - - - - - - - - - - - - beta12orEarlier - Assign a protein tertiary structure (3D coordinates) from raw experimental data. - - + + + + 1.15 + + + A format for storage, exchange, and processing of protein identifications created from ms/ms-derived peptide sequence data. + + + No human-consumable information about this format is available (see http://tools.proteomecenter.org/wiki/index.php?title=Formats:protXML). + protXML - + - - Protein model validation - - - - - - - - - - - - - - - - - - - - - Evaluate the quality or correctness a protein three-dimensional model. - Model validation might involve checks for atomic packing, steric clashes (bumps), volume irregularities, agreement with electron density maps, number of amino acid residues, percentage of residues with missing or bad atoms, irregular Ramachandran Z-scores, irregular Chi-1 / Chi-2 normality scores, RMS-Z score on bonds and angles etc. - WHATIF: CorrectedPDBasXML - Protein structure validation - WHATIF: UseFileDB - The PDB file format has had difficulties, inconsistencies and errors. Corrections can include identifying a meaningful sequence, removal of alternate atoms, correction of nomenclature problems, removal of incomplete residues and spurious waters, addition or removal of water, modelling of missing side chains, optimisation of cysteine bonds, regularisation of bond lengths, bond angles and planarities etc. - beta12orEarlier - - + + + + + 1.15 + + A linked data format enables publishing structured data as linked data (Linked Data), so that the data can be interlinked and become more useful through semantic queries. + Linked Data format + Semantic Web format + + + Linked data format - + - - Molecular model refinement - - - Protein model refinement - WHATIF: CorrectedPDBasXML - beta12orEarlier - Refine (after evaluation) a model of a molecular structure (typically a protein structure) to reduce steric clashes, volume irregularities etc. - - + + + + + 1.15 + + jsonld + + + + JSON-LD, or JavaScript Object Notation for Linked Data, is a method of encoding Linked Data using JSON. + JavaScript Object Notation for Linked Data + + + JSON-LD - + - - Phylogenetic tree generation - - - - - - - - - - - - - - - Phylogenetic trees are usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. - Phylogenetic tree construction - Construct a phylogenetic tree. - beta12orEarlier - - + + + 1.15 + + yaml|yml + + + YAML (YAML Ain't Markup Language) is a human-readable tree-structured data serialisation language. + YAML Ain't Markup Language + + + Data in YAML format can be serialised into text, or binary format. + YAML version 1.2 is a superset of JSON; prior versions were "not strictly compatible". + YAML - + - - Phylogenetic tree analysis - - - - - - - - - - - - - - beta12orEarlier - Analyse an existing phylogenetic tree or trees, typically to detect features or make predictions. - - + + + 1.16 + Tabular format + + Tabular data represented as values in a text file delimited by some character. + Delimiter-separated values + + + DSV - + - - Phylogenetic tree comparison - - - beta12orEarlier - Compare two or more phylogenetic trees. - For example, to produce a consensus tree, subtrees, supertrees, calculate distances between trees or test topological similarity between trees (e.g. a congruence index) etc. - - + + + 1.16 + csv + + + + Tabular data represented as comma-separated values in a text file. + Comma-separated values + + + CSV - + - - Phylogenetic tree editing - - - - - - - - - - - - - - - Edit a phylogenetic tree. - beta12orEarlier - - + + + + 1.16 + "Raw" result file from SEQUEST database search. + + + SEQUEST .out file - + - - Phylogenetic footprinting / shadowing - - - - - - - - A phylogenetic 'shadow' represents the additive differences between individual sequences. By masking or 'shadowing' variable positions a conserved sequence is produced with few or none of the variations, which is then compared to the sequences of interest to identify significant regions of conservation. - beta12orEarlier - Infer a phylogenetic tree by comparing orthologous sequences in different species, particularly many closely related species (phylogenetic shadowing). - - + + + + 1.16 + http://open-ms.sourceforge.net/schemas/ + XML file format for files containing information about peptide identifications from mass spectrometry data analysis carried out with OpenMS. + + + idXML - + - - Protein folding simulation - - beta12orEarlier - Simulate the folding of a protein. - - + + + 1.16 + Data table formatted such that it can be passed/streamed within the KNIME platform. + + + KNIME datatable format - + - - Protein folding pathway prediction - - - Predict the folding pathway(s) or non-native structural intermediates of a protein. - beta12orEarlier - - + + + + + 1.16 + + UniProtKB XML sequence features format is an XML format available for downloading UniProt entries. + UniProt XML + UniProt XML format + UniProtKB XML format + + + UniProtKB XML - + - - Protein SNP mapping - - - - - - - - - beta12orEarlier - Map and model the effects of single nucleotide polymorphisms (SNPs) on protein structure(s). - - + + + + 1.16 + + UniProtKB RDF sequence features format is an RDF format available for downloading UniProt entries (in RDF/XML). + UniProt RDF + UniProt RDF format + UniProtKB RDF format + UniProt RDF/XML + UniProt RDF/XML format + UniProtKB RDF/XML + UniProtKB RDF/XML format + + + UniProtKB RDF - + - - Protein modelling (mutation) - - + + + + + + - - + + - - + + - Methods might predict silent or pathological mutations. - Protein mutation modelling - Predict the effect of point mutation on a protein structure, in terms of strucural effects and protein folding, stability and function. - beta12orEarlier - - - - - - - - - - Immunogen design - - true - Design molecules that elicit an immune response (immunogens). - beta12orEarlier - beta12orEarlier - - + + + + + + + + + + + + + + + + + + + + 1.16 + + + + Work in progress. 'BioXSD' belongs to the 'BioXSD|GTrack' ecosystem of generic formats. 'BioJSON' is the JSON format based on the common, unified 'BioXSD data model', a.k.a. 'BioXSD|BioJSON|BioYAML'. + + BioJSON is a BioXSD-schema-based JSON format of sequence-based data and some other common data - sequence records, alignments, feature records, references to resources, and more - optimised for integrative bioinformatics, web applications and APIs, and object-oriented programming. + BioJSON (BioXSD data model) + BioJSON format (BioXSD) + BioXSD BioJSON + BioXSD BioJSON format + BioXSD JSON + BioXSD JSON format + BioXSD in JSON + BioXSD in JSON format + BioXSD+JSON + BioXSD/GTrack BioJSON + BioXSD|BioJSON|BioYAML BioJSON + BioXSD|GTrack BioJSON + + + BioJSON (BioXSD) - + - - Zinc finger prediction - + + + + + + - - + + - - + + - Predict and optimise zinc finger protein domains for DNA/RNA binding (for example for transcription factors and nucleases). - beta12orEarlier - - + + + + + + + + + + + + + + + + + + + + 1.16 + + + + Work in progress. 'BioXSD' belongs to the 'BioXSD|GTrack' ecosystem of generic formats. 'BioYAML' is the YAML format based on the common, unified 'BioXSD data model', a.k.a. 'BioXSD|BioJSON|BioYAML'. + + BioYAML is a BioXSD-schema-based YAML format of sequence-based data and some other common data - sequence records, alignments, feature records, references to resources, and more - optimised for integrative bioinformatics, web APIs, human readability and editting, and object-oriented programming. + BioXSD BioYAML + BioXSD BioYAML format + BioXSD YAML + BioXSD YAML format + BioXSD in YAML + BioXSD in YAML format + BioXSD+YAML + BioXSD/GTrack BioYAML + BioXSD|BioJSON|BioYAML BioYAML + BioXSD|GTrack BioYAML + BioYAML (BioXSD data model) + BioYAML (BioXSD) + BioYAML format + BioYAML format (BioXSD) + + + BioYAML - + - - Enzyme kinetics calculation - + + + + - - + + - - + + - beta12orEarlier - Calculate Km, Vmax and derived data for an enzyme reaction. - - + 1.16 + + + BioJSON is a JSON format of single multiple sequence alignments, with their annotations, features, and custom visualisation and application settings for the Jalview workbench. + BioJSON format (Jalview) + JSON (Jalview) + JSON format (Jalview) + Jalview BioJSON + Jalview BioJSON format + Jalview JSON + Jalview JSON format + + + BioJSON (Jalview) - + - - Formatting - - beta12orEarlier - Reformat a file of data (or equivalent entity in memory). - Format conversion - File formatting - Reformatting - File reformatting - File format conversion - - + + + + + + 1.16 + + + 'GSuite' belongs to the 'BioXSD|GTrack' ecosystem of generic formats, and particular to its subset, the 'GTrack ecosystem' (GTrack, GSuite, BTrack). 'GSuite' is the tabular format for an annotated collection of individual GTrack files. + + + GSuite is a tabular format for collections of genome or sequence feature tracks, suitable for integrative multi-track analysis. GSuite contains links to genome/sequence tracks, with additional metadata. + BioXSD/GTrack GSuite + BioXSD|GTrack GSuite + GSuite (GTrack ecosystem of formats) + GSuite format + GTrack|BTrack|GSuite GSuite + GTrack|GSuite|BTrack GSuite + + + GSuite + - + - - Format validation - - - Test and validate the format and content of a data file. - File format validation - beta12orEarlier - - + + + + + + 1.16 + 'BTrack' belongs to the 'BioXSD|GTrack' ecosystem of generic formats, and particular to its subset, the 'GTrack ecosystem' (GTrack, GSuite, BTrack). 'BTrack' is the binary, optionally compressed HDF5-based version of the GTrack and GSuite formats. + BTrack is an HDF5-based binary format for genome or sequence feature tracks and their collections, suitable for integrative multi-track analysis. BTrack is a binary, compressed alternative to the GTrack and GSuite formats. + BTrack (GTrack ecosystem of formats) + BTrack format + BioXSD/GTrack BTrack + BioXSD|GTrack BTrack + GTrack|BTrack|GSuite BTrack + GTrack|GSuite|BTrack BTrack + + + BTrack - + - - Visualisation - + + + - - + + - - + + - - + + - beta12orEarlier - Visualise, plot or render (graphically) biomolecular data such as molecular sequences or structures. - Rendering - - + 1.16 + + + + + + + Multi-Crop Passport Descriptors is a format available in 2 successive versions, V.1 (FAO/IPGRI 2001) and V.2 (FAO/Bioversity 2012). + + + + + The FAO/Bioversity/IPGRI Multi-Crop Passport Descriptors (MCPD) is an international standard format for exchange of germplasm information. + Bioversity MCPD + FAO MCPD + MCPD format + Multi-Crop Passport Descriptors + Multi-Crop Passport Descriptors format + IPGRI MCPD + MCPD V.1 + MCPD V.2 + + + MCPD + - + - - Sequence database search - - - - - - - - + + - - + + - Search a sequence database by sequence comparison and retrieve similar sequences. - -sequences matching a given sequence motif or pattern, such as a Prosite pattern or regular expression. - beta12orEarlier - This excludes direct retrieval methods (e.g. the dbfetch program). - - + 1.16 + Data format of an annotated text, e.g. with recognised entities, concepts, and relations. + + + Annotated text format - + - - Structure database search - - - - - - - - beta12orEarlier - Search a tertiary structure database, typically by sequence and/or structure comparison, or some other means, and retrieve structures and associated data. - - + + + + + 1.16 + + + JSON format of annotated scientific text used by PubAnnotations and other tools. + + + PubAnnotation format - + - - Protein secondary database search - - 1.8 - beta12orEarlier - true - Search a secondary protein database (of classification information) to assign a protein sequence(s) to a known protein family or group. - - + + + + + 1.16 + + + BioC is a standardised XML format for sharing and integrating text data and annotations. + + + BioC - + - - Motif database search - - beta12orEarlier - Screen a sequence against a motif or pattern database. - true - 1.8 - - + + + + + + 1.16 + + + Native textual export format of annotated scientific text from PubTator. + + + PubTator format - + - - Sequence profile database search - - true - beta12orEarlier - Search a database of sequence profiles with a query sequence. - 1.4 - - + + + + + 1.16 + + + A format of text annotation using the linked-data Open Annotation Data Model, serialised typically in RDF or JSON-LD. + + + Open Annotation format + - + - - Transmembrane protein database search - - true - beta12orEarlier - Search a database of transmembrane proteins, for example for sequence or structural similarities. - beta12orEarlier - - + + + + 1.16 + + + + + + + + + + + + + A family of similar formats of text annotation, used by BRAT and other tools, known as BioNLP Shared Task format (BioNLP 2009 Shared Task on Event Extraction, BioNLP Shared Task 2011, BioNLP Shared Task 2013), BRAT format, BRAT standoff format, and similar. + BRAT format + BRAT standoff format + + + BioNLP Shared Task format - + - - Sequence retrieval (by code) - - Query a database and retrieve sequences with a given entry code or accession number. - true - 1.6 - beta12orEarlier - - + + + + + + + + + 1.16 + A query language (format) for structured database queries. + Query format + + + Query language - + - - Sequence retrieval (by keyword) - - true - Query a database and retrieve sequences containing a given keyword. - beta12orEarlier - 1.6 - - + + + 1.16 + sql + + + + SQL (Structured Query Language) is the de-facto standard query language (format of queries) for querying and manipulating data in relational databases. + Structured Query Language + + + SQL + + + + + + + + + + 1.16 + + xq|xqy|xquery + + XQuery (XML Query) is a query language (format of queries) for querying and manipulating structured and unstructured data, usually in the form of XML, text, and with vendor-specific extensions for other data formats (JSON, binary, etc.). + XML Query + + + XQuery + + + + + + + + + + 1.16 + + + SPARQL (SPARQL Protocol and RDF Query Language) is a semantic query language for querying and manipulating data stored in Resource Description Framework (RDF) format. + SPARQL Protocol and RDF Query Language + + + SPARQL + + + + + + + + + + + beta12orEarlier + Function + A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs). + Computational method + Computational operation + Computational procedure + Computational subroutine + Function (programming) + Lambda abstraction + Mathematical function + Mathematical operation + Computational tool + Process + sumo:Function + + + Special cases are: a) An operation that consumes no input (has no input arguments). Such operation is either a constant function, or an operation depending only on the underlying state. b) An operation that may modify the underlying state but has no output. c) The singular-case operation with no input or output, that still may modify the underlying state. + Operation + http://en.wikipedia.org/wiki/Function_(computer_science) + http://en.wikipedia.org/wiki/Function_(mathematics) + http://en.wikipedia.org/wiki/Subroutine + http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Method + http://purl.org/biotop/biotop.owl#Function + http://semanticscience.org/resource/SIO_000017 + http://semanticscience.org/resource/SIO_000649 + http://wsio.org/operation_001 + http://www.ebi.ac.uk/swo/SWO_0000003 + http://www.ifomis.org/bfo/1.1/snap#Continuant + http://www.ifomis.org/bfo/1.1/snap#Function + http://www.ifomis.org/bfo/1.1/snap#Quality + http://www.ifomis.org/bfo/1.1/span#Process + http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#process + http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality + http://www.onto-med.de/ontologies/gfo.owl#Function + http://www.onto-med.de/ontologies/gfo.owl#Perpetuant + http://www.onto-med.de/ontologies/gfo.owl#Process + + + + Function + Operation is a function that is computational. It typically has input(s) and output(s), which are always data. + + + + + Computational tool + Computational tool provides one or more operations. + + + + + Process + Process can have a function (as its quality/attribute), and can also perform an operation with inputs and outputs. + - + - - Sequence similarity search - - - Structure database search (by sequence) - Sequence database search (by sequence) - beta12orEarlier - Search a sequence database and retrieve sequences that are similar to a query sequence. - - + + + + + + + + + + + + + + + beta12orEarlier + Search or query a data resource and retrieve entries and / or annotation. + Database retrieval + Query + + + Query and retrieval - + - - Sequence database search (by motif or pattern) - - 1.8 - Search a sequence database and retrieve sequences matching a given sequence motif or pattern, such as a Prosite pattern or regular expression. - beta12orEarlier + + + beta12orEarlier + beta13 + + Search database to retrieve all relevant references to a particular entity or entry. + + Data retrieval (database cross-reference) true - - - + - - Sequence database search (by amino acid composition) - - true - Search a sequence database and retrieve sequences of a given amino acid composition. - 1.6 - beta12orEarlier - - + + + + + + + + + + + + + + + beta12orEarlier + Annotate an entity (typically a biological or biomedical database entity) with terms from a controlled vocabulary. + + + This is a broad concept and is used a placeholder for other, more specific concepts. + Annotation - - - - Sequence database search (by property) - - Search a sequence database and retrieve sequences with a specified property, typically a physicochemical or compositional property. - beta12orEarlier - - - - - - - + - - Sequence database search (by sequence using word-based methods) - - beta12orEarlier - Word-based methods (for example BLAST, gapped BLAST, MEGABLAST, WU-BLAST etc.) are usually quicker than alignment-based methods. They may or may not handle gaps. - 1.6 - true - Sequence similarity search (word-based methods) - Search a sequence database and retrieve sequences that are similar to a query sequence using a word-based method. - - + + + + + + + + + beta12orEarlier + Generate an index of (typically a file of) biological data. + Data indexing + Database indexing + + + Indexing - + - - Sequence database search (by sequence using profile-based methods) - + + + beta12orEarlier + 1.6 + + Analyse an index of biological data. + + Data index analysis true - Sequence similarity search (profile-based methods) - Search a sequence database and retrieve sequences that are similar to a query sequence using a sequence profile-based method, or with a supplied profile as query. - beta12orEarlier - This includes tools based on PSI-BLAST. - 1.6 - - - + - - Sequence database search (by sequence using local alignment-based methods) - - Search a sequence database for sequences that are similar to a query sequence using a local alignment-based method. - 1.6 - beta12orEarlier + + + beta12orEarlier + beta12orEarlier + + Retrieve basic information about a molecular sequence. + + Annotation retrieval (sequence) true - Sequence similarity search (local alignment-based methods) - This includes tools based on the Smith-Waterman algorithm or FASTA. - - - + - - Sequence database search (by sequence using global alignment-based methods) - - This includes tools based on the Needleman and Wunsch algorithm. - Search sequence(s) or a sequence database for sequences that are similar to a query sequence using a global alignment-based method. - 1.6 - Sequence similarity search (global alignment-based methods) - beta12orEarlier - true - - + + + + beta12orEarlier + Generate a molecular sequence by some means. + + + Sequence generation - + - - Sequence database search (by sequence for primer sequences) - - true - beta12orEarlier - Search a DNA database (for example a database of conserved sequence tags) for matches to Sequence-Tagged Site (STS) primer sequences. - 1.6 - STSs are genetic markers that are easily detected by the polymerase chain reaction (PCR) using specific primers. - Sequence similarity search (primer sequences) - - + + + + beta12orEarlier + Edit or change a molecular sequence, either randomly or specifically. + + + Sequence editing - + - - Sequence database search (by molecular weight) - - Search sequence(s) or a sequence database for sequences which match a set of peptide masses, for example a peptide mass fingerprint from mass spectrometry. - 1.6 - Protein fingerprinting - true - beta12orEarlier - Peptide mass fingerprinting - - + + + beta12orEarlier + Merge two or more (typically overlapping) molecular sequences. + Sequence splicing + Paired-end merging + Paired-end stitching + Read merging + Read stitching + + + Sequence merging - + - - Sequence database search (by isoelectric point) - - 1.6 - beta12orEarlier - Search sequence(s) or a sequence database for sequences of a given isoelectric point. - true - - + + + + beta12orEarlier + Convert a molecular sequence from one type to another. + + + Sequence conversion - + - - Structure retrieval (by code) - - Query a tertiary structure database and retrieve entries with a given entry code or accession number. - 1.6 - beta12orEarlier - true - - + + + + + + + + + + + + + + + beta12orEarlier + Calculate sequence complexity, for example to find low-complexity regions in sequences. + + + Sequence complexity calculation - + - - Structure retrieval (by keyword) - - true - 1.6 - Query a tertiary structure database and retrieve entries containing a given keyword. - beta12orEarlier - - + + + + + + + + + + + + + + + beta12orEarlier + Calculate sequence ambiguity, for example identity regions in protein or nucleotide sequences with many ambiguity codes. + + + Sequence ambiguity calculation - + - - Structure database search (by sequence) - - beta12orEarlier - true - Search a tertiary structure database and retrieve structures with a sequence similar to a query sequence. - 1.8 - - + + + + + + + + + + + + + + + + beta12orEarlier + Calculate character or word composition or frequency of a molecular sequence. + + + Sequence composition calculation - + - - Structural similarity search - - + + - - + + - beta12orEarlier - Search a database of molecular structure and retrieve structures that are similar to a query structure. - Structure database search (by structure) - Structure retrieval by structure - - + beta12orEarlier + Find and/or analyse repeat sequences in (typically nucleotide) sequences. + + + Repeat sequences include tandem repeats, inverted or palindromic repeats, DNA microsatellites (Simple Sequence Repeats or SSRs), interspersed repeats, maximal duplications and reverse, complemented and reverse complemented repeats etc. Repeat units can be exact or imperfect, in tandem or dispersed, of specified or unspecified length. + Repeat sequence analysis - + - - Sequence annotation - + + + - - + + - - + + - beta12orEarlier - Annotate a molecular sequence record with terms from a controlled vocabulary. - - + beta12orEarlier + Discover new motifs or conserved patterns in sequences or sequence alignments (de-novo discovery). + Motif discovery + + + Motifs and patterns might be conserved or over-represented (occur with improbable frequency). + Sequence motif discovery - + - - Genome annotation - - beta12orEarlier - Annotate a genome sequence with terms from a controlled vocabulary. - - + + + + + + + + + + + + + + + + beta12orEarlier + Find (scan for) known motifs, patterns and regular expressions in molecular sequence(s). + Motif scanning + Sequence signature detection + Sequence signature recognition + Motif detection + Motif recognition + Motif search + Sequence motif detection + Sequence motif search + Sequence profile search + + + Sequence motif recognition - + - - Nucleic acid sequence reverse and complement - - beta12orEarlier - Generate the reverse and / or complement of a nucleotide sequence. - - + + + + + + + + + + + + + + + + beta12orEarlier + Find motifs shared by molecular sequences. + + + Sequence motif comparison - + - - Random sequence generation - - Generate a random sequence, for example, with a specific character composition. - beta12orEarlier - - + + + beta12orEarlier + beta13 + + Analyse the sequence, conformational or physicochemical properties of transcription regulatory elements in DNA sequences. + + For example transcription factor binding sites (TFBS) analysis to predict accessibility of DNA to binding factors. + Transcription regulatory sequence analysis + true - + - - Nucleic acid restriction digest - - - - - - - - - beta12orEarlier - Generate digest fragments for a nucleotide sequence containing restriction sites. - - + + + + beta12orEarlier + Identify common, conserved (homologous) or synonymous transcriptional regulatory motifs (transcription factor binding sites). + + + For example cross-species comparison of transcription factor binding sites (TFBS). Methods might analyse co-regulated or co-expressed genes, or sets of oppositely expressed genes. + Conserved transcription regulatory sequence identification - + - - Protein sequence cleavage - - + + + - - + + - - + + - beta12orEarlier - Cleave a protein sequence into peptide fragments (by enzymatic or chemical cleavage) and calculate the fragment masses. - - + beta12orEarlier + Extract, calculate or predict non-positional (physical or chemical) properties of a protein from processing a protein (3D) structure. + Protein structural property calculation + + + This might be a residue-level search for properties such as solvent accessibility, hydropathy, secondary structure, ligand-binding etc. + Protein property calculation (from structure) - + - - Sequence mutation and randomization - - beta12orEarlier - Mutate a molecular sequence a specified amount or shuffle it to produce a randomized sequence with the same overall composition. - - + + + + beta12orEarlier + Analyse flexibility and motion in protein structure. + + + Use this concept for analysis of flexible and rigid residues, local chain deformability, regions undergoing conformational change, molecular vibrations or fluctuational dynamics, domain motions or other large-scale structural transitions in a protein structure. + Protein flexibility and motion analysis - + - - Sequence masking - - Mask characters in a molecular sequence (replacing those characters with a mask character). - For example, SNPs or repeats in a DNA sequence might be masked. - beta12orEarlier - - + + + + + + + + + + beta12orEarlier + Identify or screen for 3D structural motifs in protein structure(s). + Protein structural feature identification + + + This includes conserved substructures and conserved geometry, such as spatial arrangement of secondary structure or protein backbone. Methods might use structure alignment, structural templates, searches for similar electrostatic potential and molecular surface shape, surface-mapping of phylogenetic information etc. + Protein structural motif recognition - + - - Sequence cutting - - Cut (remove) characters or a region from a molecular sequence. - beta12orEarlier - - + + + + + + + + + + beta12orEarlier + Identify structural domains in a protein structure from first principles (for example calculations on structural compactness). + + + Protein domain recognition - + - - Restriction site creation - - Create (or remove) restriction sites in sequences, for example using silent mutations. - beta12orEarlier - - + + + beta12orEarlier + Analyse the architecture (spatial arrangement of secondary structure) of protein structure(s). + + + Protein architecture analysis - + - - DNA translation - + + - - + + - beta12orEarlier - Translate a DNA sequence into protein. - - + beta12orEarlier + WHATIF: SymShellFiveXML + WHATIF: SymShellOneXML + WHATIF: SymShellTenXML + WHATIF: SymShellTwoXML + WHATIF:ListContactsNormal + WHATIF:ListContactsRelaxed + WHATIF:ListSideChainContactsNormal + WHATIF:ListSideChainContactsRelaxed + Calculate or extract inter-atomic, inter-residue or residue-atom contacts, distances and interactions in protein structure(s). + + + Residue interaction calculation - + - - DNA transcription - + + - - + + - beta12orEarlier - Transcribe a nucleotide sequence into mRNA sequence(s). - - + beta12orEarlier + WHATIF:CysteineTorsions + WHATIF:ResidueTorsions + WHATIF:ResidueTorsionsBB + WHATIF:ShowTauAngle + Calculate, visualise or analyse phi/psi angles of a protein structure. + Backbone torsion angle calculation + Cysteine torsion angle calculation + Tau angle calculation + Torsion angle calculation + + + Protein geometry calculation - + - - Sequence composition calculation (nucleic acid) - - true - Calculate base frequency or word composition of a nucleotide sequence. - 1.8 - beta12orEarlier - - + + + + + beta12orEarlier + Calculate (or predict) physical or chemical properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence. + Protein property rendering + + + This includes methods to render and visualise the properties of a protein sequence. + Protein property calculation - + - - Sequence composition calculation (protein) - - 1.8 - Calculate amino acid frequency or word composition of a protein sequence. - beta12orEarlier - true - - + + + + + + + + + + + + + + + + beta12orEarlier + Predict antigenicity, allergenicity / immunogenicity, allergic cross-reactivity etc of peptides and proteins. + Immunogenicity prediction + Hopp and Woods plotting + MHC peptide immunogenicity prediction + + + This includes methods that generate a graphical rendering of antigenicity of a protein, such as a Hopp and Woods plot. + This is usually done in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data. + Peptide immunogenicity prediction - + - - Repeat sequence detection - - - beta12orEarlier - Find (and possibly render) short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences. - - + + + + + + + + + + + + + + + + beta12orEarlier + Predict, recognise and identify positional features in molecular sequences such as key functional sites or regions. + Sequence feature prediction + Sequence feature recognition + Motif database search + SO:0000110 + + + Sequence feature detection - + - - Repeat sequence organisation analysis - - - beta12orEarlier - Analyse repeat sequence organization such as periodicity. - - + + + beta12orEarlier + beta13 + + Extract a sequence feature table from a sequence database entry. + + Data retrieval (feature table) + true - + - - Protein hydropathy calculation (from structure) - - - - Analyse the hydrophobic, hydrophilic or charge properties of a protein structure. - beta12orEarlier - - + + + beta12orEarlier + 1.6 + + Query the features (in a feature table) of molecular sequence(s). + + Feature table query + true - + - - Protein solvent accessibility calculation - + + + - - + + - - + + - beta12orEarlier - Calculate solvent accessible or buried surface areas in protein structures. - - - - - - - - - - Protein hydropathy cluster calculation - - - beta12orEarlier - Identify clusters of hydrophobic or charged residues in a protein structure. - - + + + + + + + beta12orEarlier + Compare the feature tables of two or more molecular sequences. + Feature comparison + Feature table comparison + + + Sequence feature comparison - + - - Protein dipole moment calculation - - - - - - - - beta12orEarlier - Calculate whether a protein structure has an unusually large net charge (dipole moment). - - + + + beta12orEarlier + beta13 + + Display basic information about a sequence alignment. + + Data retrieval (sequence alignment) + true - + - - Protein surface and interior calculation - + + - - + + - beta12orEarlier - Identify the protein surface and interior, surface accessible pockets, interior inaccessible cavities etc. - - + beta12orEarlier + Analyse a molecular sequence alignment. + + + Sequence alignment analysis - + - - Protein binding site prediction (from structure) - - - Identify or predict catalytic residues, active sites or other ligand-binding sites in protein structures. - beta12orEarlier - Ligand-binding and active site prediction (from structure) - Binding site prediction (from structure) - - + + + + beta12orEarlier + Compare (typically by aligning) two molecular sequence alignments. + + + See also 'Sequence profile alignment'. + Sequence alignment comparison - + - - Protein-nucleic acid binding site analysis - - - - - - - - Analyse RNA or DNA-binding sites in protein structure. - beta12orEarlier - - + + + + beta12orEarlier + Convert a molecular sequence alignment from one type to another (for example amino acid to coding nucleotide sequence). + + + Sequence alignment conversion - + - - Protein peeling - - beta12orEarlier - Decompose a structure into compact or globular fragments (protein peeling). - - + + + beta12orEarlier + beta13 + + Process (read and / or write) physicochemical property data of nucleic acids. + + Nucleic acid property processing + true - + - - Protein distance matrix calculation - + + + - - + + - beta12orEarlier - Calculate a matrix of distance between residues (for example the C-alpha atoms) in a protein structure. - - + beta12orEarlier + Calculate or predict physical or chemical properties of nucleic acid molecules, including any non-positional properties of the molecular sequence. + + + Nucleic acid property calculation - + - - Protein contact map calculation - + + - - + + - beta12orEarlier - Calculate a residue contact map (typically all-versus-all inter-residue contacts) for a protein structure. - - + beta12orEarlier + Predict splicing alternatives or transcript isoforms from analysis of sequence data. + + + Splice transcript prediction - + - - Protein residue cluster calculation - + + + - - + + - Cluster of contacting residues might be key structural residues. - Calculate clusters of contacting residues in protein structures. - beta12orEarlier - - + beta12orEarlier + Detect frameshifts in DNA sequences, including frameshift sites and signals, and frameshift errors from sequencing projects. + Frameshift error detection + + + Methods include sequence alignment (if related sequences are available) and word-based sequence comparison. + Frameshift detection - + - - Hydrogen bond calculation - - - - - - - - WHATIF:ShowHydrogenBonds - WHATIF:HasHydrogenBonds - The output might include the atoms involved in the bond, bond geometric parameters and bond enthalpy. - beta12orEarlier - WHATIF:ShowHydrogenBondsM - Identify potential hydrogen bonds between amino acids and other groups. - - + + + + beta12orEarlier + Detect vector sequences in nucleotide sequence, typically by comparison to a set of known vector sequences. + + + Vector sequence detection - + - - Residue non-canonical interaction detection - - - beta12orEarlier - Calculate non-canonical atomic interactions in protein structures. - - + + + + + beta12orEarlier + Predict secondary structure of protein sequences. + Secondary structure prediction (protein) + + + Methods might use amino acid composition, local sequence information, multiple sequence alignments, physicochemical features, estimated energy content, statistical algorithms, hidden Markov models, support vector machines, kernel machines, neural networks etc. + Protein secondary structure prediction - + - - Ramachandran plot calculation - + + - - + + - Calculate a Ramachandran plot of a protein structure. - beta12orEarlier - - + beta12orEarlier + Predict super-secondary structure of protein sequence(s). + + + Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. + Protein super-secondary structure prediction - + - - Ramachandran plot validation - - - - - - - + + + + beta12orEarlier + Predict and/or classify transmembrane proteins or transmembrane (helical) domains or regions in protein sequences. + + + Transmembrane protein prediction + + + + + + + + - - + + - beta12orEarlier - Validate a Ramachandran plot of a protein structure. - - + beta12orEarlier + Analyse transmembrane protein(s), typically by processing sequence and / or structural data, and write an informative report for example about the protein and its transmembrane domains / regions. + + + Use this (or child) concept for analysis of transmembrane domains (buried and exposed faces), transmembrane helices, helix topology, orientation, inter-helical contacts, membrane dipping (re-entrant) loops and other secondary structure etc. Methods might use pattern discovery, hidden Markov models, sequence alignment, structural profiles, amino acid property analysis, comparison to known domains or some combination (hybrid methods). + Transmembrane protein analysis - + - - Protein molecular weight calculation - + + + - - + + - - + + - Calculate the molecular weight of a protein sequence or fragments. - beta12orEarlier - - + beta12orEarlier + Predict tertiary structure of a molecular (biopolymer) sequence. + + + Structure prediction - + - - Protein extinction coefficient calculation - + + + - - + + - beta12orEarlier - Predict extinction coefficients or optical density of a protein sequence. - - + beta12orEarlier + Predict contacts, non-covalent interactions and distance (constraints) between amino acids in protein sequences. + + + Methods usually involve multiple sequence alignment analysis. + Residue interaction prediction - + - - Protein pH-dependent property calculation - + + - - + + - - + + - Calculate pH-dependent properties from pKa calculations of a protein sequence. - beta12orEarlier - - + beta12orEarlier + Analyse experimental protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc. + + + Protein interaction raw data analysis - + - - Protein hydropathy calculation (from sequence) - - - Hydropathy calculation on a protein sequence. - beta12orEarlier - - + + + beta12orEarlier + 1.12 + Identify or predict protein-protein interactions, interfaces, binding sites etc in protein sequences. + + + Protein-protein interaction prediction (from protein sequence) + true - + - - Protein titration curve plotting - - - - - - - - - beta12orEarlier - Plot a protein titration curve. - - + + + beta12orEarlier + 1.12 + Identify or predict protein-protein interactions, interfaces, binding sites etc in protein structures. + + + Protein-protein interaction prediction (from protein structure) + true - + - - Protein isoelectric point calculation - + + + - - + + - beta12orEarlier - Calculate isoelectric point of a protein sequence. - - - - - - - - - - Protein hydrogen exchange rate calculation - - - + + - Estimate hydrogen exchange rate of a protein sequence. - beta12orEarlier - - + beta12orEarlier + Analyse a network of protein interactions. + + + Protein interaction network analysis - + - - Protein hydrophobic region calculation - - Calculate hydrophobic or hydrophilic / charged regions of a protein sequence. - beta12orEarlier - - + + + + beta12orEarlier + Compare two or more networks of protein interactions. + + + Protein interaction network comparison - + - - Protein aliphatic index calculation - + + + + - - + + - beta12orEarlier - Calculate aliphatic index (relative volume occupied by aliphatic side chains) of a protein. - - + beta12orEarlier + Predict RNA secondary structure (for example knots, pseudoknots, alternative structures etc). + + + Methods might use RNA motifs, predicted intermolecular contacts, or RNA sequence-structure compatibility (inverse RNA folding). + RNA secondary structure prediction - + - - Protein hydrophobic moment plotting - - + + + + - - + + - beta12orEarlier - Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. - Calculate the hydrophobic moment of a peptide sequence and recognize amphiphilicity. - - + beta12orEarlier + Analyse some aspect of RNA/DNA folding, typically by processing sequence and/or structural data. + Nucleic acid folding + Nucleic acid folding modelling + Nucleic acid folding prediction + + + Nucleic acid folding analysis - + - - Protein globularity prediction - - - - - - - - Predict the stability or globularity of a protein sequence, whether it is intrinsically unfolded etc. - beta12orEarlier - - + + + beta12orEarlier + beta13 + + Retrieve information on restriction enzymes or restriction enzyme sites. + + Data retrieval (restriction enzyme annotation) + true - + - - Protein solubility prediction - - - - - - - - Predict the solubility or atomic solvation energy of a protein sequence. - beta12orEarlier - - + + + beta12orEarlier + beta13 + + Identify genetic markers in DNA sequences. + + A genetic marker is any DNA sequence of known chromosomal location that is associated with and specific to a particular gene or trait. This includes short sequences surrounding a SNP, Sequence-Tagged Sites (STS) which are well suited for PCR amplification, a longer minisatellites sequence etc. + Genetic marker identification + true - + - - Protein crystallizability prediction - + + + - - + + - beta12orEarlier - Predict crystallizability of a protein sequence. - - - - - - - - - - Protein signal peptide detection (eukaryotes) - - beta12orEarlier - Detect or predict signal peptides (and typically predict subcellular localization) of eukaryotic proteins. - - + beta12orEarlier + Generate a genetic (linkage) map of a DNA sequence (typically a chromosome) showing the relative positions of genetic markers based on estimation of non-physical distances. + Functional mapping + Genetic map construction + Genetic map generation + Linkage mapping + QTL mapping + + + Mapping involves ordering genetic loci along a chromosome and estimating the physical distance between loci. A genetic map shows the relative (not physical) position of known genes and genetic markers. + This includes mapping of the genetic architecture of dynamic complex traits (functional mapping), e.g. by characterisation of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs). + Genetic mapping - + - - Protein signal peptide detection (bacteria) - - Detect or predict signal peptides (and typically predict subcellular localization) of bacterial proteins. - beta12orEarlier - - + + + + + + + + + + + + + + + beta12orEarlier + Analyse genetic linkage. + + + For example, estimate how close two genes are on a chromosome by calculating how often they are transmitted together to an offspring, ascertain whether two genes are linked and parental linkage, calculate linkage map distance etc. + Linkage analysis - + - - MHC peptide immunogenicity prediction - - Predict MHC class I or class II binding peptides, promiscuous binding peptides, immunogenicity etc. - beta12orEarlier - - + + + + + + + + + + beta12orEarlier + Calculate codon usage statistics and create a codon usage table. + Codon usage table construction + + + Codon usage table generation - + - - Protein feature prediction (from sequence) - - Methods typically involve scanning for known motifs, patterns and regular expressions. - beta12orEarlier - true - Sequence feature detection (protein) - 1.6 - Predict, recognise and identify positional features in protein sequences such as functional sites or regions and secondary structure. - - + + + + beta12orEarlier + Compare two or more codon usage tables. + + + Codon usage table comparison - + - - Nucleic acid feature detection - - + + - - + + - - + + - Sequence feature detection (nucleic acid) - Predict, recognise and identify features in nucleotide sequences such as functional sites or regions, typically by scanning for known motifs, patterns and regular expressions. - Methods typically involve scanning for known motifs, patterns and regular expressions. - beta12orEarlier - Nucleic acid feature recognition - Nucleic acid feature prediction - - - - - - - - - - Epitope mapping - - - - + + - beta12orEarlier - Predict antigenic determinant sites (epitopes) in protein sequences. - Epitope mapping is commonly done during vaccine design. - - - - - - - - - - Protein post-translation modification site prediction - - - + + - Predict post-translation modification sites in protein sequences. - beta12orEarlier - Methods might predict sites of methylation, N-terminal myristoylation, N-terminal acetylation, sumoylation, palmitoylation, phosphorylation, sulfation, glycosylation, glycosylphosphatidylinositol (GPI) modification sites (GPI lipid anchor signals) etc. - - + + + + + + + beta12orEarlier + Process (read and / or write) codon usage data, e.g. analyse codon usage tables or codon usage in molecular sequences. + synon: Codon usage data analysis + synon: Codon usage table analysis + + + Codon usage analysis - + - - Protein signal peptide detection - - + + + - - + + - beta12orEarlier - Methods might use sequence motifs and features, amino acid composition, profiles, machine-learned classifiers, etc. - Detect or predict signal peptides and signal peptide cleavage sites in protein sequences. - - + + + + + + + beta12orEarlier + Identify and plot third base position variability in a nucleotide sequence. + + + Base position variability plotting - + - - Protein binding site prediction (from sequence) - - - Binding site prediction (from sequence) - Predict catalytic residues, active sites or other ligand-binding sites in protein sequences. - Ligand-binding and active site prediction (from sequence) - Protein binding site detection - beta12orEarlier - - + + + beta12orEarlier + Find exact character or word matches between molecular sequences without full sequence alignment. + + + Sequence word comparison - + - - Protein-nucleic acid binding prediction - - beta12orEarlier - Predict RNA and DNA-binding binding sites in protein sequences. - - + + + + + + + + + + + + + + + + beta12orEarlier + Calculate a sequence distance matrix or otherwise estimate genetic distances between molecular sequences. + Phylogenetic distance matrix generation + Sequence distance matrix construction + + + Sequence distance matrix generation - + - - Protein folding site prediction - - - Predict protein sites that are key to protein folding, such as possible sites of nucleation or stabilization. - beta12orEarlier - - + + + + + + + + + beta12orEarlier + Compare two or more molecular sequences, identify and remove redundant sequences based on some criteria. + + + Sequence redundancy removal - + - - Protein cleavage site prediction - + + + + - - + + - beta12orEarlier - Detect or predict cleavage sites (enzymatic or chemical) in protein sequences. - - + beta12orEarlier + Build clusters of similar sequences, typically using scores from pair-wise alignment or other comparison of the sequences. + Sequence cluster construction + Sequence cluster generation + + + The clusters may be output or used internally for some other purpose. + Sequence clustering - + - - Epitope mapping (MHC Class I) - - 1.8 - true - beta12orEarlier - Predict epitopes that bind to MHC class I molecules. - - + + + + + + + + + + + beta12orEarlier + Align (identify equivalent sites within) molecular sequences. + Sequence alignment construction + Sequence alignment generation + Consensus-based sequence alignment + + + Sequence alignment - + - - Epitope mapping (MHC Class II) - - Predict epitopes that bind to MHC class II molecules. - 1.8 + + + beta12orEarlier + beta13 + + Align two or more molecular sequences of different types (for example genomic DNA to EST, cDNA or mRNA). + + Hybrid sequence alignment construction true - beta12orEarlier - - - - + - - Whole gene prediction - - beta12orEarlier - Detect, predict and identify whole gene structure in DNA sequences. This includes protein coding regions, exon-intron structure, regulatory regions etc. - - + + + beta12orEarlier + Align molecular sequences using sequence and structural information. + Sequence alignment (structure-based) + Sequence alignment generation (structure-based) + Structure-based sequence alignment construction + Structure-based sequence alignment generation + + + Structure-based sequence alignment - + - - Gene component prediction - - Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc. - beta12orEarlier - Detect, predict and identify genetic elements such as promoters, coding regions, splice sites, etc in DNA sequences. - - + + + + + + + + + + + beta12orEarlier + Align (superimpose) molecular tertiary structures. + + + Structure alignment - + - - Transposon prediction - - beta12orEarlier - Detect or predict transposons, retrotransposons / retrotransposition signatures etc. - - + + + + + + + + + + + + + + + + + + + + + + beta12orEarlier + Generate some type of sequence profile (for example a hidden Markov model) from a sequence alignment. + Sequence profile construction + + + Sequence profile generation - + - - PolyA signal detection - - Detect polyA signals in nucleotide sequences. - beta12orEarlier - - + + + + + + + + + + + + + + + + + + + + + + beta12orEarlier + Generate some type of structural (3D) profile or template from a structure or structure alignment. + Structural profile construction + Structural profile generation + + + 3D profile generation - + - - Quadruplex formation site detection - + + - - + + - - + + - beta12orEarlier - Quadruplex structure prediction - Detect quadruplex-forming motifs in nucleotide sequences. - Quadruplex (4-stranded) structures are formed by guanine-rich regions and are implicated in various important biological processes and as therapeutic targets. - - + + + + + + + beta12orEarlier + Align sequence profiles (representing sequence alignments). + Profile-to-profile alignment + Sequence profile alignment + + + Methods might perform one-to-one, one-to-many or many-to-many comparisons. See also 'Sequence alignment comparison'. + Profile-profile alignment - + - - CpG island and isochore detection - + + - - + + - An isochore is long region (> 3 KB) of DNA with very uniform GC content, in contrast to the rest of the genome. Isochores tend tends to have more genes, higher local melting or denaturation temperatures, and different flexibility. Methods might calculate fractional GC content or variation of GC content, predict methylation status of CpG islands etc. This includes methods that visualise CpG rich regions in a nucleotide sequence, for example plot isochores in a genome sequence. - beta12orEarlier - Find CpG rich regions in a nucleotide sequence or isochores in genome sequences. - CpG island and isochores rendering - CpG island and isochores detection - - + + + + + + + beta12orEarlier + Align structural (3D) profiles or templates (representing structures or structure alignments). + 3D profile alignment + Structural profile alignment + + + Methods might perform one-to-one, one-to-many or many-to-many comparisons. + 3D profile-to-3D profile alignment - + - - Restriction site recognition - + + - - + + - beta12orEarlier - Find and identify restriction enzyme cleavage sites (restriction sites) in (typically) DNA sequences, for example to generate a restriction map. - - + + + + + + + + + + + + + beta12orEarlier + Align molecular sequence(s) to sequence profile(s). + Sequence-profile alignment + + + A sequence profile typically represents a sequence alignment. Methods might perform one-to-one, one-to-many or many-to-many comparisons. + Sequence-to-profile alignment - + - - Nucleosome formation or exclusion sequence prediction - - beta12orEarlier - Identify or predict nucleosome exclusion sequences (nucleosome free regions) in DNA. - - + + + + + + + + + + + + + + + + beta12orEarlier + Align molecular sequence(s) to structural (3D) profile(s) or template(s) (representing a structure or structure alignment). + Sequence-3D profile alignment + + + Methods might perform one-to-one, one-to-many or many-to-many comparisons. + Sequence-to-3D-profile alignment - + - - Splice site prediction - + + + - - + + - beta12orEarlier - Identify, predict or analyse splice sites in nucleotide sequences. - Methods might require a pre-mRNA or genomic DNA sequence. - - + + + + + + + beta12orEarlier + Align molecular sequence to structure in 3D space (threading). + Sequence-structure alignment + + + Use this concept for methods that evaluate sequence-structure compatibility by assessing residue interactions in 3D. Methods might perform one-to-one, one-to-many or many-to-many comparisons. + Protein threading - + - - Integrated gene prediction - - Predict whole gene structure using a combination of multiple methods to achieve better predictions. - beta12orEarlier - - + + + + + + beta12orEarlier + Recognize (predict and identify) known protein structural domains or folds in protein sequence(s). + Protein domain prediction + Protein fold prediction + + + Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH. + Protein fold recognition - + - - Operon prediction - - Find operons (operators, promoters and genes) in bacteria genes. - beta12orEarlier - - + + + + + + + + + beta12orEarlier + Search for and retrieve data concerning or describing some core data, as distinct from the primary data that is being described. + Data retrieval (documentation) + Data retrieval (metadata) + + + This includes documentation, general information and other metadata on entities such as databases, database entries and tools. + Metadata retrieval - + - - Coding region prediction - - Predict protein-coding regions (CDS or exon) or open reading frames in nucleotide sequences. - ORF prediction - ORF finding - beta12orEarlier - - + + + + + + + + + beta12orEarlier + Query scientific literature, in search for articles, article data, concepts, named entities, or for statistics. + + + Literature search - + - - Selenocysteine insertion sequence (SECIS) prediction - + + + - - + + - Predict selenocysteine insertion sequence (SECIS) in a DNA sequence. - SECIS elements are around 60 nucleotides in length with a stem-loop structure directs the cell to translate UGA codons as selenocysteines. - beta12orEarlier - - + + + + + + + + + + + + + beta12orEarlier + Text analysis + Process and analyse text (typically scientific literature) to extract information from it. + Literature mining + Text analytics + Text data mining + Article analysis + Literature analysis + + + Text mining + - + - - Regulatory element prediction - + + - - + + - Identify or predict transcription regulatory motifs, patterns, elements or regions in DNA sequences. - Translational regulatory element prediction - Transcription regulatory element prediction - This includes promoters, enhancers, silencers and boundary elements / insulators, regulatory protein or transcription factor binding sites etc. Methods might be specific to a particular genome and use motifs, word-based / grammatical methods, position-specific frequency matrices, discriminative pattern analysis etc. - beta12orEarlier - - + beta12orEarlier + Perform in-silico (virtual) PCR. + + + Virtual PCR - + - - Translation initiation site prediction - + + - - + + - Predict translation initiation sites, possibly by searching a database of sites. - beta12orEarlier - - + + + + + + + + + + + + + beta12orEarlier + Design or predict oligonucleotide primers for PCR and DNA amplification etc. + PCR primer prediction + PCR primer design (based on gene structure) + PCR primer design (for conserved primers) + PCR primer design (for gene transcription profiling) + PCR primer design (for genotyping polymorphisms) + PCR primer design (for large scale sequencing) + PCR primer design (for methylation PCRs) + + + Primer design involves predicting or selecting primers that are specific to a provided PCR template. Primers can be designed with certain properties such as size of product desired, primer size etc. The output might be a minimal or overlapping primer set. + This includes predicting primers based on gene structure, promoters, exon-exon junctions, predicting primers that are conserved across multiple genomes or species, primers for for gene transcription profiling, for genotyping polymorphisms, for example single nucleotide polymorphisms (SNPs), for large scale sequencing, or for methylation PCRs. + PCR primer design - + - - Promoter prediction - - Identify or predict whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in DNA sequences. - Methods might recognize CG content, CpG islands, splice sites, polyA signals etc. - beta12orEarlier - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + beta12orEarlier + Predict and/or optimize oligonucleotide probes for DNA microarrays, for example for transcription profiling of genes, or for genomes and gene families. + Microarray probe prediction + + + Microarray probe design - + - - Transcription regulatory element prediction (DNA-cis) - - beta12orEarlier - Cis-regulatory elements (cis-elements) regulate the expression of genes located on the same strand. Cis-elements are found in the 5' promoter region of the gene, in an intron, or in the 3' untranslated region. Cis-elements are often binding sites of one or more trans-acting factors. - Identify, predict or analyse cis-regulatory elements (TATA box, Pribnow box, SOS box, CAAT box, CCAAT box, operator etc.) in DNA sequences. - - + + + + + + + + + + + + + + + + beta12orEarlier + Combine (align and merge) overlapping fragments of a DNA sequence to reconstruct the original sequence. + + + For example, assemble overlapping reads from paired-end sequencers into contigs (a contiguous sequence corresponding to read overlaps). Or assemble contigs, for example ESTs and genomic DNA fragments, depending on the detected fragment overlaps. + Sequence assembly - + - - Transcription regulatory element prediction (RNA-cis) - - Cis-regulatory elements (cis-elements) regulate genes located on the same strand from which the element was transcribed. A riboswitch is a region of an mRNA molecule that bind a small target molecule that regulates the gene's activity. - Identify, predict or analyse cis-regulatory elements (for example riboswitches) in RNA sequences. - beta12orEarlier - - + + + beta12orEarlier + 1.16 + Standardize or normalize microarray data. + + + Microarray data standardisation and normalisation + true - + - - Transcription regulatory element prediction (trans) - - - - - - - - beta12orEarlier - Trans-regulatory elements regulate genes distant from the gene from which they were transcribed. - Identify or predict functional RNA sequences with a gene regulatory role (trans-regulatory elements) or targets. - Functional RNA identification - - + + + beta12orEarlier + beta12orEarlier + + Process (read and / or write) SAGE, MPSS or SBS experimental data. + + Sequencing-based expression profile data processing + true - + - - Matrix/scaffold attachment site prediction - - MAR/SAR sites often flank a gene or gene cluster and are found nearby cis-regulatory sequences. They might contribute to transcription regulation. - Identify matrix/scaffold attachment regions (MARs/SARs) in DNA sequences. - beta12orEarlier - - + + + + + + + + + + beta12orEarlier + Perform cluster analysis of gene expression data to identify groups with similar gene-expression profiles, for example by clustering. + + + Gene expression profile clustering - + - - Transcription factor binding site prediction - - beta12orEarlier - Identify or predict transcription factor binding sites in DNA sequences. - - + + + + + + + + + + beta12orEarlier + Gene expression quantification + The measurement of the gene expression of multiple genes in a cell, tissue, sample etc., in order to get an impression of biological function. + Gene expression profile construction + Gene expression profile generation + Gene transcription profiling + Metagenomic inference + Non-coding RNA profiling + RNA profiling + mRNA profiling + Functional profiling + Protein profiling + + + Gene expression profiling generates some sort of gene expression profile, for example from microarray data. + Metagenomic inference is the profiling of phylogenetic marker genes in order to predict metagenome function. + Gene expression profiling + https://en.wikipedia.org/wiki/Gene_expression_profiling - + - - Exonic splicing enhancer prediction - + + + - - + + - An exonic splicing enhancer (ESE) is 6-base DNA sequence motif in an exon that enhances or directs splicing of pre-mRNA or hetero-nuclear RNA (hnRNA) into mRNA. - Identify or predict exonic splicing enhancers (ESE) in exons. - beta12orEarlier - - + beta12orEarlier + Comparison of gene expression profiles. + + + Gene expression profile comparison - + - - Sequence alignment validation - - - Evaluation might be purely sequence-based or use structural information. - Sequence alignment quality evaluation - Evaluate molecular sequence alignment accuracy. - beta12orEarlier - - + + + beta12orEarlier + beta12orEarlier + Interpret (in functional terms) and annotate gene expression data. + + + Functional profiling + true - + - - Sequence alignment analysis (conservation) - - beta12orEarlier - Analyse character conservation in a molecular sequence alignment, for example to derive a consensus sequence. - Residue conservation analysis - Use this concept for methods that calculate substitution rates, estimate relative site variability, identify sites with biased properties, derive a consensus sequence, or identify highly conserved or very poorly conserved sites, regions, blocks etc. - - + + + beta12orEarlier + beta12orEarlier + + Analyse EST or cDNA sequences. + + For example, identify full-length cDNAs from EST sequences or detect potential EST antisense transcripts. + EST and cDNA sequence analysis + true - + - - Sequence alignment analysis (site correlation) - - - Analyse correlations between sites in a molecular sequence alignment. - This is typically done to identify possible covarying positions and predict contacts or structural constraints in protein structures. - beta12orEarlier - - + + + beta12orEarlier + beta12orEarlier + + Identify and select targets for protein structural determination. + + Methods will typically navigate a graph of protein families of known structure. + Structural genomics target selection + true - + - - Chimeric sequence detection - - beta12orEarlier - A chimera includes regions from two or more phylogenetically distinct sequences. They are usually artifacts of PCR and are thought to occur when a prematurely terminated amplicon reanneals to another DNA strand and is subsequently copied to completion in later PCR cycles. - Detects chimeric sequences (chimeras) from a sequence alignment. - Sequence alignment analysis (chimeric sequence detection) - - + + + + + + + + + + + + + + + beta12orEarlier + Assign secondary structure from protein coordinate or experimental data. + + + Protein secondary structure assignment - + - - Recombination detection - - Sequence alignment analysis (recombination detection) - beta12orEarlier - Detect recombination (hotspots and coldspots) and identify recombination breakpoints in a sequence alignment. - Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on. - - - - - - - - - - Indel detection - - beta12orEarlier - Sequence alignment analysis (indel detection) - Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on. - Identify insertion, deletion and duplication events from a sequence alignment. - - - - - - - - - - Nucleosome formation potential prediction - - true - beta12orEarlier - Predict nucleosome formation potential of DNA sequences. - beta12orEarlier - - - - - - - - - - Nucleic acid thermodynamic property calculation - + + + - - + + - Calculate a thermodynamic property of DNA or DNA/RNA, such as melting temperature, enthalpy and entropy. - beta12orEarlier - - - - - - - - - - Nucleic acid melting profile plotting - - - - + + - Calculate and plot a DNA or DNA/RNA melting profile. - A melting profile is used to visualise and analyse partly melted DNA conformations. - beta12orEarlier - - + beta12orEarlier + Assign a protein tertiary structure (3D coordinates) from raw experimental data. + + + Protein structure assignment - + - - Nucleic acid stitch profile plotting - + + + - - + + - A stitch profile represents the alternative conformations that partly melted DNA can adopt in a temperature range. - beta12orEarlier - Calculate and plot a DNA or DNA/RNA stitch profile. - - - - - - - - - - Nucleic acid melting curve plotting - - - + + - Calculate and plot a DNA or DNA/RNA melting curve. - beta12orEarlier - - + beta12orEarlier + WHATIF: CorrectedPDBasXML + WHATIF: UseFileDB + WHATIF: UseResidueDB + Evaluate the quality or correctness a protein three-dimensional model. + Protein structure validation + Residue validation + + + Model validation might involve checks for atomic packing, steric clashes (bumps), volume irregularities, agreement with electron density maps, number of amino acid residues, percentage of residues with missing or bad atoms, irregular Ramachandran Z-scores, irregular Chi-1 / Chi-2 normality scores, RMS-Z score on bonds and angles etc. + The PDB file format has had difficulties, inconsistencies and errors. Corrections can include identifying a meaningful sequence, removal of alternate atoms, correction of nomenclature problems, removal of incomplete residues and spurious waters, addition or removal of water, modelling of missing side chains, optimisation of cysteine bonds, regularisation of bond lengths, bond angles and planarities etc. + This includes methods that calculate poor quality residues. The scoring function to identify poor quality residues may consider residues with bad atoms or atoms with high B-factor, residues in the N- or C-terminal position, adjacent to an unstructured residue, non-canonical residues, glycine and proline (or adjacent to these such residues). + Protein model validation - + - - Nucleic acid probability profile plotting - - - - - - - - beta12orEarlier - Calculate and plot a DNA or DNA/RNA probability profile. - - + + + + beta12orEarlier + WHATIF: CorrectedPDBasXML + Refine (after evaluation) a model of a molecular structure (typically a protein structure) to reduce steric clashes, volume irregularities etc. + Protein model refinement + + + Molecular model refinement - + - - Nucleic acid temperature profile plotting - + + + - - + + - Calculate and plot a DNA or DNA/RNA temperature profile. - beta12orEarlier - - + + + + + + + beta12orEarlier + Construct a phylogenetic tree. + Phylogenetic tree construction + + + Phylogenetic trees are usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. + Phylogenetic tree generation - + - - Nucleic acid curvature calculation - + + - - + + - Calculate curvature and flexibility / stiffness of a nucleotide sequence. - beta12orEarlier - This includes properties such as. - - + beta12orEarlier + Analyse an existing phylogenetic tree or trees, typically to detect features or make predictions. + + + Phylogenetic tree analysis - + - - microRNA detection - - Identify or predict microRNA sequences (miRNA) and precursors or microRNA targets / binding sites in a DNA sequence. - beta12orEarlier - - + + + + beta12orEarlier + Compare two or more phylogenetic trees. + + + For example, to produce a consensus tree, subtrees, supertrees, calculate distances between trees or test topological similarity between trees (e.g. a congruence index) etc. + Phylogenetic tree comparison - + - - tRNA gene prediction - + + + - - + + - Identify or predict tRNA genes in genomic sequences (tRNA). - beta12orEarlier - - - - - - - - - - siRNA binding specificity prediction - - - + + - beta12orEarlier - Assess binding specificity of putative siRNA sequence(s), for example for a functional assay, typically with respect to designing specific siRNA sequences. - - - - - - - - - - Protein secondary structure prediction (integrated) - - Predict secondary structure of protein sequence(s) using multiple methods to achieve better predictions. - beta12orEarlier - - + beta12orEarlier + Edit a phylogenetic tree. + + + Phylogenetic tree editing - + - - Protein secondary structure prediction (helices) - - beta12orEarlier - Predict helical secondary structure of protein sequences. - - + + + + + + + + + beta12orEarlier + Infer a phylogenetic tree by comparing orthologous sequences in different species, particularly many closely related species (phylogenetic shadowing). + + + A phylogenetic 'shadow' represents the additive differences between individual sequences. By masking or 'shadowing' variable positions a conserved sequence is produced with few or none of the variations, which is then compared to the sequences of interest to identify significant regions of conservation. + Phylogenetic footprinting / shadowing - + - - Protein secondary structure prediction (turns) - - Predict turn structure (for example beta hairpin turns) of protein sequences. - beta12orEarlier - - + + + beta12orEarlier + Simulate the folding of a protein. + + + Protein folding simulation - + - - Protein secondary structure prediction (coils) - - beta12orEarlier - Predict open coils, non-regular secondary structure and intrinsically disordered / unstructured regions of protein sequences. - - + + + + beta12orEarlier + Predict the folding pathway(s) or non-native structural intermediates of a protein. + + + Protein folding pathway prediction - + - - Protein secondary structure prediction (disulfide bonds) - - beta12orEarlier - Predict cysteine bonding state and disulfide bond partners in protein sequences. - - + + + beta12orEarlier + 1.12 + Map and model the effects of single nucleotide polymorphisms (SNPs) on protein structure(s). + + + Protein SNP mapping + true - + - - GPCR prediction - - - beta12orEarlier - G protein-coupled receptor (GPCR) prediction - Predict G protein-coupled receptors (GPCR). - - + + + + + + + + + + + + + + + + beta12orEarlier + Predict the effect of point mutation on a protein structure, in terms of strucural effects and protein folding, stability and function. + Protein mutation modelling + Protein SNP mapping + Rotamer likelihood prediction + + + This includes 1) rotamer likelihood prediction: the prediction of rotamer likelihoods for all 20 amino acid types at each position in a protein structure, where output typically includes, for each residue position, the likelihoods for the 20 amino acid types with estimated reliability of the 20 likelihoods. 2) Protein SNP mapping, which maps and modesl the effects of single nucleotide polymorphisms (SNPs) on protein structure(s). Methods might predict silent or pathological mutations. + Protein modelling (mutation) - + - - GPCR analysis - - - - - - - - Analyse G-protein coupled receptor proteins (GPCRs). - beta12orEarlier - G protein-coupled receptor (GPCR) analysis - - + + + beta12orEarlier + beta12orEarlier + Design molecules that elicit an immune response (immunogens). + + + Immunogen design + true - + - - Protein structure prediction - - - - + + - - + + - - + + - beta12orEarlier - Predict tertiary structure (backbone and side-chain conformation) of protein sequences. - - + beta12orEarlier + Predict and optimise zinc finger protein domains for DNA/RNA binding (for example for transcription factors and nucleases). + + + Zinc finger prediction - + - - Nucleic acid structure prediction - - - + + - - + + - - + + - beta12orEarlier - Methods might identify thermodynamically stable or evolutionarily conserved structures. - Predict tertiary structure of DNA or RNA. - - + beta12orEarlier + Calculate Km, Vmax and derived data for an enzyme reaction. + + + Enzyme kinetics calculation - + - - Ab initio structure prediction - - Predict tertiary structure of protein sequence(s) without homologs of known structure. - de novo structure prediction - beta12orEarlier - - + + + beta12orEarlier + Reformat a file of data (or equivalent entity in memory). + File format conversion + File formatting + File reformatting + Format conversion + Reformatting + + + Formatting - + - - Protein modelling - - - - - - - - - - Comparative modelling - beta12orEarlier - Build a three-dimensional protein model based on known (for example homologs) structures. - The model might be of a whole, part or aspect of protein structure. Molecular modelling methods might use sequence-structure alignment, structural templates, molecular dynamics, energy minimization etc. - Homology modelling - Homology structure modelling - Protein structure comparative modelling - - + + + beta12orEarlier + Test and validate the format and content of a data file. + File format validation + + + Format validation - + - - Molecular docking - - + + - - + + - - + + - - + + - Model the structure of a protein in complex with a small molecule or another macromolecule. - beta12orEarlier - This includes protein-protein interactions, protein-nucleic acid, protein-ligand binding etc. Methods might predict whether the molecules are likely to bind in vivo, their conformation when bound, the strength of the interaction, possible mutations to achieve bonding and so on. - Docking simulation - Protein docking - - + beta12orEarlier + Visualise, plot or render (graphically) biomolecular data such as molecular sequences or structures. + Rendering + + + Visualisation - + - - Protein modelling (backbone) - - Model protein backbone conformation. - Methods might require a preliminary C(alpha) trace. - beta12orEarlier - - + + + + + + + + + + beta12orEarlier + Search a sequence database by sequence comparison and retrieve similar sequences. + +sequences matching a given sequence motif or pattern, such as a Prosite pattern or regular expression. + + + This excludes direct retrieval methods (e.g. the dbfetch program). + Sequence database search - + - - Protein modelling (side chains) - - beta12orEarlier - Methods might use a residue rotamer library. - Model, analyse or edit amino acid side chain conformation in protein structure, optimize side-chain packing, hydrogen bonding etc. - - + + + + + + + + + beta12orEarlier + Search a tertiary structure database, typically by sequence and/or structure comparison, or some other means, and retrieve structures and associated data. + + + Structure database search - + - - Protein modelling (loops) - - beta12orEarlier - Model loop conformation in protein structures. - - + + + beta12orEarlier + 1.8 + Search a secondary protein database (of classification information) to assign a protein sequence(s) to a known protein family or group. + + + Protein secondary database search + true - + - - Protein-ligand docking - - - - - - - - - - - - - - beta12orEarlier - Methods aim to predict the position and orientation of a ligand bound to a protein receptor or enzyme. - Ligand-binding simulation - Model protein-ligand (for example protein-peptide) binding using comparative modelling or other techniques. - Virtual ligand screening - - + + + beta12orEarlier + 1.8 + + Screen a sequence against a motif or pattern database. + + Motif database search + true - + - - Structured RNA prediction and optimisation - - - - - - - - - - - - - - Nucleic acid folding family identification - RNA inverse folding - beta12orEarlier - Predict or optimise RNA sequences (sequence pools) with likely secondary and tertiary structure for in vitro selection. - - + + + beta12orEarlier + 1.4 + + Search a database of sequence profiles with a query sequence. + + Sequence profile database search + true - + - - SNP detection - - - - Find single nucleotide polymorphisms (SNPs) between sequences. - Single nucleotide polymorphism detection - beta12orEarlier - This includes functional SNPs for large-scale genotyping purposes, disease-associated non-synonymous SNPs etc. - - + + + beta12orEarlier + beta12orEarlier + + Search a database of transmembrane proteins, for example for sequence or structural similarities. + + Transmembrane protein database search + true - + - - Radiation Hybrid Mapping - - - - - - - - Generate a physical (radiation hybrid) map of genetic markers in a DNA sequence using provided radiation hybrid (RH) scores for one or more markers. - beta12orEarlier - - + + + beta12orEarlier + 1.6 + + Query a database and retrieve sequences with a given entry code or accession number. + + Sequence retrieval (by code) + true - + - - Functional mapping - - beta12orEarlier + + + beta12orEarlier + 1.6 + + Query a database and retrieve sequences containing a given keyword. + + Sequence retrieval (by keyword) true - This can involve characterization of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs). - Map the genetic architecture of dynamic complex traits. - beta12orEarlier - - - + - - Haplotype mapping - - - - - - - - - Haplotype map generation - Haplotype inference - Infer haplotypes, either alleles at multiple loci that are transmitted together on the same chromosome, or a set of single nucleotide polymorphisms (SNPs) on a single chromatid that are statistically associated. - beta12orEarlier - Haplotype inference can help in population genetic studies and the identification of complex disease genes, , and is typically based on aligned single nucleotide polymorphism (SNP) fragments. Haplotype comparison is a useful way to characterize the genetic variation between individuals. An individual's haplotype describes which nucleotide base occurs at each position for a set of common SNPs. Tools might use combinatorial functions (for example parsimony) or a likelihood function or model with optimization such as minimum error correction (MEC) model, expectation-maximization algorithm (EM), genetic algorithm or Markov chain Monte Carlo (MCMC). - Haplotype reconstruction - - + + + + + beta12orEarlier + Search a sequence database and retrieve sequences that are similar to a query sequence. + Sequence database search (by sequence) + Structure database search (by sequence) + + + Sequence similarity search - + - - Linkage disequilibrium calculation - - - - - - - - beta12orEarlier - Linkage disequilibrium is identified where a combination of alleles (or genetic markers) occurs more or less frequently in a population than expected by chance formation of haplotypes. - Calculate linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome). - - + + + beta12orEarlier + 1.8 + Search a sequence database and retrieve sequences matching a given sequence motif or pattern, such as a Prosite pattern or regular expression. + + + Sequence database search (by motif or pattern) + true - + - - Genetic code prediction - - - - - - - - - beta12orEarlier - Predict genetic code from analysis of codon usage data. - - + + + beta12orEarlier + 1.6 + + Search a sequence database and retrieve sequences of a given amino acid composition. + + Sequence database search (by amino acid composition) + true - + - - Dotplot plotting - - - - - - - - - - beta12orEarlier - Draw a dotplot of sequence similarities identified from word-matching or character comparison. - - + + + beta12orEarlier + Search a sequence database and retrieve sequences with a specified property, typically a physicochemical or compositional property. + + + Sequence database search (by property) - + - - Pairwise sequence alignment - - - - - - - - Pairwise sequence alignment generation - Pairwise sequence alignment - Methods might perform one-to-one, one-to-many or many-to-many comparisons. - Align exactly two molecular sequences. - Pairwise sequence alignment construction - beta12orEarlier - - + + + beta12orEarlier + 1.6 + + Search a sequence database and retrieve sequences that are similar to a query sequence using a word-based method. + + Word-based methods (for example BLAST, gapped BLAST, MEGABLAST, WU-BLAST etc.) are usually quicker than alignment-based methods. They may or may not handle gaps. + Sequence database search (by sequence using word-based methods) + true - + - - Multiple sequence alignment - - Multiple sequence alignment construction - Align two or more molecular sequences. - This includes methods that use an existing alignment, for example to incorporate sequences into an alignment, or combine several multiple alignments into a single, improved alignment. - Multiple sequence alignment - beta12orEarlier - Multiple sequence alignment generation - - + + + beta12orEarlier + 1.6 + + Search a sequence database and retrieve sequences that are similar to a query sequence using a sequence profile-based method, or with a supplied profile as query. + + This includes tools based on PSI-BLAST. + Sequence database search (by sequence using profile-based methods) + true - + - - Pairwise sequence alignment generation (local) - - beta12orEarlier - Local pairwise sequence alignment construction - Locally align exactly two molecular sequences. - Pairwise sequence alignment (local) + + + beta12orEarlier + 1.6 + + Search a sequence database for sequences that are similar to a query sequence using a local alignment-based method. + + This includes tools based on the Smith-Waterman algorithm or FASTA. + Sequence database search (by sequence using local alignment-based methods) true - Local alignment methods identify regions of local similarity. - 1.6 - Pairwise sequence alignment construction (local) - - - - + - - Pairwise sequence alignment generation (global) - - Pairwise sequence alignment construction (global) - Global pairwise sequence alignment construction - 1.6 + + + beta12orEarlier + 1.6 + + Search sequence(s) or a sequence database for sequences that are similar to a query sequence using a global alignment-based method. + + This includes tools based on the Needleman and Wunsch algorithm. + Sequence database search (by sequence using global alignment-based methods) true - Globally align exactly two molecular sequences. - beta12orEarlier - Global alignment methods identify similarity across the entire length of the sequences. - Pairwise sequence alignment (global) - - - - + - - Local sequence alignment - - Multiple sequence alignment (local) - Local multiple sequence alignment construction - beta12orEarlier - Local alignment methods identify regions of local similarity. - Multiple sequence alignment construction (local) - Sequence alignment generation (local) - Sequence alignment (local) - Locally align two or more molecular sequences. - - + + + beta12orEarlier + 1.6 + + Search a DNA database (for example a database of conserved sequence tags) for matches to Sequence-Tagged Site (STS) primer sequences. + + STSs are genetic markers that are easily detected by the polymerase chain reaction (PCR) using specific primers. + Sequence database search (by sequence for primer sequences) + true - + - - Global sequence alignment - - Global multiple sequence alignment construction - Multiple sequence alignment (global) - beta12orEarlier - Sequence alignment (global) - Multiple sequence alignment construction (global) - Globally align two or more molecular sequences. - Sequence alignment generation (global) - Global alignment methods identify similarity across the entire length of the sequences. - - + + + beta12orEarlier + 1.6 + Search sequence(s) or a sequence database for sequences which match a set of peptide masses, for example a peptide mass fingerprint from mass spectrometry. + + + Sequence database search (by molecular weight) + true - + - - Constrained sequence alignment - - beta12orEarlier - Align two or more molecular sequences with user-defined constraints. - Multiple sequence alignment construction (constrained) - Sequence alignment generation (constrained) - Multiple sequence alignment (constrained) - Sequence alignment (constrained) - Constrained multiple sequence alignment construction - - + + + beta12orEarlier + 1.6 + + Search sequence(s) or a sequence database for sequences of a given isoelectric point. + + Sequence database search (by isoelectric point) + true - + - - Consensus-based sequence alignment - - Consensus multiple sequence alignment construction - Sequence alignment (consensus) - beta12orEarlier - Align two or more molecular sequences using multiple methods to achieve higher quality. - Sequence alignment generation (consensus) - Multiple sequence alignment construction (consensus) - Multiple sequence alignment (consensus) - - + + + beta12orEarlier + 1.6 + + Query a tertiary structure database and retrieve entries with a given entry code or accession number. + + Structure retrieval (by code) + true - + - - Tree-based sequence alignment - - - - - - - - Sequence alignment generation (phylogenetic tree-based) - This is supposed to give a more biologically meaningful alignment than standard alignments. - beta12orEarlier - Phylogenetic tree-based multiple sequence alignment construction - Align multiple sequences using relative gap costs calculated from neighbors in a supplied phylogenetic tree. - Sequence alignment (phylogenetic tree-based) - Multiple sequence alignment construction (phylogenetic tree-based) - Multiple sequence alignment (phylogenetic tree-based) - - + + + beta12orEarlier + 1.6 + + Query a tertiary structure database and retrieve entries containing a given keyword. + + Structure retrieval (by keyword) + true - + - - Secondary structure alignment generation - - beta12orEarlier - 1.6 - Secondary structure alignment construction - Secondary structure alignment + + + beta12orEarlier + 1.8 + Search a tertiary structure database and retrieve structures with a sequence similar to a query sequence. + + + Structure database search (by sequence) true - Align molecular secondary structure (represented as a 1D string). - - - + - - Protein secondary structure alignment generation - - - - - - - - - Protein secondary structure alignment construction - Align protein secondary structures. - beta12orEarlier - Secondary structure alignment (protein) - Protein secondary structure alignment - - + + + + beta12orEarlier + Search a database of molecular structure and retrieve structures that are similar to a query structure. + Structure database search (by structure) + Structure retrieval by structure + + + Structural similarity search - + - - RNA secondary structure alignment - - + + - - + + - - + + - RNA secondary structure alignment generation - RNA secondary structure alignment - Align RNA secondary structures. - RNA secondary structure alignment construction - Secondary structure alignment (RNA) - beta12orEarlier - - + beta12orEarlier + Annotate a molecular sequence record with terms from a controlled vocabulary. + + + Sequence annotation - + - - Pairwise structure alignment - - beta12orEarlier - Pairwise structure alignment generation - Pairwise structure alignment construction - Align (superimpose) exactly two molecular tertiary structures. - - + + + beta12orEarlier + Annotate a genome sequence with terms from a controlled vocabulary. + Metagenome annotation + + + Genome annotation - + - - Multiple structure alignment construction - - Align (superimpose) two or more molecular tertiary structures. - This includes methods that use an existing alignment. - 1.6 - true - Multiple structure alignment - beta12orEarlier - - + + + beta12orEarlier + Generate the reverse and / or complement of a nucleotide sequence. + + + Nucleic acid sequence reverse and complement - + - - Structure alignment (protein) - - beta13 - true - beta12orEarlier - Align protein tertiary structures. - - + + + beta12orEarlier + Generate a random sequence, for example, with a specific character composition. + + + Random sequence generation - - - - Structure alignment (RNA) - - beta13 - true - Align RNA tertiary structures. - beta12orEarlier - - - - - + - + + + + + + + + + + beta12orEarlier + Generate digest fragments for a nucleotide sequence containing restriction sites. + + + Nucleic acid restriction digest + + - - Pairwise structure alignment generation (local) - - Locally align (superimpose) exactly two molecular tertiary structures. - Pairwise structure alignment (local) - Local alignment methods identify regions of local similarity, common substructures etc. - Pairwise structure alignment construction (local) - 1.6 - true - Local pairwise structure alignment construction - beta12orEarlier - - - + + + + + + + + + + + + + + + + + + + beta12orEarlier + Cleave a protein sequence into peptide fragments (by enzymatic or chemical cleavage) and calculate the fragment masses. + + + Protein sequence cleavage - + - - Pairwise structure alignment generation (global) - - Global pairwise structure alignment construction - Global alignment methods identify similarity across the entire structures. - true - beta12orEarlier - 1.6 - Pairwise structure alignment construction (global) - Globally align (superimpose) exactly two molecular tertiary structures. - Pairwise structure alignment (global) - - - + + + beta12orEarlier + Mutate a molecular sequence a specified amount or shuffle it to produce a randomised sequence with the same overall composition. + + + Sequence mutation and randomisation - + - - Local structure alignment - - Local multiple structure alignment construction - Local alignment methods identify regions of local similarity, common substructures etc. - Structure alignment construction (local) - beta12orEarlier - Locally align (superimpose) two or more molecular tertiary structures. - Multiple structure alignment construction (local) - Multiple structure alignment (local) - Structure alignment generation (local) - - + + + beta12orEarlier + Mask characters in a molecular sequence (replacing those characters with a mask character). + + + For example, SNPs or repeats in a DNA sequence might be masked. + Sequence masking - + - - Global structure alignment - - Structure alignment construction (global) - Multiple structure alignment (global) - Structure alignment generation (global) - Multiple structure alignment construction (global) - beta12orEarlier - Global alignment methods identify similarity across the entire structures. - Global multiple structure alignment construction - Globally align (superimpose) two or more molecular tertiary structures. - - + + + beta12orEarlier + Cut (remove) characters or a region from a molecular sequence. + + + Sequence cutting - + - - Profile-to-profile alignment (pairwise) - - Sequence alignment generation (pairwise profile) - Methods might perform one-to-one, one-to-many or many-to-many comparisons. - Pairwise sequence profile alignment construction - Sequence profile alignment construction (pairwise) - Sequence profile alignment (pairwise) - beta12orEarlier - Align exactly two molecular profiles. - Sequence profile alignment generation (pairwise) - - + + + beta12orEarlier + Create (or remove) restriction sites in sequences, for example using silent mutations. + + + Restriction site creation - + - - Sequence alignment generation (multiple profile) - - Align two or more molecular profiles. - 1.6 - true - Sequence profile alignment generation (multiple) - beta12orEarlier - Sequence profile alignment (multiple) - Sequence profile alignment construction (multiple) - Multiple sequence profile alignment construction - - + + + + + + + + + beta12orEarlier + Translate a DNA sequence into protein. + + + DNA translation - + - - 3D profile-to-3D profile alignment (pairwise) - - Methods might perform one-to-one, one-to-many or many-to-many comparisons. - Pairwise structural (3D) profile alignment construction - Structural (3D) profile alignment (pairwise) - Structural profile alignment construction (pairwise) - Align exactly two molecular Structural (3D) profiles. - beta12orEarlier - Structural profile alignment generation (pairwise) - - + + + + + + + + + beta12orEarlier + Transcribe a nucleotide sequence into mRNA sequence(s). + + + DNA transcription - + - - Structural profile alignment generation (multiple) - + + + beta12orEarlier + 1.8 + Calculate base frequency or word composition of a nucleotide sequence. + + + Sequence composition calculation (nucleic acid) true - Structural profile alignment construction (multiple) - Align two or more molecular 3D profiles. - Multiple structural (3D) profile alignment construction - beta12orEarlier - Structural (3D) profile alignment (multiple) - 1.6 - - - + - - Data retrieval (tool metadata) - - Data retrieval (tool annotation) - 1.6 - Search and retrieve names of or documentation on bioinformatics tools, for example by keyword or which perform a particular function. - beta12orEarlier + + + beta12orEarlier + 1.8 + Calculate amino acid frequency or word composition of a protein sequence. + + + Sequence composition calculation (protein) true - Tool information retrieval - - - + - - Data retrieval (database metadata) - - beta12orEarlier - true - Data retrieval (database annotation) - Search and retrieve names of or documentation on bioinformatics databases or query terms, for example by keyword. - Database information retrieval - 1.6 - - + + + + beta12orEarlier + Find (and possibly render) short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences. + + + Repeat sequence detection - + - - PCR primer design (for large scale sequencing) - - - - - - - - Predict primers for large scale sequencing. - beta12orEarlier - - + + + + beta12orEarlier + Analyse repeat sequence organisation such as periodicity. + + + Repeat sequence organisation analysis - + - - PCR primer design (for genotyping polymorphisms) - - beta12orEarlier - Predict primers for genotyping polymorphisms, for example single nucleotide polymorphisms (SNPs). - - + + + beta12orEarlier + 1.12 + Analyse the hydrophobic, hydrophilic or charge properties of a protein structure. + + + Protein hydropathy calculation (from structure) + true - + - - PCR primer design (for gene transcription profiling) - + + - - + + - Predict primers for gene transcription profiling. - beta12orEarlier - - + beta12orEarlier + WHATIF:AtomAccessibilitySolvent + WHATIF:AtomAccessibilitySolventPlus + Calculate solvent accessible or buried surface areas in protein or other molecular structures. + Protein solvent accessibility calculation + + + Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). + Accessible surface calculation - + - - PCR primer design (for conserved primers) - - Predict primers that are conserved across multiple genomes or species. - beta12orEarlier - - + + + beta12orEarlier + 1.12 + Identify clusters of hydrophobic or charged residues in a protein structure. + + + Protein hydropathy cluster calculation + true - + - - PCR primer design (based on gene structure) - + + - - + + - Predict primers based on gene structure, promoters, exon-exon junctions etc. - beta12orEarlier - - + beta12orEarlier + Calculate whether a protein structure has an unusually large net charge (dipole moment). + + + Protein dipole moment calculation - + - - PCR primer design (for methylation PCRs) - - beta12orEarlier - Predict primers for methylation PCRs. - - + + + beta12orEarlier + WHATIF:AtomAccessibilityMolecular + WHATIF:AtomAccessibilityMolecularPlus + WHATIF:ResidueAccessibilityMolecular + WHATIF:ResidueAccessibilitySolvent + WHATIF:ResidueAccessibilityVacuum + WHATIF:ResidueAccessibilityVacuumMolecular + WHATIF:TotAccessibilityMolecular + WHATIF:TotAccessibilitySolvent + Calculate the molecular surface area in proteins and other macromolecules. + Protein atom surface calculation + Protein residue surface calculation + Protein surface and interior calculation + Protein surface calculation + + + Molecular surface calculation - + - - Sequence assembly (mapping assembly) - - Sequence assembly by combining fragments using an existing backbone sequence, typically a reference genome. - beta12orEarlier - The final sequence will resemble the backbone sequence. Mapping assemblers are usually much faster and less memory intensive than de-novo assemblers. - - + + + beta12orEarlier + 1.12 + Identify or predict catalytic residues, active sites or other ligand-binding sites in protein structures. + + + Protein binding site prediction (from structure) + true - + - - Sequence assembly (de-novo assembly) - - Sequence assembly by combining fragments without the aid of a reference sequence or genome. - De-novo assemblers are much slower and more memory intensive than mapping assemblers. - beta12orEarlier - - + + + + + + + + + beta12orEarlier + Analyse RNA or DNA-binding sites in protein structure. + + + Protein-nucleic acid binding site analysis - + - - Sequence assembly (genome assembly) - - Sequence assembly capable on a very large scale such as assembly of whole genomes. - beta12orEarlier - - + + + beta12orEarlier + Decompose a structure into compact or globular fragments (protein peeling). + + + Protein peeling - + - - Sequence assembly (EST assembly) - - beta12orEarlier - Sequence assembly for EST sequences (transcribed mRNA). - Assemblers must handle (or be complicated by) alternative splicing, trans-splicing, single-nucleotide polymorphism (SNP), recoding, and post-transcriptional modification. - - + + + + + + + + + beta12orEarlier + Calculate a matrix of distance between residues (for example the C-alpha atoms) in a protein structure. + + + Protein distance matrix calculation - + - - Tag mapping - - + + - - + + - Tag mapping might assign experimentally obtained tags to known transcripts or annotate potential virtual tags in a genome. - Tag to gene assignment - Make gene to tag assignments (tag mapping) of SAGE, MPSS and SBS data, by annotating tags with ontology concepts. - beta12orEarlier - - + beta12orEarlier + Calculate a residue contact map (typically all-versus-all inter-residue contacts) for a protein structure. + + + Protein contact map calculation - + - - SAGE data processing - - beta12orEarlier - Serial analysis of gene expression data processing - beta12orEarlier - Process (read and / or write) serial analysis of gene expression (SAGE) data. - true - - + + + + + + + + + beta12orEarlier + Calculate clusters of contacting residues in protein structures. + + + This includes for example clusters of hydrophobic or charged residues, or clusters of contacting residues which have a key structural or functional role. + Residue cluster calculation - + - - MPSS data processing - - beta12orEarlier - Process (read and / or write) massively parallel signature sequencing (MPSS) data. - true - Massively parallel signature sequencing data processing - beta12orEarlier - - + + + + + + + + + beta12orEarlier + WHATIF:HasHydrogenBonds + WHATIF:ShowHydrogenBonds + WHATIF:ShowHydrogenBondsM + Identify potential hydrogen bonds between amino acids and other groups. + + + The output might include the atoms involved in the bond, bond geometric parameters and bond enthalpy. + Hydrogen bond calculation - + - - SBS data processing - - beta12orEarlier - Sequencing by synthesis data processing - beta12orEarlier - Process (read and / or write) sequencing by synthesis (SBS) data. + + + beta12orEarlier + 1.12 + + Calculate non-canonical atomic interactions in protein structures. + + Residue non-canonical interaction detection true - - - + - - Heat map generation - - + + - - + + - beta12orEarlier - The heat map usually uses a coloring scheme to represent clusters. They can show how expression of mRNA by a set of genes was influenced by experimental conditions. - Heat map construction - Generate a heat map of gene expression from microarray data. - - + beta12orEarlier + Calculate a Ramachandran plot of a protein structure. + + + Ramachandran plot calculation - + - - Gene expression profile analysis - - true - Functional profiling - beta12orEarlier - Analyse one or more gene expression profiles, typically to interpret them in functional terms. - 1.6 - - + + + + + + + + + + + + + + + beta12orEarlier + Validate a Ramachandran plot of a protein structure. + + + Ramachandran plot validation - + - - Gene expression profile pathway mapping - - - + + - - + + - beta12orEarlier - Map a gene expression profile to known biological pathways, for example, to identify or reconstruct a pathway. - - + + + + + + + beta12orEarlier + Calculate the molecular weight of a protein sequence or fragments. + + + Protein molecular weight calculation - + - - Protein secondary structure assignment (from coordinate data) - - - beta12orEarlier - Assign secondary structure from protein coordinate data. - - + + + + + + + + + beta12orEarlier + Predict extinction coefficients or optical density of a protein sequence. + + + Protein extinction coefficient calculation - + - - Protein secondary structure assignment (from CD data) - + + - - + + - Assign secondary structure from circular dichroism (CD) spectroscopic data. - beta12orEarlier - - + + + + + + + beta12orEarlier + Calculate pH-dependent properties from pKa calculations of a protein sequence. + + + Protein pH-dependent property calculation - + - - Protein structure assignment (from X-ray crystallographic data) - + + + beta12orEarlier + 1.12 + Hydropathy calculation on a protein sequence. + + + Protein hydropathy calculation (from sequence) true - 1.7 - Assign a protein tertiary structure (3D coordinates) from raw X-ray crystallography data. - beta12orEarlier - - - + - - Protein structure assignment (from NMR data) - - beta12orEarlier - Assign a protein tertiary structure (3D coordinates) from raw NMR spectroscopy data. - true - 1.7 - - + + + + + + + + + + beta12orEarlier + Plot a protein titration curve. + + + Protein titration curve plotting - + - - Phylogenetic tree generation (data centric) - - Phylogenetic tree construction (data centric) - beta12orEarlier - Construct a phylogenetic tree from a specific type of data. - - + + + + + + + + + beta12orEarlier + Calculate isoelectric point of a protein sequence. + + + Protein isoelectric point calculation - + - - Phylogenetic tree generation (method centric) - - Phylogenetic tree construction (method centric) - Construct a phylogenetic tree using a specific method. - beta12orEarlier - - + + + + + + + + + beta12orEarlier + Estimate hydrogen exchange rate of a protein sequence. + + + Protein hydrogen exchange rate calculation - + - - Phylogenetic tree generation (from molecular sequences) - - - Phylogenetic tree construction from molecular sequences. - beta12orEarlier - Phylogenetic tree construction (from molecular sequences) - Methods typically compare multiple molecular sequence and estimate evolutionary distances and relationships to infer gene families or make functional predictions. - - + + + beta12orEarlier + Calculate hydrophobic or hydrophilic / charged regions of a protein sequence. + + + Protein hydrophobic region calculation - + - - Phylogenetic tree generation (from continuous quantitative characters) - + + - - + + - Phylogenetic tree construction (from continuous quantitative characters) - beta12orEarlier - Phylogenetic tree construction from continuous quantitative character data. - - + beta12orEarlier + Calculate aliphatic index (relative volume occupied by aliphatic side chains) of a protein. + + + Protein aliphatic index calculation - + - - Phylogenetic tree generation (from gene frequencies) - - - - - - - + + + - - + + - Phylogenetic tree construction (from gene frequencies) - Phylogenetic tree construction from gene frequency data. - beta12orEarlier - - + beta12orEarlier + Calculate the hydrophobic moment of a peptide sequence and recognize amphiphilicity. + + + Hydrophobic moment is a peptides hydrophobicity measured for different angles of rotation. + Protein hydrophobic moment plotting - + - - Phylogenetic tree construction (from polymorphism data) - + + - - + + - Phylogenetic tree construction from polymorphism data including microsatellites, RFLP (restriction fragment length polymorphisms), RAPD (random-amplified polymorphic DNA) and AFLP (amplified fragment length polymorphisms) data. - Phylogenetic tree generation (from polymorphism data) - beta12orEarlier - - + beta12orEarlier + Predict the stability or globularity of a protein sequence, whether it is intrinsically unfolded etc. + + + Protein globularity prediction - + - - Phylogenetic species tree construction - - Construct a phylogenetic species tree, for example, from a genome-wide sequence comparison. - Phylogenetic species tree generation - beta12orEarlier - - + + + + + + + + + beta12orEarlier + Predict the solubility or atomic solvation energy of a protein sequence. + + + Protein solubility prediction - + - - Phylogenetic tree generation (parsimony methods) - - Phylogenetic tree construction (parsimony methods) - Construct a phylogenetic tree by computing a sequence alignment and searching for the tree with the fewest number of character-state changes from the alignment. - This includes evolutionary parsimony (invariants) methods. - beta12orEarlier - - + + + + + + + + + beta12orEarlier + Predict crystallizability of a protein sequence. + + + Protein crystallizability prediction - + - - Phylogenetic tree generation (minimum distance methods) - - This includes neighbor joining (NJ) clustering method. - beta12orEarlier - Phylogenetic tree construction (minimum distance methods) - Construct a phylogenetic tree by computing (or using precomputed) distances between sequences and searching for the tree with minimal discrepancies between pairwise distances. - - + + + beta12orEarlier + Detect or predict signal peptides (and typically predict subcellular localisation) of eukaryotic proteins. + + + Protein signal peptide detection (eukaryotes) - + - - Phylogenetic tree generation (maximum likelihood and Bayesian methods) - - Phylogenetic tree construction (maximum likelihood and Bayesian methods) - Construct a phylogenetic tree by relating sequence data to a hypothetical tree topology using a model of sequence evolution. - Maximum likelihood methods search for a tree that maximizes a likelihood function, i.e. that is most likely given the data and model. Bayesian analysis estimate the probability of tree for branch lengths and topology, typically using a Monte Carlo algorithm. - beta12orEarlier - - + + + beta12orEarlier + Detect or predict signal peptides (and typically predict subcellular localisation) of bacterial proteins. + + + Protein signal peptide detection (bacteria) - + - - Phylogenetic tree generation (quartet methods) - - beta12orEarlier - Phylogenetic tree construction (quartet methods) - Construct a phylogenetic tree by computing four-taxon trees (4-trees) and searching for the phylogeny that matches most closely. - - + + + beta12orEarlier + 1.12 + Predict MHC class I or class II binding peptides, promiscuous binding peptides, immunogenicity etc. + + + MHC peptide immunogenicity prediction + true + - + - - Phylogenetic tree generation (AI methods) - - Construct a phylogenetic tree by using artificial-intelligence methods, for example genetic algorithms. - Phylogenetic tree construction (AI methods) - beta12orEarlier - - + + + beta12orEarlier + 1.6 + + Predict, recognise and identify positional features in protein sequences such as functional sites or regions and secondary structure. + + Methods typically involve scanning for known motifs, patterns and regular expressions. + Protein feature prediction (from sequence) + true - + - - DNA substitution modelling - - + + + - - + + - - + + - Sequence alignment analysis (phylogenetic modelling) - beta12orEarlier - Identify a plausible model of DNA substitution that explains a DNA sequence alignment. - - + beta12orEarlier + Predict, recognise and identify features in nucleotide sequences such as functional sites or regions, typically by scanning for known motifs, patterns and regular expressions. + Sequence feature detection (nucleic acid) + Nucleic acid feature prediction + Nucleic acid feature recognition + + + Methods typically involve scanning for known motifs, patterns and regular expressions. + Nucleic acid feature detection - + - - Phylogenetic tree analysis (shape) - - Phylogenetic tree topology analysis - Analyse the shape (topology) of a phylogenetic tree. - beta12orEarlier - - + + + + + + + + + + beta12orEarlier + Predict antigenic determinant sites (epitopes) in protein sequences. + + + Epitope mapping is commonly done during vaccine design. + Epitope mapping - + - - Phylogenetic tree bootstrapping - - - Apply bootstrapping or other measures to estimate confidence of a phylogenetic tree. - beta12orEarlier - - + + + + + + + + + beta12orEarlier + Predict post-translation modification sites in protein sequences. + + + Methods might predict sites of methylation, N-terminal myristoylation, N-terminal acetylation, sumoylation, palmitoylation, phosphorylation, sulfation, glycosylation, glycosylphosphatidylinositol (GPI) modification sites (GPI lipid anchor signals) etc. + Protein post-translation modification site prediction - + - - Phylogenetic tree analysis (gene family prediction) - - - - - - - + + + - - + + - Predict families of genes and gene function based on their position in a phylogenetic tree. - beta12orEarlier - - + beta12orEarlier + Detect or predict signal peptides and signal peptide cleavage sites in protein sequences. + + + Methods might use sequence motifs and features, amino acid composition, profiles, machine-learned classifiers, etc. + Protein signal peptide detection - + - - Phylogenetic tree analysis (natural selection) - - beta12orEarlier - Stabilizing/purifying (directional) selection favors a single phenotype and tends to decrease genetic diversity as a population stabilizes on a particular trait, selecting out trait extremes or deleterious mutations. In contrast, balancing selection maintain genetic polymorphisms (or multiple alleles), whereas disruptive (or diversifying) selection favors individuals at both extremes of a trait. - Analyse a phylogenetic tree to identify allele frequency distribution and change that is subject to evolutionary pressures (natural selection, genetic drift, mutation and gene flow). Identify type of natural selection (such as stabilizing, balancing or disruptive). - - + + + beta12orEarlier + 1.12 + Predict catalytic residues, active sites or other ligand-binding sites in protein sequences. + + + Protein binding site prediction (from sequence) + true - + - - Phylogenetic tree generation (consensus) - - - Compare two or more phylogenetic trees to produce a consensus tree. - Methods typically test for topological similarity between trees using for example a congruence index. - beta12orEarlier - Phylogenetic tree construction (consensus) - - + + + beta12orEarlier + Predict RNA and DNA-binding binding sites in protein sequences. + + + Protein-nucleic acid binding prediction - + - - Phylogenetic sub/super tree detection - - beta12orEarlier - Compare two or more phylogenetic trees to detect subtrees or supertrees. - - + + + + beta12orEarlier + Predict protein sites that are key to protein folding, such as possible sites of nucleation or stabilisation. + + + Protein folding site prediction - + - - Phylogenetic tree distances calculation - + + - - + + - beta12orEarlier - Compare two or more phylogenetic trees to calculate distances between trees. - - + beta12orEarlier + Detect or predict cleavage sites (enzymatic or chemical) in protein sequences. + + + Protein cleavage site prediction - + - - Phylogenetic tree annotation - - beta12orEarlier - http://www.evolutionaryontology.org/cdao.owl#CDAOAnnotation - Annotate a phylogenetic tree with terms from a controlled vocabulary. - - + + + beta12orEarlier + 1.8 + Predict epitopes that bind to MHC class I molecules. + + + Epitope mapping (MHC Class I) + true - + - - Immunogenicity prediction - - - - - - - - - - - - - - - - - - - - beta12orEarlier - Peptide immunogen prediction - Predict and optimise peptide ligands that elicit an immunological response. - - + + + beta12orEarlier + 1.8 + Predict epitopes that bind to MHC class II molecules. + + + + Epitope mapping (MHC Class II) + true - + - - DNA vaccine design - - - - - - - - - - - - - - - beta12orEarlier - Predict or optimise DNA to elicit (via DNA vaccination) an immunological response. - - + + + beta12orEarlier + 1.12 + Detect, predict and identify whole gene structure in DNA sequences. This includes protein coding regions, exon-intron structure, regulatory regions etc. + + + Whole gene prediction + true - + - - Sequence formatting - - - - - - - - - - - - - - beta12orEarlier - Reformat (a file or other report of) molecular sequence(s). - Sequence file format conversion - - - + + + beta12orEarlier + 1.12 + Detect, predict and identify genetic elements such as promoters, coding regions, splice sites, etc in DNA sequences. + + + Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc. + Gene component prediction + true + - + - - Sequence alignment formatting - - - - - - - - - - - - - - Reformat (a file or other report of) molecular sequence alignment(s). - beta12orEarlier - - + + + beta12orEarlier + Detect or predict transposons, retrotransposons / retrotransposition signatures etc. + + + Transposon prediction - + - - Codon usage table formatting - - - - - - - - - - - - - - - Reformat a codon usage table. - beta12orEarlier - - + + + beta12orEarlier + Detect polyA signals in nucleotide sequences. + + + PolyA signal detection - + - - Sequence visualisation - - - - - - - - + + - - + + - beta12orEarlier - Visualise, format or render a molecular sequence, possibly with sequence features or properties shown. - Sequence rendering - - + beta12orEarlier + Detect quadruplex-forming motifs in nucleotide sequences. + Quadruplex structure prediction + + + Quadruplex (4-stranded) structures are formed by guanine-rich regions and are implicated in various important biological processes and as therapeutic targets. + Quadruplex formation site detection - + - - Sequence alignment visualisation - - + + - - + + - - - - - - - Sequence alignment rendering - Visualise, format or print a molecular sequence alignment. - beta12orEarlier - - + beta12orEarlier + Find CpG rich regions in a nucleotide sequence or isochores in genome sequences. + CpG island and isochores detection + CpG island and isochores rendering + + + An isochore is long region (> 3 KB) of DNA with very uniform GC content, in contrast to the rest of the genome. Isochores tend tends to have more genes, higher local melting or denaturation temperatures, and different flexibility. Methods might calculate fractional GC content or variation of GC content, predict methylation status of CpG islands etc. This includes methods that visualise CpG rich regions in a nucleotide sequence, for example plot isochores in a genome sequence. + CpG island and isochore detection - + - - Sequence cluster visualisation - - - - - - - + + - - + + - Sequence cluster rendering - beta12orEarlier - Visualise, format or render sequence clusters. - - + beta12orEarlier + Find and identify restriction enzyme cleavage sites (restriction sites) in (typically) DNA sequences, for example to generate a restriction map. + + + Restriction site recognition - + - - Phylogenetic tree visualisation - - - - - - - - - Render or visualise a phylogenetic tree. - Phylogenetic tree rendering - beta12orEarlier - - + + + beta12orEarlier + Identify or predict nucleosome exclusion sequences (nucleosome free regions) in DNA. + + + Nucleosome formation or exclusion sequence prediction - + - - RNA secondary structure visualisation - - + + - - + + - RNA secondary structure rendering - Visualise RNA secondary structure, knots, pseudoknots etc. - beta12orEarlier - - + beta12orEarlier + Identify, predict or analyse splice sites in nucleotide sequences. + + + Methods might require a pre-mRNA or genomic DNA sequence. + Splice site prediction - + - - Protein secondary structure rendering - Protein secondary structure visualisation - - - - - - - - Render and visualise protein secondary structure. - beta12orEarlier - - + + + beta12orEarlier + Predict whole gene structure using a combination of multiple methods to achieve better predictions. + + + Integrated gene prediction - + - - Structure visualisation - - - - - - - - - - - - - - - Structure rendering - Visualise or render a molecular tertiary structure, for example a high-quality static picture or animation. - beta12orEarlier - - + + + beta12orEarlier + Find operons (operators, promoters and genes) in bacteria genes. + + + Operon prediction - + - - Microarray data rendering - - - + + + beta12orEarlier + Predict protein-coding regions (CDS or exon) or open reading frames in nucleotide sequences. + ORF finding + ORF prediction + + + Coding region prediction + + + + + + + + - - + + - Visualise microarray data. - beta12orEarlier - - + beta12orEarlier + Predict selenocysteine insertion sequence (SECIS) in a DNA sequence. + + + SECIS elements are around 60 nucleotides in length with a stem-loop structure directs the cell to translate UGA codons as selenocysteines. + Selenocysteine insertion sequence (SECIS) prediction - + - - Protein interaction network rendering - Protein interaction network visualisation - + + - - + + - - beta12orEarlier - Identify and analyse networks of protein interactions. - - + beta12orEarlier + Identify or predict transcription regulatory motifs, patterns, elements or regions in DNA sequences. + Transcription regulatory element prediction + Translational regulatory element prediction + + + This includes promoters, enhancers, silencers and boundary elements / insulators, regulatory protein or transcription factor binding sites etc. Methods might be specific to a particular genome and use motifs, word-based / grammatical methods, position-specific frequency matrices, discriminative pattern analysis etc. + Regulatory element prediction - + - - Map drawing - + + - - + + - beta12orEarlier - DNA map drawing - Map rendering - Draw or visualise a DNA map. - - + beta12orEarlier + Predict translation initiation sites, possibly by searching a database of sites. + + + Translation initiation site prediction - + - - Sequence motif rendering - - Render a sequence with motifs. - true - beta12orEarlier - beta12orEarlier - - + + + beta12orEarlier + Identify or predict whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in DNA sequences. + + + Methods might recognize CG content, CpG islands, splice sites, polyA signals etc. + Promoter prediction - + - - Restriction map drawing - - + + + beta12orEarlier + Identify, predict or analyse cis-regulatory elements (TATA box, Pribnow box, SOS box, CAAT box, CCAAT box, operator etc.) in DNA sequences. + + + Cis-regulatory elements (cis-elements) regulate the expression of genes located on the same strand. Cis-elements are found in the 5' promoter region of the gene, in an intron, or in the 3' untranslated region. Cis-elements are often binding sites of one or more trans-acting factors. + Transcription regulatory element prediction (DNA-cis) + + + + + + + + + beta12orEarlier + Identify, predict or analyse cis-regulatory elements (for example riboswitches) in RNA sequences. + + + Cis-regulatory elements (cis-elements) regulate genes located on the same strand from which the element was transcribed. A riboswitch is a region of an mRNA molecule that bind a small target molecule that regulates the gene's activity. + Transcription regulatory element prediction (RNA-cis) + + + + + + + + - - + + - Draw or visualise restriction maps in DNA sequences. - beta12orEarlier - - + beta12orEarlier + Identify or predict functional RNA sequences with a gene regulatory role (trans-regulatory elements) or targets. + Functional RNA identification + + + Trans-regulatory elements regulate genes distant from the gene from which they were transcribed. + Transcription regulatory element prediction (trans) - + - - DNA linear map rendering - - beta12orEarlier - beta12orEarlier - true - Draw a linear maps of DNA. - - + + + beta12orEarlier + Identify matrix/scaffold attachment regions (MARs/SARs) in DNA sequences. + + + MAR/SAR sites often flank a gene or gene cluster and are found nearby cis-regulatory sequences. They might contribute to transcription regulation. + Matrix/scaffold attachment site prediction - + - - Plasmid map drawing - - beta12orEarlier - DNA circular map rendering - Draw a circular maps of DNA, for example a plasmid map. - - + + + beta12orEarlier + Identify or predict transcription factor binding sites in DNA sequences. + + + Transcription factor binding site prediction - + - - Operon drawing - + + - - + + - Visualise operon structure etc. - beta12orEarlier - Operon rendering - - + beta12orEarlier + Identify or predict exonic splicing enhancers (ESE) in exons. + + + An exonic splicing enhancer (ESE) is 6-base DNA sequence motif in an exon that enhances or directs splicing of pre-mRNA or hetero-nuclear RNA (hnRNA) into mRNA. + Exonic splicing enhancer prediction - + - - Nucleic acid folding family identification - - true - beta12orEarlier - Identify folding families of related RNAs. - beta12orEarlier - - + + + + beta12orEarlier + Evaluate molecular sequence alignment accuracy. + Sequence alignment quality evaluation + + + Evaluation might be purely sequence-based or use structural information. + Sequence alignment validation - + - - Nucleic acid folding energy calculation - - beta12orEarlier - Compute energies of nucleic acid folding, e.g. minimum folding energies for DNA or RNA sequences or energy landscape of RNA mutants. - - + + + beta12orEarlier + Analyse character conservation in a molecular sequence alignment, for example to derive a consensus sequence. + Residue conservation analysis + + + Use this concept for methods that calculate substitution rates, estimate relative site variability, identify sites with biased properties, derive a consensus sequence, or identify highly conserved or very poorly conserved sites, regions, blocks etc. + Sequence alignment analysis (conservation) - + - - Annotation retrieval - - beta12orEarlier - Use this concepts for tools which retrieve pre-existing annotations, not for example prediction methods that might make annotations. - Retrieve existing annotation (or documentation), typically annotation on a database entity. - beta12orEarlier + + + + beta12orEarlier + Analyse correlations between sites in a molecular sequence alignment. + + + This is typically done to identify possible covarying positions and predict contacts or structural constraints in protein structures. + Sequence alignment analysis (site correlation) + + + + + + + + + beta12orEarlier + Detects chimeric sequences (chimeras) from a sequence alignment. + Sequence alignment analysis (chimeric sequence detection) + + + A chimera includes regions from two or more phylogenetically distinct sequences. They are usually artifacts of PCR and are thought to occur when a prematurely terminated amplicon reanneals to another DNA strand and is subsequently copied to completion in later PCR cycles. + Chimeric sequence detection + + + + + + + + + beta12orEarlier + Detect recombination (hotspots and coldspots) and identify recombination breakpoints in a sequence alignment. + Sequence alignment analysis (recombination detection) + + + Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on. + Recombination detection + + + + + + + + + + beta12orEarlier + Identify insertion, deletion and duplication events from a sequence alignment. + Indel discovery + Sequence alignment analysis (indel detection) + + + Tools might use a genetic algorithm, quartet-mapping, bootscanning, graphical methods, random forest model and so on. + Indel detection + + + + + + + + + beta12orEarlier + beta12orEarlier + + Predict nucleosome formation potential of DNA sequences. + + Nucleosome formation potential prediction true - - - + - - Protein function prediction - - + + - - + + - beta12orEarlier - Predict general functional properties of a protein. - For functional properties that can be mapped to a sequence, use 'Sequence feature detection (protein)' instead. - - + beta12orEarlier + Calculate a thermodynamic property of DNA or DNA/RNA, such as melting temperature, enthalpy and entropy. + + + Nucleic acid thermodynamic property calculation - + - - Protein function comparison - - + + + - - + + - Compare the functional properties of two or more proteins. - beta12orEarlier - - + beta12orEarlier + Calculate and plot a DNA or DNA/RNA melting profile. + + + A melting profile is used to visualise and analyse partly melted DNA conformations. + Nucleic acid melting profile plotting - + - - Sequence submission - - Submit a molecular sequence to a database. - beta12orEarlier - 1.6 - true - - + + + + + + + + + beta12orEarlier + Calculate and plot a DNA or DNA/RNA stitch profile. + + + A stitch profile represents the alternative conformations that partly melted DNA can adopt in a temperature range. + Nucleic acid stitch profile plotting - + - - Gene regulatory network analysis - + + - - + + - beta12orEarlier - Analyse a known network of gene regulation. - - - + beta12orEarlier + Calculate and plot a DNA or DNA/RNA melting curve. + + + Nucleic acid melting curve plotting - + - - Loading - + + - - + + - Data loading - WHATIF:UploadPDB - Prepare or load a user-specified data file so that it is available for use. - beta12orEarlier - - + beta12orEarlier + Calculate and plot a DNA or DNA/RNA probability profile. + + + Nucleic acid probability profile plotting - + - - Sequence retrieval - - This includes direct retrieval methods (e.g. the dbfetch program) but not those that perform calculations on the sequence. - Data retrieval (sequences) - 1.6 - Query a sequence data resource (typically a database) and retrieve sequences and / or annotation. - beta12orEarlier - true - - + + + + + + + + + beta12orEarlier + Calculate and plot a DNA or DNA/RNA temperature profile. + + + Nucleic acid temperature profile plotting - + - - Structure retrieval - - true - WHATIF:EchoPDB - beta12orEarlier - WHATIF:DownloadPDB - This includes direct retrieval methods but not those that perform calculations on the sequence or structure. - Query a tertiary structure data resource (typically a database) and retrieve structures, structure-related data and annotation. - 1.6 - - + + + + + + + + + beta12orEarlier + Calculate curvature and flexibility / stiffness of a nucleotide sequence. + + + This includes properties such as. + Nucleic acid curvature calculation - + - - Surface rendering - - - beta12orEarlier - WHATIF:GetSurfaceDots - Calculate the positions of dots that are homogeneously distributed over the surface of a molecule. - A dot has three coordinates (x,y,z) and (typically) a color. - - + + + beta12orEarlier + Identify or predict microRNA sequences (miRNA) and precursors or microRNA targets / binding sites in a DNA sequence. + + + microRNA detection - + - - Protein atom surface calculation (accessible) - - beta12orEarlier - WHATIF:AtomAccessibilitySolventPlus - WHATIF:AtomAccessibilitySolvent - Calculate the solvent accessibility ('accessible surface') for each atom in a structure. - Waters are not considered. - - + + + + + + + + + beta12orEarlier + Identify or predict tRNA genes in genomic sequences (tRNA). + + + tRNA gene prediction - + - - Protein atom surface calculation (accessible molecular) - - beta12orEarlier - Calculate the solvent accessibility ('accessible molecular surface') for each atom in a structure. - Waters are not considered. - WHATIF:AtomAccessibilityMolecular - WHATIF:AtomAccessibilityMolecularPlus - - + + + + + + + + + beta12orEarlier + Assess binding specificity of putative siRNA sequence(s), for example for a functional assay, typically with respect to designing specific siRNA sequences. + + + siRNA binding specificity prediction - + - - Protein residue surface calculation (accessible) - - WHATIF:ResidueAccessibilitySolvent - beta12orEarlier - Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). - Calculate the solvent accessibility ('accessible surface') for each residue in a structure. - - + + + beta12orEarlier + Predict secondary structure of protein sequence(s) using multiple methods to achieve better predictions. + + + Protein secondary structure prediction (integrated) - + - - Protein residue surface calculation (vacuum accessible) - - Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). - Calculate the solvent accessibility ('vacuum accessible surface') for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to. - WHATIF:ResidueAccessibilityVacuum - beta12orEarlier - - + + + beta12orEarlier + Predict helical secondary structure of protein sequences. + + + Protein secondary structure prediction (helices) - + - - Protein residue surface calculation (accessible molecular) - - Calculate the solvent accessibility ('accessible molecular surface') for each residue in a structure. - WHATIF:ResidueAccessibilityMolecular - Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). - beta12orEarlier - - + + + beta12orEarlier + Predict turn structure (for example beta hairpin turns) of protein sequences. + + + Protein secondary structure prediction (turns) - + - - Protein residue surface calculation (vacuum molecular) - - Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). - beta12orEarlier - Calculate the solvent accessibility ('vacuum molecular surface') for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to. - WHATIF:ResidueAccessibilityVacuumMolecular - - + + + beta12orEarlier + Predict open coils, non-regular secondary structure and intrinsically disordered / unstructured regions of protein sequences. + + + Protein secondary structure prediction (coils) - + - - Protein surface calculation (accessible molecular) - - WHATIF:TotAccessibilityMolecular - beta12orEarlier - Calculate the solvent accessibility ('accessible molecular surface') for a structure as a whole. - - + + + beta12orEarlier + Predict cysteine bonding state and disulfide bond partners in protein sequences. + + + Protein secondary structure prediction (disulfide bonds) - + - - Protein surface calculation (accessible) - - WHATIF:TotAccessibilitySolvent - Calculate the solvent accessibility ('accessible surface') for a structure as a whole. - beta12orEarlier - - + + + + beta12orEarlier + Predict G protein-coupled receptors (GPCR). + G protein-coupled receptor (GPCR) prediction + + + GPCR prediction - + - - Backbone torsion angle calculation - - beta12orEarlier - WHATIF:ResidueTorsionsBB - Calculate for each residue in a protein structure all its backbone torsion angles. - - + + + + + + + + + beta12orEarlier + Analyse G-protein coupled receptor proteins (GPCRs). + G protein-coupled receptor (GPCR) analysis + + + GPCR analysis - + - - Full torsion angle calculation - - beta12orEarlier - Calculate for each residue in a protein structure all its torsion angles. - WHATIF:ResidueTorsions - - + + + + + + + + + + + + beta12orEarlier + Predict tertiary structure (backbone and side-chain conformation) of protein sequences. + + + Protein structure prediction - + - - Cysteine torsion angle calculation - - beta12orEarlier - Calculate for each cysteine (bridge) all its torsion angles. - WHATIF:CysteineTorsions - - + + + + + + + + + + + beta12orEarlier + Predict tertiary structure of DNA or RNA. + + + Methods might identify thermodynamically stable or evolutionarily conserved structures. + Nucleic acid structure prediction - + - - Tau angle calculation - - WHATIF:ShowTauAngle - beta12orEarlier - Tau is the backbone angle N-Calpha-C (angle over the C-alpha). - For each amino acid in a protein structure calculate the backbone angle tau. - - + + + beta12orEarlier + Predict tertiary structure of protein sequence(s) without homologs of known structure. + de novo structure prediction + + + Ab initio structure prediction - + - - Cysteine bridge detection - - WHATIF:ShowCysteineBridge - Detect cysteine bridges (from coordinate data) in a protein structure. - beta12orEarlier - - + + + + + + + + + + + beta12orEarlier + Build a three-dimensional protein model based on known (for example homologs) structures. + Comparative modelling + Homology modelling + Homology structure modelling + Protein structure comparative modelling + + + The model might be of a whole, part or aspect of protein structure. Molecular modelling methods might use sequence-structure alignment, structural templates, molecular dynamics, energy minimisation etc. + Protein modelling - + - - Free cysteine detection - - beta12orEarlier - A free cysteine is neither involved in a cysteine bridge, nor functions as a ligand to a metal. - Detect free cysteines in a protein structure. - WHATIF:ShowCysteineFree - - + + + + + + + + + + + + + + + + beta12orEarlier + Model the structure of a protein in complex with a small molecule or another macromolecule. + Docking simulation + Protein docking + + + This includes protein-protein interactions, protein-nucleic acid, protein-ligand binding etc. Methods might predict whether the molecules are likely to bind in vivo, their conformation when bound, the strength of the interaction, possible mutations to achieve bonding and so on. + Molecular docking - + - - Metal-bound cysteine detection - - beta12orEarlier - WHATIF:ShowCysteineMetal - Detect cysteines that are bound to metal in a protein structure. - - + + + beta12orEarlier + Model protein backbone conformation. + + + Methods might require a preliminary C(alpha) trace. + Protein modelling (backbone) - + - - Residue contact calculation (residue-nucleic acid) - - - - beta12orEarlier - WHATIF:ShowProteiNucleicContacts - Calculate protein residue contacts with nucleic acids in a structure. - WHATIF:HasNucleicContacts - - + + + beta12orEarlier + Model, analyse or edit amino acid side chain conformation in protein structure, optimize side-chain packing, hydrogen bonding etc. + + + Methods might use a residue rotamer library. + Protein modelling (side chains) - + - - Residue contact calculation (residue-metal) - - - WHATIF:HasMetalContacts - beta12orEarlier - Calculate protein residue contacts with metal in a structure. - WHATIF:HasMetalContactsPlus - - + + + beta12orEarlier + Model loop conformation in protein structures. + + + Protein modelling (loops) - + - - Residue contact calculation (residue-negative ion) - - Calculate ion contacts in a structure (all ions for all side chain atoms). - WHATIF:HasNegativeIonContactsPlus - beta12orEarlier - WHATIF:HasNegativeIonContacts - - + + + + + + + + + + + + + + + beta12orEarlier + Model protein-ligand (for example protein-peptide) binding using comparative modelling or other techniques. + Ligand-binding simulation + Virtual ligand screening + + + Methods aim to predict the position and orientation of a ligand bound to a protein receptor or enzyme. + Protein-ligand docking - + - - Residue bump detection - - WHATIF:ShowBumps - beta12orEarlier - Detect 'bumps' between residues in a structure, i.e. those with pairs of atoms whose Van der Waals' radii interpenetrate more than a defined distance. - - + + + + + + + + + beta12orEarlier + Predict or optimise RNA sequences (sequence pools) with likely secondary and tertiary structure for in vitro selection. + Nucleic acid folding family identification + RNA inverse folding + + + Structured RNA prediction and optimisation - + - - Residue symmetry contact calculation - - Calculate the number of symmetry contacts made by residues in a protein structure. - WHATIF:SymmetryContact - A symmetry contact is a contact between two atoms in different asymmetric unit. - beta12orEarlier - - + + + + + beta12orEarlier + Find single nucleotide polymorphisms (SNPs) between sequences. + SNP discovery + Single nucleotide polymorphism detection + + + This includes functional SNPs for large-scale genotyping purposes, disease-associated non-synonymous SNPs etc. + SNP detection - + - - Residue contact calculation (residue-ligand) - - - beta12orEarlier - Calculate contacts between residues and ligands in a protein structure. - WHATIF:ShowDrugContactsShort - WHATIF:ShowLigandContacts - WHATIF:ShowDrugContacts - - + + + + + + + + + beta12orEarlier + Generate a physical (radiation hybrid) map of genetic markers in a DNA sequence using provided radiation hybrid (RH) scores for one or more markers. + + + Radiation Hybrid Mapping - + - - Salt bridge calculation - - Salt bridges are interactions between oppositely charged atoms in different residues. The output might include the inter-atomic distance. - WHATIF:HasSaltBridgePlus - WHATIF:ShowSaltBridges - beta12orEarlier - WHATIF:HasSaltBridge - WHATIF:ShowSaltBridgesH - Calculate (and possibly score) salt bridges in a protein structure. - - + + + beta12orEarlier + beta12orEarlier + + Map the genetic architecture of dynamic complex traits. + + This can involve characterisation of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs). + Functional mapping + true - + - - Rotamer likelihood prediction - - WHATIF:ShowLikelyRotamers - WHATIF:ShowLikelyRotamers500 - Predict rotamer likelihoods for all 20 amino acid types at each position in a protein structure. - WHATIF:ShowLikelyRotamers800 - WHATIF:ShowLikelyRotamers600 - WHATIF:ShowLikelyRotamers900 - Output typically includes, for each residue position, the likelihoods for the 20 amino acid types with estimated reliability of the 20 likelihoods. - WHATIF:ShowLikelyRotamers700 - WHATIF:ShowLikelyRotamers400 - WHATIF:ShowLikelyRotamers300 - WHATIF:ShowLikelyRotamers200 - WHATIF:ShowLikelyRotamers100 - beta12orEarlier - - + + + + + + + + + + beta12orEarlier + Infer haplotypes, either alleles at multiple loci that are transmitted together on the same chromosome, or a set of single nucleotide polymorphisms (SNPs) on a single chromatid that are statistically associated. + Haplotype inference + Haplotype map generation + Haplotype reconstruction + + + Haplotype inference can help in population genetic studies and the identification of complex disease genes, , and is typically based on aligned single nucleotide polymorphism (SNP) fragments. Haplotype comparison is a useful way to characterize the genetic variation between individuals. An individual's haplotype describes which nucleotide base occurs at each position for a set of common SNPs. Tools might use combinatorial functions (for example parsimony) or a likelihood function or model with optimisation such as minimum error correction (MEC) model, expectation-maximisation algorithm (EM), genetic algorithm or Markov chain Monte Carlo (MCMC). + Haplotype mapping - + - - Proline mutation value calculation - - Calculate for each position in a protein structure the chance that a proline, when introduced at this position, would increase the stability of the whole protein. - WHATIF:ProlineMutationValue - beta12orEarlier - - + + + + + + + + + beta12orEarlier + Calculate linkage disequilibrium; the non-random association of alleles or polymorphisms at two or more loci (not necessarily on the same chromosome). + + + Linkage disequilibrium is identified where a combination of alleles (or genetic markers) occurs more or less frequently in a population than expected by chance formation of haplotypes. + Linkage disequilibrium calculation - + - - Residue packing validation - - beta12orEarlier - Identify poorly packed residues in protein structures. - WHATIF: PackingQuality - - + + + + + + + + + + beta12orEarlier + Predict genetic code from analysis of codon usage data. + + + Genetic code prediction - + - - Dihedral angle validation - - WHATIF: ImproperQualitySum - Identify for each residue in a protein structure any improper dihedral (phi/psi) angles. - beta12orEarlier - WHATIF: ImproperQualityMax - - + + + + + + + + + + + beta12orEarlier + Draw a dotplot of sequence similarities identified from word-matching or character comparison. + + + Dotplot plotting - + - - PDB file sequence retrieval - - Extract a molecular sequence from a PDB file. - beta12orEarlier - WHATIF: PDB_sequence - true - beta12orEarlier - - + + + + + + + + + beta12orEarlier + Align exactly two molecular sequences. + Pairwise alignment + + + Methods might perform one-to-one, one-to-many or many-to-many comparisons. + Pairwise sequence alignment - + - - HET group detection - - Identify HET groups in PDB files. - WHATIF: HETGroupNames - beta12orEarlier - A HET group usually corresponds to ligands, lipids, but might also (not consistently) include groups that are attached to amino acids. Each HET group is supposed to have a unique three letter code and a unique name which might be given in the output. - - + + + beta12orEarlier + Align more than two molecular sequences. + Multiple alignment + + + This includes methods that use an existing alignment, for example to incorporate sequences into an alignment, or combine several multiple alignments into a single, improved alignment. + Multiple sequence alignment - + - - DSSP secondary structure assignment - - Determine for residue the DSSP determined secondary structure in three-state (HSC). - beta12orEarlier - WHATIF: ResidueDSSP - beta12orEarlier + + + beta12orEarlier + 1.6 + + + Locally align exactly two molecular sequences. + + Local alignment methods identify regions of local similarity. + Pairwise sequence alignment generation (local) true - - - + - - Structure formatting - - Reformat (a file or other report of) tertiary structure data. - beta12orEarlier - WHATIF: PDBasXML - - + + + beta12orEarlier + 1.6 + + + Globally align exactly two molecular sequences. + + Global alignment methods identify similarity across the entire length of the sequences. + Pairwise sequence alignment generation (global) + true - + - - Protein cysteine and disulfide bond assignment - + + + beta12orEarlier + Locally align two or more molecular sequences. + Local sequence alignment + Sequence alignment (local) + Smith-Waterman + + + Local alignment methods identify regions of local similarity. + Local alignment + + + + + + + + + beta12orEarlier + Globally align two or more molecular sequences. + Global sequence alignment + Sequence alignment (global) + + + Global alignment methods identify similarity across the entire length of the sequences. + Global alignment + + + + + + + + + beta12orEarlier + Align two or more molecular sequences with user-defined constraints. + Multiple sequence alignment (constrained) + Sequence alignment (constrained) + + + Constrained sequence alignment + + + + + + + + + beta12orEarlier + 1.16 + Align two or more molecular sequences using multiple methods to achieve higher quality. + + + Consensus-based sequence alignment + true + + + + + + + + - - + + - Assign cysteine bonding state and disulfide bond partners in protein structures. - beta12orEarlier - - + beta12orEarlier + Align multiple sequences using relative gap costs calculated from neighbors in a supplied phylogenetic tree. + Multiple sequence alignment (phylogenetic tree-based) + Multiple sequence alignment construction (phylogenetic tree-based) + Phylogenetic tree-based multiple sequence alignment construction + Sequence alignment (phylogenetic tree-based) + Sequence alignment generation (phylogenetic tree-based) + + + This is supposed to give a more biologically meaningful alignment than standard alignments. + Tree-based sequence alignment - + - - Residue validation - - Identify poor quality amino acid positions in protein structures. - beta12orEarlier - WHATIF: UseResidueDB - The scoring function to identify poor quality residues may consider residues with bad atoms or atoms with high B-factor, residues in the N- or C-terminal position, adjacent to an unstructured residue, non-canonical residues, glycine and proline (or adjacent to these such residues). - - + + + beta12orEarlier + 1.6 + + Align molecular secondary structure (represented as a 1D string). + + Secondary structure alignment generation + true - + - - Structure retrieval (water) - - beta12orEarlier - 1.6 - WHATIF:MovedWaterPDB - true - Query a tertiary structure database and retrieve water molecules. - - + + + + + + + + + + beta12orEarlier + Align protein secondary structures. + Protein secondary structure alignment + Protein secondary structure alignment construction + Secondary structure alignment (protein) + + + Protein secondary structure alignment generation - + - - siRNA duplex prediction - + + + - - + + - beta12orEarlier - Identify or predict siRNA duplexes in RNA. - - + + + + + + + beta12orEarlier + Align RNA secondary structures. + RNA secondary structure alignment construction + RNA secondary structure alignment generation + Secondary structure alignment (RNA) + + + RNA secondary structure alignment - + - - Sequence alignment refinement - - - Refine an existing sequence alignment. - beta12orEarlier - - + + + beta12orEarlier + Align (superimpose) exactly two molecular tertiary structures. + Structure alignment (pairwise) + + + Pairwise structure alignment - + - - Listfile processing - - 1.6 - Process an EMBOSS listfile (list of EMBOSS Uniform Sequence Addresses). - true - beta12orEarlier - - + + + beta12orEarlier + Align (superimpose) more than two molecular tertiary structures. + Structure alignment (multiple) + + + This includes methods that use an existing alignment. + Multiple structure alignment - + - - Sequence file editing - - - beta12orEarlier - Perform basic (non-analytical) operations on a report or file of sequences (which might include features), such as file concatenation, removal or ordering of sequences, creation of subset or a new file of sequences. - - + + + beta12orEarlier + beta13 + + Align protein tertiary structures. + + Structure alignment (protein) + true - + - - Sequence alignment file processing - - beta12orEarlier - Perform basic (non-analytical) operations on a sequence alignment file, such as copying or removal and ordering of sequences. - 1.6 + + + beta12orEarlier + beta13 + + Align RNA tertiary structures. + + Structure alignment (RNA) true - - - + - - Small molecule data processing - - beta13 + + + beta12orEarlier + 1.6 + + + Locally align (superimpose) exactly two molecular tertiary structures. + + Local alignment methods identify regions of local similarity, common substructures etc. + Pairwise structure alignment generation (local) true - beta12orEarlier - Process (read and / or write) physicochemical property data for small molecules. - - - + - - Data retrieval (ontology annotation) - - beta13 - Ontology information retrieval + + + beta12orEarlier + 1.6 + + + Globally align (superimpose) exactly two molecular tertiary structures. + + Global alignment methods identify similarity across the entire structures. + Pairwise structure alignment generation (global) true - Search and retrieve documentation on a bioinformatics ontology. - beta12orEarlier - - - + - - Data retrieval (ontology concept) - - Query an ontology and retrieve concepts or relations. - true - beta13 - beta12orEarlier - Ontology retrieval - - + + + beta12orEarlier + Locally align (superimpose) two or more molecular tertiary structures. + Structure alignment (local) + + + Local alignment methods identify regions of local similarity, common substructures etc. + Local structure alignment - + - - Representative sequence identification - - - - - - - - Identify a representative sequence from a set of sequences, typically using scores from pair-wise alignment or other comparison of the sequences. - beta12orEarlier - - + + + beta12orEarlier + Globally align (superimpose) two or more molecular tertiary structures. + Structure alignment (global) + + + Global alignment methods identify similarity across the entire structures. + Global structure alignment - + - - Structure file processing - - Perform basic (non-analytical) operations on a file of molecular tertiary structural data. - 1.6 - beta12orEarlier + + + beta12orEarlier + 1.16 + Align exactly two molecular profiles. + + + Methods might perform one-to-one, one-to-many or many-to-many comparisons. + Profile-profile alignment (pairwise) true - - - + - - Data retrieval (sequence profile) - - Query a profile data resource and retrieve one or more profile(s) and / or associated annotation. + + + beta12orEarlier + 1.6 + + Align two or more molecular profiles. + + Sequence alignment generation (multiple profile) true - This includes direct retrieval methods that retrieve a profile by, e.g. the profile name. - beta13 - beta12orEarlier - - - + - - Statistical calculation - - Statistical analysis - Perform a statistical data operation of some type, e.g. calibration or validation. - beta12orEarlier + + + beta12orEarlier + 1.16 + Align exactly two molecular Structural (3D) profiles. + + + 3D profile-to-3D profile alignment (pairwise) true - - - + - - 3D-1D scoring matrix generation - - - - - - - - - - - - - - - - beta12orEarlier - 3D-1D scoring matrix construction - A 3D-1D scoring matrix scores the probability of amino acids occurring in different structural environments. - Calculate a 3D-1D scoring matrix from analysis of protein sequence and structural data. - - + + + beta12orEarlier + 1.6 + + Align two or more molecular 3D profiles. + + Structural profile alignment generation (multiple) + true - + - - Transmembrane protein visualisation - - - - - - - - - Visualise transmembrane proteins, typically the transmembrane regions within a sequence. - beta12orEarlier - Transmembrane protein rendering - - + + + beta12orEarlier + 1.6 + + Search and retrieve names of or documentation on bioinformatics tools, for example by keyword or which perform a particular function. + + Data retrieval (tool metadata) + true - + - - Demonstration - - beta12orEarlier + + + beta12orEarlier + 1.6 + + Search and retrieve names of or documentation on bioinformatics databases or query terms, for example by keyword. + + Data retrieval (database metadata) true - An operation performing purely illustrative (pedagogical) purposes. - beta13 - - + - - Data retrieval (pathway or network) - - beta12orEarlier + + + beta12orEarlier + 1.13 + Predict primers for large scale sequencing. + + + PCR primer design (for large scale sequencing) true - Query a biological pathways database and retrieve annotation on one or more pathways. - beta13 - - - + - - Data retrieval (identifier) - - beta12orEarlier - Query a database and retrieve one or more data identifiers. - beta13 + + + beta12orEarlier + 1.13 + Predict primers for genotyping polymorphisms, for example single nucleotide polymorphisms (SNPs). + + + PCR primer design (for genotyping polymorphisms) true - - - + - - Nucleic acid density plotting - - - beta12orEarlier - Calculate a density plot (of base composition) for a nucleotide sequence. - - + + + beta12orEarlier + 1.13 + Predict primers for gene transcription profiling. + + + PCR primer design (for gene transcription profiling) + true - + - - Sequence analysis - - - - - - - - Analyse one or more known molecular sequences. - beta12orEarlier - Sequence analysis (general) - - + + + beta12orEarlier + 1.13 + Predict primers that are conserved across multiple genomes or species. + + + PCR primer design (for conserved primers) + true - + - - Sequence motif processing - + + + beta12orEarlier + 1.13 + + + PCR primer design (based on gene structure) true - 1.6 - Process (read and / or write) molecular sequence motifs. - beta12orEarlier - - - + - - Protein interaction data processing - - 1.6 - Process (read and / or write) protein interaction data. + + + beta12orEarlier + 1.13 + Predict primers for methylation PCRs. + + + PCR primer design (for methylation PCRs) true - beta12orEarlier - - - + - - Protein structure analysis - - - - - - - - - - - - - - - Structure analysis (protein) - beta12orEarlier - Analyse protein tertiary structural data. - - + + + beta12orEarlier + Sequence assembly by combining fragments using an existing backbone sequence, typically a reference genome. + Sequence assembly (mapping assembly) + + + The final sequence will resemble the backbone sequence. Mapping assemblers are usually much faster and less memory intensive than de-novo assemblers. + Mapping assembly - + - - Annotation processing - - true - beta12orEarlier - beta12orEarlier - Process (read and / or write) annotation of some type, typically annotation on an entry from a biological or biomedical database entity. - - + + + beta12orEarlier + Sequence assembly by combining fragments without the aid of a reference sequence or genome. + De Bruijn graph + Sequence assembly (de-novo assembly) + + + De-novo assemblers are much slower and more memory intensive than mapping assemblers. + De-novo assembly - + - - Sequence feature analysis - - beta12orEarlier - true - Analyse features in molecular sequences. - beta12orEarlier - - + + + beta12orEarlier + The process of assembling many short DNA sequences together such thay they represent the original chromosomes from which the DNA originated. + Sequence assembly (genome assembly) + + + Genome assembly - + - - Utility operation - - - - - - - - Basic (non-analytical) operations of some data, either a file or equivalent entity in memory. - File processing - beta12orEarlier - Report handling - File handling - Data file processing - - + + + beta12orEarlier + Sequence assembly for EST sequences (transcribed mRNA). + Sequence assembly (EST assembly) + + + Assemblers must handle (or be complicated by) alternative splicing, trans-splicing, single-nucleotide polymorphism (SNP), recoding, and post-transcriptional modification. + EST assembly - + - - Gene expression analysis - - Analyse gene expression and regulation data. - beta12orEarlier - true - beta12orEarlier - - + + + + beta12orEarlier + Make sequence tag to gene assignments (tag mapping) of SAGE, MPSS and SBS data. + Tag to gene assignment + + + Sequence tag mapping assigns experimentally obtained sequence tags to known transcripts or annotate potential virtual sequence tags in a genome. + Sequence tag mapping - + - - Structural profile processing - - beta12orEarlier - 1.6 - Process (read and / or write) one or more structural (3D) profile(s) or template(s) of some type. - 3D profile processing + + + beta12orEarlier + beta12orEarlier + + Process (read and / or write) serial analysis of gene expression (SAGE) data. + + SAGE data processing true - - - + - - Data index processing - - Database index processing + + + beta12orEarlier + beta12orEarlier + + Process (read and / or write) massively parallel signature sequencing (MPSS) data. + + MPSS data processing true - Process (read and / or write) an index of (typically a file of) biological data. - 1.6 - beta12orEarlier - - - + - - Sequence profile processing - + + + beta12orEarlier + beta12orEarlier + + Process (read and / or write) sequencing by synthesis (SBS) data. + + SBS data processing true - beta12orEarlier - Process (read and / or write) some type of sequence profile. - 1.6 - - - + - - Protein function analysis - + + + - - + + - This is a broad concept and is used a placeholder for other, more specific concepts. - beta12orEarlier - Analyse protein function, typically by processing protein sequence and/or structural data, and generate an informative report. - - + beta12orEarlier + Generate a heat map of gene expression from e.g. microarray data. + Heat map construction + + + The heat map usually uses a coloring scheme to represent clusters. They can show how expression of mRNA by a set of genes was influenced by experimental conditions. + Heat map generation - + - - Protein folding analysis - - - - - - - - - - - - - - - This is a broad concept and is used a placeholder for other, more specific concepts. - Analyse protein folding, typically by processing sequence and / or structural data, and write an informative report. - Protein folding modelling - beta12orEarlier - - + + + beta12orEarlier + 1.6 + + Analyse one or more gene expression profiles, typically to interpret them in functional terms. + + Gene expression profile analysis + true - + - - Protein secondary structure analysis - + + + + - - + + - - - - - - - Analyse known protein secondary structure data. - beta12orEarlier - Secondary structure analysis (protein) - - + beta12orEarlier + Map a gene expression profile to known biological pathways, for example, to identify or reconstruct a pathway. + + + Gene expression profile pathway mapping - + - - Physicochemical property data processing - - beta13 - true - Process (read and / or write) data on the physicochemical property of a molecule. - beta12orEarlier - - + + + + beta12orEarlier + Assign secondary structure from protein coordinate data. + + + Protein secondary structure assignment (from coordinate data) - + - - Primer and probe design - - + + - - + + - Primer and probe prediction - beta12orEarlier - Predict oligonucleotide primers or probes. - - + beta12orEarlier + Assign secondary structure from circular dichroism (CD) spectroscopic data. + + + Protein secondary structure assignment (from CD data) - + - - Operation (typed) - - Computation - Calculation - Processing - Process (read and / or write) data of a specific type, for example applying analytical methods. - beta12orEarlier - - + + + beta12orEarlier + 1.7 + Assign a protein tertiary structure (3D coordinates) from raw X-ray crystallography data. + + + Protein structure assignment (from X-ray crystallographic data) + true - + - - Database search - - - - - - - - beta12orEarlier - Typically the query is compared to each entry and high scoring matches (hits) are returned. For example, a BLAST search of a sequence database. - Search a database (or other data resource) with a supplied query and retrieve entries (or parts of entries) that are similar to the query. - - + + + beta12orEarlier + 1.7 + Assign a protein tertiary structure (3D coordinates) from raw NMR spectroscopy data. + + + Protein structure assignment (from NMR data) + true - + - - Data retrieval - - - - - - - - Information retrieval - beta12orEarlier - Retrieve an entry (or part of an entry) from a data resource that matches a supplied query. This might include some primary data and annotation. The query is a data identifier or other indexed term. For example, retrieve a sequence record with the specified accession number, or matching supplied keywords. - - + + + beta12orEarlier + Construct a phylogenetic tree from a specific type of data. + Phylogenetic tree construction (data centric) + + + Phylogenetic tree generation (data centric) - + - - Prediction and recognition - - beta12orEarlier - Recognition - Prediction - Predict, recognise, detect or identify some properties of a biomolecule. - Detection - - + + + beta12orEarlier + Construct a phylogenetic tree using a specific method. + Phylogenetic tree construction (method centric) + + + Phylogenetic tree generation (method centric) - + - - Comparison - - beta12orEarlier - Compare two or more things to identify similarities. - - + + + + beta12orEarlier + Phylogenetic tree construction from molecular sequences. + Phylogenetic tree construction (from molecular sequences) + + + Methods typically compare multiple molecular sequence and estimate evolutionary distances and relationships to infer gene families or make functional predictions. + Phylogenetic tree generation (from molecular sequences) - + - - Optimisation and refinement - - beta12orEarlier - Refine or optimise some data model. - - + + + + + + + + + beta12orEarlier + Phylogenetic tree construction from continuous quantitative character data. + Phylogenetic tree construction (from continuous quantitative characters) + + + Phylogenetic tree generation (from continuous quantitative characters) - + - - Modelling and simulation - + + + + + + + + - - + + - beta12orEarlier - Model or simulate some biological entity or system. - - + beta12orEarlier + Phylogenetic tree construction from gene frequency data. + Phylogenetic tree construction (from gene frequencies) + + + Phylogenetic tree generation (from gene frequencies) - + - - Data handling - - true - beta12orEarlier - Perform basic operations on some data or a database. - beta12orEarlier - - + + + + + + + + + beta12orEarlier + Phylogenetic tree construction from polymorphism data including microsatellites, RFLP (restriction fragment length polymorphisms), RAPD (random-amplified polymorphic DNA) and AFLP (amplified fragment length polymorphisms) data. + Phylogenetic tree generation (from polymorphism data) + + + Phylogenetic tree construction (from polymorphism data) - + - - Validation - - beta12orEarlier - Validation and standardisation - Validate some data. - - + + + beta12orEarlier + Construct a phylogenetic species tree, for example, from a genome-wide sequence comparison. + Phylogenetic species tree generation + + + Phylogenetic species tree construction - + - - Mapping - - This is a broad concept and is used a placeholder for other, more specific concepts. - Map properties to positions on an biological entity (typically a molecular sequence or structure), or assemble such an entity from constituent parts. - beta12orEarlier - - + + + beta12orEarlier + Construct a phylogenetic tree by computing a sequence alignment and searching for the tree with the fewest number of character-state changes from the alignment. + Phylogenetic tree construction (parsimony methods) + + + This includes evolutionary parsimony (invariants) methods. + Phylogenetic tree generation (parsimony methods) - + - - Design - - beta12orEarlier - Design a biological entity (typically a molecular sequence or structure) with specific properties. - true - - + + + beta12orEarlier + Construct a phylogenetic tree by computing (or using precomputed) distances between sequences and searching for the tree with minimal discrepancies between pairwise distances. + Phylogenetic tree construction (minimum distance methods) + + + This includes neighbor joining (NJ) clustering method. + Phylogenetic tree generation (minimum distance methods) - + - - Microarray data processing - - beta12orEarlier - Process (read and / or write) microarray data. - beta12orEarlier - true - - + + + beta12orEarlier + Construct a phylogenetic tree by relating sequence data to a hypothetical tree topology using a model of sequence evolution. + Phylogenetic tree construction (maximum likelihood and Bayesian methods) + + + Maximum likelihood methods search for a tree that maximizes a likelihood function, i.e. that is most likely given the data and model. Bayesian analysis estimate the probability of tree for branch lengths and topology, typically using a Monte Carlo algorithm. + Phylogenetic tree generation (maximum likelihood and Bayesian methods) - + - - Codon usage table processing - - Process (read and / or write) a codon usage table. - beta12orEarlier - - + + + beta12orEarlier + Construct a phylogenetic tree by computing four-taxon trees (4-trees) and searching for the phylogeny that matches most closely. + Phylogenetic tree construction (quartet methods) + + + Phylogenetic tree generation (quartet methods) - + - - Data retrieval (codon usage table) - - Retrieve a codon usage table and / or associated annotation. - beta12orEarlier - true - beta13 - - + + + beta12orEarlier + Construct a phylogenetic tree by using artificial-intelligence methods, for example genetic algorithms. + Phylogenetic tree construction (AI methods) + + + Phylogenetic tree generation (AI methods) - + - - Gene expression profile processing - - 1.6 - Process (read and / or write) a gene expression profile. - true - beta12orEarlier - - + + + + + + + + + + + + + + + + beta12orEarlier + Identify a plausible model of DNA substitution that explains a molecular (DNA or protein) sequence alignment. + Sequence alignment analysis (phylogenetic modelling) + + + DNA substitution modelling - + - - Functional enrichment - - - - - - - - - beta12orEarlier - Gene expression profile annotation - The Gene Ontology (GO) is invariably used, the input is a set of Gene IDs and the output of the analysis is typically a ranked list of GO terms, each associated with a p-value. - Analyse a set of genes (genes corresponding to an expression profile, or any other set) with respect to concepts from an ontology of gene functions. - GO term enrichment - - + + + beta12orEarlier + Analyse the shape (topology) of a phylogenetic tree. + Phylogenetic tree topology analysis + + + Phylogenetic tree analysis (shape) - + - - Gene regulatory network prediction - - + + + + beta12orEarlier + Apply bootstrapping or other measures to estimate confidence of a phylogenetic tree. + + + Phylogenetic tree bootstrapping + + + + + + + + - - + + - - + + - Predict a network of gene regulation. - beta12orEarlier - - + beta12orEarlier + Predict families of genes and gene function based on their position in a phylogenetic tree. + + + Phylogenetic tree analysis (gene family prediction) - + - - Pathway or network processing - - - - - - - - Generate, analyse or handle a biological pathway or network. - beta12orEarlier - - + + + beta12orEarlier + Analyse a phylogenetic tree to identify allele frequency distribution and change that is subject to evolutionary pressures (natural selection, genetic drift, mutation and gene flow). Identify type of natural selection (such as stabilizing, balancing or disruptive). + + + Stabilizing/purifying (directional) selection favors a single phenotype and tends to decrease genetic diversity as a population stabilizes on a particular trait, selecting out trait extremes or deleterious mutations. In contrast, balancing selection maintain genetic polymorphisms (or multiple alleles), whereas disruptive (or diversifying) selection favors individuals at both extremes of a trait. + Phylogenetic tree analysis (natural selection) - + - - RNA secondary structure analysis - - - - - - - - beta12orEarlier - Process (read and / or write) RNA secondary structure data. - - + + + + beta12orEarlier + Compare two or more phylogenetic trees to produce a consensus tree. + Phylogenetic tree construction (consensus) + + + Methods typically test for topological similarity between trees using for example a congruence index. + Phylogenetic tree generation (consensus) - + - - Structure processing (RNA) - - Process (read and / or write) RNA tertiary structure data. - beta12orEarlier - beta13 - true - - + + + beta12orEarlier + Compare two or more phylogenetic trees to detect subtrees or supertrees. + + + Phylogenetic sub/super tree detection - + - - RNA structure prediction - + + - - + + - beta12orEarlier - Predict RNA tertiary structure. - - + beta12orEarlier + Compare two or more phylogenetic trees to calculate distances between trees. + + + Phylogenetic tree distances calculation - + - - DNA structure prediction - - - - - - - - Predict DNA tertiary structure. - beta12orEarlier - - + + + beta12orEarlier + Annotate a phylogenetic tree with terms from a controlled vocabulary. + + + Phylogenetic tree annotation + http://www.evolutionaryontology.org/cdao.owl#CDAOAnnotation - + - - Phylogenetic tree processing - + + + beta12orEarlier + 1.12 + Predict and optimise peptide ligands that elicit an immunological response. + + + Immunogenicity prediction + true + + + + + + + + - - + + - beta12orEarlier - Process (read and / or write) a phylogenetic tree. - - + beta12orEarlier + Predict or optimise DNA to elicit (via DNA vaccination) an immunological response. + + + DNA vaccine design - + - - Protein secondary structure processing - - Process (read and / or write) protein secondary structure data. - 1.6 + + + beta12orEarlier + 1.12 + Reformat (a file or other report of) molecular sequence(s). + + + Sequence formatting true - beta12orEarlier - - - + - - Protein interaction network processing - + + + beta12orEarlier + 1.12 + Reformat (a file or other report of) molecular sequence alignment(s). + + + Sequence alignment formatting true - beta12orEarlier - Process (read and / or write) a network of protein interactions. - 1.6 - - - + - - Sequence processing - - Sequence processing (general) - Process (read and / or write) one or more molecular sequences and associated annotation. + + + beta12orEarlier + 1.12 + Reformat a codon usage table. + + + Codon usage table formatting true - beta12orEarlier - 1.6 - - - + - - Sequence processing (protein) - - Process (read and / or write) a protein sequence and associated annotation. - beta12orEarlier - true - 1.6 - - + + + + + + + + + + + + + + + + beta12orEarlier + Visualise, format or render a molecular sequence or sequences such as a sequence alignment, possibly with sequence features or properties shown. + Sequence rendering + Sequence alignment visualisation + + + Sequence visualisation - + - - Sequence processing (nucleic acid) - - 1.6 + + + beta12orEarlier + 1.15 + Visualise, format or print a molecular sequence alignment. + + + Sequence alignment visualisation true - beta12orEarlier - Process (read and / or write) a nucleotide sequence and associated annotation. - - - + - - Sequence comparison - - - - - - - - + + - - + + + beta12orEarlier + Visualise, format or render sequence clusters. + Sequence cluster rendering + + + Sequence cluster visualisation + + + + + + + + + - - + + - Compare two or more molecular sequences. - beta12orEarlier - - + beta12orEarlier + Render or visualise a phylogenetic tree. + Phylogenetic tree rendering + + + Phylogenetic tree visualisation - + - - Sequence cluster processing - - Process (read and / or write) a sequence cluster. + + + beta12orEarlier + 1.15 + Visualise RNA secondary structure, knots, pseudoknots etc. + + + RNA secondary structure visualisation true - beta12orEarlier - 1.6 - - - + - - Feature table processing - - Process (read and / or write) a sequence feature table. - 1.6 + + + beta12orEarlier + 1.15 + Render and visualise protein secondary structure. + + + Protein secondary structure visualisation true - beta12orEarlier - - - + - - Gene prediction - + + + - - + + - - + + - Gene and gene component prediction - beta12orEarlier - Detect, predict and identify genes or components of genes in DNA sequences. - Gene finding - - + beta12orEarlier + Visualise or render molecular structure, for example a high-quality static picture or animation. This includes secondary structure such as knots, pseudoknots etc. as well as tertiary and quaternary structure. + Structure rendering + Protein secondary structure visualisation + RNA secondary structure visualisation + + + Structure visualisation - + - - GPCR classification - - + + + + - - + + - beta12orEarlier - G protein-coupled receptor (GPCR) classification - Classify G-protein coupled receptors (GPCRs) into families and subfamilies. - - + beta12orEarlier + Visualise microarray data. + + + Microarray data rendering - + - - GPCR coupling selectivity prediction - - - + + - - + + - Predict G-protein coupled receptor (GPCR) coupling selectivity. - beta12orEarlier - - + beta12orEarlier + Identify and analyse networks of protein interactions. + + + + Protein interaction network rendering + Protein interaction network visualisation - + - - Structure processing (protein) - - true - 1.6 - beta12orEarlier - Process (read and / or write) a protein tertiary structure. - - + + + + + + + + + beta12orEarlier + Draw or visualise a DNA map. + DNA map drawing + Map rendering + + + Map drawing - + - - Protein atom surface calculation - - Waters are not considered. - Calculate the solvent accessibility for each atom in a structure. - beta12orEarlier - - + + + beta12orEarlier + beta12orEarlier + + Render a sequence with motifs. + + Sequence motif rendering + true - + - - Protein residue surface calculation - - beta12orEarlier - Calculate the solvent accessibility for each residue in a structure. - - + + + + + + + + + + beta12orEarlier + Draw or visualise restriction maps in DNA sequences. + + + Restriction map drawing - + - - Protein surface calculation - - beta12orEarlier - Calculate the solvent accessibility of a structure as a whole. - - + + + beta12orEarlier + beta12orEarlier + + Draw a linear maps of DNA. + + DNA linear map rendering + true - + - - Sequence alignment processing - - beta12orEarlier - true - Process (read and / or write) a molecular sequence alignment. - 1.6 - - + + + beta12orEarlier + DNA circular map rendering + Draw a circular maps of DNA, for example a plasmid map. + + + Plasmid map drawing - + - - Protein-protein interaction prediction - - - - - - - + + - - + + - Identify or predict protein-protein interactions, interfaces, binding sites etc. - beta12orEarlier - - + beta12orEarlier + Visualise operon structure etc. + Operon rendering + + + Operon drawing - + - - Structure processing - + + + beta12orEarlier + beta12orEarlier + + Identify folding families of related RNAs. + + Nucleic acid folding family identification true - 1.6 - Process (read and / or write) a molecular tertiary structure. - beta12orEarlier - - - + - - Map annotation - - Annotate a DNA map of some type with terms from a controlled vocabulary. - true - beta12orEarlier - 1.6 - - + + + beta12orEarlier + Compute energies of nucleic acid folding, e.g. minimum folding energies for DNA or RNA sequences or energy landscape of RNA mutants. + + + Nucleic acid folding energy calculation - + - - Data retrieval (protein annotation) - - Retrieve information on a protein. - beta13 + + + beta12orEarlier + beta12orEarlier + + Retrieve existing annotation (or documentation), typically annotation on a database entity. + + Use this concepts for tools which retrieve pre-existing annotations, not for example prediction methods that might make annotations. + Annotation retrieval true - Protein information retrieval - beta12orEarlier - - - + - - Data retrieval (phylogenetic tree) - - beta12orEarlier - beta13 - Retrieve a phylogenetic tree from a data resource. - true - - + + + + + + + + + + beta12orEarlier + Predict general functional properties of a protein. + + + For functional properties that can be mapped to a sequence, use 'Sequence feature detection (protein)' instead. + Protein function prediction - + - - Data retrieval (protein interaction annotation) - - Retrieve information on a protein interaction. - true - beta13 - beta12orEarlier - - + + + + + + + + + + beta12orEarlier + Compare the functional properties of two or more proteins. + + + Protein function comparison - + - - Data retrieval (protein family annotation) - - beta12orEarlier - Protein family information retrieval - beta13 - Retrieve information on a protein family. + + + beta12orEarlier + 1.6 + + Submit a molecular sequence to a database. + + Sequence submission true - - - + - - Data retrieval (RNA family annotation) - - true - Retrieve information on an RNA family. - RNA family information retrieval - beta12orEarlier - beta13 - - + + + + + + + + + beta12orEarlier + Analyse a known network of gene regulation. + + + Gene regulatory network analysis - + - - Data retrieval (gene annotation) - - beta12orEarlier - Gene information retrieval - Retrieve information on a specific gene. - true - beta13 - - + + + + + + + + + beta12orEarlier + WHATIF:UploadPDB + Prepare or load a user-specified data file so that it is available for use. + Data loading + + + Loading - + - - Data retrieval (genotype and phenotype annotation) - - Retrieve information on a specific genotype or phenotype. - Genotype and phenotype information retrieval - beta12orEarlier - beta13 + + + beta12orEarlier + 1.6 + + Query a sequence data resource (typically a database) and retrieve sequences and / or annotation. + + This includes direct retrieval methods (e.g. the dbfetch program) but not those that perform calculations on the sequence. + Sequence retrieval true - - - + - - Protein architecture comparison - - - Compare the architecture of two or more protein structures. - beta12orEarlier - - + + + beta12orEarlier + 1.6 + + WHATIF:DownloadPDB + WHATIF:EchoPDB + Query a tertiary structure data resource (typically a database) and retrieve structures, structure-related data and annotation. + + This includes direct retrieval methods but not those that perform calculations on the sequence or structure. + Structure retrieval + true - + - - Protein architecture recognition - - - - beta12orEarlier - Includes methods that try to suggest the most likely biological unit for a given protein X-ray crystal structure based on crystal symmetry and scoring of putative protein-protein interfaces. - Identify the architecture of a protein structure. - - + + + + beta12orEarlier + WHATIF:GetSurfaceDots + Calculate the positions of dots that are homogeneously distributed over the surface of a molecule. + + + A dot has three coordinates (x,y,z) and (typically) a color. + Surface rendering - + - - Molecular dynamics simulation - - - - - - - - - - - - - - - - - - - - - - Simulate molecular (typically protein) conformation using a computational model of physical forces and computer simulation. - beta12orEarlier - - + + + beta12orEarlier + 1.12 + Calculate the solvent accessibility ('accessible surface') for each atom in a structure. + + + Waters are not considered. + Protein atom surface calculation (accessible) + true - + - - Nucleic acid sequence analysis - - - - - - - - - - - - - - - Analyse a nucleic acid sequence (using methods that are only applicable to nucleic acid sequences). - beta12orEarlier - Sequence analysis (nucleic acid) - - + + + beta12orEarlier + 1.12 + Calculate the solvent accessibility ('accessible molecular surface') for each atom in a structure. + + + Waters are not considered. + Protein atom surface calculation (accessible molecular) + true - + - - Protein sequence analysis - - - - - - - - - Analyse a protein sequence (using methods that are only applicable to protein sequences). - Sequence analysis (protein) - beta12orEarlier - - + + + beta12orEarlier + 1.12 + Calculate the solvent accessibility ('accessible surface') for each residue in a structure. + + + Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). + Protein residue surface calculation (accessible) + true - + - - Structure analysis - - - - - - - - beta12orEarlier - Analyse known molecular tertiary structures. - - + + + beta12orEarlier + 1.12 + Calculate the solvent accessibility ('vacuum accessible surface') for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to. + + + Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). + Protein residue surface calculation (vacuum accessible) + true - + - - Nucleic acid structure analysis - - - - - - - - - - - - - - - Analyse nucleic acid tertiary structural data. - beta12orEarlier - - + + + beta12orEarlier + 1.12 + Calculate the solvent accessibility ('accessible molecular surface') for each residue in a structure. + + + Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). + Protein residue surface calculation (accessible molecular) + true - + - - Secondary structure processing - - 1.6 - Process (read and / or write) a molecular secondary structure. + + + beta12orEarlier + 1.12 + Calculate the solvent accessibility ('vacuum molecular surface') for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to. + + + Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain). + Protein residue surface calculation (vacuum molecular) true - beta12orEarlier - - - + - - Structure comparison - - - - - - - - - beta12orEarlier - Compare two or more molecular tertiary structures. - - + + + beta12orEarlier + 1.12 + Calculate the solvent accessibility ('accessible molecular surface') for a structure as a whole. + + + Protein surface calculation (accessible molecular) + true - + - - Helical wheel drawing - - - - - - - - Helical wheel rendering - beta12orEarlier - Render a helical wheel representation of protein secondary structure. - - + + + beta12orEarlier + 1.12 + Calculate the solvent accessibility ('accessible surface') for a structure as a whole. + + + Protein surface calculation (accessible) + true - + - - Topology diagram drawing - - - - - - - - Topology diagram rendering - beta12orEarlier - Render a topology diagram of protein secondary structure. - - + + + beta12orEarlier + 1.12 + Calculate for each residue in a protein structure all its backbone torsion angles. + + + Backbone torsion angle calculation + true - + - - Protein structure comparison - - - - - - - - - - beta12orEarlier - Structure comparison (protein) - Methods might identify structural neighbors, find structural similarities or define a structural core. - Compare protein tertiary structures. - - + + + beta12orEarlier + 1.12 + Calculate for each residue in a protein structure all its torsion angles. + + + Full torsion angle calculation + true - + - - Protein secondary structure comparison - - - - Compare protein secondary structures. - beta12orEarlier - Secondary structure comparison (protein) - Protein secondary structure - - + + + beta12orEarlier + 1.12 + Calculate for each cysteine (bridge) all its torsion angles. + + + Cysteine torsion angle calculation + true - + - - Protein subcellular localization prediction - - - - - - - - - The prediction might include subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or export (extracellular proteins) of a protein. - Predict the subcellular localization of a protein sequence. - Protein targeting prediction - beta12orEarlier - - + + + beta12orEarlier + 1.12 + For each amino acid in a protein structure calculate the backbone angle tau. + + + Tau is the backbone angle N-Calpha-C (angle over the C-alpha). + Tau angle calculation + true - + - - Residue contact calculation (residue-residue) - - beta12orEarlier - Calculate contacts between residues in a protein structure. - - + + + beta12orEarlier + WHATIF:ShowCysteineBridge + Detect cysteine bridges (from coordinate data) in a protein structure. + + + Cysteine bridge detection - + - - Hydrogen bond calculation (inter-residue) - - - Identify potential hydrogen bonds between amino acid residues. - beta12orEarlier - - + + + beta12orEarlier + WHATIF:ShowCysteineFree + Detect free cysteines in a protein structure. + + + A free cysteine is neither involved in a cysteine bridge, nor functions as a ligand to a metal. + Free cysteine detection - + - - Protein interaction prediction - - - - - - - - - - - - - - - Predict the interactions of proteins with other molecules. - beta12orEarlier - - + + + + beta12orEarlier + WHATIF:ShowCysteineMetal + Detect cysteines that are bound to metal in a protein structure. + + + Metal-bound cysteine detection - + - - Codon usage data processing - - beta12orEarlier - beta13 - Process (read and / or write) codon usage data. + + + beta12orEarlier + 1.12 + Calculate protein residue contacts with nucleic acids in a structure. + + + Residue contact calculation (residue-nucleic acid) true - - - + - - Gene expression data analysis - - - - - - - - beta12orEarlier - Gene expression profile analysis - Gene expression (microarray) data processing - Microarray data processing - Gene expression data processing - Process (read and / or write) gene expression (typically microarray) data, including analysis of one or more gene expression profiles, typically to interpret them in functional terms. - - + + + beta12orEarlier + Calculate protein residue contacts with metal in a structure. + Residue-metal contact calculation + + + Protein-metal contact calculation - + - - Gene regulatory network processing - - 1.6 - beta12orEarlier - Process (read and / or write) a network of gene regulation. + + + beta12orEarlier + 1.12 + Calculate ion contacts in a structure (all ions for all side chain atoms). + + + Residue contact calculation (residue-negative ion) true - - + - - Pathway or network analysis - - - - - - - - Analyse a known biological pathway or network. - Pathway analysis - Network analysis - beta12orEarlier - - + + + beta12orEarlier + WHATIF:ShowBumps + Detect 'bumps' between residues in a structure, i.e. those with pairs of atoms whose Van der Waals' radii interpenetrate more than a defined distance. + + + Residue bump detection - + - - Sequencing-based expression profile data analysis - - Analyse SAGE, MPSS or SBS experimental data, typically to identify or quantify mRNA transcripts. - beta12orEarlier - beta12orEarlier + + + beta12orEarlier + 1.12 + WHATIF:SymmetryContact + Calculate the number of symmetry contacts made by residues in a protein structure. + + + A symmetry contact is a contact between two atoms in different asymmetric unit. + Residue symmetry contact calculation true - - - + - - Splicing model analysis - - - - - - - - - - Analyse, characterize and model alternative splicing events from comparing multiple nucleic acid sequences. - Splicing analysis - beta12orEarlier - - + + + beta12orEarlier + 1.12 + Calculate contacts between residues and ligands in a protein structure. + + + Residue contact calculation (residue-ligand) + true - + - - Microarray raw data analysis - - beta12orEarlier - beta12orEarlier + + + beta12orEarlier + WHATIF:HasSaltBridge + WHATIF:HasSaltBridgePlus + WHATIF:ShowSaltBridges + WHATIF:ShowSaltBridgesH + Calculate (and possibly score) salt bridges in a protein structure. + + + Salt bridges are interactions between oppositely charged atoms in different residues. The output might include the inter-atomic distance. + Salt bridge calculation + + + + + + + + + beta12orEarlier + 1.12 + WHATIF:ShowLikelyRotamers + WHATIF:ShowLikelyRotamers100 + WHATIF:ShowLikelyRotamers200 + WHATIF:ShowLikelyRotamers300 + WHATIF:ShowLikelyRotamers400 + WHATIF:ShowLikelyRotamers500 + WHATIF:ShowLikelyRotamers600 + WHATIF:ShowLikelyRotamers700 + WHATIF:ShowLikelyRotamers800 + WHATIF:ShowLikelyRotamers900 + Predict rotamer likelihoods for all 20 amino acid types at each position in a protein structure. + + + Output typically includes, for each residue position, the likelihoods for the 20 amino acid types with estimated reliability of the 20 likelihoods. + Rotamer likelihood prediction true - Analyse raw microarray data. - - - + - - Nucleic acid analysis - - - - - - - - Process (read and / or write) nucleic acid sequence or structural data. - Nucleic acid data processing - beta12orEarlier - - + + + beta12orEarlier + 1.12 + WHATIF:ProlineMutationValue + Calculate for each position in a protein structure the chance that a proline, when introduced at this position, would increase the stability of the whole protein. + + + Proline mutation value calculation + true - + - - Protein analysis - - - - - - - - beta12orEarlier - Protein data processing - Process (read and / or write) protein sequence or structural data. - - + + + beta12orEarlier + WHATIF: PackingQuality + Identify poorly packed residues in protein structures. + + + Residue packing validation - + - - Sequence data processing - - beta12orEarlier - Process (read and / or write) molecular sequence data. - beta13 + + + beta12orEarlier + WHATIF: ImproperQualityMax + WHATIF: ImproperQualitySum + Validate protein geometry, for example bond lengths, bond angles, torsion angles, chiralities, planaraties etc. + + + Protein geometry validation + + + + + + + + + beta12orEarlier + beta12orEarlier + WHATIF: PDB_sequence + Extract a molecular sequence from a PDB file. + + + PDB file sequence retrieval true - - + - - Structural data processing - - Process (read and / or write) molecular structural data. - beta13 + + + beta12orEarlier + 1.12 + Identify HET groups in PDB files. + + + A HET group usually corresponds to ligands, lipids, but might also (not consistently) include groups that are attached to amino acids. Each HET group is supposed to have a unique three letter code and a unique name which might be given in the output. + HET group detection true - beta12orEarlier - - - + - - Text processing - + + + beta12orEarlier + beta12orEarlier + + Determine for residue the DSSP determined secondary structure in three-state (HSC). + + DSSP secondary structure assignment true - beta12orEarlier - Process (read and / or write) text. - 1.6 - - - + - - Protein sequence alignment analysis - - - - - - - - - - Analyse a protein sequence alignment, typically to detect features or make predictions. - beta12orEarlier - Sequence alignment analysis (protein) - - + + + beta12orEarlier + 1.12 + WHATIF: PDBasXML + Reformat (a file or other report of) tertiary structure data. + + + Structure formatting + true - + - - Nucleic acid sequence alignment analysis - - - + + - - + + - beta12orEarlier - Sequence alignment analysis (nucleic acid) - Analyse a protein sequence alignment, typically to detect features or make predictions. - - + beta12orEarlier + Assign cysteine bonding state and disulfide bond partners in protein structures. + + + Protein cysteine and disulfide bond assignment - + - - Nucleic acid sequence comparison - - - - Sequence comparison (nucleic acid) - Compare two or more nucleic acid sequences. - beta12orEarlier - - + + + beta12orEarlier + 1.12 + Identify poor quality amino acid positions in protein structures. + + + Residue validation + true - + - - Protein sequence comparison - - - - beta12orEarlier - Sequence comparison (protein) - Compare two or more protein sequences. - - + + + beta12orEarlier + 1.6 + + WHATIF:MovedWaterPDB + Query a tertiary structure database and retrieve water molecules. + + Structure retrieval (water) + true - + - - DNA back-translation - + + - - + + - beta12orEarlier - Back-translate a protein sequence into DNA. - - + beta12orEarlier + Identify or predict siRNA duplexes in RNA. + + + siRNA duplex prediction - + - - Sequence editing (nucleic acid) - - 1.8 - true - Edit or change a nucleic acid sequence, either randomly or specifically. - beta12orEarlier - - + + + + beta12orEarlier + Refine an existing sequence alignment. + + + Sequence alignment refinement - + - - Sequence editing (protein) - - Edit or change a protein sequence, either randomly or specifically. - beta12orEarlier + + + beta12orEarlier + 1.6 + + Process an EMBOSS listfile (list of EMBOSS Uniform Sequence Addresses). + + Listfile processing true - 1.8 - - - + - - Sequence generation (nucleic acid) - - Generate a nucleic acid sequence by some means. - beta12orEarlier - - + + + + beta12orEarlier + Perform basic (non-analytical) operations on a report or file of sequences (which might include features), such as file concatenation, removal or ordering of sequences, creation of subset or a new file of sequences. + + + Sequence file editing - + - - Sequence generation (protein) - - - Generate a protein sequence by some means. - beta12orEarlier - - + + + beta12orEarlier + 1.6 + + Perform basic (non-analytical) operations on a sequence alignment file, such as copying or removal and ordering of sequences. + + Sequence alignment file processing + true - + - - Nucleic acid sequence visualisation - - Visualise, format or render a nucleic acid sequence. + + + beta12orEarlier + beta13 + + Process (read and / or write) physicochemical property data for small molecules. + + Small molecule data processing true - Various nucleic acid sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here. - 1.8 - beta12orEarlier - - - + - - Protein sequence visualisation - + + + beta12orEarlier + beta13 + + Search and retrieve documentation on a bioinformatics ontology. + + Data retrieval (ontology annotation) true - beta12orEarlier - Visualise, format or render a protein sequence. - 1.8 - Various protein sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here. - - - + - - Nucleic acid structure comparison - - - - Compare nucleic acid tertiary structures. - beta12orEarlier - Structure comparison (nucleic acid) - - + + + beta12orEarlier + beta13 + + Query an ontology and retrieve concepts or relations. + + Data retrieval (ontology concept) + true - + - - Structure processing (nucleic acid) - - 1.6 - beta12orEarlier - true - Process (read and / or write) nucleic acid tertiary structure data. - - + + + beta12orEarlier + Identify a representative sequence from a set of sequences, typically using scores from pair-wise alignment or other comparison of the sequences. + + + Representative sequence identification - + - - DNA mapping - - - - - - - - - - - - - - - - - - - - beta12orEarlier - Generate a map of a DNA sequence annotated with positional or non-positional features of some type. - - + + + beta12orEarlier + 1.6 + + Perform basic (non-analytical) operations on a file of molecular tertiary structural data. + + Structure file processing + true - + - - Map data processing - - DNA map data processing - Process (read and / or write) a DNA map of some type. - beta12orEarlier + + + beta12orEarlier + beta13 + + Query a profile data resource and retrieve one or more profile(s) and / or associated annotation. + + This includes direct retrieval methods that retrieve a profile by, e.g. the profile name. + Data retrieval (sequence profile) true - 1.6 - - - + - - Protein hydropathy calculation - + + + beta12orEarlier + Perform a statistical data operation of some type, e.g. calibration or validation. + Statistical analysis + Statistical testing + Gibbs sampling + + + Statistical calculation + + + + + + + + + + - - + + - - + + - beta12orEarlier - Analyse the hydrophobic, hydrophilic or charge properties of a protein (from analysis of sequence or structural information). - - + beta12orEarlier + Calculate a 3D-1D scoring matrix from analysis of protein sequence and structural data. + 3D-1D scoring matrix construction + + + A 3D-1D scoring matrix scores the probability of amino acids occurring in different structural environments. + 3D-1D scoring matrix generation - + - - Protein binding site prediction - + + + - - + + - Ligand-binding and active site prediction - beta12orEarlier - Binding site prediction - Identify or predict catalytic residues, active sites or other ligand-binding sites in protein sequences or structures. - - + beta12orEarlier + Visualise transmembrane proteins, typically the transmembrane regions within a sequence. + Transmembrane protein rendering + + + Transmembrane protein visualisation - + - - Sequence tagged site (STS) mapping - - - - - - - - beta12orEarlier - Sequence mapping - An STS is a short subsequence of known sequence and location that occurs only once in the chromosome or genome that is being mapped. Sources of STSs include 1. expressed sequence tags (ESTs), simple sequence length polymorphisms (SSLPs), and random genomic sequences from cloned genomic DNA or database sequences. - Generate a physical DNA map (sequence map) from analysis of sequence tagged sites (STS). - - + + + beta12orEarlier + beta13 + An operation performing purely illustrative (pedagogical) purposes. + + Demonstration + true - + - - Alignment - - - - - - - - - Compare two or more entities, typically the sequence or structure (or derivatives) of macromolecules, to identify equivalent subunits. - Alignment - Alignment generation - beta12orEarlier - Alignment construction - - + + + beta12orEarlier + beta13 + + Query a biological pathways database and retrieve annotation on one or more pathways. + + Data retrieval (pathway or network) + true - + - - Protein fragment weight comparison - - - beta12orEarlier - Calculate the molecular weight of a protein (or fragments) and compare it another protein or reference data. - - + + + beta12orEarlier + beta13 + + Query a database and retrieve one or more data identifiers. + + Data retrieval (identifier) + true - + - - Protein property comparison - - - - - - - - Compare the physicochemical properties of two or more proteins (or reference data). - beta12orEarlier - - + + + + beta12orEarlier + Calculate a density plot (of base composition) for a nucleotide sequence. + + + Nucleic acid density plotting - + - - Secondary structure comparison - + + - - + + - Compare two or more molecular secondary structures. - beta12orEarlier - - - - - - - - - - Hopp and Woods plotting - - - beta12orEarlier - Generate a Hopp and Woods plot of antigenicity of a protein. - - + beta12orEarlier + Analyse one or more known molecular sequences. + Sequence analysis (general) + + + Sequence analysis - + - - Microarray cluster textual view generation - - beta12orEarlier - Visualise gene clusters with gene names. - - + + + beta12orEarlier + Analyse molecular sequence motifs. + Sequence motif processing + + + Sequence motif analysis - + - - Microarray wave graph plotting - - Microarray wave graph rendering - Microarray cluster temporal graph rendering - beta12orEarlier - This view can be rendered as a pie graph. The distance matrix is sorted by cluster number and typically represented as a diagonal matrix with distance values displayed in different color shades. - Visualise clustered gene expression data as a set of waves, where each wave corresponds to a gene across samples on the X-axis. - - + + + beta12orEarlier + 1.6 + + Process (read and / or write) protein interaction data. + + Protein interaction data processing + true - + - - Microarray dendrograph plotting - - Microarray dendrograph rendering - Generate a dendrograph of raw, preprocessed or clustered microarray data. - beta12orEarlier - Microarray checks view rendering - Microarray view rendering - - + + + + + + + + + + + + + + + + beta12orEarlier + Analyse protein tertiary structural data. + Structure analysis (protein) + + + Protein structure analysis - + - - Microarray proximity map plotting - - beta12orEarlier - Microarray distance map rendering - Generate a plot of distances (distance matrix) between genes. - Microarray proximity map rendering - - + + + beta12orEarlier + beta12orEarlier + + Process (read and / or write) annotation of some type, typically annotation on an entry from a biological or biomedical database entity. + + Annotation processing + true - + - - Microarray tree or dendrogram rendering - - Microarray 2-way dendrogram rendering - beta12orEarlier - Visualise clustered gene expression data using a gene tree, array tree and color coded band of gene expression. - Microarray matrix tree plot rendering - - + + + beta12orEarlier + beta12orEarlier + + Analyse features in molecular sequences. + + Sequence feature analysis + true - + - - Microarray principal component plotting - - beta12orEarlier - Microarray principal component rendering - Generate a line graph drawn as sum of principal components (Eigen value) and individual expression values. - - + + + + + + + + + beta12orEarlier + Basic (non-analytical) operations of some data, either a file or equivalent entity in memory, such that the same basic type of data is consumed as input and generated as output. + File handling + File processing + Report handling + Utility operation + Processing + + + Data handling - + - - Microarray scatter plot plotting - - Generate a scatter plot of microarray data, typically after principal component analysis. - beta12orEarlier - Microarray scatter plot rendering - - + + + beta12orEarlier + beta12orEarlier + + Analyse gene expression and regulation data. + + Gene expression analysis + true - + - - Whole microarray graph plotting - - Visualise gene expression data where each band (or line graph) corresponds to a sample. - beta12orEarlier - Whole microarray graph rendering - - + + + beta12orEarlier + 1.6 + + Process (read and / or write) one or more structural (3D) profile(s) or template(s) of some type. + + Structural profile processing + true - + - - Microarray tree-map rendering - - beta12orEarlier - Visualise gene expression data after hierarchical clustering for representing hierarchical relationships. - - + + + beta12orEarlier + 1.6 + + Process (read and / or write) an index of (typically a file of) biological data. + + Data index processing + true - + - - Microarray Box-Whisker plot plotting - - beta12orEarlier - Visualise raw and pre-processed gene expression data, via a plot showing over- and under-expression along with mean, upper and lower quartiles. - - + + + beta12orEarlier + 1.6 + + Process (read and / or write) some type of sequence profile. + + Sequence profile processing + true - + - - Physical mapping - + + - - + + + beta12orEarlier + Analyse protein function, typically by processing protein sequence and/or structural data, and generate an informative report. + + + This is a broad concept and is used a placeholder for other, more specific concepts. + Protein function analysis + + + + + + + + + - - + + - beta12orEarlier - Generate a physical (sequence) map of a DNA sequence showing the physical distance (base pairs) between features or landmarks such as restriction sites, cloned DNA fragments, genes and other genetic markers. - - + + + + + + + beta12orEarlier + Analyse protein folding, typically by processing sequence and / or structural data, and write an informative report. + Protein folding modelling + + + This is a broad concept and is used a placeholder for other, more specific concepts. + Protein folding analysis - + - - Analysis - - Apply analytical methods to existing data of a specific type. - For non-analytical operations, see the 'Processing' branch. - beta12orEarlier - - - + + + + + + + + + + + + + + + beta12orEarlier + Analyse known protein secondary structure data. + Secondary structure analysis (protein) + + + Protein secondary structure analysis - + - - Alignment analysis - - Process or analyse an alignment of molecular sequences or structures. + + + beta12orEarlier + beta13 + + Process (read and / or write) data on the physicochemical property of a molecule. + + Physicochemical property data processing true - beta12orEarlier - 1.8 - - - + - - Article analysis - - - - - - - + + + - - + + - - - - - - - Analyse a body of scientific text (typically a full text article from a scientific journal.) - beta12orEarlier - Article analysis - - + beta12orEarlier + Predict oligonucleotide primers or probes. + Primer and probe prediction + + + Primer and probe design - + - - Molecular interaction analysis - - Analyse the interactions of two or more molecules (or parts of molecules) that are known to interact. - beta12orEarlier - beta13 + + + beta12orEarlier + 1.12 + Process (read and / or write) data of a specific type, for example applying analytical methods. + + + Operation (typed) true - - + - - Protein interaction analysis - + + - - + + + beta12orEarlier + Search a database (or other data resource) with a supplied query and retrieve entries (or parts of entries) that are similar to the query. + Search + + + Typically the query is compared to each entry and high scoring matches (hits) are returned. For example, a BLAST search of a sequence database. + Database search + + + + + + + + - - + + - beta12orEarlier - Analyse known protein-protein, protein-DNA/RNA or protein-ligand interactions. - - + beta12orEarlier + Information retrieval + Retrieve an entry (or part of an entry) from a data resource that matches a supplied query. This might include some primary data and annotation. The query is a data identifier or other indexed term. For example, retrieve a sequence record with the specified accession number, or matching supplied keywords. + Retrieval + + + Data retrieval - + - - Residue contact calculation - - Calculate contacts between residues and some other group in a protein structure. - beta12orEarlier - - + + + beta12orEarlier + Predict, recognise, detect or identify some properties of a biomolecule. + Detection + Prediction + Recognition + + + Prediction and recognition - + - - Alignment processing - - true - Process (read and / or write) an alignment of two or more molecular sequences, structures or derived data. - 1.6 - beta12orEarlier - - - + + + beta12orEarlier + Compare two or more things to identify similarities. + + + Comparison - + - - Structure alignment processing - - Process (read and / or write) a molecular tertiary (3D) structure alignment. - 1.6 - beta12orEarlier - true - - + + + beta12orEarlier + Refine or optimise some data model. + + + Optimisation and refinement - + - - Codon usage bias calculation - + + - - + + - Calculate codon usage bias. - beta12orEarlier - - + beta12orEarlier + Model or simulate some biological entity or system, typically using mathematical techniques including dynamical systems, statistical models, differential equations, and game theoretic models. + Mathematical modelling + + + Modelling and simulation - + - - Codon usage bias plotting - - - - - - - - - beta12orEarlier - Generate a codon usage bias plot. - - + + + beta12orEarlier + beta12orEarlier + Perform basic operations on some data or a database. + + + Data handling + true - + - - Codon usage fraction calculation - - - - - - - - Calculate the differences in codon usage fractions between two sequences, sets of sequences, codon usage tables etc. - beta12orEarlier - - + + + beta12orEarlier + Validate some data. + Quality control + + + Validation - + - - Classification - - beta12orEarlier - Assign molecular sequences, structures or other biological data to a specific group or category according to qualities it shares with that group or category. - - + + + beta12orEarlier + Map properties to positions on an biological entity (typically a molecular sequence or structure), or assemble such an entity from constituent parts. + + + This is a broad concept and is used a placeholder for other, more specific concepts. + Mapping - + - - Molecular interaction data processing - - beta13 + + + beta12orEarlier + Design a biological entity (typically a molecular sequence or structure) with specific properties. + + + Design + + + + + + + + + beta12orEarlier + beta12orEarlier + + Process (read and / or write) microarray data. + + Microarray data processing true - beta12orEarlier - Process (read and / or write) molecular interaction data. - - + - - Sequence classification - - - beta12orEarlier - Assign molecular sequence(s) to a group or category. - - + + + beta12orEarlier + Process (read and / or write) a codon usage table. + + + Codon usage table processing - + - - Structure classification - - - Assign molecular structure(s) to a group or category. - beta12orEarlier - - + + + beta12orEarlier + beta13 + + Retrieve a codon usage table and / or associated annotation. + + Data retrieval (codon usage table) + true - + - - Protein comparison - - Compare two or more proteins (or some aspect) to identify similarities. - beta12orEarlier - - + + + beta12orEarlier + 1.6 + + Process (read and / or write) a gene expression profile. + + Gene expression profile processing + true - + - - Nucleic acid comparison - - beta12orEarlier - Compare two or more nucleic acids to identify similarities. - - + + + + + + + + + + + + + + + + + 1.8 + beta12orEarlier + Analysis of a set of genes, corresponding e.g. to a gene expression profile, annotated with Gene Ontology (GO) concepts, where eventual over-/under-representation of certain GO concept within the studied set of genes is revealed. + Gene-set over-represenation analysis + GO-term enrichment + Gene Ontology concept enrichment + Gene Ontology term enrichment + + + The Gene Ontology (GO) is typically used, the input is a set of Gene IDs, and the output of the analysis is typically a ranked list of GO concepts, each associated with a p-value. + Gene-set enrichment analysis + - + - - Prediction and recognition (protein) - - beta12orEarlier - Predict, recognise, detect or identify some properties of proteins. - - + + + + + + + + + + + + + + + + beta12orEarlier + Predict a network of gene regulation. + + + Gene regulatory network prediction - + - - Prediction and recognition (nucleic acid) - - beta12orEarlier - Predict, recognise, detect or identify some properties of nucleic acids. - - + + + beta12orEarlier + 1.12 + Generate, analyse or handle a biological pathway or network. + + + Pathway or network processing + true - + - - Structure editing - + + - - + + - beta13 - Edit, convert or otherwise change a molecular tertiary structure, either randomly or specifically. - - + beta12orEarlier + Process (read and / or write) RNA secondary structure data. + + + RNA secondary structure analysis - + - - Sequence alignment editing - - Edit, convert or otherwise change a molecular sequence alignment, either randomly or specifically. - beta13 - - + + + beta12orEarlier + beta13 + Process (read and / or write) RNA tertiary structure data. + + + Structure processing (RNA) + true - + - - Pathway or network visualisation - - + + - - + + - Render (visualise) a biological pathway or network. - Pathway or network rendering - beta13 - - + beta12orEarlier + Predict RNA tertiary structure. + + + RNA structure prediction - + - - Protein function prediction (from sequence) - - beta13 + + + + + + + + + beta12orEarlier + Predict DNA tertiary structure. + + + DNA structure prediction + + + + + + + + + beta12orEarlier + 1.12 + Generate, process or analyse phylogenetic tree or trees. + + + Phylogenetic tree processing true - Predict general (non-positional) functional properties of a protein from analysing its sequence. - For functional properties that are positional, use 'Protein site detection' instead. - 1.6 - - - + - - Protein sequence feature detection - - - - Protein site recognition - Predict, recognise and identify functional or other key sites within protein sequences, typically by scanning for known motifs, patterns and regular expressions. - Protein site prediction - Sequence profile database search - Protein site detection - Protein secondary database search - Sequence feature detection (protein) - beta13 - - + + + beta12orEarlier + 1.6 + + Process (read and / or write) protein secondary structure data. + + Protein secondary structure processing + true - + - - Protein property calculation (from sequence) - - - beta13 - Calculate (or predict) physical or chemical properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence. - - + + + beta12orEarlier + 1.6 + + Process (read and / or write) a network of protein interactions. + + Protein interaction network processing + true - + - - Protein feature prediction (from structure) - - beta13 - 1.6 + + + beta12orEarlier + 1.6 + + Process (read and / or write) one or more molecular sequences and associated annotation. + + Sequence processing true - Predict, recognise and identify positional features in proteins from analysing protein structure. - - - + - - Protein feature detection - - - - - - - - - - - - - - - Features includes functional sites or regions, secondary structure, structural domains and so on. Methods might use fingerprints, motifs, profiles, hidden Markov models, sequence alignment etc to provide a mapping of a query protein sequence to a discriminatory element. This includes methods that search a secondary protein database (Prosite, Blocks, ProDom, Prints, Pfam etc.) to assign a protein sequence(s) to a known protein family or group. - - Predict, recognise and identify positional features in proteins from analysing protein sequences or structures. - beta13 - Protein feature recognition - Protein feature prediction - - + + + beta12orEarlier + 1.6 + Process (read and / or write) a protein sequence and associated annotation. + + + Sequence processing (protein) + true - + - - Database search (by sequence) - - Sequence screening + + + beta12orEarlier + 1.6 + + Process (read and / or write) a nucleotide sequence and associated annotation. + + Sequence processing (nucleic acid) true - 1.6 - Screen a molecular sequence(s) against a database (of some type) to identify similarities between the sequence and database entries. - beta13 - - - + - - Protein interaction network prediction - + + + - - + + - - + + - beta13 - Predict a network of protein interactions. - - + beta12orEarlier + Compare two or more molecular sequences. + + + Sequence comparison - + - - Nucleic acid design - - - beta13 - Design (or predict) nucleic acid sequences with specific chemical or physical properties. - - + + + beta12orEarlier + 1.6 + + Process (read and / or write) a sequence cluster. + + Sequence cluster processing + true - + - - Editing - - beta13 - Edit a data entity, either randomly or specifically. - - + + + beta12orEarlier + 1.6 + + Process (read and / or write) a sequence feature table. + + Feature table processing + true - + - - Sequence assembly validation - - + + - - + + - - + + + beta12orEarlier + Detect, predict and identify genes or components of genes in DNA sequences, including promoters, coding regions, splice sites, etc. + Gene and gene component prediction + Gene calling + Gene finding + Gene component prediction + Whole gene prediction + + + Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc. + Gene prediction + + + + + + + + + beta12orEarlier + 1.16 + Classify G-protein coupled receptors (GPCRs) into families and subfamilies. + + + GPCR classification + true + + + + + + + + + + - - + + - 1.1 - Evaluate a DNA sequence assembly, typically for purposes of quality control. - - + beta12orEarlier + Predict G-protein coupled receptor (GPCR) coupling selectivity. + + + GPCR coupling selectivity prediction - + - - Genome alignment - - Align two or more (tpyically huge) molecular sequences that represent genomes. - Genome alignment construction - 1.1 - Genome alignment - - + + + beta12orEarlier + 1.6 + Process (read and / or write) a protein tertiary structure. + + + Structure processing (protein) + true - + - - Localized reassembly - - Reconstruction of a sequence assembly in a localised area. - 1.1 - - + + + beta12orEarlier + 1.12 + Calculate the solvent accessibility for each atom in a structure. + + + Waters are not considered. + Protein atom surface calculation + true - + - - Sequence assembly visualisation - - Assembly rendering - Sequence assembly rendering - Render and visualise a DNA sequence assembly. - 1.1 - Assembly visualisation - - + + + beta12orEarlier + 1.12 + Calculate the solvent accessibility for each residue in a structure. + + + Protein residue surface calculation + true - + - - Base-calling - - - - - - - - Phred base calling - 1.1 - Identify base (nucleobase) sequence from a fluorescence 'trace' data generated by an automated DNA sequencer. - Base calling - Phred base-calling - - + + + beta12orEarlier + 1.12 + Calculate the solvent accessibility of a structure as a whole. + + + Protein surface calculation + true - + - - Bisulfite mapping - - 1.1 - Bisulfite mapping follows high-throughput sequencing of DNA which has undergone bisulfite treatment followed by PCR amplification; unmethylated cytosines are specifically converted to thymine, allowing the methylation status of cytosine in the DNA to be detected. - The mapping of methylation sites in a DNA (genome) sequence. - Bisulfite sequence alignment - Bisulfite sequence mapping - - + + + beta12orEarlier + 1.6 + + Process (read and / or write) a molecular sequence alignment. + + Sequence alignment processing + true - + - - Sequence contamination filtering - + + + - - + + - beta12orEarlier - Identify and filter a (typically large) sequence data set to remove sequences from contaminants in the sample that was sequenced. - - + + + + + + + beta12orEarlier + Identify or predict protein-protein interactions, interfaces, binding sites etc. + + + Protein-protein interaction prediction - + - - Trim ends - - 1.1 - Trim sequences (typically from an automated DNA sequencer) to remove misleading ends. - For example trim polyA tails, introns and primer sequence flanking the sequence of amplified exons, or other unwanted sequence. - - + + + beta12orEarlier + 1.6 + + Process (read and / or write) a molecular tertiary structure. + + Structure processing + true - + - - Trim vector - - Trim sequences (typically from an automated DNA sequencer) to remove sequence-specific end regions, typically contamination from vector sequences. - 1.1 - - + + + beta12orEarlier + 1.6 + + Annotate a DNA map of some type with terms from a controlled vocabulary. + + Map annotation + true - + - - Trim to reference - - 1.1 - Trim sequences (typically from an automated DNA sequencer) to remove the sequence ends that extend beyond an assembled reference sequence. - - + + + beta12orEarlier + beta13 + + Retrieve information on a protein. + + Data retrieval (protein annotation) + true - + - - Sequence trimming - - 1.1 - Cut (remove) the end from a molecular sequence. - - + + + beta12orEarlier + beta13 + + Retrieve a phylogenetic tree from a data resource. + + Data retrieval (phylogenetic tree) + true - + - - Genome feature comparison - - Genomic elements that might be compared include genes, indels, single nucleotide polymorphisms (SNPs), retrotransposons, tandem repeats and so on. - Compare the features of two genome sequences. - 1.1 - - + + + beta12orEarlier + beta13 + + Retrieve information on a protein interaction. + + Data retrieval (protein interaction annotation) + true - + - - Sequencing error detection - - - - - - - - Short read error correction - Short-read error correction - beta12orEarlier - Detect errors in DNA sequences generated from sequencing projects). - - + + + beta12orEarlier + beta13 + + Retrieve information on a protein family. + + Data retrieval (protein family annotation) + true - + - - Genotyping - - 1.1 - Methods might consider cytogenetic analyses, copy number polymorphism (and calculate copy number calls for copy-number variation(CNV) regions), single nucleotide polymorphism (SNP), , rare copy number variation (CNV) identification, loss of heterozygosity data and so on. - Analyse DNA sequence data to identify differences between the genetic composition (genotype) of an individual compared to other individual's or a reference sequence. - - + + + beta12orEarlier + beta13 + + Retrieve information on an RNA family. + + Data retrieval (RNA family annotation) + true - + - - Genetic variation analysis - - - 1.1 - Sequence variation analysis - Genetic variation annotation provides contextual interpretation of coding SNP consequences in transcripts. It allows comparisons to be made between variation data in different populations or strains for the same transcript. - Genetic variation annotation - Analyse a genetic variation, for example to annotate its location, alleles, classification, and effects on individual transcripts predicted for a gene model. - - + + + beta12orEarlier + beta13 + + Retrieve information on a specific gene. + + Data retrieval (gene annotation) + true - + - - Read mapping - - - Short oligonucleotide alignment - Oligonucleotide mapping - Oligonucleotide alignment generation - Short read mapping - Oligonucleotide alignment construction - The purpose of read mapping is to identify the location of sequenced fragments within a reference genome and assumes that there is, in fact, at least local similarity between the fragment and reference sequences. - Oligonucleotide alignment - Read alignment - 1.1 - Short read alignment - Align short oligonucleotide sequences (reads) to a larger (genomic) sequence. - Short sequence read mapping - - + + + beta12orEarlier + beta13 + + Retrieve information on a specific genotype or phenotype. + + Data retrieval (genotype and phenotype annotation) + true - + - - Split read mapping - - A varient of oligonucleotide mapping where a read is mapped to two separate locations because of possible structural variation. - 1.1 - - + + + + beta12orEarlier + Compare the architecture of two or more protein structures. + + + Protein architecture comparison - + - - DNA barcoding - - Analyse DNA sequences in order to identify a DNA barcode; short fragment(s) of DNA that are useful to diagnose the taxa of biological organisms. - 1.1 - Sample barcoding - - + + + + + beta12orEarlier + Identify the architecture of a protein structure. + + + Includes methods that try to suggest the most likely biological unit for a given protein X-ray crystal structure based on crystal symmetry and scoring of putative protein-protein interfaces. + Protein architecture recognition - + - - SNP calling - - Identify single nucleotide change in base positions in sequencing data that differ from a reference genome and which might, especially by reference to population frequency or functional data, indicate a polymorphism. - Operations usually score confidence in the prediction or some other statistical measure of evidence. - 1.1 - - + + + + + + + + + + + + + + + + + + + + + + + beta12orEarlier + Simulate molecular (typically protein) conformation using a computational model of physical forces and computer simulation. + + + Molecular dynamics simulation - + - - Mutation detection - - Polymorphism detection - Detect mutations in multiple DNA sequences, for example, from the alignment and comparison of the fluorescent traces produced by DNA sequencing hardware. - 1.1 - - + + + + + + + + + + + + + + + + beta12orEarlier + Analyse a nucleic acid sequence (using methods that are only applicable to nucleic acid sequences). + Sequence analysis (nucleic acid) + + + Nucleic acid sequence analysis - + - - Chromatogram visualisation - - Visualise, format or render an image of a Chromatogram. - Chromatogram viewing - 1.1 - - + + + + + + + + + + beta12orEarlier + Analyse a protein sequence (using methods that are only applicable to protein sequences). + Sequence analysis (protein) + + + Protein sequence analysis - + - - Methylation analysis - - 1.1 - Determine cytosine methylation states in nucleic acid sequences. - - + + + + + + + + + beta12orEarlier + Analyse known molecular tertiary structures. + + + Structure analysis - + - - Methylation calling - - - 1.1 - Determine cytosine methylation status of specific positions in a nucleic acid sequences. - - + + + + + + + + + + + + + + + + beta12orEarlier + Analyse nucleic acid tertiary structural data. + + + Nucleic acid structure analysis - + - - Methylation level analysis (global) - - 1.1 - Global methylation analysis - Measure the overall level of methyl cytosines in a genome from analysis of experimental data, typically from chromatographic methods and methyl accepting capacity assay. - - + + + beta12orEarlier + 1.6 + + Process (read and / or write) a molecular secondary structure. + + Secondary structure processing + true - + - - Methylation level analysis (gene-specific) - - Gene-specific methylation analysis - Many different techniques are available for this. - Measure the level of methyl cytosines in specific genes. - 1.1 - - + + + + + + + + + + beta12orEarlier + Compare two or more molecular tertiary structures. + + + Structure comparison - + - - Genome visualisation - - 1.1 - Genome visualization - Visualise, format or render a nucleic acid sequence that is part of (and in context of) a complete genome sequence. - Genome rendering - Genome visualisation - Genome viewing - Genome browsing - - + + + + + + + + + beta12orEarlier + Render a helical wheel representation of protein secondary structure. + Helical wheel rendering + + + Helical wheel drawing - + - - Genome comparison - - Compare the sequence or features of two or more genomes, for example, to find matching regions. - 1.1 - Genomic region matching - - + + + + + + + + + beta12orEarlier + Render a topology diagram of protein secondary structure. + Topology diagram rendering + + + Topology diagram drawing - + - - Genome indexing - + + + + - - + + - Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment. - Generate an index of a genome sequence. - 1.1 - - + beta12orEarlier + Compare protein tertiary structures. + Structure comparison (protein) + + + Methods might identify structural neighbors, find structural similarities or define a structural core. + Protein structure comparison - + - - Genome indexing (Burrows-Wheeler) - - The Burrows-Wheeler Transform (BWT) is a permutation of the genome based on a suffix array algorithm. - Generate an index of a genome sequence using the Burrows-Wheeler algorithm. - 1.1 - - + + + + + beta12orEarlier + Compare protein secondary structures. + Protein secondary structure + Secondary structure comparison (protein) + + + Protein secondary structure comparison - + - - Genome indexing (suffix arrays) - - 1.1 - Generate an index of a genome sequence using a suffix arrays algorithm. - suffix arrays - A suffix array consists of the lexicographically sorted list of suffixes of a genome. - - + + + + + + + + + + beta12orEarlier + Predict the subcellular localisation of a protein sequence. + Protein targeting prediction + + + The prediction might include subcellular localisation (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or export (extracellular proteins) of a protein. + Protein subcellular localisation prediction - + - - Spectral analysis - - Spectral analysis - 1.1 - Spectrum analysis - Analyse a spectrum from a mass spectrometry (or other) experiment. - Mass spectrum analysis - - + + + beta12orEarlier + 1.12 + Calculate contacts between residues in a protein structure. + + + Residue contact calculation (residue-residue) + true - + - - Peak detection - - - - - - - - 1.1 - Peak finding - Peak assignment - Identify peaks in a spectrum from a mass spectrometry, NMR, or some other spectrum-generating experiment. - - + + + beta12orEarlier + 1.12 + Identify potential hydrogen bonds between amino acid residues. + + + Hydrogen bond calculation (inter-residue) + true - + - - Scaffolding - - + + + - - + + - Scaffold construction - Link together a non-contiguous series of genomic sequences into a scaffold, consisting of sequences separated by gaps of known length. The sequences that are linked are typically typically contigs; contiguous sequences corresponding to read overlaps. - 1.1 - Scaffold may be positioned along a chromosome physical map to create a "golden path". - Scaffold generation - - + + + + + + + beta12orEarlier + Predict the interactions of proteins with other molecules. + + + Protein interaction prediction - + - - Scaffold gap completion - - Fill the gaps in a sequence assembly (scaffold) by merging in additional sequences. - Different techniques are used to generate gap sequences to connect contigs, depending on the size of the gap. For small (5-20kb) gaps, PCR amplification and sequencing is used. For large (>20kb) gaps, fragments are cloned (e.g. in BAC (Bacterial artificial chromosomes) vectors) and then sequenced. - 1.1 - - + + + beta12orEarlier + beta13 + + Process (read and / or write) codon usage data. + + Codon usage data processing + true - + - - Sequencing quality control - - - Raw sequence data quality control. - Analyse raw sequence data from a sequencing pipeline and identify problems. - Sequencing QC - 1.1 - - + + + + + + + + + beta12orEarlier + Process (read and / or write) gene expression (typically microarray) data, including analysis of one or more gene expression profiles, typically to interpret them in functional terms. + Gene expression data analysis + Microarray data analysis + RNA-seq analysis + + + Gene expression analysis - + - - Read pre-processing - - - Sequence read pre-processing - This is a broad concept and is used a placeholder for other, more specific concepts. For example process paired end reads to trim low quality ends remove short sequences, identify sequence inserts, detect chimeric reads, or remove low quality sequnces including vector, adaptor, low complexity and contaminant sequences. Sequences might come from genomic DNA library, EST libraries, SSH library and so on. - Pre-process sequence reads to ensure (or improve) quality and reliability. - 1.1 - - + + + beta12orEarlier + 1.6 + Process (read and / or write) a network of gene regulation. + + + Gene regulatory network processing + true - + - - Species frequency estimation - + + - - + + - Estimate the frequencies of different species from analysis of the molecular sequences, typically of DNA recovered from environmental samples. - 1.1 - - + beta12orEarlier + Generate, process or analyse a biological pathway or network. + Network analysis + Pathway analysis + + + Pathway or network analysis - + - - Peak calling - - Chip-sequencing combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to generate a set of reads, which are aligned to a genome sequence. The enriched areas contain the binding sites of DNA-associated proteins. For example, a transcription factor binding site. ChIP-on-chip in contrast combines chromatin immunoprecipitation ('ChIP') with microarray ('chip'). - Identify putative protein-binding regions in a genome sequence from analysis of Chip-sequencing data or ChIP-on-chip data. - Protein binding peak detection - 1.1 - - + + + beta12orEarlier + beta12orEarlier + + Analyse SAGE, MPSS or SBS experimental data, typically to identify or quantify mRNA transcripts. + + Sequencing-based expression profile data analysis + true - + - - Differential expression analysis - - Identify (typically from analysis of microarray or RNA-seq data) genes whose expression levels are significantly different between two sample groups. - Differentially expressed gene identification - Differential expression analysis is used, for example, to identify which genes are up-regulated (increased expression) or down-regulated (decreased expression) between a group treated with a drug and a control groups. - 1.1 - - + + + + + + + + + + + beta12orEarlier + Analyse, characterize and model alternative splicing events from comparing multiple nucleic acid sequences. + Splicing analysis + + + Splicing model analysis - + - - Gene set testing - - 1.1 - Gene sets can be defined beforehand by biological function, chromosome locations and so on. - Analyse gene expression patterns (typically from DNA microarray datasets) to identify sets of genes that are associated with a specific trait, condition, clinical outcome etc. - - + + + beta12orEarlier + beta12orEarlier + + Analyse raw microarray data. + + Microarray raw data analysis + true - + - - Variant classification - - - Classify variants based on their potential effect on genes, especially functional effects on the expressed proteins. - 1.1 - Variants are typically classified by their position (intronic, exonic, etc.) in a gene transcript and (for variants in coding exons) by their effect on the protein sequence (synonymous, non-synonymous, frameshifting, etc.) - - + + + + + + + + + beta12orEarlier + Process (read and / or write) nucleic acid sequence or structural data. + Nucleic acid data processing + + + Nucleic acid analysis - + - - Variant prioritization - - Variant prioritization can be used for example to produce a list of variants responsible for 'knocking out' genes in specific genomes. Methods amino acid substitution, aggregative approaches, probabilistic approach, inheritance and unified likelihood-frameworks. - Identify biologically interesting variants by prioritizing individual variants, for example, homozygous variants absent in control genomes. - 1.1 - - + + + + + + + + + beta12orEarlier + Process (read and / or write) protein sequence or structural data. + Protein data processing + + + Protein analysis - + - - Variant calling - - Variant mapping - 1.1 - Identify and map genomic alterations, including single nucleotide polymorphisms, short indels and structural variants, in a genome sequence. - Methods often utilise a database of aligned reads. - - + + + beta12orEarlier + beta13 + Process (read and / or write) molecular sequence data. + + + Sequence data processing + true - + - - Structural variation discovery - - Detect large regions in a genome subject to copy-number variation, or other structural variations in genome(s). - 1.1 - Methods might involve analysis of whole-genome array comparative genome hybridization or single-nucleotide polymorphism arrays, paired-end mapping of sequencing data, or from analysis of short reads from new sequencing technologies. - - + + + beta12orEarlier + beta13 + + Process (read and / or write) molecular structural data. + + Structural data processing + true - + - - Exome analysis - - 1.1 - Targeted exome capture - Exome sequencing is considered a cheap alternative to whole genome sequencing. - Exome sequence analysis - Anaylse sequencing data from experiments aiming to selectively sequence the coding regions of the genome. - - + + + beta12orEarlier + 1.6 + + + Process (read and / or write) text. + + Text processing + true - + - - Read depth analysis - - 1.1 - Analyse mapping density (read depth) of (typically) short reads from sequencing platforms, for example, to detect deletions and duplications. - - + + + + + + + + + + + beta12orEarlier + Analyse a protein sequence alignment, typically to detect features or make predictions. + Sequence alignment analysis (protein) + + + Protein sequence alignment analysis - + - - Gene expression QTL analysis - + + + + - - + + - expression quantitative trait loci profiling - 1.1 - eQTL profiling - Combine classical quantitative trait loci (QTL) analysis with gene expression profiling, for example, to describe describe cis- and trans-controlling elements for the expression of phenotype associated genes. - expression QTL profiling - - + beta12orEarlier + Analyse a protein sequence alignment, typically to detect features or make predictions. + Sequence alignment analysis (nucleic acid) + + + Nucleic acid sequence alignment analysis - + - - Copy number estimation - - Methods typically implement some statistical model for hypothesis testing, and methods estimate total copy number, i.e. do not distinguish the two inherited chromosomes quantities (specific copy number). - Transcript copy number estimation - 1.1 - Estimate the number of copies of loci of particular gene(s) in DNA sequences typically from gene-expression profiling technology based on microarray hybridization-based experiments. For example, estimate copy number (or marker dosage) of a dominant marker in samples from polyploid plant cells or tissues, or chromosomal gains and losses in tumors. - - + + + + + beta12orEarlier + Compare two or more nucleic acid sequences. + Sequence comparison (nucleic acid) + + + Nucleic acid sequence comparison - + - - Primer removal - - 1.2 - Remove forward and/or reverse primers from nucleic acid sequences (typically PCR products). - - + + + + + beta12orEarlier + Compare two or more protein sequences. + Sequence comparison (protein) + + + Protein sequence comparison - + - - Transcriptome assembly - - - - - - - + + - - + + - Infer a transcriptome sequence by analysis of short sequence reads. - 1.2 - - + beta12orEarlier + Back-translate a protein sequence into DNA. + + + DNA back-translation - + - - Transcriptome assembly (de novo) - - de novo transcriptome assembly + + + beta12orEarlier + 1.8 + Edit or change a nucleic acid sequence, either randomly or specifically. + + + Sequence editing (nucleic acid) true - 1.6 - 1.2 - Infer a transcriptome sequence without the aid of a reference genome, i.e. by comparing short sequences (reads) to each other. - - - + - - Transcriptome assembly (mapping) - - Infer a transcriptome sequence by mapping short reads to a reference genome. - 1.6 - 1.2 + + + beta12orEarlier + 1.8 + Edit or change a protein sequence, either randomly or specifically. + + + Sequence editing (protein) true - - - + - - Sequence coordinate conversion - - - - - - - - - - - - - - 1.3 - Convert one set of sequence coordinates to another, e.g. convert coordinates of one assembly to another, cDNA to genomic, CDS to genomic, protein translation to genomic etc. - - + + + beta12orEarlier + Generate a nucleic acid sequence by some means. + + + Sequence generation (nucleic acid) - + - - Document similarity calculation - - Calculate similarity between 2 or more documents. - 1.3 - - + + + + beta12orEarlier + Generate a protein sequence by some means. + + + Sequence generation (protein) - + - - Document clustering - - - Cluster (group) documents on the basis of their calculated similarity. - 1.3 - - + + + beta12orEarlier + 1.8 + Visualise, format or render a nucleic acid sequence. + + + Various nucleic acid sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here. + Nucleic acid sequence visualisation + true - + - - Named entity recognition - - - Entity identification - Entity chunking - Entity extraction - Recognise named entities (text tokens) within documents. - 1.3 - - + + + beta12orEarlier + 1.8 + Visualise, format or render a protein sequence. + + + Various protein sequence analysis methods might generate a sequence rendering but are not (for brevity) listed under here. + Protein sequence visualisation + true - + - - ID mapping - - - Identifier mapping - The mapping can be achieved by comparing identifier values or some other means, e.g. exact matches to a provided sequence. - 1.3 - Accession mapping - Map data identifiers to one another for example to establish a link between two biological databases for the purposes of data integration. - - + + + + + beta12orEarlier + Compare nucleic acid tertiary structures. + Structure comparison (nucleic acid) + + + Nucleic acid structure comparison - + - - Anonymisation - - Process data in such a way that makes it hard to trace to the person which the data concerns. - 1.3 - Data anonymisation - - + + + beta12orEarlier + 1.6 + Process (read and / or write) nucleic acid tertiary structure data. + + + + Structure processing (nucleic acid) + true - + - - ID retrieval - + + - - + + - id retrieval - Data retrieval (accession) - Data retrieval (ID) - Identifier retrieval - Data retrieval (id) - Accession retrieval - Search for and retrieve a data identifier of some kind, e.g. a database entry accession. - 1.3 - - + + + + + + + + + + + + + beta12orEarlier + Generate a map of a DNA sequence annotated with positional or non-positional features of some type. + + + DNA mapping - + - - Sequence checksum generation - + + + beta12orEarlier + 1.6 + + Process (read and / or write) a DNA map of some type. + + Map data processing + true + + + + + + + + - - + + - - + + - Generate a checksum of a molecular sequence. - 1.4 - - + beta12orEarlier + Analyse the hydrophobic, hydrophilic or charge properties of a protein (from analysis of sequence or structural information). + + + Protein hydropathy calculation - + - - Bibliography generation - + + + - - + + - Bibliography construction - Construct a bibliography from the scientific literature. - 1.4 - - + beta12orEarlier + Identify or predict catalytic residues, active sites or other ligand-binding sites in protein sequences or structures. + Binding site prediction + Protein binding site detection + Active site prediction + Ligand-binding site prediction + + + Protein binding site prediction - + - - Protein quaternary structure prediction - - 1.4 - Predict the structure of a multi-subunit protein and particularly how the subunits fit together. - - + + + + + + + + + beta12orEarlier + Generate a physical DNA map (sequence map) from analysis of sequence tagged sites (STS). + Sequence mapping + + + An STS is a short subsequence of known sequence and location that occurs only once in the chromosome or genome that is being mapped. Sources of STSs include 1. expressed sequence tags (ESTs), simple sequence length polymorphisms (SSLPs), and random genomic sequences from cloned genomic DNA or database sequences. + Sequence tagged site (STS) mapping - + - - Protein surface analysis - - 1.4 - Analyse the surface properties of proteins. - - - - - - - - - - Ontology comparison - - 1.4 - Compare two or more ontologies, e.g. identify differences. - - + + + + + + + + + + beta12orEarlier + Compare two or more entities, typically the sequence or structure (or derivatives) of macromolecules, to identify equivalent subunits. + Alignment construction + Alignment generation + + + Alignment - + - - Ontology comparison - - 1.4 - Compare two or more ontologies, e.g. identify differences. - - + + + + beta12orEarlier + Calculate the molecular weight of a protein (or fragments) and compare it to another protein or reference data. Generally used for protein identification. + PMF + Peptide mass fingerprinting + Protein fingerprinting + + + Protein fragment weight comparison - + - - Format detection - + + - - + + + beta12orEarlier + Compare the physicochemical properties of two or more proteins (or reference data). + + + Protein property comparison + + + + + + + + - - + + - Recognition of which format the given data is in. - 1.4 - Format identification - Format recognition - 'Format recognition' is not a bioinformatics-specific operation, but of great relevance in bioinformatics. Should be removed from EDAM if/when captured satisfactorily in a suitable domain-generic ontology. - Format inference - - - + beta12orEarlier + Compare two or more molecular secondary structures. + + + Secondary structure comparison - - The has_input "Data" (data_0006) may cause visualisation or other problems although ontologically correct. But on the other hand it may be useful to distinguish from nullary operations without inputs. - - - - - + - - Splitting - - File splitting - Split a file containing multiple data items into many files, each containing one item - 1.4 - - + + + beta12orEarlier + 1.12 + Generate a Hopp and Woods plot of antigenicity of a protein. + + + Hopp and Woods plotting + true - + - - Generation - - Construction - beta12orEarlier - For non-analytical operations, see the 'Processing' branch. - Construct some data entity. - - + + + beta12orEarlier + Visualise gene clusters with gene names. + + + Microarray cluster textual view generation - + - - Nucleic acid sequence feature detection - - - Nucleic acid site prediction - Predict, recognise and identify functional or other key sites within nucleic acid sequences, typically by scanning for known motifs, patterns and regular expressions. - Nucleic acid site recognition - 1.6 - Nucleic acid site detection - - + + + beta12orEarlier + Visualise clustered gene expression data as a set of waves, where each wave corresponds to a gene across samples on the X-axis. + Microarray cluster temporal graph rendering + Microarray wave graph rendering + + + This view can be rendered as a pie graph. The distance matrix is sorted by cluster number and typically represented as a diagonal matrix with distance values displayed in different color shades. + Microarray wave graph plotting - + - - Deposition - - Deposit some data in a database. - 1.6 - Database submission - Submission - Data submission - Data deposition - Database deposition - For non-analytical operations, see the 'Processing' branch. - - + + + beta12orEarlier + Generate a dendrograph of raw, preprocessed or clustered microarray data. + Microarray checks view rendering + Microarray view rendering + Microarray dendrograph rendering + + + Microarray dendrograph plotting - + - - Clustering - - 1.6 - Group together some data entities on the basis of similarities such that entities in the same group (cluster) are more similar to each other than to those in other groups (clusters). - - + + + beta12orEarlier + Generate a plot of distances (distance matrix) between genes. + Microarray distance map rendering + Microarray proximity map rendering + + + Microarray proximity map plotting - + - - Assembly - - XXX - 1.6 - - + + + beta12orEarlier + Visualise clustered gene expression data using a gene tree, array tree and color coded band of gene expression. + Microarray matrix tree plot rendering + Microarray 2-way dendrogram rendering + + + Microarray tree or dendrogram rendering - + - - Conversion - - 1.6 - Non-analytical data conversion. - - + + + beta12orEarlier + Generate a line graph drawn as sum of principal components (Eigen value) and individual expression values. + Microarray principal component rendering + + + Microarray principal component plotting - + - - Standardization and normalization - - 1.6 - Standardize or normalize data. - - + + + beta12orEarlier + Generate a scatter plot of microarray data, typically after principal component analysis. + Microarray scatter plot rendering + + + Microarray scatter plot plotting - + - - Aggregation - - Combine multiple files or data items into a single file or object. - 1.6 - - + + + beta12orEarlier + Visualise gene expression data where each band (or line graph) corresponds to a sample. + Whole microarray graph rendering + + + Whole microarray graph plotting - + - - Article comparison - - Compare two or more scientific articles. - 1.6 - - + + + beta12orEarlier + Visualise gene expression data after hierarchical clustering for representing hierarchical relationships. + + + Microarray tree-map rendering - + - - Calculation - - Mathemetical determination of the value of something, typically a properly of a molecule. - 1.6 - - + + + beta12orEarlier + Visualise raw and pre-processed gene expression data, via a plot showing over- and under-expression along with mean, upper and lower quartiles. + + + Microarray Box-Whisker plot plotting - + - - Pathway or network prediction - - - 1.6 - Predict a molecular pathway or network. - - + + + + + + + + + + + + + + + beta12orEarlier + Generate a physical (sequence) map of a DNA sequence showing the physical distance (base pairs) between features or landmarks such as restriction sites, cloned DNA fragments, genes and other genetic markers. + + + Physical mapping - + - - Genome assembly - - 1.6 - The process of assembling many short DNA sequences together such thay they represent the original chromosomes from which the DNA originated. - - + + + beta12orEarlier + Apply analytical methods to existing data of a specific type. + + + This excludes non-analytical methods that read and write the same basic type of data (for that, see 'Data handling'). + Analysis - + - - Plotting - - Generate a graph, or other visual representation, of data, showing the relationship between two or more variables. - 1.6 - - + + + beta12orEarlier + + Process or analyse an alignment of molecular sequences or structures. + + Alignment analysis + 1.8 + true - + - - Image analysis - - - - - - - - 1.7 - The analysis of a image (typically a digital image) of some type in order to extract information from it. - - - + + + beta12orEarlier + 1.16 + + + Analyse a body of scientific text (typically a full text article from a scientific journal.) + + Article analysis + true - + - - Diffraction data analysis - - 1.7 - Analysis of data from a diffraction experiment. - - + + + beta12orEarlier + beta13 + + Analyse the interactions of two or more molecules (or parts of molecules) that are known to interact. + + Molecular interaction analysis + true - + - - Cell migration analysis - + + - - + + - 1.7 - Analysis of cell migration images in order to study cell migration, typically in order to study the processes that play a role in the disease progression. - - - - - - - - - - Diffraction data reduction - - 1.7 - Processing of diffraction data into a corrected, ordered, and simplified form. - - - - - - - - - - Neurite measurement - - - + + - Measurement of neurites; projections (axons or dendrites) from the cell body of a neuron, from analysis of neuron images. - 1.7 - - - - - - - - - - Diffraction data integration - - 1.7 - Diffraction summation integration - Diffraction profile fitting - The evaluation of diffraction intensities and integration of diffraction maxima from a diffraction experiment. - - + beta12orEarlier + Analyse known protein-protein, protein-DNA/RNA or protein-ligand interactions. + + + Protein interaction analysis - + - - Phasing - - Phase a macromolecular crystal structure, for example by using molecular replacement or experimental phasing methods. - 1.7 - - + + + beta12orEarlier + WHATIF: HETGroupNames + WHATIF:HasMetalContacts + WHATIF:HasMetalContactsPlus + WHATIF:HasNegativeIonContacts + WHATIF:HasNegativeIonContactsPlus + WHATIF:HasNucleicContacts + WHATIF:ShowDrugContacts + WHATIF:ShowDrugContactsShort + WHATIF:ShowLigandContacts + WHATIF:ShowProteiNucleicContacts + Calculate contacts between residues, or between residues and other groups, in a protein structure, on the basis of distance calculations. + HET group detection + Residue contact calculation (residue-ligand) + Residue contact calculation (residue-metal) + Residue contact calculation (residue-negative ion) + Residue contact calculation (residue-nucleic acid) + WHATIF:SymmetryContact + + + This includes identifying HET groups, which usually correspond to ligands, lipids, but might also (not consistently) include groups that are attached to amino acids. Each HET group is supposed to have a unique three letter code and a unique name which might be given in the output. It can also include calculation of symmetry contacts, i.e. a contact between two atoms in different asymmetric unit. + Residue distance calculation - + - - Molecular replacement - - 1.7 - A technique used to construct an atomic model of an unknown structure from diffraction data, based upon an atomic model of a known structure, either a related protein or the same protein from a different crystal form. - The technique solves the phase problem, i.e. retrieve information concern phases of the structure. - - + + + beta12orEarlier + 1.6 + + + Process (read and / or write) an alignment of two or more molecular sequences, structures or derived data. + + Alignment processing + true - + - - Rigid body refinement - - 1.7 - Rigid body refinement usually follows molecular replacement in the assignment of a structure from diffraction data. - A method used to refine a structure by moving the whole molecule or parts of it as a rigid unit, rather than moving individual atoms. - - + + + beta12orEarlier + 1.6 + + Process (read and / or write) a molecular tertiary (3D) structure alignment. + + Structure alignment processing + true - + - - Single particle analysis - - + + - - + + - An image processing technique that combines and analyze multiple images of a particulate sample, in order to produce an image with clearer features that are more easily interpreted. - 1.7 - Single particle analysis is used to improve the information that can be obtained by relatively low resolution techniques, , e.g. an image of a protein or virus from transmission electron microscopy (TEM). - - - - - - - - - - Single particle alignment and classification - - - Compare (align and classify) multiple particle images from a micrograph in order to produce a representative image of the particle. - 1.7 - A micrograph can include particles in multiple different orientations and/or conformations. Particles are compared and organised into sets based on their similarity. Typically iterations of classification and alignment and are performed to optimise the final image; average images produced by classification are used as a reference image for subsequent alignment of the whole image set. - - + beta12orEarlier + Calculate codon usage bias. + + + Codon usage bias calculation - + - - Functional clustering - + + + - - + + - 1.7 - Clustering of molecular sequences on the basis of their function, typically using information from an ontology of gene function, or some other measure of functional phenotype. - Functional sequence clustering - - - - - - - - - - Taxonomic classification - - 1.7 - Classifiication of molecular sequences by assignment to some taxonomic hierarchy. - - + beta12orEarlier + Generate a codon usage bias plot. + + + Codon usage bias plotting - + - - Virulence prediction - - + + - - + + - Pathogenicity prediction - The prediction of the degree of pathogenicity of a microorganism from analysis of molecular sequences. - 1.7 - - + beta12orEarlier + Calculate the differences in codon usage fractions between two sequences, sets of sequences, codon usage tables etc. + + + Codon usage fraction calculation - + - - Gene expression correlation analysis - - - 1.7 - Gene co-expression network analysis - Analyse the correlation patterns among genes across across a variety of experiments, microarray samples etc. - - - + + + beta12orEarlier + Assign molecular sequences, structures or other biological data to a specific group or category according to qualities it shares with that group or category. + + + Classification - + - - RNA structure covariance model generation - - - - - - - - - Compute the covariance model for (a family of) RNA secondary structures. - 1.7 - - + + + beta12orEarlier + beta13 + + Process (read and / or write) molecular interaction data. + + Molecular interaction data processing + true - + - - RNA secondary structure prediction (shape-based) - - RNA shape prediction - Predict RNA secondary structure by analysis, e.g. probabilistic analysis, of the shape of RNA folds. - 1.7 - - + + + + beta12orEarlier + Assign molecular sequence(s) to a group or category. + + + Sequence classification - + - - Nucleic acid alignment folding prediction (alignment-based) - - 1.7 - Prediction of nucleic-acid folding using sequence alignments as a source of data. - - + + + + beta12orEarlier + Assign molecular structure(s) to a group or category. + + + Structure classification - + - - k-mer counting - - Count k-mers (substrings of length k) in DNA sequence data. - 1.7 - k-mer counting is used in genome and transcriptome assembly, metagenomic sequencing, and for error correction of sequence reads. - - + + + beta12orEarlier + Compare two or more proteins (or some aspect) to identify similarities. + + + Protein comparison - + - - Phylogenetic tree reconstruction - - - - - - - - Reconstructing the inner node labels of a phylogenetic tree from its leafes. - Note that this is somewhat different from simply analysing an existing tree or constructing a completely new one. - 1.7 - - + + + beta12orEarlier + Compare two or more nucleic acids to identify similarities. + + + Nucleic acid comparison - + - - Probabilistic data generation - - Generate some data from a choosen probibalistic model, possibly to evaluate algorithms. - 1.7 - - + + + beta12orEarlier + Predict, recognise, detect or identify some properties of proteins. + + + Prediction and recognition (protein) - + - - Probabilistic sequence generation - - - 1.7 - Generate sequences from some probabilistic model, e.g. a model that simulates evolution. - - + + + beta12orEarlier + Predict, recognise, detect or identify some properties of nucleic acids. + + + Prediction and recognition (nucleic acid) - + - - Antimicrobial resistance prediction - - + + - - + + - 1.7 - Identify or predict causes for antibiotic resistance from molecular sequence analysis. - - + beta13 + Edit, convert or otherwise change a molecular tertiary structure, either randomly or specifically. + + + Structure editing - + - - Enrichment - - - - - - - - - A relevant ontology will be used. The input is typically a set of identifiers or other data, and the output of the analysis is typically a ranked list of ontology terms, each associated with a p-value. - Term enrichment - 1.8 - Analyse a dataset with respect to concepts from an ontology. - - + + + beta13 + Edit, convert or otherwise change a molecular sequence alignment, either randomly or specifically. + + + Sequence alignment editing - + - - Chemical class enrichment - - + + + - - + + - 1.8 - Analyse a dataset with respect to concepts from an ontology of chemical structure. - - + beta13 + Render (visualise) a biological pathway or network. + Pathway or network rendering + + + Pathway or network visualisation - + - - Incident curve plotting - - 1.8 - Plot an incident curve such as a survival curve, death curve, mortality curve. - - + + + beta13 + 1.6 + + Predict general (non-positional) functional properties of a protein from analysing its sequence. + + For functional properties that are positional, use 'Protein site detection' instead. + Protein function prediction (from sequence) + true - + - - Variant pattern analysis - - Methods often utilise a database of aligned reads. - Identify and map patterns of genomic variations. - 1.8 - - + + + + + beta13 + Predict, recognise and identify functional or other key sites within protein sequences, typically by scanning for known motifs, patterns and regular expressions. + Protein site detection + Sequence feature detection (protein) + Protein secondary database search + Protein site prediction + Protein site recognition + Sequence profile database search + + + Protein sequence feature detection - + - - Mathematical modelling - - Model some biological system using mathematical techniques including dynamical systems, statistical models, differential equations, and game theoretic models. - beta12orEarlier - - + + + + beta13 + Calculate (or predict) physical or chemical properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence. + + + Protein property calculation (from sequence) - + - - Topic - - - - - - http://purl.org/biotop/biotop.owl#Quality - http://bioontology.org/ontologies/ResearchArea.owl#Area_of_Research - http://www.onto-med.de/ontologies/gfo.owl#Category - http://www.ifomis.org/bfo/1.1/snap#Quality - http://www.onto-med.de/ontologies/gfo.owl#Perpetuant - A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other. - http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality - beta12orEarlier - http://www.ifomis.org/bfo/1.1/snap#Continuant - sumo:FieldOfStudy - http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Method - - + + + beta13 + 1.6 + + Predict, recognise and identify positional features in proteins from analysing protein structure. + + Protein feature prediction (from structure) + true - + - - Nucleic acids - - Nucleic acid bioinformatics - Nucleic acid analysis - Nucleic acid informatics - http://purl.bioontology.org/ontology/MSH/D017423 - Nucleic acid properties - Nucleic acid physicochemistry - http://purl.bioontology.org/ontology/MSH/D017422 - beta12orEarlier - Topic concerning the processing and analysis of nucleic acid sequence, structural and other data. - - + + + + + + + + + + + + + + + + beta13 + Predict, recognise and identify positional features in proteins from analysing protein sequences or structures. + Protein feature prediction + Protein feature recognition + + + Features includes functional sites or regions, secondary structure, structural domains and so on. Methods might use fingerprints, motifs, profiles, hidden Markov models, sequence alignment etc to provide a mapping of a query protein sequence to a discriminatory element. This includes methods that search a secondary protein database (Prosite, Blocks, ProDom, Prints, Pfam etc.) to assign a protein sequence(s) to a known protein family or group. + + Protein feature detection - + - - Proteins - - Topic concerning archival, processing and analysis of protein data, typically molecular sequence and structural data. - Protein bioinformatics - Protein informatics - Protein databases - Protein analysis - http://purl.bioontology.org/ontology/MSH/D020539 - beta12orEarlier - - + + + beta13 + 1.6 + + Screen a molecular sequence(s) against a database (of some type) to identify similarities between the sequence and database entries. + + Database search (by sequence) + true - + - - Metabolites - - Metabolite structures - Topic concerning the structures of reactants or products of metabolism, for example small molecules such as including vitamins, polyols, nucleotides and amino acids. - This concept excludes macromolecules such as proteins and nucleic acids. - beta12orEarlier - - + + + + + + + + + + + + + + + beta13 + Predict a network of protein interactions. + + + Protein interaction network prediction - + - - Sequence analysis - - beta12orEarlier - Sequence databases - Sequences - http://purl.bioontology.org/ontology/MSH/D017421 - BioCatalogue:Sequence Analysis - Topic concerning the archival, processing and analysis of molecular sequences (monomer composition of polymers) including molecular sequence data resources, sequence sites, alignments, motifs and profiles. - - - + + + + beta13 + Design (or predict) nucleic acid sequences with specific chemical or physical properties. + + + Nucleic acid design - + - - Structure analysis - - Computational structural biology - Topic concerning the curation, processing and analysis of the structure of biological molecules, typically proteins and nucleic acids and other macromolecules. - http://purl.bioontology.org/ontology/MSH/D015394 - Structure analysis - Structural bioinformatics - Structure databases - This includes related concepts such as structural properties, alignments and structural motifs. - Structure data resources - beta12orEarlier - - - + + + beta13 + Edit a data entity, either randomly or specifically. + + + Editing - + - - Structure prediction - - Topic concerning the prediction of molecular (secondary or tertiary) structure. - beta12orEarlier - - + + + + + + + + + + + + + + + + + + + + + + 1.1 + Evaluate a DNA sequence assembly, typically for purposes of quality control. + Assembly QC + Assembly quality evaluation + Sequence assembly QC + Sequence assembly quality evaluation + + + Sequence assembly validation - + - - Alignment - - beta12orEarlier - true - Topic concerning the alignment (equivalence between sites) of molecular sequences, structures or profiles (representing a sequence or structure alignment). - beta12orEarlier - - - + + + 1.1 + Align two or more (tpyically huge) molecular sequences that represent genomes. + Genome alignment construction + + + Genome alignment - + - - Phylogeny - - Phylogeny reconstruction - Phylogenetic stratigraphy - beta12orEarlier - BioCatalogue:Tree Inference - Phylogenetic dating - Phylogenetic clocks - Topic concerning the study of evolutionary relationships amongst organisms. - http://purl.bioontology.org/ontology/MSH/D010802 - Phylogenetic simulation - BioCatalogue:Phylogeny - This includes diverse phylogenetic methods, including phylogenetic tree construction, typically from molecular sequence or morphological data, methods that simulate DNA sequence evolution, a phylogenetic tree or the underlying data, or which estimate or use molecular clock and stratigraphic (age) data, methods for studying gene evolution etc. - BioCatalogue:Evolutionary Distance Measurements - - - + + + 1.1 + Reconstruction of a sequence assembly in a localised area. + + + Localised reassembly - + - - Functional genomics - - - beta12orEarlier - Topic concerning the study of gene or protein functions and their interactions in totality in a given organism, tissue, cell etc. - BioCatalogue:Functional Genomics - - - + + + 1.1 + Render and visualise a DNA sequence assembly. + Assembly rendering + Assembly visualisation + Sequence assembly rendering + + + Sequence assembly visualisation - + - - Ontology and terminology - - BioCatalogue:Ontology - Terminology - beta12orEarlier - http://purl.bioontology.org/ontology/MSH/D002965 - Applied ontology - Ontology - Topic concerning the conceptualisation, categorisation and nomenclature (naming) of entities or phenomena within biology or bioinformatics. This includes formal ontologies, controlled vocabularies, structured glossary, symbols and terminology or other related resource. - BioCatalogue:Ontology Lookup - Ontologies - - - + + + + + + + + + 1.1 + Identify base (nucleobase) sequence from a fluorescence 'trace' data generated by an automated DNA sequencer. + Base calling + Phred base calling + Phred base-calling + + + Base-calling - + - - Data search, query and retrieval - - beta12orEarlier - Data retrieval - This includes, for example, search, query and retrieval of molecular sequences and associated data. - Data search - BioCatalogue:Identifier Retrieval - BioCatalogue:Data Retrieval - BioCatalogue:Sequence Retrieval - BioCatalogue:Image Retrieval - BioCatalogue:Structure Retrieval - Topic concerning the search and query of data sources (typically biological databases or ontologies) in order to retrieve entries or other information. - Data query - - + + + 1.1 + The mapping of methylation sites in a DNA (genome) sequence. + Bisulfite sequence alignment + Bisulfite sequence mapping + + + Bisulfite mapping follows high-throughput sequencing of DNA which has undergone bisulfite treatment followed by PCR amplification; unmethylated cytosines are specifically converted to thymine, allowing the methylation status of cytosine in the DNA to be detected. + Bisulfite mapping - + - - Bioinformatics - - - This includes data processing in general, including basic handling of files and databases, datatypes, workflows and annotation. - http://purl.bioontology.org/ontology/MSH/D016247 - Topic concerning the archival, curation, processing and analysis of complex biological data. - beta12orEarlier - - - + + + + + + + + + beta12orEarlier + Identify and filter a (typically large) sequence data set to remove sequences from contaminants in the sample that was sequenced. + + + Sequence contamination filtering - + - - Data visualisation - - Data rendering - Topic for the rendering (drawing on a computer screen) or visualisation of molecular sequences, structures or other biomolecular data. - Data rendering and visualisation - beta12orEarlier - - + + + 1.1 + 1.12 + Trim sequences (typically from an automated DNA sequencer) to remove misleading ends. + + + For example trim polyA tails, introns and primer sequence flanking the sequence of amplified exons, or other unwanted sequence. + Trim ends + true - + - - Nucleic acid thermodynamics - - Topic concerning the study of the thermodynamic properties of a nucleic acid. + + + 1.1 + 1.12 + Trim sequences (typically from an automated DNA sequencer) to remove sequence-specific end regions, typically contamination from vector sequences. + + + Trim vector true - 1.3 - - - + - - Nucleic acid structure analysis - - Includes secondary and tertiary nucleic acid structural data, nucleic acid thermodynamic, thermal and conformational properties including DNA or DNA/RNA denaturation (melting) etc. - DNA melting - Nucleic acid denaturation - RNA alignment - Topic concerning the archival, curation, processing and analysis of nucleic acid structural information, such as whole structures, structural features and alignments, and associated annotation. - RNA structure alignment - beta12orEarlier - Nucleic acid structure - Nucleic acid thermodynamics - RNA structure - - + + + 1.1 + 1.12 + Trim sequences (typically from an automated DNA sequencer) to remove the sequence ends that extend beyond an assembled reference sequence. + + + Trim to reference + true - + - - RNA - - beta12orEarlier - Topic concerning RNA sequences and structures. - - + + + 1.1 + Cut (remove) the end from a molecular sequence. + Trimming + Barcode sequence removal + Trim ends + Trim to reference + Trim vector + + + This includes + +ennd trimming +Trim sequences (typically from an automated DNA sequencer) to remove misleading ends. +For example trim polyA tails, introns and primer sequence flanking the sequence of amplified exons, or other unwanted sequence. + +trimming to a reference sequence, +Trim sequences (typically from an automated DNA sequencer) to remove the sequence ends that extend beyond an assembled reference sequence. + +vector trimming +Trim sequences (typically from an automated DNA sequencer) to remove sequence-specific end regions, typically contamination from vector sequences. + + Sequence trimming - + - - Nucleic acid restriction - - 1.3 - beta12orEarlier - Topic for the study of restriction enzymes, their cleavage sites and the restriction of nucleic acids. - true - - + + + 1.1 + Compare the features of two genome sequences. + + + Genomic elements that might be compared include genes, indels, single nucleotide polymorphisms (SNPs), retrotransposons, tandem repeats and so on. + Genome feature comparison - + - - Mapping - - Topic concerning the mapping of complete (typically nucleotide) sequences. - Genetic linkage - Linkage - Linkage mapping - Synteny - DNA mapping - beta12orEarlier - This includes resources that aim to identify, map or analyse genetic markers in DNA sequences, for example to produce a genetic (linkage) map of a chromosome or genome or to analyse genetic linkage and synteny. It also includes resources for physical (sequence) maps of a DNA sequence showing the physical distance (base pairs) between features or landmarks such as restriction sites, cloned DNA fragments, genes and other genetic markers. - - + + + + + + + + + beta12orEarlier + Detect errors in DNA sequences generated from sequencing projects). + Short read error correction + Short-read error correction + + + Sequencing error detection - + - - Genetic codes and codon usage - - beta12orEarlier - true - Topic concerning the study of codon usage in nucleotide sequence(s), genetic codes and so on. - 1.3 - Codon usage analysis - - + + + 1.1 + Analyse DNA sequence data to identify differences between the genetic composition (genotype) of an individual compared to other individual's or a reference sequence. + + + Methods might consider cytogenetic analyses, copy number polymorphism (and calculate copy number calls for copy-number variation(CNV) regions), single nucleotide polymorphism (SNP), , rare copy number variation (CNV) identification, loss of heterozygosity data and so on. + Genotyping - + - - Protein expression - - Translation - Topic concerning the translation of mRNA into protein and subsequent protein processing in the cell. - beta12orEarlier - - - + + + + 1.1 + Analyse a genetic variation, for example to annotate its location, alleles, classification, and effects on individual transcripts predicted for a gene model. + Genetic variation annotation + Sequence variation analysis + + + Genetic variation annotation provides contextual interpretation of coding SNP consequences in transcripts. It allows comparisons to be made between variation data in different populations or strains for the same transcript. + Genetic variation analysis - + - - Gene finding - - beta12orEarlier - Gene prediction - true - 1.3 - This includes the study of promoters, coding regions, splice sites, etc. Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc. - Topic that aims to identify, predict, model or analyse genes or gene structure in DNA sequences. - Gene discovery - BioCatalogue:Gene Prediction - - + + + + 1.1 + Align short oligonucleotide sequences (reads) to a larger (genomic) sequence. + Oligonucleotide alignment + Oligonucleotide alignment construction + Oligonucleotide alignment generation + Oligonucleotide mapping + Read alignment + Short oligonucleotide alignment + Short read alignment + Short read mapping + Short sequence read mapping + + + The purpose of read mapping is to identify the location of sequenced fragments within a reference genome and assumes that there is, in fact, at least local similarity between the fragment and reference sequences. + Read mapping - + - - Transcription - - 1.3 - Topic concerning the transcription of DNA into mRNA. - beta12orEarlier - true - - + + + 1.1 + A varient of oligonucleotide mapping where a read is mapped to two separate locations because of possible structural variation. + + + Split read mapping - + - - Promoters - - true - beta12orEarlier - BioCatalogue:Promoter Prediction - Topic concerning promoters in DNA sequences (region of DNA that facilitates the transcription of a particular gene by binding RNA polymerase and transcription factor proteins). - beta13 - - + + + 1.1 + Analyse DNA sequences in order to identify a DNA 'barcode'; marker genes or any short fragment(s) of DNA that are useful to diagnose the taxa of biological organisms. + Sample barcoding + DNA barcoding + + + Community profiling - + - - Nucleic acid folding - - beta12orEarlier - true - Topic concerning the folding (in 3D space) of nucleic acid molecules. - beta12orEarlier - - + + + 1.1 + Identify single nucleotide change in base positions in sequencing data that differ from a reference genome and which might, especially by reference to population frequency or functional data, indicate a polymorphism. + + + Operations usually score confidence in the prediction or some other statistical measure of evidence. + SNP calling - + - - Gene structure - - - This includes the study of promoters, coding regions etc. - beta12orEarlier - Gene features - Topic concerning gene structure, regions which make an RNA product and features such as promoters, coding regions, gene fusion, splice sites etc. - - - + + + 1.1 + Detect mutations in multiple DNA sequences, for example, from the alignment and comparison of the fluorescent traces produced by DNA sequencing hardware. + Polymorphism detection + Mutation detection + + + Polymorphism detection - + - - Proteomics - - beta12orEarlier - Protein and peptide identification - Peptide identification - Proteomics includes any methods (especially high-throughput) that separate, characterize and identify expressed proteins such as mass spectrometry, two-dimensional gel electrophoresis and protein microarrays, as well as in-silico methods that perform proteolytic or mass calculations on a protein sequence and other analyses of protein expression data, for example in different cells or tissues. - http://purl.bioontology.org/ontology/MSH/D040901 - Topic concerning protein and peptide identification, especially in the study of whole proteomes of organisms. - Protein expression - BioCatalogue:Proteomics - - - + + + 1.1 + Visualise, format or render an image of a Chromatogram. + Chromatogram viewing + + + Chromatogram visualisation - + - - Structural genomics - - - BioCatalogue:Structural Genomics - beta12orEarlier - Topic concerning the elucidation of the three dimensional structure for all (available) proteins in a given organism. - - - + + + 1.1 + Determine cytosine methylation states in nucleic acid sequences. + + + Methylation analysis - + - - Protein properties - - Topic concerning the study of the physical and biochemical properties of peptides and proteins, for example the hydrophobic, hydrophilic and charge properties of a protein. - Protein hydropathy - Protein physicochemistry - beta12orEarlier - - + + + + 1.1 + Determine cytosine methylation status of specific positions in a nucleic acid sequences. + + + Methylation calling - + - - Protein interactions - - - Protein-nucleic acid interactions - Protein-RNA interaction - This includes experimental (e.g. yeast two-hybrid) and computational analysis techniques. - Protein-protein interactions - Protein-ligand interactions - beta12orEarlier - Protein-DNA interaction - BioCatalogue:Ligand Interaction - Topic concerning protein-protein, protein-DNA/RNA and protein-ligand interactions, including analysis of known interactions and prediction of putative interactions. - BioCatalogue:Protein Interaction - - + + + 1.1 + Measure the overall level of methyl cytosines in a genome from analysis of experimental data, typically from chromatographic methods and methyl accepting capacity assay. + Global methylation analysis + + + Methylation level analysis (global) - + - - Protein folding, stability and design - - Topic concerning protein stability, folding (in 3D space) and protein sequence-structure-function relationships. This includes for example study of inter-atomic or inter-residue interactions in protein (3D) structures, the effect of mutation, and the design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein. - Protein folding - Protein stability - beta12orEarlier - Protein residue interactions - Protein design - Rational protein design - - + + + 1.1 + Measure the level of methyl cytosines in specific genes. + Gene-specific methylation analysis + + + Many different techniques are available for this. + Methylation level analysis (gene-specific) - + - - Two-dimensional gel electrophoresis - - Topic concerning two-dimensional gel electrophoresis image and related data. - beta13 - beta12orEarlier - true - - + + + 1.1 + Visualise, format or render a nucleic acid sequence that is part of (and in context of) a complete genome sequence. + Genome browser + Genome browsing + Genome rendering + Genome viewing + + + Genome visualisation - + - - Mass spectrometry - - beta12orEarlier - Topic concerning an analytical chemistry technique that measures the mass-to-charge ratio and abundance of irons in the gas phase. - - - + + + 1.1 + Compare the sequence or features of two or more genomes, for example, to find matching regions. + Genomic region matching + + + Genome comparison - + - - Protein microarrays - - Topic concerning protein microarray data. - true - beta12orEarlier - beta13 - - + + + + + + + + + 1.1 + Generate an index of a genome sequence. + Burrows-Wheeler + Genome indexing (Burrows-Wheeler) + Genome indexing (suffix arrays) + Suffix arrays + + + Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment. The Burrows-Wheeler Transform (BWT) is a permutation of the genome based on a suffix array algorithm. A suffix array consists of the lexicographically sorted list of suffixes of a genome. + Genome indexing - + - - Protein hydropathy - - Topic for the study of the hydrophobic, hydrophilic and charge properties of a protein. - beta12orEarlier + + + 1.1 + 1.12 + Generate an index of a genome sequence using the Burrows-Wheeler algorithm. + + + The Burrows-Wheeler Transform (BWT) is a permutation of the genome based on a suffix array algorithm. + Genome indexing (Burrows-Wheeler) true - 1.3 - - - + - - Protein targeting and localization - - Protein targeting - Protein sorting - Topic concerning the study of how proteins are transported within and without the cell, including signal peptides, protein subcellular localization and export. - Protein localization - beta12orEarlier - - + + + 1.1 + 1.12 + Generate an index of a genome sequence using a suffix arrays algorithm. + + + A suffix array consists of the lexicographically sorted list of suffixes of a genome. + Genome indexing (suffix arrays) + true - + - - Protein cleavage sites and proteolysis - - true - Topic concerning enzyme or chemical cleavage sites and proteolytic or mass calculations on a protein sequence. - beta12orEarlier - 1.3 - - + + + + + + + + + 1.1 + Analyse one or more spectra from mass spectrometry (or other) experiments. + Mass spectrum analysis + Spectrum analysis + + + Spectral analysis - + - - Protein structure comparison - - Topic concerning the comparison of two or more protein structures. - beta12orEarlier - true - Use this concept for methods that are exclusively for protein structure. - beta12orEarlier - - - + + + + + + + + + 1.1 + Identify peaks in a spectrum from a mass spectrometry, NMR, or some other spectrum-generating experiment. + Peak assignment + Peak finding + + + Peak detection - + - - Protein residue interactions - - The processing and analysis of inter-atomic or inter-residue interactions in protein (3D) structures. - Protein residue interactions - true - 1.3 - beta12orEarlier - - + + + + + + + + + + 1.1 + Link together a non-contiguous series of genomic sequences into a scaffold, consisting of sequences separated by gaps of known length. The sequences that are linked are typically typically contigs; contiguous sequences corresponding to read overlaps. + Scaffold construction + Scaffold generation + + + Scaffold may be positioned along a chromosome physical map to create a "golden path". + Scaffolding - + - - Protein-protein interactions - - Protein interaction networks - true - beta12orEarlier - 1.3 - Topic concerning protein-protein interactions, individual interactions and networks, protein complexes, protein functional coupling etc. - - + + + 1.1 + Fill the gaps in a sequence assembly (scaffold) by merging in additional sequences. + + + Different techniques are used to generate gap sequences to connect contigs, depending on the size of the gap. For small (5-20kb) gaps, PCR amplification and sequencing is used. For large (>20kb) gaps, fragments are cloned (e.g. in BAC (Bacterial artificial chromosomes) vectors) and then sequenced. + Scaffold gap completion - + - - Protein-ligand interactions - - beta12orEarlier - Topic concerning protein-ligand (small molecule) interactions. - true - 1.3 - - + + + + 1.1 + Raw sequence data quality control. + Sequencing QC + + + Analyse raw sequence data from a sequencing pipeline and identify (and possiby fix) problems. + Sequencing quality control - + - - Protein-nucleic acid interactions - - beta12orEarlier - Topic concerning protein-DNA/RNA interactions. - 1.3 - true - - + + + + 1.1 + Pre-process sequence reads to ensure (or improve) quality and reliability. + Sequence read pre-processing + + + For example process paired end reads to trim low quality ends remove short sequences, identify sequence inserts, detect chimeric reads, or remove low quality sequnces including vector, adaptor, low complexity and contaminant sequences. Sequences might come from genomic DNA library, EST libraries, SSH library and so on. + Read pre-processing - + - - Protein design - - 1.3 - beta12orEarlier - Topic concerning the design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein. - true - - + + + + + + + + + 1.1 + Estimate the frequencies of different species from analysis of the molecular sequences, typically of DNA recovered from environmental samples. + + + Species frequency estimation - + - - G protein-coupled receptors (GPCR) - - true - Topic concerning G-protein coupled receptors (GPCRs). - beta12orEarlier - beta12orEarlier - - + + + 1.1 + Identify putative protein-binding regions in a genome sequence from analysis of Chip-sequencing data or ChIP-on-chip data. + Protein binding peak detection + Peak-pair calling + + + Chip-sequencing combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to generate a set of reads, which are aligned to a genome sequence. The enriched areas contain the binding sites of DNA-associated proteins. For example, a transcription factor binding site. ChIP-on-chip in contrast combines chromatin immunoprecipitation ('ChIP') with microarray ('chip'). "Peak-pair calling" is similar to "Peak calling" in the context of ChIP-exo. + Peak calling - + - - Carbohydrates - - beta12orEarlier - Topic concerning carbohydrates, typically including structural information. - - + + + + 1.1 + Identify from molecular sequence analysis (typically from analysis of microarray or RNA-seq data) genes whose expression levels are significantly different between two sample groups. + Differential gene analysis + Differentially expressed gene identification + + + Differential gene expression analysis is used, for example, to identify which genes are up-regulated (increased expression) or down-regulated (decreased expression) between a group treated with a drug and a control groups. + Differential gene expression analysis - + - - Lipids - - beta12orEarlier - Topic concerning lipids and their structures. - - + + + 1.1 + Analyse gene expression patterns (typically from DNA microarray datasets) to identify sets of genes that are associated with a specific trait, condition, clinical outcome etc. + + + Gene sets can be defined beforehand by biological function, chromosome locations and so on. + Gene set testing - + - - Small molecules - - Small molecules include organic molecules, metal-organic compounds, small polypeptides, small polysaccharides and oligonucleotides. Structural data is usually included. - Topic concerning small molecules of biological significance, typically archival, curation, processing and analysis of structural information. - CHEBI:23367 - beta12orEarlier - - + + + + 1.1 + Classify variants based on their potential effect on genes, especially functional effects on the expressed proteins. + + + Variants are typically classified by their position (intronic, exonic, etc.) in a gene transcript and (for variants in coding exons) by their effect on the protein sequence (synonymous, non-synonymous, frameshifting, etc.) + Variant classification - + - - Sequence editing - - beta12orEarlier - true - beta12orEarlier - Edit, convert or otherwise change a molecular sequence, either randomly or specifically. - - - + + + 1.1 + Identify biologically interesting variants by prioritizing individual variants, for example, homozygous variants absent in control genomes. + + + Variant prioritisation can be used for example to produce a list of variants responsible for 'knocking out' genes in specific genomes. Methods amino acid substitution, aggregative approaches, probabilistic approach, inheritance and unified likelihood-frameworks. + Variant prioritisation - + - - Sequence composition, complexity and repeats - - Repeat sequences - beta12orEarlier - Sequence complexity - Low complexity sequences - Sequence repeats - Topic concerning the archival, processing and analysis of the basic character composition of molecular sequences, for example character or word frequency, ambiguity, complexity, particularly regions of low complexity, and repeats or the repetitive nature of molecular sequences. - Sequence composition - BioCatalogue:Repeats - - + + + 1.1 + Identify and map genomic alterations, including single nucleotide polymorphisms, short indels and structural variants, in a genome sequence. + Variant mapping + Allele calling + Germ line variant calling + Somatic variant calling + + + Methods often utilise a database of aligned reads. + Somatic variant calling is the detection of variations established in somatic cells and hence not inherited as a germ line variant. + Variant detection + Variant calling - + - - Sequence motifs - - beta12orEarlier - Motifs - true - 1.3 - Topic concerning conserved patterns (motifs) in molecular sequences, that (typically) describe functional or other key sites. - - + + + 1.1 + Detect large regions in a genome subject to copy-number variation, or other structural variations in genome(s). + + + Methods might involve analysis of whole-genome array comparative genome hybridisation or single-nucleotide polymorphism arrays, paired-end mapping of sequencing data, or from analysis of short reads from new sequencing technologies. + Structural variation discovery - + - - Sequence comparison - - BioCatalogue:Nucleotide Sequence Similarity - The comparison might be on the basis of sequence, physico-chemical or some other properties of the sequences. - beta12orEarlier - BioCatalogue:Protein Sequence Similarity - Topic concerning the comparison of two or more molecular sequences, for example sequence alignment and clustering. - - + + + 1.1 + Anaylse sequencing data from experiments aiming to selectively sequence the coding regions of the genome. + Exome sequence analysis + + + Exome analysis + Exome assembly - + - - Sequence sites, features and motifs - - Sequence features - Functional sites - Sequence motifs - Topic concerning the archival, detection, prediction and analysis of -positional features such as functional and other key sites, in molecular sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them. - Sequence profiles - Sequence sites - HMMs - beta12orEarlier - - + + + 1.1 + Analyse mapping density (read depth) of (typically) short reads from sequencing platforms, for example, to detect deletions and duplications. + + + Read depth analysis - + - - Sequence database search - - beta12orEarlier - Search and retrieve molecular sequences that are similar to a sequence-based query (typically a simple sequence). - beta12orEarlier - true - The query is a sequence-based entity such as another sequence, a motif or profile. - - + + + + + + + + + 1.1 + Combine classical quantitative trait loci (QTL) analysis with gene expression profiling, for example, to describe describe cis- and trans-controlling elements for the expression of phenotype associated genes. + Gene expression QTL profiling + Gene expression quantitative trait loci profiling + eQTL profiling + + + Gene expression QTL analysis - + - - Sequence clustering - - This includes systems that generate, process and analyse sequence clusters. - beta12orEarlier - true - Topic concerning the comparison and grouping together of molecular sequences on the basis of their similarities. - 1.7 - Sequence clusters - - + + + 1.1 + Estimate the number of copies of loci of particular gene(s) in DNA sequences typically from gene-expression profiling technology based on microarray hybridisation-based experiments. For example, estimate copy number (or marker dosage) of a dominant marker in samples from polyploid plant cells or tissues, or chromosomal gains and losses in tumors. + Transcript copy number estimation + + + Methods typically implement some statistical model for hypothesis testing, and methods estimate total copy number, i.e. do not distinguish the two inherited chromosomes quantities (specific copy number). + Copy number estimation - + - - Protein structural motifs and surfaces - - - This includes conformation of conserved substructures, conserved geometry (spatial arrangement) of secondary structure or protein backbone, solvent-exposed surfaces, internal cavities, the analysis of shape, hydropathy, electrostatic patches, role and functions etc. - Protein structural features - Structural motifs - Protein 3D motifs - Topic concerning (3D) structural features or common 3D motifs within protein structures, including the surface of a protein structure, such as biological interfaces with other molecules. - beta12orEarlier - Protein structural motifs - Protein surfaces - - + + + 1.2 + Adapter removal + Remove forward and/or reverse primers from nucleic acid sequences (typically PCR products). + + + Primer removal - + - - Structural (3D) profiles - - The processing, analysis or use of some type of structural (3D) profile or template; a computational entity (typically a numerical matrix) that is derived from and represents a structure or structure alignment. - true - beta12orEarlier - 1.3 - Structural profiles - - + + + + + + + + + + + + + + + 1.2 + Infer a transcriptome sequence by analysis of short sequence reads. + + + Transcriptome assembly - + - - Protein structure prediction - - - beta12orEarlier - Topic concerning the prediction, modelling, recognition or design of protein secondary or tertiary structure or other structural features. - BioCatalogue:Protein Structure Prediction - - + + + 1.2 + 1.6 + + Infer a transcriptome sequence without the aid of a reference genome, i.e. by comparing short sequences (reads) to each other. + de novo transcriptome assembly + + Transcriptome assembly (de novo) + true - + - - Nucleic acid structure prediction - - - DNA structure prediction - Nucleic acid design - RNA structure prediction - beta12orEarlier - Nucleic acid folding - Topic concerning the folding of nucleic acid molecules and the prediction or design of nucleic acid (typically RNA) sequences with specific conformations. - - + + + 1.2 + 1.6 + + Infer a transcriptome sequence by mapping short reads to a reference genome. + + Transcriptome assembly (mapping) + true - + - - Ab initio structure prediction - - 1.7 - Topic concerning the prediction of three-dimensional structure of a (typically protein) sequence from first principles, using a physics-based or empirical scoring function and without using explicit structural templates. - true - beta12orEarlier - - + + + + + + + + + + + + + + + 1.3 + Convert one set of sequence coordinates to another, e.g. convert coordinates of one assembly to another, cDNA to genomic, CDS to genomic, protein translation to genomic etc. + + + Sequence coordinate conversion - + - - Homology modelling - - 1.4 - true - beta12orEarlier - Topic concerning the modelling of the three-dimensional structure of a protein using known sequence and structural data. - - + + + 1.3 + Calculate similarity between 2 or more documents. + + + Document similarity calculation - + - - Molecular dynamics - - This includes resources concerning flexibility and motion in protein and other molecular structures. - Topic concerning the simulation of molecular (typically protein) conformation using a computational model of physical forces and computer simulation. - Molecular flexibility - Molecular motions - beta12orEarlier - - + + + + 1.3 + Cluster (group) documents on the basis of their calculated similarity. + + + Document clustering + - + - - Molecular docking - - beta12orEarlier - Topic concerning the modelling the structure of proteins in complex with small molecules or other macromolecules. - - + + + 1.3 + Recognise named entities, ontology concepts, tags, events, and dictionary terms within documents. + Concept mining + Entity chunking + Entity extraction + Entity identification + Event extraction + Named-entity recognition + + + Named-entity and concept recognition + + - + - - Protein secondary structure prediction - - Topic concerning the prediction of secondary or supersecondary structure of protein sequences. - beta12orEarlier - 1.3 - true - - - + + + + 1.3 + Map data identifiers to one another for example to establish a link between two biological databases for the purposes of data integration. + Accession mapping + Identifier mapping + + + The mapping can be achieved by comparing identifier values or some other means, e.g. exact matches to a provided sequence. + ID mapping - + - - Protein tertiary structure prediction - - 1.3 - true - beta12orEarlier - Topic concerning the prediction of tertiary structure of protein sequences. - - - + + + 1.3 + Process data in such a way that makes it hard to trace to the person which the data concerns. + Data anonymisation + + + Anonymisation - + - - Protein fold recognition - - For example threading, or the alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment). - Topic concerning the recognition (prediction and assignment) of known protein structural domains or folds in protein sequence(s). - beta12orEarlier - - + + + + + + + + + 1.3 + Search for and retrieve a data identifier of some kind, e.g. a database entry accession. + Accession retrieval + Data retrieval (ID) + Data retrieval (accession) + Data retrieval (id) + Identifier retrieval + id retrieval + + + ID retrieval - + - - Sequence alignment - - This includes the generation of alignments (the identification of equivalent sites), the analysis of alignments, editing, visualisation, alignment databases, the alignment (equivalence between sites) of sequence profiles (representing sequence alignments) and so on. - beta12orEarlier - Topic concerning the alignment of molecular sequences or sequence profiles (representing sequence alignments). - 1.7 - true - - + + + + + + + + + + + + + + + 1.4 + Generate a checksum of a molecular sequence. + + + Sequence checksum generation - + - - Structure alignment - - Topic concerning the superimposition of molecular tertiary structures or structural (3D) profiles (representing a structure or structure alignment). - This includes the generation, storage, analysis, rendering etc. of structure alignments. - true - 1.7 - beta12orEarlier - - + + + + + + + + + 1.4 + Construct a bibliography from the scientific literature. + Bibliography construction + + + Bibliography generation - + - - Threading - - Sequence-structure alignment - 1.3 - Topic concerning the alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment). - beta12orEarlier - true - - + + + 1.4 + Predict the structure of a multi-subunit protein and particularly how the subunits fit together. + + + Protein quaternary structure prediction - + - - Sequence profiles and HMMs - - true - Topic concerning sequence profiles; typically a positional, numerical matrix representing a sequence alignment. - beta12orEarlier - 1.3 - Sequence profiles include position-specific scoring matrix (position weight matrix), hidden Markov models etc. - - + + + + + + + + + + + + + + + 1.4 + Analyse the surface properties of proteins or other macromolecules, including surface accessible pockets, interior inaccessible cavities etc. + + + Molecular surface analysis - + - - Phylogeny reconstruction - - BioCatalogue:Evolutionary Distance Measurements - Topic concerning the reconstruction of a phylogeny (evolutionary relatedness amongst organisms), for example, by building a phylogenetic tree. - 1.3 - true - Currently too specific for the topic sub-ontology (but might be unobsoleted). - beta12orEarlier - BioCatalogue:Tree Inference - - + + + 1.4 + Compare two or more ontologies, e.g. identify differences. + + + Ontology comparison - + - - Phylogenomics - - - beta12orEarlier - Topic concerning the integrated study of evolutionary relationships and whole genome data, for example, in the analysis of species trees, horizontal gene transfer and evolutionary reconstruction. - - - + + + 1.4 + 1.9 + Compare two or more ontologies, e.g. identify differences. + + + Ontology comparison - + - - Virtual PCR - - beta13 - Polymerase chain reaction - beta12orEarlier - PCR - true - Topic concerning simulated polymerase chain reaction (PCR). - - + + + + + + + + + + + + + + + + 1.4 + Recognition of which format the given data is in. + Format identification + Format inference + Format recognition + + + 'Format recognition' is not a bioinformatics-specific operation, but of great relevance in bioinformatics. Should be removed from EDAM if/when captured satisfactorily in a suitable domain-generic ontology. + Format detection + + + + + The has_input "Data" (data_0006) may cause visualisation or other problems although ontologically correct. But on the other hand it may be useful to distinguish from nullary operations without inputs. + - + - - Sequence assembly - - Assembly - Topic concerning the assembly of fragments of a DNA sequence to reconstruct the original sequence. - beta12orEarlier - This covers for example the alignment of sequences of (typically millions) of short reads to a reference genome. - - + + + 1.4 + Split a file containing multiple data items into many files, each containing one item + File splitting + + + Splitting - + - - Genetic variation - - - http://purl.bioontology.org/ontology/MSH/D014644 - DNA variation - Mutation - Polymorphism - beta12orEarlier - Topic concerning stable, naturally occuring mutations in a nucleotide sequence including alleles, naturally occurring mutations such as single base nucleotide substitutions, deletions and insertions, RFLPs and other polymorphisms. - - + + + beta12orEarlier + Construct some data entity. + Construction + + + For non-analytical operations, see the 'Processing' branch. + Generation - + - - Microarrays - - BioCatalogue:Microarrays - true - http://purl.bioontology.org/ontology/MSH/D046228 - 1.3 - Topic concerning microarrays, for example, to process microarray data or design probes and experiments. - DNA microarrays - beta12orEarlier - - + + + + 1.6 + Predict, recognise and identify functional or other key sites within nucleic acid sequences, typically by scanning for known motifs, patterns and regular expressions. + Nucleic acid site detection + Nucleic acid site prediction + Nucleic acid site recognition + + + Nucleic acid sequence feature detection - + - - Pharmacology - - Computational pharmacology - beta12orEarlier - Pharmacoinformatics - Topic concerning the study of drugs and their effects or responses in living systems. - - - + + + 1.6 + Deposit some data in a database or some other type of repository or software system. + Data deposition + Data submission + Database deposition + Database submission + Submission + + + For non-analytical operations, see the 'Processing' branch. + Deposition - + - - Gene expression - - This includes the study of codon usage in nucleotide sequence(s), genetic codes and so on. - BioCatalogue:Microarrays - Gene expression profiling - Expression profiling - beta12orEarlier - Topic concerning the analysis of levels and patterns of synthesis of gene products (proteins and functional RNA) including interpretation in functional terms of gene expression data. - http://edamontology.org/topic_0197 - Gene expression levels are analysed by identifying, quantifying or comparing mRNA transcripts, for example using microarrays, RNA-seq, northern blots, gene-indexed expression profiles etc. - http://purl.bioontology.org/ontology/MSH/D015870 - Gene expression analysis - DNA microarrays - Codon usage - - - + + + 1.6 + Group together some data entities on the basis of similarities such that entities in the same group (cluster) are more similar to each other than to those in other groups (clusters). + + + Clustering - + - - Gene regulation - - Topic concerning primarily the regulation of gene expression. - beta12orEarlier - - + + + 1.6 + Construct some entity (typically a molecule sequence) from component pieces. + + + Assembly - + - - Pharmacogenomics - - - beta12orEarlier - Topic concerning the influence of genotype on drug response, for example by correlating gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity. - - - + + + 1.6 + Convert a data set from one form to another. + + + Conversion - + - - Medicinal chemistry - - - This includes methods that search compound collections, generate or analyse drug 3D conformations, identify drug targets with structural docking etc. - Topic concerning the design and chemical synthesis of bioactive molecules, for example drugs or potential drug compounds, for medicinal purposes. - Drug design - beta12orEarlier - - - + + + 1.6 + Standardize or normalize data by some statistical method. + Normalisation + Standardisation + + + In the simplest normalisation means adjusting values measured on different scales to a common scale (often between 0.0 and 1.0), but can refer to more sophisticated adjustment whereby entire probability distributions of adjusted values are brought into alignment. Standardisation typically refers to an operation whereby a range of values are standardised to measure how many standard deviations a value is from its mean. + Standardisation and normalisation - + - - Fish - - beta12orEarlier - Topic concerning fish, e.g. information on a specific fish genome including molecular sequences, genes and annotation. - true - 1.3 - - + + + 1.6 + Combine multiple files or data items into a single file or object. + + + Aggregation - + - - Flies - - Topic concerning flies, e.g. information on a specific fly genome including molecular sequences, genes and annotation. - 1.3 - true - beta12orEarlier - - + + + + + + + + + 1.6 + Compare two or more scientific articles. + + + Article comparison - + - - Mice or rats - - The resource may be specific to a group of mice / rats or all mice / rats. - true - beta12orEarlier - 1.3 - Topic concerning mice or rats, e.g. information on a specific genome including molecular sequences, genes and annotation. - - + + + 1.6 + Mathemetical determination of the value of something, typically a properly of a molecule. + + + Calculation - + - - Worms - - Topic concerning worms, e.g. information on a specific worm genome including molecular sequences, genes and annotation. - true - 1.3 - beta12orEarlier - - + + + + 1.6 + Predict a molecular pathway or network. + + + Pathway or network prediction - + - - Literature analysis - - beta12orEarlier - 1.3 - The processing and analysis of the bioinformatics literature and bibliographic data, such as literature search and query. + + + 1.6 + 1.12 + The process of assembling many short DNA sequences together such thay they represent the original chromosomes from which the DNA originated. + + + + Genome assembly true - - - + - - Data mining - - Topic concerning the analysis of the biomedical and informatics literature. - beta12orEarlier - Text data mining - Literature analysis - Text mining - Literature mining - - - + + + 1.6 + Generate a graph, or other visual representation, of data, showing the relationship between two or more variables. + + + Plotting - + - - Data deposition, annotation and curation - - Topic concerning the organisation and maintenance of a collection of biological database entries (or other such entities) including the annotation of entries, typically with terms from a controlled vocabulary. - Database curation - beta12orEarlier - - - + + + + + + + + + 1.7 + Image processing + The analysis of a image (typically a digital image) of some type in order to extract information from it. + + + Image analysis - + - - File management - - Routine data management - Topic concerning basic manipulations of files or reports of generic biological data. - beta12orEarlier - This includes editing, reformatting, conversion, transformation, validation, debugging, indexing and so on. - Utility software - - + + + 1.7 + Analysis of data from a diffraction experiment. + + + Diffraction data analysis - + - - Sequence annotation - - beta12orEarlier - beta12orEarlier - true - Annotate a molecular sequence. - - + + + + + + + + + 1.7 + Analysis of cell migration images in order to study cell migration, typically in order to study the processes that play a role in the disease progression. + + + Cell migration analysis - + - - Genome annotation - - beta12orEarlier - true - beta12orEarlier - Annotate a genome. - BioCatalogue:Genome Annotation - - - + + + 1.7 + Processing of diffraction data into a corrected, ordered, and simplified form. + + + Diffraction data reduction - + - - NMR - - - ROESY - NOESY - Nuclear Overhauser Effect Spectroscopy - HOESY - beta12orEarlier - Heteronuclear Overhauser Effect Spectroscopy - Nuclear magnetic resonance spectroscopy - Spectroscopy - NMR spectroscopy - Topic concerning an analytical technique that exploits the magenetic properties of certain atomic nuclei to provide information on the structure, dynamics, reaction state and chemical environment of molecules. - Rotational Frame Nuclear Overhauser Effect Spectroscopy - - - + + + + + + + + + 1.7 + Measurement of neurites; projections (axons or dendrites) from the cell body of a neuron, from analysis of neuron images. + + + Neurite measurement - + - - Sequence classification - - beta12orEarlier - Topic concerning the classification of molecular sequences based on some measure of their similarity. - Methods including sequence motifs, profile and other diagnostic elements which (typically) represent conserved patterns (of residues or properties) in molecular sequences. - - + + + 1.7 + The evaluation of diffraction intensities and integration of diffraction maxima from a diffraction experiment. + Diffraction profile fitting + Diffraction summation integration + + + Diffraction data integration - + - - Protein classification - - 1.3 - true - Topic concerning primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc. - beta12orEarlier - - + + + 1.7 + Phase a macromolecular crystal structure, for example by using molecular replacement or experimental phasing methods. + + + Phasing - + - - Sequence motif or profile - - beta12orEarlier - true - This includes comparison, discovery, recognition etc. of sequence motifs. - beta12orEarlier - Topic concerning sequence motifs, or sequence profiles derived from an alignment of molecular sequences of a particular type. - - - + + + 1.7 + A technique used to construct an atomic model of an unknown structure from diffraction data, based upon an atomic model of a known structure, either a related protein or the same protein from a different crystal form. + + + The technique solves the phase problem, i.e. retrieve information concern phases of the structure. + Molecular replacement - + - - Protein modifications - - GO:0006464 - Topic concerning protein chemical modifications, e.g. post-translational modifications. - Protein post-translational modification - MOD:00000 - EDAM does not describe all possible protein modifications. For fine-grained annotation of protein modification use the Gene Ontology (children of concept GO:0006464) and/or the Protein Modifications ontology (children of concept MOD:00000) - beta12orEarlier - - + + + 1.7 + A method used to refine a structure by moving the whole molecule or parts of it as a rigid unit, rather than moving individual atoms. + + + Rigid body refinement usually follows molecular replacement in the assignment of a structure from diffraction data. + Rigid body refinement - + - - Molecular interactions, pathways and networks - - BioCatalogue:Pathway Retrieval - Biological networks - Network or pathway analysis - beta13 - Molecular interactions - Biological models - Biological pathways - Topic concerning molecular interactions, biological pathways, networks and other models. - http://edamontology.org/topic_3076 - BioCatalogue:Pathways - - - + + + + + + + + + + 1.7 + An image processing technique that combines and analyze multiple images of a particulate sample, in order to produce an image with clearer features that are more easily interpreted. + + + Single particle analysis is used to improve the information that can be obtained by relatively low resolution techniques, , e.g. an image of a protein or virus from transmission electron microscopy (TEM). + Single particle analysis - + - - Informatics - - true - A database concerning biological data management and modelling, including datatypes, workflows and models. A sub-discipline of bioinformatics; the application of information technology to a specialised biological area. - beta12orEarlier - beta12orEarlier - - + + + + 1.7 + Compare (align and classify) multiple particle images from a micrograph in order to produce a representative image of the particle. + + + A micrograph can include particles in multiple different orientations and/or conformations. Particles are compared and organised into sets based on their similarity. Typically iterations of classification and alignment and are performed to optimise the final image; average images produced by classification are used as a reference image for subsequent alignment of the whole image set. + Single particle alignment and classification - + - - Literature data resources - - Data resources for the biological or biomedical literature, either a primary source of literature or some derivative. - true - 1.3 - beta12orEarlier - - + + + + + + + + + 1.7 + Clustering of molecular sequences on the basis of their function, typically using information from an ontology of gene function, or some other measure of functional phenotype. + Functional sequence clustering + + + Functional clustering - + - - Laboratory information management - - Topic concerning laboratory management and resources, for example, catalogues of biological resources for use in the lab including cell lines, viruses, plasmids, phages, DNA probes and primers and so on. - beta12orEarlier - Laboratory resources - - - - + + + 1.7 + Classifiication (typically of molecular sequences) by assignment to some taxonomic hierarchy. + Taxonomy assignment + + + Taxonomic classification - + - - Cell and tissue culture - - Tissue culture - 1.3 - true - Topic concerning general cell culture or data on a specific cell lines. - Cell culture - beta12orEarlier - - + + + + + + + + + + 1.7 + The prediction of the degree of pathogenicity of a microorganism from analysis of molecular sequences. + Pathogenicity prediction + + + Virulence prediction - + - - Ecology - - Topic concerning the ecological and environmental sciences and especially the application of information technology (ecoinformatics). - http://purl.bioontology.org/ontology/MSH/D004777 - Ecological informatics - beta12orEarlier - Computational ecology - Ecoinformatics - Environmental science - - - + + + + 1.7 + Analyse the correlation patterns among genes across across a variety of experiments, microarray samples etc. + + Gene co-expression network analysis + + + Gene expression correlation analysis - + - - Electron microscopy - - - SEM - Scanning electron microscopy - TEM - Topic concerning the study of matter by studying the interference pattern from firing electrons at a sample, to analyse structures at resolutions higher than can be achieved using light. - - Transmission electron microscopy - beta12orEarlier - Electron crystallography - Electron diffraction experiment - Single particle electron microscopy - - - + + + + + + + + + 1.7 + Identify a correlation, i.e. a statistical relationship between two random variables or two sets of data. + + + Correlation - + - - Cell cycle - - beta13 - Topic concerning the cell cycle including key genes and proteins. - beta12orEarlier - true - - + + + + + + + + + + 1.7 + Compute the covariance model for (a family of) RNA secondary structures. + + + RNA structure covariance model generation - + - - Peptides and amino acids - - beta12orEarlier - Topic concerning the physicochemical, biochemical or structural properties of amino acids or peptides. - Amino acids - Peptides - - + + + 1.7 + Predict RNA secondary structure by analysis, e.g. probabilistic analysis, of the shape of RNA folds. + RNA shape prediction + + + RNA secondary structure prediction (shape-based) - + - - Organelles - - Cell membrane - Cytoplasm - Organelle genes and proteins - Smooth endoplasmic reticulum - Topic concerning a specific organelle, or organelles in general, typically the genes and proteins (or genome and proteome). - beta12orEarlier - Lysosome - Centriole - Ribosome - Nucleus - true - Mitochondria - Golgi apparatus - Rough endoplasmic reticulum - 1.3 - - + + + 1.7 + Prediction of nucleic-acid folding using sequence alignments as a source of data. + + + Nucleic acid folding prediction (alignment-based) - + - - Ribosomes - - beta12orEarlier - Ribosome genes and proteins - Topic concerning ribosomes, typically of ribosome-related genes and proteins. - 1.3 - true - - + + + 1.7 + Count k-mers (substrings of length k) in DNA sequence data. + + + k-mer counting is used in genome and transcriptome assembly, metagenomic sequencing, and for error correction of sequence reads. + k-mer counting - + - - Scents - - A database about scents. - beta12orEarlier - beta13 - true - - + + + + + + + + + 1.7 + Reconstructing the inner node labels of a phylogenetic tree from its leafes. + + + Note that this is somewhat different from simply analysing an existing tree or constructing a completely new one. + Phylogenetic tree reconstruction - + - - Drugs and target structures - - - Drug structures - Topic concerning the structures of drugs, drug target, their interactions and binding affinities. - beta12orEarlier - Target structures - - - + + + 1.7 + Generate some data from a choosen probibalistic model, possibly to evaluate algorithms. + + + Probabilistic data generation - + - - Organisms - - This may include information on the genome (including molecular sequences and map, genes and annotation), proteome, as well as more general information about an organism. - beta12orEarlier - Topic concerning a specific organism, or group of organisms, used to study a particular aspect of biology. - Model organisms - - - + + + + 1.7 + Generate sequences from some probabilistic model, e.g. a model that simulates evolution. + + + Probabilistic sequence generation - + - - Genomics - - BioCatalogue:Genomics - http://purl.bioontology.org/ontology/MSH/D023281 - Topic concerning whole genomes of one or more organisms, or genomes in general, such as meta-information on genomes, genome projects, gene names etc. - beta12orEarlier - - - + + + + + + + + + + 1.7 + Identify or predict causes for antibiotic resistance from molecular sequence analysis. + + + Antimicrobial resistance prediction - + - - Gene families - - beta12orEarlier - Gene family - Gene system - Topic concerning particular gene(s), gene family or other gene group or system and their encoded proteins. - Genes, gene family or system - Gene and protein families - - - + + + + + + + + + 1.8 + Analysis of a set of objects, such as genes, annotated with given categories, where eventual over-/under-representation of certain categories within the studied set of objects is revealed. + Enrichment + Enrichment analysis + Functional enrichment + + + Categories from a relevant ontology can be used. The input is typically a set of genes or other biological objects, possibly represented by their identifiers, and the output of the analysis is typically a ranked list of categories, each associated with a statistical metric of over-/under-representation within the studied data. + Over-representation analysis - + - - Chromosomes - - beta12orEarlier - Topic concerning chromosomes. - - + + + + + + + + + 1.8 + Analyse a dataset with respect to concepts from an ontology of chemical structure. + + + Chemical class enrichment - + - - Genotype and phenotype - - Genotype and phenotype resources - Topic concerning the study of genetic constitution of a living entity, such as an individual, and organism, a cell and so on, typically with respect to a particular observable phenotypic traits, or resources concerning such traits, which might be an aspect of biochemistry, physiology, morphology, anatomy, development and so on. - Genotyping - beta12orEarlier - - - + + + 1.8 + Plot an incident curve such as a survival curve, death curve, mortality curve. + + + Incident curve plotting - + - - Gene expression and microarray - - Topic concerning gene expression e.g. microarray data, northern blots, gene-indexed expression profiles etc. - true - beta12orEarlier - beta12orEarlier - - - + + + 1.8 + Identify and map patterns of genomic variations. + + + Methods often utilise a database of aligned reads. + Variant pattern analysis - + - - Sequence design - - Probes - This includes the design of primers for PCR and DNA amplification or the design of molecular probes. - http://purl.bioontology.org/ontology/MSH/D015335 - Gene design - Probe design - Topic concerning molecular probes (e.g. a peptide probe or DNA microarray probe) or primers (e.g. for PCR). - in silico cloning - Primer design - Primers - beta12orEarlier - - + + + beta12orEarlier + 1.12 + Model some biological system using mathematical techniques including dynamical systems, statistical models, differential equations, and game theoretic models. + + + Mathematical modelling + true - + - - Pathology - - Topic concerning diseases, including diseases in general and the genes, gene variations and proteins involved in one or more specific diseases. - beta12orEarlier - Diseases - - - + + + + + + + + + 1.9 + Visualise images resulting from various types of microscopy. + + + Microscope image visualisation - + - - Specific protein resources - - 1.3 - Topic concerning a particular protein, protein family or other group of proteins. - true - Specific protein - beta12orEarlier - - + + + 1.9 + Annotate an image of some sort, typically with terms from a controlled vocabulary. + + + Image annotation - + - - Taxonomy - - beta12orEarlier - Topic concerning organism classification, identification and naming. - - + + + 1.9 + Replace missing data with substituted values, usually by using some statistical or other mathematical approach. + Data imputation + + + Imputation - + - - Protein sequence analysis - - beta12orEarlier - 1.8 - Topic concerning archival, processing and analysis of protein sequences and sequence-based entities such as alignments, motifs and profiles. - true - - + + + 1.9 + Visualise, format or render data from an ontology, typically a tree of terms. + Ontology browsing + + + Ontology visualisation - + - - Nucleic acid sequence analysis - - beta12orEarlier - BioCatalogue:Nucleotide Sequence Analysis - 1.8 - true - Topic concerning the archival, processing and analysis of nucleotide sequences and and sequence-based entities such as alignments, motifs and profiles. - - - + + + beta12orEarlier + A method for making numerical assessments about the maximum percent of time that a conformer of a flexible macromolecule can exist and still be compatible with the experimental data. + + + Maximum occurence analysis - + - - Repeat sequences - - true - beta12orEarlier - Topic concerning the repetitive nature of molecular sequences. - 1.3 - - + + + + 1.9 + Compare the models or schemas used by two or more databases, or any other general comparison of databases rather than a detailed comparison of the entries themselves. + Data model comparison + Schema comparison + + + Database comparison - + - - Low complexity sequences - - true - Topic concerning the (character) complexity of molecular sequences, particularly regions of low complexity. - 1.3 - beta12orEarlier - - + + + + + + + + + 1.9 + Simulate the bevaviour of a biological pathway or network. + Network topology simulation + Pathway simulation + + + Network simulation - + - - Proteome - - Topic concerning a specific proteome including protein sequences and annotation. - beta12orEarlier - beta13 - true - - + + + 1.9 + Analyze read counts from RNA-seq experiments. + + + RNA-seq read count analysis - + - - DNA - - DNA analysis - beta12orEarlier - Topic concerning DNA sequences and structure, including processes such as methylation and replication. - The DNA sequences might be coding or non-coding sequences. - - + + + 1.9 + Identify and remove redudancy from a set of small molecule structures. + + + Chemical redundancy removal - + - - Coding RNA - - EST - cDNA - mRNA - Topic concerning protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames - This includes expressed sequence tag (EST) or complementary DNA (cDNA) sequences. - beta12orEarlier - - + + + 1.9 + Analyze time series data from an RNA-seq experiment. + + + RNA-seq time series data analysis - + - - Functional, regulatory and non-coding RNA - - - ncRNA - Non-coding RNA - Functional RNA - Regulatory RNA - Non-coding RNA includes piwi-interacting RNA (piRNA), small nuclear RNA (snRNA) and small nucleolar RNA (snoRNA). Regulatory RNA includes microRNA (miRNA) - short single stranded RNA molecules that regulate gene expression, and small interfering RNA (siRNA). - Topic concerning non-coding or functional RNA sequences, including regulatory RNA sequences, ribosomal RNA (rRNA) and transfer RNA (tRNA). - beta12orEarlier - - + + + 1.9 + Simulate gene expression data, e.g. for purposes of benchmarking. + + + Simulated gene expression data generation - + - - rRNA - - 1.3 - true - Topic concerning one or more ribosomal RNA (rRNA) sequences. - - + + + 1.12 + Identify semantic relations among entities and concepts within a text, using text mining techniques. + Relationship inference + + + Relation inference - + - - tRNA - - 1.3 - true - Topic concerning one or more transfer RNA (tRNA) sequences. - - + + + + + + + + + 1.12 + Re-adjust the output of mass spectrometry experiments with shifted ppm values. + + + Mass spectra calibration - + - - Protein secondary structure - - true - beta12orEarlier - Topic concerning protein secondary structure or secondary structure alignments. - 1.8 - This includes assignment, analysis, comparison, prediction, rendering etc. of secondary structure data. - - + + + + + + + + + 1.12 + Align multiple data sets using information from chromatography and/or peptide identification, from mass spectrometry experiments. + + + Chromatographic alignment - + - - RNA structure - - 1.3 - Topic concerning RNA secondary or tertiary structure and alignments. - beta12orEarlier - true - - + + + + + + + + + 1.12 + The removal of isotope peaks in a spectrum, to represent the fragment ion as one data point. + Deconvolution + + + Deisotoping is commonly done to reduce complexity, and done in conjunction with the charge state deconvolution. + Deisotoping - + - - Protein tertiary structure - - 1.8 - Topic concerning protein tertiary structures. - true - beta12orEarlier - - + + + + + + + + + 1.12 + Technique for determining the amount of proteins in a sample. + Protein quantitation + + + Protein quantification - + - - Nucleic acid classification - - 1.3 - true - Topic concerning classification of nucleic acid sequences and structures. - beta12orEarlier - - - - + + + + + + + + + 1.12 + Determination of peptide sequence from mass spectrum. + Peptide-spectrum-matching + + + Peptide identification + + - + - - Protein families - - Topic concerning primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc., curation of a particular protein or protein family, or any other proteins that have been classified as members of a common group. - beta12orEarlier - Protein sequence classification - Protein secondary databases - A protein families database might include the classifier (e.g. a sequence profile) used to build the classification. - - - + + + + + + + + + + + + + + + 1.12 + Calculate the isotope distribution of a given chemical species. + + + Isotopic distributions calculation - + - - Protein domains and folds - - Topic concerning protein tertiary structural domains and folds. - beta12orEarlier - Protein folds - BioCatalogue:Domains - Protein domains - - + + + 1.12 + Prediction of retention times in a mass spectrometry experiment based on compositional and structural properties of the separated species. + Retention times calculation + + + Retention times prediction - + - - Nucleic acid sequence alignment - - beta12orEarlier - true - Topic concerning nucleotide sequence alignments. - 1.3 - - + + + 1.12 + Quantification without the use of chemical tags. + + + Label-free quantification - + - - Protein sequence alignment - - 1.3 - beta12orEarlier - true - A sequence profile typically represents a sequence alignment. - Topic concerning protein sequence alignments. - - + + + 1.12 + Quantification based on the use of chemical tags. + + + Labeled quantification - + - - Nucleic acid sites and features - - beta12orEarlier - 1.3 - true - Topic concerning the archival, detection, prediction and analysis of -positional features such as functional sites in nucleotide sequences. - - - + + + 1.12 + Quantification by Selected/multiple Reaction Monitoring workflow (XIC quantitation of precursor / fragment mass pair). + + + MRM/SRM - + - - Protein sites and features - - beta12orEarlier - 1.3 - Topic concerning the detection, identification and analysis of positional features in proteins, such as functional sites. - true - - - + + + 1.12 + Calculate number of identified MS2 spectra as approximation of peptide / protein quantity. + + + Spectral counting - + - - Transcription factors and regulatory sites - - - - Transcription factor proteins either promote (as an activator) or block (as a repressor) the binding to DNA of RNA polymerase. Regulatory sites including transcription factor binding site as well as promoters, enhancers, silencers and boundary elements / insulators. - BioCatalogue:Transcription Factors - Topic concerning proteins that bind to DNA and control transcription of DNA to mRNA (transcription factors) and also transcriptional regulatory sites, elements and regions (such as promoters, enhancers, silencers and boundary elements / insulators) in nucleotide sequences. - Transcriptional regulatory sites - TFBS - Transcription factors - beta12orEarlier - Transcription factor binding sites - - + + + 1.12 + Quantification analysis using stable isotope labeling by amino acids in cell culture. + + + SILAC - + - - Phosphorylation sites - - 1.0 - true - Topic concerning protein phosphorylation and phosphorylation sites in protein sequences. - beta12orEarlier - - - + + + 1.12 + Quantification analysis using the AB SCIEX iTRAQ isobaric labelling workflow, wherein 2-8 reporter ions are measured in MS2 spectra near 114 m/z. + + + iTRAQ - + - - Metabolic pathways - - beta12orEarlier - Topic concerning metabolic pathways. - - + + + 1.12 + Quantification analysis using labeling based on 18O-enriched H2O. + + + 18O labeling - + - - Signaling pathways - - Topic concerning signaling pathways. - Signal transduction pathways - beta12orEarlier - - + + + 1.12 + Quantification analysis using the Thermo Fisher tandem mass tag labelling workflow. + + + TMT-tag - + - - Protein and peptide identification - - 1.3 - beta12orEarlier - true - - + + + 1.12 + Quantification analysis using chemical labeling by stable isotope dimethylation + + + Dimethyl - + - - Workflows - - Topic concerning biological or biomedical analytical workflows or pipelines. - beta12orEarlier - true - 1.0 - + + + 1.12 + Peptide sequence tags are used as piece of information about a peptide obtained by tandem mass spectrometry. + + + Tag-based peptide identification - + - - Data types and objects - - Topic concerning structuring data into basic types and (computational) objects. - beta12orEarlier - 1.0 - true - - + + + + 1.12 + Analytical process that derives a peptide’s amino acid sequence from its tandem mass spectrum (MS/MS) without the assistance of a sequence database. + + + de Novo sequencing - + - - Theoretical biology - - 1.3 - true - - + + + 1.12 + Identification of post-translational modifications (PTMs) of peptides/proteins in mass spectrum. + + + PTM identification - + - - Mitochondria - - beta12orEarlier - true - Topic concerning mitochondria, typically of mitochondrial genes and proteins. - 1.3 - - + + + + 1.12 + Determination of best matches between MS/MS spectrum and a database of protein or nucleic acid sequences. + + + Peptide database search - + - - Plants - - Plant - The resource may be specific to a plant, a group of plants or all plants. - Plant biology - Topic concerning plants, e.g. information on a specific plant genome including molecular sequences, genes and annotation. - Botany - beta12orEarlier - - + + + 1.12 + Peptide database search for identification of known and unknown PTMs looking for mass difference mismatches. + Modification-tolerant peptide database search + Unrestricted peptide database search + + + Blind peptide database search - + - - Viruses - - Virology - Topic concerning viruses, e.g. sequence and structural data, interactions of viral proteins, or a viral genome including molecular sequences, genes and annotation. - beta12orEarlier - The resource may be specific to a virus, a group of viruses or all viruses. - - + + + + 1.12 + Statistical estimation of false discovery rate from score distribution for peptide-spectrum-matches, following a peptide database search. + + + Validation of peptide-spectrum matches - + - - Fungi - - Mycology - beta12orEarlier - Topic concerning fungi and molds, e.g. information on a specific fungal genome including molecular sequences, genes and annotation. - The resource may be specific to a fungus, a group of fungi or all fungi. - Yeast - - + + + 1.12 + Estimation of false discovery rate by comparison to search results with a database containing incorrect information. + + + Target-Decoy - + - - Pathogens - - beta12orEarlier - The resource may be specific to a pathogen, a group of pathogens or all pathogens. - Topic concerning pathogens, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation. - - + + + 1.12 + Analyse data in order to deduce properties of an underlying distribution or population. + Empirical Bayes + + + Statistical inference - + - - Arabidopsis - - Topic concerning Arabidopsis-specific data. - beta12orEarlier - 1.3 - true - - + + + 1.12 + A statistical calculation to estimate the relationships among variables. + Regression + + + Regression analysis - + - - Rice - - true - 1.3 - Topic concerning rice-specific data. - beta12orEarlier - - + + + + + + + + + 1.12 + Model a metabolic network, for example, to reconstruct pathways or to simulate metabolism. + Metabolic network reconstruction + Metabolic network simulation + Metabolic reconstruction + + + Metabolic network modelling - + - - Genetic mapping and linkage - - Linkage mapping - beta12orEarlier - 1.3 - true - Genetic linkage - Informatics resources that aim to identify, map or analyse genetic markers in DNA sequences, for example to produce a genetic (linkage) map of a chromosome or genome or to analyse genetic linkage and synteny. - - + + + 1.12 + Predict the effect or function of an individual single nucleotide polymorphism (SNP). + + + SNP annotation - + - - Comparative genomics - - Topic concerning the study (typically comparison) of the sequence, structure or function of multiple genomes. - beta12orEarlier - BioCatalogue:Comparative Genomics - - - + + + 1.12 + Prediction of genes or gene components from first principles, i.e. without reference to existing genes. + Gene prediction (ab-initio) + + + Ab-initio gene prediction - + - - Mobile genetic elements - - - Transposons - beta12orEarlier - Topic concerning mobile genetic elements, such as transposons, Plasmids, Bacteriophage elements and Group II introns. - - + + + 1.12 + Prediction of genes or gene components by reference to homologous genes. + Gene prediction (homology-based) + + + Homology-based gene prediction - + - - Human disease - - beta13 - true - beta12orEarlier - Topic concerning human diseases, typically describing the genes, mutations and proteins implicated in disease. - - + + + 1.12 + Construction of a statistical model, or a set of assumptions around some observed data, usually by describing a set of probability distributions which approximate the distribution of data. + + + Statistical modelling - + - - Immunology - - Topic concerning the application of information technology to immunology such as immunological processes, immunological genes, proteins and peptide ligands, antigens and so on. - Immunoinformatics - Computational immunology - http://purl.bioontology.org/ontology/MSH/D007120 - http://purl.bioontology.org/ontology/MSH/D007125 - beta12orEarlier - - - + + + + 1.12 + Compare two or more molecular surfaces. + + + Molecular surface comparison - + - - Membrane and lipoproteins - - beta12orEarlier - Membrane proteins - Lipoproteins - Transmembrane proteins - Topic concerning lipoproteins (protein-lipid assemblies), and proteins or region of a protein that spans or are associated with a membrane. - - + + + 1.12 + Annotate one or more sequences with functional information, such as cellular processes or metaobolic pathways, by reference to a controlled vocabulary - invariably the Gene Ontology (GO). + + + Gene functional annotation - + - - Enzymes - - beta12orEarlier - Topic concerning proteins that catalyze chemical reaction, the kinetics of enzyme-catalysed reactions, enzyme nomenclature etc. - Enzymology - - + + + + 1.12 + Variant filtering is used to eliminate false positive variants based for example on base calling quality, strand and position information, and mapping info. + + + Variant filtering - + - - Primers - - Nucleic acid features (primers) - Topic concerning PCR primers and hybridization oligos in a nucleic acid sequence. - beta12orEarlier - Primer binding sites - - - + + + 1.12 + Differential binding analysis identifies binding sites in nucleic acid sequences that are statistically significantly differentially bound between sample groups. + + + Differential binding analysis - + - - PolyA signal or sites - - beta12orEarlier - Nucleic acid features (PolyA signal or site) - PolyA signal - A polyA signal is required for endonuclease cleavage of an RNA transcript that is followed by polyadenylation. A polyA site is a site on an RNA transcript to which adenine residues will be added during post-transcriptional polyadenylation. - PolyA site - Topic concerning regions or sites in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript. - - - + + + 1.13 + Analyze data from RNA-seq experiments. + + + RNA-Seq analysis - + - - CpG island and isochores - - beta12orEarlier - Nucleic acid features (CpG island and isochore) - Topic concerning CpG rich regions (isochores) in a nucleotide sequence. - - - + + + 1.1 + Visualise, format or render a mass spectrum. + + + Mass spectrum visualisation - + - - Restriction sites - - Topic concerning restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence. - Nucleic acid features (restriction sites) - beta12orEarlier - Nucleic acid restriction sites (report) - - - + + + 1.13 + Filter a set of files or data items according to some property. + Sequence filtering + + + Filtering - + - - Splice sites - - - Topic concerning splice sites in a nucleotide sequence or alternative RNA splicing events. - Nucleic acid features (splice sites) - Nucleic acid report (RNA splicing) - beta12orEarlier - Nucleic acid report (RNA splice model) - - - + + + 1.1 + Identification of the best reference for mapping for a specific dataset from a list of potential references, when performing genetic variation analysis. + + + Reference identification - + - - Matrix/scaffold attachment sites - - Nucleic acid features (matrix/scaffold attachment sites) - beta12orEarlier - Topic concerning matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence. - - - + + + 1.14 + Label-free quantification by integration of ion current (ion counting). + Ion current integration + + + Ion counting - + - - Operon - - Gene features (operon) - Topic concerning operons (operators, promoters and genes) from a bacterial genome. - beta12orEarlier - Nucleic acid features (operon) - The report for a query sequence or gene might include the predicted operon leader and trailer gene, gene composition of the operon and associated information, as well as information on the query. - - - + + + 1.14 + Chemical tagging free amino groups of intact proteins with stable isotopes. + ICPL + + + Isotope-coded protein label - + - - Promoters - - beta12orEarlier - Nucleic acid features (promoters) - Topic concerning whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in a DNA sequence. - - - + + + 1.14 + Labeling all proteins and (possibly) all amino acids using C-13 or N-15 enriched grown medium or feed. + C-13 metabolic labeling + N-15 metabolic labeling + + + This includes N-15 metabolic labeling (labeling all proteins and (possibly) all amino acids using N-15 enriched grown medium or feed) and C-13 metabolic labeling (labeling all proteins and (possibly) all amino acids using C-13 enriched grown medium or feed). + Metabolic labeling - + - - Structural biology - - Topic concerning the molecular structure of biological molecules, particularly macromolecules such as proteins and nucleic acids. - Structural assignment - Structure determination - This includes experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, microscopy etc., including the assignment or modelling of molecular structure from such data. - 1.3 - This includes Informatics concerning data generated from the use of microscopes, including optical, electron and scanning probe microscopy. Includes methods for digitizing microscope images and viewing the produced virtual slides and associated data on a computer screen. - Structural determination - - - + + + 1.15 + Construction of a single sequence assembly of all reads from different samples, typically as part of a comparative metagenomic analysis. + Sequence assembly (cross-assembly) + + + Cross-assembly - + - - Protein membrane regions - - - 1.8 - Protein features (membrane regions) - This might include the location and size of the membrane spanning segments and intervening loop regions, transmembrane region IN/OUT orientation relative to the membrane, plus the following data for each amino acid: A Z-coordinate (the distance to the membrane center), the free energy of membrane insertion (calculated in a sliding window over the sequence) and a reliability score. The z-coordinate implies information about re-entrant helices, interfacial helices, the tilt of a transmembrane helix and loop lengths. - Topic concerning trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements. - Intramembrane regions - Protein transmembrane regions - Transmembrane regions - - - + + + 1.15 + The comparison of samples from a metagenomics study, for example, by comparison of metagenome shotgun reads or assembled contig sequences, by comparison of functional profiles, or some other method. + + + Sample comparison - + - - Structure comparison - - Topic concerning the comparison of two or more molecular structures, for example structure alignment and clustering. - This might involve comparison of secondary or tertiary (3D) structural information. - beta12orEarlier - - - + + + + 1.15 + Differential protein analysis + The analysis, using proteomics techniques, to identify proteins whose encoding genes are differentially expressed under a given experimental setup. + + + Differential protein expression analysis - + - - Function analysis - - Protein function prediction - BioCatalogue:Function Prediction - Topic concerning the study of gene and protein function including the prediction of functional properties of a protein. - Protein function analysis - beta12orEarlier - - - + + + 1.15 + The analysis, using any of diverse techniques, to identify genes that are differentially expressed under a given experimental setup. + + + Differential gene expression analysis - + - - Prokaryotes and archae - - The resource may be specific to a prokaryote, a group of prokaryotes or all prokaryotes. - beta12orEarlier - Topic concerning specific bacteria or archaea, e.g. information on a specific prokaryote genome including molecular sequences, genes and annotation. - - + + + 1.15 + Visualise, format or render data arising from an analysis of multiple samples from a metagenomics/community experiment. + + + Multiple sample visualisation - + - - Protein databases - - true - 1.3 - beta12orEarlier - Protein data resources - Topic concerning protein data resources. - - + + + 1.15 + The extrapolation of empirical characteristics of individuals or populations, backwards in time, to their common ancestors. + Character mapping + Character optimisation + + + Ancestral reconstruction is often used to recover possible ancestral character states of ancient, extinct organisms. + Ancestral reconstruction - + - - Structure determination - - Topic concerning experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, microscopy etc., including the assignment or modelling of molecular structure from such data. - beta12orEarlier - true - 1.3 - - + + + 1.16 + Site localisation of post-translational modifications in peptide or protein mass spectra. + PTM scoring + Site localisation + + + PTM localisation - + - - Cell biology - - beta12orEarlier - Topic concerning cells, such as key genes and proteins involved in the cell cycle. - - + + + 1.16 + Operations concerning the handling and use of other tools. + + + Service management - + - - Classification - - beta13 - beta12orEarlier - Topic focused on identifying, grouping, or naming things in a structured way according to some schema based on observable relationships. - true - - + + + 1.16 + An operation supporting the browsing or discovery of other tools and services. + + + Service discovery - + - - Lipoproteins - - true - 1.3 - Topic concerning lipoproteins (protein-lipid assemblies). - beta12orEarlier - - + + + 1.16 + An operation supporting the aggregation of other services (at least two) into a funtional unit, for the automation of some task. + + + Service composition - + - - Phylogeny visualisation - - true - Visualise a phylogeny, for example, render a phylogenetic tree. - BioCatalogue:Tree Display - beta12orEarlier - beta12orEarlier - - + + + 1.16 + An operation supporting the calling (invocation) of other tools and services. + + + Service invocation - + - - Cheminformatics - - - Chemical informatics - BioCatalogue:Chemoinformatics - Topic concerning the application of information technology to chemistry in biological research environment. - beta12orEarlier - Chemoinformatics - - - + + + + + + + + + 1.16 + A data mining method typically used for studying biological networks based on pairwise correlations between variables. + WGCNA + Weighted gene co-expression network analysis + + + Weighted correlation network analysis - + - - Systems biology - - http://en.wikipedia.org/wiki/Systems_biology - BioCatalogue:Model Execution - This includes databases of models and methods to construct or analyse a model. - BioCatalogue:Model Creation - Topic concerning the holistic modelling and analysis of complex biological systems and the interactions therein. - Biological models - http://purl.bioontology.org/ontology/MSH/D049490 - BioCatalogue:Model Analysis - BioCatalogue:Systems Biology - beta12orEarlier - Biological system modelling - Biological modelling - - - + + + + + + + + + + 1.16 + Identification of protein, for example from one or more peptide identifications by tandem mass spectrometry. + Protein inference + + + Protein identification - + - - Statistics - - Topic concerning the application of statistical methods to biological problems. - Biostatistics - http://en.wikipedia.org/wiki/Biostatistics - BioCatalogue:Biostatistics - beta12orEarlier - http://purl.bioontology.org/ontology/MSH/D056808 - - - + + + + + + + + + + + + + + + + + + + + + + 1.16 + Text annotation is the operation of adding notes, data and metadata, recognised entities and concepts, and their relations to a text (such as a scientific article). + Article annotation + Literature annotation + + + Text annotation + - + - - Structure database search - - The query is a structure-based entity such as another structure, a 3D (structural) motif, 3D profile or template. - beta12orEarlier - Search for and retrieve molecular structures that are similar to a structure-based query (typically another structure or part of a structure). - beta12orEarlier - true - - + + + + beta12orEarlier + A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other. + sumo:FieldOfStudy + + + Topic + http://bioontology.org/ontologies/ResearchArea.owl#Area_of_Research + http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Method + http://purl.org/biotop/biotop.owl#Quality + http://www.ifomis.org/bfo/1.1/snap#Continuant + http://www.ifomis.org/bfo/1.1/snap#Quality + http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality + http://www.onto-med.de/ontologies/gfo.owl#Category + http://www.onto-med.de/ontologies/gfo.owl#Perpetuant - + - - Molecular modelling - - Homology modeling - Comparative modeling - Comparative modelling - beta12orEarlier - Topic concerning the construction, analysis, evaluation, refinement etc. of models of a molecules properties or behaviour. - Homology modelling - Molecular modeling - - + + + beta12orEarlier + true + The processing and analysis of nucleic acid sequence, structural and other data. + Nucleic acid bioinformatics + Nucleic acid informatics + Nucleic acid physicochemistry + Nucleic acid properties + + + Nucleic acids + http://purl.bioontology.org/ontology/MSH/D017422 + http://purl.bioontology.org/ontology/MSH/D017423 - + - - Protein function prediction - - 1.2 - beta12orEarlier - BioCatalogue:Function Prediction - true - Topic concerning the prediction of functional properties of a protein. - - + + + beta12orEarlier + true + Archival, processing and analysis of protein data, typically molecular sequence and structural data. + Protein bioinformatics + Protein informatics + Protein databases + + + Proteins + http://purl.bioontology.org/ontology/MSH/D020539 - + - - SNP - - beta12orEarlier - Single nucleotide polymorphism - A SNP is a DNA sequence variation where a single nucleotide differs between members of a species or paired chromosomes in an individual. - Topic concerning single nucleotide polymorphisms (SNP) and associated data, for example, the discovery and annotation of SNPs. - - + + + beta12orEarlier + 1.13 + The structures of reactants or products of metabolism, for example small molecules such as including vitamins, polyols, nucleotides and amino acids. + + + Metabolites + true - + - - Transmembrane protein prediction - - Predict transmembrane domains and topology in protein sequences. - beta12orEarlier - beta12orEarlier - true - - - + + + beta12orEarlier + true + The archival, processing and analysis of molecular sequences (monomer composition of polymers) including molecular sequence data resources, sequence sites, alignments, motifs and profiles. + Sequences + Sequence databases + + + + Sequence analysis + http://purl.bioontology.org/ontology/MSH/D017421 - + - - Nucleic acid structure comparison - - beta12orEarlier - true - Topic concerning the comparison two or more nucleic acid (typically RNA) secondary or tertiary structures. - beta12orEarlier - Use this concept for methods that are exclusively for nucleic acid structures. - - - + + + beta12orEarlier + true + The curation, processing and analysis of the structure of biological molecules, typically proteins and nucleic acids and other macromolecules. + Structural bioinformatics + Computational structural biology + Structure data resources + Structure databases + + + + This includes related concepts such as structural properties, alignments and structural motifs. + Structure analysis + http://purl.bioontology.org/ontology/MSH/D015394 - + - - Exons - - Gene features (exon) - Topic concerning exons in a nucleotide sequences. - beta12orEarlier - - - + + + beta12orEarlier + true + The prediction of molecular structure, including the prediction, modelling, recognition or design of protein secondary or tertiary structure or other structural features, and the folding of nucleic acid molecules and the prediction or design of nucleic acid (typically RNA) sequences with specific conformations. + + + DNA structure prediction + Nucleic acid design + Nucleic acid folding + Nucleic acid structure prediction + Protein fold recognition + Protein structure prediction + RNA structure prediction + + + This includes the recognition (prediction and assignment) of known protein structural domains or folds in protein sequence(s), for example by threading, or the alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment). + Structure prediction - + - - Gene transcription features - - GC signals (report) - CAAT signals (report) - -35 signals (report) - Gene transcriptional features - This includes promoters, CAAT signals, TATA signals, -35 signals, -10 signals, GC signals, primer binding sites for initiation of transcription or reverse transcription, enhancer, attenuator, terminators and ribosome binding sites. - Enhancers (report) - Terminators (report) - Ribosome binding sites (report) - -10 signals (report) - Topic concerning transcription of DNA into RNA including the regulation of transcription. - beta12orEarlier - TATA signals (report) - Attenuators (report) - - - + + + beta12orEarlier + beta12orEarlier + + + The alignment (equivalence between sites) of molecular sequences, structures or profiles (representing a sequence or structure alignment). + + Alignment + true - + - - DNA mutation - - - Mutation annotation - beta12orEarlier - Nucleic acid features (mutation) - Topic concerning DNA mutation. - - - + + + + beta12orEarlier + true + The study of evolutionary relationships amongst organisms. + Phylogenetic clocks + Phylogenetic dating + Phylogenetic simulation + Phylogenetic stratigraphy + Phylogeny reconstruction + + + + This includes diverse phylogenetic methods, including phylogenetic tree construction, typically from molecular sequence or morphological data, methods that simulate DNA sequence evolution, a phylogenetic tree or the underlying data, or which estimate or use molecular clock and stratigraphic (age) data, methods for studying gene evolution etc. + Phylogeny + http://purl.bioontology.org/ontology/MSH/D010802 - + - - Oncology - - Topic concerning the study of cancer, for example, genes and proteins implicated in cancer. - beta12orEarlier - Cancer - Cancer biology - - - + + + + beta12orEarlier + true + The study of gene or protein functions and their interactions in totality in a given organism, tissue, cell etc. + + + + Functional genomics - + - - Toxins and targets - - - Toxins - Topic concerning structural and associated data for toxic chemical substances. - Targets - beta12orEarlier - - - + + + beta12orEarlier + true + The conceptualisation, categorisation and nomenclature (naming) of entities or phenomena within biology or bioinformatics. This includes formal ontologies, controlled vocabularies, structured glossary, symbols and terminology or other related resource. + Applied ontology + Ontologies + Ontology + Terminology + + + + Ontology and terminology + http://purl.bioontology.org/ontology/MSH/D002965 - + - - Introns - - Gene features (intron) - Nucleic acid features (intron) - Topic concerning introns in a nucleotide sequences. - beta12orEarlier - - - + + + beta12orEarlier + 1.13 + The search and query of data sources (typically databases or ontologies) in order to retrieve entries or other information. + + + Information retrieval + true - + - - Tool topic - - beta12orEarlier - A topic concerning primarily bioinformatics software tools, typically the broad function or purpose of a tool. - true - beta12orEarlier - - + + + beta12orEarlier + true + VT 1.5.6 Bioinformatics + The archival, curation, processing and analysis of complex biological data. + + + + This includes data processing in general, including basic handling of files and databases, datatypes, workflows and annotation. + Bioinformatics + http://purl.bioontology.org/ontology/MSH/D016247 - + - - Study topic - - A general area of bioinformatics study, typically the broad scope or category of content of a bioinformatics journal or conference proceeding. - beta12orEarlier - true - beta12orEarlier - - + + + beta12orEarlier + true + Computer graphics + VT 1.2.5 Computer graphics + Rendering (drawing on a computer screen) or visualisation of molecular sequences, structures or other biomolecular data. + Data rendering + + + Data visualisation - + - - Nomenclature - + + + 1.3 + + The study of the thermodynamic properties of a nucleic acid. + + Nucleic acid thermodynamics true - 1.3 - Topic concerning biological nomenclature (naming), symbols and terminology. - beta12orEarlier - - - + - - Disease genes and proteins - - 1.3 - true - Topic concerning the genes, gene variations and proteins involved in one or more specific diseases. - beta12orEarlier - - + + + + beta12orEarlier + The archival, curation, processing and analysis of nucleic acid structural information, such as whole structures, structural features and alignments, and associated annotation. + Nucleic acid structure + DNA melting + Nucleic acid denaturation + Nucleic acid thermodynamics + RNA alignment + RNA structure + RNA structure alignment + + + Includes secondary and tertiary nucleic acid structural data, nucleic acid thermodynamic, thermal and conformational properties including DNA or DNA/RNA denaturation (melting) etc. + Nucleic acid structure analysis - + - - Protein structure analysis - - Protein structure - http://edamontology.org/topic_3040 - beta12orEarlier - Topic concerning protein secondary or tertiary structural data and/or associated annotation. - - - + + + beta12orEarlier + RNA sequences and structures. + Small RNA + + + RNA - + - - Humans - - beta12orEarlier + + + beta12orEarlier + 1.3 + + Topic for the study of restriction enzymes, their cleavage sites and the restriction of nucleic acids. + + Nucleic acid restriction true - Topic concerning the human genome, including molecular sequences, genes, annotation, maps and viewers, the human proteome or human beings in general. - 1.3 - - - + - - Gene resources - - Gene resource - beta12orEarlier - 1.3 - Informatics resource (typically a database) primarily focussed on genes. - Gene database - true - - + + + beta12orEarlier + true + The mapping of complete (typically nucleotide) sequences. Mapping (in the sense of short read alignment, or more generally, just alignment) has application in RNA-Seq analysis (mapping of transcriptomics reads), variant discovery (e.g. mapping of exome capture), and re-sequencing (mapping of WGS reads). + Genetic linkage + Linkage + Linkage mapping + Synteny + + This includes resources that aim to identify, map or analyse genetic markers in DNA sequences, for example to produce a genetic (linkage) map of a chromosome or genome or to analyse genetic linkage and synteny. It also includes resources for physical (sequence) maps of a DNA sequence showing the physical distance (base pairs) between features or landmarks such as restriction sites, cloned DNA fragments, genes and other genetic markers. It also covers for example the alignment of sequences of (typically millions) of short reads to a reference genome. + Mapping - + - - Yeast - - Topic concerning yeast, e.g. information on a specific yeast genome including molecular sequences, genes and annotation. - beta12orEarlier + + + beta12orEarlier + 1.3 + + The study of codon usage in nucleotide sequence(s), genetic codes and so on. + + Genetic codes and codon usage true - 1.3 - - - + - - Eukaryotes - - Eukaryote - Topic concerning eukaryotes or data concerning eukaryotes, e.g. information on a specific eukaryote genome including molecular sequences, genes and annotation. - The resource may be specific to a eukaryote, a group of eukaryotes or all eukaryotes. - beta12orEarlier - - + + + beta12orEarlier + The translation of mRNA into protein and subsequent protein processing in the cell. + Translation + + + + Protein expression - + - - Invertebrates - - The resource may be specific to an invertebrate, a group of invertebrates or all invertebrates. - beta12orEarlier - Topic concerning invertebrates, e.g. information on a specific invertebrate genome including molecular sequences, genes and annotation. - - + + + beta12orEarlier + 1.3 + + Methods that aims to identify, predict, model or analyse genes or gene structure in DNA sequences. + + This includes the study of promoters, coding regions, splice sites, etc. Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc. + Gene finding + true - + - - Vertebrates - - The resource may be specific to a vertebrate, a group of vertebrates or all vertebrates. - Topic concerning vertebrates, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation. - beta12orEarlier - - + + + beta12orEarlier + 1.3 + + The transcription of DNA into mRNA. + + Transcription + true - + - - Unicellular eukaryotes - - beta12orEarlier - The resource may be specific to a unicellular eukaryote, a group of unicellular eukaryotes or all unicellular eukaryotes. - Topic concerning unicellular eukaryotes, e.g. information on a unicellular eukaryote genome including molecular sequences, genes and annotation. - - + + + beta12orEarlier + beta13 + + Promoters in DNA sequences (region of DNA that facilitates the transcription of a particular gene by binding RNA polymerase and transcription factor proteins). + + Promoters + true - + - - Protein structure alignment - - beta12orEarlier - Topic concerning protein secondary or tertiary structure alignments. + + + beta12orEarlier + beta12orEarlier + The folding (in 3D space) of nucleic acid molecules. + + + Nucleic acid folding true - 1.3 - - - + - - X-ray diffraction - - - beta12orEarlier - X-ray microscopy - Topic concerning the study of matter and their structure by means of the diffraction of X-rays, typically the diffraction pattern caused by the regularly spaced atoms of a crystalline sample. - Crystallography - X-ray crystallography - - - + + + beta12orEarlier + true + Gene structure, regions which make an RNA product and features such as promoters, coding regions, gene fusion, splice sites etc. + + Gene features + Fusion genes + + + This includes the study of promoters, coding regions etc. + This incudes operons (operators, promoters and genes) from a bacterial genome. For example the operon leader and trailer gene, gene composition of the operon and associated information. + Gene structure - + - - Ontologies, nomenclature and classification - - true - 1.3 - http://purl.bioontology.org/ontology/MSH/D002965 - beta12orEarlier - Topic concerning conceptualisation, categorisation and naming of entities or phenomena within biology or bioinformatics. - - + + + beta12orEarlier + true + Protein and peptide identification, especially in the study of whole proteomes of organisms. + Metaproteomics + Peptide identification + Protein and peptide identification + + + + Includes metaproteomics: proteomics analysis of an environmental sample. + Proteomics includes any methods (especially high-throughput) that separate, characterize and identify expressed proteins such as mass spectrometry, two-dimensional gel electrophoresis and protein microarrays, as well as in-silico methods that perform proteolytic or mass calculations on a protein sequence and other analyses of protein production data, for example in different cells or tissues. + Proteomics + http://purl.bioontology.org/ontology/MSH/D040901 - + - - Immunoproteins, genes and antigens - - - Topic concerning immunity-related genes, proteins and their ligands. - Immunopeptides - Antigens - This includes T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF) / antibodies, major histocompatibility complex superfamily (MhcSF), etc." - beta12orEarlier - Immunoproteins - Immunogenes - - - + + + + beta12orEarlier + true + The elucidation of the three dimensional structure for all (available) proteins in a given organism. + + + + Structural genomics - + - - Molecules - - CHEBI:23367 - beta12orEarlier - Topic concerning specific molecules, including large molecules built from repeating subunits (macromolecules) and small molecules of biological significance. - beta12orEarlier - true - - + + + beta12orEarlier + true + The study of the physical and biochemical properties of peptides and proteins, for example the hydrophobic, hydrophilic and charge properties of a protein. + Protein physicochemistry + Protein hydropathy + + + Protein properties - + - - Toxicology - - - Topic concerning toxins and the adverse effects of these chemical substances on living organisms. - beta12orEarlier - Toxicoinformatics - Computational toxicology - Toxicology - - - + + + + beta12orEarlier + true + Protein-protein, protein-DNA/RNA and protein-ligand interactions, including analysis of known interactions and prediction of putative interactions. + Protein interaction networks + Protein-DNA interaction + Protein-RNA interaction + Protein-ligand interactions + Protein-nucleic acid interactions + Protein-protein interactions + + + This includes experimental (e.g. yeast two-hybrid) and computational analysis techniques. + Protein interactions - + - - High-throughput sequencing - - Next-generation sequencing - beta13 - true - Topic concerning parallelized sequencing processes that are capable of sequencing many thousands of sequences simultaneously. - beta12orEarlier - - + + + beta12orEarlier + true + Protein stability, folding (in 3D space) and protein sequence-structure-function relationships. This includes for example study of inter-atomic or inter-residue interactions in protein (3D) structures, the effect of mutation, and the design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein. + Protein design + Protein folding + Protein residue interactions + Protein stability + Rational protein design + + + Protein folding, stability and design - + - - Structural clustering - - 1.7 - Structure classification + + + beta12orEarlier + beta13 + + Two-dimensional gel electrophoresis image and related data. + + Two-dimensional gel electrophoresis true - Topic concerning the comparison and grouping together of molecular structures on the basis of similarity; generate, process or analyse structural clusters. - beta12orEarlier - - - + - - Gene regulatory networks - - - Topic concerning gene regulatory networks. - beta12orEarlier - - + + + beta12orEarlier + 1.13 + An analytical chemistry technique that measures the mass-to-charge ratio and abundance of irons in the gas phase. + + + Mass spectrometry + true - + - - Disease (specific) - - Informatics resources dedicated to one or more specific diseases (not diseases in general). - beta12orEarlier + + + beta12orEarlier + beta13 + + Protein microarray data. + + Protein microarrays true - beta12orEarlier - - - + - - VNTR - - Nucleic acid features (VNTR) - Variable number of tandem repeat polymorphism - beta12orEarlier - VNTR annotation - VNTRs occur in non-coding regions of DNA and consists sub-sequence that is repeated a multiple (and varied) number of times. - Topic concerning variable number of tandem repeat (VNTR) polymorphism in a DNA sequence. - - - + + + beta12orEarlier + 1.3 + + The study of the hydrophobic, hydrophilic and charge properties of a protein. + + Protein hydropathy + true - + - - Microsatellites - - beta12orEarlier - Nucleic acid features (microsatellite) - Topic concerning microsatellite polymorphism in a DNA sequence. - A microsatellite polymorphism is a very short subsequence that is repeated a variable number of times between individuals. These repeats consist of the nucleotides cytosine and adenosine. - Microsatellite annotation - - - + + + beta12orEarlier + The study of how proteins are transported within and without the cell, including signal peptides, protein subcellular localisation and export. + Protein localisation + Protein sorting + Protein targeting + + + Protein targeting and localisation - + - - RFLP - - Topic concerning restriction fragment length polymorphisms (RFLP) in a DNA sequence. - An RFLP is defined by the presence or absence of a specific restriction site of a bacterial restriction enzyme. - RFLP annotation - beta12orEarlier - Nucleic acid features (RFLP) - - - + + + beta12orEarlier + 1.3 + + Enzyme or chemical cleavage sites and proteolytic or mass calculations on a protein sequence. + + Protein cleavage sites and proteolysis + true - + - - DNA polymorphism - - - Nucleic acid features (polymorphism) - Polymorphism annotation - beta12orEarlier - Topic concerning DNA polymorphism. - - - + + + beta12orEarlier + beta12orEarlier + The comparison of two or more protein structures. + + + Use this concept for methods that are exclusively for protein structure. + Protein structure comparison + true - + - - Nucleic acid design - - Topic for the design of nucleic acid sequences with specific conformations. - 1.3 - beta12orEarlier + + + beta12orEarlier + 1.3 + + The processing and analysis of inter-atomic or inter-residue interactions in protein (3D) structures. + + Protein residue interactions true - - - + - - Primer or probe design - - 1.3 - Topic concerning the design of primers for PCR and DNA amplification or the design of molecular probes. + + + beta12orEarlier + 1.3 + + Protein-protein interactions, individual interactions and networks, protein complexes, protein functional coupling etc. + + Protein-protein interactions true - beta13 - - - + - - Structure databases - - beta13 + + + beta12orEarlier + 1.3 + + Protein-ligand (small molecule) interactions. + + Protein-ligand interactions true - 1.2 - Structure data resources - Topic concerning molecular secondary or tertiary (3D) structural data resources, typically of proteins and nucleic acids. - - - + - - Nucleic acid structure - + + + beta12orEarlier + 1.3 + + Protein-DNA/RNA interactions. + + Protein-nucleic acid interactions true - beta13 - Topic concerning nucleic acid (secondary or tertiary) structure, such as whole structures, structural features and associated annotation. - 1.2 - - - + - - Sequence databases - + + + beta12orEarlier + 1.3 + + The design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein. + + Protein design true - beta13 - Sequence data resources - Sequence data - Sequence data resource - 1.3 - Topic concerning molecular sequence data resources, including sequence sites, alignments, motifs and profiles. - - - + - - Nucleic acid sequences - - beta13 - 1.3 - Topic concerning nucleotide sequences and associated concepts such as sequence sites, alignments, motifs and profiles. + + + beta12orEarlier + beta12orEarlier + + G-protein coupled receptors (GPCRs). + + G protein-coupled receptors (GPCR) true - Nucleotide sequences - - - + - - Protein sequences - - Topic concerning protein sequences and associated concepts such as sequence sites, alignments, motifs and profiles. - beta13 - 1.3 - true - - + + + beta12orEarlier + true + Carbohydrates, typically including structural information. + + + Carbohydrates - + - - Protein interaction networks - - 1.3 - true - - + + + beta12orEarlier + true + Lipids and their structures. + Lipidomics + + + Lipids - + - - Molecular biology - - beta13 - Topic concerning the molecular basis of biological activity, particularly the macromolecules (e.g. proteins and nucleic acids) that are essential to life. - - - + + + beta12orEarlier + true + Small molecules of biological significance, typically archival, curation, processing and analysis of structural information. + Amino acids + Chemical structures + Drug structures + Drug targets + Drugs and target structures + Metabolite structures + Metabolites + Peptides + Peptides and amino acids + Target structures + Targets + Toxins + Toxins and targets + CHEBI:23367 + + + Small molecules include organic molecules, metal-organic compounds, small polypeptides, small polysaccharides and oligonucleotides. Structural data is usually included. + This concept excludes macromolecules such as proteins and nucleic acids. + This includes the structures of drugs, drug target, their interactions and binding affinities. Also the structures of reactants or products of metabolism, for example small molecules such as including vitamins, polyols, nucleotides and amino acids. Also the physicochemical, biochemical or structural properties of amino acids or peptides. Also structural and associated data for toxic chemical substances. + Small molecules + + - + - - Mammals - + + + beta12orEarlier + beta12orEarlier + + + Edit, convert or otherwise change a molecular sequence, either randomly or specifically. + + Sequence editing true - Topic concerning mammals, e.g. information on a specific mammal genome including molecular sequences, genes and annotation. - beta13 - 1.3 - - - + - - Biodiversity - - beta13 - Topic concerning the degree of variation of life forms within a given ecosystem, biome or an entire planet. - http://purl.bioontology.org/ontology/MSH/D044822 - - - + + + beta12orEarlier + true + The archival, processing and analysis of the basic character composition of molecular sequences, for example character or word frequency, ambiguity, complexity, particularly regions of low complexity, and repeats or the repetitive nature of molecular sequences. + Low complexity sequences + Nucleic acid repeats + Protein repeats + Protein sequence repeats + Repeat sequences + Sequence complexity + Sequence composition + Sequence repeats + + + This includes repetitive elements within a nucleic acid sequence, e.g. +long terminal repeats (LTRs); sequences (typically retroviral) directly repeated at both ends of a sequence and other types of repeating unit. + This includes short repetitive subsequences (repeat sequences) in a protein sequence. + Sequence composition, complexity and repeats - + - - Sequence clusters and classification - - Topic concerning the comparison, grouping together and classification of macromolecules on the basis of sequence similarity. - This includes the results of sequence clustering, ortholog identification, assignment to families, annotation etc. - Sequence families - 1.3 + + + beta12orEarlier + 1.3 + + Conserved patterns (motifs) in molecular sequences, that (typically) describe functional or other key sites. + Motifs + + Sequence motifs true - Sequence clusters - beta13 - - - + - - Genetics - - Topic concerning the study of genes, genetic variation and heredity in living organisms. - Gene database - http://purl.bioontology.org/ontology/MSH/D005823 - Genetics data resources - beta13 - Gene resource - - - + + + beta12orEarlier + 1.12 + The comparison of two or more molecular sequences, for example sequence alignment and clustering. + + + The comparison might be on the basis of sequence, physico-chemical or some other properties of the sequences. + Sequence comparison + true - + - - Quantitative genetics - - beta13 - Topic concerning the genes and genetic mechanisms such as Mendelian inheritance that underly continuous phenotypic traits (such as height or weight). - - + + + beta12orEarlier + true + The archival, detection, prediction and analysis of positional features such as functional and other key sites, in molecular sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them. + Functional sites + HMMs + Sequence features + Sequence motifs + Sequence profiles + Sequence sites + + + Sequence sites, features and motifs - + - - Population genetics - - Topic concerning the distribution of allele frequencies in a population of organisms and its change subject to evolutionary processes including natural selection, genetic drift, mutation and gene flow. - beta13 - - - + + + beta12orEarlier + beta12orEarlier + + Search and retrieve molecular sequences that are similar to a sequence-based query (typically a simple sequence). + + The query is a sequence-based entity such as another sequence, a motif or profile. + Sequence database search + true - + - - Regulatory RNA - - Topic concerning regulatory RNA sequences including microRNA (miRNA) and small interfering RNA (siRNA). - 1.3 + + + beta12orEarlier + 1.7 + The comparison and grouping together of molecular sequences on the basis of their similarities. + + + This includes systems that generate, process and analyse sequence clusters. + Sequence clustering true - beta13 - - - + - - Documentation and help - - Topic concerning the documentation of resources such as tools, services and databases and how to get help. - Help - beta13 - Documentation - - - + + + beta12orEarlier + true + Structural features or common 3D motifs within protein structures, including the surface of a protein structure, such as biological interfaces with other molecules. + Protein 3D motifs + Protein structural features + Protein structural motifs + Protein surfaces + Structural motifs + + + This includes conformation of conserved substructures, conserved geometry (spatial arrangement) of secondary structure or protein backbone, solvent-exposed surfaces, internal cavities, the analysis of shape, hydropathy, electrostatic patches, role and functions etc. + Protein structural motifs and surfaces - + - - Genetic organisation - - 1.3 - beta13 - Topic concerning the structural and functional organisation of genes and other genetic elements. + + + beta12orEarlier + 1.3 + + The processing, analysis or use of some type of structural (3D) profile or template; a computational entity (typically a numerical matrix) that is derived from and represents a structure or structure alignment. + + Structural (3D) profiles true - - - + - - Medical informatics - - - Topic concerning the application of information technology to health, disease and biomedicine. - Health informatics - Clinical informatics - Biomedical informatics - Translational medicine - Healthcare informatics - beta13 - Health and disease - Molecular medicine - - - + + + beta12orEarlier + 1.12 + The prediction, modelling, recognition or design of protein secondary or tertiary structure or other structural features. + + + Protein structure prediction + true - + - - Developmental biology - - Topic concerning how organisms grow and develop. - beta13 - - - + + + beta12orEarlier + 1.12 + The folding of nucleic acid molecules and the prediction or design of nucleic acid (typically RNA) sequences with specific conformations. + + + Nucleic acid structure prediction + true - + - - Embryology - - beta13 - Topic concerning the development of organisms between the one-cell stage (typically the zygote) and the end of the embryonic stage. - - - + + + beta12orEarlier + 1.7 + The prediction of three-dimensional structure of a (typically protein) sequence from first principles, using a physics-based or empirical scoring function and without using explicit structural templates. + + + Ab initio structure prediction + true - + - - Anatomy - - beta13 - Topic concerning the form and function of the structures of living organisms. - - - + + + beta12orEarlier + 1.4 + + The modelling of the three-dimensional structure of a protein using known sequence and structural data. + + Homology modelling + true - + - - Literature and reference - - Literature search - beta13 - Literature sources - Topic concerning the scientific literature, reference information and documentation. - http://purl.bioontology.org/ontology/MSH/D011642 - - - + + + beta12orEarlier + true + Molecular flexibility + Molecular motions + The study and simulation of molecular (typically protein) conformation using a computational model of physical forces and computer simulation. + Protein dynamics + + + This includes resources concerning flexibility and motion in protein and other molecular structures. + Molecular dynamics - + - - Biology - - Biological science - beta13 - Topic concerning a particular biological science, especially observable traits such as aspects of biochemistry, physiology, morphology, anatomy, development and so on. - - - + + + beta12orEarlier + true + 1.12 + The modelling the structure of proteins in complex with small molecules or other macromolecules. + + + Molecular docking + true - + - - Data management - - Topic concerning the general handling of data stored in digital archives such as databanks, databases proper, web portals and other data resources. - Databases - Data acquisition - beta13 - http://purl.bioontology.org/ontology/MSH/D030541 - Data handling - Information management - Databases - Knowledge management - Data processing - - - + + + beta12orEarlier + 1.3 + The prediction of secondary or supersecondary structure of protein sequences. + + + Protein secondary structure prediction + true - + - - Sequence feature detection - - 1.3 - Topic concerning the detection of the positional features, such as functional and other key sites, in molecular sequences. + + + beta12orEarlier + 1.3 + The prediction of tertiary structure of protein sequences. + + + Protein tertiary structure prediction true - beta13 - http://purl.bioontology.org/ontology/MSH/D058977 - - - + - - Nucleic acid feature detection - + + + beta12orEarlier + 1.12 + The recognition (prediction and assignment) of known protein structural domains or folds in protein sequence(s). + + + Protein fold recognition true - Topic concerning the detection of positional features such as functional sites in nucleotide sequences. - beta13 - 1.3 - - - + - - Protein feature detection - - beta13 - Topic concerning the detection, identification and analysis of positional protein sequence features, such as functional sites. - 1.3 + + + beta12orEarlier + 1.7 + The alignment of molecular sequences or sequence profiles (representing sequence alignments). + + + This includes the generation of alignments (the identification of equivalent sites), the analysis of alignments, editing, visualisation, alignment databases, the alignment (equivalence between sites) of sequence profiles (representing sequence alignments) and so on. + Sequence alignment true - - - + - - Biological system modelling - - BioCatalogue:Model Analysis - BioCatalogue:Model Execution - 1.2 + + + beta12orEarlier + 1.7 + The superimposition of molecular tertiary structures or structural (3D) profiles (representing a structure or structure alignment). + + + This includes the generation, storage, analysis, rendering etc. of structure alignments. + Structure alignment true - beta13 - Topic for modelling biological systems in mathematical terms. - - - + - - Data acquisition - - Topic concerning the acquisition of biological data. - beta13 - - + + + beta12orEarlier + 1.3 + The alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment). + + + Threading + true - + - - Genes and proteins resources - - 1.3 - Topic concerning specific genes and/or their encoded proteins or a family or other grouping of related genes and proteins. - Gene family - beta13 - Gene and protein families + + + beta12orEarlier + 1.3 + + Sequence profiles; typically a positional, numerical matrix representing a sequence alignment. + + Sequence profiles include position-specific scoring matrix (position weight matrix), hidden Markov models etc. + Sequence profiles and HMMs true - - - + - - Protein topological domains - - - Protein features (topological domains) - Topic concerning topological domains such as cytoplasmic regions in a protein. - 1.8 - - - + + + beta12orEarlier + 1.3 + + The reconstruction of a phylogeny (evolutionary relatedness amongst organisms), for example, by building a phylogenetic tree. + + Currently too specific for the topic sub-ontology (but might be unobsoleted). + Phylogeny reconstruction + true - + - - Protein variants - - beta13 - Topic concerning protein sequence variants produced e.g. from alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting. - - - + + + + beta12orEarlier + true + The integrated study of evolutionary relationships and whole genome data, for example, in the analysis of species trees, horizontal gene transfer and evolutionary reconstruction. + + + + Phylogenomics - + - - Expression signals - - - beta13 - Topic concerning regions within a nucleic acid sequence containing a signal that alters a biological function. - Nucleic acid features (expression signal) - - - + + + beta12orEarlier + beta13 + + Simulated polymerase chain reaction (PCR). + + Virtual PCR + true - + - - DNA binding sites - - - This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes). - beta13 - Topic concerning nucleic acids binding to some other molecule. - Nucleic acid features (binding) - - - + + + beta12orEarlier + true + The assembly of fragments of a DNA sequence to reconstruct the original sequence. + Assembly + + + Assembly has two broad types, de-novo and re-sequencing. Re-sequencing is a specialised case of assembly, where an assembled (typically de-novo assembled) reference genome is available and is about 95% identical to the re-sequenced genome. All other cases of assembly are 'de-novo'. + Sequence assembly - + - - Nucleic acid repeats - - beta13 - This includes long terminal repeats (LTRs); sequences (typically retroviral) directly repeated at both ends of a defined sequence and other types of repeating unit. - Topic concerning repetitive elements within a nucleic acid sequence. - - - + + + beta12orEarlier + true + Stable, naturally occuring mutations in a nucleotide sequence including alleles, naturally occurring mutations such as single base nucleotide substitutions, deletions and insertions, RFLPs and other polymorphisms. + DNA variation + Mutation + Polymorphism + Somatic mutations + + + Genetic variation + http://purl.bioontology.org/ontology/MSH/D014644 - + - - DNA replication and recombination - - This includes binding sites for initiation of replication (origin of replication), regions where transfer is initiated during the conjugation or mobilization (origin of transfer), starting sites for DNA duplication (origin of replication) and regions which are eliminated through any of kind of recombination. - Nucleosome exclusion sequences - Nucleic acid features (replication and recombination) - beta13 - Topic concerning DNA replication or recombination. - - - + + + beta12orEarlier + 1.3 + + Microarrays, for example, to process microarray data or design probes and experiments. + + Microarrays + http://purl.bioontology.org/ontology/MSH/D046228 + true - + - - Signal or transit peptide - - Topic concerning coding sequences for a signal or transit peptide. - beta13 - Nucleic acid features (signal or transit peptide) - A signal peptide coding sequence encodes an N-terminal domain of a secreted protein, which is involved in attaching the polypeptide to a membrane leader sequence. A transit peptide coding sequence encodes an N-terminal domain of a nuclear-encoded organellar protein; which is involved in import of the protein into the organelle. - - - + + + beta12orEarlier + true + VT 3.1.7 Pharmacology and pharmacy + The study of drugs and their effects or responses in living systems. + Computational pharmacology + Pharmacoinformatics + + + + Pharmacology - + - - Sequence tagged sites - - Nucleic acid features (STS) - Topic concerning sequence tagged sites (STS) in nucleic acid sequences. - beta13 - Sequence tagged sites are short DNA sequences that are unique within a genome and serve as a mapping landmark, detectable by PCR they allow a genome to be mapped via an ordering of STSs. - - - + + + beta12orEarlier + true + http://edamontology.org/topic_0197 + The analysis of levels and patterns of synthesis of gene products (proteins and functional RNA) including interpretation in functional terms of gene expression data. + Codon usage + DNA microarrays + Gene expression profiling + Transcription + + + + Gene expression levels are analysed by identifying, quantifying or comparing mRNA transcripts, for example using microarrays, RNA-seq, northern blots, gene-indexed expression profiles etc. + This includes the study of codon usage in nucleotide sequence(s), genetic codes and so on. + Gene expression + + http://purl.bioontology.org/ontology/MSH/D015870 - + - - Sequencing - - Topic concerning the determination of complete (typically nucleotide) sequences, including those of genomes (full genome sequencing, de novo sequencing and resequencing), amplicons and transcriptomes. - http://purl.bioontology.org/ontology/MSH/D059014 - 1.1 - NGS - Next generation sequencing - Next gen sequencing - - - + + + beta12orEarlier + true + The regulation of gene expression. + Regulatory genomics + + + Gene regulation - + - - ChIP-seq - - true - 1.3 - Chip sequencing - Chip seq - 1.1 - Chip-sequencing - Topic concerning the analysis of protein-DNA interactions where chromatin immunoprecipitation (ChIP) is used in combination with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. - - + + + + beta12orEarlier + true + The influence of genotype on drug response, for example by correlating gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity. + Pharmacogenetics + + + + Pharmacogenomics - + - - RNA-Seq - - Small RNA-seq - Whole transcriptome shotgun sequencing - RNA-seq - 1.1 - 1.3 - A topic concerning high-throughput sequencing of cDNA to measure the RNA content (transcriptome) of a sample, for example, to investigate how different alleles of a gene are expressed, detect post-transcriptional mutations or identify gene fusions. - Small RNA-Seq - WTSS - This includes small RNA profiling (small RNA-Seq), for example to find novel small RNAs, characterize mutations and analyze expression of small RNAs. - true - - + + + + beta12orEarlier + true + VT 3.1.4 Medicinal chemistry + The design and chemical synthesis of bioactive molecules, for example drugs or potential drug compounds, for medicinal purposes. + Drug design + + + + This includes methods that search compound collections, generate or analyse drug 3D conformations, identify drug targets with structural docking etc. + Medicinal chemistry - + - - DNA methylation - - Topic concerning DNA methylation including bisulfite sequencing, methylation sites and analysis, for example of patterns and profiles of DNA methylation in a population, tissue etc. + + + beta12orEarlier + 1.3 + + Information on a specific fish genome including molecular sequences, genes and annotation. + + Fish true - 1.3 - http://purl.bioontology.org/ontology/MSH/D019175 - 1.1 - - - + - - Metabolomics - - Topic concerning the systematic study of metabolites, the chemical processes they are involved, and the chemical fingerprints of specific cellular processes in a whole cell, tissue, organ or organism. - http://purl.bioontology.org/ontology/MSH/D055432 - 1.1 - - - + + + beta12orEarlier + 1.3 + + Information on a specific fly genome including molecular sequences, genes and annotation. + + Flies + true - + - - Epigenomics - - - Epigenetics concerns the heritable changes in gene expression owing to mechanisms other than DNA sequence variation. - 1.1 - http://purl.bioontology.org/ontology/MSH/D057890 - Topic concerning the study of the epigenetic modifications of a whole cell, tissue, organism etc. - - - + + + beta12orEarlier + Information on a specific mouse or rat genome including molecular sequences, genes and annotation. + + + The resource may be specific to a group of mice / rats or all mice / rats. + Mice or rats - + - - Metagenomics - - - http://purl.bioontology.org/ontology/MSH/D056186 - Ecogenomics - Community genomics - Environmental genomics - Topic concerning the study of genetic material recovered from environmental samples, and associated environmental data. - 1.1 - - - + + + beta12orEarlier + 1.3 + + Information on a specific worm genome including molecular sequences, genes and annotation. + + Worms + true - + - - Structural variation - - - 1.1 - Topic concerning variation in chromosome structure including microscopic and submicroscopic types of variation such as deletions, duplications, copy-number variants, insertions, inversions and translocations. - Genomic structural variation - - + + + beta12orEarlier + 1.3 + The processing and analysis of the bioinformatics literature and bibliographic data, such as literature search and query. + + + Literature analysis + true - + - - DNA packaging - - beta12orEarlier - Topic concerning DNA-histone complexes (chromatin), organisation of chromatin into nucleosomes and packaging into higher-order structures. - http://purl.bioontology.org/ontology/MSH/D042003 - - + + + + beta12orEarlier + The processing and analysis of natural language, such as scientific literature in English, in order to extract data and information, or to enable human-computer interaction. + NLP + BioNLP + Literature mining + Text analytics + Text data mining + Text mining + + + + Natural language processing + + + - + - - DNA-Seq - - 1.1 - A topic concerning high-throughput sequencing of randomly fragmented genomic DNA, for example, to investigate whole-genome sequencing and resequencing, SNP discovery, identification of copy number variations and chromosomal rearrangements. - 1.3 - DNA-seq - true - - + + + beta12orEarlier + Deposition and curation of database accessions, including annotation, typically with terms from a controlled vocabulary. + Database curation + + + + Data submission, annotation and curation - + - - RNA-Seq alignment - + + + beta12orEarlier + 1.13 + The management and manipulation of digital documents, including database records, files and reports. + + + Document, record and content management true - Topic concerning the alignment of sequences of (typically millions) of short reads to a reference genome. This is a specialised topic within sequence alignment, especially because of complications arising from RNA splicing. - 1.3 - RNA-seq alignment - beta12orEarlier - - - + - - ChIP-on-chip - + + + beta12orEarlier + beta12orEarlier + + Annotation of a molecular sequence. + + Sequence annotation true - 1.3 - Topic concerning experimental techniques that combine chromatin immunoprecipitation ('ChIP') with microarray ('chip'). ChIP-on-chip is used for high-throughput study protein-DNA interactions. - 1.1 - ChIP-chip - - - + - - Data security - - Topic concerning the protection of data, for example, patient health data. - Privacy - 1.3 - Security - Security - - + + + beta12orEarlier + beta12orEarlier + + + Annotation of a genome. + + Genome annotation + true - + - - Sample collections - - samples - biobanking - Topic concerning biological samples and specimens. - 1.3 - biosamples - Specimen collections - - - + + + + beta12orEarlier + Spectroscopy + An analytical technique that exploits the magenetic properties of certain atomic nuclei to provide information on the structure, dynamics, reaction state and chemical environment of molecules. + NMR spectroscopy + Nuclear magnetic resonance spectroscopy + HOESY + Heteronuclear Overhauser Effect Spectroscopy + NOESY + Nuclear Overhauser Effect Spectroscopy + ROESY + Rotational Frame Nuclear Overhauser Effect Spectroscopy + + + + NMR - + - - Biochemistry - - - Chemical biology - 1.3 - Topic concerning chemical substances and physico-chemical processes and that occur within living organisms. - Biological chemistry - - - + + + beta12orEarlier + 1.12 + The classification of molecular sequences based on some measure of their similarity. + + + Methods including sequence motifs, profile and other diagnostic elements which (typically) represent conserved patterns (of residues or properties) in molecular sequences. + Sequence classification + true - + - - Phylogenetics - - - Topic concerning the study of evolutionary relationships amongst organisms from analysis of genetic information (typically gene or protein sequences). - 1.3 - http://purl.bioontology.org/ontology/MSH/D010802 - - + + + beta12orEarlier + 1.3 + + primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc. + + Protein classification + true - + - - Epigenetics - - Topic concerning the study of heritable changes, for example in gene expression or phenotype, caused by mechanisms other than changes in the DNA sequence. - DNA methylation - This includes sub-topics such as histone modification and DNA methylation. - http://purl.bioontology.org/ontology/MSH/D019175 - Histone modification - 1.3 - - - + + + beta12orEarlier + beta12orEarlier + + Sequence motifs, or sequence profiles derived from an alignment of molecular sequences of a particular type. + + This includes comparison, discovery, recognition etc. of sequence motifs. + Sequence motif or profile + true - + - - Biotechnology - - Topic concerning the exploitation of biological process, structure and function for industrial purposes, for example the genetic manipulation of microorganisms for the antibody production. - 1.3 - - - + + + beta12orEarlier + true + Protein chemical modifications, e.g. post-translational modifications. + Protein post-translational modification + Post-translation modifications + Protein chemical modifications + Protein post-translational modifications + GO:0006464 + MOD:00000 + + + EDAM does not describe all possible protein modifications. For fine-grained annotation of protein modification use the Gene Ontology (children of concept GO:0006464) and/or the Protein Modifications ontology (children of concept MOD:00000) + Protein modifications - + - - Phenomics - - - Topic concerning phenomes, or the study of the change in phenotype (the physical and biochemical traits of organisms) in response to genetic and environmental factors. - 1.3 - - - + + + beta13 + true + http://edamontology.org/topic_3076 + Molecular interactions, biological pathways, networks and other models. + Biological models + Biological networks + Biological pathways + Cellular process pathways + Disease pathways + Environmental information processing pathways + Gene regulatory networks + Genetic information processing pathways + Interactions + Molecular interactions + Networks + Pathways + Signal transduction pathways + Signaling pathways + + + + Molecular interactions, pathways and networks - + - - Evolutionary biology - - Topic concerning the evolutionary processes, from the genetic to environmental scale, that produced life in all its diversity. - 1.3 - - - + + + beta12orEarlier + true + VT 1.3 Information sciences + VT 1.3.3 Information retrieval + VT 1.3.4 Information management + VT 1.3.5 Knowledge management + VT 1.3.99 Other + The study and practice of information processing and use of computer information systems. + Information management + Information science + Knowledge management + + Informatics - + - - Physiology - - 1.3 - Topic concerning the functions of living organisms and their constituent parts. - - - + + + beta12orEarlier + 1.3 + Data resources for the biological or biomedical literature, either a primary source of literature or some derivative. + + + Literature data resources + true - + - - Microbiology - - Topic concerning the biology of microorganisms. - 1.3 - - - + + + beta12orEarlier + true + + Laboratory management and resources, for example, catalogues of biological resources for use in the lab including cell lines, viruses, plasmids, phages, DNA probes and primers and so on. + Laboratory resources + + + + Laboratory information management - + - - Parasitology - - Topic concerning the biology of parasites. - Topic concerning the branch of medicine that deals with the anatomy, functions and disorders of the nervous system. - 1.3 - - - + + + beta12orEarlier + 1.3 + + General cell culture or data on a specific cell lines. + + Cell and tissue culture + true - + - - Medicine - - Experimental medicine - Topic concerning research in support of healing by diagnosis, treatment, and prevention of disease. - 1.3 - Biomedical research - - - + + + beta12orEarlier + true + Environmental science + VT 1.5.15 Ecology + The ecological and environmental sciences and especially the application of information technology (ecoinformatics). + Computational ecology + Ecoinformatics + Ecological informatics + + + + Ecology + http://purl.bioontology.org/ontology/MSH/D004777 - + - - Neurobiology - - Neuroscience - 1.3 - Topic concerning the study of the nervous system and brain; its anatomy, physiology and function. - - - + + + + beta12orEarlier + Electron diffraction experiment + The study of matter by studying the interference pattern from firing electrons at a sample, to analyse structures at resolutions higher than can be achieved using light. + + Electron crystallography + SEM + Scanning electron microscopy + Single particle electron microscopy + TEM + Transmission electron microscopy + + + + Electron microscopy - + - - Public health and epidemiology - - Topic concerning the the patterns, cause, and effect of disease within populations. - 1.3 - Public health - Epidemiology - - - + + + beta12orEarlier + beta13 + + The cell cycle including key genes and proteins. + + Cell cycle + true - + - - Biophysics - - - 1.3 - Topic concerning the use of physics to study biological system. - - - + + + beta12orEarlier + 1.13 + The physicochemical, biochemical or structural properties of amino acids or peptides. + + + Peptides and amino acids + true - + - - Computational biology - - - BioCatalogue:Model Execution - This includes the modeling and treatment of biological processes and systems in mathematical terms (theoretical biology). - Mathematical biology - Topic concerning the development and application of theory, analytical methods, mathematical models and computational simulation of biological systems. - Theoretical biology - 1.3 - Biomathematics - - - + + + beta12orEarlier + 1.3 + + A specific organelle, or organelles in general, typically the genes and proteins (or genome and proteome). + + Organelles + true - + - - Transcriptomics - - - Transcriptome - 1.3 - Topic concerning the analysis of transcriptomes, or a set of all the RNA molecules in a specific cell, tissue etc. - - - + + + beta12orEarlier + 1.3 + + Ribosomes, typically of ribosome-related genes and proteins. + + Ribosomes + true - + - - Chemistry - - 1.3 - Topic concerning the composition and properties of matter, reactions, and the use of reactions to create new substances. - - - + + + beta12orEarlier + beta13 + + A database about scents. + + Scents + true - + - - Mathematics - - Topic concerning the is the study of numbers (quantity) and other topics including structure, space, and change. - Maths - 1.3 - - - + + + beta12orEarlier + 1.13 + The structures of drugs, drug target, their interactions and binding affinities. + + + Drugs and target structures + true - + - - Computer science - - 1.3 - Topic concerning the theory and practical use of computer systems. - - - + + + beta12orEarlier + true + A specific organism, or group of organisms, used to study a particular aspect of biology. + Organisms + + + + This may include information on the genome (including molecular sequences and map, genes and annotation), proteome, as well as more general information about an organism. + Model organisms - + - - Physics - - Topic concerning the study of matter, space and time, and related concepts such as energy and force. - 1.3 - - - + + + beta12orEarlier + true + Whole genomes of one or more organisms, or genomes in general, such as meta-information on genomes, genome projects, gene names etc. + Personal genomics + + + + Genomics + http://purl.bioontology.org/ontology/MSH/D023281 - + - - RNA splicing - - - Topic concerning RNA splicing; post-transcription RNA modification involving the removal of introns and joining of exons. - This includes the study of splice sites, splicing patterns, splice alternatives or variants, isoforms, etc. - 1.3 - - + + + + beta12orEarlier + true + Particular gene(s), gene family or other gene group or system and their encoded proteins.Primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc., curation of a particular protein or protein family, or any other proteins that have been classified as members of a common group. + Genes, gene family or system + Gene families + Gene family + Gene system + Protein families + Protein sequence classification + + + + A protein families database might include the classifier (e.g. a sequence profile) used to build the classification. + Gene and protein families - + - - Molecular genetics - - Topic concerning the structure and function of genes at a molecular level. - 1.3 - - - + + + beta12orEarlier + 1.13 + Study of chromosomes. + + + Chromosomes + true - + - - Respiratory medicine - - Respiratory disease - Pulmonary medicine - 1.3 - Pulmonary disorders - Pulmonology - Topic concerning the study of respiratory system. - - - + + + beta12orEarlier + true + The study of genetic constitution of a living entity, such as an individual, and organism, a cell and so on, typically with respect to a particular observable phenotypic traits, or resources concerning such traits, which might be an aspect of biochemistry, physiology, morphology, anatomy, development and so on. + Genotype and phenotype resources + Genotyping + Phenotyping + + + + Genotype and phenotype - + - - Metabolic disease - - 1.4 - 1.3 + + + beta12orEarlier + beta12orEarlier + + Gene expression e.g. microarray data, northern blots, gene-indexed expression profiles etc. + + Gene expression and microarray true - Topic concerning the study of metabolic diseases. - - - + - - Infectious disease - - Transmissable disease - Communicable disease - Topic concerning the branch of medicine that deals with the prevention, diagnosis and management of transmissable disease with clinically evident illness resulting from infection with pathogenic biological agents (viruses, bacteria, fungi, protozoa, parasites and prions). - 1.3 - - - + + + beta12orEarlier + true + Molecular probes (e.g. a peptide probe or DNA microarray probe) or PCR primers and hybridisation oligos in a nucleic acid sequence. + + Primers + Probes + + + This includes the design of primers for PCR and DNA amplification or the design of molecular probes. + Probes and primers + http://purl.bioontology.org/ontology/MSH/D015335 - + - - Rare diseases - - 1.3 - Topic concerning the study of rare diseases. - - - + + + beta12orEarlier + true + VT 3.1.6 Pathology + Diseases, including diseases in general and the genes, gene variations and proteins involved in one or more specific diseases. + Disease + + + + Pathology - + - - Computational chemistry - - - 1.3 - Topic concerning the development and application of theory, analytical methods, mathematical models and computational simulation of chemical systems. - - - + + + beta12orEarlier + 1.3 + + A particular protein, protein family or other group of proteins. + Specific protein + + Specific protein resources + true - + - - Neurology - - Topic concerning the branch of medicine that deals with the anatomy, functions and disorders of the nervous system. - Neurological disorders - 1.3 - - - + + + beta12orEarlier + true + VT 1.5.25 Taxonomy + Organism classification, identification and naming. + + + Taxonomy - + - - Cardiology - - Cardiovascular medicine - 1.3 - Topic concerning the diseases and abnormalities of the heart and circulatory system. - Heart disease - Cardiovascular disease - - - + + + beta12orEarlier + 1.8 + Archival, processing and analysis of protein sequences and sequence-based entities such as alignments, motifs and profiles. + + + Protein sequence analysis + true - + - - Drug discovery - - - This includes methods that search compound collections, generate or analyse drug 3D conformations, identify drug targets with structural docking etc. - Topic concerning the discovery and design of drugs or potential drug compounds. - 1.3 - - - + + + beta12orEarlier + 1.8 + The archival, processing and analysis of nucleotide sequences and and sequence-based entities such as alignments, motifs and profiles. + + + + Nucleic acid sequence analysis + true - + - - Biobank - - biobanking - 1.3 - Topic concerning repositories of biological samples, typically human, for basic biological and clinical research. - Tissue collection - - - + + + beta12orEarlier + 1.3 + + The repetitive nature of molecular sequences. + + Repeat sequences + true - + - - Mouse clinic - - 1.3 - Topic concerning laboratory study of mice, for example, phenotyping, and mutagenesis of mouse cell lines. - - - + + + beta12orEarlier + 1.3 + + The (character) complexity of molecular sequences, particularly regions of low complexity. + + Low complexity sequences + true - + - - Microbial collection - - 1.3 - Topic concerning collections of microbial cells including bacteria, yeasts and moulds. - - - + + + beta12orEarlier + beta13 + + A specific proteome including protein sequences and annotation. + + Proteome + true - + - - Cell culture collection - - Topic concerning collections of cells grown under laboratory conditions, specifically, cells from multi-cellular eukaryotes and especially animal cells. - 1.3 - - - + + + beta12orEarlier + DNA sequences and structure, including processes such as methylation and replication. + DNA analysis + Ancient DNA + Chromosomes + + + The DNA sequences might be coding or non-coding sequences. + DNA - + - - Clone library - - 1.3 - Topic concerning collections of DNA, including both collections of cloned molecules, and populations of micro-organisms that store and propagate cloned DNA. - - - + + + beta12orEarlier + 1.13 + Protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames + + + Coding RNA + true - + - - Translational medicine - - Topic concerning 'translating' the output of basic and biomedical research into better diagnostic tools, medicines, medical procedures, policies and advice. - 1.3 - - - + + + + beta12orEarlier + true + Non-coding or functional RNA sequences, including regulatory RNA sequences, ribosomal RNA (rRNA) and transfer RNA (tRNA). + Functional RNA + Non-coding RNA + Regulatory RNA + miRNA + microRNA + ncRNA + piRNA + piwi-interacting RNA + siRNA + small interfering RNA + small nuclear RNA + small nucleolar RNA + snRNA + snoRNA + + + Non-coding RNA includes piwi-interacting RNA (piRNA), small nuclear RNA (snRNA) and small nucleolar RNA (snoRNA). Regulatory RNA includes microRNA (miRNA) - short single stranded RNA molecules that regulate gene expression, and small interfering RNA (siRNA). + Functional, regulatory and non-coding RNA - + - - Compound libraries and screening - - Translational medicine - Chemical library - Topic concerning collections of chemicals, typically for use in high-throughput screening experiments. - Compound library - Chemical screening - 1.3 - - - + + + 1.3 + + One or more ribosomal RNA (rRNA) sequences. + + rRNA + true - + - - Biomedical science - - - Topic concerning biological science that is (typically) performed in the context of medicine. - 1.3 - - - + + + 1.3 + + One or more transfer RNA (tRNA) sequences. + + tRNA + true - + - - Data identity and mapping - - 1.3 - Topic concerning the identity of biological data and the mapping of entities in different databases. - - - + + + beta12orEarlier + 1.8 + Protein secondary structure or secondary structure alignments. + + + This includes assignment, analysis, comparison, prediction, rendering etc. of secondary structure data. + Protein secondary structure + true - + - - Sequence search - - 1.3 - Sequence database search - Topic concerning the search and retrieval from a database on the basis of molecular sequence similarity. - - + + + beta12orEarlier + 1.3 + + RNA secondary or tertiary structure and alignments. + + RNA structure + true - + - - Biomarkers - - Diagnostic markers - 1.4 - Topic concerning objective indicators of biological state often used to assess health, and determinate treatment. - - + + + beta12orEarlier + 1.8 + Protein tertiary structures. + + + Protein tertiary structure + true - + - - Laboratory techniques - - Topic concerning the procedures used to conduct an experiment. - Lab techniques - 1.4 - - - + + + beta12orEarlier + 1.3 + + Classification of nucleic acid sequences and structures. + + Nucleic acid classification + true - + - - Data analysis - - Topic concerning the process of systematically applying statistical and / or logical techniques to describe and illustrate, condense and recap, and evaluate data. - 1.4 - - - + + + beta12orEarlier + 1.14 + Primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc., curation of a particular protein or protein family, or any other proteins that have been classified as members of a common group. + + + Protein families + true - + - - Data integration - - Topic concerning the combination of data from different sources to provide users with a unified view of these data. - 1.4 - - - + + + beta12orEarlier + true + Protein tertiary structural domains and folds in a protein or polypeptide chain. + Intramembrane regions + Protein domains + Protein folds + Protein membrane regions + Protein structural domains + Protein topological domains + Protein transmembrane regions + Transmembrane regions + + + This includes topological domains such as cytoplasmic regions in a protein. + This includes trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements. For example, the location and size of the membrane spanning segments and intervening loop regions, transmembrane region IN/OUT orientation relative to the membrane, plus the following data for each amino acid: A Z-coordinate (the distance to the membrane center), the free energy of membrane insertion (calculated in a sliding window over the sequence) and a reliability score. The z-coordinate implies information about re-entrant helices, interfacial helices, the tilt of a transmembrane helix and loop lengths. + Protein folds and structural domains - + - - Biomaterials - - Diagnostic markers - 1.4 - Topic concerning any matter, surface or construct that interacts with a biological system. - - - + + + beta12orEarlier + 1.3 + Nucleotide sequence alignments. + + + Nucleic acid sequence alignment + true - + - - Chemical biology - - - 1.4 - Topic concerning the use of synthetic chemistry to study and manipulate biological systems. - - - + + + beta12orEarlier + 1.3 + + Protein sequence alignments. + + A sequence profile typically represents a sequence alignment. + Protein sequence alignment + true - + - - Analytical chemistry - - 1.4 - Topic concerning the study of the separation, identification, and quantification of the chemical components of natural and artificial materials. - - - + + + beta12orEarlier + 1.3 + + + The archival, detection, prediction and analysis of +positional features such as functional sites in nucleotide sequences. + + Nucleic acid sites and features + true - + - - Synthetic chemistry - - Synthetic organic chemistry - 1.4 - Topic concerning the use of chemistry to create new compounds. - - - + + + beta12orEarlier + 1.3 + + + The detection, identification and analysis of positional features in proteins, such as functional sites. + + Protein sites and features + true - + - - Computer programming - - Topic concerning the process that leads from an original formulation of a computing problem to executable programs. - 1.4 - Software development - - - + + + + + beta12orEarlier + Proteins that bind to DNA and control transcription of DNA to mRNA (transcription factors) and also transcriptional regulatory sites, elements and regions (such as promoters, enhancers, silencers and boundary elements / insulators) in nucleotide sequences. + -10 signals + -35 signals + Attenuators + CAAT signals + CAT box + CCAAT box + CpG islands + Enhancers + GC signals + Isochores + Promoters + TATA signals + TFBS + Terminators + Transcription factor binding sites + Transcription factors + Transcriptional regulatory sites + + + This includes CpG rich regions (isochores) in a nucleotide sequence. + This includes promoters, CAAT signals, TATA signals, -35 signals, -10 signals, GC signals, primer binding sites for initiation of transcription or reverse transcription, enhancer, attenuator, terminators and ribosome binding sites. + Transcription factor proteins either promote (as an activator) or block (as a repressor) the binding to DNA of RNA polymerase. Regulatory sites including transcription factor binding site as well as promoters, enhancers, silencers and boundary elements / insulators. + Transcription factors and regulatory sites - + - - Drug development - - 1.4 - Topic concerning the process of bringing a new drug to market once a lead compounds has been identified through drug discovery. - Medicine development - Drug development science - Medicines development - - - + + + beta12orEarlier + 1.0 + + + Protein phosphorylation and phosphorylation sites in protein sequences. + + Phosphorylation sites + true - + - - Drug formulation and delivery - - Drug delivery - Drug formulation - Topic concerning the process of formulating abd administering a pharmaceutical compound to achieve a therapeutic effect. - 1.4 - - - + + + beta12orEarlier + 1.13 + Metabolic pathways. + + + Metabolic pathways + true - + - - Pharmacokinetics and pharmacodynamics - - Pharmacodynamics - Pharmacokinetics - Topic concerning the study of how a drug interacts with the body. - Drug distribution - 1.4 - Drug excretion - Drug absorption - ADME - Drug metabolism - Drug metabolism - - - + + + beta12orEarlier + 1.13 + Signaling pathways. + + + Signaling pathways + true - + - - Medicines research and development - Medicine research and development - - Health care research - Drug discovery and development - 1.4 - Topic concerning the discovery, development and approval of medicines. - - - + + + beta12orEarlier + 1.3 + + + Protein and peptide identification + true - + - - Safety sciences - - 1.4 - Drug safety - Topic concerning the safety (or lack) of drugs and other medical interventions. - - - + + + beta12orEarlier + Biological or biomedical analytical workflows or pipelines. + Pipelines + + Workflows - + - - Pharmacovigilence - - 1.4 - Pharmacovigilence concerns safety once a drug has gone to market. - Topic concerning the detection, assesment, understanding and prevention of adverse effects of medicines. - - - + + + beta12orEarlier + 1.0 + + Structuring data into basic types and (computational) objects. + + Data types and objects + true - + - - Preclinical and clinical studies - - Topic concerning the testing of new medicines, vaccines or procedures on animals (preclinical) and humans (clinical) prior to their approval by regulatory authorities. - Preclinical studies - 1.4 - Clinical studies - - - + + + 1.3 + + + Theoretical biology + true - + - - Imaging - - This includes diffraction experiments that are based upon the interference of waves, typically electromagnetic waves such as X-rays or visible light, by some object being studied, typical in order to produce an image of the object or determine its structure. - 1.4 - Microscopy - Diffraction experiment - Topic concerning the visual representation of an object. - - - + + + beta12orEarlier + 1.3 + + Mitochondria, typically of mitochondrial genes and proteins. + + Mitochondria + true - + - - Biological imaging - - 1.4 - Topic concerning the use of imaging techniques to understand biology. - - - + + + beta12orEarlier + Botany + Plant biology + Plant science + VT 1.5.10 Botany + VT 1.5.22 Plant science + Plants, e.g. information on a specific plant genome including molecular sequences, genes and annotation. + Plant + + + The resource may be specific to a plant, a group of plants or all plants. + Plants - + - - Medical imaging - - Topic concerning the use of imaging techniques for clinical purposes for medical research. - 1.4 - - - + + + beta12orEarlier + Virology + VT 1.5.28 Virology + Viruses, e.g. sequence and structural data, interactions of viral proteins, or a viral genome including molecular sequences, genes and annotation. + + + The resource may be specific to a virus, a group of viruses or all viruses. + Viruses - + - - Light microscopy - - Topic concerning the use of optical instruments to magnify the image of an object. - 1.4 - - - + + + beta12orEarlier + Mycology + VT 1.5.21 Mycology + Fungi and molds, e.g. information on a specific fungal genome including molecular sequences, genes and annotation. + Yeast + + + The resource may be specific to a fungus, a group of fungi or all fungi. + Fungi - + - - Laboratory animal science - - 1.4 - Topic concerning the use of animals and alternatives in experimental research. - - - + + + beta12orEarlier + Pathogens, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation. + + + The resource may be specific to a pathogen, a group of pathogens or all pathogens. + Pathogens - + - - Marine biology - - 1.4 - Topic concerning the study of organisms in the ocean or brackish waters. - - - + + + beta12orEarlier + 1.3 + + Arabidopsis-specific data. + + Arabidopsis + true - + - - Molecular medicine - - 1.4 - Topic concerning the identification of molecular and genetic causes of disease and the development of interventions to correct them. - - - + + + beta12orEarlier + 1.3 + + Rice-specific data. + + Rice + true - + - - Nutritional science - - Topic concerning the study of the effects of food components on the metabolism, health, performance and disease resistance of humans and animals. It also includes the study of human behaviours related to food choices. - 1.4 - Nutrition science - - - + + + beta12orEarlier + 1.3 + + Informatics resources that aim to identify, map or analyse genetic markers in DNA sequences, for example to produce a genetic (linkage) map of a chromosome or genome or to analyse genetic linkage and synteny. + + Genetic mapping and linkage + true - + - - Omics - - Topic concerning the collective characterisation and quantification of pools of biological molecules that translate into the structure, function, and dynamics of an organism or organisms. - 1.4 - - - + + + beta12orEarlier + true + The study (typically comparison) of the sequence, structure or function of multiple genomes. + + + + Comparative genomics - + - - Quality affairs - - Good clinical practice - Good manufacturing practice - Topic concerning the processes that need to be in place to ensure the quality of products for human or animal use. - Quality assurance - Good laboratory practice - 1.4 - - - + + + beta12orEarlier + Mobile genetic elements, such as transposons, Plasmids, Bacteriophage elements and Group II introns. + Transposons + + + Mobile genetic elements - + - - Regulatory affairs - - Topic concerning the protection of public health by controlling the safety and efficacy of products in areas including pharmaceuticals, veterinary medicine, medical devices, pesticides, agrochemicals, cosmetics, and complementary medicines. - 1.4 - - - + + + beta12orEarlier + beta13 + + Human diseases, typically describing the genes, mutations and proteins implicated in disease. + + Human disease + true - + - - Regnerative medicine - - Stem cell research - 1.4 - Topic concerning biomedical approaches to clinical interventions that involve the use of stem cells. - - - + + + beta12orEarlier + true + VT 3.1.3 Immunology + The application of information technology to immunology such as immunological processes, immunological genes, proteins and peptide ligands, antigens and so on. + Computational immunology + Immunoinformatics + + + + Immunology + http://purl.bioontology.org/ontology/MSH/D007120 + http://purl.bioontology.org/ontology/MSH/D007125 - + - - Systems medicine - - 1.4 - Topic concerning an interdisciplinary field of study that looks at the dynamic systems of the human body as part of an integrted whole, incoporating biochemical, physiological, and environmental interactions that sustain life. - - - + + + beta12orEarlier + true + Lipoproteins (protein-lipid assemblies), and proteins or region of a protein that spans or are associated with a membrane. + Lipoproteins + Membrane proteins + Transmembrane proteins + + + Membrane and lipoproteins - + - - Veterinary medicine - - 1.4 - Topic concerning the branch of medicine that deals with the prevention, diagnosis, and treatment of disease, disorder and injury in animals. - - - + + + beta12orEarlier + true + Proteins that catalyze chemical reaction, the kinetics of enzyme-catalysed reactions, enzyme nomenclature etc. + Enzymology + + + Enzymes - + - - Bioengineering - - 1.4 - Diagnostic markers - Topic concerning the application of biological concepts and methods to the analytical and synthetic methodologies of engineering. - - - + + + beta12orEarlier + 1.13 + PCR primers and hybridisation oligos in a nucleic acid sequence. + + + Primers + true - + - - Geriatric medicine - - Ageing - Topic concerning the branch of medicine dealing with the diagnosis, treatment and prevention of disease in older people, and the problems specific to aging. - Aging - 1.4 - Geriatrics - - - + + + beta12orEarlier + 1.13 + Regions or sites in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript. + + + PolyA signal or sites + true - + - - Allergy, clinical immunology and immunotherapeutics. - - Topic concerning health issues related to the immune system and their prevention, diagnosis and mangement. - 1.4 - Immune disorders - Clinical immunology - Immunomodulators - Allergy - Immunotherapeutics - - - + + + beta12orEarlier + 1.13 + CpG rich regions (isochores) in a nucleotide sequence. + + + CpG island and isochores + true - + - - Pain medicine - - Topic concerning with the prevention of pain and the evaluation, treatment and rehabilitation of persons in pain. - Ageing - 1.4 - Algiatry - - - + + + beta12orEarlier + 1.13 + Restriction enzyme recognition sites (restriction sites) in a nucleic acid sequence. + + + Restriction sites + true - + - - Anaesthesiology - - Anaesthetics - 1.4 - Topic concerning anaesthesia and anaesthetics. - - - + + + beta12orEarlier + 1.13 + + + Splice sites in a nucleotide sequence or alternative RNA splicing events. + + Splice sites + true - + - - Critical care medicine - - Acute medicine - Geriatrics - Emergency medicine - 1.4 - Topic concerning the multidisciplinary that cares for patients with acute, life-threatening illness or injury. - - - + + + beta12orEarlier + 1.13 + Matrix/scaffold attachment regions (MARs/SARs) in a DNA sequence. + + + Matrix/scaffold attachment sites + true - + - - Dermatology - - Dermatological disorders - Topic concerning the branch of medicine that deals with prevention, diagnosis and treatment of disorders of the skin, scalp, hair and nails. - 1.4 - - - + + + beta12orEarlier + 1.13 + Operons (operators, promoters and genes) from a bacterial genome. + + + Operon + true - + - - Dentistry - - 1.4 - Topic concerning the study, diagnosis, prevention and treatments of disorders of the oral cavity, maxillofacial area and adjacent structures. - - - + + + beta12orEarlier + 1.13 + Whole promoters or promoter elements (transcription start sites, RNA polymerase binding site, transcription factor binding sites, promoter enhancers etc) in a DNA sequence. + + + Promoters + true - + - - Ear, nose and throat medicine - - Topic concerning the branch of medicine that deals with the prevention, diagnosis, and treatment of disorders of the ear, nose and throat. - Otolaryngology - 1.4 - Audiovestibular medicine - Head and neck disorders - - - + + + 1.3 + true + This includes Informatics concerning data generated from the use of microscopes, including optical, electron and scanning probe microscopy. Includes methods for digitizing microscope images and viewing the produced virtual slides and associated data on a computer screen. + VT 1.5.24 Structural biology + The molecular structure of biological molecules, particularly macromolecules such as proteins and nucleic acids. + Structural assignment + Structural determination + Structure determination + + + + This includes experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, microscopy etc., including the assignment or modelling of molecular structure from such data. + Structural biology - + - - Endocrinology and metabolism - - 1.4 - Metabolic disorders - Metabolism - Topic concerning the branch of medicine dealing with diseases of endocrine organs, hormone systems, their target organs, and disorders of the pathways of glucose and lipid metabolism. - Endocrinology - Endocrine disorders - - - + + + 1.8 + 1.13 + Trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements. + + + Protein membrane regions + true - + - - Haematology - - Topic concerning the branch of medicine that deals with the blood, blood-forming organs and blood diseases. - Haematological disorders - 1.4 - Blood disorders - - - + + + beta12orEarlier + 1.13 + The comparison of two or more molecular structures, for example structure alignment and clustering. + + + This might involve comparison of secondary or tertiary (3D) structural information. + Structure comparison + true - + - - Gastroenterology - - Gastrointestinal disorders - 1.4 - Topic concerning the branch of medicine that deals with disorders of the oesophagus, stomach, duodenum, jejenum, ileum, large intestine, sigmoid colon and rectum. - - - + + + beta12orEarlier + true + The study of gene and protein function including the prediction of functional properties of a protein. + Protein function analysis + Protein function prediction + + + + Function analysis - + - - Gender medicine - - Topic concerning the study of the biological and physiological differences between males and females and how they effect differences in disease presentation and management. - 1.4 - - - + + + beta12orEarlier + Bacteriology + VT 1.5.2 Bacteriology + Specific bacteria or archaea, e.g. information on a specific prokaryote genome including molecular sequences, genes and annotation. + + + The resource may be specific to a prokaryote, a group of prokaryotes or all prokaryotes. + Prokaryotes and Archaea - + - - Gynaecology and obstetrics - - 1.4 - Topic concerning the branch of medicine that deals with the health of the female reproductive system, pregnancy and birth. - Gynaecology - Gynaecological disorders - Obstetrics - - - + + + beta12orEarlier + 1.3 + + Protein data resources. + + Protein databases + true - + - - Hepatic and biliary medicine - - Hepatobiliary medicine - Liver disorders - 1.4 - Topic concerning the branch of medicine that deals with the liver, gallbladder, bile ducts and bile. - - - + + + beta12orEarlier + 1.3 + + Experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, microscopy etc., including the assignment or modelling of molecular structure from such data. + + Structure determination + true - + - - Infectious tropical disease - - 1.4 - Topic concerning the branch of medicine that deals with the infectious diseases of the tropics. - - - + + + beta12orEarlier + true + VT 1.5.11 Cell biology + Cells, such as key genes and proteins involved in the cell cycle. + Cellular processes + + + Cell biology - + - - Trauma medicine - - 1.4 - Topic concerning the branch of medicine that treats body wounds or shock produced by sudden physical injury, as from violence or accident. - - - + + + beta12orEarlier + beta13 + + Topic focused on identifying, grouping, or naming things in a structured way according to some schema based on observable relationships. + + Classification + true - + - - Medical toxicology - - Topic concerning the branch of medicine that deals with the diagnosis, management and prevention of poisoning and other adverse health effects caused by medications, occupational and environmental toxins, and biological agents. - 1.4 - - - + + + beta12orEarlier + 1.3 + + Lipoproteins (protein-lipid assemblies). + + Lipoproteins + true - + - - Musculoskeletal medicine - - Topic concerning the branch of medicine that deals with the prevention, diagnosis, and treatment of disorders of the muscle, bone and connective tissue. It incorporates aspects of orthopaedics, rheumatology, rehabilitation medicine and pain medicine. - Musculoskeletal disorders - 1.4 - - - + + + beta12orEarlier + beta12orEarlier + + Visualise a phylogeny, for example, render a phylogenetic tree. + + Phylogeny visualisation + true - + - - Opthalmology - - 1.4 - Eye disoders - Audiovestibular medicine - Topic concerning the branch of medicine that deals with disorders of the eye, including eyelid, optic nerve/visual pathways and occular muscles. - - - + + + beta12orEarlier + true + The application of information technology to chemistry in biological research environment. + Chemical informatics + Chemoinformatics + + + + Cheminformatics - + - - Paediatrics - - 1.4 - Topic concerning the branch of medicine that deals with the medical care of infants, children and adolescents. - Child health - - - + + + beta12orEarlier + true + The holistic modelling and analysis of complex biological systems and the interactions therein. + Biological modelling + Biological system modelling + + + + This includes databases of models and methods to construct or analyse a model. + Systems biology + + http://purl.bioontology.org/ontology/MSH/D049490 - + - - Psychiatry - - 1.4 - Psychiatric disorders - Topic concerning the branch of medicine that deals with the mangement of mental illness, emotional disturbance and abnormal behaviour. - Mental health - - - + + + beta12orEarlier + The application of statistical methods to biological problems. + Biostatistics + Probability + Statistics + + + + Statistics and probability + http://en.wikipedia.org/wiki/Biostatistics + http://purl.bioontology.org/ontology/MSH/D056808 - + - - Reproductive health - - Topic concerning the health of the reproductive processes, functions and systems at all stages of life. - Reproductive disorders - Family planning - Audiovestibular medicine - Fertility medicine - 1.4 - - - + + + beta12orEarlier + beta12orEarlier + + Search for and retrieve molecular structures that are similar to a structure-based query (typically another structure or part of a structure). + + The query is a structure-based entity such as another structure, a 3D (structural) motif, 3D profile or template. + Structure database search + true - + - - Surgery - - Topic concerning the use of operative, manual and instrumental techniques on a patient to investigate and/or treat a pathological condition or help improve bodily function or appearance. - 1.4 - - - + + + beta12orEarlier + true + The construction, analysis, evaluation, refinement etc. of models of a molecules properties or behaviour, including the modelling the structure of proteins in complex with small molecules or other macromolecules (docking). + Comparative modelling + Homology modeling + Homology modelling + Molecular docking + + + Molecular modelling - + - - Urology and nephrology - - Topic concerning the branches of medicine and physiology focussing on the function and disorders of the urinary system in males and females, the reproductive system in males, and the kidney. - 1.4 - Urology - Kidney disease - Urological disorders - Nephrology - - - + + + beta12orEarlier + 1.2 + + The prediction of functional properties of a protein. + + Protein function prediction + true - + - - Complementary medicine - - Topic concerning medical therapies that fall beyond the scope of conventional medicine but may be used alongside it in the treatment of disease and ill health. - Holistic medicine - 1.4 - Alternative medicine - - - + + + beta12orEarlier + 1.13 + Single nucleotide polymorphisms (SNP) and associated data, for example, the discovery and annotation of SNPs. + + + SNP + true - + - - MRI - - Nuclear magnetic resonance imaging - Topic concerning techniques that uses magnetic fields and radiowaves to form images, typically to investigate the anatomy and physiology of the human body. - 1.7 - MRT - Magnetic resonance tomography - NMRI - Magnetic resonance imaging - - - + + + beta12orEarlier + beta12orEarlier + + + Predict transmembrane domains and topology in protein sequences. + + Transmembrane protein prediction + true - + - - Neutron diffraction - - - Neutron microscopy - Elastic neutron scattering - 1.7 - Topic concerning the study of matter by studying the diffraction pattern from firing neutrons at a sample, typically to determine atomic and/or magnetic structure. - Neutron diffraction experiment - - + + + beta12orEarlier + beta12orEarlier + + + The comparison two or more nucleic acid (typically RNA) secondary or tertiary structures. + + Use this concept for methods that are exclusively for nucleic acid structures. + Nucleic acid structure comparison + true - + - - Tomography - - X-ray tomography - Electron tomography - Topic concerning imaging in sections (sectioning), through the use of a wave-generating device (tomograph) that generates an image (a tomogram). - 1.7 - - + + + beta12orEarlier + 1.13 + Exons in a nucleotide sequences. + + + Exons + true - + - - Data mining - - 1.7 - Topic concerning the discovery of patterns in large data sets and the extraction and trasnsformation of those patterns into a useful format. - Knowledge Discovery in Databases - KDD - - + + + beta12orEarlier + 1.13 + Transcription of DNA into RNA including the regulation of transcription. + + + Gene transcription + true - + - - Machine learning - - A topic concerning the application of artificial intelligence methods to algorithms, in order to create methods that can learn from data in order to generate an ouput, rather than relying on explicitly encoded information only. - 1.7 - - + + + + beta12orEarlier + DNA mutation. + + + DNA mutation - + - - Biological databases - - 1.8 - Topic concerning databases of biological information including the results of scientific experiments, the application of high-throughput technology, computational analysis and the the scientific literature. - - + + + beta12orEarlier + true + VT 3.2.16 Oncology + The study of cancer, for example, genes and proteins implicated in cancer. + Cancer biology + Cancer + + + + Oncology - + - - Animals - - The resource may be specific to a plant, a group of plants or all plants. - 1.8 - Animal biology - Zoology - Animal - Metazoa - Topic concerning animals, e.g. information on a specific animal genome including molecular sequences, genes and annotation. - - + + + beta12orEarlier + 1.13 + Structural and associated data for toxic chemical substances. + + + Toxins and targets + true - + - - Protein sites, features and motifs - - Topic concerning the biologiy, archival, detection, prediction and analysis of positional features such as functional and other key sites, in protein sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them. - Protein sequence features - Protein functional sites - 1.8 - - + + + beta12orEarlier + 1.13 + Introns in a nucleotide sequences. + + + Introns + true - + - - Nucleic acid sites, features and motifs - - Nucleic acid sequence features - 1.8 - Nucleic acid functional sites - Topic concerning the biologiy, archival, detection, prediction and analysis of positional features such as functional and other key sites, in nucleic acid sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them. - - + + + beta12orEarlier + beta12orEarlier + A topic concerning primarily bioinformatics software tools, typically the broad function or purpose of a tool. + + + Tool topic + true - + - - Gene transcript features - - - Topic concerning features of a messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules. - Nucleic acid features (mRNA features) - mRNA features - This includes 5'untranslated region (5'UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3'untranslated regions (3'UTR). - 1.8 - - + + + beta12orEarlier + beta12orEarlier + A general area of bioinformatics study, typically the broad scope or category of content of a bioinformatics journal or conference proceeding. + + + Study topic + true - + - - Protein-ligand interactions - - Topic concerning protein-ligand (small molecule) interaction(s). - 1.8 - - + + + beta12orEarlier + 1.3 + + Biological nomenclature (naming), symbols and terminology. + + Nomenclature + true - + - - Protein-drug interactions - - Topic concerning protein-drug interaction(s). - 1.8 - - + + + beta12orEarlier + 1.3 + + The genes, gene variations and proteins involved in one or more specific diseases. + + Disease genes and proteins + true - + - - Genotyping experiment - - 1.8 - Topic concerning genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods. - - + + + + beta12orEarlier + true + http://edamontology.org/topic_3040 + Protein secondary or tertiary structural data and/or associated annotation. + Protein structure + + + + Protein structure analysis - + - - GWAS study - - 1.8 - Genome-wide association study - Topic concerning genome-wide association study experiments. - - + + + beta12orEarlier + The human genome, including molecular sequences, genes, annotation, maps and viewers, the human proteome or human beings in general. + + + Humans - + - - Microarray experiment - - Topic concerning microarray experiments including conditions, protocol, sample:data relationships etc. - 1.8 - This might specify which raw data file relates to which sample and information on hybridisations, e.g. which are technical and which are biological replicates. - - + + + beta12orEarlier + 1.3 + + Informatics resource (typically a database) primarily focussed on genes. + + Gene resources + true - + - - PCR experiment - - 1.8 - Topic concerning PCR experiments, e.g. quantitative real-time PCR. - - + + + beta12orEarlier + 1.3 + + Yeast, e.g. information on a specific yeast genome including molecular sequences, genes and annotation. + + Yeast + true - + - - Proteomics experiment - - 1.8 - Topic concerning proteomics experiments. - - + + + beta12orEarlier + Eukaryotes or data concerning eukaryotes, e.g. information on a specific eukaryote genome including molecular sequences, genes and annotation. + Eukaryote + + + The resource may be specific to a eukaryote, a group of eukaryotes or all eukaryotes. + Eukaryotes - + - - 2D PAGE experiment - - Topic concerning two-dimensional gel electrophoresis experiments, gels or spots in a gel. - 1.8 - - + + + beta12orEarlier + Invertebrates, e.g. information on a specific invertebrate genome including molecular sequences, genes and annotation. + + + The resource may be specific to an invertebrate, a group of invertebrates or all invertebrates. + Invertebrates - + - - Northern blot experiment - - Topic concerning Northern Blot experiments. - 1.8 - - + + + beta12orEarlier + Vertebrates, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation. + + + The resource may be specific to a vertebrate, a group of vertebrates or all vertebrates. + Vertebrates - + - - RNAi experiment - - 1.8 - Topic concerning RNAi experiments. - - + + + beta12orEarlier + Unicellular eukaryotes, e.g. information on a unicellular eukaryote genome including molecular sequences, genes and annotation. + + + The resource may be specific to a unicellular eukaryote, a group of unicellular eukaryotes or all unicellular eukaryotes. + Unicellular eukaryotes - + - - Simulation experiment - - 1.8 - Topic concerning biological computational model experiments (simulation), for example the minimum information required in order to permit its correct interpretation and reproduction. - - + + + beta12orEarlier + 1.3 + + Protein secondary or tertiary structure alignments. + + Protein structure alignment + true - + - - Protein-nucleic acid interactions - - 1.8 - Topic concerning protein-DNA/RNA interaction(s). - - + + + + beta12orEarlier + The study of matter and their structure by means of the diffraction of X-rays, typically the diffraction pattern caused by the regularly spaced atoms of a crystalline sample. + Crystallography + X-ray crystallography + X-ray microscopy + + + + X-ray diffraction - + - - Protein-protein interactions - - Topic concerning protein-protein interaction(s), including interactions between protein domains. - Domain-domain interactions - 1.8 - Protein interaction networks - - + + + beta12orEarlier + 1.3 + + Conceptualisation, categorisation and naming of entities or phenomena within biology or bioinformatics. + + Ontologies, nomenclature and classification + http://purl.bioontology.org/ontology/MSH/D002965 + true - + - - Cellular process pathways - - 1.8 - Topic concernning cellular process pathways. - - + + + + beta12orEarlier + Immunity-related genes, proteins and their ligands. + Antigens + Immunogenes + Immunopeptides + Immunoproteins + + + + This includes T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF) / antibodies, major histocompatibility complex superfamily (MhcSF), etc." + Immunoproteins, genes and antigens - + - - Disease pathways - - Topic concerning disease pathways, typically of human disease. - Pathway or network (disease) - 1.8 - - + + + beta12orEarlier + beta12orEarlier + + Specific molecules, including large molecules built from repeating subunits (macromolecules) and small molecules of biological significance. + CHEBI:23367 + + Molecules + true - + - - Environmental information processing pathways - - Topic concerning environmental information processing pathways. - 1.8 - Pathway or network (environmental information processing) - - + + + + beta12orEarlier + true + VT 3.1.9 Toxicology + Toxins and the adverse effects of these chemical substances on living organisms. + Computational toxicology + Toxicoinformatics + + + + Toxicology - + - - Genetic information processing pathways - - Topic concerning genetic information processing pathways. - Pathway or network (genetic information processing) - 1.8 - - + + + beta12orEarlier + beta13 + + Parallelised sequencing processes that are capable of sequencing many thousands of sequences simultaneously. + Next-generation sequencing + + High-throughput sequencing + true - + - - Protein super-secondary structure - - Protein features (super-secondary) - 1.8 - Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. - Topic concerning super-secondary structure of protein sequence(s). - - + + + beta12orEarlier + 1.7 + The comparison and grouping together of molecular structures on the basis of similarity; generate, process or analyse structural clusters. + + + Structural clustering + true - + - - Protein active sites - - Enzyme active site - 1.8 - Topic concerning catalytic residues (active site) of an enzyme. - Protein features (active sites) - - + + + beta12orEarlier + 1.13 + Gene regulatory networks. + + + Gene regulatory networks + true - + - - Protein binding sites - - 1.8 - Topic concerning ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids. - Protein features (binding sites) - - + + + beta12orEarlier + beta12orEarlier + + Informatics resources dedicated to one or more specific diseases (not diseases in general). + + Disease (specific) + true - + - - Protein-nucleic acid binding sites - - Topic concerning RNA and DNA-binding proteins and binding sites in protein sequences. - 1.8 - Protein features (nucleic acid binding sites) - - + + + beta12orEarlier + 1.13 + Variable number of tandem repeat (VNTR) polymorphism in a DNA sequence. + + + VNTR + true - + - - Protein cleavage sites - - Topic concerning cleavage sites (for a proteolytic enzyme or agent) in a protein sequence. - Protein features (cleavage sites) - 1.8 - - + + + beta12orEarlier + 1.13 + + Microsatellite polymorphism in a DNA sequence. + + + Microsatellites + true - + - - Protein chemical modifications - - Topic concerning chemical modification of a protein. - Protein features (chemical modifications) - MOD:00000 - 1.8 - GO:0006464 - - + + + beta12orEarlier + 1.13 + + Restriction fragment length polymorphisms (RFLP) in a DNA sequence. + + + RFLP + true - + - - Protein disordered structure - - Topic concerning disordered structure in a protein. - 1.8 - Protein features (disordered structure) - - + + + + beta12orEarlier + true + DNA polymorphism. + Microsatellites + RFLP + SNP + Single nucleotide polymorphism + VNTR + Variable number of tandem repeat polymorphism + + + Includes microsatellite polymorphism in a DNA sequence. A microsatellite polymorphism is a very short subsequence that is repeated a variable number of times between individuals. These repeats consist of the nucleotides cytosine and adenosine. + Includes restriction fragment length polymorphisms (RFLP) in a DNA sequence. An RFLP is defined by the presence or absence of a specific restriction site of a bacterial restriction enzyme. + Includes single nucleotide polymorphisms (SNP) and associated data, for example, the discovery and annotation of SNPs. A SNP is a DNA sequence variation where a single nucleotide differs between members of a species or paired chromosomes in an individual. + Includes variable number of tandem repeat (VNTR) polymorphism in a DNA sequence. VNTRs occur in non-coding regions of DNA and consists sub-sequence that is repeated a multiple (and varied) number of times. + DNA polymorphism - + - - Protein domains - - - The report will typically include a graphic of the location of domains in a sequence, with associated data such as lists of related sequences, literature references, etc. - 1.8 - Topic concerning structural domains or 3D folds in a protein or polypeptide chain. - Protein structural domains - Protein features (domains) - - + + + beta12orEarlier + 1.3 + + Topic for the design of nucleic acid sequences with specific conformations. + + Nucleic acid design + true - + - - Protein key folding sites - - - Protein features (key folding sites) - 1.8 - Topic concerning key residues involved in protein folding. - - + + + beta13 + 1.3 + + The design of primers for PCR and DNA amplification or the design of molecular probes. + + Primer or probe design + true - + - - Protein post-translational modifications - - Protein features (post-translation modifications) - Post-translation modifications - Topic concerning post-translation modifications in a protein sequence, typically describing the specific sites involved. - 1.8 - - + + + beta13 + 1.2 + + Molecular secondary or tertiary (3D) structural data resources, typically of proteins and nucleic acids. + + Structure databases + true - + - - Protein secondary structure - - - The location and size of the secondary structure elements and intervening loop regions is typically given. The report can include disulphide bonds and post-translationally formed peptide bonds (crosslinks). - Protein features (secondary structure) - Topic concerning secondary structure (predicted or real) of a protein. - 1.8 - - + + + beta13 + 1.2 + + Nucleic acid (secondary or tertiary) structure, such as whole structures, structural features and associated annotation. + + Nucleic acid structure + true - + - - Protein sequence repeats - - 1.8 - Topic concerning short repetitive subsequences (repeat sequences) in a protein sequence. - Protein features (repeats) - Protein repeats - - + + + beta13 + 1.3 + + Molecular sequence data resources, including sequence sites, alignments, motifs and profiles. + + Sequence databases + true - + - - Protein signal peptides - - Protein features (signal peptides) - 1.8 - Topic concerning signal peptides or signal peptide cleavage sites in protein sequences. - - + + + beta13 + 1.3 + + Nucleotide sequences and associated concepts such as sequence sites, alignments, motifs and profiles. + + Nucleic acid sequences + true - + - - data visualization algorithm - + + + beta13 + 1.3 + Protein sequences and associated concepts such as sequence sites, alignments, motifs and profiles. + + + Protein sequences + true - + - - data cleaning algorithm - + + + 1.3 + + + Protein interaction networks + true - + - - data selection algorithm - + + + beta13 + true + VT 1.5.4 Biochemistry and molecular biology + The molecular basis of biological activity, particularly the macromolecules (e.g. proteins and nucleic acids) that are essential to life. + + + + Molecular biology - + - - data integration algorithm - + + + beta13 + 1.3 + + Mammals, e.g. information on a specific mammal genome including molecular sequences, genes and annotation. + + Mammals + true - + - - data processing task - - A data processing task is an information processing objective that specifies the objective that a data processing algorithm execution process needs to achieve when executed on a dataset to produce as output a new dataset. + + + beta13 + true + VT 1.5.5 Biodiversity conservation + The degree of variation of life forms within a given ecosystem, biome or an entire planet. + + + + Biodiversity + http://purl.bioontology.org/ontology/MSH/D044822 - + - - data construction algorithm - + + + beta13 + 1.3 + + The comparison, grouping together and classification of macromolecules on the basis of sequence similarity. + + This includes the results of sequence clustering, ortholog identification, assignment to families, annotation etc. + Sequence clusters and classification + true - + - - generalization specification - - A generalization is a broad name for an output of a execution of a data mining algorithm on a specific dataset. A generalization specification is an informational entity that specifies the type of the generalization such as: decision trees, decision rules, neural networks, itemsets etc. - Generalization specification of a directive informational entity class that specifies the type of generalization. It includes information about the types of data used to produced the generalization and the language in which the generalization is expressed. - OntoDM + + + beta13 + true + The study of genes, genetic variation and heredity in living organisms. + Heredity + + + + Genetics + http://purl.bioontology.org/ontology/MSH/D005823 - - A generalization is a broad name for an output of a execution of a data mining algorithm on a specific dataset. A generalization specification is an informational entity that specifies the type of the generalization such as: decision trees, decision rules, neural networks, itemsets etc. - - - - - + - - ensemble specification - - A ensemble of generalizations specification is a generalization specification and denotes a type of generalization that is produced by a ensemble algorithm. This algorithm produces a set of generalizations at its output. - An ensemble specification denotes a type of generalization which is an output of an execution of a ensemble algorithm. -Ensembles are sets of generalizations (have as parts single generalizations) with a defined procedure of their combination into a single generalization when executed in a process. - OntoDM + + + beta13 + true + The genes and genetic mechanisms such as Mendelian inheritance that underly continuous phenotypic traits (such as height or weight). + + + Quantitative genetics - - An ensemble specification denotes a type of generalization which is an output of an execution of a ensemble algorithm. -Ensembles are sets of generalizations (have as parts single generalizations) with a defined procedure of their combination into a single generalization when executed in a process. - - - - - + - - data mining algorithm - - A data mining algorithm is an algorithm that has as its objective a data mining task and outputs as a result a generalization specified by a generalization specification. + + + beta13 + true + The distribution of allele frequencies in a population of organisms and its change subject to evolutionary processes including natural selection, genetic drift, mutation and gene flow. + + + + Population genetics - + - - pattern specification - - A patten specification is a single generalization specification and denotes a pattern P on type T which is a boolean funtion on objects of type T. - A pattern P on type T specifies a Boolean function on objects of type T, i.e., has the signature p :: T → bool. A pattern on type T is true or false on an object of type T. Frawley et al. (1991) define a pattern as a statement (expression) in a given language, that describes (relationships among) the facts in (a subset of) the data. In the broadest sense, the word pattern is used to describe the output of a variety of data mining algorithms and includes probability distributions, predictive models and clusters/clusterings; however, we restrict it here to the sense that it is most commonly used, i.e., in the sense of frequent pattern mining. - OntoDM + + + beta13 + 1.3 + Regulatory RNA sequences including microRNA (miRNA) and small interfering RNA (siRNA). + + + Regulatory RNA + true - - A pattern P on type T specifies a Boolean function on objects of type T, i.e., has the signature p :: T → bool. A pattern on type T is true or false on an object of type T. Frawley et al. (1991) define a pattern as a statement (expression) in a given language, that describes (relationships among) the facts in (a subset of) the data. In the broadest sense, the word pattern is used to describe the output of a variety of data mining algorithms and includes probability distributions, predictive models and clusters/clusterings; however, we restrict it here to the sense that it is most commonly used, i.e., in the sense of frequent pattern mining. - - - - - + - - probability distribution estimation task - - Estimating the (Joint) Probability Distribution. A set of data (of type -T) is often assumed to be a sample taken from a population according to a -probability distribution. A probability distribution/density function assigns a -non-negative probability/density to each object of type T. Probably the most -general data mining task (Hand et al. 2001) is the task of estimating the (joint) -probability distribution D over type T from a set of data items or a sample -drawn from that distribution. -As mentioned above, in the most typical case we would have T = Tuple(T1, -. . ., Tk), where each of T1, . . ., Tk is Boolean, Discrete(S) or Real. We talk about -the joint probability distribution to emphasize the difference to the marginal -distributions of each of the variables of type T1, . . ., Tk: the joint distribution -captures the interactions among the variables. -Representing multi-variate distributions is a non-trivial task. Two approaches -are commonly used in data mining. In the density-based clustering paradigm, -mixtures of multi-variate Gaussian distributions are typically considered (Hand -et al. 2001). Probabilistic graphical models, most notably Bayesian networks, -represent graphically the (in)dependencies between the variables: Learning their -structure and parameters is an important approach to the problem of estimating -the joint probability distribution. + + + beta13 + 1.13 + The documentation of resources such as tools, services and databases and how to get help. + + + Documentation and help + true - + - - pattern discovery task - - the task of pattern discovery is to find all local patterns from a given -pattern language that satisfy the required conditions. A prototypical instantiation -of this task is the task of finding frequent itemsets (sets of items, such as -{bread, butter}), which are often found together in a transaction (e.g., a market -basket) (Aggrawal et al 1993). The condition that a pattern (itemset) has to -satisfy in this case is to appear in (hold true for) a sufficiently high proportion -(called support and denoted by s) of the transactions in the input dataset. -With the increasing interest in mining complex data, mining frequent patterns -is also considered for structured data. We can thus talk about mining frequent -subsequences or mining frequent subgraphs in sequence or graph data. We can -consider as frequency the multiple occurrences of a pattern in a single data -structure (e.g., sequence or graph) or the single occurrences of a pattern in -multiple data structures. + + + beta13 + 1.3 + + The structural and functional organisation of genes and other genetic elements. + + Genetic organisation + true - + - - data mining task - - A data mining task is an objective specification that specifies the objective that a data mining algorithm needs to achieve when executed on a dataset to produce as output a generalization. + + + beta13 + true + Molecular medicine + Translational medicine + The application of information technology to health, disease and biomedicine. + Biomedical informatics + Clinical informatics + Health and disease + Health informatics + Healthcare informatics + + + + Medical informatics - + - - predictive model specification - - A predictive model M for types Td, Tc specifies a function that takes an object of type Td and returns one of type Tc, i.e., has the signature m :: Td → Tc. Most often, predictive modelling is concerned with classification, where Tc would be Boolean (for binary classification) or Discrete(S) (for multi-class classification), or regression, where Tc would be Real. In our case, we allow both Td (description) and Tc (class/target) to be arbitrarily complex data types. - OntoDM - Predictive model specification is a single generalization specification and denotes a type of generalization that represents a mapping taking objects of type Td and returns objects of type To. + + + beta13 + true + VT 1.5.14 Developmental biology + How organisms grow and develop. + + + + Developmental biology - - A predictive model M for types Td, Tc specifies a function that takes an object of type Td and returns one of type Tc, i.e., has the signature m :: Td → Tc. Most often, predictive modelling is concerned with classification, where Tc would be Boolean (for binary classification) or Discrete(S) (for multi-class classification), or regression, where Tc would be Real. In our case, we allow both Td (description) and Tc (class/target) to be arbitrarily complex data types. - - - - - + - - predictive modeling task - - Learning a (Probabilistic) Predictive Model. In this task, we are given -a dataset that consists of examples of the form (d, c), where each d is of type -Td and each c is of type Tc. We will refer to d as the description and c as the -class or target. To learn a predictive model means to find a mapping from the -description to the target, m :: Td → Tc, that fits the data closely. This means -that the observed target values and the target values predicted by the model, -i.e., c and ˆc = m(d), have to match closely. + + + beta13 + true + The development of organisms between the one-cell stage (typically the zygote) and the end of the embryonic stage. + + + + Embryology - + - - probability distribution estimation algorithm - + + + beta13 + true + VT 3.1.1 Anatomy and morphology + The form and function of the structures of living organisms. + + + + Anatomy - + - - clustering task - - Clustering. Clustering in general is concerned with grouping objects into classes -of similar objects (Kaufman and Rousseeuw 1990). Given a set of examples (object -descriptions), the task of clustering is to partition these examples into subsets, -called clusters. + + + beta13 + true + The scientific literature, language processing, reference information, and documentation. + Bibliography + Citations + Documentation + References + Scientific literature + + + + This includes the documentation of resources such as tools, services and databases, user support, how to get help etc. + Literature and language + http://purl.bioontology.org/ontology/MSH/D011642 - + - - probability distribution specification - - A probability distribution D on type T specifies a mapping from objects of type T to non-negative Reals, i.e., has the signature d :: T → R0+. For uncountably infinite types, probability densities are used instead. The sum of all probabilities (the integral of the probability densities) over T is constrained to amount to one. - A probability distribution specification is a single generalization specification and denotes a type of generalization that is a mapping from objects of type T to non-negative reals. This generalization is an output of a probability distribution estimation algorithm. - OntoDM + + + beta13 + true + VT 1.5 Biological sciences + VT 1.5.1 Aerobiology + VT 1.5.13 Cryobiology + + VT 1.5.23 Reproductive biology + VT 1.5.3 Behavioural biology + VT 1.5.7 Biological rhythm + VT 1.5.8 Biology + VT 1.5.99 Other + A particular biological science, especially observable traits such as aspects of biochemistry, physiology, morphology, anatomy, development and so on. + Biological science + Aerobiology + Behavioural biology + Biological rhythms + Chronobiology + Cryobiology + Reproductive biology + + + + Biology - - A probability distribution D on type T specifies a mapping from objects of type T to non-negative Reals, i.e., has the signature d :: T → R0+. For uncountably infinite types, probability densities are used instead. The sum of all probabilities (the integral of the probability densities) over T is constrained to amount to one. - - - - - + - - data processing algorithm - - A data processing algorithm is an algorithm that has as its objective a data processing task and has data items both as input and output. - Allyson Lister + + + beta13 + true + VT 1.3.1 Data management + The development and use of architectures, policies, practices and procedures for management of data. + + + + Data management + http://purl.bioontology.org/ontology/MSH/D030541 - + - - single generalization specification - - A single generalization specification is a generalization specification and denotes a type of generalization that is produced by a single generalization data mining algorithm. This algorithm produces only one generalization at its output. - Examples of such generalization types are: decision trees, desicion rules, neural networks, frequent itemsets, clusters etc. - OntoDM + + + beta13 + 1.3 + + The detection of the positional features, such as functional and other key sites, in molecular sequences. + + Sequence feature detection + http://purl.bioontology.org/ontology/MSH/D058977 + true - + - - ensemble algorithm - - - Ensemble algorithms are algorithms that generate an ensemble when executed on a dataset. The ensemble algorithms include a specification of single generalization algorithms which are executed in oreder to produce the single generalizations that compose the ensemble. + + + beta13 + 1.3 + + The detection of positional features such as functional sites in nucleotide sequences. + + Nucleic acid feature detection + true + + -Examples of ensemble algorithms include bagging, boosting, stacking, random forests, random subspaces,bagging of random subspaces etc. -For example, bagging of decision trees algorithm includes the specification of a bagging algorithm and having a decision tree algorithm for generating the base models composing the ensemble. + + + + + beta13 + 1.3 + + The detection, identification and analysis of positional protein sequence features, such as functional sites. + + Protein feature detection + true - + - - single generalization algorithm - - single generalization algorithms are data mining algorithms that given a dataset on input produce a generalization at the output. + + + beta13 + 1.2 + + Topic for modelling biological systems in mathematical terms. + + Biological system modelling + true - + - - data visualization task - - data visualization task is information processing objective achieved by a data visualization algorithm execution process. + + + beta13 + The acquisition of data, typically measurements of physical systems using any type of sampling system, or by another other means. + + + Data acquisition - + - - process - process - - BFO - the life of an organism, the process of sleeping, the process of cell-division - A processual entity that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities. + + + beta13 + 1.3 + + Specific genes and/or their encoded proteins or a family or other grouping of related genes and proteins. + + Genes and proteins resources + true - + - - material entity - - A material entity is a real world physical object. It is an entity that exists in full during the length of time of its existence, persists through this time while maintaining its identity and has no temporal parts. For example a heart, a human, a fly, a microarray. - An independent continuant [snap:IndependentContinuant] that is spatially extended whose identity is independent of that of other entities and can be maintained through time. Note: Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology. - BFO - Collection of random bacteria, a chair, dorsal surface of the body. - James Malone + + + 1.8 + 1.13 + Topological domains such as cytoplasmic regions in a protein. + + + Protein topological domains + true - - A material entity is a real world physical object. It is an entity that exists in full during the length of time of its existence, persists through this time while maintaining its identity and has no temporal parts. For example a heart, a human, a fly, a microarray. - - - - - + - - programming language - - A language in which source code is written, intended to executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it. - IAO + + + beta13 + true + + Protein sequence variants produced e.g. from alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting. + + + Protein variants - + - - data - data - - - - - - - - - - - Data is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. - IAO - http://www.ontobee.org/browser/rdf.php?o=IAO&iri=http://purl.obolibrary.org/obo/IAO_0000027 + + + beta13 + 1.12 + + Regions within a nucleic acid sequence containing a signal that alters a biological function. + + Expression signals + true - + - - information content entity - information content entity - - IAO - An information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity. - Examples of information content entites include journal articles, data, graphical layouts, and graphs. + + + + beta13 + + Nucleic acids binding to some other molecule. + Matrix-attachment region + Matrix/scaffold attachment region + Nucleosome exclusion sequences + Restriction sites + Ribosome binding sites + Scaffold-attachment region + + + This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes), restriction enzyme recognition sites (restriction sites) etc. + This includes sites involved with DNA replication and recombination. This includes binding sites for initiation of replication (origin of replication), regions where transfer is initiated during the conjugation or mobilisation (origin of transfer), starting sites for DNA duplication (origin of replication) and regions which are eliminated through any of kind of recombination. Also nucleosome exclusion regions, i.e. specific patterns or regions which exclude nucleosomes (the basic structural units of eukaryotic chromatin which play a significant role in regulating gene expression). + DNA binding sites - + - - algorithm - algorithm - - IAO - A plan specification which describes inputs, output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. - An algorithm is a set of instructions for performing a paticular calculation. + + + beta13 + 1,13 + Repetitive elements within a nucleic acid sequence. + + + This includes long terminal repeats (LTRs); sequences (typically retroviral) directly repeated at both ends of a defined sequence and other types of repeating unit. + Nucleic acid repeats + true - - An algorithm is a set of instructions for performing a paticular calculation. - - - - - + - - data format specification - data format specification - - - - A data format specification is the information content borne by the document published defining the specification. - IAO - The ISO document specifying what encompasses an XML document; The instructions in a XSD file. - The syntax by which data is specified which renders it valid for a given format. + + + beta13 + true + DNA replication or recombination. + + + DNA replication and recombination - - - The syntax by which data is specified which renders it valid for a given format. - - - - + - - version name - version name - - - - - - - - - - - - - - - - - - IAO - A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name. + + + beta13 + 1.13 + Coding sequences for a signal or transit peptide. + + + Signal or transit peptide + true - + - - organization - organization - - An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. - http://purl.obolibrary.org/obo/OBI_0000245 + + + beta13 + 1.13 + Sequence tagged sites (STS) in nucleic acid sequences. + + + Sequence tagged sites + true - + - - sequence feature format - + + + 1.1 + true + The determination of complete (typically nucleotide) sequences, including those of genomes (full genome sequencing, de novo sequencing and resequencing), amplicons and transcriptomes. + DNA-Seq + Amplicon sequencing + Chromosome walking + High throughput sequencing + High-throughput sequencing + NGS + Next gen sequencing + Next generation sequencing + Primer walking + Resequencing + + + + Amplicon sequencing is the ultra-deep sequencing of PCR products (amplicons), usually for the purpose of efficient genetic variant identification and characterisation in specific genomic regions. + Sequencing + http://purl.bioontology.org/ontology/MSH/D059014 - + - - matlab software - - - - - - - + + + + 1.1 + The analysis of protein-DNA interactions where chromatin immunoprecipitation (ChIP) is used in combination with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. + Chip Seq + Chip sequencing + Chip-sequencing + + ChIP-seq - + - - 2-sample pooled t-test - + + + 1.1 + A topic concerning high-throughput sequencing of cDNA to measure the RNA content (transcriptome) of a sample, for example, to investigate how different alleles of a gene are expressed, detect post-transcriptional mutations or identify gene fusions. + RNA-seq + Small RNA-Seq + Small RNA-seq + WTSS + Whole transcriptome shotgun sequencing + miRNA-seq + + This includes small RNA profiling (small RNA-Seq), for example to find novel small RNAs, characterize mutations and analyze expression of small RNAs. + RNA-Seq - + - - 50-50 MANOVA - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 50-50 Manova is software in which the 50-50 MANOVA algorithm is implemented. - General linear modeling of fixed-effects models with multiple responses is performed. The function calculates 50-50 MANOVA p-values, ordinary univariate p-values and adjusted p-values using rotation testing. - Nandini Badarinarayan - http://rss.acs.unt.edu/Rdoc/library/ffmanova/html/ffmanova.html + + + 1.1 + 1.3 + DNA methylation including bisulfite sequencing, methylation sites and analysis, for example of patterns and profiles of DNA methylation in a population, tissue etc. + + + DNA methylation + true - + - - ABarray - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Nandini Badarinarayan - The ABarray is designed to work with Applied Biosystems whole genome microarray platform, as well as any other platform whose data can be tranformed into expression data matrix. - http://www.bioconductor.org/packages/2.4/bioc/html/ABarray.html + + + 1.1 + true + The systematic study of metabolites, the chemical processes they are involved, and the chemical fingerprints of specific cellular processes in a whole cell, tissue, organ or organism. + + + + Metabolomics + + http://purl.bioontology.org/ontology/MSH/D055432 - + - - 'ACME' - - The ACME algorithm is quite straightforward. Using a user-dened quantile of the data,called the threshold, any probes in the data that are above that threshold are considered positive probes. A p-value is then assigned to each probe. + + + + 1.1 + true + The study of the epigenetic modifications of a whole cell, tissue, organism etc. + + + + Epigenetics concerns the heritable changes in gene expression owing to mechanisms other than DNA sequence variation. + Epigenomics + http://purl.bioontology.org/ontology/MSH/D057890 - + - - Algorithms for Calculating Microarray Enrichment - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ACME (Algorithms for Calculating Microarray Enrichment) is a set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other experiments that result in regions of the genome showing "enrichment". It does not rely on a specific array technology (although the array should be a "tiling" array), is very general (can be applied in experiments resulting in regions of enrichment), and is very insensitive to array noise or normalization methods. It is also very fast and can be applied on whole-genome tiling array experiments quite easily with enough memory. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/ACME.html + + + + 1.1 + true + Community genomics + Ecogenomics + Environmental genomics + Environmental omics + The study of genetic material recovered from environmental samples, and associated environmental data. + Biome sequencing + Environmental sequencing + Shotgun metagenomics + + + + Metagenomics + http://purl.bioontology.org/ontology/MSH/D056186 - + - - Affymetrix Expression Console - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Expression Console™ software supports probe set summarization and CHP file generation for 3' expression (e.g., GeneChip® Human Genome U133 Plus 2.0 Array), gene-level (e.g., GeneChip® Human Gene 1.0 ST array) and exon-level arrays (e.g., GeneChip® Human Exon 1.0 ST Array). The Expression Console workflow provides the user with a choice of the more commonly used probe set summarization algorithms - Nandini Badarinarayan - http://www.affymetrix.com/ + + + + 1.1 + Variation in chromosome structure including microscopic and submicroscopic types of variation such as deletions, duplications, copy-number variants, insertions, inversions and translocations. + Genomic structural variation + Structural variation + + + DNA structural variation - + - - AIDA - - - - - - - - - - - - - - - - - - AIDA is a modular software package for evaluation and documentation of images that were obtained with digital devices such as CCD cameras, flat bed scanners, or BAS / FLA- scanners from Fuji. Additionally, AIDA allows the loading of loading a variety of images in other image formats (e.g.: TIFF, JPEG, Bmp, gel). AIDA can control all scanning devices offering a TWAIN compatible driver. - Nandini Badarinarayan - http://www.raytest.de/index2.html + + + beta12orEarlier + DNA-histone complexes (chromatin), organisation of chromatin into nucleosomes and packaging into higher-order structures. + Nucleosome positioning + + + DNA packaging + http://purl.bioontology.org/ontology/MSH/D042003 - + - - Average log expression across arrays (ALE) - + + + 1.1 + 1.3 + + A topic concerning high-throughput sequencing of randomly fragmented genomic DNA, for example, to investigate whole-genome sequencing and resequencing, SNP discovery, identification of copy number variations and chromosomal rearrangements. + + DNA-Seq + true - + - - ALL/AML data set - + + + beta12orEarlier + 1.3 + + The alignment of sequences of (typically millions) of short reads to a reference genome. This is a specialised topic within sequence alignment, especially because of complications arising from RNA splicing. + + RNA-Seq alignment + true - + - - AMDIS - + + + 1.1 + Experimental techniques that combine chromatin immunoprecipitation ('ChIP') with microarray ('chip'). ChIP-on-chip is used for high-throughput study protein-DNA interactions. + ChIP-Chip + ChIP-chip + ChiP + + ChIP-on-chip - + - - ANCOVA - - The ANCOVA global test is a test for the association between expression values and clinical entities. The test is carried out by comparison of linear models via the extra sum of squares principle. If the mean expression level for at least one gene diers between corresponding models the global null hypothesis, which is the intersection of all single gene null hypotheses, is violated. FDR + + + 1.3 + The protection of data, such as patient health data, from damage or unwanted access from unauthorised users. + Data privacy + + + Data security - + - - 'ANOVA' - - ANNOVA - ANOVA or Analysis of Variance is a hypothesis testing algorithm which a variable is partitioned into components attributable to different sources of variation. + + + 1.3 + Biological samples and specimens. + Specimen collections + biosamples + samples + + + + Sample collections - + - - AP-MS data - + + + + 1.3 + true + VT 1.5.4 Biochemistry and molecular biology + Chemical substances and physico-chemical processes and that occur within living organisms. + Biological chemistry + + + + Biochemistry - + - - ARACNE algorithm - + + + + 1.3 + true + The study of evolutionary relationships amongst organisms from analysis of genetic information (typically gene or protein sequences). + + + Phylogenetics + http://purl.bioontology.org/ontology/MSH/D010802 - + - - ARR - + + + 1.3 + true + Topic concerning the study of heritable changes, for example in gene expression or phenotype, caused by mechanisms other than changes in the DNA sequence. + DNA methylation + Histone modification + + + + This includes sub-topics such as histone modification and DNA methylation (methylation sites and analysis, for example of patterns and profiles of DNA methylation in a population, tissue etc.) + Epigenetics + http://purl.bioontology.org/ontology/MSH/D019175 - + - - AWS algorithm - + + + 1.3 + true + The exploitation of biological process, structure and function for industrial purposes, for example the genetic manipulation of microorganisms for the antibody production. + + + + Biotechnology - + - - Absolute Expression Analysis - - Nandini Badarinarayan + + + + + 1.3 + true + Phenomes, or the study of the change in phenotype (the physical and biochemical traits of organisms) in response to genetic and environmental factors. + + + + Phenomics - + - - Absolute Expression Analysis - - Nandini Badarinarayan + + + 1.3 + true + VT 1.5.16 Evolutionary biology + The evolutionary processes, from the genetic to environmental scale, that produced life in all its diversity. + + + + Evolutionary biology - + - - 'AffyCompatible' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Nandini Badarinarayan - The AffyCompatible package provides an interface to Affymetrix chip annotation and sample attribute files. The package allows an easy way for users to download and manage local data bases of Affynmetrix NetAffx annotation files. The package also provides access to GeneChip Operating System (GCOS) and GeneChip Command Console (AGCC)-compatible sample annotation files. - http://bioconductor.org/packages/2.4/bioc/html/AffyCompatible.html + + + 1.3 + true + VT 3.1.8 Physiology + The functions of living organisms and their constituent parts. + + + + Physiology - + - - 'AffyExpress' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Nandini Badarinarayan - The purpose of this package is to provide a comprehensive and easy-to-use tool for quality assessment and to identify differentially expressed genes in the Affymetrix gene expression data. - http://bioconductor.org/packages/2.4/bioc/html/AffyExpress.html + + + 1.3 + true + VT 1.5.20 Microbiology + The biology of microorganisms. + + + + Microbiology - + - - Affymetrix GCOS v1.2 - - Nandini Badarinarayan + + + 1.3 + true + The biology of parasites. + + + + Parasitology - + - - Affymetrix GeneChip Operating Software - - - - - - - - - - - - - - - - - - Affymetrix GCOS software - GCOS software - GeneChip Operating Software - Nandini Badarinarayan - The Affymetrix GeneChip Operating Software (GCOS) is an operating system software that controls Affymetrix instruments, acquires data, and executes gene expression analysis. In addition, GCOS contains an embedded database that manages both experiment information and data. - http://www.affymetrix.com + + + 1.3 + true + VT 3.1 Basic medicine + VT 3.2 Clinical medicine + VT 3.2.9 General and internal medicine + Research in support of healing by diagnosis, treatment, and prevention of disease. + Biomedical research + Clinical medicine + Experimental medicine + General medicine + Internal medicine + + + + Medicine - + - - Affymetrix Software - - - - - - - - - - - - - Nandini Badarinarayan + + + 1.3 + true + Neuroscience + VT 3.1.5 Neuroscience + The study of the nervous system and brain; its anatomy, physiology and function. + + + + Neurobiology - + - - Agi4x44PreProcess - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Nandini Badarinarayan - Preprocessing of Agilent 4x44 array data - http://bioconductor.org/packages/2.4/bioc/html/Agi4x44PreProcess.html + + + 1.3 + true + VT 3.3.1 Epidemiology + Topic concerning the the patterns, cause, and effect of disease within populations. + Epidemiology + Public health + + + + Public health and epidemiology - + - - Agilent Feature Extraction 5.1.1 - - Nandini Badarinarayan + + + + 1.3 + true + VT 1.5.9 Biophysics + The use of physics to study biological system. + + + + Biophysics - + - - Agilent Feature Extraction software version 7.1 - - Nandini Badarinarayan + + + 1.3 + true + VT 1.5.12 Computational biology + VT 1.5.19 Mathematical biology + VT 1.5.26 Theoretical biology + The development and application of theory, analytical methods, mathematical models and computational simulation of biological systems. + Biomathematics + Mathematical biology + Theoretical biology + + + + This includes the modeling and treatment of biological processes and systems in mathematical terms (theoretical biology). + Computational biology - + - - Agilent Feature Extraction software version 7.5 - - Nandini Badarinarayan + + + + 1.3 + true + The analysis of transcriptomes, or a set of all the RNA molecules in a specific cell, tissue etc. + Comparative transcriptomics + Metatranscriptomics + Transcriptome + + + + Transcriptomics - + - - Agilent Feature Extraction software version A.5.1.1 - - Nandini Badarinarayan + + + 1.3 + Chemical science + Polymer science + VT 1.7.10 Polymer science + VT 1.7 Chemical sciences + VT 1.7.2 Chemistry + VT 1.7.3 Colloid chemistry + VT 1.7.5 Electrochemistry + VT 1.7.6 Inorganic and nuclear chemistry + VT 1.7.7 Mathematical chemistry + VT 1.7.8 Organic chemistry + VT 1.7.9 Physical chemistry + The composition and properties of matter, reactions, and the use of reactions to create new substances. + Inorganic chemistry + Mathematical chemistry + Nuclear chemistry + Organic chemistry + Physical chemistry + + + + Chemistry - + - - Agilent Scan Control - - - - - - - - - - - - - - - - - - Nandini Badarinarayan - Scan Control Application software - Scan Control Software is the user interface software that controls the Agilent scanner. This software is usable only with the Agilent high-resolution scanner (G2565CA) or high-resolution scanner upgrade. It will not function with earlier scanner versions - http://www.chem.agilent.com/ + + + 1.3 + VT 1.1.99 Other + VT:1.1 Mathematics + The study of numbers (quantity) and other topics including structure, space, and change. + Maths + + + + Mathematics - + - - Agilent Technologies Software - - - - - - - - - - - - - - - - - - Nandini Badarinarayan + + + 1.3 + VT 1.2 Computer sciences + VT 1.2.99 Other + The theory and practical use of computer systems. + + + + Computer science - + - - 'AnnotationDbi' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Nandini Badarinarayan - This package provides user interface and database connection code for annotation data packages using SQLite data storage. - http://bioconductor.org/packages/2.4/bioc/html/AnnotationDbi.html + + + 1.3 + The study of matter, space and time, and related concepts such as energy and force. + + + + Physics - + - - Applied Biosystems 1700 Expression Array System Software - - - - - - - - - - - - - - - - - - Microarrays are powerful tools for discovering levels of gene expression. Geneservice have invested in the latest gene expression microarray system from Applied Biosystems so that the widest choice of platform is available to our customers. The key features of this system are: -Sensitivity: a detection threshold of as little as a femtomole of expresseed mRNA and requiring as little as 500ng of starting total RNA. -Content: each probe is associated with a gene sequence buiult on unique Celera data and validated by public RefSeqs all of which have been curated. -Pipeline: complete integrated solutions for gene expression research including Applied Biosystems Bioinformatic tools and ready-to-go gene expression TaqMan assays for validation of results. - Nandini Badarinarayan - http://www.geneservice.co.uk/services/geneexpression/overview_1700.jsp + + + + 1.3 + true + RNA splicing; post-transcription RNA modification involving the removal of introns and joining of exons. + Alternative splicing + Splice sites + + + This includes the study of splice sites, splicing patterns, alternative splicing events and variants, isoforms, etc.. + RNA splicing - + - - ArrayGauge - - - - - - - - - - - - - - - - - - ArrayGauge [FUJIFILM] - Fujifilm ArrayGauge™ software is specifically designed for Macroarray and Microarray samples, with all the practical functions necessary for the most powerful array analysis. -Its ultra-friendly navigation and functions can handle any kind of array (CLONTECH, Genome Systems, Research Genetics - even hand-made arrays). It already includes virtually every contemporary cDNA membrane template on the market, with the flexibility to handle others as they develop. - Nandini Badarinarayan - http://www.fujifilm.com/products/life_science_systems/science_imaging/arraygauge/ + + + + 1.3 + true + The structure and function of genes at a molecular level. + + + + Molecular genetics - + - - ArrayNorm - - - - - - - - - - - - - - - - - - ArrayNorm is an platform-independent Java tool for normalization and statistical analysis for microarray-experiment data. It provides modules for visualization (scatterplot, histogram, boxplot, etc.), normalization and analysis. - Nandini Badarinarayan - http://bin.tugraz.at/Tools/ArrayNorm.html + + + 1.3 + true + VT 3.2.25 Respiratory systems + The study of respiratory system. + Pulmonary medicine + Pulmonology + Pulmonary disorders + Respiratory disease + + + + Respiratory medicine - + - - 'ArrayTools' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Nandini Badarinarayan - This package is designed to provide solutions for quality assessment and to detect differentially expressed genes for the Affymetrix GeneChips, including both 3' -arrays and gene 1.0-ST arrays. - http://bioconductor.org/packages/2.4/bioc/html/ArrayTools.html + + + 1.3 + 1.4 + + The study of metabolic diseases. + + Metabolic disease + true - + - - ArrayVision - - - - - - - - - - - - - - - - - - - Nandini Badarinarayan - This software implements a robust algorithm for spot finding and quantitation, quality metrics, and use of pre-made protocols ensure accuracy and reproducibility. Choices for background correction, normalization, and ratio calculation between arrays provides flexibility.Wizard guides simplify operation.Automatic batch processing increases throughput and saves time.Data easily exported to Microsoft™ Excel or database programs for flexibility in reporting. + + + 1.3 + VT 3.3.4 Infectious diseases + The branch of medicine that deals with the prevention, diagnosis and management of transmissable disease with clinically evident illness resulting from infection with pathogenic biological agents (viruses, bacteria, fungi, protozoa, parasites and prions). + Communicable disease + Transmissable disease + + + + Infectious disease - + - - ArrayVision 6.0 (Imaging Research Inc.) - - Nandini Badarinarayan + + + 1.3 + The study of rare diseases. + + + + Rare diseases - + - - Array_vision_(Interfocus) - - Nandini Badarinarayan + + + + 1.3 + true + Topic concerning the development and application of theory, analytical methods, mathematical models and computational simulation of chemical systems. + VT 1.7.4 Computational chemistry + + + + Computational chemistry - + - - AtlasImage - - - - - - - - - - - - - - - - - - Computer software for the analysis and comparison of Atlas™ nylon and plastic arrays. - Nandini Badarinarayan - http://www.clontech.com/images/pacs/634650-PA27475.pdf + + + 1.3 + true + The branch of medicine that deals with the anatomy, functions and disorders of the nervous system. + Neurological disorders + + + + Neurology - + - - Axon GenePix Pro 3 - - Nandini Badarinarayan + + + 1.3 + true + VT 3.2.22 Peripheral vascular disease + VT 3.2.4 Cardiac and Cardiovascular systems + The diseases and abnormalities of the heart and circulatory system. + Cardiovascular medicine + Cardiovascular disease + Heart disease + + + + Cardiology - + - - BAC - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Nandini Badarinarayan - This package uses a Bayesian hierarchical model to detect enriched regions from ChIP-chip experiments - http://bioconductor.org/packages/2.4/bioc/html/BAC.html + + + + 1.3 + true + The discovery and design of drugs or potential drug compounds. + + + + This includes methods that search compound collections, generate or analyse drug 3D conformations, identify drug targets with structural docking etc. + Drug discovery - + - - Binning clustering method - - binning clustering method- The algorithm uses single-linkage clustering to join compounds into similarity groups, where every member in a cluster shares with at least one other member a similarity value above a user-specified threshold. The algorithm is optimized for speed and memory -eciency by avoiding the calculation of an all-against-all distance matrix. + + + 1.3 + true + Repositories of biological samples, typically human, for basic biological and clinical research. + Tissue collection + biobanking + + + + Biobank - + - - 'BCRANK' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Functions and classes for de novo prediction of transcription factor binding consensus by heuristic search - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/BCRANK.html + + + 1.3 + Laboratory study of mice, for example, phenotyping, and mutagenesis of mouse cell lines. + + + + Mouse clinic - + - - obsolete_BED format - - true - Marked as obsolete by Allyson Lister. - After 0.4 release. - Equivalence with EDAM term "BED" (format_3003). + + + 1.3 + Collections of microbial cells including bacteria, yeasts and moulds. + + + + Microbial collection - + - - BGL - - BGL implements Depth First Search, Breadth First Search,Dijkstra's, Bellman Ford's and DAG,Johnson's and Floyd Warshall's.Kruskal's algorithm and Prim's algorithm Cuthill-McKee's algorithm Minimum degree Ordering + + + 1.3 + Collections of cells grown under laboratory conditions, specifically, cells from multi-cellular eukaryotes and especially animal cells. + + + + Cell culture collection - + - - 'BGmix' - - - - - - - - - - - - - - - - - - - - - - - - - - Bayesian models for differential gene expression - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/BGmix.html + + + 1.3 + Collections of DNA, including both collections of cloned molecules, and populations of micro-organisms that store and propagate cloned DNA. + + + + Clone library - + - - BLAST - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - BLAST, or Basic Local Alignment Search Tool in full, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. - James Malone - Nandini Badarinarayan - The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. - http://blast.ncbi.nlm.nih.gov/Blast.cgi - Allyson Lister: added 'achieves objective' axioms for pairwise and multiple sequence alignment classes. + + + 1.3 + true + 'translating' the output of basic and biomedical research into better diagnostic tools, medicines, medical procedures, policies and advice. + + + + Translational medicine - + - - Iterative Bayesian Model Averaging (BMA) - + + + 1.3 + Collections of chemicals, typically for use in high-throughput screening experiments. + Chemical library + Chemical screening + Compound library + + + + Compound libraries and screening - + - - Base-Pair-Distance Kernel - + + + 1.3 + true + VT 3.3 Health sciences + Topic concerning biological science that is (typically) performed in the context of medicine. + Health science + + + + Biomedical science - + - - BPMAP - - - - - - - - http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/bpmap.html, accessed 22 May 2013. - BPMAP is a binary data format specification created by Affymetrix where the data is stored in big-endian format. The BPMAP format contains information relating to the design of the Affymetrix tiling arrays. - Allyson Lister + + + 1.3 + Topic concerning the identity of biological entities, or reports on such entities, and the mapping of entities and records in different databases. + + + + Data identity and mapping - + - - BRB-ArrayTools - - - - - - - - - - - - - - - - - - BRB-ArrayTools is an integrated package for the visualization and statistical analysis of DNA microarray gene expression data. It was developed by professional statisticians experienced in the analysis of microarray data and involved in the development of improved methods for the design and analysis of microarray based experiments. The system incorporates a variety of powerful analytic and visualization tools developed specifically for microarray data analysis. - Nandini Badarinarayan - http://linus.nci.nih.gov/BRB-ArrayTools.html + + + 1.3 + 1.12 + The search and retrieval from a database on the basis of molecular sequence similarity. + Sequence database search + + + Sequence search + true - + - - 'BSgenome' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Nandini Badarinarayan - This document describes the process of forging a BSgenome data package. It is intended for Bioconductor -users who want to make a new BSgenome data package - http://bioconductor.org/packages/2.4/bioc/html/BSgenome.html + + + 1.4 + true + Objective indicators of biological state often used to assess health, and determinate treatment. + Diagnostic markers + + + Biomarkers - + - - BZScan - - - - - - - - - - - - - - - - - - BZScan is a free java tool for automatic quantification of DNA microarrays with radioactive labeling. BZScan provides saturation, overshining, and background noise correction, it also gives quality control measures. It can work either in a fully automatic "batch mode" or at different levels of manual operation. - Nandini Badarinarayan - http://tagc.univ-mrs.fr/bioinformatics/bzscan/ - + + + 1.4 + The procedures used to conduct an experiment. + Lab techniques + + + + Laboratory techniques + - + - - BaldiLongT - + + + 1.4 + The development of policies, models and standards that cover data acquisitioin, storage and integration, such that it can be put to use, typically through a process of systematically applying statistical and / or logical techniques to describe, illustrate, summarise or evaluate data. + Data analysis + Data architecture + Data design + + + + Data architecture, analysis and design - + - - BasReader 3.01 - - - - - - - - - - - - - - - - - - Nandini Badarinarayan - This program may be used to read out image data from all scanners of the FujiFilm BAS series (BAS1000, BAS1500, BAS1800, BAS2000, BAS2500, BAS3000, BAS5000) and the FujiFilm FLA scanners (FLA-2000, FLA-3000). - http://www.rubion.rub.de/labor/pdf/BASREAD.pdf + + + 1.4 + The combination and integration of data from different sources, for example into a central repository or warehouse, to provide users with a unified view of these data. + + + Data integration + Data warehousing + + + + Data integration and warehousing - + - - Bayesian Model - + + + 1.4 + Any matter, surface or construct that interacts with a biological system. + + + + Biomaterials - + - - Beadstudio - - - - - - - - - - - - - - - - - - BeadStudio Software is a modular analysis tool for genotyping, gene expression, and methylation applications - Nandini Badarinarayan - http://www.illumina.com/pages.ilmn?ID=35 + + + + 1.4 + true + The use of synthetic chemistry to study and manipulate biological systems. + + + + Chemical biology - + - - 'BicARE' - - - - - - - - - - - - - - - - - - - - - - - - Nandini Badarinarayan - This package is dedicated to biclustering analysis which allows to discover sets of genes that have the same expression pattern accross a set of samples - http://bioconductor.org/packages/2.4/bioc/html/BicARE.html + + + 1.4 + VT 1.7.1 Analytical chemistry + The study of the separation, identification, and quantification of the chemical components of natural and artificial materials. + + + + Analytical chemistry - + - - 'BioMVCClass' - - - - - - - - Creates classes used in model-view-controller (MVC) design - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/BioMVCClass.html + + + 1.4 + The use of chemistry to create new compounds. + Synthetic organic chemistry + + + + Synthetic chemistry - + - - 'Biobase' - - - - - - - - Functions that are needed by many other packages or which replace R functions - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/Biobase.html + + + 1.4 + 1.2.12 Programming languages + Software engineering + VT 1.2.1 Algorithms + VT 1.2.14 Software engineering + VT 1.2.7 Data structures + The process that leads from an original formulation of a computing problem to executable programs. + Computer programming + Software development + Programming languages + Algorithms + Data structures + + + + Software engineering - + - - 'BiocCaseStudies' - - - - - - - - Nandini Badarinarayan - Software and data to support the case studies. - http://bioconductor.org/packages/2.4/bioc/html/BiocCaseStudies.html + + + 1.4 + true + The process of bringing a new drug to market once a lead compounds has been identified through drug discovery. + Drug development science + Medicine development + Medicines development + + + + Drug development - + - - BioConductor Software - - - - - - - - - - - - - - - - - - - Bioconductor - Bioconductor is an open source and open development software project to provide tools for the analysis and comprehension of genomic data. Bioconductor is based primarily on the R programming language, but does contain contributions in other programming languages. - Nandini Badarinarayan - http://www.bioconductor.org/overview - This is a defined class which will be populated if a piece of software identifies itself as having the value 'Bioconductor' for the 'is published by' property. (Allyson Lister) + + + 1.4 + The process of formulating abd administering a pharmaceutical compound to achieve a therapeutic effect. + Biotherapeutics + Drug delivery + Drug formulation + + + + Drug formulation and delivery - + - - 'Biostrings' - - - - - - - - - - - - - - - - - - - - Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or set of sequences. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/Biostrings.html + + + 1.4 + true + Drug metabolism + The study of how a drug interacts with the body. + ADME + Drug absorption + Drug distribution + Drug excretion + Pharmacodynamics + Pharmacokinetics + + + + Pharmacokinetics and pharmacodynamics - + - - BlueFuse - - - - - - - - - - - - - - - - - - BlueFuse for Microarrays is a powerful software solution for the analysis of microarray expression and arrayCGH experiments. Operation is simple and fully automated, saving time, removing operator error and subjectivity and ensuring experimental reproducibility. - BlueFuse [BlueGnome] - Nandini Badarinarayan - http://www.cambridgebluegnome.com/bluefuse.htm + + + 1.4 + Health care research + Health care science + The discovery, development and approval of medicines. + Drug discovery and development + + + + Medicine research and development + Medicines research and development - + - - 'BufferedMatrix' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Nandini Badarinarayan - This package creates a tabular style data object where most data is stored outside main memory. A buffer is used to speed up access to data. - http://bioconductor.org/packages/2.4/bioc/html/BufferedMatrix.html + + + 1.4 + The safety (or lack) of drugs and other medical interventions. + Drug safety + + + + Safety sciences - + - - 'BufferedMatrixMethods' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Nandini Badarinarayan - This package involves microarray Data related methods that utlize BufferedMatrix objects - http://bioconductor.org/packages/2.4/bioc/html/BufferedMatrixMethods.html + + + 1.4 + The detection, assesment, understanding and prevention of adverse effects of medicines. + + + + Pharmacovigilence concerns safety once a drug has gone to market. + Pharmacovigilence - + - - 'CALIB' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Nandini Badarinarayan - This package contains functions for normalizing spotted microarray data, based on a physically motivated calibration model. The model parameters and error distributions are estiamted from external control spikes. - http://bioconductor.org/packages/2.4/bioc/html/CALIB.html + + + + 1.4 + The testing of new medicines, vaccines or procedures on animals (preclinical) and humans (clinical) prior to their approval by regulatory authorities. + Clinical studies + Clinical study + Preclinical studies + Preclinical study + + + + Preclinical and clinical studies - + - - 'CAMERA' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Annotation of peaklists generated by xcms, rule based annotation of isotopes and adducts, EIC correlation based tagging of unknown adducts and fragments - Nandini Badarinarayan + + + 1.4 + true + The visual representation of an object. + Diffraction experiment + Microscopy + Microscopy imaging + + + + This includes diffraction experiments that are based upon the interference of waves, typically electromagnetic waves such as X-rays or visible light, by some object being studied, typical in order to produce an image of the object or determine its structure. + Imaging - + - - CBS - - The circular binary segmentation (CBS) algorithm divides the genome into regions of equal copy number . The algorithm tests for change-points using a maximal t-statistic with a permutation reference distribution to obtain the corresponding p-value. The number of computations required for the maximal test statistic is O(N^2),where N is the number of markers. This makes the full permutation approach computationally prohibitive for the newer arrays that contain tens of thousands markers and highlights the need for a faster algorithm. + + + 1.4 + The use of imaging techniques to understand biology. + + + + Biological imaging - + - - CBS algorithm - + + + 1.4 + VT 3.2.13 Medical imaging + VT 3.2.14 Nuclear medicine + VT 3.2.24 Radiology + The use of imaging techniques for clinical purposes for medical research. + Nuclear medicine + Radiology + + + + Medical imaging - + - - CDF binary format - - - - - - - - http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/cdf.html, accessed 22 May 2013. - The CDF binary format is a binary data format specification created by Affymetrix was created for faster access and smaller file size in comparison to the CDF ASCII format. The values in the file are stored in little-endian format. CDF binary format describes the layout for an Affymetrix GeneChip array. An array may contain Expression, Genotyping, CustomSeq, Copy Number and/or Tag probe sets. All probe set names within an array are unique. Multiple copies of a probe set may exist on a single array as long as each copy has a unique name. - It is unclear whether, originally, this format was intended to be the ASCII or binary version of the CDF format. As such, this class has been renamed as the binary format, and a new class created (CDF ASCII format) to make both options available. + + + 1.4 + The use of optical instruments to magnify the image of an object. + + + + Light microscopy - + - - CEL binary format - - - - - - - - Allyson Lister - CEL binary format is a binary data format specification created by Affymetrix where values are stored in little-endian format. The CEL format stores the results of the intensity calculations on the pixel values of the DAT file. This includes an intensity value, standard deviation of the intensity, the number of pixels used to calculate the intensity value, a flag to indicate an outlier as calculated by the algorithm and a user defined flag indicating the feature should be excluded from future analysis. The file stores the previously stated data for each feature on the probe array. - It is unclear whether, originally, this format was intended to be the ASCII or binary version of the CEL format. As such, this class has been renamed as the binary format, and a new class created (CEL ASCII format) to make both options available. (22/05/2013) - http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/cel.html, accessed 22 May 2013. + + + 1.4 + The use of animals and alternatives in experimental research. + + + + Laboratory animal science - + - - 'CGHbase' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Contains functions and classes that are needed by arrayCGH packages. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/CGHbase.html + + + 1.4 + true + VT 1.5.18 Marine and Freshwater biology + The study of organisms in the ocean or brackish waters. + + + + Marine biology - + - - 'CGHcall' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Calls aberrations for array CGH data using a six state mixture model as well as several biological concepts that are ignored by existing algorithms. Visualization of profiles is also provided. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/CGHcall.html + + + 1.4 + true + The identification of molecular and genetic causes of disease and the development of interventions to correct them. + + + + Molecular medicine - + - - 'CGHregions' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Dimension Reduction for Array CGH Data with Minimal Information Loss - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/CGHregions.html + + + 1.4 + VT 3.3.7 Nutrition and Dietetics + The study of the effects of food components on the metabolism, health, performance and disease resistance of humans and animals. It also includes the study of human behaviours related to food choices. + Nutrition science + Dietetics + + + + Nutritional science - + - - CHP binary format - - - - - - - - CHP binary format is a binary data format specification created by Affymetrix, stored in little-endian format and used to store expression, resequencing and genotyping results from algorithms implemented in the GCOS 1.2, 1.3 and 1.4 and BRLMM Analysis Tool software applications. - http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/chp.html, http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/chp-xda.html, accessed 22 May 2013. - As this is a child of Binary format, it is assumed that this class is intended to represent the binary form of this format. As described in the definition sources, there are other formats for CHP available. - Allyson Lister + + + 1.4 + true + The collective characterisation and quantification of pools of biological molecules that translate into the structure, function, and dynamics of an organism or organisms. + + + + Omics - + - - CLR algorithm - + + + 1.4 + The processes that need to be in place to ensure the quality of products for human or animal use. + Quality assurance + Good clinical practice + Good laboratory practice + Good manufacturing practice + + + + Quality affairs - + - - 'CMA' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Nandini Badarinarayan - This package provides a comprehensive collection of various microarray-based classification algorithms both from Machine Learning and Statistics. Variable Selection, Hyperparameter tuning, Evaluation and Comparison can be performed combined or stepwise in a user-friendly environment. - http://bioconductor.org/packages/2.4/bioc/html/CMA.html + + + 1.4 + The protection of public health by controlling the safety and efficacy of products in areas including pharmaceuticals, veterinary medicine, medical devices, pesticides, agrochemicals, cosmetics, and complementary medicines. + + + + Regulatory affairs - + - - CMA - - CMA- it implements k-fold cross validation, MCMC cross validation, bootstrap and (t.test or welch.test or wilcox.test or f.test or kruskal.test or One-step Recursive Feature Elimination or random forest variable importance measure or lasso or elastic net or componentwise boosting) + + + 1.4 + true + Biomedical approaches to clinical interventions that involve the use of stem cells. + Stem cell research + + + + Regnerative medicine - + - - 'CORREP' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Multivariate correlation estimation and statistical inference. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/CORREP.html + + + 1.4 + true + An interdisciplinary field of study that looks at the dynamic systems of the human body as part of an integrted whole, incoporating biochemical, physiological, and environmental interactions that sustain life. + + + + Systems medicine - + - - CRLMM algorithm - - This algorithm offers improved confidence scores, quality scores for SNP’s and batches, higher accuracy on different datasets and better performance. + + + 1.4 + Topic concerning the branch of medicine that deals with the prevention, diagnosis, and treatment of disease, disorder and injury in animals. + + + + Veterinary medicine - + - - Continuous Wavelet Transform (CWT)-based peak detection algorithm - + + + 1.4 + The application of biological concepts and methods to the analytical and synthetic methodologies of engineering. + + + + Bioengineering - + - - CARMAweb - - - - - - - - - - - - - - - - - - CARMAweb allows the analysis of Affymetrix GeneChip, ABI microarrays and two color microarrays. -The analysis includes normalization and data preprocessing, detection for differentially expressed genes, cluster analysis and GO analysis. All calculations (except the cluster analysis) are performed in R using functions provided by the BioConductor packages. - CarmaWEB - Nandini Badarinarayan - https://carmaweb.genome.tugraz.at/carma/ + + + 1.4 + true + Ageing + Aging + Gerontology + VT 3.2.10 Geriatrics and gerontology + The branch of medicine dealing with the diagnosis, treatment and prevention of disease in older people, and the problems specific to aging. + Geriatrics + + + + Geriatric medicine - + - - Category analysis - + + + 1.4 + true + VT 3.2.1 Allergy + Health issues related to the immune system and their prevention, diagnosis and mangement. + Allergy + Clinical immunology + Immune disorders + Immunomodulators + Immunotherapeutics + + + + Allergy, clinical immunology and immunotherapeutics. - + - - Category - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A collection of tools for performing category analysis. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/Category.html + + + 1.4 + true + The prevention of pain and the evaluation, treatment and rehabilitation of persons in pain. + Algiatry + + + + Pain medicine - + - - 'ChemmineR' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ChemMineR is an open source compound mining framework. It contains functions for atom descriptor calculation, structure similarity searching, clustering of compound libraries and various utilities for managing complex compound data. It also offers a wide range of visualization functions for compound clusters and chemical structures. The package is integrated with the online ChemMine environment and allows bidirectional communications between the two services. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/ChemmineR.html + + + 1.4 + VT 3.2.2 Anaesthesiology + Anaesthesia and anaesthetics. + Anaesthetics + + + + Anaesthesiology - + - - ChipReader 3.1 - - - - - - - - - - - - - - - - - - Nandini Badarinarayan - VersArray ChipReader - Versarray ChipReader systems are highly sensitive laser confocal systems designed for rapid imaging of microarrays. These are advanced scanners that meet your expectations, differentiating between a spot response and background level, and optimizing the signal on the bottom as well as the top end of the range for increased sensitivity. Results with versarray chipreader systems have a low background, enhanced weak signal detection, and virtually no photobleaching for a long dye lifetime. - http://www.bio-medicine.org/ + + + 1.4 + VT 3.2.5 Critical care/Emergency medicine + The multidisciplinary that cares for patients with acute, life-threatening illness or injury. + Acute medicine + Emergency medicine + + + + Critical care medicine - + - - ChipSkipper - - - - - - - - - - - - - - - - - - ChipSkipper - an integrated tool for analysis, evaluation and quantitation of DNA micro-array data - ChipSkipper Microarray Data Evaluation Software - ChipSkipper [EMBL] - Nandini Badarinarayan - http://angiogenesis.dkfz.de/software/chipskipper/index.htm + + + 1.4 + VT 3.2.7 Dermatology and venereal diseases + The branch of medicine that deals with prevention, diagnosis and treatment of disorders of the skin, scalp, hair and nails. + Dermatological disorders + + + + Dermatology - + - - ChipSkipper V0.99 - - Nandini Badarinarayan + + + 1.4 + The study, diagnosis, prevention and treatments of disorders of the oral cavity, maxillofacial area and adjacent structures. + + + + Dentistry - + - - multiscan - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A multiscan is an R package for combining multiple scans - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/multiscan.html + + + 1.4 + VT 3.2.20 Otorhinolaryngology + The branch of medicine that deals with the prevention, diagnosis, and treatment of disorders of the ear, nose and throat. + Audiovestibular medicine + Otolaryngology + Otorhinolaryngology + Head and neck disorders + + + + Ear, nose and throat medicine - + - - affy - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Nandini Badarinarayan - The affy package contains functions for exploratory oligonucleotide array analysis. The dependance to tkWidgets only concerns few convenience functions. 'affy' is fully functional without it. - http://bioconductor.org/packages/2.4/bioc/html/affy.html + + + 1.4 + true + The branch of medicine dealing with diseases of endocrine organs, hormone systems, their target organs, and disorders of the pathways of glucose and lipid metabolism. + Endocrine disorders + Endocrinology + Metabolic disorders + Metabolism + + + + Endocrinology and metabolism - + - - affycomp - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Nandini Badarinarayan - The affycomp package contains functions that can be used to compare expression measures for Affymetrix Oligonucleotide Arrays. - http://bioconductor.org/packages/2.4/bioc/html/affycomp.html + + + 1.4 + true + VT 3.2.11 Hematology + The branch of medicine that deals with the blood, blood-forming organs and blood diseases. + Blood disorders + Haematological disorders + + + + Haematology - + - - PCMG - - PCMG- a bipartite graph in which one set of nodes represents proteins, the other set represents complexes, and an edge from a protein node to a complex node represents membership of the protein in that complex. + + + 1.4 + true + VT 3.2.8 Gastroenterology and hepatology + The branch of medicine that deals with disorders of the oesophagus, stomach, duodenum, jejenum, ileum, large intestine, sigmoid colon and rectum. + Gastrointestinal disorders + + + + Gastroenterology - + - - Feature Extraction Software - - - - - - - - Nandini Badarinarayan + + + 1.4 + The study of the biological and physiological differences between males and females and how they effect differences in disease presentation and management. + + + + Gender medicine - + - - Chi-square - + + + 1.4 + true + VT 3.2.15 Obstetrics and gynaecology + The branch of medicine that deals with the health of the female reproductive system, pregnancy and birth. + Gynaecological disorders + Gynaecology + Obstetrics + + + + Gynaecology and obstetrics - + - - Annotation-Driven Clustering - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Nandini Badarinarayan - adSplit implements clustering of microarray gene expression profiles according to functional annotations. For each term genes are annotated to, splits into two subclasses are computed and a significance of the supporting gene set is determined. - http://bioconductor.org/packages/2.4/bioc/html/adSplit.html + + + 1.4 + true + The branch of medicine that deals with the liver, gallbladder, bile ducts and bile. + Hepatobiliary medicine + Liver disorders + + + + Hepatic and biliary medicine - + - - distance calculation - + + + 1.4 + 1.13 + The branch of medicine that deals with the infectious diseases of the tropics. + + + Infectious tropical disease + true - + - - R software - - - - - - - - Nandini Badarinarayan - Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. - http://www.stat.berkeley.edu/users/terry/zarray/Software/smacode.html + + + 1.4 + The branch of medicine that treats body wounds or shock produced by sudden physical injury, as from violence or accident. + + + + Trauma medicine - + - - BCRANK - - BCRANK is a method that takes a ranked list of genomic regions as input and outputs short DNA sequences that are overrepresented in some part of the list. + + + 1.4 + true + The branch of medicine that deals with the diagnosis, management and prevention of poisoning and other adverse health effects caused by medications, occupational and environmental toxins, and biological agents. + + + + Medical toxicology - + - - Cosmo - - cosmo allows the user to target the motif search by specifying a set of constraints that the unknown position weight matrix must satisfy. The algorithm is based on a probabilistic model that describes the DNA sequences of interest through a two- component multinomial mixture model with estimates of the position weight matrix entries obtained by maximizing the observed data likelihood over the smaller parameter space corresponding to the imposed constraints. It includes methods such as Probabilistic models and one-occurrence-per-sequence and zero-or-one-occurrence-per-sequence and two-component mixture + + + 1.4 + VT 3.2.19 Orthopaedics + VT 3.2.26 Rheumatology + The branch of medicine that deals with the prevention, diagnosis, and treatment of disorders of the muscle, bone and connective tissue. It incorporates aspects of orthopaedics, rheumatology, rehabilitation medicine and pain medicine. + Musculoskeletal disorders + Orthopaedics + Rheumatology + + + + Musculoskeletal medicine - + - - F test - + + + 1.4 + Optometry + VT 3.2.17 Ophthalmology + VT 3.2.18 Optometry + The branch of medicine that deals with disorders of the eye, including eyelid, optic nerve/visual pathways and occular muscles. + Eye disoders + + + + Opthalmology - + - - MAGE-TAB inputting software - - - - - - - - - - - - - - - - - - Nandini Badarinarayan + + + 1.4 + VT 3.2.21 Paediatrics + The branch of medicine that deals with the medical care of infants, children and adolescents. + Child health + + + + Paediatrics - + - - Text data set - + + + 1.4 + Mental health + VT 3.2.23 Psychiatry + The branch of medicine that deals with the mangement of mental illness, emotional disturbance and abnormal behaviour. + Psychiatric disorders + + + + Psychiatry - + - - CSV data set - + + + 1.4 + VT 3.2.3 Andrology + The health of the reproductive processes, functions and systems at all stages of life. + Andrology + Family planning + Fertility medicine + Reproductive disorders + + + + Reproductive health - + - - Non-linear functional regression model - - non-linear functional regression model with both additive and multiplicative error terms + + + 1.4 + VT 3.2.28 Transplantation + The use of operative, manual and instrumental techniques on a patient to investigate and/or treat a pathological condition or help improve bodily function or appearance. + Transplantation + + + + Surgery - + - - 'CoCiteStats' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A collection of software tools for dealing with co-citation data. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/CoCiteStats.html - - + + + 1.4 + VT 3.2.29 Urology and nephrology + The branches of medicine and physiology focussing on the function and disorders of the urinary system in males and females, the reproductive system in males, and the kidney. + Kidney disease + Nephrology + Urological disorders + Urology + + + + Urology and nephrology + + - + - - CodeLink Expression Analysis Software - - - - - - - - - - - - - - - - - - Nandini Badarinarayan - This software has a series of analytical tools to address the manufacturing, detection and data analysis components of a microarray experiment. Together, these tools help optimize performance in an expression profiling study. - http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=101854 + + + 1.4 + Alternative medicine + Holistic medicine + Integrative medicine + VT 3.2.12 Integrative and Complementary medicine + Medical therapies that fall beyond the scope of conventional medicine but may be used alongside it in the treatment of disease and ill health. + + + + Complementary medicine - + - - CodeLink Expression Scanning Software - - - - - - - - - - - - - - - - - - Nandini Badarinarayan - Slides are scanned using CodeLink Expression Scanning Software + + + 1.7 + Techniques that uses magnetic fields and radiowaves to form images, typically to investigate the anatomy and physiology of the human body. + MRT + Magnetic resonance imaging + + Magnetic resonance tomography + NMRI + Nuclear magnetic resonance imaging + + + MRI - + - - Complex Estimation Algorithm - + + + + 1.7 + The study of matter by studying the diffraction pattern from firing neutrons at a sample, typically to determine atomic and/or magnetic structure. + Neutron diffraction experiment + Elastic neutron scattering + Neutron microscopy + + + Neutron diffraction - + - - Cyber-T - - - - - - - - - - - - - - - - - - Cyber-T may be used to statistically determine what the probability is that a specific gene is differentially expressed by determining an associated p-value statistic. - Nandini Badarinarayan - http://dmaf.biochem.uci.edu/affymetrix_analysis_software.html + + + 1.7 + Imaging in sections (sectioning), through the use of a wave-generating device (tomograph) that generates an image (a tomogram). + Electron tomography + X-ray tomography + + + Tomography - + - - 'DEDS' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Nandini Badarinarayan - This library contains functions that calculate various statistics of differential expression for microarray data, including t statistics, fold change, F statistics, SAM, moderated t and F statistics and B statistics. It also implements a new methodology called DEDS (Differential Expression via Distance Summary), which selects differentially expressed genes by integrating and summarizing a set of statistics using a weighted distance approach. - http://bioconductor.org/packages/2.4/bioc/html/DEDS.html + + + 1.7 + true + KDD + Knowledge discovery in databases + VT 1.3.2 Data mining + The discovery of patterns in large data sets and the extraction and trasnsformation of those patterns into a useful format. + Pattern recognition + + + Data mining - + - - 'DFP' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Nandini Badarinarayan - This package provides a supervised technique able to identify differentially expressed genes. The Fuzzy Patterns are built by means of applying 3 Membership Functions to discretized gene expression values. - http://bioconductor.org/packages/2.4/bioc/html/DFP.html + + + 1.7 + Artificial Intelligence + VT 1.2.2 Artificial Intelligence (expert systems, machine learning, robotics) + A topic concerning the application of artificial intelligence methods to algorithms, in order to create methods that can learn from data in order to generate an ouput, rather than relying on explicitly encoded information only. + + + Machine learning - + - - Discriminant Fuzzy Pattern Algorithm - - A DFP version of a FP (fuzzy pattern) only includes those genes that can serve to differentiate it from the rest of the patterns.This algorithm is based on the discretization of float values (gene expression values) stored in an ExpressionSet object into labels combining 'Low', 'Medium' and 'High' + + + 1.8 + The general handling of data stored in digital archives such as databanks, databases proper, web portals and other data resources. + + Database administration + Databases + Biological databases + Content management + Data maintenance + Document management + Document, record and content management + File management + Record management + + + This includes databases for the results of scientific experiments, the application of high-throughput technology, computational analysis and the scientific literature. It covers the management and manipulation of digital documents, including database records, files and reports. + Database management - + - - DFW - + + + 1.8 + Animal biology + Zoology + VT 1.5.29 Zoology + Animals, e.g. information on a specific animal genome including molecular sequences, genes and annotation. + Animal + Metazoa + + + The resource may be specific to a plant, a group of plants or all plants. + Animals - + - - Digital gene expression (DGE) datasets - + + + + 1.8 + The biology, archival, detection, prediction and analysis of positional features such as functional and other key sites, in protein sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them. + Protein sequence features + Signal peptide cleavage sites + + + A signal peptide coding sequence encodes an N-terminal domain of a secreted protein, which is involved in attaching the polypeptide to a membrane leader sequence. A transit peptide coding sequence encodes an N-terminal domain of a nuclear-encoded organellar protein; which is involved in import of the protein into the organelle. + Protein sites, features and motifs - + - - 'DNAcopy' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Nandini Badarinarayan - Segments DNA copy number data using circular binary segmentation to detect regions with abnormal copy number - http://bioconductor.org/packages/2.4/bioc/html/DNAcopy.html + + + + 1.8 + The biology, archival, detection, prediction and analysis of positional features such as functional and other key sites, in nucleic acid sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them. + Nucleic acid functional sites + Nucleic acid sequence features + Primer binding sites + Sequence tagged sites + + + Sequence tagged sites are short DNA sequences that are unique within a genome and serve as a mapping landmark, detectable by PCR they allow a genome to be mapped via an ordering of STSs. + Nucleic acid sites, features and motifs - + - - 'DynDoc' - - - - - - - - - - - - - - - - - - - - - - - - A set of functions to create and interact with dynamic documents and vignettes. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/DynDoc.html + + + + 1.8 + Transcription of DNA into RNA and features of a messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules. + mRNA features + Coding RNA + EST + Exons + Fusion transcripts + Gene transcript features + Introns + PolyA signal + PolyA site + Signal peptide coding sequence + Transit peptide coding sequence + cDNA + mRNA + + + This includes 5'untranslated region (5'UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3'untranslated regions (3'UTR). + This includes Introns, and protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames. Also expressed sequence tag (EST) or complementary DNA (cDNA) sequences. + This includes coding sequences for a signal or transit peptide. A signal peptide coding sequence encodes an N-terminal domain of a secreted protein, which is involved in attaching the polypeptide to a membrane leader sequence. A transit peptide coding sequence encodes an N-terminal domain of a nuclear-encoded organellar protein; which is involved in import of the protein into the organelle. + This includes regions or sites in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript. A polyA signal is required for endonuclease cleavage of an RNA transcript that is followed by polyadenylation. A polyA site is a site on an RNA transcript to which adenine residues will be added during post-transcriptional polyadenylation. + Gene transcripts - + - - 'EBImage' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - EBImage is an R package which provides general purpose functionality for the reading, writing, processing and analysis of images. Furthermore, in the context of microscopy based cellular assays, EBImage offers tools to transform the images, segment cells and extract quantitative cellular descriptors. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/EBImage.html + + + 1.8 + 1.13 + Protein-ligand (small molecule) interaction(s). + Protein-drug interactions + + + Protein-ligand interactions + true - + - - 'EBarrays' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - EBarrays provides tools for the analysis of replicated/unreplicated microarray data. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/EBarrays.html + + + 1.8 + 1.13 + Protein-drug interaction(s). + + + Protein-drug interactions + true - + - - Expectation-Maximization(EM) algorithm - + + + 1.8 + Genotype experiment including case control, population, and family studies. These might use array based methods and re-sequencing methods. + + + Genotyping experiment - + - - Empirical Bayes rule - + + + 1.8 + Genome-wide association study experiments. + Genome-wide association study + + + GWAS study - + - - Expert 2100 - - - - - - - - - - - - - - - - - - Exper 2100 offers powerful data evaluation tools for all available assays, automatic and manual integration, smear analysis and many assay-specific tools. - Nandini Badarinarayan - http://www.chem.agilent.com/en-US/products/instruments/lab-on-a-chip/2100expertsoftware/pages/default.aspx + + + 1.8 + Microarray experiments including conditions, protocol, sample:data relationships etc. + Microarrays + ChIP-on-chip + Genotyping array + Methylation array + MicroRNA array + Multichannel microarray + One channel microarray + Proprietary platform micoarray + Reverse phase protein array + Tissue microarray + Two channel microarray + mRNA microarray + miRNA array + + + This might specify which raw data file relates to which sample and information on hybridisations, e.g. which are technical and which are biological replicates. + Microarray experiment - + - - obsolete_FACS ( fluorescence-activated cell sorter) - - true - 0.5 - Marked as obsolete by Allyson Lister. - This class had no definition, and seemed incorrectly placed as an algorithm, as from its name it seemed to only be an experimental method. + + + 1.8 + PCR experiments, e.g. quantitative real-time PCR. + + + PCR experiment - + - - FACS data - - FACS data is data which describes flow cytometry data sets. - Allyson Lister - http://www.bioconductor.org/packages/2.12/bioc/vignettes/prada/inst/doc/fcs3.html, accessed 29 May 2013. + + + 1.8 + Proteomics experiments. + 2D PAGE experiment + Mass spectrometry + Northern blot experiment + + + This includes two-dimensional gel electrophoresis (2D PAGE) experiments, gels or spots in a gel. Also mass spectrometry - an analytical chemistry technique that measures the mass-to-charge ratio and abundance of irons in the gas phase. Also Northern blot experiments. + Proteomics experiment - + - - FARMS - + + + 1.8 + 1.13 + Two-dimensional gel electrophoresis experiments, gels or spots in a gel. + + + 2D PAGE experiment + true - + - - obsolete_FASTA - - true - Obsoleted after the 0.4 release. - Equivalence with EDAM term format_1929. Please use this term instead. - Marked as obsolete by Allyson Lister. + + + 1.8 + 1.13 + Northern Blot experiments. + + + Northern blot experiment + true - + - - FC - + + + 1.8 + RNAi experiments. + + + RNAi experiment - + - - obsolete_FCS - - true - Marked as obsolete by Allyson Lister - 0.5 - Obsoleted as it was a generic term where there was no way of knowing for sure which format it was - or which version the format was in. Perhaps could have been annotated and moved, but this class was only identified after a new class (http://www.ebi.ac.uk/swo/data/SWO_3000061) had been created. Please use the new class (SWO_3000061) or its versioned children instead of this obsolete class. + + + 1.8 + Biological computational model experiments (simulation), for example the minimum information required in order to permit its correct interpretation and reproduction. + + + Simulation experiment - + - - 'FDR' - + + + 1.8 + 1.13 + Protein-DNA/RNA interaction(s). + + + Protein-nucleic acid interactions + true - + - - Fixed effect model - + + + 1.8 + 1.13 + Protein-protein interaction(s), including interactions between protein domains. + + + Protein-protein interactions + true - + - - Agilent Feature Extraction Software - - - - - - - - - - - - - - - - - - - - - - - - Feature Extraction Software - Feature Extraction Software [Agilent Technologies] - Feature Extraction software - Nandini Badarinarayan - The software automatically finds and places microarray grids, rejects outlier pixels, accurately determines feature intensities and ratios, flags outlier pixels, and calculates statistical confidences. Application-specific QC reports summarize results and provide an at-a-glance quality assessment - http://www.chem.agilent.com/en-us/products/instruments/dnamicroarrays/featureextractionsoftware/pages/default.aspx + + + 1.8 + 1.13 + Cellular process pathways. + + + Cellular process pathways + true - + - - Firth's bias reduction procedure - + + + 1.8 + 1.13 + Disease pathways, typically of human disease. + + + Disease pathways + true - + - - Fischer's Exact Test - + + + 1.8 + 1.13 + Environmental information processing pathways. + + + Environmental information processing pathways + true - + - - FoxDimmicT - + + + 1.8 + 1.13 + Genetic information processing pathways. + + + Genetic information processing pathways + true - + - - GACK - - - - - - - - - - - - - - - - - - Dynamically chooses cutoffs for grouping into present/divergent genes based on the shape of the distribution. More resistant to variation in hybridization data than CCACK. - Nandini Badarinarayan - http://falkow.stanford.edu/whatwedo/software/software.html + + + 1.8 + 1.13 + Super-secondary structure of protein sequence(s). + + + Protein super-secondary structure + true - + - - GASSCO method - + + + 1.8 + 1.13 + Catalytic residues (active site) of an enzyme. + + + Protein active sites + true - + - - GC-RMA Quantification - - - - - - - - - - - - - - - - - - GC-RMA Quantification (Stratagene ArrayAssist Expression Software) - Nandini Badarinarayan - Single-user desktop software package for analyzing microarray data from multiple microarray platforms. - http://www.biocompare.com/ProductDetails/475470/ArrayAssist-Expression-Software-(1-year-academic-license).html + + + 1.8 + Binding sites in proteins, including cleavage sites (for a proteolytic enzyme or agent), key residues involved in protein folding, catalytic residues (active site) of an enzyme, ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids, RNA and DNA-binding proteins and binding sites etc. + Enzyme active site + Protein cleavage sites + Protein functional sites + Protein key folding sites + Protein-nucleic acid binding sites + + + Protein binding sites - + - - GEMTools 2.4 - - - - - - - - - - - - - - - - - - Incyte GEMTools software is an enterprise solution for managing gene expression data using the SQL Server and Oracle relational databases. It was one of the first integrated software packages designed with an easy-to-use interface to help scientist track and analyze the vast amounts of gene expression data generated from microarray experiments. GEMTools can be used quantify and graphically display your gene expression data. Incyte Genomics relied on the GEMTools for internal operations and to track each well, probe, cDNA target, and other components of GEM arrays through ordering, fabrication, image analysis, and final data delivery. - Nandini Badarinarayan - http://www.baymedia.com/gemtools/ + + + 1.8 + 1.13 + RNA and DNA-binding proteins and binding sites in protein sequences. + + + Protein-nucleic acid binding sites + true - + - - GEO data type - + + + 1.8 + 1.13 + Cleavage sites (for a proteolytic enzyme or agent) in a protein sequence. + + + Protein cleavage sites + true - + - - GEO Matrix Series format - + + + 1.8 + 1.13 + Chemical modification of a protein. + + + Protein chemical modifications + true - + - - GEOmetadb - - - - - - - - - - - - - - - - - - - - - - - - Nandini Badarinarayan - The NCBI Gene Expression Omnibus (GEO) represents the largest public repository of microarray data. However, finding data of interest can be challenging using current tools. GEOmetadb is an attempt to make access to the metadata associated with samples, platforms, and datasets much more feasible. This is accomplished by parsing all the NCBI GEO metadata into a SQLite database that can be stored and queried locally. GEOmetadb is simply a thin wrapper around the SQLite database along with associated documentation. Finally, the SQLite database is updated regularly as new data is added to GEO and can be downloaded at will for the most up-to-date metadata. - http://bioconductor.org/packages/2.4/bioc/html/GEOmetadb.html + + + 1.8 + Disordered structure in a protein. + Protein features (disordered structure) + + + Protein disordered structure - + - - GEOquery - - - - - - - - - - - - - - - - - - - - - - - - Nandini Badarinarayan - The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data. Given the rich and varied nature of these data, it is only natural to want to apply BioConductor tools to these data. - http://bioconductor.org/packages/2.4/bioc/html/GEOquery.html + + + 1.8 + 1.13 + Structural domains or 3D folds in a protein or polypeptide chain. + + + Protein domains + true - + - - GGBase - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Nandini Badarinarayan - This package is an infrastructure for dealing with hapmap SNP reports, GWAS, etc. - http://bioconductor.org/packages/2.4/bioc/html/GGBase.html + + + 1.8 + 1.13 + Key residues involved in protein folding. + + + Protein key folding sites + true - + - - Gamma Gamma Model - + + + 1.8 + 1.13 + Post-translation modifications in a protein sequence, typically describing the specific sites involved. + + + Protein post-translational modifications + true - + - - GGtools - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Nandini Badarinarayan - This package deals with hapmap SNP reports, GWAS, etc. - http://bioconductor.org/packages/2.4/bioc/html/GGtools.html + + + 1.8 + Secondary structure (predicted or real) of a protein, including super-secondary structure. + Protein features (secondary structure) + Protein super-secondary structure + + + Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc. + The location and size of the secondary structure elements and intervening loop regions is typically given. The report can include disulphide bonds and post-translationally formed peptide bonds (crosslinks). + Protein secondary structure - + - - GLAD - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Analysis of array CGH data : detection of breakpoints in genomic profiles and assignment of a status (gain, normal or lost) to each chromosomal regions identified. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/GLAD.html + + + 1.8 + 1.13 + Short repetitive subsequences (repeat sequences) in a protein sequence. + + + Protein sequence repeats + true - + - - Modified version of the GLAD algorithm (Gain and Loss Analysis of DNA) - + + + 1.8 + 1.13 + Signal peptides or signal peptide cleavage sites in protein sequences. + + + Protein signal peptides + true - + - - GLEAMS software - - - - - - - - - - - - - - - - - - Microarray image quantification is performed using GLEAMS software - Nandini Badarinarayan - http://hmg.oxfordjournals.org/cgi/reprint/12/17/2145.pdf + + + 1.12 + An experiment for studying protein-protein interactions. + Co-immunoprecipitation + Phage display + Yeast one-hybrid + Yeast two-hybrid + + + Protein interaction experiment - + - - GMS - - Nandini Badarinarayan + + + 1.10 + VT 1.1.1 Applied mathematics + The application of mathematics to specific problems in science, typically by the formulation and analysis of mathematical models. + + + Applied mathematics - + - - GOstats - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A set of tools for interacting with GO and microarray data. A variety of basic manipulation tools for graphs, hypothesis testing and other simple calculations - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/GOstats.html + + + 1.10 + VT 1.1.1 Pure mathematics + The study of abstract mathematical concepts. + + + Pure mathematics - + - - Gene Recommender algorithm - + + + 1.10 + The control of data entry and maintenance to ensure the data meets defined standards, qualities or constraints. + Data stewardship + + + Data governance + http://purl.bioontology.org/ontology/MSH/D030541 - + - - GSEABase - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Nandini Badarinarayan - This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA). - http://bioconductor.org/packages/2.4/bioc/html/GSEABase.html + + + 1.10 + The quality, integrity, and cleaning up of data. + Data clean-up + Data integrity + Data quality + + + Data quality management - + - - GSEAlm - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Models and methods for fitting linear models to gene expression data, together with tools for computing and using various regression diagnostics. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/GSEAlm.html + + + 1.10 + VT 1.5.18 Marine and Freshwater biology + The study of organisms in freshwater ecosystems. + + + + Freshwater biology - + - - Gamma-Gamma hierarchical model - + + + 1.10 + true + VT 3.1.2 Human genetics + The study of inheritatnce in human beings. + + + + Human genetics - + - - Gaussian locally weighted regression - + + + 1.10 + VT 3.3.14 Tropical medicine + Health problems that are prevalent in tropical and subtropical regions. + + + + Tropical medicine - + - - Gene-Set Enrichment Analysis - + + + 1.10 + true + VT 3.3.14 Tropical medicine + VT 3.4 Medical biotechnology + VT 3.4.1 Biomedical devices + VT 3.4.2 Health-related biotechnology + Biotechnology applied to the medical sciences and the development of medicines. + Pharmaceutical biotechnology + + + + Medical biotechnology - + - - GeneData Expressionist Analyst v4.0.5 - - - - - - - - - - - - - - - - - - Genedata Expressionist® is an enterprise solution that integrates, stores and analyzes transcriptomics, proteomics and metabolomics data as well as a wide variety of phenotypic data. - Nandini Badarinarayan - http://www.genedata.com/products/expressionist/overview.html + + + 1.10 + true + VT 3.4.5 Molecular diagnostics + Health problems that are prevalent in tropical and subtropical regions. + Molecular diagnostics + + + + Personalised medicine - + - - Gene Pix - - - - - - - - - - - - - - - - - - Gene Pix - GenePix is the industry standard microarray image analysis software because of its unique combination of imaging and analysis tools, visualizations, automation capabilities, performance and ease of use. - Genepix - Nandini Badarinarayan - http://www.moleculardevices.com/pages/software/gn_genepix_pro.html + + + 1.12 + Experimental techniques to purify a protein-DNA crosslinked complex. Usually sequencing follows e.g. in the techniques ChIP-chip, ChIP-seq and MeDIP-seq. + + Chromatin immunoprecipitation + + + + Immunoprecipitation experiment - + - - GenePix 3.0.6 - - Nandini Badarinarayan + + + 1.12 + + Laboratory technique to sequence the complete DNA sequence of an organism's genome at a single time. + WGS + Whole genome resequencing + + Whole genome sequencing - + - - GenePix 4.1 - - Nandini Badarinarayan + + + 1.12 + + Laboratory technique to sequence the methylated regions in DNA. + MeDIP-chip + MeDIP-seq + mDIP + Bisulfite sequencing + MeDIP + Methylated DNA immunoprecipitation (MeDIP) + Methylation sequencing + + Methylated DNA immunoprecipitation - + - - GenePix 4100A - - GenePix 4100A [Axon Instruments] - Nandini Badarinarayan + + + 1.1 + + Laboratory technique to sequence all the protein-coding regions in a genome, i.e., the exome. + Exome analysis + Exome capture + Targeted exome capture + + + Exome sequencing is considered a cheap alternative to whole genome sequencing. + Exome sequencing - + - - GenePix 5.0.1 - - Nandini Badarinarayan + + + 1.12 + + true + The design of an experiment intended to test a hypothesis, and describe or explain empirical data obtained under various experimental conditions. + Design of experiments + Experimental design + Studies + + + Experimental design and studies - + - - GenePix - - GenePix [Axon Instruments] - Nandini Badarinarayan + + + + 1.12 + The design of an experiment involving non-human animals. + Challenge study + + + Animal study - + - - GenePix Pro - - Nandini Badarinarayan + + + + 1.13 + true + The ecology of microorganisms including their relationship with one another and their environment. + Environmental microbiology + Microbiome + + + Microbial ecology - + - - GenePix Pro 3 - - Nandini Badarinarayan + + + data visualization algorithm - + - - GenePix Pro 5.0 - - Nandini Badarinarayan + + + data cleaning algorithm - + - - GenePix Pro 6.0 - - Nandini Badarinarayan + + + data selection algorithm - + - - GenePix Pro 6 [Axon Instruments] - - Nandini Badarinarayan + + + data integration algorithm - + - - GenePix Pro [Axon Instruments] - - Axon GenePix Pro - Nandini Badarinarayan + + + A data processing task is an information processing objective that specifies the objective that a data processing algorithm execution process needs to achieve when executed on a dataset to produce as output a new dataset. + data processing task - + - - GeneR - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Nandini Badarinarayan - Package manipulating nucleotidic sequences (Embl, Fasta, GenBank) - http://bioconductor.org/packages/2.4/bioc/html/GeneR.html + + + data construction algorithm - + - - GeneRegionScan - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - A package with focus on analysis of discrete regions of the genome. This package is useful for investigation of one or a few genes using Affymetrix data, since it will extract probe level data using the Affymetrix Power Tools application and wrap these data into a ProbeLevelSet. A ProbeLevelSet directly extends the expressionSet, but includes additional information about the sequence of each probe and the probe set it is derived from. The package includes a number of functions used for plotting these probe level data as a function of location along sequences of mRNA-strands. This can be used for analysis of variable splicing, and is especially well suited for use with exon-array data - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/GeneRegionScan.html + + + A generalization is a broad name for an output of a execution of a data mining algorithm on a specific dataset. A generalization specification is an informational entity that specifies the type of the generalization such as: decision trees, decision rules, neural networks, itemsets etc. + Generalization specification of a directive informational entity class that specifies the type of generalization. It includes information about the types of data used to produced the generalization and the language in which the generalization is expressed. + OntoDM + generalization specification + + + + A generalization is a broad name for an output of a execution of a data mining algorithm on a specific dataset. A generalization specification is an informational entity that specifies the type of the generalization such as: decision trees, decision rules, neural networks, itemsets etc. + + - + - - GeneRfold - - - - - - - - - - - - - - - - - + + + A ensemble of generalizations specification is a generalization specification and denotes a type of generalization that is produced by a ensemble algorithm. This algorithm produces a set of generalizations at its output. + An ensemble specification denotes a type of generalization which is an output of an execution of a ensemble algorithm. +Ensembles are sets of generalizations (have as parts single generalizations) with a defined procedure of their combination into a single generalization when executed in a process. + OntoDM + ensemble specification + + + + + An ensemble specification denotes a type of generalization which is an output of an execution of a ensemble algorithm. +Ensembles are sets of generalizations (have as parts single generalizations) with a defined procedure of their combination into a single generalization when executed in a process. + + + + + + + + + + A data mining algorithm is an algorithm that has as its objective a data mining task and outputs as a result a generalization specified by a generalization specification. + data mining algorithm + + + + + + + + + A patten specification is a single generalization specification and denotes a pattern P on type T which is a boolean funtion on objects of type T. + A pattern P on type T specifies a Boolean function on objects of type T, i.e., has the signature p :: T → bool. A pattern on type T is true or false on an object of type T. Frawley et al. (1991) define a pattern as a statement (expression) in a given language, that describes (relationships among) the facts in (a subset of) the data. In the broadest sense, the word pattern is used to describe the output of a variety of data mining algorithms and includes probability distributions, predictive models and clusters/clusterings; however, we restrict it here to the sense that it is most commonly used, i.e., in the sense of frequent pattern mining. + OntoDM + pattern specification + + + + + A pattern P on type T specifies a Boolean function on objects of type T, i.e., has the signature p :: T → bool. A pattern on type T is true or false on an object of type T. Frawley et al. (1991) define a pattern as a statement (expression) in a given language, that describes (relationships among) the facts in (a subset of) the data. In the broadest sense, the word pattern is used to describe the output of a variety of data mining algorithms and includes probability distributions, predictive models and clusters/clusterings; however, we restrict it here to the sense that it is most commonly used, i.e., in the sense of frequent pattern mining. + + + + + + + + + + Estimating the (Joint) Probability Distribution. A set of data (of type +T) is often assumed to be a sample taken from a population according to a +probability distribution. A probability distribution/density function assigns a +non-negative probability/density to each object of type T. Probably the most +general data mining task (Hand et al. 2001) is the task of estimating the (joint) +probability distribution D over type T from a set of data items or a sample +drawn from that distribution. +As mentioned above, in the most typical case we would have T = Tuple(T1, +. . ., Tk), where each of T1, . . ., Tk is Boolean, Discrete(S) or Real. We talk about +the joint probability distribution to emphasize the difference to the marginal +distributions of each of the variables of type T1, . . ., Tk: the joint distribution +captures the interactions among the variables. +Representing multi-variate distributions is a non-trivial task. Two approaches +are commonly used in data mining. In the density-based clustering paradigm, +mixtures of multi-variate Gaussian distributions are typically considered (Hand +et al. 2001). Probabilistic graphical models, most notably Bayesian networks, +represent graphically the (in)dependencies between the variables: Learning their +structure and parameters is an important approach to the problem of estimating +the joint probability distribution. + probability distribution estimation task + + + + + + + + + the task of pattern discovery is to find all local patterns from a given +pattern language that satisfy the required conditions. A prototypical instantiation +of this task is the task of finding frequent itemsets (sets of items, such as +{bread, butter}), which are often found together in a transaction (e.g., a market +basket) (Aggrawal et al 1993). The condition that a pattern (itemset) has to +satisfy in this case is to appear in (hold true for) a sufficiently high proportion +(called support and denoted by s) of the transactions in the input dataset. +With the increasing interest in mining complex data, mining frequent patterns +is also considered for structured data. We can thus talk about mining frequent +subsequences or mining frequent subgraphs in sequence or graph data. We can +consider as frequency the multiple occurrences of a pattern in a single data +structure (e.g., sequence or graph) or the single occurrences of a pattern in +multiple data structures. + pattern discovery task + + + + + + + + + A data mining task is an objective specification that specifies the objective that a data mining algorithm needs to achieve when executed on a dataset to produce as output a generalization. + data mining task + + + + + + + + + OntoDM + A predictive model M for types Td, Tc specifies a function that takes an object of type Td and returns one of type Tc, i.e., has the signature m :: Td → Tc. Most often, predictive modelling is concerned with classification, where Tc would be Boolean (for binary classification) or Discrete(S) (for multi-class classification), or regression, where Tc would be Real. In our case, we allow both Td (description) and Tc (class/target) to be arbitrarily complex data types. + Predictive model specification is a single generalization specification and denotes a type of generalization that represents a mapping taking objects of type Td and returns objects of type To. + predictive model specification + + + + + A predictive model M for types Td, Tc specifies a function that takes an object of type Td and returns one of type Tc, i.e., has the signature m :: Td → Tc. Most often, predictive modelling is concerned with classification, where Tc would be Boolean (for binary classification) or Discrete(S) (for multi-class classification), or regression, where Tc would be Real. In our case, we allow both Td (description) and Tc (class/target) to be arbitrarily complex data types. + + + + + + + + + + Learning a (Probabilistic) Predictive Model. In this task, we are given +a dataset that consists of examples of the form (d, c), where each d is of type +Td and each c is of type Tc. We will refer to d as the description and c as the +class or target. To learn a predictive model means to find a mapping from the +description to the target, m :: Td → Tc, that fits the data closely. This means +that the observed target values and the target values predicted by the model, +i.e., c and ˆc = m(d), have to match closely. + predictive modeling task + + + + + + + + + probability distribution estimation algorithm + + + + + + + + + Clustering. Clustering in general is concerned with grouping objects into classes +of similar objects (Kaufman and Rousseeuw 1990). Given a set of examples (object +descriptions), the task of clustering is to partition these examples into subsets, +called clusters. + clustering task + + + + + + + + + A probability distribution D on type T specifies a mapping from objects of type T to non-negative Reals, i.e., has the signature d :: T → R0+. For uncountably infinite types, probability densities are used instead. The sum of all probabilities (the integral of the probability densities) over T is constrained to amount to one. + A probability distribution specification is a single generalization specification and denotes a type of generalization that is a mapping from objects of type T to non-negative reals. This generalization is an output of a probability distribution estimation algorithm. + OntoDM + probability distribution specification + + + + + A probability distribution D on type T specifies a mapping from objects of type T to non-negative Reals, i.e., has the signature d :: T → R0+. For uncountably infinite types, probability densities are used instead. The sum of all probabilities (the integral of the probability densities) over T is constrained to amount to one. + + + + + + + + + + Allyson Lister + A data processing algorithm is an algorithm that has as its objective a data processing task and has data items both as input and output. + data processing algorithm + + + + + + + + + Examples of such generalization types are: decision trees, desicion rules, neural networks, frequent itemsets, clusters etc. + A single generalization specification is a generalization specification and denotes a type of generalization that is produced by a single generalization data mining algorithm. This algorithm produces only one generalization at its output. + OntoDM + single generalization specification + + + + + + + + + + Ensemble algorithms are algorithms that generate an ensemble when executed on a dataset. The ensemble algorithms include a specification of single generalization algorithms which are executed in oreder to produce the single generalizations that compose the ensemble. + +Examples of ensemble algorithms include bagging, boosting, stacking, random forests, random subspaces,bagging of random subspaces etc. + +For example, bagging of decision trees algorithm includes the specification of a bagging algorithm and having a decision tree algorithm for generating the base models composing the ensemble. + ensemble algorithm + + + + + + + + + single generalization algorithms are data mining algorithms that given a dataset on input produce a generalization at the output. + single generalization algorithm + + + + + + + + + data visualization task is information processing objective achieved by a data visualization algorithm execution process. + data visualization task + + + + + + + + + the life of an organism, the process of sleeping, the process of cell-division + A processual entity that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities. + BFO + process + process + + + + + + + + + Collection of random bacteria, a chair, dorsal surface of the body. + A material entity is a real world physical object. It is an entity that exists in full during the length of time of its existence, persists through this time while maintaining its identity and has no temporal parts. For example a heart, a human, a fly, a microarray. + An independent continuant [snap:IndependentContinuant] that is spatially extended whose identity is independent of that of other entities and can be maintained through time. Note: Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology. + BFO + James Malone + material entity + + + + + A material entity is a real world physical object. It is an entity that exists in full during the length of time of its existence, persists through this time while maintaining its identity and has no temporal parts. For example a heart, a human, a fly, a microarray. + + + + + + + + + + A language in which source code is written, intended to executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it. + IAO + programming language + + + + + + + + - - + + + Data is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. + IAO + data + http://www.ontobee.org/browser/rdf.php?o=IAO&iri=http://purl.obolibrary.org/obo/IAO_0000027 + + + + + + + + + Examples of information content entites include journal articles, data, graphical layouts, and graphs. + An information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity. + IAO + information content entity + information content entity + + + + + + + + + A plan specification which describes inputs, output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata. + An algorithm is a set of instructions for performing a paticular calculation. + IAO + algorithm + algorithm + + + + + An algorithm is a set of instructions for performing a paticular calculation. + + + + + + + + + + The ISO document specifying what encompasses an XML document; The instructions in a XSD file. + A data format specification is the information content borne by the document published defining the specification. + The syntax by which data is specified which renders it valid for a given format. + IAO + data format specification + + + + + The syntax by which data is specified which renders it valid for a given format. + + + + + + + + + - - + + - - - - - - - + + + + + + - + - Nandini Badarinarayan - Package manipulating sequences with fold routines - http://bioconductor.org/packages/2.4/bioc/html/GeneRfold.html + A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name. + IAO + version name + version name - + - - GeneSelectMMD - - - - - - - - + + + An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. + http://purl.obolibrary.org/obo/OBI_0000245 + organization + organization + + + + + + + + + sequence feature format + + + + + + + + - - + + - + + + matlab software + + + + + + + + + 2-sample pooled t-test + + + + + + + + - + - + - - + + @@ -56144,130 +55538,75 @@ The analysis includes normalization and data preprocessing, detection for differ - - - - - - - - - - - - + + - - + + - - - - - - - - - - - - + + - Gene selection based on a mixture of marginal distributions - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/GeneSelectMMD.html + 50-50 Manova is software in which the 50-50 MANOVA algorithm is implemented. + General linear modeling of fixed-effects models with multiple responses is performed. The function calculates 50-50 MANOVA p-values, ordinary univariate p-values and adjusted p-values using rotation testing. + http://rss.acs.unt.edu/Rdoc/library/ffmanova/html/ffmanova.html + Nandini Badarinarayan + 50-50 MANOVA - + - - GeneSelector - - - - - - - - - - - - - + + - - + + - - + + - - + + - - + + - - + + - - - - - - - - - - - Nandini Badarinarayan - The term 'GeneSelector' refers to a filter selecting those genes which are consistently identified as differentially expressed using various statistical procedures. 'Selected' genes are those present at the top of the list in various featured ranking methods (currently 15). In addition, the stability of the findings can be taken in account in the final ranking by examining perturbed versions of the original data set, e.g. by leaving samples, swapping class labels, generating bootstrap replicates or adding noise. - http://bioconductor.org/packages/2.4/bioc/html/GeneSelector.html - - - - - - - - GeneSpring - - - - + - + - - + + @@ -56276,20 +55615,14 @@ The analysis includes normalization and data preprocessing, detection for differ - - - - - - - + - + - - + + @@ -56298,14 +55631,14 @@ The analysis includes normalization and data preprocessing, detection for differ - + - + - - + + @@ -56314,143 +55647,111 @@ The analysis includes normalization and data preprocessing, detection for differ - + - + - - + + - Nandini Badarinarayan - Set of functions and class definitions to be able to read and write GeneSpring specific data objects and covert them to BioConductor objects - http://bioconductor.org/packages/2.4/bioc/html/GeneSpring.html + + + + + + + The ABarray is designed to work with Applied Biosystems whole genome microarray platform, as well as any other platform whose data can be tranformed into expression data matrix. + http://www.bioconductor.org/packages/2.4/bioc/html/ABarray.html + Nandini Badarinarayan + ABarray - + - - GeneSpringGX - - Nandini Badarinarayan + + + The ACME algorithm is quite straightforward. Using a user-dened quantile of the data,called the threshold, any probes in the data that are above that threshold are considered positive probes. A p-value is then assigned to each probe. + 'ACME' - + - - GeneTac Analyser - + + - + - - - - - + + - Genetic Analyzer is a multi-color fluorescence-based DNA analysis system with 16 capillaries operating in parallel, offers high-quality data and efficient sample processing - Nandini Badarinarayan - https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catNavigate2&catID=600530 - - - - - - - - GeneTraffic - - - + + - + - + - - + + - Nandini Badarinarayan - Set of functions and class definitions to be able to read GeneTraffic specific data from a project summary zip file and covert them to BioConductor objects (for 1 color projects affy's ExpressionSet, for 2 color projects marray's marrayRaw) - http://bioconductor.org/packages/2.4/bioc/html/GeneTraffic.html - - - - - - - - GenePix Pro 4.0 - - GenePix Pro v4.0 scanning software - Genepix Pro 4.0 - Nandini Badarinarayan - - - - - - - - GenePix Pro 3.0 - - Genepix pro 3.0 - Nandini Badarinarayan + + + + + + + ACME (Algorithms for Calculating Microarray Enrichment) is a set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other experiments that result in regions of the genome showing "enrichment". It does not rely on a specific array technology (although the array should be a "tiling" array), is very general (can be applied in experiments resulting in regions of enrichment), and is very insensitive to array noise or normalization methods. It is also very fast and can be applied on whole-genome tiling array experiments quite easily with enough memory. + http://bioconductor.org/packages/2.4/bioc/html/ACME.html + Nandini Badarinarayan + Algorithms for Calculating Microarray Enrichment - + - - GeneticsBase - - - - - - - + + - + - + - - + + @@ -56459,14 +55760,14 @@ The analysis includes normalization and data preprocessing, detection for differ - + - + - - + + @@ -56475,49 +55776,32 @@ The analysis includes normalization and data preprocessing, detection for differ - - + + - - - - - - - + + - - + + - Nandini Badarinarayan - This package (GeneticsBase) provides a foundation of efficient data structures and easy-to-use manipulation functions. - http://bioconductor.org/packages/2.4/bioc/html/GeneticsBase.html - - - - - - - - GeneticsDesign - - + - + - - + + @@ -56526,60 +55810,196 @@ The analysis includes normalization and data preprocessing, detection for differ - + - + - - + + + Expression Console™ software supports probe set summarization and CHP file generation for 3' expression (e.g., GeneChip® Human Genome U133 Plus 2.0 Array), gene-level (e.g., GeneChip® Human Gene 1.0 ST array) and exon-level arrays (e.g., GeneChip® Human Exon 1.0 ST Array). The Expression Console workflow provides the user with a choice of the more commonly used probe set summarization algorithms + http://www.affymetrix.com/ + Nandini Badarinarayan + Affymetrix Expression Console + + + + + + + + - - + + + + + + + + + + + + - Nandini Badarinarayan - This package contains functions useful for designing genetics studies, including power and sample-size calculations. - http://bioconductor.org/packages/2.4/bioc/html/GeneticsDesign.html + AIDA is a modular software package for evaluation and documentation of images that were obtained with digital devices such as CCD cameras, flat bed scanners, or BAS / FLA- scanners from Fuji. Additionally, AIDA allows the loading of loading a variety of images in other image formats (e.g.: TIFF, JPEG, Bmp, gel). AIDA can control all scanning devices offering a TWAIN compatible driver. + http://www.raytest.de/index2.html + Nandini Badarinarayan + AIDA - + + + + + Average log expression across arrays (ALE) + + + + + + + + + ALL/AML data set + + + + + + + + + AMDIS + + + + + + + + + The ANCOVA global test is a test for the association between expression values and clinical entities. The test is carried out by comparison of linear models via the extra sum of squares principle. If the mean expression level for at least one gene diers between corresponding models the global null hypothesis, which is the intersection of all single gene null hypotheses, is violated. FDR + ANCOVA + + + + + + + + + ANOVA or Analysis of Variance is a hypothesis testing algorithm which a variable is partitioned into components attributable to different sources of variation. + ANNOVA + 'ANOVA' + + + + + + + + + AP-MS data + + + + + + + + + ARACNE algorithm + + + + + + + + + ARR + + - - GeneticsPed - + + + + + + AWS algorithm + + + + + + + + + Nandini Badarinarayan + Absolute Expression Analysis + + + + + + + + + Nandini Badarinarayan + Absolute Expression Analysis + + + + + + + + - - + + - - + + + + + + + + + + + + - + - + - - + + @@ -56588,93 +56008,60 @@ The analysis includes normalization and data preprocessing, detection for differ - - + + - - - - - - - - - - - - Classes and methods for handling pedigree data. It also includes functions to calculate genetic relationship measures as relationship and inbreeding coefficients and other utilities. Note that package is not yet stable - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/GeneticsPed.html + The AffyCompatible package provides an interface to Affymetrix chip annotation and sample attribute files. The package allows an easy way for users to download and manage local data bases of Affynmetrix NetAffx annotation files. The package also provides access to GeneChip Operating System (GCOS) and GeneChip Command Console (AGCC)-compatible sample annotation files. + http://bioconductor.org/packages/2.4/bioc/html/AffyCompatible.html + Nandini Badarinarayan + 'AffyCompatible' - + - - GenomeGraphs - + + - - - - - - - - - - - - + + - - + + - + - + - - + + - Genomic data analyses requires integrated visualization of known genomic information and new experimental data. GenomeGraphs uses the biomaRt package to perform live annotation queries to Ensembl and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data. Another strength of GenomeGraphs is to plot different data types such as array CGH, gene expression, sequencing and other data, together in one plot using the same genome coordinate system. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/GenomeGraphs.html - - - - - - - - GlobalAncova - - + - + - - + + @@ -56683,14 +56070,14 @@ The analysis includes normalization and data preprocessing, detection for differ - + - + - - + + @@ -56699,78 +56086,134 @@ The analysis includes normalization and data preprocessing, detection for differ - - + + + + + + + + + + + + - - + + - - + + - - + + - GlobalAncova approach: After appropriate normalisation, gene-expression-data appear rather symmetrical and outliers are no real problem, so least squares should be rather robust. ANCOVA with interaction yields saturated data modelling e.g. different means per group and gene. Covariate adjustment can help to correct for possible selection bias. Variance homogeneity and uncorrelated residuals cannot be expected. Application of ordinary least squares gives unbiased, but no longer optimal estimates (Gauss-Markov-Aitken). Therefore, using the classical F-test is inappropriate, due to correlation. The test statistic however mirrors deviations from the null hypothesis. In combination with a permutation approach, empirical significance levels can be approximated. Alternatively, an approximation yields asymptotic p-values. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/GlobalAncova.html + The purpose of this package is to provide a comprehensive and easy-to-use tool for quality assessment and to identify differentially expressed genes in the Affymetrix gene expression data. + http://bioconductor.org/packages/2.4/bioc/html/AffyExpress.html + Nandini Badarinarayan + 'AffyExpress' - + + + + + Nandini Badarinarayan + Affymetrix GCOS v1.2 + + + + + - - GOSemSim - + + - + - + - - + + + The Affymetrix GeneChip Operating Software (GCOS) is an operating system software that controls Affymetrix instruments, acquires data, and executes gene expression analysis. In addition, GCOS contains an embedded database that manages both experiment information and data. + Affymetrix GCOS software + GCOS software + GeneChip Operating Software + http://www.affymetrix.com + Nandini Badarinarayan + Affymetrix GeneChip Operating Software + + + + + + + + + + + + + + + + + + + + Nandini Badarinarayan + Affymetrix Software + + + + + + + + - - + + - - + + - + - + - - + + @@ -56779,38 +56222,30 @@ The analysis includes normalization and data preprocessing, detection for differ - - - - - Methods for estimating GO semantic similarities. Implemented five methods proposed by Resnik, Schlicker(Rel), Jiang, Lin and Wang respectively. Support five species: human, rat, mouse, fly, and yeast. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/GOSemSim.html - - - - - - - - GraphAT - - - - - + + + + + + + + + + + + - + - + - - + + @@ -56819,14 +56254,14 @@ The analysis includes normalization and data preprocessing, detection for differ - + - + - - + + @@ -56835,32 +56270,30 @@ The analysis includes normalization and data preprocessing, detection for differ - - + + + + + + + + + + + + - Functions and data used in Balasubramanian, et al. (2004) - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/GraphAT.html - - - - - - - - GraphAlignment - - + - + - - + + @@ -56869,135 +56302,145 @@ The analysis includes normalization and data preprocessing, detection for differ - - + + - - + + - - - - - - - - - - - - + + - Graph alignment is an extension package for the R programming environment which provides functions for finding an alignment between two networks based on link and node similarity scores. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/GraphAlignment.html + Preprocessing of Agilent 4x44 array data + http://bioconductor.org/packages/2.4/bioc/html/Agi4x44PreProcess.html + Nandini Badarinarayan + Agi4x44PreProcess - + - - GridGrinder - - - - - - - - - - - - - - - - - - Nandini Badarinarayan - Software for microarray image analysis. - http://www.oxfordjournals.org/nar/webserver/summary/825 + + + Nandini Badarinarayan + Agilent Feature Extraction 5.1.1 - + - - Hexagon binning algorithm - + + + Nandini Badarinarayan + Agilent Feature Extraction software version 7.1 - + + + + + Nandini Badarinarayan + Agilent Feature Extraction software version 7.5 + + + + + + + + + Nandini Badarinarayan + Agilent Feature Extraction software version A.5.1.1 + + - - HELP - + + + + + - + - + - - + + - - - - - - - + Scan Control Software is the user interface software that controls the Agilent scanner. This software is usable only with the Agilent high-resolution scanner (G2565CA) or high-resolution scanner upgrade. It will not function with earlier scanner versions + Scan Control Application software + http://www.chem.agilent.com/ + Nandini Badarinarayan + Agilent Scan Control + + + + + + + + - + - + - - + + - + + + Nandini Badarinarayan + Agilent Technologies Software + + + + + + + + - - + + - + - + - - + + @@ -57006,14 +56449,14 @@ The analysis includes normalization and data preprocessing, detection for differ - + - + - - + + @@ -57022,257 +56465,159 @@ The analysis includes normalization and data preprocessing, detection for differ - - - - - - - + - - + + + + + - - - - - - - Nandini Badarinarayan - The package contains a modular pipeline for analysis of HELP microarray data, and includes graphical and mathematical tools with more general applications - http://bioconductor.org/packages/2.4/bioc/html/HELP.html + This package provides user interface and database connection code for annotation data packages using SQLite data storage. + http://bioconductor.org/packages/2.4/bioc/html/AnnotationDbi.html + Nandini Badarinarayan + 'AnnotationDbi' - + - - HEM - + + - + - + - - + + + Microarrays are powerful tools for discovering levels of gene expression. Geneservice have invested in the latest gene expression microarray system from Applied Biosystems so that the widest choice of platform is available to our customers. The key features of this system are: +Sensitivity: a detection threshold of as little as a femtomole of expresseed mRNA and requiring as little as 500ng of starting total RNA. +Content: each probe is associated with a gene sequence buiult on unique Celera data and validated by public RefSeqs all of which have been curated. +Pipeline: complete integrated solutions for gene expression research including Applied Biosystems Bioinformatic tools and ready-to-go gene expression TaqMan assays for validation of results. + http://www.geneservice.co.uk/services/geneexpression/overview_1700.jsp + Nandini Badarinarayan + Applied Biosystems 1700 Expression Array System Software + + + + + + + + - - - - - - - - - - - - - - - - - - - + - + - - + + - - - - - - - - - - - - - Nandini Badarinarayan - This package fits heterogeneous error models for analysis of microarray data - http://bioconductor.org/packages/2.4/bioc/html/HEM.html - - - - - - - - Heterogeneous Error Model (HEM) - - - - - - - - - Hubert’s gamma - - - - - - - - - Hidden Markov Model - - - - - - - - - Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) algorithm - - - - - - - - - Hidden Variable Dynamic Modelling HVDM) - - Technique which predicts a given transcription factor activity and then uses this infor- mation to predict its targets. - - - - - - - - HaarSeg algorithm - - - - - - - - - Hardy-Weinberg equilibrium - + Fujifilm ArrayGauge™ software is specifically designed for Macroarray and Microarray samples, with all the practical functions necessary for the most powerful array analysis. +Its ultra-friendly navigation and functions can handle any kind of array (CLONTECH, Genome Systems, Research Genetics - even hand-made arrays). It already includes virtually every contemporary cDNA membrane template on the market, with the flexibility to handle others as they develop. + ArrayGauge [FUJIFILM] + http://www.fujifilm.com/products/life_science_systems/science_imaging/arraygauge/ + Nandini Badarinarayan + ArrayGauge - + - - Harshlight - - - - - - - + + - + - + - - + + + ArrayNorm is an platform-independent Java tool for normalization and statistical analysis for microarray-experiment data. It provides modules for visualization (scatterplot, histogram, boxplot, etc.), normalization and analysis. + http://bin.tugraz.at/Tools/ArrayNorm.html + Nandini Badarinarayan + ArrayNorm + + + + + + + + - - + + - - + + - + - + - - + + - Nandini Badarinarayan - The package is used to detect extended, diffuse and compact blemishes on microarray chips. Harshlight automatically marks the areas in a collection of chips (affybatch objects) and a corrected AffyBatch object is returned, in which the defected areas are substituted with NAs or the median of the values of the same probe in the other chips in the collection. The new version handle the substitue value as whole matrix to solve the memory problem. - http://bioconductor.org/packages/2.4/bioc/html/Harshlight.html - - - - - - - - Heatplus - - - - - - - - + - + - - + + @@ -57281,86 +56626,130 @@ The analysis includes normalization and data preprocessing, detection for differ - - + + + This package is designed to provide solutions for quality assessment and to detect differentially expressed genes for the Affymetrix GeneChips, including both 3' -arrays and gene 1.0-ST arrays. + http://bioconductor.org/packages/2.4/bioc/html/ArrayTools.html + Nandini Badarinarayan + 'ArrayTools' + + + + + + + + - + - + - - + + - Add an extra graphical display at the bottom of a heat map, indicating for each column a) whether it has one of several binary properties or not, and b) the value of a quantitative variable. A cutting threshold for the sample dendrogram can also be specified, and the resulting clustering of the columns is indicated by coloring both the dendrogram and the extra variable display. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/Heatplus.html + This software implements a robust algorithm for spot finding and quantitation, quality metrics, and use of pre-made protocols ensure accuracy and reproducibility. Choices for background correction, normalization, and ratio calculation between arrays provides flexibility.Wizard guides simplify operation.Automatic batch processing increases throughput and saves time.Data easily exported to Microsoft™ Excel or database programs for flexibility in reporting. + Nandini Badarinarayan + + ArrayVision - + + + + + Nandini Badarinarayan + ArrayVision 6.0 (Imaging Research Inc.) + + + + + + + + + Nandini Badarinarayan + Array_vision_(Interfocus) + + + + + - - HilbertVis - + + - + - + - - + + + Computer software for the analysis and comparison of Atlas™ nylon and plastic arrays. + http://www.clontech.com/images/pacs/634650-PA27475.pdf + Nandini Badarinarayan + AtlasImage + + + + + + + + + Nandini Badarinarayan + Axon GenePix Pro 3 + + + + + + + + - - + + - - - - - - - - - - - - + + - + - + - - + + @@ -57369,60 +56758,66 @@ The analysis includes normalization and data preprocessing, detection for differ - - + + + + + + + - - + + - Functions to visualize long vectors of integer data by means of Hilbert curves - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/HilbertVis.html + This package uses a Bayesian hierarchical model to detect enriched regions from ChIP-chip experiments + http://bioconductor.org/packages/2.4/bioc/html/BAC.html + Nandini Badarinarayan + BAC - + + + + + binning clustering method- The algorithm uses single-linkage clustering to join compounds into similarity groups, where every member in a cluster shares with at least one other member a similarity value above a user-specified threshold. The algorithm is optimized for speed and memory +eciency by avoiding the calculation of an all-against-all distance matrix. + Binning clustering method + + + - - HilbertVisGUI - + + + + - - - - - - - - - - - - + + - - + + - + - + - - + + @@ -57431,160 +56826,117 @@ The analysis includes normalization and data preprocessing, detection for differ - - - - - - - + - + - - + + - An interactive tool to visualize long vectors of integer data by means of Hilbert curves - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/HilbertVisGUI.html - - - - - - - - Hypergeometric probability - + Functions and classes for de novo prediction of transcription factor binding consensus by heuristic search + http://bioconductor.org/packages/2.4/bioc/html/BCRANK.html + Nandini Badarinarayan + 'BCRANK' - + - - ICS-501 (version 2.3) Image Capture System - - - - - - - - - - - - - - - - - - Nandini Badarinarayan + + + Marked as obsolete by Allyson Lister. + After 0.4 release. + Equivalence with EDAM term "BED" (format_3003). + obsolete_BED format + true - + - - Iteratively ReWeighted Least Squares - + + + BGL implements Depth First Search, Breadth First Search,Dijkstra's, Bellman Ford's and DAG,Johnson's and Floyd Warshall's.Kruskal's algorithm and Prim's algorithm Cuthill-McKee's algorithm Minimum degree Ordering + BGL - + - - IRanges - + + - - + + - - - - - - - - - - - - + + - - + + - - + + + Bayesian models for differential gene expression + http://bioconductor.org/packages/2.4/bioc/html/BGmix.html + Nandini Badarinarayan + 'BGmix' + + + + + + + + - + - + - - + + - Nandini Badarinarayan - The IRanges class and its extensions are low-level containers for storing sets of integer ranges. A typical use of these containers in biology is for representing a set of chromosome regions. More specific extensions of the IRanges class will typically allow the storage of additional information attached to each chromosome region as well as a hierarchical relationship between these regions. - http://bioconductor.org/packages/2.4/bioc/html/IRanges.html - - - - - - - - ITALICS - - - - - - - - + - + - - + + @@ -57593,20 +56945,14 @@ The analysis includes normalization and data preprocessing, detection for differ - - - - - - - + - + - - + + @@ -57615,350 +56961,474 @@ The analysis includes normalization and data preprocessing, detection for differ - - + + + + + + + + + + + + - - + + - - + + - A Method to normalize of Affymetrix GeneChip Human Mapping 100K and 500K set - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/ITALICS.html + BLAST, or Basic Local Alignment Search Tool in full, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. + The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. + http://blast.ncbi.nlm.nih.gov/Blast.cgi + Allyson Lister: added 'achieves objective' axioms for pairwise and multiple sequence alignment classes. + James Malone + Nandini Badarinarayan + BLAST - + - - ILLUMINA data - + + + Iterative Bayesian Model Averaging (BMA) - + - - ImaGene4.1 software - - Nandini Badarinarayan + + + Base-Pair-Distance Kernel - + - - ImaGene 3.0 - - Nandini Badarinarayan + + + + + + + + + BPMAP is a binary data format specification created by Affymetrix where the data is stored in big-endian format. The BPMAP format contains information relating to the design of the Affymetrix tiling arrays. + http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/bpmap.html, accessed 22 May 2013. + Allyson Lister + BPMAP - + - - ImageQuant - + + - + - + - - + + - ImageQuant (Molecular Dynamics) - Nandini Badarinarayan - This is a general image analysis program used in the study of electrophoretic separations, dot blots, slot blots, microplate assays, TLC assays, and plaque assays. ImageQuant provides a point-and-click environment for fast analysis of qualitative and quantitative assays. With tools for accurate volume integration, ImageQuant generates accurate lane profiles even for curved or slanted lanes. - http://www.research.bidmc.harvard.edu/AcademicIT/ImageQuant.asp + BRB-ArrayTools is an integrated package for the visualization and statistical analysis of DNA microarray gene expression data. It was developed by professional statisticians experienced in the analysis of microarray data and involved in the development of improved methods for the design and analysis of microarray based experiments. The system incorporates a variety of powerful analytic and visualization tools developed specifically for microarray data analysis. + http://linus.nci.nih.gov/BRB-ArrayTools.html + Nandini Badarinarayan + BRB-ArrayTools - + - - ImageReader - - Nandini Badarinarayan + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + This document describes the process of forging a BSgenome data package. It is intended for Bioconductor +users who want to make a new BSgenome data package + http://bioconductor.org/packages/2.4/bioc/html/BSgenome.html + Nandini Badarinarayan + 'BSgenome' - + - - ImaGene - + + - + - + - - + + - ImaGene [BioDiscovery] - ImaGene microarray image analysis software by biodiscovery for microarrays, protein arrays and CGH analysis. - Imagene - Nandini Badarinarayan - http://www.biodiscovery.com/index/imagene + BZScan is a free java tool for automatic quantification of DNA microarrays with radioactive labeling. BZScan provides saturation, overshining, and background noise correction, it also gives quality control measures. It can work either in a fully automatic "batch mode" or at different levels of manual operation. + http://tagc.univ-mrs.fr/bioinformatics/bzscan/ + Nandini Badarinarayan + BZScan - + - - Imagene v4.0 - - Nandini Badarinarayan + + + BaldiLongT - + - - Initial microarray data processing (data filtering, local normalisation and quality control) - + + - + - + - - + + - Nandini Badarinarayan - These scripts are for primer design and initial microarray data processing and are available as .zip files: - http://www.bahlerlab.info/resources/ + This program may be used to read out image data from all scanners of the FujiFilm BAS series (BAS1000, BAS1500, BAS1800, BAS2000, BAS2500, BAS3000, BAS5000) and the FujiFilm FLA scanners (FLA-2000, FLA-3000). + http://www.rubion.rub.de/labor/pdf/BASREAD.pdf + Nandini Badarinarayan + BasReader 3.01 - + - - Jaccard’s index - + + + Bayesian Model - + - - Jaguar - + + - + - + - - + + - Image analysis software - Nandini Badarinarayan + BeadStudio Software is a modular analysis tool for genotyping, gene expression, and methylation applications + http://www.illumina.com/pages.ilmn?ID=35 + Nandini Badarinarayan + Beadstudio - + - - KCsmart - + + - - + + - + - + - - + + + This package is dedicated to biclustering analysis which allows to discover sets of genes that have the same expression pattern accross a set of samples + http://bioconductor.org/packages/2.4/bioc/html/BicARE.html + Nandini Badarinarayan + 'BicARE' + + + + + + + + + + + + + + + Creates classes used in model-view-controller (MVC) design + http://bioconductor.org/packages/2.4/bioc/html/BioMVCClass.html + Nandini Badarinarayan + 'BioMVCClass' + + + + + + + + - - + + + Functions that are needed by many other packages or which replace R functions + http://bioconductor.org/packages/2.4/bioc/html/Biobase.html + Nandini Badarinarayan + 'Biobase' + + + + + + + + - - - - - - - - - - - - + + + + + Software and data to support the case studies. + http://bioconductor.org/packages/2.4/bioc/html/BiocCaseStudies.html + Nandini Badarinarayan + 'BiocCaseStudies' + + + + + + + + + + + + + + + + + + + + + + + + Bioconductor is an open source and open development software project to provide tools for the analysis and comprehension of genomic data. Bioconductor is based primarily on the R programming language, but does contain contributions in other programming languages. + http://www.bioconductor.org/overview + Bioconductor + Nandini Badarinarayan + This is a defined class which will be populated if a piece of software identifies itself as having the value 'Bioconductor' for the 'is published by' property. (Allyson Lister) + BioConductor Software + + + + + + + + - - + + - - + + - - - - - - - - - - - - + + - Multi sample aCGH analysis package using kernel convolution - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/KCsmart.html + Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or set of sequences. + http://bioconductor.org/packages/2.4/bioc/html/Biostrings.html + Nandini Badarinarayan + 'Biostrings' - + - - KEGGSOAP - + + - + - + - - + + + BlueFuse for Microarrays is a powerful software solution for the analysis of microarray expression and arrayCGH experiments. Operation is simple and fully automated, saving time, removing operator error and subjectivity and ensuring experimental reproducibility. + BlueFuse [BlueGnome] + http://www.cambridgebluegnome.com/bluefuse.htm + Nandini Badarinarayan + BlueFuse + + + + + + + + - - + + - + - + - - + + - A package that provides a client interface to the KEGG SOAP server - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/KEGGSOAP.html - - - - - - - - KEGGgraph - - + - + - - + + @@ -57967,14 +57437,14 @@ The analysis includes normalization and data preprocessing, detection for differ - + - + - - + + @@ -57983,72 +57453,48 @@ The analysis includes normalization and data preprocessing, detection for differ - - - - - - - - + + + + + + + + + + + + - KEGGGraph is an interface between KEGG pathway and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated KGML (KEGG XML) files into graph models maintaining all essential pathway attributes. The package offers functionalities including parsing, graph operation, visualization and etc. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/KEGGgraph.html - - - - - - - - KGML - - - - - - - - - 'KLD' - - - - - - - - - Kolmogorov Smirnov rank-sum based algorithm - - KS measures how biased the ranks of a subset of items are among the ranks of the entire set + This package creates a tabular style data object where most data is stored outside main memory. A buffer is used to speed up access to data. + http://bioconductor.org/packages/2.4/bioc/html/BufferedMatrix.html + Nandini Badarinarayan + 'BufferedMatrix' - + - - LBE - + + - - + + - + - + - - + + @@ -58057,85 +57503,64 @@ The analysis includes normalization and data preprocessing, detection for differ - - - - - - - + - + - - + + + This package involves microarray Data related methods that utlize BufferedMatrix objects + http://bioconductor.org/packages/2.4/bioc/html/BufferedMatrixMethods.html + Nandini Badarinarayan + 'BufferedMatrixMethods' + + + + + + + + - - + + - + - + - - + + - LBE is an efficient procedure for estimating the proportion of true null hypotheses, the false discovery rate (and so the q-values) in the framework of estimating procedures based on the marginal distribution of the p-values without assumption for the alternative hypothesis. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/LBE.html - - - - - - - - LC-MS data - - - - - - - - - LMGene - - - - - - - - + - + - - + + @@ -58144,99 +57569,155 @@ The analysis includes normalization and data preprocessing, detection for differ - - + + - - + + + + + This package contains functions for normalizing spotted microarray data, based on a physically motivated calibration model. The model parameters and error distributions are estiamted from external control spikes. + http://bioconductor.org/packages/2.4/bioc/html/CALIB.html + Nandini Badarinarayan + 'CALIB' + + + + + + + + + + + + - - + + + + + + + + + + + + - + - + - - + + - LMGene package for analysis of microarray data using a linear model and glog data transformation in the R statistical package - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/LMGene.html + + + + + + + Annotation of peaklists generated by xcms, rule based annotation of isotopes and adducts, EIC correlation based tagging of unknown adducts and fragments + Nandini Badarinarayan + 'CAMERA' - + - - Locally Moderated Weighted-t (LMW) method - + + + The circular binary segmentation (CBS) algorithm divides the genome into regions of equal copy number . The algorithm tests for change-points using a maximal t-statistic with a permutation reference distribution to obtain the corresponding p-value. The number of computations required for the maximal test statistic is O(N^2),where N is the number of markers. This makes the full permutation approach computationally prohibitive for the newer arrays that contain tens of thousands markers and highlights the need for a faster algorithm. + CBS - + - - Lognormal Normal Model - + + + CBS algorithm - + - - Lognormal Normal with Modied Variance Model - + + + + + + + + + The CDF binary format is a binary data format specification created by Affymetrix was created for faster access and smaller file size in comparison to the CDF ASCII format. The values in the file are stored in little-endian format. CDF binary format describes the layout for an Affymetrix GeneChip array. An array may contain Expression, Genotyping, CustomSeq, Copy Number and/or Tag probe sets. All probe set names within an array are unique. Multiple copies of a probe set may exist on a single array as long as each copy has a unique name. + http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/cdf.html, accessed 22 May 2013. + It is unclear whether, originally, this format was intended to be the ASCII or binary version of the CDF format. As such, this class has been renamed as the binary format, and a new class created (CDF ASCII format) to make both options available. + CDF binary format - + - - LPE - + + - - + + + CEL binary format is a binary data format specification created by Affymetrix where values are stored in little-endian format. The CEL format stores the results of the intensity calculations on the pixel values of the DAT file. This includes an intensity value, standard deviation of the intensity, the number of pixels used to calculate the intensity value, a flag to indicate an outlier as calculated by the algorithm and a user defined flag indicating the feature should be excluded from future analysis. The file stores the previously stated data for each feature on the probe array. + http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/cel.html, accessed 22 May 2013. + Allyson Lister + It is unclear whether, originally, this format was intended to be the ASCII or binary version of the CEL format. As such, this class has been renamed as the binary format, and a new class created (CEL ASCII format) to make both options available. (22/05/2013) + CEL binary format + + + + + + + + - - + + - + - + - - + + @@ -58245,26 +57726,14 @@ The analysis includes normalization and data preprocessing, detection for differ - - - - - - - - - - - - - + - + - - + + @@ -58273,60 +57742,50 @@ The analysis includes normalization and data preprocessing, detection for differ - - + + - - + + - Nandini Badarinarayan - This LPE library is used to do significance analysis of microarray data with small number of replicates. It uses resampling based FDR adjustment, and gives less conservative results than traditional 'BH' or 'BY' procedures. Data accepted is raw data in txt format from MAS4, MAS5 or dChip. Data can also be supplied after normalization. LPE library is primarily used for analyzing data between two conditions. To use it for paired data, see LPEP library. For using LPE in multiple conditions, use HEM library. - http://bioconductor.org/packages/2.4/bioc/html/LPE.html + Contains functions and classes that are needed by arrayCGH packages. + http://bioconductor.org/packages/2.4/bioc/html/CGHbase.html + Nandini Badarinarayan + 'CGHbase' - + - - LPEadj - + + - - + + - - - - - - - - - - - - + + - + - + - - + + @@ -58335,32 +57794,14 @@ The analysis includes normalization and data preprocessing, detection for differ - - - - - - - - - - - - - - - - - - - + - + - - + + @@ -58369,346 +57810,140 @@ The analysis includes normalization and data preprocessing, detection for differ - - + + - - + + - Nandini Badarinarayan - Two options are added to the LPE algorithm. The original LPE method sets all variances below the max variance in the ordered distribution of variances to the maximum variance. in LPEadj this option is turned off by default. The second option is to use a variance adjustment based on sample size rather than pi/2. By default the LPEadj uses the sample size based variance adjustment. - http://bioconductor.org/packages/2.4/bioc/html/LPEadj.html - - - - - - - - publisher role - - A publisher role is a role borne by an organization or individual in which they are responsible for making software available to a particular consumer group. Such organizations or individuals do need to be involved in the development of the software. - James Malone - - - - - - - - Langmuir Isotherm - - - - - - - - - Laplace mixture model - - - - - - - - - Library Search Algorithm - - - - - - - - - Loess algorithm - - - - - - - - - Logic regression - - - - - - - - - MAANOVA v1.2 package for MATLAB - - Nandini Badarinarayan - Tools for analyzing Micro Array experiments - http://cran.r-project.org/web/packages/maanova/index.html - - - - - - - - Median Average Difference Algorithm - - - - - - - - - obsolete_MAGE-ML - - true - Marked as obsolete by Allyson Lister. - Equivalence with EDAM format_3161. - Obsoleted after the 0.4 release. + + + + + + + Calls aberrations for array CGH data using a six state mixture model as well as several biological concepts that are ignored by existing algorithms. Visualization of profiles is also provided. + http://bioconductor.org/packages/2.4/bioc/html/CGHcall.html + Nandini Badarinarayan + 'CGHcall' - + - - MANOR - - - - - - - - - - - - - - - - - - - + + - - + + - - + + - + - - + + + + + - Nandini Badarinarayan - We propose importation, normalization, visualization, and quality control functions to correct identified sources of variability in array-CGH experiments. - http://bioconductor.org/packages/2.4/bioc/html/MANOR.html - - - - - - - - MAQC data - - - - - - - - - MIcroarray Analysis Suite - - + - + - - + + - Affymetrix MicroArraySuite - Affymetrix® Microarray Suite (MAS) is the core software product in the Affymetrix Software System providing instrument control, data acquisition, and data analysis for the entire GeneChip® platform. - MAS - Nandini Badarinarayan - http://www.affymetrix.com/support/technical/datasheets/mas_datasheet.pdf - - - - - - - - MicroArraySuite 5.0 - - MAS 5.0 software - Nandini Badarinarayan - - - - - - - - MATLAB language - + Dimension Reduction for Array CGH Data with Minimal Information Loss + http://bioconductor.org/packages/2.4/bioc/html/CGHregions.html + Nandini Badarinarayan + 'CGHregions' - + - - MAVI Pro - + + - - - - - - - - - - - - + + - Nandini Badarinarayan - - - - - - - - Multivariate correlation estimator - - - - - - - - - Markov Chain Monte Carlo - + CHP binary format is a binary data format specification created by Affymetrix, stored in little-endian format and used to store expression, resequencing and genotyping results from algorithms implemented in the GCOS 1.2, 1.3 and 1.4 and BRLMM Analysis Tool software applications. + http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/chp.html, http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/chp-xda.html, accessed 22 May 2013. + Allyson Lister + As this is a child of Binary format, it is assumed that this class is intended to represent the binary form of this format. As described in the definition sources, there are other formats for CHP available. + CHP binary format - + - - MCR algorithm - - minimum common regions (MCR) algorithm- Minimal common regions (MCRs) are dened as contiguous spans having at least a recurrence rate dened by a parameter (recurrence) across samples. + + + CLR algorithm - + - - MCRestimate - - - - - - - - - - - - - - - - - + + - - + + - - - - - - - - - - - - + + - Nandini Badarinarayan - This package includes a function for combining preprocessing and classification methods to calculate misclassification errors - http://bioconductor.org/packages/2.4/bioc/html/MCRestimate.html - - - - - - - - MEDME - - + - + - - + + @@ -58717,14 +57952,14 @@ The analysis includes normalization and data preprocessing, detection for differ - + - + - - + + @@ -58733,56 +57968,48 @@ The analysis includes normalization and data preprocessing, detection for differ - - + + - MEDME allows the prediction of absolute and relative methylation levels based on measures obtained by MeDIP-microarray experiments - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/MEDME.html - - - - - - - - 'MI' - + This package provides a comprehensive collection of various microarray-based classification algorithms both from Machine Learning and Statistics. Variable Selection, Hyperparameter tuning, Evaluation and Comparison can be performed combined or stepwise in a user-friendly environment. + http://bioconductor.org/packages/2.4/bioc/html/CMA.html + Nandini Badarinarayan + 'CMA' - + - - Mutual information matrix (MIM) - + + + CMA- it implements k-fold cross validation, MCMC cross validation, bootstrap and (t.test or welch.test or wilcox.test or f.test or kruskal.test or One-step Recursive Feature Elimination or random forest variable importance measure or lasso or elastic net or componentwise boosting) + CMA - + - - MLInterfaces - + + - - + + - + - + - - + + @@ -58791,14 +58018,14 @@ The analysis includes normalization and data preprocessing, detection for differ - + - + - - + + @@ -58807,113 +58034,177 @@ The analysis includes normalization and data preprocessing, detection for differ - - + + + + + + + + - Nandini Badarinarayan - Uniform interfaces to machine learning code for data in Bioconductor containers - http://bioconductor.org/packages/2.4/bioc/html/MLInterfaces.html + Multivariate correlation estimation and statistical inference. + http://bioconductor.org/packages/2.4/bioc/html/CORREP.html + Nandini Badarinarayan + 'CORREP' - + - - MMD - - MMD describes the distributions of gene expression levels directly via the marginal distributions. It includes EM algorithm, FDR, it is the percentage of nondifferentially expressed genes among selected genes), false non-discovery rate (denoted as FNDR; it is the percentage of differentially expressed genes among unselected genes),false positive rate (denoted as FPR; it is the percentage of selected genes among nondifferentially expressed genes), and false negative rate (denoted as FNR; it is the percentage of un-selected genes among differentially expressed genes), + + + This algorithm offers improved confidence scores, quality scores for SNP’s and batches, higher accuracy on different datasets and better performance. + CRLMM algorithm - + + + + + Continuous Wavelet Transform (CWT)-based peak detection algorithm + + + + + - - MVCClass - + + - + - + - - + + + CARMAweb allows the analysis of Affymetrix GeneChip, ABI microarrays and two color microarrays. +The analysis includes normalization and data preprocessing, detection for differentially expressed genes, cluster analysis and GO analysis. All calculations (except the cluster analysis) are performed in R using functions provided by the BioConductor packages. + CarmaWEB + https://carmaweb.genome.tugraz.at/carma/ + Nandini Badarinarayan + CARMAweb + + + + + + + + + Category analysis + + + + + + + + + + + + + + + + + + + + - - + + + + + + + - - + + - + - + - - + + - Creates classes used in model-view-controller (MVC) design - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/MVCClass.html - - - - - - - - Mahalanobis distance - + + + + + + + + + + + + + A collection of tools for performing category analysis. + http://bioconductor.org/packages/2.4/bioc/html/Category.html + Nandini Badarinarayan + Category - + - - MantelCorr - + + + + + + + + - - + + - + - + - - + + @@ -58922,14 +58213,14 @@ The analysis includes normalization and data preprocessing, detection for differ - + - + - - + + @@ -58938,113 +58229,164 @@ The analysis includes normalization and data preprocessing, detection for differ - - + + + + + + + + + + + + - - + + - Computes Mantel cluster correlations from a (p x n) numeric data matrix (e.g. microarray gene-expression data) - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/MantelCorr.html + ChemMineR is an open source compound mining framework. It contains functions for atom descriptor calculation, structure similarity searching, clustering of compound libraries and various utilities for managing complex compound data. It also offers a wide range of visualization functions for compound clusters and chemical structures. The package is integrated with the online ChemMine environment and allows bidirectional communications between the two services. + http://bioconductor.org/packages/2.4/bioc/html/ChemmineR.html + Nandini Badarinarayan + 'ChemmineR' - + - - MassSpecWavelet - + + - + - + - - + + + Versarray ChipReader systems are highly sensitive laser confocal systems designed for rapid imaging of microarrays. These are advanced scanners that meet your expectations, differentiating between a spot response and background level, and optimizing the signal on the bottom as well as the top end of the range for increased sensitivity. Results with versarray chipreader systems have a low background, enhanced weak signal detection, and virtually no photobleaching for a long dye lifetime. + VersArray ChipReader + http://www.bio-medicine.org/ + Nandini Badarinarayan + ChipReader 3.1 + + + + + + + + - + - + - - + + + ChipSkipper - an integrated tool for analysis, evaluation and quantitation of DNA micro-array data + ChipSkipper Microarray Data Evaluation Software + ChipSkipper [EMBL] + http://angiogenesis.dkfz.de/software/chipskipper/index.htm + Nandini Badarinarayan + ChipSkipper + + + + + + + + + Nandini Badarinarayan + ChipSkipper V0.99 + + + + + + + + - - + + - - + + - Nandini Badarinarayan - Processing Mass Spectrometry spectrum by using wavelet based algorithm - http://bioconductor.org/packages/2.4/bioc/html/MassSpecWavelet.html - - - - - - - - MeasurementError.cor - - - + + + + + + + + + - - + + - - + + + A multiscan is an R package for combining multiple scans + http://bioconductor.org/packages/2.4/bioc/html/multiscan.html + Nandini Badarinarayan + multiscan + + + + + + + + - + - - - - - + + @@ -59052,43 +58394,39 @@ The analysis includes normalization and data preprocessing, detection for differ - + + + + + + + - - - - - - - - - + + + + + + + + + + + + + - Nandini Badarinarayan - Two-stage measurement error model for correlation estimation with smaller bias than the usual sample correlation - http://bioconductor.org/packages/2.4/bioc/html/MeasurementError.cor.html - - - - - - - - MergeMaid - - + - - - - - + + + @@ -59096,27 +58434,44 @@ The analysis includes normalization and data preprocessing, detection for differ - - + + + + + + + + + + - - + + + The affy package contains functions for exploratory oligonucleotide array analysis. The dependance to tkWidgets only concerns few convenience functions. 'affy' is fully functional without it. + http://bioconductor.org/packages/2.4/bioc/html/affy.html + Nandini Badarinarayan + affy + + + + + + + + - + - - - - - + + @@ -59124,21 +58479,24 @@ The analysis includes normalization and data preprocessing, detection for differ - - + + + + + + + + - + - - - - - + + @@ -59146,114 +58504,108 @@ The analysis includes normalization and data preprocessing, detection for differ - + - - - - - + + - Nandini Badarinarayan - The functions in this R extension are intended for cross-study comparison of gene expression array data. Required from the user is gene expression matrices, their corresponding gene-id vectors and other useful information, and they could be 'list','matrix', or 'ExpressionSet'. The main function is 'mergeExprs' which transforms the input objects into data in the merged format, such that common genes in different datasets can be easily found. And the function 'intcor' calculate the correlation coefficients. Other functions use the output from 'modelOutcome' to graphically display the results and cross-validate associations of gene expression data with survival. - http://bioconductor.org/packages/2.4/bioc/html/MergeMaid.html + The affycomp package contains functions that can be used to compare expression measures for Affymetrix Oligonucleotide Arrays. + http://bioconductor.org/packages/2.4/bioc/html/affycomp.html + Nandini Badarinarayan + affycomp - + + + + + PCMG- a bipartite graph in which one set of nodes represents proteins, the other set represents complexes, and an edge from a protein node to a complex node represents membership of the protein in that complex. + PCMG + + + + + - - Mfuzz - + + - - - - - - - - - - - - + + + Nandini Badarinarayan + Feature Extraction Software + + + + + + + + + Chi-square + + + + + + + + - - - - - - - - - - - - + + - - + + - - + + - + - + - - + + - Nandini Badarinarayan - Package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface) - http://bioconductor.org/packages/2.4/bioc/html/Mfuzz.html - - - - - - - - MiPP - - + - + - - + + @@ -59262,206 +58614,176 @@ The analysis includes normalization and data preprocessing, detection for differ - - - - - - - + - + - - + + - - - - - - - - - - - - - Nandini Badarinarayan - This package finds optimal sets of genes that seperate samples into two or more classes. - http://bioconductor.org/packages/2.4/bioc/html/MiPP.html - - - - - - - - Misclassification-Penalized Posteriors (MiPP) - + adSplit implements clustering of microarray gene expression profiles according to functional annotations. For each term genes are annotated to, splits into two subclasses are computed and a significance of the supporting gene set is determined. + http://bioconductor.org/packages/2.4/bioc/html/adSplit.html + Nandini Badarinarayan + Annotation-Driven Clustering - + - - MicroArraySuite 4.0 - - Nandini Badarinarayan + + + distance calculation - + - - Mixed model equations - + + + + + + + + + Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. + http://www.stat.berkeley.edu/users/terry/zarray/Software/smacode.html + Nandini Badarinarayan + R software - + - - 'Needleman-Wunsch' - + + + BCRANK is a method that takes a ranked list of genomic regions as input and outputs short DNA sequences that are overrepresented in some part of the list. + BCRANK - + - - Nested Effects Models - - This includes exhaustive enumeration, triple-based inference,pairwise heuristic, module based inference, greedy hillclimbing + + + cosmo allows the user to target the motif search by specifying a set of constraints that the unknown position weight matrix must satisfy. The algorithm is based on a probabilistic model that describes the DNA sequences of interest through a two- component multinomial mixture model with estimates of the position weight matrix entries obtained by maximizing the observed data likelihood over the smaller parameter space corresponding to the imposed constraints. It includes methods such as Probabilistic models and one-occurrence-per-sequence and zero-or-one-occurrence-per-sequence and two-component mixture + Cosmo - + - - Nonlinear Estimation by Iterative Partial Least Squares - + + + F test - + - - OCplus - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - + - + - - + + - - Nandini Badarinarayan - This package allows to characterize the operating characeristics of a microarray experiment, i.e. the trade-off between false discovery rate and the power to detect truly regulated genes. The package includes tools both for planned experiments (for sample size assessment) and for already collected data (identification of differentially expressed genes). - http://bioconductor.org/packages/2.4/bioc/html/OCplus.html + + + Nandini Badarinarayan + MAGE-TAB inputting software - + + + + + Text data set + + + + + + + + + CSV data set + + + + + + + + + non-linear functional regression model with both additive and multiplicative error terms + Non-linear functional regression model + + + + + - - OLIN - + + + + + + + + - - + + - - + + - - + + - + - + - - + + @@ -59470,212 +58792,186 @@ The analysis includes normalization and data preprocessing, detection for differ - - - - - - - + - + - - + + - Functions for normalisation of two-color microarrays by optimised local regression and for detection of artefacts in microarray data - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/OLIN.html + + + + + + + A collection of software tools for dealing with co-citation data. + http://bioconductor.org/packages/2.4/bioc/html/CoCiteStats.html + Nandini Badarinarayan + 'CoCiteStats' - + - - OLINgui - - - - - - - - - - - - - - - - - - - + + - + - + - - + + + This software has a series of analytical tools to address the manufacturing, detection and data analysis components of a microarray experiment. Together, these tools help optimize performance in an expression profiling study. + http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=101854 + Nandini Badarinarayan + CodeLink Expression Analysis Software + + + + + + + + - - - - - - - - - - - - - + - + - - + + - Graphical user interface for the OLIN package - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/OLINgui.html + Slides are scanned using CodeLink Expression Scanning Software + Nandini Badarinarayan + CodeLink Expression Scanning Software - + + + + + Complex Estimation Algorithm + + + + + - - Optiquant - + + - + - + - - + + - Computer software for image acquisition, analysis and reporting, for use in the life sciences - Nandini Badarinarayan - http://www.findownersearch.com/optiquant/7766418/ + Cyber-T may be used to statistically determine what the probability is that a specific gene is differentially expressed by determining an associated p-value statistic. + http://dmaf.biochem.uci.edu/affymetrix_analysis_software.html + Nandini Badarinarayan + Cyber-T - + - - OrderedList - + + - - - - - - - - - - - - + + + + + + + + - - + + - - + + - - + + - + - + - - + + - Detection of similarities between ordered lists of genes. Thereby, either simple lists can be compared or gene expression data can be used to deduce the lists. Significance of similarities is evaluated by shuffling lists or by resampling in microarray data, respectively. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/OrderedList.html - - - - - - - - OutlierD - - + - + - - + + @@ -59684,69 +58980,50 @@ The analysis includes normalization and data preprocessing, detection for differ - - + + - - + + + This library contains functions that calculate various statistics of differential expression for microarray data, including t statistics, fold change, F statistics, SAM, moderated t and F statistics and B statistics. It also implements a new methodology called DEDS (Differential Expression via Distance Summary), which selects differentially expressed genes by integrating and summarizing a set of statistics using a weighted distance approach. + http://bioconductor.org/packages/2.4/bioc/html/DEDS.html + Nandini Badarinarayan + 'DEDS' + + + + + + + + - - - - - - - - - - - - + + - - + + - Nandini Badarinarayan - This package detects outliers using quantile regression on the M-A scatterplots of high-throughput data. - http://bioconductor.org/packages/2.4/bioc/html/OutlierD.html - - - - - - - - Presence-Absence calls with Negative Probesets (PANP) - - - - - - - - - PAnnBuilder - - + - + - - + + @@ -59755,14 +59032,14 @@ The analysis includes normalization and data preprocessing, detection for differ - + - + - - + + @@ -59771,53 +59048,66 @@ The analysis includes normalization and data preprocessing, detection for differ - - + + - Nandini Badarinarayan - Processing annotation data from public data repositories and building annoation data packages. - http://bioconductor.org/packages/2.4/bioc/html/PAnnBuilder.html + This package provides a supervised technique able to identify differentially expressed genes. The Fuzzy Patterns are built by means of applying 3 Membership Functions to discretized gene expression values. + http://bioconductor.org/packages/2.4/bioc/html/DFP.html + Nandini Badarinarayan + 'DFP' - + - - Pearson correlation estimator - + + + A DFP version of a FP (fuzzy pattern) only includes those genes that can serve to differentiate it from the rest of the patterns.This algorithm is based on the discretization of float values (gene expression values) stored in an ExpressionSet object into labels combining 'Low', 'Medium' and 'High' + Discriminant Fuzzy Pattern Algorithm - + - - PCpheno - - - - - - - + + + DFW + + + + + + + + + Digital gene expression (DGE) datasets + + + + + + + + - - + + - + - + - - + + @@ -59826,76 +59116,82 @@ The analysis includes normalization and data preprocessing, detection for differ - - - - - - - - - - - - - + - + - - + + + Segments DNA copy number data using circular binary segmentation to detect regions with abnormal copy number + http://bioconductor.org/packages/2.4/bioc/html/DNAcopy.html + Nandini Badarinarayan + 'DNAcopy' + + + + + + + + + + + + + + - + - + - - + + - - - - - - - Nandini Badarinarayan - Tools to integrate, annotate, and link phenotypes to cellular organizational units such as protein complexes and pathways. - http://bioconductor.org/packages/2.4/bioc/html/PCpheno.html + A set of functions to create and interact with dynamic documents and vignettes. + http://bioconductor.org/packages/2.4/bioc/html/DynDoc.html + Nandini Badarinarayan + 'DynDoc' - + - - PGSEA - + + + + + + + + - + - + - - + + @@ -59904,14 +59200,14 @@ The analysis includes normalization and data preprocessing, detection for differ - + - + - - + + @@ -59920,70 +59216,72 @@ The analysis includes normalization and data preprocessing, detection for differ - - - - - - - + - + - - + + - Nandini Badarinarayan - Parametric Analysis of Gene Set Enrichment - http://bioconductor.org/packages/2.4/bioc/html/PGSEA.html - - - - - - - - 'PLM' - - it is where we fit a model with probe level and chip level parameters on a probeset by probeset basis + EBImage is an R package which provides general purpose functionality for the reading, writing, processing and analysis of images. Furthermore, in the context of microscopy based cellular assays, EBImage offers tools to transform the images, segment cells and extract quantitative cellular descriptors. + http://bioconductor.org/packages/2.4/bioc/html/EBImage.html + Nandini Badarinarayan + 'EBImage' - + - - PLPE - + + + + + + + + + + + + + + + + + + + + - - + + - - + + - + - + - - + + @@ -59992,14 +59290,14 @@ The analysis includes normalization and data preprocessing, detection for differ - + - + - - + + @@ -60008,273 +59306,447 @@ The analysis includes normalization and data preprocessing, detection for differ - - + + + + + + + + + + + + - - + + - Nandini Badarinarayan - This package performs tests for paired high-throughput data. - http://bioconductor.org/packages/2.4/bioc/html/PLPE.html + EBarrays provides tools for the analysis of replicated/unreplicated microarray data. + http://bioconductor.org/packages/2.4/bioc/html/EBarrays.html + Nandini Badarinarayan + 'EBarrays' - + - - Probe level Locally moderated Weighted median-t (PLW) method - + + + Expectation-Maximization(EM) algorithm - + - - PPC algorithm - + + + Empirical Bayes rule - + - - PROcess - - - - - - - - - - - - - - - - - - - - - - - - - + + - + - + - - + + + Exper 2100 offers powerful data evaluation tools for all available assays, automatic and manual integration, smear analysis and many assay-specific tools. + http://www.chem.agilent.com/en-US/products/instruments/lab-on-a-chip/2100expertsoftware/pages/default.aspx + Nandini Badarinarayan + Expert 2100 + + + + + + + + + Marked as obsolete by Allyson Lister. + 0.5 + This class had no definition, and seemed incorrectly placed as an algorithm, as from its name it seemed to only be an experimental method. + obsolete_FACS ( fluorescence-activated cell sorter) + true + + + + + + + + + FACS data is data which describes flow cytometry data sets. + http://www.bioconductor.org/packages/2.12/bioc/vignettes/prada/inst/doc/fcs3.html, accessed 29 May 2013. + Allyson Lister + FACS data + + + + + + + + + FARMS + + + + + + + + + Marked as obsolete by Allyson Lister. + Obsoleted after the 0.4 release. + Equivalence with EDAM term format_1929. Please use this term instead. + obsolete_FASTA + true + + + + + + + + + FC + + + + + + + + + Marked as obsolete by Allyson Lister + 0.5 + Obsoleted as it was a generic term where there was no way of knowing for sure which format it was - or which version the format was in. Perhaps could have been annotated and moved, but this class was only identified after a new class (http://www.ebi.ac.uk/swo/data/SWO_3000061) had been created. Please use the new class (SWO_3000061) or its versioned children instead of this obsolete class. + obsolete_FCS + true + + + + + + + + + 'FDR' + + + + + + + + + Fixed effect model + + + + + + + + - + - + - - + + - A package for processing protein mass spectrometry data. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/PROcess.html + + + + + + + The software automatically finds and places microarray grids, rejects outlier pixels, accurately determines feature intensities and ratios, flags outlier pixels, and calculates statistical confidences. Application-specific QC reports summarize results and provide an at-a-glance quality assessment + Feature Extraction Software + Feature Extraction Software [Agilent Technologies] + Feature Extraction software + http://www.chem.agilent.com/en-us/products/instruments/dnamicroarrays/featureextractionsoftware/pages/default.aspx + Nandini Badarinarayan + Agilent Feature Extraction Software - + - - Propagation of uncertainty in microarray analysis - - Included are summarisation, differential expression detection, clustering and PCA methods, together with useful plotting and data manipulation functions + + + Firth's bias reduction procedure - + + + + + Fischer's Exact Test + + + + + + + + + FoxDimmicT + + + + + - - Pathways 2.01 software - + + - + - + - - + + - Nandini Badarinarayan - The background intensity data from the spot quantification programs may be used to correct spot intensity. This software measures background globally as: BGLow (low background), BGAvg (Average background), BGRms (root mean square background). - http://maexplorer.sourceforge.net/MaeRefMan/hmaeDoc2.4.2.html - - - - - - - - Power Law Global Error Model (PLGEM) analysis method - + Dynamically chooses cutoffs for grouping into present/divergent genes based on the shape of the distribution. More resistant to variation in hybridization data than CCACK. + http://falkow.stanford.edu/whatwedo/software/software.html + Nandini Badarinarayan + GACK - + - - Probe Cell Analysis - - Nandini Badarinarayan + + + GASSCO method - + - - PLIER (Probe Logarithmic Error Intensity Estimate) method - + + + + + + + + + + + + + + + + + + + Single-user desktop software package for analyzing microarray data from multiple microarray platforms. + GC-RMA Quantification (Stratagene ArrayAssist Expression Software) + http://www.biocompare.com/ProductDetails/475470/ArrayAssist-Expression-Software-(1-year-academic-license).html + Nandini Badarinarayan + GC-RMA Quantification - + - - QuantArray scanner software - + + - + - + - - + + - Nandini Badarinarayan - QuantArray - QuantArray® is a powerful microarray analysis software that enables researchers to -easily and accurately visualize and quantitate gene expression data. - http://las.perkinelmer.com/content/relatedmaterials/brochures/bro_quantarray.pdf + Incyte GEMTools software is an enterprise solution for managing gene expression data using the SQL Server and Oracle relational databases. It was one of the first integrated software packages designed with an easy-to-use interface to help scientist track and analyze the vast amounts of gene expression data generated from microarray experiments. GEMTools can be used quantify and graphically display your gene expression data. Incyte Genomics relied on the GEMTools for internal operations and to track each well, probe, cDNA target, and other components of GEM arrays through ordering, fabrication, image analysis, and final data delivery. + http://www.baymedia.com/gemtools/ + Nandini Badarinarayan + GEMTools 2.4 - + - - QuantArray, PackaardBiochip technologies - - Nandini Badarinarayan + + + GEO data type - + - - QuantArray version 2 - - Nandini Badarinarayan + + + GEO Matrix Series format - + - - Radial basis function - + + + + + + + + + + + + + + + + + + + + + + + + + The NCBI Gene Expression Omnibus (GEO) represents the largest public repository of microarray data. However, finding data of interest can be challenging using current tools. GEOmetadb is an attempt to make access to the metadata associated with samples, platforms, and datasets much more feasible. This is accomplished by parsing all the NCBI GEO metadata into a SQLite database that can be stored and queried locally. GEOmetadb is simply a thin wrapper around the SQLite database along with associated documentation. Finally, the SQLite database is updated regularly as new data is added to GEO and can be downloaded at will for the most up-to-date metadata. + http://bioconductor.org/packages/2.4/bioc/html/GEOmetadb.html + Nandini Badarinarayan + GEOmetadb - + - - RBGL - + + - - + + - - + + + + + + + + + + + + + The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data. Given the rich and varied nature of these data, it is only natural to want to apply BioConductor tools to these data. + http://bioconductor.org/packages/2.4/bioc/html/GEOquery.html + Nandini Badarinarayan + GEOquery + + + + + + + + - - + + - - + + + + + + + + + + + + - + - + - - + + @@ -60283,14 +59755,14 @@ easily and accurately visualize and quantitate gene expression data. - + - + - - + + @@ -60299,51 +59771,57 @@ easily and accurately visualize and quantitate gene expression data. - + - + - - + + - A fairly extensive and comprehensive interface to the graph algorithms contained in the BOOST library. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/RBGL.html + This package is an infrastructure for dealing with hapmap SNP reports, GWAS, etc. + http://bioconductor.org/packages/2.4/bioc/html/GGBase.html + Nandini Badarinarayan + GGBase - + - - R interface to boost graph library algorithm (RBGL) - + + + Gamma Gamma Model - + - - RBioinf - + + + + + + + + - + - + - - + + @@ -60352,14 +59830,14 @@ easily and accurately visualize and quantitate gene expression data. - + - + - - + + @@ -60368,295 +59846,355 @@ easily and accurately visualize and quantitate gene expression data. - - + + + + + + + + + + + + - - + + + + + + + + + + + + - Functions and datasets and examples to accompany the monograph R For Bioinformatics. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/RBioinf.html + This package deals with hapmap SNP reports, GWAS, etc. + http://bioconductor.org/packages/2.4/bioc/html/GGtools.html + Nandini Badarinarayan + GGtools - - - - Random effects model - - - - - - - - - Recursive Feature Elimination (RFE) - - for the Support Vector Machine (SVM), as presented in [3] and the Nearest Shrunken Centroid (NSC) - - - - - + - - RLMM - - - - - - - - - - - - - - - - - - - - - - - - - + + - - + + - - + + - - + + + + + + + + + + + + - - + + + + + + + + + + + + - A Genotype Calling Algorithm for Affymetrix SNP Arrays - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/RLMM.html + Analysis of array CGH data : detection of breakpoints in genomic profiles and assignment of a status (gain, normal or lost) to each chromosomal regions identified. + http://bioconductor.org/packages/2.4/bioc/html/GLAD.html + Nandini Badarinarayan + GLAD - - - - Regression model - - - - - - + - - RMA - + + + Modified version of the GLAD algorithm (Gain and Loss Analysis of DNA) - + - - RMA+ - + + + + + + + + + + + + + + + + + + + Microarray image quantification is performed using GLEAMS software + http://hmg.oxfordjournals.org/cgi/reprint/12/17/2145.pdf + Nandini Badarinarayan + GLEAMS software - + - - RMA++ - + + + Nandini Badarinarayan + GMS - + - - RMAExpress - + + + + + + + + + + + + + + - - + + - + - - - - - - - - - - - + + + + + + + + + - - + + + + + + + + + + + + - + - - + + + + + - Nandini Badarinarayan - RMAExpress is a standalone GUI program for Windows (and Linux) to compute gene expression summary values for Affymetrix Genechip® data using the Robust Multichip Average expression summary and to carry out quality assessment using probe-level metrics. It does not require R nor is it dependent on any component of the BioConductor project. If focuses on processing 3' IVT expression arrays, exon and WT gene arrays. - http://rmaexpress.bmbolstad.com/ - - - - - - - - RMAExpress 2.0 - - Nandini Badarinarayan + + + + + + + + + + + + + + + + + + + + + + + A set of tools for interacting with GO and microarray data. A variety of basic manipulation tools for graphs, hypothesis testing and other simple calculations + http://bioconductor.org/packages/2.4/bioc/html/GOstats.html + Nandini Badarinarayan + GOstats - + - - RMAExpress quantification - - Nandini Badarinarayan + + + Gene Recommender algorithm - + - - RMAGEML - + + - - - - - - - + + - - + + + + + + + + + + + + - - + + + + + + + + + + + + - + - + - - + + - Nandini Badarinarayan - This package can be used to handle MAGEML documents in Bioconductor - http://bioconductor.org/packages/2.4/bioc/html/RMAGEML.html + This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA). + http://bioconductor.org/packages/2.4/bioc/html/GSEABase.html + Nandini Badarinarayan + GSEABase - + - - RNAither - + + - - + + - - + + - - + + - + - - + + + + + @@ -60664,452 +60202,819 @@ easily and accurately visualize and quantitate gene expression data. - - + + + + + + + + + + + + - Nandini Badarinarayan - RNAither analyzes cell-based RNAi screens, and includes quality assessment, customizable normalization and statistical tests, leading to lists of significant genes and biological processes - http://bioconductor.org/packages/2.4/bioc/html/RNAither.html - - - - - - - - ROC - - - + + - - + + + Models and methods for fitting linear models to gene expression data, together with tools for computing and using various regression diagnostics. + http://bioconductor.org/packages/2.4/bioc/html/GSEAlm.html + Nandini Badarinarayan + GSEAlm + + + + + + + + + Gamma-Gamma hierarchical model + + + + + + + + + Gaussian locally weighted regression + + + + + + + + + Gene-Set Enrichment Analysis + + + + + + + + - - + + + + + + + + + + + + + Genedata Expressionist® is an enterprise solution that integrates, stores and analyzes transcriptomics, proteomics and metabolomics data as well as a wide variety of phenotypic data. + http://www.genedata.com/products/expressionist/overview.html + Nandini Badarinarayan + GeneData Expressionist Analyst v4.0.5 + + + + + + + + - + - - - - + + + + + + + + + - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/ROC.html - utilities for ROC, with uarray focus + GenePix is the industry standard microarray image analysis software because of its unique combination of imaging and analysis tools, visualizations, automation capabilities, performance and ease of use. + Gene Pix + Genepix + http://www.moleculardevices.com/pages/software/gn_genepix_pro.html + Nandini Badarinarayan + Gene Pix - + + + + + Nandini Badarinarayan + GenePix 3.0.6 + + + + + + + + + Nandini Badarinarayan + GenePix 4.1 + + + + + + + + + GenePix 4100A [Axon Instruments] + Nandini Badarinarayan + GenePix 4100A + + + + + + + + + Nandini Badarinarayan + GenePix 5.0.1 + + + - - RWebServices - + + + + + GenePix [Axon Instruments] + Nandini Badarinarayan + GenePix + + + + + + + + + Nandini Badarinarayan + GenePix Pro + + + + + + + + + Nandini Badarinarayan + GenePix Pro 3 + + + + + + + + + Nandini Badarinarayan + GenePix Pro 5.0 + + + + + + + + + Nandini Badarinarayan + GenePix Pro 6.0 + + + + + + + + + Nandini Badarinarayan + GenePix Pro 6 [Axon Instruments] + + + + + + + + + Axon GenePix Pro + Nandini Badarinarayan + GenePix Pro [Axon Instruments] + + + + + + + + - - - - - - - - - - - - - - - + + - + - - - - + + + + + + + + + - - + + + + + + + + + + + + - - + + + + + + + + + + + + - Nandini Badarinarayan - This package provides mechanisms for automatic function prototyping and exposure of R functionality in a web services environment. - http://bioconductor.org/packages/2.4/bioc/html/RWebServices.html + Package manipulating nucleotidic sequences (Embl, Fasta, GenBank) + http://bioconductor.org/packages/2.4/bioc/html/GeneR.html + Nandini Badarinarayan + GeneR - + - - RankProd - + + - - + + - - + + + + + + + + + + + + - - + + + + + + + + + + + + + A package with focus on analysis of discrete regions of the genome. This package is useful for investigation of one or a few genes using Affymetrix data, since it will extract probe level data using the Affymetrix Power Tools application and wrap these data into a ProbeLevelSet. A ProbeLevelSet directly extends the expressionSet, but includes additional information about the sequence of each probe and the probe set it is derived from. The package includes a number of functions used for plotting these probe level data as a function of location along sequences of mRNA-strands. This can be used for analysis of variable splicing, and is especially well suited for use with exon-array data + http://bioconductor.org/packages/2.4/bioc/html/GeneRegionScan.html + Nandini Badarinarayan + GeneRegionScan + + + + + + + + - - + + - - + + + + + + + + + + + + - + - - - - + + + + + + + + + - Nandini Badarinarayan - Rank Product method for identifying differentially expressed genes with application in meta-analysis - http://bioconductor.org/packages/2.4/bioc/html/RankProd.html + Package manipulating sequences with fold routines + http://bioconductor.org/packages/2.4/bioc/html/GeneRfold.html + Nandini Badarinarayan + GeneRfold - + - - RbcBook1 - + + - - + + - Nandini Badarinarayan - Support for Springer monograph on Bioconductor - http://bioconductor.org/packages/2.4/bioc/html/RbcBook1.html - - - - - - - - Rdbi - - - + + - - + + + + + + + + + + + + - - + + + + + + + + + + + + - + - - - - + + + + + + + + + - Generic database methods - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/Rdbi.html + + + + + + + Gene selection based on a mixture of marginal distributions + http://bioconductor.org/packages/2.4/bioc/html/GeneSelectMMD.html + Nandini Badarinarayan + GeneSelectMMD - + - - RdbiPgSQL - + + - - + + - - - - - - - + + - - + + - - + + - Nandini Badarinarayan - Provides methods for accessing data stored in PostgreSQL tables. - http://bioconductor.org/packages/2.4/bioc/html/RdbiPgSQL.html - - - - - - - - Rdisop - - - + + - - - - - - - + + + + + + + + - - + + - - + + - Decomposition of Isotopic Patterns - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/Rdisop.html + The term 'GeneSelector' refers to a filter selecting those genes which are consistently identified as differentially expressed using various statistical procedures. 'Selected' genes are those present at the top of the list in various featured ranking methods (currently 15). In addition, the stability of the findings can be taken in account in the final ranking by examining perturbed versions of the original data set, e.g. by leaving samples, swapping class labels, generating bootstrap replicates or adding noise. + http://bioconductor.org/packages/2.4/bioc/html/GeneSelector.html + Nandini Badarinarayan + GeneSelector - + - - RefPlus - + + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - - + + + + + + + + + + + + - + - - - + + + + + - Nandini Badarinarayan - The package contains functions for pre-processing Affymetrix data using the RMA+ and the RMA++ methods. - http://bioconductor.org/packages/2.4/bioc/html/RefPlus.html + Set of functions and class definitions to be able to read and write GeneSpring specific data objects and covert them to BioConductor objects + http://bioconductor.org/packages/2.4/bioc/html/GeneSpring.html + Nandini Badarinarayan + GeneSpring - + - - Resourcerer - + + + Nandini Badarinarayan + GeneSpringGX + + + + + + + + - - + + + + + + + + + + + + + Genetic Analyzer is a multi-color fluorescence-based DNA analysis system with 16 capillaries operating in parallel, offers high-quality data and efficient sample processing + https://products.appliedbiosystems.com/ab/en/US/adirect/ab?cmd=catNavigate2&catID=600530 + Nandini Badarinarayan + GeneTac Analyser + + + + + + + + - - + + - - + + + + + + + + + + + + - Nandini Badarinarayan - This package allows user either to read an annotation data file from TIGR Resourcerer as a matrix or convert the file into a Bioconductor annotation data package using the AnnBuilder package. - http://bioconductor.org/packages/2.4/bioc/html/Resourcerer.html + Set of functions and class definitions to be able to read GeneTraffic specific data from a project summary zip file and covert them to BioConductor objects (for 1 color projects affy's ExpressionSet, for 2 color projects marray's marrayRaw) + http://bioconductor.org/packages/2.4/bioc/html/GeneTraffic.html + Nandini Badarinarayan + GeneTraffic - + + + + + GenePix Pro v4.0 scanning software + Genepix Pro 4.0 + Nandini Badarinarayan + GenePix Pro 4.0 + + + + + + + + + Genepix pro 3.0 + Nandini Badarinarayan + GenePix Pro 3.0 + + + - - Rgraphviz - + + + + - - + + - - + + - + - - - - + + + + + + + + + - - + + + + + + + - Nandini Badarinarayan - Provides plotting capabilities for R graph objects - http://bioconductor.org/packages/2.4/bioc/html/Rgraphviz.html - - - - - - - - Ringo - - - + + + + + + + + + + + + - - + + + This package (GeneticsBase) provides a foundation of efficient data structures and easy-to-use manipulation functions. + http://bioconductor.org/packages/2.4/bioc/html/GeneticsBase.html + Nandini Badarinarayan + GeneticsBase + + + + + + + + - - + + - + - - + + + + + @@ -61117,395 +61022,426 @@ easily and accurately visualize and quantitate gene expression data. - + - + - - + + - - - - - 2 - - - Nandini Badarinarayan - The package Ringo facilitates the primary analysis of ChIP-chip data. The main functionalities of the package are data read-in, quality assessment, data visualisation and identification of genomic regions showing enrichment in ChIP-chip. The package has functions to deal with two-color oligonucleotide microarrays from NimbleGen used in ChIP-chip projects - http://bioconductor.org/packages/2.4/bioc/html/Ringo.html + This package contains functions useful for designing genetics studies, including power and sample-size calculations. + http://bioconductor.org/packages/2.4/bioc/html/GeneticsDesign.html + Nandini Badarinarayan + GeneticsDesign - + - - Rintact - + + - - + + - - - - - - - + + - - + + + + + + + - + - - - - + + + + + + + + + - - + + - Nandini Badarinarayan - Queries and data structures for protein interactions - http://bioconductor.org/packages/2.4/bioc/html/Rintact.html + Classes and methods for handling pedigree data. It also includes functions to calculate genetic relationship measures as relationship and inbreeding coefficients and other utilities. Note that package is not yet stable + http://bioconductor.org/packages/2.4/bioc/html/GeneticsPed.html + Nandini Badarinarayan + GeneticsPed - + - - Rmagpie - - - - - - - + + - - + + - - + + + + + + + + + + + + - - - - - - - - + + + + + + + + + + + + - Microarray Classification is designed for both biologists and statisticians. It offers the ability to train a classifier on a labelled microarray dataset and to then use that classifier to predict the class of new observations. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/Rmagpie.html - - - - - - - - Rnw - - - - - - - - - Robust likelihood-based survival modeling - + Genomic data analyses requires integrated visualization of known genomic information and new experimental data. GenomeGraphs uses the biomaRt package to perform live annotation queries to Ensembl and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data. Another strength of GenomeGraphs is to plot different data types such as array CGH, gene expression, sequencing and other data, together in one plot using the same genome coordinate system. + http://bioconductor.org/packages/2.4/bioc/html/GenomeGraphs.html + Nandini Badarinarayan + GenomeGraphs - + - - Rosetta Resolver - + + - - + + - Nandini Badarinarayan - The Rosetta Resolver® system provides a central analysis center and repository for biologists, statisticians, and bioinformaticians for the evaluation of gene expression data from microarrays and qPCR studies. - http://www.rosettabio.com/products/resolver - - - - - - - - RpsiXML - - - - - - - - + + - - + + + + + + + + + + + + - + - - - - + + + + + + + + + - - + + - - + + - Nandini Badarinarayan - Queries, data structure and interface to visualization of interaction datasets. This package inplements the PSI-MI 2.5 standard and supports up to now 8 databases. Further databases supporting PSI-MI 2.5 standard will be added continuously. - http://bioconductor.org/packages/2.4/bioc/html/RpsiXML.html + GlobalAncova approach: After appropriate normalisation, gene-expression-data appear rather symmetrical and outliers are no real problem, so least squares should be rather robust. ANCOVA with interaction yields saturated data modelling e.g. different means per group and gene. Covariate adjustment can help to correct for possible selection bias. Variance homogeneity and uncorrelated residuals cannot be expected. Application of ordinary least squares gives unbiased, but no longer optimal estimates (Gauss-Markov-Aitken). Therefore, using the classical F-test is inappropriate, due to correlation. The test statistic however mirrors deviations from the null hypothesis. In combination with a permutation approach, empirical significance levels can be approximated. Alternatively, an approximation yields asymptotic p-values. + http://bioconductor.org/packages/2.4/bioc/html/GlobalAncova.html + Nandini Badarinarayan + GlobalAncova - + - - Rredland - - - - - - - + + - - + + - - + + - + - - - - + + + + + + + + + - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/Rredland.html - interface to redland RDF utilities - - - - - - - - Rtreemix - - + - - - - + + + + + + + - - + + + Methods for estimating GO semantic similarities. Implemented five methods proposed by Resnik, Schlicker(Rel), Jiang, Lin and Wang respectively. Support five species: human, rat, mouse, fly, and yeast. + http://bioconductor.org/packages/2.4/bioc/html/GOSemSim.html + Nandini Badarinarayan + GOSemSim + + + + + + + + - - + + - - + + - + - - - - + + + + + + + + + - - + + + + + + + + + + + + - Nandini Badarinarayan - Rtreemix is a package that offers an environment for estimating the mutagenetic trees mixture models from cross-sectional data and using them for various predictions. It includes functions for fitting the trees mixture models, likelihood computations, model comparisons, waiting time estimations, stability analysis, etc. - http://bioconductor.org/packages/2.4/bioc/html/Rtreemix.html + Functions and data used in Balasubramanian, et al. (2004) + http://bioconductor.org/packages/2.4/bioc/html/GraphAT.html + Nandini Badarinarayan + GraphAT - + - - Ruuid - - - - - - - + + - - + + - - + + - - + + + + + + + + + + + + - + - - - - + + + + + + + + + - A package to provide UUID values in R - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/Ruuid.html + Graph alignment is an extension package for the R programming environment which provides functions for finding an alignment between two networks based on link and node similarity scores. + http://bioconductor.org/packages/2.4/bioc/html/GraphAlignment.html + Nandini Badarinarayan + GraphAlignment - + - - S-Score algorithm - + + + + + + + + + + + + + + + + + + + Software for microarray image analysis. + http://www.oxfordjournals.org/nar/webserver/summary/825 + Nandini Badarinarayan + GridGrinder - + - - Serial Analysis of Gene Expression (SAGE) - + + + Hexagon binning algorithm - + - - SAGx - + + - + - - + + @@ -61513,20 +61449,20 @@ easily and accurately visualize and quantitate gene expression data. - - + + - + - + - - + + @@ -61535,220 +61471,314 @@ easily and accurately visualize and quantitate gene expression data. - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - A package for retrieval, preparation and analysis of data from the Affymetrix GeneChip. In particular the issue of identifying differentially expressed genes is addressed. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/SAGx.html - - - - - - - - SAM - - Note: It is unclear from just the label what is meant by a SAM algorithm. It may or may not be related to the SAM sequence alignment software described by the class SWO_0000077 (Allyson Lister) - - - - - - - - SAS/STAT Software, Version 8 - - - + + - Nandini Badarinarayan - Statistical Analysis with a number of procedures, providing statistical information such as analysis of variance, regression, multivariate analysis, and categorical data analysis. - http://en.wikipedia.org/wiki/SAS_System + The package contains a modular pipeline for analysis of HELP microarray data, and includes graphical and mathematical tools with more general applications + http://bioconductor.org/packages/2.4/bioc/html/HELP.html + Nandini Badarinarayan + HELP - + - - SBMLR - + + - - - - - - - - - - - - - - + + + + + + + + + + + + + + - - + + - - + + - + - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + - Nandini Badarinarayan - This package contains a systems biology markup language (SBML) interface and biochemical system analysis tools with illustrative examples. - http://bioconductor.org/packages/2.4/bioc/html/SBMLR.html + This package fits heterogeneous error models for analysis of microarray data + http://bioconductor.org/packages/2.4/bioc/html/HEM.html + Nandini Badarinarayan + HEM - + - - SBMLR format - + + + Heterogeneous Error Model (HEM) - + - - obsolete_SBML file - - true - Identical to http://www.ebi.ac.uk/swo/data/SWO_3000037 - 0.4 - Marked as obsolete by Allyson Lister + + + Hubert’s gamma - + - - obsolete_SBML model - - true - 0.5 - Marked as obsolete by Allyson Lister. - 'SBML model' was classed as a child of algorithm, when this clearly isn't the case. As SWO already contained 'SBML file' (to cover the data format itself), there was no need for this class at all. The one class (SBMLR) which referenced this class had the relevant axiom deleted. For referencing the SBML format, please use the class 'SBML file'. + + + Hidden Markov Model - + - - SDF format - + + + Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH) algorithm - + - - SIM - + + + Technique which predicts a given transcription factor activity and then uses this infor- mation to predict its targets. + Hidden Variable Dynamic Modelling HVDM) + + + + + + + + + HaarSeg algorithm + + + + + + + + + Hardy-Weinberg equilibrium + + + + + + + + - - - - - - - - - - + + - - + + - - + + + + + + + + + + + + + + + + + + - - + + + + + + + + + + + + - Finds associations between DNA copy number and gene expression. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/SIM.html + The package is used to detect extended, diffuse and compact blemishes on microarray chips. Harshlight automatically marks the areas in a collection of chips (affybatch objects) and a corrected AffyBatch object is returned, in which the defected areas are substituted with NAs or the median of the values of the same probe in the other chips in the collection. The new version handle the substitue value as whole matrix to solve the memory problem. + http://bioconductor.org/packages/2.4/bioc/html/Harshlight.html + Nandini Badarinarayan + Harshlight - + - - SLGI - + + - - + + - - + + + + + + + + + + + + - + - + - - + + @@ -61757,36 +61787,39 @@ easily and accurately visualize and quantitate gene expression data. - - + + - A variety of data files and functions for the analysis of genetic interactions - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/SLGI.html + Add an extra graphical display at the bottom of a heat map, indicating for each column a) whether it has one of several binary properties or not, and b) the value of a quantitative variable. A cutting threshold for the sample dendrogram can also be specified, and the resulting clustering of the columns is indicated by coloring both the dendrogram and the extra variable display. + http://bioconductor.org/packages/2.4/bioc/html/Heatplus.html + Nandini Badarinarayan + Heatplus - + - - SLqPCR - + + - - + + - + - - + + + + + @@ -61794,14 +61827,14 @@ easily and accurately visualize and quantitate gene expression data. - + - + - - + + @@ -61810,55 +61843,76 @@ easily and accurately visualize and quantitate gene expression data. - + - - - - + + + + + + + + + - - + + + + + + + + - Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/SLqPCR.html + Functions to visualize long vectors of integer data by means of Hilbert curves + http://bioconductor.org/packages/2.4/bioc/html/HilbertVis.html + Nandini Badarinarayan + HilbertVis - + - - SMAP - + + - - + + - - + + + + + + + + + + + + - + - + - - + + @@ -61867,12 +61921,15 @@ easily and accurately visualize and quantitate gene expression data. - + - - + + + + + @@ -61880,57 +61937,83 @@ easily and accurately visualize and quantitate gene expression data. - - + + + An interactive tool to visualize long vectors of integer data by means of Hilbert curves + http://bioconductor.org/packages/2.4/bioc/html/HilbertVisGUI.html + Nandini Badarinarayan + HilbertVisGUI + + + + + + + + + Hypergeometric probability + + + + + + + + - + - - - - + + + + + + + + + - Functions and classes for DNA copy number profiling of array-CGH data - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/SMAP.html + Nandini Badarinarayan + ICS-501 (version 2.3) Image Capture System - + - - SNPRMA algorithm - + + + Iteratively ReWeighted Least Squares - + - - SNPchip - + + - - + + - + - - - + + + + + @@ -61938,80 +62021,78 @@ easily and accurately visualize and quantitate gene expression data. - - - - - - - + - - - - + + + + + + + + + - - + + - - - - - - - - - + + - Nandini Badarinarayan - This package defines classes and functions for plotting copy number and genotype in high throughput SNP platforms such as Affymetrix and Illumina. In particular, SNPchip is a useful add-on to the oligo package for visualizing SNP-level estimates after pre-processing. - http://bioconductor.org/packages/2.4/bioc/html/SNPchip.html + The IRanges class and its extensions are low-level containers for storing sets of integer ranges. A typical use of these containers in biology is for representing a set of chromosome regions. More specific extensions of the IRanges class will typically allow the storage of additional information attached to each chromosome region as well as a hierarchical relationship between these regions. + http://bioconductor.org/packages/2.4/bioc/html/IRanges.html + Nandini Badarinarayan + IRanges - + - - SPIA - + + - - + + - - + + - - + + - + + + + + + + - + - - + + @@ -62020,213 +62101,232 @@ easily and accurately visualize and quantitate gene expression data. - - - - - - - + - - + + + + + - Nandini Badarinarayan - This package implements the Signaling Pathway Impact Analysis (SPIA) which uses the information form a list of differentially expressed genes and their log fold changes together with signaling pathways topology, in order to identify the pathways most relevant to the condition under the study. - http://bioconductor.org/packages/2.4/bioc/html/SPIA.html + + + + + + + A Method to normalize of Affymetrix GeneChip Human Mapping 100K and 500K set + http://bioconductor.org/packages/2.4/bioc/html/ITALICS.html + Nandini Badarinarayan + ITALICS - + - - Semantic Similarity Measures - - Semantic Similarity Measures- Four methods proposed by Resnik[Philip, 1999], Jiang[Jiang and Conrath, -1997], Lin[Lin, 1998] and Schlicker[Schlicker et al., 2006] respectively have -presented to determine the semantic similarities of two GO terms based -on the annotation statistics of their common ancestor terms. Wang [Wang -et al., 2007] proposed a new method to measure the similarities based on -the graph structure of GO. + + + ILLUMINA data - + - - SSPA - - - - - - - - - - - - - - - - - - - + + + Nandini Badarinarayan + ImaGene4.1 software + + + + + + + + + Nandini Badarinarayan + ImaGene 3.0 + + + + + + + + - + - + - - + + - Nandini Badarinarayan - Sample size and power analysis for microarray data, where two groups are analysed. - http://bioconductor.org/packages/2.4/bioc/html/SSPA.html - - - - - - - - SVDimpute algorithm - - - - - - - - - software developer role - - James Malone - Software developer role is a role borne by an organization or individual in which they are responsible for authoring software. + This is a general image analysis program used in the study of electrophoretic separations, dot blots, slot blots, microplate assays, TLC assays, and plaque assays. ImageQuant provides a point-and-click environment for fast analysis of qualitative and quantitative assays. With tools for accurate volume integration, ImageQuant generates accurate lane profiles even for curved or slanted lanes. + ImageQuant (Molecular Dynamics) + http://www.research.bidmc.harvard.edu/AcademicIT/ImageQuant.asp + Nandini Badarinarayan + ImageQuant - + - - obsolete_Information processing - - Information processing is a process in which input information is analysed or transformed in order to produce information as output. - James Malone - true - Present both in the original file (SWO_0000393) and in the core file (SWO_0000003), and each have different identifiers. SWO_0000393 was initially created within the originalsoftwareontology.owl and later moved to swo_core.owl. SWO_0000003 was retained and SWO_0000393 deemed obsolete. Please use SWO_0000003 instead. - 0.4 - Marked as obsolete by Allyson Lister. + + + Nandini Badarinarayan + ImageReader - + - - software developer organization - + + + - - + + + + + + + + + + + + - - - An organization or legal entity (including single person) that is responsible for developing software. Developing includes aspects of design, coding and testing. + + ImaGene microarray image analysis software by biodiscovery for microarrays, protein arrays and CGH analysis. + ImaGene [BioDiscovery] + Imagene + http://www.biodiscovery.com/index/imagene + Nandini Badarinarayan + ImaGene - + - - software publisher organization - - - - - - - - An organization or legal entity (including single person) that is responsible for publishing software. Publishing here includes tasks such as designing and producing physical products, technical customer support, licensing arrangements and marketing. + + + Nandini Badarinarayan + Imagene v4.0 - + - - 50-50 MANOVA algorithm - - Classical multivariate analysis-of-variance tests perform poorly in cases with several highly correlated responses and the tests collapse when the number of responses exceeds the number of observations. This paper presents a new method which handles this problem. The dimensionality of the data is reduced by using principal component decompositions and the final tests are still based on the classical test statistics and their distributions. The methodology is illustrated with an example from the production of sausages with responses from near infrared reflectance spectroscopy. A closely related method for testing relationships in uniresponse regression with collinear explanatory variables is also presented. The new test, which is called the 50-50 F-test, uses the first k components to calculate SSMODEL. The next d components are not involved in SSERROR and they are called buffer components. - Langsrud, &Oslash. (2002), 50-50 Multivariate Analysis of Variance for Collinear Responses, The Statistician, 51, 305-317. + + + + + + + + + + + + + + + + + + + These scripts are for primer design and initial microarray data processing and are available as .zip files: + http://www.bahlerlab.info/resources/ + Nandini Badarinarayan + Initial microarray data processing (data filtering, local normalisation and quality control) - + - - obsolete_html - - true - 0.4 - Marked as obsolete by Allyson Lister. - There is one EDAM html class (EDAM_format:2331) and one SWO class (SWO_0000399) within swo_data.owl. EDAM_format:2331 was retained and SWO_0000399 deemed obsolete, as EDAM_format:2331 has a better location in the hierarchy and is an imported term. All axioms belonging to SWO_0000399 were transferred to EDAM_format:2331. Please use EDAM_format:2331 (in this ontology via its full URI http://edamontology.org/format_2331) instead. + + + Jaccard’s index - + - - ArrayExpress Bioconductor - + + - + - + - - + + + Image analysis software + Nandini Badarinarayan + Jaguar + + + + + + + + + + + + + + + + + + + + - + - + - - + + @@ -62235,14 +62335,14 @@ the graph structure of GO. - + - + - - + + @@ -62251,20 +62351,14 @@ the graph structure of GO. - - - - - - - + - + - - + + @@ -62273,99 +62367,185 @@ the graph structure of GO. - - + + + + + + + + + + + Multi sample aCGH analysis package using kernel convolution + http://bioconductor.org/packages/2.4/bioc/html/KCsmart.html + Nandini Badarinarayan + KCsmart + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - - + + - ArrayExpress Bioconductor package is software that read in MAGE-TAB format files from the ArrayExpress FTP site and converts them to R objects. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/ArrayExpress.html + A package that provides a client interface to the KEGG SOAP server + http://bioconductor.org/packages/2.4/bioc/html/KEGGSOAP.html + Nandini Badarinarayan + KEGGSOAP - + - - Gene list - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + KEGGGraph is an interface between KEGG pathway and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated KGML (KEGG XML) files into graph models maintaining all essential pathway attributes. The package offers functionalities including parsing, graph operation, visualization and etc. + http://bioconductor.org/packages/2.4/bioc/html/KEGGgraph.html + Nandini Badarinarayan + KEGGgraph - + - - Clustered data set - + + + KGML - + - - R data frame - + + + 'KLD' - + - - R language - + + + KS measures how biased the ranks of a subset of items are among the ranks of the entire set + Kolmogorov Smirnov rank-sum based algorithm - + - - ScISI - - - - - - - - - - - - + + - - + + - - + + - + - - + + + + + @@ -62373,293 +62553,186 @@ the graph structure of GO. - + - - + + + + + - Nandini Badarinarayan - Package to create In Silico Interactomes - http://bioconductor.org/packages/2.4/bioc/html/ScISI.html - - - - - - - - ScanAlyze - - - + + + + + + + + + + + + - Nandini Badarinarayan - Processes fluorescent images of microarrays - http://smd.stanford.edu/resources/restech.shtml - - - - - - - - ScanArray - - - + + - Nandini Badarinarayan - ScanArray Express - ScanArray Express [PerkinElmer] - ScanArray Express provides superior spot finding and quantization algorithm. This combined with template adjustment features drives excellence in analysis performance. - http://las.perkinelmer.com/Catalog/ProductInfoPage.htm?ProductID=7000060 - - - - - - - - ScanArray v3.1 software - - Nandini Badarinarayan - ScanArray version 3.1 + LBE is an efficient procedure for estimating the proportion of true null hypotheses, the false discovery rate (and so the q-values) in the framework of estimating procedures based on the marginal distribution of the p-values without assumption for the alternative hypothesis. + http://bioconductor.org/packages/2.4/bioc/html/LBE.html + Nandini Badarinarayan + LBE - + - - scanning software - - Nandini Badarinarayan + + + LC-MS data - + - - Scanning software G2565AA version A6.3.1 - + + - - + + - High resolution scanning with pixel sizes of 2, 3, 5, and 10 microns enables users to scan a range of array types from ultra-high density commercial arrays as well as low-density home-brew arrays.Low level detection resulting from optimized precision optics, broad dynamic range, minimal spectral cross talk allowing users to detect weak features, achieve rapid, accurate and dependable results - Nandini Badarinarayan - http://www.chem.agilent.com/en-us/products/instruments/dnamicroarrays/dnamicroarrayscanner/pages/default.aspx - - - - - - - - ShortRead - - - + + - + - - - - + + + + + + + + + - - + + + + + + + + + + + + - - + + - Base classes, functions, and methods for representation of high-throughput, short-read sequencing data. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/ShortRead.html - - - - - - - - Signaling Pathway Impact Analysis (SPIA) algorithm - - - - - - - - - Silicon Genetics Genespring - - - + + - Nandini Badarinarayan - SiliconGenetics GeneSpring - The GeneSpring-R integration package will allow you to expand the capability of GeneSpring by integrating R programs seamlessly into GeneSpring. With the integration package you will be able to use the power of R and BioConductor scripts in GeneSpring's rich graphical environment - http://www.silicongenetics.com/cgi/SiG.cgi/Support/gs_r_int.smf - - - - - - - - Similarity score - + LMGene package for analysis of microarray data using a linear model and glog data transformation in the R statistical package + http://bioconductor.org/packages/2.4/bioc/html/LMGene.html + Nandini Badarinarayan + LMGene - + - - 'Smith-Waterman' - + + + Locally Moderated Weighted-t (LMW) method - + - - Spot quantification - - Nandini Badarinarayan + + + Lognormal Normal Model - + - - Spotfinder [TIGR] - - - - - - - - - - - - - - Nandini Badarinarayan - TIGR Spotfinder was designed for the rapid, reproducible and computer-aided analysis of microarray images and the quantification of gene expression - http://www.tm4.org/contributors.html + + + Lognormal Normal with Modied Variance Model - + - - Spotfire - + + - - + + - Nandini Badarinarayan - Spotfire’s interactive, visual capabilities for data analysis empower individuals to easily see trends, patterns outliers and unanticipated relationships in data with unprecedented speed and adaptability. - http://spotfire.tibco.com/Products/Info.aspx - - - - - - - - TAS Software - - - + + - Nandini Badarinarayan - Tiling Analysis Software (TAS) is a freely downloadable tool for analysis, with which one can perform a simulation to assess the likelihood that an observed probe overlap region is different from the expected overlap with no enrichment from binding, and can derive an interval overlap report and/or computation of summary statistics. - http://dmaf.biochem.uci.edu/affymetrix_analysis_software.html - - - - - - - - obsolete_TIFF image - - true - 0.4 - SWO_0000434 was initially created within the originalsoftwareontology.owl and later moved to swo_data.owl. SWO_3000016, with the label 'TIFF', is also present, and stored within swo_data.owl. SWO_3000016 was retained and SWO_0000434 deemed obsolete, as SWO_3000016 has a better location in the hierarchy. All axioms belonging to SWO_0000434 were transferred to SWO_3000016. Please use SWO_3000016 instead. - Marked as obsolete by Allyson Lister. - - - - - - - - TargetSearch - - - + + - + - - + - - + + @@ -62668,12 +62741,15 @@ the graph structure of GO. - + - - + + + + + @@ -62681,129 +62757,94 @@ the graph structure of GO. - - + + - - + + - Nandini Badarinarayan - This packages provides a targeted pre-processing method for GC-MS data. - http://bioconductor.org/packages/2.4/bioc/html/TargetSearch.html - - - - - - - - Theodore Ts’o’s - + + + + + + + This LPE library is used to do significance analysis of microarray data with small number of replicates. It uses resampling based FDR adjustment, and gives less conservative results than traditional 'BH' or 'BY' procedures. Data accepted is raw data in txt format from MAS4, MAS5 or dChip. Data can also be supplied after normalization. LPE library is primarily used for analyzing data between two conditions. To use it for paired data, see LPEP library. For using LPE in multiple conditions, use HEM library. + http://bioconductor.org/packages/2.4/bioc/html/LPE.html + Nandini Badarinarayan + LPE - + - - TypeInfo - + + - - + + - - - - - - - - - - - - + + - - + + - + - - + + - - + + - + - A prototype for a mechanism for specifying the types of parameters and the return value for an R function. This is meta-information that can be used to generate stubs for servers and various interfaces to these functions - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/TypeInfo.html - - - - - - - - Variance-stabilizing transformation (VST) algorithm - - - - - - - - - VanillaICE - - + - - - - + + + + + + + + + - - - - - - - + - + - - + + @@ -62812,168 +62853,308 @@ the graph structure of GO. - - + + + + + + + + - - + + - Hidden Markov Models for characterizing chromosomal alterations in high throughput SNP arrays - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/VanillaICE.html + Two options are added to the LPE algorithm. The original LPE method sets all variances below the max variance in the ordered distribution of variances to the maximum variance. in LPEadj this option is turned off by default. The second option is to use a variance adjustment based on sample size rather than pi/2. By default the LPEadj uses the sample size based variance adjustment. + http://bioconductor.org/packages/2.4/bioc/html/LPEadj.html + Nandini Badarinarayan + LPEadj - + - - WilcEbam - + + + A publisher role is a role borne by an organization or individual in which they are responsible for making software available to a particular consumer group. Such organizations or individuals do need to be involved in the development of the software. + James Malone + publisher role - + - - Wilcoxon - + + + Langmuir Isotherm - + + + + + Laplace mixture model + + - - XDE - + + + + + + Library Search Algorithm + + + + + + + + + Loess algorithm + + + + + + + + + Logic regression + + + + + + + + + Tools for analyzing Micro Array experiments + http://cran.r-project.org/web/packages/maanova/index.html + Nandini Badarinarayan + MAANOVA v1.2 package for MATLAB + + + + + + + + + Median Average Difference Algorithm + + + + + + + + + Marked as obsolete by Allyson Lister. + Obsoleted after the 0.4 release. + Equivalence with EDAM format_3161. + obsolete_MAGE-ML + true + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - - + + - + - - + + + We propose importation, normalization, visualization, and quality control functions to correct identified sources of variability in array-CGH experiments. + http://bioconductor.org/packages/2.4/bioc/html/MANOR.html + Nandini Badarinarayan + MANOR + + + + + + + + + MAQC data + + + + + + + + - + - - + + + + + + Affymetrix® Microarray Suite (MAS) is the core software product in the Affymetrix Software System providing instrument control, data acquisition, and data analysis for the entire GeneChip® platform. + Affymetrix MicroArraySuite + MAS + http://www.affymetrix.com/support/technical/datasheets/mas_datasheet.pdf + Nandini Badarinarayan + MIcroarray Analysis Suite + + + + + + + + + MAS 5.0 software + Nandini Badarinarayan + MicroArraySuite 5.0 + + + + + + + + + MATLAB language + + + + + + + + - + - + - - + + - - - - - - - Nandini Badarinarayan - XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression - http://bioconductor.org/packages/2.4/bioc/html/XDE.html + Nandini Badarinarayan + MAVI Pro - + - - XDotsReader - - - - - - - - Analysis Software for Integrated Image Analysis for Spot Detection , Position and Quantification - Nandini Badarinarayan - http://www.cose.fr/us_dots.html + + + Multivariate correlation estimator - + - - obsolete_XML - - true - 5. SWO_0000448 was initially created within the originalsoftwareontology.owl and later moved to swo_data.owl. SWO_3000005 is also present within swo_data.owl. SWO_3000005 was retained and SWO_0000448 deemed obsolete, as SWO_3000005 has a better location in the hierarchy. All axioms belonging to SWO_0000448 were transferred to SWO_3000005. Please use SWO_3000005 instead. - 0.4 - Marked as obsolete by Allyson Lister. + + + Markov Chain Monte Carlo - + - - Xba.CQV and Xba.regions - + + + minimum common regions (MCR) algorithm- Minimal common regions (MCRs) are dened as contiguous spans having at least a recurrence rate dened by a parameter (recurrence) across samples. + MCR algorithm - + - - Array Comparative Genomic Hybridization - + + + + + + + + - + - + - - + + @@ -62982,48 +63163,48 @@ the graph structure of GO. - + - + - - + + + This package includes a function for combining preprocessing and classification methods to calculate misclassification errors + http://bioconductor.org/packages/2.4/bioc/html/MCRestimate.html + Nandini Badarinarayan + MCRestimate + + + + + + + + - - - - - - - - - - - - - - + + - + - + - - + + @@ -63032,218 +63213,265 @@ the graph structure of GO. - - - - - Nandini Badarinarayan - The aCGH package functions for reading data from image analysis output files and clone information files, creation of aCGH S3 objects for storing these data. Basic methods for accessing/replacing, subsetting, printing and plotting aCGH objects. - http://bioconductor.org/packages/2.4/bioc/html/aCGH.html - - - - - - - - Acuity - - - - + - + - - + + - Acuity is the complete enterprise microarray informatics platform for microarray data storage, data filtering and data analysis. It analysis tools for quality, visualizations for discovery and Data Management for Security. - Nandini Badarinarayan - http://www.bio-medicine.org/ + MEDME allows the prediction of absolute and relative methylation levels based on measures obtained by MeDIP-microarray experiments + http://bioconductor.org/packages/2.4/bioc/html/MEDME.html + Nandini Badarinarayan + MEDME - + - - affxparser - - - - - - - - - - - - - + + + 'MI' + + + + + + + + + Mutual information matrix (MIM) + + + + + + + + - - + + - - + + - - + + + + + + + + + + + + - - + + + + + + + + + + + + - Nandini Badarinarayan - affxparser is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR). It provides methods for fast and memory efficient parsing of Affymetrix files using the Affymetrix' Fusion SDK. - http://bioconductor.org/packages/2.4/bioc/html/affxparser.html + Uniform interfaces to machine learning code for data in Bioconductor containers + http://bioconductor.org/packages/2.4/bioc/html/MLInterfaces.html + Nandini Badarinarayan + MLInterfaces - + + + + + MMD describes the distributions of gene expression levels directly via the marginal distributions. It includes EM algorithm, FDR, it is the percentage of nondifferentially expressed genes among selected genes), false non-discovery rate (denoted as FNDR; it is the percentage of differentially expressed genes among unselected genes),false positive rate (denoted as FPR; it is the percentage of selected genes among nondifferentially expressed genes), and false negative rate (denoted as FNR; it is the percentage of un-selected genes among differentially expressed genes), + MMD + + + + + - - affyContam - + + - - + + - + - - - - - - - - - - - + + + + + + + + + - + - - - - - - - - - - - + + + + + + + + + - - + + - Nandini Badarinarayan - affyContam is software which provides the in silico creation of quality problems in CEL-level data to help evaluate performance of quality metrics. In essence, it creates structured corruption within CEL data to demonstrate QA effectiveness. - http://bioconductor.org/packages/2.4/bioc/html/affyContam.html (access unknown); http://www.bioconductor.org/packages/2.12/bioc/vignettes/affyContam/inst/doc/affyContam.pdf, accessed 22 May 2013. - Allyson Lister + Creates classes used in model-view-controller (MVC) design + http://bioconductor.org/packages/2.4/bioc/html/MVCClass.html + Nandini Badarinarayan + MVCClass - + + + + + Mahalanobis distance + + + - - affyImGUI - + + + + + + + + + + - - + + - + - - - - + + + + + + + - - + + + + + + + + + + + + - A Graphical User Interface for affy analysis using the limma Microarray package - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/affylmGUI.html - Removed the links to specified data inputs, as this software is a GUI wrapper for another package, and it is this package which takes the inputs. (Allyson Lister 22/05/2013) + + + + + + + Computes Mantel cluster correlations from a (p x n) numeric data matrix (e.g. microarray gene-expression data) + http://bioconductor.org/packages/2.4/bioc/html/MantelCorr.html + Nandini Badarinarayan + MantelCorr - + - - 'affyPLM' - + + - - - - - - - + + + + + + + + - + - + - - + + @@ -63252,97 +63480,70 @@ the graph structure of GO. - + - - - + + + + + - - - - - - - - - - - - - - - - - - - - A package that extends and improves the functionality of the base affy package. Routines that make heavy use of compiled code for speed. Central focus is on implementation of methods for fitting probe-level models and tools using these models. PLM based quality assessment tools. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/affyPLM.html + Processing Mass Spectrometry spectrum by using wavelet based algorithm + http://bioconductor.org/packages/2.4/bioc/html/MassSpecWavelet.html + Nandini Badarinarayan + MassSpecWavelet - + - - affyPara - + + - - + + - - - - - - - - - - + + - + - - - - - - - - - - - + + + + + + + + + - + - + - - + + @@ -63351,181 +63552,211 @@ the graph structure of GO. - - + + - Nandini Badarinarayan - The package contains parallelized functions for exploratory oligonucleotide array analysis. The package is designed for large numbers of microarray data. - http://bioconductor.org/packages/2.4/bioc/html/affyPara.html + Two-stage measurement error model for correlation estimation with smaller bias than the usual sample correlation + http://bioconductor.org/packages/2.4/bioc/html/MeasurementError.cor.html + Nandini Badarinarayan + MeasurementError.cor - + - - affyQCReport - + + - - + + - - + + - - - - - - - - - - - - - - + + - - + + + + + + + + + + + + - + - + - - + + - Nandini Badarinarayan - This package creates a QC report for an AffyBatch object. The report is intended to allow the user to quickly assess the quality of a set of arrays in an AffyBatch object. - http://bioconductor.org/packages/2.4/bioc/html/affyQCReport.html - - - - - - - - affyTiling - - - + + + + + + + + + + + + - + - - + + + + + + The functions in this R extension are intended for cross-study comparison of gene expression array data. Required from the user is gene expression matrices, their corresponding gene-id vectors and other useful information, and they could be 'list','matrix', or 'ExpressionSet'. The main function is 'mergeExprs' which transforms the input objects into data in the merged format, such that common genes in different datasets can be easily found. And the function 'intcor' calculate the correlation coefficients. Other functions use the output from 'modelOutcome' to graphically display the results and cross-validate associations of gene expression data with survival. + http://bioconductor.org/packages/2.4/bioc/html/MergeMaid.html + Nandini Badarinarayan + MergeMaid + + + + + + + + - - + + - - + + - - + + + + + + + + + + + + - + - - - - - - - - - - - + + + + + + + + + - Nandini Badarinarayan - This package provides easy, fast functions for the extraction and annotation of individual probes from Affymetrix tiling arrays. - http://bioconductor.org/packages/2.4/bioc/html/AffyTiling.html - - - - - - - - 'affycoretools' - - + - - + + + + + + Package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface) + http://bioconductor.org/packages/2.4/bioc/html/Mfuzz.html + Nandini Badarinarayan + Mfuzz + + + + + + + + + + + + + + - - + + - + - - - + + + + + @@ -63533,287 +63764,359 @@ the graph structure of GO. - + - - - - + + + + + + + - - + + - Nandini Badarinarayan - Various wrapper functions that have been written to streamline the more common analyses that a core Biostatistician might see - http://bioconductor.org/packages/2.4/bioc/html/affycoretools.html + This package finds optimal sets of genes that seperate samples into two or more classes. + http://bioconductor.org/packages/2.4/bioc/html/MiPP.html + Nandini Badarinarayan + MiPP - + + + + + Misclassification-Penalized Posteriors (MiPP) + + - - affyio - + + + + + + Nandini Badarinarayan + MicroArraySuite 4.0 + + + + + + + + + Mixed model equations + + + + + + + + + 'Needleman-Wunsch' + + + + + + + + + This includes exhaustive enumeration, triple-based inference,pairwise heuristic, module based inference, greedy hillclimbing + Nested Effects Models + + + + + + + + + Nonlinear Estimation by Iterative Partial Least Squares + + + + + + + + - - + + - - + + - + - - - - - - - - - - - - - + + + + + + + + + - - - - - - - + - - - - - - - - - - - - - + + + + + + + + + - Nandini Badarinarayan - Routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing the CEL and CDF file formats. - http://bioconductor.org/packages/2.4/bioc/html/affyio.html - - - - - - - - affypdnn - - + - + - - + + + This package allows to characterize the operating characeristics of a microarray experiment, i.e. the trade-off between false discovery rate and the power to detect truly regulated genes. The package includes tools both for planned experiments (for sample size assessment) and for already collected data (identification of differentially expressed genes). + http://bioconductor.org/packages/2.4/bioc/html/OCplus.html + Nandini Badarinarayan + OCplus + + + + + + + + - - - - - - - - + + - - + + - Nandini Badarinarayan - The package contains functions to perform the PDNN method described by Li Zhang et al. - http://bioconductor.org/packages/2.4/bioc/html/affypdnn.html - - - - - - - - altcdfenvs - - + - - - - + + + + + + + + + - - + + + + + + + + + + + + - - + + - - + + - Nandini Badarinarayan - altcdfenvs is a software package for alternative CDF environments (aka probeset mappings) and contains convenience data structures and functions to handle cdfenvs. - http://www.bioconductor.org/packages/release/bioc/html/altcdfenvs.html, accessed May 28 2013. - Allyson Lister + Functions for normalisation of two-color microarrays by optimised local regression and for detection of artefacts in microarray data + http://bioconductor.org/packages/2.4/bioc/html/OLIN.html + Nandini Badarinarayan + OLIN - + - - annaffy - + + - - + + - - - - - - - + + - - + + + + + + + + + + + + - - + + + + + + + + + + + + - Nandini Badarinarayan - This package functions for handling data from Bioconductor Affymetrix annotation data packages.Allows searching biological metadata using various criteria. - http://bioconductor.org/packages/2.4/bioc/html/annaffy.html - - - - - - - - 'annotate' - - - + + - - + + - - + + - Nandini Badarinarayan - Using R enviroments for annotation. - http://bioconductor.org/packages/2.4/bioc/html/annotate.html + Graphical user interface for the OLIN package + http://bioconductor.org/packages/2.4/bioc/html/OLINgui.html + Nandini Badarinarayan + OLINgui - + - - data annotation - + + + + + + + + + + + + + + + + + + + Computer software for image acquisition, analysis and reporting, for use in the life sciences + http://www.findownersearch.com/optiquant/7766418/ + Nandini Badarinarayan + Optiquant - + - - annotationTools - + + + + + + + + - - + + - + - - + + + + + @@ -63821,200 +64124,213 @@ the graph structure of GO. - - - - - - - + - - - - + + + + + + + + + - - + + - Nandini Badarinarayan - This package functions to annotate microarrays, find orthologs, and integrate heterogeneous gene expression profiles using annotation and other molecular biology information available as flat file database (plain text files). - http://bioconductor.org/packages/2.4/bioc/html/annotationTools.html - - - - - - - - Annotation data packages - + Detection of similarities between ordered lists of genes. Thereby, either simple lists can be compared or gene expression data can be used to deduce the lists. Significance of similarities is evaluated by shuffling lists or by resampling in microarray data, respectively. + http://bioconductor.org/packages/2.4/bioc/html/OrderedList.html + Nandini Badarinarayan + OrderedList - + - - 'apComplex' - + + + + + + + + - - + + - - + + + + + + + + + + + + - - + + + + + + + + + + + + - - + + - Nandini Badarinarayan - This package functions to estimate a bipartite graph of protein complex membership using AP-MS data. - http://bioconductor.org/packages/2.4/bioc/html/apComplex.html + This package detects outliers using quantile regression on the M-A scatterplots of high-throughput data. + http://bioconductor.org/packages/2.4/bioc/html/OutlierD.html + Nandini Badarinarayan + OutlierD - + - - aroma.light - - - - - - - + + + Presence-Absence calls with Negative Probesets (PANP) + + + + + + + + - - + + - + - - - - + + + + + + + + + - + - - - + + + + + - - - - - - - Nandini Badarinarayan - This package functions as methods for microarray analysis that take basic data types such as matrices and lists of vectors. These methods can be used standalone, be utilized in other packages, or be wrapped up in higher-level classes. - http://bioconductor.org/packages/2.4/bioc/html/aroma.light.html + Processing annotation data from public data repositories and building annoation data packages. + http://bioconductor.org/packages/2.4/bioc/html/PAnnBuilder.html + Nandini Badarinarayan + PAnnBuilder - + + + + + Pearson correlation estimator + + + + + - - arrayMvout - + + - - + + - - + + - - + + - + - + - - - - - - - - - + + - Nandini Badarinarayan - This package supports the application of diverse quality metrics to AffyBatch instances, summarizing these metrics via PCA, and then performing parametric outlier detection on the PCs to identify aberrant arrays with a fixed Type I error rate - http://bioconductor.org/packages/2.4/bioc/html/arrayMvout.html - - - - - - - - arrayQuality - - + - - + + + + + @@ -64022,49 +64338,61 @@ the graph structure of GO. - - - - - - - + - - + + + + + - Nandini Badarinarayan - This package functions for performing print-run and array level quality assessment. - http://bioconductor.org/packages/2.4/bioc/html/arrayQuality.html + + + + + + + + + + + + + Tools to integrate, annotate, and link phenotypes to cellular organizational units such as protein complexes and pathways. + http://bioconductor.org/packages/2.4/bioc/html/PCpheno.html + Nandini Badarinarayan + PCpheno - + - - arrayQualityMetrics - + + - - + + - + - - + + + + + @@ -64072,212 +64400,183 @@ the graph structure of GO. - + - - - - + + + + + + + + + - - - - - Nandini Badarinarayan - This package generates a quality metrics report on ExpressionSet, NChannelSet, AffyBatch or BeadLevelList objects containing microarray data with one or two channels. - http://bioconductor.org/packages/2.4/bioc/html/arrayQualityMetrics.html - - - - - - - - arrayWoRx 2.0 - - Nandini Badarinarayan - - - - - - - - arrayWoRx - - - - - + + + + + + + + + + + + - Applied Precision MicroArray Scanner Model arrayWoRx Comprehensive system that fully automates the image capture and quantitation of microarrays. by integrating Slid handling, fluorescent microscopy, and sophisticated spot scan and analysis software the systems detects and measures the fluorescence intensity at each of the specified elements in a microarray. The intensity data can be presented as image data, graphical representation, or as numerical data. - Nandini Badarinarayan - http://www.hitechtrader.com/detail.cfm?autonumber=64022 - - - - - - - - Associative T method - + Parametric Analysis of Gene Set Enrichment + http://bioconductor.org/packages/2.4/bioc/html/PGSEA.html + Nandini Badarinarayan + PGSEA - + - - AvgNRRs - + + + it is where we fit a model with probe level and chip level parameters on a probeset by probeset basis + 'PLM' - + - - 'beadarray' - + + - - + + - - + + - Nandini Badarinarayan - The package is able to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided. - http://bioconductor.org/packages/2.4/bioc/html/beadarray.html - - - - - - - - 'beadarraySNP' - - - + + + + + + + + + + + + - - + + + + + + + + + + + + - - + + - - + + - Importing data from Illumina SNP experiments and performing copy number calculations and reports. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/beadarraySNP.html + This package performs tests for paired high-throughput data. + http://bioconductor.org/packages/2.4/bioc/html/PLPE.html + Nandini Badarinarayan + PLPE - + - - 'betr' - - - - - - - - - - - - - - - - - - - - - - - - - + + + Probe level Locally moderated Weighted median-t (PLW) method + + + + + + + + + PPC algorithm + + + + + + + + - - - - - - - + + - - + + - Nandini Badarinarayan - betr is a software package which implements the BETR (Bayesian Estimation of Temporal Regulation) algorithm to identify differentially expressed genes in microarray time-course data. - http://www.bioconductor.org/packages/2.12/bioc/html/betr.html, accessed 28 May 2013. - Allyson Lister - - - - - - - - bgafun - - + - - - - + + + + + + + + + - + - - + + + + + @@ -64285,333 +64584,208 @@ the graph structure of GO. - - + + - - + + - BGAfun is a method to identify specifity determining residues in protein families - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/bgafun.html + A package for processing protein mass spectrometry data. + http://bioconductor.org/packages/2.4/bioc/html/PROcess.html + Nandini Badarinarayan + PROcess - + + + + + Included are summarisation, differential expression detection, clustering and PCA methods, together with useful plotting and data manipulation functions + Propagation of uncertainty in microarray analysis + + - - bgx - + + + + + - - - - - - - - - - - - - - - - - - - - - - - - - + - + - - + + - - - - - - - Bayesian integrated analysis of Affymetrix GeneChips - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/bgx.html + The background intensity data from the spot quantification programs may be used to correct spot intensity. This software measures background globally as: BGLow (low background), BGAvg (Average background), BGRms (root mean square background). + http://maexplorer.sourceforge.net/MaeRefMan/hmaeDoc2.4.2.html + Nandini Badarinarayan + Pathways 2.01 software - + - - Bitmap object - + + + Power Law Global Error Model (PLGEM) analysis method - + - - bioDist - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Nandini Badarinarayan - The bioDist package contains some distance functions that have been shown to be useful in a number of dierent biological or bioinformatic problems. The return values are typically instances of the S3 class dist. - http://bioconductor.org/packages/2.4/bioc/html/bioDist.html + + + Nandini Badarinarayan + Probe Cell Analysis - + - - 'biocDatasets' - - - - - - - - Nandini Badarinarayan - Synthetic datasets to a) demonstrate the usage of bioconductor packages, b) write unit tests, while keeping dependencies and ressources usage minimal. - http://bioconductor.org/packages/2.4/bioc/html/biocDatasets.html + + + PLIER (Probe Logarithmic Error Intensity Estimate) method - + - - 'biocGraph' - + + - + - - + + + + + - - - - - - - - - - - - - Nandini Badarinarayan - This package provides examples and code that make use of the different graph related packages produced by Bioconductor. - http://bioconductor.org/packages/2.4/bioc/html/biocGraph.html + QuantArray® is a powerful microarray analysis software that enables researchers to +easily and accurately visualize and quantitate gene expression data. + QuantArray + http://las.perkinelmer.com/content/relatedmaterials/brochures/bro_quantarray.pdf + Nandini Badarinarayan + QuantArray scanner software - + - - 'biocViews' - - - - - - - - - - - - - - Categorized views of R package repositories - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/biocViews.html + + + Nandini Badarinarayan + QuantArray, PackaardBiochip technologies - + - - biomaRT - - - - - - - - - - - - - - - - - - - - - - - - - Nandini Badarinarayan - The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. - http://bioconductor.org/packages/2.4/bioc/html/biomaRt.html + + + Nandini Badarinarayan + QuantArray version 2 - + - - Bootstrap - + + + Radial basis function - + - - 'bridge' - + + - - + + - - + + - + - - + + + + + - Nandini Badarinarayan - The bridge package consists of several functions for testing for dierential expression among mul- -tiple samples - http://bioconductor.org/packages/2.4/bioc/html/bridge.html - - - - - - - - cdt - - - - - - - - - 'cellHTS' - - - + + + + + + + + + + + + - + - - + + + + + @@ -64619,63 +64793,60 @@ tiple samples - - + + - - - - - - - - - + + - Analysis of cell-based RNA interference screens - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/cellHTS.html + A fairly extensive and comprehensive interface to the graph algorithms contained in the BOOST library. + http://bioconductor.org/packages/2.4/bioc/html/RBGL.html + Nandini Badarinarayan + RBGL - + + + + + R interface to boost graph library algorithm (RBGL) + + + + + - - 'cellHTS2' - + + - - - - - - - - - + + - - + + - + - - - + + + + + @@ -64683,404 +64854,382 @@ tiple samples - - + + + + + + + + + + + + - Analysis of cell-based RNA interference screens - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/cellHTS2.html + Functions and datasets and examples to accompany the monograph R For Bioinformatics. + http://bioconductor.org/packages/2.4/bioc/html/RBioinf.html + Nandini Badarinarayan + RBioinf - + + + + + Random effects model + + + + + + + + + for the Support Vector Machine (SVM), as presented in [3] and the Nearest Shrunken Centroid (NSC) + Recursive Feature Elimination (RFE) + + - - cghMCR - + + + + + - - + + - - + + - + - - - - - - - - - + + + + + + + + + + + - - + + - - + + - - - - - - - + + - Based on the algothrim proposed by Dr. Lynda Chin's lab, this package provides functions that identify chromosome regions that show gains/losses commonly observed across different samples profiled using arrayCGH platform. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/cghMCR.html + A Genotype Calling Algorithm for Affymetrix SNP Arrays + http://bioconductor.org/packages/2.4/bioc/html/RLMM.html + Nandini Badarinarayan + RLMM - + - - chamber slide format - + + + Regression model - + - - cls - - http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#CLS:_Categorical_.28e.g_tumor_vs_normal.29_class_file_format_.28.2A.cls.29 - Categorical (e.g tumor vs normal) class file format + + + RMA - + - - 'clusterStab' - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Nandini Badarinarayan - This package can be used to estimate the number of clusters in a set of microarray data, as well as test the stability of these clusters. - http://bioconductor.org/packages/2.4/bioc/html/clusterStab.html + + + RMA+ - + - - obsolete_Clustering algorithm - - true - 0.4 - Marked as obsolete by Allyson Lister. - The original label for this class, 'Clustering algorithm', was used in two separate class URIs. The first was SWO_0000500, initially created within the originalsoftwareontology.owl. The second URI is stored within swo_algorithms.owl and is an import from OntoDM (OntoDM_170075). As the SWO class contains no annotation beyond its label, and because OntoDM has more structure surrounding its algorithm classes, the OntoDM class was retained and the SWO class was deemed obsolete. The 6 usages of the SWO class were refactored to reference the OntoDM term and then the SWO class was marked as obsolete. Please use OntoDM_170075 instead. + + + RMA++ - + - - 'codelink' - + + - + - - - - + + + + - + - - - - - - + + + + + + + + + + + - - + + - - - - - - - - - - - + + - Nandini Badarinarayan - This packages allow reading into R of Codelink bioarray data exported as text from the Codelink software. Also includes some functions to ease the manipulation and pre-processing of data, such in background correction and normalization. - http://bioconductor.org/packages/2.4/bioc/html/codelink.html + RMAExpress is a standalone GUI program for Windows (and Linux) to compute gene expression summary values for Affymetrix Genechip® data using the Robust Multichip Average expression summary and to carry out quality assessment using probe-level metrics. It does not require R nor is it dependent on any component of the BioConductor project. If focuses on processing 3' IVT expression arrays, exon and WT gene arrays. + http://rmaexpress.bmbolstad.com/ + Nandini Badarinarayan + RMAExpress - + - - dataset comparison - + + + Nandini Badarinarayan + RMAExpress 2.0 - + - - Concordance - + + + Nandini Badarinarayan + RMAExpress quantification - + - - convert - + + - - + + - + - - + + - + - - - - + + + + + + + + + - - + + - Define coerce methods for microarray data objects. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/convert.html + This package can be used to handle MAGEML documents in Bioconductor + http://bioconductor.org/packages/2.4/bioc/html/RMAGEML.html + Nandini Badarinarayan + RMAGEML - + - - copa - - - - - - - + + - - - - - - - + + - - - - - - - - - + + - - - - - - - - - + + - - + + - + - - - - - + + - COPA is a method to find genes that undergo recurrent fusion in a given cancer type by finding pairs of genes that have mutually exclusive outlier profiles. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/copa.html + RNAither analyzes cell-based RNAi screens, and includes quality assessment, customizable normalization and statistical tests, leading to lists of significant genes and biological processes + http://bioconductor.org/packages/2.4/bioc/html/RNAither.html + Nandini Badarinarayan + RNAither - + - - cosmo - + + + + + + + + + + + + + + - - + + + + + + + - - + + + utilities for ROC, with uarray focus + http://bioconductor.org/packages/2.4/bioc/html/ROC.html + Nandini Badarinarayan + ROC + + + + + + + + - - + + - + - + - - - - + + + + + @@ -65089,383 +65238,365 @@ tiple samples - + - - - - - - - - - - - - - - + + + + - - + + - Nandini Badarinarayan - cosmo searches a set of unaligned DNA sequences for a shared motif that may, for example, represent a common transcription factor binding site. The algorithm is similar to MEME, but also allows the user to specify a set of constraints that the position weight matrix of the unknown motif must satisfy. Such constraints may include bounds on the information content across certain regions of the unknown motif, for example, and can often be formulated on the basis of prior knowledge about the structure of the transcription factor in question. The unknown motif width, the distribution of motif occurrences (OOPS, ZOOPS, or TCM), as well as the appropriate constraint set can be selected data-adaptively. - http://bioconductor.org/packages/2.4/bioc/html/cosmo.html + This package provides mechanisms for automatic function prototyping and exposure of R functionality in a web services environment. + http://bioconductor.org/packages/2.4/bioc/html/RWebServices.html + Nandini Badarinarayan + RWebServices - + - - cosmoGUI - + + - - + + - - + + - - - - - - - - - - - - - - - - - + + - + - - - - - - - - - + + - - + + - - + + - Nandini Badarinarayan - cosmoGUI allows the user to interactively define constraint sets that can be used by the cosmo package to supervise the search for shared motifs in a set of DNA sequences. The constraints can be either adapted from a set of commonly used templates or defined from scratch. - http://bioconductor.org/packages/2.4/bioc/html/cosmoGUI.html + Rank Product method for identifying differentially expressed genes with application in meta-analysis + http://bioconductor.org/packages/2.4/bioc/html/RankProd.html + Nandini Badarinarayan + RankProd - + - - covdesc file - + + + + + + + + + Support for Springer monograph on Bioconductor + http://bioconductor.org/packages/2.4/bioc/html/RbcBook1.html + Nandini Badarinarayan + RbcBook1 - + - - database creation - - An objective in which the aim is to create a new database instance. - James Malone - PERSON: James Malone + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Generic database methods + http://bioconductor.org/packages/2.4/bioc/html/Rdbi.html + Nandini Badarinarayan + Rdbi - + - - crlmm - + + - - + + - - + + + + + + + - - - - - - - - - - - - + + - - + + + Provides methods for accessing data stored in PostgreSQL tables. + http://bioconductor.org/packages/2.4/bioc/html/RdbiPgSQL.html + Nandini Badarinarayan + RdbiPgSQL + + + + + + + + - - + + - + - - - - - - - - - + + - Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 6.0. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/crlmm.html + + + + + + + + + + + + + Decomposition of Isotopic Patterns + http://bioconductor.org/packages/2.4/bioc/html/Rdisop.html + Nandini Badarinarayan + Rdisop - + - - ctc - - - - - - - + + - - + + - - + + - - + + - + - - - - - - - - - - - - - + + + - Nandini Badarinarayan - Tools for export and import classification trees and clusters to other programs - http://bioconductor.org/packages/2.4/bioc/html/ctc.html + The package contains functions for pre-processing Affymetrix data using the RMA+ and the RMA++ methods. + http://bioconductor.org/packages/2.4/bioc/html/RefPlus.html + Nandini Badarinarayan + RefPlus - + - - dChip - + + - - + + - Analysis and visualization of gene expression and SNP microarrays - Nandini Badarinarayan - http://www.bioinformatics.org/dchip/ - - - - - - - - daMA - - - + + - - + + + This package allows user either to read an annotation data file from TIGR Resourcerer as a matrix or convert the file into a Bioconductor annotation data package using the AnnBuilder package. + http://bioconductor.org/packages/2.4/bioc/html/Resourcerer.html + Nandini Badarinarayan + Resourcerer + + + + + + + + - - + + - + - - + + - - + + - - - - - - - - - + + - Nandini Badarinarayan - This package contains functions for the efficient design of factorial two-colour microarray experiments and for the statistical analysis of factorial microarray data. - http://bioconductor.org/packages/2.4/bioc/html/daMA.html - - - - - - - - .data - - - - - - - - - dcf - - debian control file format - - - - - - - - design file - + Provides plotting capabilities for R graph objects + http://bioconductor.org/packages/2.4/bioc/html/Rgraphviz.html + Nandini Badarinarayan + Rgraphviz - + - - 'diffGeneAnalysis' - + + + + + + + + + + + + + + - + - - + + + + + @@ -65473,436 +65604,419 @@ tiple samples - - + + + + + + + + + - - + + - - + + 2 + - Analyze microarray data - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/diffGeneAnalysis.html + The package Ringo facilitates the primary analysis of ChIP-chip data. The main functionalities of the package are data read-in, quality assessment, data visualisation and identification of genomic regions showing enrichment in ChIP-chip. The package has functions to deal with two-color oligonucleotide microarrays from NimbleGen used in ChIP-chip projects + http://bioconductor.org/packages/2.4/bioc/html/Ringo.html + Nandini Badarinarayan + Ringo - + - - 'domainsignatures' - + + - - + + - - + + + + + + + - - + + + + + + + - - + + - - + + - Find significantly enriched gene classifications in a list of functionally undescribed genes based on their InterPro domain structure. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/domainsignatures.html + Queries and data structures for protein interactions + http://bioconductor.org/packages/2.4/bioc/html/Rintact.html + Nandini Badarinarayan + Rintact - + - - 'dualKS' - + + - - - - - - - - - + + - - + + - - + + - - - - - - - - - + + - - - - - - - - - + + - Nandini Badarinarayan - This package implements a Kolmogorov Smirnov rank-sum based algorithm for training and classification of gene expression data sets. One of the chief strengths of this approach is that it is amenable to the "multiclass" problem. That is, it can discriminate between more than 2 classes. - http://bioconductor.org/packages/2.4/bioc/html/dualKS.html + Microarray Classification is designed for both biologists and statisticians. It offers the ability to train a classifier on a labelled microarray dataset and to then use that classifier to predict the class of new observations. + http://bioconductor.org/packages/2.4/bioc/html/Rmagpie.html + Nandini Badarinarayan + Rmagpie - + + + + + Rnw + + + + + + + + + Robust likelihood-based survival modeling + + + + + - - dyebias - + + - - + + + The Rosetta Resolver® system provides a central analysis center and repository for biologists, statisticians, and bioinformaticians for the evaluation of gene expression data from microarrays and qPCR studies. + http://www.rosettabio.com/products/resolver + Nandini Badarinarayan + Rosetta Resolver + + + + + + + + - - + + - + - - - - - - - - - - - - - - - - - + + + + - + - - - - - - - + + + + - - + + - - + + - Gene-specific dye-bias correction of two-color microarray data using the GASSCO method - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/dyebias.html - - - - - - - - Dynamic programming algorithm - + Queries, data structure and interface to visualization of interaction datasets. This package inplements the PSI-MI 2.5 standard and supports up to now 8 databases. Further databases supporting PSI-MI 2.5 standard will be added continuously. + http://bioconductor.org/packages/2.4/bioc/html/RpsiXML.html + Nandini Badarinarayan + RpsiXML - + - - ecolitk - - - - - - - - - - - - - - - - - + + - - + + - - + + - - + + + + + + + - - + + - Meta-data and tools to work with E. coli. The tools are mostly plotting functions to work with circular genomes. They can used with other genomes/plasmids. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/ecolitk.html + interface to redland RDF utilities + http://bioconductor.org/packages/2.4/bioc/html/Rredland.html + Nandini Badarinarayan + Rredland - + - - edd - + + - + - - - - + + + + + + - - - - - - - - - + + + + + + + + - + - - - - - - - - - + + + + - - + + - - + + - Nandini Badarinarayan - This package provides tools for evaluating cohort distributions of gene expression levels - http://bioconductor.org/packages/2.4/bioc/html/edd.html + Rtreemix is a package that offers an environment for estimating the mutagenetic trees mixture models from cross-sectional data and using them for various predictions. It includes functions for fitting the trees mixture models, likelihood computations, model comparisons, waiting time estimations, stability analysis, etc. + http://bioconductor.org/packages/2.4/bioc/html/Rtreemix.html + Nandini Badarinarayan + Rtreemix - + - - 'edgeR' - + + - - + + - - - - - - - - - + + - - + + - + - - - - - - + + + + - - + + - Estimation and Testing for Differential Expression in Multiple Digital Gene Expression Libraries. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/edgeR.html + A package to provide UUID values in R + http://bioconductor.org/packages/2.4/bioc/html/Ruuid.html + Nandini Badarinarayan + Ruuid - + - - exonmap - - - - - - - + + + S-Score algorithm + + + + + + + + + Serial Analysis of Gene Expression (SAGE) + + + + + + + + - + - - - - - - - - - - - - - + + + + + + - - + + - + - + - - + + @@ -65911,212 +66025,221 @@ tiple samples - - - - - - - - - - - - - + + + A package for retrieval, preparation and analysis of data from the Affymetrix GeneChip. In particular the issue of identifying differentially expressed genes is addressed. + http://bioconductor.org/packages/2.4/bioc/html/SAGx.html + Nandini Badarinarayan + SAGx + + + + + + + + + Note: It is unclear from just the label what is meant by a SAM algorithm. It may or may not be related to the SAM sequence alignment software described by the class SWO_0000077 (Allyson Lister) + SAM + + + + + + + + - - - - - - - - - + + - Nandini Badarinarayan - This package provides fine grained annotation of Affymetrix exon arrays, including mappings between the array probes and probesets and the Ensembl exons, transcripts and genes they target. - http://bioconductor.org/packages/2.4/bioc/html/exonmap.html + Statistical Analysis with a number of procedures, providing statistical information such as analysis of variance, regression, multivariate analysis, and categorical data analysis. + http://en.wikipedia.org/wiki/SAS_System + Nandini Badarinarayan + SAS/STAT Software, Version 8 - + - - 'explorase' - + + - - + + - + - - - - - - + + + + + + + + + + + - - + + + + + + + + + + + + + + - - + + - Nandini Badarinarayan - This package explores and analyzes *omics data with R and GGobi - http://bioconductor.org/packages/2.4/bioc/html/explorase.html + This package contains a systems biology markup language (SBML) interface and biochemical system analysis tools with illustrative examples. + http://bioconductor.org/packages/2.4/bioc/html/SBMLR.html + Nandini Badarinarayan + SBMLR - + - - 'externalVector' - - - - - - - - Basic class definitions and generics for external pointer based vector objects for R. A simple in-memory implementation is also provided - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/externalVector.html + + + SBMLR format - + - - f-test - + + + Marked as obsolete by Allyson Lister + 0.4 + Identical to http://www.ebi.ac.uk/swo/data/SWO_3000037 + obsolete_SBML file + true - + + + + + Marked as obsolete by Allyson Lister. + 0.5 + 'SBML model' was classed as a child of algorithm, when this clearly isn't the case. As SWO already contained 'SBML file' (to cover the data format itself), there was no need for this class at all. The one class (SBMLR) which referenced this class had the relevant axiom deleted. For referencing the SBML format, please use the class 'SBML file'. + obsolete_SBML model + true + + + + + + + + + SDF format + + + + + - - factDesign - + + - - + + - - + + - - - - - - - - - - - + + - + - - - + + + - - - - - - - - - - - - - - - - - - - Nandini Badarinarayan - This package provides a set of tools for analyzing data from a factorial designed microarray experiment, or any microarray experiment for which a linear model is appropriate. The functions can be used to evaluate tests of contrast of biological interest and perform single outlier detection. - http://bioconductor.org/packages/2.4/bioc/html/factDesign.html + Finds associations between DNA copy number and gene expression. + http://bioconductor.org/packages/2.4/bioc/html/SIM.html + Nandini Badarinarayan + SIM - + - - fbat - + + - - + + - - - - - - - + + - + - - + + + + + @@ -66124,64 +66247,50 @@ tiple samples - - - - - - - - - - - - - + + - Nandini Badarinarayan - This package implements a broad class of Family Based Association Tests for genetids data, with adjustments for population admixture using the code from the 'FBAT' software program - http://bioconductor.org/packages/2.4/bioc/html/fbat.html + A variety of data files and functions for the analysis of genetic interactions + http://bioconductor.org/packages/2.4/bioc/html/SLGI.html + Nandini Badarinarayan + SLGI - + - - fdrame - - - - - - - + + - - + + - + - - + + - + - - + + + + + @@ -66189,66 +66298,69 @@ tiple samples - - + + + + + + + + + - - + + - Nandini Badarinarayan - This package contains two main functions. The first is fdr.ma which takes normalized expression data array, experimental design and computes adjusted p-values It returns the fdr adjusted p-values and plots, according to the methods described in (Reiner, Yekutieli and Benjamini 2002). The second, is fdr.gui() which creates a simple graphic user interface to access fdr.ma - http://bioconductor.org/packages/2.4/bioc/html/fdrame.html + Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH + http://bioconductor.org/packages/2.4/bioc/html/SLqPCR.html + Nandini Badarinarayan + SLqPCR - + - - flagme - + + - - + + - - + + - + - - - - - - - - - + + - + - - + + + + + @@ -66256,15 +66368,12 @@ tiple samples - + - - - - - + + @@ -66272,47 +66381,46 @@ tiple samples - - + + - Fragment-level analysis of gas chromatography - mass spectrometry metabolomics data - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/flagme.html + Functions and classes for DNA copy number profiling of array-CGH data + http://bioconductor.org/packages/2.4/bioc/html/SMAP.html + Nandini Badarinarayan + SMAP - + + + + + SNPRMA algorithm + + - - flowClust - + + + + + - - - - - - - - - - - - + + - + - - - + + + @@ -66320,75 +66428,29 @@ tiple samples - - - - - - - - - - - - - - - - - - - - - - - - - - + + - Nandini Badarinarayan - Robust model-based clustering using a t-mixture model with Box-Cox transformation. Note: users should have GSL installed - http://bioconductor.org/packages/2.4/bioc/html/flowClust.html - - - - - - - - flowCore - - + - - - - - - - - - + + - + - - - - - + + @@ -66396,95 +66458,64 @@ tiple samples - - - - - - - - + + - Nandini Badarinarayan - This package provides S4 data structures and basic functions to deal with flow cytometry data. - http://bioconductor.org/packages/2.4/bioc/html/flowCore.html + This package defines classes and functions for plotting copy number and genotype in high throughput SNP platforms such as Affymetrix and Illumina. In particular, SNPchip is a useful add-on to the oligo package for visualizing SNP-level estimates after pre-processing. + http://bioconductor.org/packages/2.4/bioc/html/SNPchip.html + Nandini Badarinarayan + SNPchip - + - - flowFlowJo - - - - - - - - - - - - + + - - - - - - - + + - - + + - - + + - + - - + + + + + - FlowJo is a commercial GUI based software package from TreeStar Inc. for the visualization and analysis of flow cytometry data. One of the FlowJo standard export file types is the "FlowJo Workspace". This is an XML document that describes files and manipulations that have been performed in the FlowJo GUI environment. This package can take apart the FlowJo workspace and deliver the data into R in the flowCore paradigm. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/flowFlowJo.html - - - - - - - - flowQ - - + - - + + @@ -66492,55 +66523,59 @@ tiple samples - - - - - - - - - - - - - - - - - - - + + - Nandini Badarinarayan - This package provides quality control and quality assessment tools for flow cytometry data. - http://bioconductor.org/packages/2.4/bioc/html/flowQ.html + This package implements the Signaling Pathway Impact Analysis (SPIA) which uses the information form a list of differentially expressed genes and their log fold changes together with signaling pathways topology, in order to identify the pathways most relevant to the condition under the study. + http://bioconductor.org/packages/2.4/bioc/html/SPIA.html + Nandini Badarinarayan + SPIA - + + + + + Semantic Similarity Measures- Four methods proposed by Resnik[Philip, 1999], Jiang[Jiang and Conrath, +1997], Lin[Lin, 1998] and Schlicker[Schlicker et al., 2006] respectively have +presented to determine the semantic similarities of two GO terms based +on the annotation statistics of their common ancestor terms. Wang [Wang +et al., 2007] proposed a new method to measure the similarities based on +the graph structure of GO. + Semantic Similarity Measures + + + - - flowStats - + + + + + + + + + + - - + + - + - + - - + + @@ -66549,147 +66584,140 @@ tiple samples - - - - - - - - - - - - - - - - - - - + + - Nandini Badarinarayan - This package contains methods and functionality to analyse flow data that is beyond the basic infrastructure provided by the flowCore package. - http://bioconductor.org/packages/2.4/bioc/html/flowStats.html + Sample size and power analysis for microarray data, where two groups are analysed. + http://bioconductor.org/packages/2.4/bioc/html/SSPA.html + Nandini Badarinarayan + SSPA - + - - flowUtils - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Nandini Badarinarayan - This package provides utilities for flow cytometry data. - http://bioconductor.org/packages/2.4/bioc/html/flowUtils.html + + + SVDimpute algorithm - + - - flowViz - - - - - - - - + + + Software developer role is a role borne by an organization or individual in which they are responsible for authoring software. + James Malone + software developer role + + + + + + + + + Information processing is a process in which input information is analysed or transformed in order to produce information as output. + James Malone + Marked as obsolete by Allyson Lister. + 0.4 + Present both in the original file (SWO_0000393) and in the core file (SWO_0000003), and each have different identifiers. SWO_0000393 was initially created within the originalsoftwareontology.owl and later moved to swo_core.owl. SWO_0000003 was retained and SWO_0000393 deemed obsolete. Please use SWO_0000003 instead. + obsolete_Information processing + true + + + + + + + + - - + + - - + + + An organization or legal entity (including single person) that is responsible for developing software. Developing includes aspects of design, coding and testing. + software developer organization + + + + + + + + - - - - - - - + + - + + + An organization or legal entity (including single person) that is responsible for publishing software. Publishing here includes tasks such as designing and producing physical products, technical customer support, licensing arrangements and marketing. + software publisher organization + + + + + + + + + Classical multivariate analysis-of-variance tests perform poorly in cases with several highly correlated responses and the tests collapse when the number of responses exceeds the number of observations. This paper presents a new method which handles this problem. The dimensionality of the data is reduced by using principal component decompositions and the final tests are still based on the classical test statistics and their distributions. The methodology is illustrated with an example from the production of sausages with responses from near infrared reflectance spectroscopy. A closely related method for testing relationships in uniresponse regression with collinear explanatory variables is also presented. The new test, which is called the 50-50 F-test, uses the first k components to calculate SSMODEL. The next d components are not involved in SSERROR and they are called buffer components. + Langsrud, &Oslash. (2002), 50-50 Multivariate Analysis of Variance for Collinear Responses, The Statistician, 51, 305-317. + 50-50 MANOVA algorithm + + + + + + + + + Marked as obsolete by Allyson Lister. + 0.4 + There is one EDAM html class (EDAM_format:2331) and one SWO class (SWO_0000399) within swo_data.owl. EDAM_format:2331 was retained and SWO_0000399 deemed obsolete, as EDAM_format:2331 has a better location in the hierarchy and is an imported term. All axioms belonging to SWO_0000399 were transferred to EDAM_format:2331. Please use EDAM_format:2331 (in this ontology via its full URI http://edamontology.org/format_2331) instead. + obsolete_html + true + + + + + + + + - + - - + + + + + - Nandini Badarinarayan - Provides visualization tools for flow cytometry data - http://bioconductor.org/packages/2.4/bioc/html/flowViz.html - - - - - - - - gaga - - + - - + + + + + @@ -66697,14 +66725,14 @@ tiple samples - + - + - - + + @@ -66713,18 +66741,21 @@ tiple samples - - + + - + - - + + + + + @@ -66732,117 +66763,93 @@ tiple samples - + - - - - + + + + + + + + + - - - - - - - Nandini Badarinarayan - This package fits Rossell's generalizations of the Gamma-Gamma hierarchical model for microarray data analysis, which substantially improve the quality of the fit at a low computational cost. The model can be fit via empirical Bayes (Expectation-Maximization and Simulated Annealing) and fully Bayesian techniques (Gibbs and Metropolis-Hastings posterior sampling). - http://bioconductor.org/packages/2.4/bioc/html/gaga.html + ArrayExpress Bioconductor package is software that read in MAGE-TAB format files from the ArrayExpress FTP site and converts them to R objects. + http://bioconductor.org/packages/2.4/bioc/html/ArrayExpress.html + Nandini Badarinarayan + ArrayExpress Bioconductor - + - - 'gaggle' - - - - - - - - Nandini Badarinarayan - This package contains functions connecting R with the Gaggle - http://bioconductor.org/packages/2.4/bioc/html/gaggle.html + + + Gene list - + - - gcRMA quantification - - - - - - - - - - - - - - - - - - Background adjustment using sequence information - Nandini Badarinarayan - http://www.bioconductor.org/packages/2.3/bioc/html/gcrma.html + + + Clustered data set - + + + + + R data frame + + + + + - - gcrma - + + + R language + + + + + + + + - - + + - + - - - - - - - - - + + - - - - - - - + - - + + @@ -66850,295 +66857,319 @@ tiple samples - - + + + + + + + + + - - - - - - - + + - Background adjustment using sequence information - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/gcrma.html + Package to create In Silico Interactomes + http://bioconductor.org/packages/2.4/bioc/html/ScISI.html + Nandini Badarinarayan + ScISI - + - - gct - - http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#GCT:_Gene_Cluster_Text_file_format_.28.2A.gct.29 - Gene Cluster Text file format + + + + + + + + + Processes fluorescent images of microarrays + http://smd.stanford.edu/resources/restech.shtml + Nandini Badarinarayan + ScanAlyze - + - - 'genArise' - - - - - - - - - - - - - - - - - - - + + - - - - - - - - - - + + - Nandini Badarinarayan - genArise is an easy to use tool for dual color microarray data. Its GUI-Tk based environment let any non-experienced user performs a basic, but not simple, data analysis just following a wizard. In addition it provides some tools for the developer. - http://bioconductor.org/packages/2.4/bioc/html/genArise.html + ScanArray Express provides superior spot finding and quantization algorithm. This combined with template adjustment features drives excellence in analysis performance. + ScanArray Express + ScanArray Express [PerkinElmer] + http://las.perkinelmer.com/Catalog/ProductInfoPage.htm?ProductID=7000060 + Nandini Badarinarayan + ScanArray - + - - gene2pathway - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Nandini Badarinarayan - The package takes a list of genes and predicts to which KEGG pathway each gene maps to. This is done by looking at the InterPro domains of each gene. Each prediction is assigned a confidence score. The package also allows to predict connected component membership of genes within signaling pathways. Separate models for each organism supported by KEGG can be trained. - http://bioconductor.org/packages/2.4/bioc/html/gene2pathway.html + + + ScanArray version 3.1 + Nandini Badarinarayan + ScanArray v3.1 software - + + + + + Nandini Badarinarayan + scanning software + + + + + - - geneRecommender - + + - - + + + High resolution scanning with pixel sizes of 2, 3, 5, and 10 microns enables users to scan a range of array types from ultra-high density commercial arrays as well as low-density home-brew arrays.Low level detection resulting from optimized precision optics, broad dynamic range, minimal spectral cross talk allowing users to detect weak features, achieve rapid, accurate and dependable results + http://www.chem.agilent.com/en-us/products/instruments/dnamicroarrays/dnamicroarrayscanner/pages/default.aspx + Nandini Badarinarayan + Scanning software G2565AA version A6.3.1 + + + + + + + + - - + + - - + + - + - - + + - - + + + Base classes, functions, and methods for representation of high-throughput, short-read sequencing data. + http://bioconductor.org/packages/2.4/bioc/html/ShortRead.html + Nandini Badarinarayan + ShortRead + + + + + + + + + Signaling Pathway Impact Analysis (SPIA) algorithm + + + + + + + + - - - - - - - - - + + - Nandini Badarinarayan - This package contains a targeted clustering algorithm for the analysis of microarray data. The algorithm can aid in the discovery of new genes with similar functions to a given list of genes already known to have closely related functions. - http://bioconductor.org/packages/2.4/bioc/html/geneRecommender.html + The GeneSpring-R integration package will allow you to expand the capability of GeneSpring by integrating R programs seamlessly into GeneSpring. With the integration package you will be able to use the power of R and BioConductor scripts in GeneSpring's rich graphical environment + SiliconGenetics GeneSpring + http://www.silicongenetics.com/cgi/SiG.cgi/Support/gs_r_int.smf + Nandini Badarinarayan + Silicon Genetics Genespring - + - - Gene array analysis algorithm - + + + Similarity score - + - - gene expression analysis - + + + 'Smith-Waterman' - + - - Gene expression dataset - + + + Nandini Badarinarayan + Spot quantification - + - - genefilter - + + - - + + - - + + + TIGR Spotfinder was designed for the rapid, reproducible and computer-aided analysis of microarray images and the quantification of gene expression + http://www.tm4.org/contributors.html + Nandini Badarinarayan + Spotfinder [TIGR] + + + + + + + + - - + + + Spotfire’s interactive, visual capabilities for data analysis empower individuals to easily see trends, patterns outliers and unanticipated relationships in data with unprecedented speed and adaptability. + http://spotfire.tibco.com/Products/Info.aspx + Nandini Badarinarayan + Spotfire + + + + + + + + - - + + + Tiling Analysis Software (TAS) is a freely downloadable tool for analysis, with which one can perform a simulation to assess the likelihood that an observed probe overlap region is different from the expected overlap with no enrichment from binding, and can derive an interval overlap report and/or computation of summary statistics. + http://dmaf.biochem.uci.edu/affymetrix_analysis_software.html + Nandini Badarinarayan + TAS Software + + + + + + + + + Marked as obsolete by Allyson Lister. + 0.4 + SWO_0000434 was initially created within the originalsoftwareontology.owl and later moved to swo_data.owl. SWO_3000016, with the label 'TIFF', is also present, and stored within swo_data.owl. SWO_3000016 was retained and SWO_0000434 deemed obsolete, as SWO_3000016 has a better location in the hierarchy. All axioms belonging to SWO_0000434 were transferred to SWO_3000016. Please use SWO_3000016 instead. + obsolete_TIFF image + true + + + + + + + + - - + + + + + + + + + - - - - - - - + + - Nandini Badarinarayan - Some basic functions for filtering genes - http://bioconductor.org/packages/2.4/bioc/html/genefilter.html - - - - - - - - genemeta - - - + + - + - - - - - - - - + + + + + + @@ -67146,169 +67177,206 @@ tiple samples - - - - - - - - + + - A collection of meta-analysis tools for analysing high throughput experimental data - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/GeneMeta.html - http://bioconductor.org/packages/2.4/bioc/html/GeneMeta.html + This packages provides a targeted pre-processing method for GC-MS data. + http://bioconductor.org/packages/2.4/bioc/html/TargetSearch.html + Nandini Badarinarayan + TargetSearch - + + + + + Theodore Ts’o’s + + + + + - - geneplotter - + + + + + + + + - - + + + + + + + + + + + + - - + + + + + + + + + + + + - - + + - Nandini Badarinarayan - Some basic functions for plotting genetic data - http://bioconductor.org/packages/2.4/bioc/html/geneplotter.html + A prototype for a mechanism for specifying the types of parameters and the return value for an R function. This is meta-information that can be used to generate stubs for servers and various interfaces to these functions + http://bioconductor.org/packages/2.4/bioc/html/TypeInfo.html + Nandini Badarinarayan + TypeInfo - + + + + + Variance-stabilizing transformation (VST) algorithm + + + + + - - genomeIntervals - + + - - + + - - + + - + - - + + - - + + + + + + + + + + + + - - - - - - - - - - - - - - + + - Nandini Badarinarayan - Tools for operation on genomic intervals. - http://bioconductor.org/packages/2.4/bioc/html/genomeIntervals.html + Hidden Markov Models for characterizing chromosomal alterations in high throughput SNP arrays + http://bioconductor.org/packages/2.4/bioc/html/VanillaICE.html + Nandini Badarinarayan + VanillaICE - + - - obsolete_gff format - - true - Equivalence with EDAM format_2305. - Obsoleted after the 0.4 release. - Marked as obsolete by Allyson Lister. + + + WilcEbam - + - - Global test - - global test allows the unit of analysis of the microarray experiment to be shifted from the single gene level to the pathway level, where a ‘pathway’ may be any set of genes, e.g. chosen using the Gene Ontology database or from earlier experiments. + + + Wilcoxon - + - - globaltest - + + - - + + + + + + + + + - - + + - - + + - + - + - - + + @@ -67317,97 +67385,125 @@ tiple samples - - + + + + + + + + + - - + + - Nandini Badarinarayan - Testing whether sets of genes (e.g. KEGG pathways of GO terms) are significantly associated with a clinical variable of interest. - http://bioconductor.org/packages/2.4/bioc/html/globaltest.html + XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression + http://bioconductor.org/packages/2.4/bioc/html/XDE.html + Nandini Badarinarayan + XDE - + - - gmt format - + + + + + + + + + Analysis Software for Integrated Image Analysis for Spot Detection , Position and Quantification + http://www.cose.fr/us_dots.html + Nandini Badarinarayan + XDotsReader - + + + + + Marked as obsolete by Allyson Lister. + 0.4 + 5. SWO_0000448 was initially created within the originalsoftwareontology.owl and later moved to swo_data.owl. SWO_3000005 is also present within swo_data.owl. SWO_3000005 was retained and SWO_0000448 deemed obsolete, as SWO_3000005 has a better location in the hierarchy. All axioms belonging to SWO_0000448 were transferred to SWO_3000005. Please use SWO_3000005 instead. + obsolete_XML + true + + + + + + + + + Xba.CQV and Xba.regions + + + + + - - goProfiles - + + - - + + - - + + - - + + - - + + - + - - - + + + + + - Nandini Badarinarayan - The package implements methods to compare lists of genes based on comparing the corresponding 'functional profiles'. - http://bioconductor.org/packages/2.4/bioc/html/goProfiles.html - - - - - - - - goTools - - + - + - - + + @@ -67416,201 +67512,216 @@ tiple samples - - - - - - - - - - - - - - + + + + + + + + + + + + + The aCGH package functions for reading data from image analysis output files and clone information files, creation of aCGH S3 objects for storing these data. Basic methods for accessing/replacing, subsetting, printing and plotting aCGH objects. + http://bioconductor.org/packages/2.4/bioc/html/aCGH.html + Nandini Badarinarayan + Array Comparative Genomic Hybridization + + + + + + + + - - + + + + + + + + + + + + - Nandini Badarinarayan - Wraper functions for description/comparison of oligo ID list using Gene Ontology database - http://bioconductor.org/packages/2.4/bioc/html/goTools.html + Acuity is the complete enterprise microarray informatics platform for microarray data storage, data filtering and data analysis. It analysis tools for quality, visualizations for discovery and Data Management for Security. + http://www.bio-medicine.org/ + Nandini Badarinarayan + Acuity - + - - gpls - + + - - - - - - - + + - - + + - - + + - - - - - - - + + - - + + - Classification using generalized partial least squares for two-group and multi-group (more than 2 group) classification. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/gpls.html - - - - - - - - gpr format - - GenePix Pro Results file format + + + + + + + affxparser is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR). It provides methods for fast and memory efficient parsing of Affymetrix files using the Affymetrix' Fusion SDK. + http://bioconductor.org/packages/2.4/bioc/html/affxparser.html + Nandini Badarinarayan + affxparser - + - - graph - + + + + + + + + - + - - + + + + + + + + + - + - - - - - - + + + + + + + + + + + - - + + + affyContam is software which provides the in silico creation of quality problems in CEL-level data to help evaluate performance of quality metrics. In essence, it creates structured corruption within CEL data to demonstrate QA effectiveness. + http://bioconductor.org/packages/2.4/bioc/html/affyContam.html (access unknown); http://www.bioconductor.org/packages/2.12/bioc/vignettes/affyContam/inst/doc/affyContam.pdf, accessed 22 May 2013. + Allyson Lister + Nandini Badarinarayan + affyContam + + + + + + + + - - + + + + + + + + + - - + + - - + + - A package that implements some simple graph handling capabilities. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/graph.html - - - - - - - - gtr - - - - - - - - - gxl format - - - - - - - - - obsolete_Heatmap - - true - Marked as obsolete by Allyson Lister. - Obsoleted after the 0.4 release. - Equivalence with EDAM data_1636. + A Graphical User Interface for affy analysis using the limma Microarray package + http://bioconductor.org/packages/2.4/bioc/html/affylmGUI.html + Nandini Badarinarayan + Removed the links to specified data inputs, as this software is a GUI wrapper for another package, and it is this package which takes the inputs. (Allyson Lister 22/05/2013) + affyImGUI - + - - hexbin - + + - + - - + + + @@ -67618,96 +67729,97 @@ tiple samples - - - - - - - - + + - - + + + + + + + - + - - - - + + + + + + + + + - - + + + + + + + + + - Binning and plotting functions for hexagonal bins. Now uses and relies on grid graphics and formal (S4) classes and methods. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/hexbin.html + A package that extends and improves the functionality of the base affy package. Routines that make heavy use of compiled code for speed. Central focus is on implementation of methods for fitting probe-level models and tools using these models. PLM based quality assessment tools. + http://bioconductor.org/packages/2.4/bioc/html/affyPLM.html + Nandini Badarinarayan + 'affyPLM' - - - - Hierarchical clustering - - - - - - + - - hopach - + + - - + + - + - - - - - - - - - + + + + + + + + + + + - - - - - - - + - - + + + + + @@ -67715,523 +67827,652 @@ tiple samples - - + + + + + + + + + + - Nandini Badarinarayan - The HOPACH clustering algorithm builds a hierarchical tree of clusters by recursively partitioning a data set, while ordering and possibly collapsing clusters at each level. The algorithm uses the Mean/Median Split Silhouette (MSS) criteria to identify the level of the tree with maximally homogeneous clusters. It also runs the tree down to produce a final ordered list of the elements. The non-parametric bootstrap allows one to estimate the probability that each element belongs to each cluster (fuzzy clustering). - http://bioconductor.org/packages/2.4/bioc/html/hopach.html - - - - - - - - HTML report - - - + + + The package contains parallelized functions for exploratory oligonucleotide array analysis. The package is designed for large numbers of microarray data. + http://bioconductor.org/packages/2.4/bioc/html/affyPara.html + Nandini Badarinarayan + affyPara - - - - Hypergeometric enrichment - - - - - - + - - hypergraph - + + - - + + - + - - + + + + + + + + + - - + + + + + + + + + + + + - - + + - - + + - A package that implements some simple capabilities for representing and manipulating hypergraphs. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/hypergraph.html + This package creates a QC report for an AffyBatch object. The report is intended to allow the user to quickly assess the quality of a set of arrays in an AffyBatch object. + http://bioconductor.org/packages/2.4/bioc/html/affyQCReport.html + Nandini Badarinarayan + affyQCReport - + - - Icens - + + - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - + - - - - - + + - Many functions for computing the NPMLE for censored and truncated data. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/Icens.html + + + + + + + This package provides easy, fast functions for the extraction and annotation of individual probes from Affymetrix tiling arrays. + http://bioconductor.org/packages/2.4/bioc/html/AffyTiling.html + Nandini Badarinarayan + affyTiling - + - - idiogram - + + - - + + + + + + + + + - - + + - + - - - - + + + + + + - + - - + + + - A package for plotting genomic data by chromosomal location - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/idiogram.html - - - - - - - - obsolete_Image - - true - Marked as obsolete by Allyson Lister. - Obsoleted after the 0.4 release. - Equivalence with EDAM data_2968 + + + + + + + Various wrapper functions that have been written to streamline the more common analyses that a core Biostatistician might see + http://bioconductor.org/packages/2.4/bioc/html/affycoretools.html + Nandini Badarinarayan + 'affycoretools' - + - - impute - + + + + + + + + - - + + + + + + + + + + + + + + + + - - + + + + + + + + + + + + + + + + - - + + - - + + - Imputation for microarray data (currently KNN only) - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/impute.html + Routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing the CEL and CDF file formats. + http://bioconductor.org/packages/2.4/bioc/html/affyio.html + Nandini Badarinarayan + affyio - + - - iterativeBMA - + + - - + + - - + + + + + + + + + + + + - - + + - - - - - - - - - + + - Nandini Badarinarayan - The iterative Bayesian Model Averaging (BMA) algorithm is a variable selection and classification algorithm with an application of classifying 2-class microarray samples, as described in Yeung, Bumgarner and Raftery (Bioinformatics 2005, 21: 2394-2402). - http://bioconductor.org/packages/2.4/bioc/html/iterativeBMA.html + The package contains functions to perform the PDNN method described by Li Zhang et al. + http://bioconductor.org/packages/2.4/bioc/html/affypdnn.html + Nandini Badarinarayan + affypdnn - + - - iterativeBMAsurv - - - - - - - + + - - + + - + - - + + - - + + - - + + - Nandini Badarinarayan - The iterative Bayesian Model Averaging (BMA) algorithm for survival analysis is a variable selection method for applying survival analysis to microarray data. - http://bioconductor.org/packages/2.4/bioc/html/iterativeBMAsurv.html - - - - - - - - Iterative local regression and model selection - + altcdfenvs is a software package for alternative CDF environments (aka probeset mappings) and contains convenience data structures and functions to handle cdfenvs. + http://www.bioconductor.org/packages/release/bioc/html/altcdfenvs.html, accessed May 28 2013. + Allyson Lister + Nandini Badarinarayan + altcdfenvs - + - - obsolete_.java file - - true - Marked as obsolete by Allyson Lister. - The original label for this class, .java file, was used in two separate class URIs. The first was SWO_0000585, initially created within the originalsoftwareontology.owl. The second URI is stored within swo_data.owl and is SWO_3000034. As SWO_3000034 is properly modelled as a child of 'Programming language format' this class was retained and SWO_0000585 deemed obsolete. The usages of SWO_0000585 were refactored to reference 3. SWO_3000034, and SWO_0000585 was marked as obsolete. Please use SWO_3000034 instead. - 0.4 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + This package functions for handling data from Bioconductor Affymetrix annotation data packages.Allows searching biological metadata using various criteria. + http://bioconductor.org/packages/2.4/bioc/html/annaffy.html + Nandini Badarinarayan + annaffy - + - - obsolete_jpeg - - true - SWO_0000586 (jpeg) was initially created within the originalsoftwareontology.owl and later moved to swo_data.owl. SWO_3000017, with the label 'JPEG', is also present, and stored within swo_data.owl. SWO_3000017 was retained and SWO_ 0000586 deemed obsolete, as SWO_3000017 has a better location in the hierarchy. All axioms belonging to SWO_0000586 were transferred to SWO_3000017. Please use SWO_3000017 instead. - 0.4 - Marked as obsolete by Allyson Lister. + + + + + + + + + + + + + + + + + + + + + Using R enviroments for annotation. + http://bioconductor.org/packages/2.4/bioc/html/annotate.html + Nandini Badarinarayan + 'annotate' - + - - k-cores - + + + data annotation - + - - k-means - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + This package functions to annotate microarrays, find orthologs, and integrate heterogeneous gene expression profiles using annotation and other molecular biology information available as flat file database (plain text files). + http://bioconductor.org/packages/2.4/bioc/html/annotationTools.html + Nandini Badarinarayan + annotationTools - + - - k-nearest neighbour classification - + + + Annotation data packages - + - - keggorth - + + - - + + - - + + - - + + - - - - - - - + + - Nandini Badarinarayan - Test package for a pathway 'ontology' - http://bioconductor.org/packages/2.4/bioc/html/keggorth.html + This package functions to estimate a bipartite graph of protein complex membership using AP-MS data. + http://bioconductor.org/packages/2.4/bioc/html/apComplex.html + Nandini Badarinarayan + 'apComplex' - + - - lapmix - - - - - - - + + - - + + - + - - - - - - - - - + + + + - - + + - - + + + + + + + + + + - - + + - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/lapmix.html - Allyson Lister - lapmix is a software package for the identification of differentially expressed genes. A hierarchical Bayesian approach is used, and the hyperparameters are estimated using empirical Bayes. - - - - - - - - Likelihood method - + This package functions as methods for microarray analysis that take basic data types such as matrices and lists of vectors. These methods can be used standalone, be utilized in other packages, or be wrapped up in higher-level classes. + http://bioconductor.org/packages/2.4/bioc/html/aroma.light.html + Nandini Badarinarayan + aroma.light - + - - limma - + + - - + + - - + + - + - + - - + + + + + + + + + @@ -68240,339 +68481,339 @@ tiple samples - - + + + This package supports the application of diverse quality metrics to AffyBatch instances, summarizing these metrics via PCA, and then performing parametric outlier detection on the PCs to identify aberrant arrays with a fixed Type I error rate + http://bioconductor.org/packages/2.4/bioc/html/arrayMvout.html + Nandini Badarinarayan + arrayMvout + + + + + + + + - - + + - - + + + + + + + + + - Data analysis, linear models and differential expression for microarray data. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/limma.html - - - - - - - - limmaGUI - - + - - - - - + + + This package functions for performing print-run and array level quality assessment. + http://bioconductor.org/packages/2.4/bioc/html/arrayQuality.html + Nandini Badarinarayan + arrayQuality + + + + + + + + - - + + - - + + + + + + + - - + + + + + + + + + - - + + - A Graphical User Interface for the limma Microarray package - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/limmaGUI.html + This package generates a quality metrics report on ExpressionSet, NChannelSet, AffyBatch or BeadLevelList objects containing microarray data with one or two channels. + http://bioconductor.org/packages/2.4/bioc/html/arrayQualityMetrics.html + Nandini Badarinarayan + arrayQualityMetrics - + - - Linear modelling - + + + Nandini Badarinarayan + arrayWoRx 2.0 - + - - lma - + + + + + + + + + Applied Precision MicroArray Scanner Model arrayWoRx Comprehensive system that fully automates the image capture and quantitation of microarrays. by integrating Slid handling, fluorescent microscopy, and sophisticated spot scan and analysis software the systems detects and measures the fluorescence intensity at each of the specified elements in a microarray. The intensity data can be presented as image data, graphical representation, or as numerical data. + http://www.hitechtrader.com/detail.cfm?autonumber=64022 + Nandini Badarinarayan + arrayWoRx - + - - Local-pooled-error - + + + Associative T method - + - - log file - + + + AvgNRRs - + - - logicFS - + + - - + + - - - - - - - + + + + + The package is able to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided. + http://bioconductor.org/packages/2.4/bioc/html/beadarray.html + Nandini Badarinarayan + 'beadarray' + + + + + + + + + + + + - - - - - - - - - - - - + + - - + + - - + + - Identification of interactions between binary variables using Logic Regression. Can, e.g., be used to find interesting SNP interactions. Contains also a bagging version of logic regression for classification. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/logicFS.html - - - - - - - - logicFS dataset - + Importing data from Illumina SNP experiments and performing copy number calculations and reports. + http://bioconductor.org/packages/2.4/bioc/html/beadarraySNP.html + Nandini Badarinarayan + 'beadarraySNP' - + - - logitT - + + - - - - - - - - - + + - - + + - - - - - - - - - - - - - - + + - - + + + + + + + - - + + - - - - - - - + + - Nandini Badarinarayan - The logitT library implements the Logit-t algorithm introduced in --A high performance test of differential gene expression for oligonucleotide arrays-- by William J Lemon, Sandya Liyanarachchi and Ming You for use with Affymetrix data stored in an AffyBatch object in R. - http://bioconductor.org/packages/2.4/bioc/html/logitT.html - - - - - - - - Logit-t algorithm - + betr is a software package which implements the BETR (Bayesian Estimation of Temporal Regulation) algorithm to identify differentially expressed genes in microarray time-course data. + http://www.bioconductor.org/packages/2.12/bioc/html/betr.html, accessed 28 May 2013. + Allyson Lister + Nandini Badarinarayan + 'betr' - + - - lumi - - - - - - - - - - - - + + - - + + - - + + + + + + + - - + + + + + + + + + - - + + - Nandini Badarinarayan - The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. - http://bioconductor.org/packages/2.4/bioc/html/lumi.html + BGAfun is a method to identify specifity determining residues in protein families + http://bioconductor.org/packages/2.4/bioc/html/bgafun.html + Nandini Badarinarayan + bgafun - + - - maCorrPlot - - - - - - - + + - - + + - + - + - - + + @@ -68582,47 +68823,55 @@ tiple samples - - - - - - - + - - - + + + + + - Graphically displays correlation in microarray data that is due to insufficient normalization - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/maCorrPlot.html + + + + + + + Bayesian integrated analysis of Affymetrix GeneChips + http://bioconductor.org/packages/2.4/bioc/html/bgx.html + Nandini Badarinarayan + bgx - + + + + + Bitmap object + + + - - maDB - + + + + - + - - - - - + + @@ -68630,184 +68879,176 @@ tiple samples - - - - - - - - - + + - - + + + + + + + - - + + - - + + - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/maDB.html - maDB allows to create a simple microarray database to store microarray experiments and annotation data into it. Affymetrix GeneChip expression values as well as values from two color microarrays can be stored into the database. Whole experiments or subsets from a experiment (or also values for a subset of genes in a subset of microarrays) can be fetched back to R. Additionally maDB provides different utility functions for the microarray data analysis like functions to draw MA plots or volcano plots with the data points color coded according to the local point density or functions that allow a replicate handling of miroarrays. + The bioDist package contains some distance functions that have been shown to be useful in a number of dierent biological or bioinformatic problems. The return values are typically instances of the S3 class dist. + http://bioconductor.org/packages/2.4/bioc/html/bioDist.html + Nandini Badarinarayan + bioDist - + - - maSigPro - + + - - - - - - - - - - + + + Synthetic datasets to a) demonstrate the usage of bioconductor packages, b) write unit tests, while keeping dependencies and ressources usage minimal. + http://bioconductor.org/packages/2.4/bioc/html/biocDatasets.html + Nandini Badarinarayan + 'biocDatasets' + + + + + + + + - - + + - - + + - + - - + + - - - - - - - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/maSigPro.html - maSigPro is a regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray experiments. + This package provides examples and code that make use of the different graph related packages produced by Bioconductor. + http://bioconductor.org/packages/2.4/bioc/html/biocGraph.html + Nandini Badarinarayan + 'biocGraph' - + - - maanova - + + - - + + - - - - - - - - - + + + Categorized views of R package repositories + http://bioconductor.org/packages/2.4/bioc/html/biocViews.html + Nandini Badarinarayan + 'biocViews' + + + + + + + + - - - - - - - - - + + - + - - - - - - - - + + + + - - - - - - - - - + + - Analysis of N-dye Micro Array experiment using mixed model effect. Containing anlysis of variance, permutation and bootstrap, cluster and consensus tree. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/maanova.html + The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. + http://bioconductor.org/packages/2.4/bioc/html/biomaRt.html + Nandini Badarinarayan + biomaRT - + + + + + Bootstrap + + + + + - - macat - + + - + - - + + @@ -68815,129 +69056,108 @@ tiple samples - - + + - - - - - - - - - - - + + + + + The bridge package consists of several functions for testing for dierential expression among mul- +tiple samples + http://bioconductor.org/packages/2.4/bioc/html/bridge.html + Nandini Badarinarayan + 'bridge' + + + + + + + + + cdt + + + + + + + + + + + + - - + + - + - - - + + - Nandini Badarinarayan - This library contains functions to investigate links between differential gene expression and the chromosomal localization of the genes. MACAT is motivated by the common observation of phenomena involving large chromosomal regions in tumor cells. MACAT is the implementation of a statistical approach for identifying significantly differentially expressed chromosome regions. The functions have been tested on a publicly available data set about acute lymphoblastic leukemia (Yeoh et al.Cancer Cell 2002), which is provided in the library 'stjudem'. - - - - - - - - made4 - - - - - - - - + - - + + - - - - - - - - - - - - - Multivariate data analysis and graphical display of microarray data. Functions include between group analysis and coinertia analysis. It contains functions that require ADE4. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/made4.html + Analysis of cell-based RNA interference screens + http://bioconductor.org/packages/2.4/bioc/html/cellHTS.html + Nandini Badarinarayan + 'cellHTS' - + - - maigesPack - + + - - + + - - - - - - - - - - - + + - + - - - + + @@ -68945,292 +69165,209 @@ tiple samples - + - - + + + - Nandini Badarinarayan - This package uses functions of various other packages together with other functions in a coordinated way to handle and analyse cDNA microarray data - http://bioconductor.org/packages/2.4/bioc/html/maigesPack.html + Analysis of cell-based RNA interference screens + http://bioconductor.org/packages/2.4/bioc/html/cellHTS2.html + Nandini Badarinarayan + 'cellHTS2' - + - - makePlatformDesign - + + - - - - - - - + + - - + + - - - - - - - + - - - - - - - - - - + + - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/makePlatformDesign.html - makePlatformDesign creates the Platform Design environments (PDenvs) required by oligo. - - - - - - - - makecdfenv - - - - - - - - + - - - - + + + + + + + + + - - - - - - - - - - - - - - + + - - + + - Nandini Badarinarayan - This package has two functions. One reads a Affymetrix chip description file (CDF) and creates a hash table environment containing the location/probe set membership mapping. The other creates a package that automatically loads that environment. - http://bioconductor.org/packages/2.4/bioc/html/makecdfenv.html + Based on the algothrim proposed by Dr. Lynda Chin's lab, this package provides functions that identify chromosome regions that show gains/losses commonly observed across different samples profiled using arrayCGH platform. + http://bioconductor.org/packages/2.4/bioc/html/cghMCR.html + Nandini Badarinarayan + cghMCR - + - - marray - - - - - - - + + + chamber slide format + + + + + + + + + Categorical (e.g tumor vs normal) class file format + http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#CLS:_Categorical_.28e.g_tumor_vs_normal.29_class_file_format_.28.2A.cls.29 + cls + + + + + + + + - - + + - - + + - - + + - + - - - - - - - - - - - - + + + + - + - - + + - Class definitions for two-color spotted microarray data. Fuctions for data input, diagnostic plots, normalization and quality checking. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/marray.html - - - - - - - - 'MAS5' - + This package can be used to estimate the number of clusters in a set of microarray data, as well as test the stability of these clusters. + http://bioconductor.org/packages/2.4/bioc/html/clusterStab.html + Nandini Badarinarayan + 'clusterStab' - + - - mas5 format - + + + Marked as obsolete by Allyson Lister. + 0.4 + The original label for this class, 'Clustering algorithm', was used in two separate class URIs. The first was SWO_0000500, initially created within the originalsoftwareontology.owl. The second URI is stored within swo_algorithms.owl and is an import from OntoDM (OntoDM_170075). As the SWO class contains no annotation beyond its label, and because OntoDM has more structure surrounding its algorithm classes, the OntoDM class was retained and the SWO class was deemed obsolete. The 6 usages of the SWO class were refactored to reference the OntoDM term and then the SWO class was marked as obsolete. Please use OntoDM_170075 instead. + obsolete_Clustering algorithm + true - + - - matchprobes - + + - - - - - - - - - - - - - - - + + - + - - - - + + + + + + - - - - - - - - - - - Basic infrastructure for using oligonucleotide microarray reporter sequence information for preprocessing and quality assessment. For general work with genomic sequences, this package is inadequate. Please refer to the Biostrings package for that. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/matchprobes.html - - - - - - - - mdqc - - - - - - - - - - + - - + + @@ -69238,133 +69375,135 @@ tiple samples - - - - - - - + - - + + + + - MDQC is a multivariate quality assessment method for microarrays based on quality control (QC) reports. The Mahalanobis distance of an array's quality attributes is used to measure the similarity of the quality of that array against the quality of the other arrays. Then, arrays with unusually high distances can be flagged as potentially low-quality. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/mdqc.html + This packages allow reading into R of Codelink bioarray data exported as text from the Codelink software. Also includes some functions to ease the manipulation and pre-processing of data, such in background correction and normalization. + http://bioconductor.org/packages/2.4/bioc/html/codelink.html + Nandini Badarinarayan + 'codelink' - + - - M-estimation regression - + + + dataset comparison - + - - metaArray - - - - - - - + + + Concordance + + + + + + + + - - + + - + - - - - - - - - - + + + + - - + + + + + + + - - + + - 1) Data transformation for meta-analysis of microarray Data: Transformation of gene expression data to signed probability scale (MCMC/EM methods) 2) Combined differential expression on raw scale: Weighted Z-score after stabilizing mean-variance relation within platform - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/metaArray.html + Define coerce methods for microarray data objects. + http://bioconductor.org/packages/2.4/bioc/html/convert.html + Nandini Badarinarayan + convert - - - - Meta data - - - - - - + - - metahdep - + + - - + + + + + + + + + - - + + - - + + + + + + + - + - + - - + + @@ -69373,168 +69512,247 @@ tiple samples - - + + + + + + + + + + + + + + + - Nandini Badarinarayan - Tools for meta-analysis in the presence of hierarchical (and/or sampling) dependence, including with gene expression studies - http://bioconductor.org/packages/2.4/bioc/html/metahdep.html + COPA is a method to find genes that undergo recurrent fusion in a given cancer type by finding pairs of genes that have mutually exclusive outlier profiles. + http://bioconductor.org/packages/2.4/bioc/html/copa.html + Nandini Badarinarayan + copa - + - - miRNApath - + + - - + + - - + + - + - - - - - - - - - + + + + + + + + + + + - - + + + + + + + + + + + + + + + + + - - + + - - + + - Nandini Badarinarayan - This package provides pathway enrichment techniques for miRNA expression data. Specifically, the set of methods handles the many-to-many relationship between miRNAs and the multiple genes they are predicted to target (and thus affect.) It also handles the gene-to-pathway relationships separately. Both steps are designed to preserve the additive effects of miRNAs on genes, many miRNAs affecting one gene, one miRNA affecting multiple genes, or many miRNAs affecting many genes. - http://bioconductor.org/packages/2.4/bioc/html/miRNApath.html + cosmo searches a set of unaligned DNA sequences for a shared motif that may, for example, represent a common transcription factor binding site. The algorithm is similar to MEME, but also allows the user to specify a set of constraints that the position weight matrix of the unknown motif must satisfy. Such constraints may include bounds on the information content across certain regions of the unknown motif, for example, and can often be formulated on the basis of prior knowledge about the structure of the transcription factor in question. The unknown motif width, the distribution of motif occurrences (OOPS, ZOOPS, or TCM), as well as the appropriate constraint set can be selected data-adaptively. + http://bioconductor.org/packages/2.4/bioc/html/cosmo.html + Nandini Badarinarayan + cosmo - + - - microRNA - + + + + + + + + + + + + + + - + - - + + + + + + + + + - - + + + + + + + + + + + + + + + + + - - + + - - - - - - - + + - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/microRNA.html, accessed 28 May 2013. - microRNA is a software package which provides data resources for microRNAs and various functions for manipulating them. - Allyson Lister + cosmoGUI allows the user to interactively define constraint sets that can be used by the cosmo package to supervise the search for shared motifs in a set of DNA sequences. The constraints can be either adapted from a set of commonly used templates or defined from scratch. + http://bioconductor.org/packages/2.4/bioc/html/cosmoGUI.html + Nandini Badarinarayan + cosmoGUI - + - - obsolete_Microarray data - - true - Obsoleted after the 0.4 release. - Equivalent to EDAM class data_2603. - Marked as obsolete by Allyson Lister. + + + covdesc file - + + + + + An objective in which the aim is to create a new database instance. + PERSON: James Malone + James Malone + database creation + + - - minet - + + + + + - - - - - - - - - + + + + + + + + - - + + + + + + + + + + + + + + - + - - - + + + + + @@ -69542,142 +69760,114 @@ tiple samples - - + + - - + + - Nandini Badarinarayan - This package implements various algorithms for inferring mutual information networks from data. All the algorithms compute the mutual information matrix in order to infer a network. Several mutual information estimators are implemented. - http://bioconductor.org/packages/2.4/bioc/html/minet.html - - - - - - - - mrnet algorithm - - - - - - - - - Multinomial probit regression with Gaussian Process priors - - - - - - - - - Multiple testing - - multiple testing which includes controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). Tests based on a variety of t- and F-statistics (including t-statistics based on regression parameters from linear and survival models as well as those based on correlation parameters) are included. - - - - - - - - Multivariate t mixture models - + Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 6.0. + http://bioconductor.org/packages/2.4/bioc/html/crlmm.html + Nandini Badarinarayan + crlmm - + - - multtest - + + - - + + - - + + - - + + - + - - - - + + + + + + + + + + + + + + + + + - - - - - - - - + + - Nandini Badarinarayan - Resampling-based multiple hypothesis testing - http://bioconductor.org/packages/2.4/bioc/html/multtest.html + Tools for export and import classification trees and clusters to other programs + http://bioconductor.org/packages/2.4/bioc/html/ctc.html + Nandini Badarinarayan + ctc - + - - Negative binomial distribution - + + + + + + + + + Analysis and visualization of gene expression and SNP microarrays + http://www.bioinformatics.org/dchip/ + Nandini Badarinarayan + dChip - + - - nem - - - - - - - + + - + - - - + + @@ -69685,341 +69875,332 @@ tiple samples - - + + + + + + + + + + + + + + + + + + + - - + + - - + + - Nandini Badarinarayan - Nested Effects Models to reconstruct phenotypic hierarchies - http://bioconductor.org/packages/2.4/bioc/html/nem.html + This package contains functions for the efficient design of factorial two-colour microarray experiments and for the statistical analysis of factorial microarray data. + http://bioconductor.org/packages/2.4/bioc/html/daMA.html + Nandini Badarinarayan + daMA - + - - Neural networks models - + + + .data - + - - obsolete_newick - - true - Marked as obsolete by Allyson Lister - Equivalence with EDAM format_1910. - Obsoleted after the 0.4 release. + + + debian control file format + dcf - + - - nnNorm - - - - - - - - - - - - - - - - - - - - - - - - + + + design file + + + + + + + + - - + + - - + + - - + + - - + + + + + + + + + - Nandini Badarinarayan - This package allows to detect and correct for spatial and intensity biases with two-channel microarray data. The normalization method implemented in this package is based on robust neural networks fitting. - http://bioconductor.org/packages/2.4/bioc/html/nnNorm.html + Analyze microarray data + http://bioconductor.org/packages/2.4/bioc/html/diffGeneAnalysis.html + Nandini Badarinarayan + 'diffGeneAnalysis' - + - - nudge - - - - - - - - - - - - + + - - + + - - + + - - + + - - + + - - - - - - - + + - Nandini Badarinarayan - Package for normalizing microarray data in single and multiple replicate experiments and fitting a normal-uniform mixture to detect differentially expressed genes in the cases where the two samples are being compared directly or indirectly (via a common reference sample) - http://bioconductor.org/packages/2.4/bioc/html/nudge.html + Find significantly enriched gene classifications in a list of functionally undescribed genes based on their InterPro domain structure. + http://bioconductor.org/packages/2.4/bioc/html/domainsignatures.html + Nandini Badarinarayan + 'domainsignatures' - + - - occugene - + + - - + + + + + + + + + - - + + - - + + - + - - - - + + + + + + - + - - - - + + + + + + - Nandini Badarinarayan - Statistical tools for building random mutagenesis libraries for prokaryotes. The package has functions for handling the occupancy distribution for a multinomial and for estimating the number of essential genes in random transposon mutagenesis libraries. - http://bioconductor.org/packages/2.4/bioc/html/occugene.html + This package implements a Kolmogorov Smirnov rank-sum based algorithm for training and classification of gene expression data sets. One of the chief strengths of this approach is that it is amenable to the "multiclass" problem. That is, it can discriminate between more than 2 classes. + http://bioconductor.org/packages/2.4/bioc/html/dualKS.html + Nandini Badarinarayan + 'dualKS' - + - - oligo - + + - - + + - - + + - + - - - - + + + + + + + + + + + + + + + - - - - - - - - - - - - - - + + - + - - - - + + + + + + + - A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/oligo.html - - - - - - - - oligoClasses - - - + + - Nandini Badarinarayan - This package contains class definitions, validity checks, and initialization methods for classes used by the oligo package. - http://bioconductor.org/packages/2.4/bioc/html/oligoClasses.html + Gene-specific dye-bias correction of two-color microarray data using the GASSCO method + http://bioconductor.org/packages/2.4/bioc/html/dyebias.html + Nandini Badarinarayan + dyebias - + - - OMICS data - + + + Dynamic programming algorithm - + - - oneChannelGUI - + + - - + + - - + + - + - - + - - + + @@ -70028,134 +70209,100 @@ tiple samples - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - - - - - - - - - - - + + - Nandini Badarinarayan - This package was developed to simplify the use of Bioconductor tools for beginners having limited or no experience in writing R code. This library provides a graphical interface allowing QC, filtering, statistical validation, and alternative splicing analysis. - http://bioconductor.org/packages/2.4/bioc/html/oneChannelGUI.html + Meta-data and tools to work with E. coli. The tools are mostly plotting functions to work with circular genomes. They can used with other genomes/plasmids. + http://bioconductor.org/packages/2.4/bioc/html/ecolitk.html + Nandini Badarinarayan + ecolitk - + - - ontoTools - + + - - + + - + - - + + - - + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/ontoTools.html - tools for working with ontologies and graphs - - - - - - - - pair file - + This package provides tools for evaluating cohort distributions of gene expression levels + http://bioconductor.org/packages/2.4/bioc/html/edd.html + Nandini Badarinarayan + edd - + - - pamr - + + - + - - - - - + + @@ -70163,94 +70310,107 @@ tiple samples - - + + - - + + - - - - - - - - + + + + + + + + + - - + + - Nandini Badarinarayan - Some functions for sample classification in microarrays - http://bioconductor.org/packages/2.4/bioc/html/pamr.html + Estimation and Testing for Differential Expression in Multiple Digital Gene Expression Libraries. + http://bioconductor.org/packages/2.4/bioc/html/edgeR.html + Nandini Badarinarayan + 'edgeR' - + - - panp - + + - - + + + + + + + + + - - + + - + - - - - - - + + + + - - + + + + + + + + + + + + + + + + - + - + - - - - - - - - - + + @@ -70259,148 +70419,108 @@ tiple samples - - - - - - - - - + + + + + + + + - A function to make gene presence/absence calls based on distance from negative strand matching probesets (NSMP) which are derived from Affymetrix annotation. PANP is applied after gene expression values are created, and therefore can be used after any preprocessing method such as MAS5 or GCRMA, or PM-only methods like RMA. NSMP sets have been established for the HGU133A and HGU133-Plus-2.0 chipsets to date. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/panp.html + This package provides fine grained annotation of Affymetrix exon arrays, including mappings between the array probes and probesets and the Ensembl exons, transcripts and genes they target. + http://bioconductor.org/packages/2.4/bioc/html/exonmap.html + Nandini Badarinarayan + exonmap - + - - parody - + + - - + + - - - - - - - + + - - + + - + - - - - - + + - Nandini Badarinarayan - Routines for univariate and multivariate outlier detection with a focus on parametric methods, but support for some methods based on resistant statistics - http://bioconductor.org/packages/2.4/bioc/html/parody.html + This package explores and analyzes *omics data with R and GGobi + http://bioconductor.org/packages/2.4/bioc/html/explorase.html + Nandini Badarinarayan + 'explorase' - + - - parse - + + + + + + + + + Basic class definitions and generics for external pointer based vector objects for R. A simple in-memory implementation is also provided + http://bioconductor.org/packages/2.4/bioc/html/externalVector.html + Nandini Badarinarayan + 'externalVector' - + - - pathRender - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Nandini Badarinarayan - build graphs from pathway databases, render them by Rgraphviz - http://bioconductor.org/packages/2.4/bioc/html/pathRender.html + + + f-test - + - - pcaMethods - + + - - - - - - - + - - - - + + + + @@ -70408,24 +70528,37 @@ tiple samples - - + + - - + + + + + + + + + + + + + + - + - - + + + @@ -70433,117 +70566,89 @@ tiple samples - - - - - - - + + - A cluster based method for missing value estimationn is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA on incomplete data as well as for accurate missing value estimation. A set of methods for printing and plotting the results is also provided. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/pcaMethods.html + This package provides a set of tools for analyzing data from a factorial designed microarray experiment, or any microarray experiment for which a linear model is appropriate. The functions can be used to evaluate tests of contrast of biological interest and perform single outlier detection. + http://bioconductor.org/packages/2.4/bioc/html/factDesign.html + Nandini Badarinarayan + factDesign - + - - pcot2 - + + - - + + + + + + + + + - - + + - + - - - - - - - - - + + + + - - + + + + + + + - - + + - Nandini Badarinarayan - PCOT2 is a permutation-based method for investigating changes in the activity of multi-gene networks. It utilizes inter-gene correlation information to detect significant alterations in gene network activities. Currently it can be applied to two-sample comparisons. - http://bioconductor.org/packages/2.4/bioc/html/pcot2.html - - - - - - - - obsolete_pdf - - true - Marked as obsolete by Allyson Lister. - 0.4 - SWO_0000652 was initially created within the originalsoftwareontology.owl and later moved to swo_data.owl. SWO_3000015 is also present and stored within swo_data.owl. SWO_3000015 was retained and SWO_0000652 deemed obsolete, as SWO_3000015 has a better location in the hierarchy. All axioms belonging to SWO_0000652 were transferred to SWO_3000015. Please use SWO_3000015 instead. + This package implements a broad class of Family Based Association Tests for genetids data, with adjustments for population admixture using the code from the 'FBAT' software program + http://bioconductor.org/packages/2.4/bioc/html/fbat.html + Nandini Badarinarayan + fbat - + - - pdInfoBuilder - - - - - - - + + - + - - - - - - - - - - - - - + + @@ -70551,45 +70656,59 @@ tiple samples - - + + + + + + + + + + + + + + + + + + + - - + + - - + + - Builds platform design information packages. These consist of a SQLite database containing feature-level data such as x, y position on chip and featureSet ID. The database also incorporates featureSet-level annotation data. The products of this packages are used by the oligo pkg. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/pdInfoBuilder.html + This package contains two main functions. The first is fdr.ma which takes normalized expression data array, experimental design and computes adjusted p-values It returns the fdr adjusted p-values and plots, according to the methods described in (Reiner, Yekutieli and Benjamini 2002). The second, is fdr.gui() which creates a simple graphic user interface to access fdr.ma + http://bioconductor.org/packages/2.4/bioc/html/fdrame.html + Nandini Badarinarayan + fdrame - + - - pdmclass - + + - + - - - - - + + @@ -70597,136 +70716,175 @@ tiple samples - - + + - - + + + + + + + + + + + + + + - - + + + + + + + + + + + + - - + + - - + + - Nandini Badarinarayan - This package can be used to classify microarray data using one of three penalized regression methods; partial least squares, principal components regression, or ridge regression. - http://bioconductor.org/packages/2.4/bioc/html/pdmclass.html - - - - - - - - pedigree data file - + Fragment-level analysis of gas chromatography - mass spectrometry metabolomics data + http://bioconductor.org/packages/2.4/bioc/html/flagme.html + Nandini Badarinarayan + flagme - + - - pgUtils - + + - - + + + + + + + + + + - - + + - + - - + + + + + + + + + - - + + + + + + + + + + + + - - + + - Functions for creating PostgreSQL database tables, with auto incrementing primary keys, selection of foreign keys to allow referencial integrity and a logging mechanism. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/pgUtils.html + Robust model-based clustering using a t-mixture model with Box-Cox transformation. Note: users should have GSL installed + http://bioconductor.org/packages/2.4/bioc/html/flowClust.html + Nandini Badarinarayan + flowClust - + - - pickgene - - - - - - - + + - - + + - + - - - - - - + + + + + + + + + + + - + - - - + + + + + @@ -70734,88 +70892,106 @@ tiple samples - - - - - - - - - - - - - + + - Functions to Analyze Microarray (Gene Expression) Data. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/pickgene.html + This package provides S4 data structures and basic functions to deal with flow cytometry data. + http://bioconductor.org/packages/2.4/bioc/html/flowCore.html + Nandini Badarinarayan + flowCore - + - - pkgDepTools - + + - - + + - - + + + + + + + - + - - + + - - + + + + + + + + + + + + + + + - Nandini Badarinarayan - This package provides tools for computing and analyzing dependency relationships among R packages. It provides tools for building a graph-based representation of the dependencies among all packages in a list of CRAN-style package repositories. There are also utilities for computing installation order of a given package. If the RCurl package is available, an estimate of the download size required to install a given package and its dependencies can be obtained. - http://bioconductor.org/packages/2.4/bioc/html/pkgDepTools.html + FlowJo is a commercial GUI based software package from TreeStar Inc. for the visualization and analysis of flow cytometry data. One of the FlowJo standard export file types is the "FlowJo Workspace". This is an XML document that describes files and manipulations that have been performed in the FlowJo GUI environment. This package can take apart the FlowJo workspace and deliver the data into R in the flowCore paradigm. + http://bioconductor.org/packages/2.4/bioc/html/flowFlowJo.html + Nandini Badarinarayan + flowFlowJo - + - - plgem - + + + + + + + + - - + + + + + + + - + - - + + @@ -70823,123 +70999,156 @@ tiple samples - - + + + This package provides quality control and quality assessment tools for flow cytometry data. + http://bioconductor.org/packages/2.4/bioc/html/flowQ.html + Nandini Badarinarayan + flowQ + + + + + + + + - - + + - - + + + + + + + - + - + - - + + - Nandini Badarinarayan - PLGEM is useful for detecting differential expression in microarray and proteomics datasets. - http://bioconductor.org/packages/2.4/bioc/html/plgem.html + + + + + + + + + + + + + This package contains methods and functionality to analyse flow data that is beyond the basic infrastructure provided by the flowCore package. + http://bioconductor.org/packages/2.4/bioc/html/flowStats.html + Nandini Badarinarayan + flowStats - + - - plier - + + + + + + + + - - + + + + + + + - - + + + + + + + - - + + - - + + - Nandini Badarinarayan - The PLIER (Probe Logarithmic Error Intensity Estimate) method produces an improved signal by accounting for experimentally observed patterns in probe behavior and handling error at the appropriately at low and high signal values. - http://bioconductor.org/packages/2.4/bioc/html/plier.html - - - - - - - - Graph plot - + This package provides utilities for flow cytometry data. + http://bioconductor.org/packages/2.4/bioc/html/flowUtils.html + Nandini Badarinarayan + flowUtils - + - - plw - + + - - + + - + - - - - - - - + + + + - + - - + + @@ -70947,15 +71156,30 @@ tiple samples - + + + + + Provides visualization tools for flow cytometry data + http://bioconductor.org/packages/2.4/bioc/html/flowViz.html + Nandini Badarinarayan + flowViz + + + + + + + + + + + - - - - - + + @@ -70963,72 +71187,31 @@ tiple samples - - - - - - - - - - - - - - + + - - + + + + + + + - Nandini Badarinarayan - Probe level Locally moderated Weighted median-t (PLW) and Locally Moderated Weighted-t (LMW). - http://bioconductor.org/packages/2.4/bioc/html/plw.html - - - - - - - - obsolete_png - - true - Marked as obsolete by Allyson Lister. - SWO_0000663 was initially created within the originalsoftwareontology.owl and later moved to swo_data.owl. SWO_3000018 is also present and stored within swo_data.owl. SWO_3000018 was retained and SWO_0000663 deemed obsolete, as SWO_3000018 has a better location in the hierarchy. All axioms belonging to SWO_0000663 were transferred to SWO_3000018 . Please use SWO_3000018 instead. - 0.4 - - - - - - - - Position weight matrix (PWM ) - - - - - - - - - ppiStats - - + - + - - + + @@ -71037,167 +71220,130 @@ tiple samples - - - - - - - - + + + + + + + + + - - + + - Nandini Badarinarayan - Tools for the analysis of protein interaction data. - http://bioconductor.org/packages/2.4/bioc/html/ppiStats.html + This package fits Rossell's generalizations of the Gamma-Gamma hierarchical model for microarray data analysis, which substantially improve the quality of the fit at a low computational cost. The model can be fit via empirical Bayes (Expectation-Maximization and Simulated Annealing) and fully Bayesian techniques (Gibbs and Metropolis-Hastings posterior sampling). + http://bioconductor.org/packages/2.4/bioc/html/gaga.html + Nandini Badarinarayan + gaga - + - - prada - - - - - - - + + - - - - - - - - - - - - + + + This package contains functions connecting R with the Gaggle + http://bioconductor.org/packages/2.4/bioc/html/gaggle.html + Nandini Badarinarayan + 'gaggle' + + + + + + + + - + - + - - - - - - + + - - - - - - - Nandini Badarinarayan - Tools for analysing and navigating data from high-throughput phenotyping experiments based on cellular assays and fluorescent detection (flow cytometry (FACS), high-content screening microscopy). - http://bioconductor.org/packages/2.4/bioc/html/prada.html + Background adjustment using sequence information + http://www.bioconductor.org/packages/2.3/bioc/html/gcrma.html + Nandini Badarinarayan + gcRMA quantification - + - - preprocessCore - - - - - - - + + - - + + - - + + - + - - + + + + + + + + + - + - - + + - A library of core preprocessing routines - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/preprocessCore.html - - - - - - - - obsolete_ps - - true - An equivalence statement is already marked for these two classes. Removed equivalence statement as the location of the obsoleted class has been changed. SWO_0000668 was initially created within the originalsoftwareontology.owl and later moved to swo_data.owl. SWO_3000024 is also present and stored within swo_data.owl. SWO_3000018 was retained and SWO_0000668 deemed obsolete, as SWO_3000024 has a better location in the hierarchy. All axioms belonging to SWO_0000668 were transferred to SWO_3000024. Please use SWO_3000024 instead. - Marked as obsolete by Allyson Lister. - 0.4 - - - - - - - - puma - - + - - + + @@ -71205,313 +71351,278 @@ tiple samples - - + + + Background adjustment using sequence information + http://bioconductor.org/packages/2.4/bioc/html/gcrma.html + Nandini Badarinarayan + gcrma + + + + + + + + + Gene Cluster Text file format + http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#GCT:_Gene_Cluster_Text_file_format_.28.2A.gct.29 + gct + + + + + + + + - - + + - - - - - - - - - + + - - - - - - - - - - - - - - + + - + - - + + + - Most analyses of Affymetrix GeneChip data are based on point estimates of expression levels and ignore the uncertainty of such estimates. By propagating uncertainty to downstream analyses we can improve results from microarray analyses. For the first time, the puma package makes a suite of uncertainty propagation methods available to a general audience. puma also offers improvements in terms of scope and speed of execution over previously available uncertainty propagation methods. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/puma.html - - - - - - - - qPCR data - + genArise is an easy to use tool for dual color microarray data. Its GUI-Tk based environment let any non-experienced user performs a basic, but not simple, data analysis just following a wizard. In addition it provides some tools for the developer. + http://bioconductor.org/packages/2.4/bioc/html/genArise.html + Nandini Badarinarayan + 'genArise' - + - - qpcrNorm - + + - - + + - - - - - - - - - + + - - + + - - + + + + + + + - - + + - Nandini Badarinarayan - The package contains functions to perform normalization of high-throughput qPCR data. Basic functions for processing raw Ct data plus functions to generate diagnostic plots are also available. - http://bioconductor.org/packages/2.4/bioc/html/qpcrNorm.html + The package takes a list of genes and predicts to which KEGG pathway each gene maps to. This is done by looking at the InterPro domains of each gene. Each prediction is assigned a confidence score. The package also allows to predict connected component membership of genes within signaling pathways. Separate models for each organism supported by KEGG can be trained. + http://bioconductor.org/packages/2.4/bioc/html/gene2pathway.html + Nandini Badarinarayan + gene2pathway - + - - qpgraph - + + - - + + - - - - - - - - - - - - + + - - + + - + - - - - - - + + + + - - + + + + + + + + + - - + + - Nandini Badarinarayan - Reverse engineering of molecular regulatory networks with qp-graphs - http://bioconductor.org/packages/2.4/bioc/html/qpgraph.html + This package contains a targeted clustering algorithm for the analysis of microarray data. The algorithm can aid in the discovery of new genes with similar functions to a given list of genes already known to have closely related functions. + http://bioconductor.org/packages/2.4/bioc/html/geneRecommender.html + Nandini Badarinarayan + geneRecommender - + - - Quantile normalization - + + + Gene array analysis algorithm - + - - Quantile regression techniques - + + + gene expression analysis - + + + + + Gene expression dataset + + - - quantsmooth - + + + + + - - + + - - + + - - - - - - - - - + + - - - - - Nandini Badarinarayan - Quantile smoothing and genomic visualization of array data - http://bioconductor.org/packages/2.4/bioc/html/quantsmooth.html - - - - - - - - qvalue - - - - - - - - - - + - - - - - - + + + + - - + + - - + + - Nandini Badarinarayan - This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values. The q-value of a test measures the proportion of false positives incurred (called the false discovery rate) when that particular test is called significant. - http://bioconductor.org/packages/2.4/bioc/html/qvalue.html + Some basic functions for filtering genes + http://bioconductor.org/packages/2.4/bioc/html/genefilter.html + Nandini Badarinarayan + genefilter - + - - rHVDM - - - - - - - + + - + - - + + + + + + + + @@ -71519,66 +71630,83 @@ tiple samples - - + + - - + + - - + + - Hidden Variable Dynamic Modeling - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/rHVDM.html + A collection of meta-analysis tools for analysing high throughput experimental data + http://bioconductor.org/packages/2.4/bioc/html/GeneMeta.html + http://bioconductor.org/packages/2.4/bioc/html/GeneMeta.html + Nandini Badarinarayan + genemeta - + - - rMAT - + + - - - - - - - - - - + + + + + + + + + + + + + + + Some basic functions for plotting genetic data + http://bioconductor.org/packages/2.4/bioc/html/geneplotter.html + Nandini Badarinarayan + geneplotter + + + + + + + + - - + + - + - + - - - - + + + + @@ -71587,86 +71715,91 @@ tiple samples - + - - - - - - - - - + + - - + + + + + + + + - Nandini Badarinarayan - R implementation from MAT program to normalize and analyze tiling arrays and ChIP-chip data. - http://bioconductor.org/packages/2.4/bioc/html/rMAT.html + Tools for operation on genomic intervals. + http://bioconductor.org/packages/2.4/bioc/html/genomeIntervals.html + Nandini Badarinarayan + genomeIntervals - + - - rama - - - - - - - - - - - - - - - - - - - - + + + Marked as obsolete by Allyson Lister. + Obsoleted after the 0.4 release. + Equivalence with EDAM format_2305. + obsolete_gff format + true + + + + + + + + + global test allows the unit of analysis of the microarray experiment to be shifted from the single gene level to the pathway level, where a ‘pathway’ may be any set of genes, e.g. chosen using the Gene Ontology database or from earlier experiments. + Global test + + + + + + + + - - + + - - + + - - - 2 + + - + - - + + + + + @@ -71674,177 +71807,110 @@ tiple samples - - - - - - - - - - - - + + - Nandini Badarinarayan - The rama package consists of several functions for robust estimation of two color microarray intensities with replicates - http://bioconductor.org/packages/2.4/bioc/html/rama.html - - - - - - - - Rank-invariant set normalization - - - - - - - - - Rank product non-parametric method - + + + + + + + Testing whether sets of genes (e.g. KEGG pathways of GO terms) are significantly associated with a clinical variable of interest. + http://bioconductor.org/packages/2.4/bioc/html/globaltest.html + Nandini Badarinarayan + globaltest - + - - .raw files - + + + gmt format - + - - rbsurv - - - - - - - - - - - - - - - - - - + + - - + + - - + + - - + + - Nandini Badarinarayan - This package selects genes associated with survival. - http://bioconductor.org/packages/2.4/bioc/html/rbsurv.html - - - - - - - - rda - - - - - - - - - reb - - - + + - + - - + + + - - - - - - - A set of functions to dentify regional expression biases - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/reb.html + The package implements methods to compare lists of genes based on comparing the corresponding 'functional profiles'. + http://bioconductor.org/packages/2.4/bioc/html/goProfiles.html + Nandini Badarinarayan + goProfiles - + - - rflowcyt - + + - - + + - - - - - - - + + - + - - + + + + + @@ -71852,188 +71918,218 @@ tiple samples - - + + - Nandini Badarinarayan - Statistical tools and data structures for analytic flow cytometry - http://bioconductor.org/packages/2.4/bioc/html/rflowcyt.html - - - - - - - - .rma format - + + + + + + + Wraper functions for description/comparison of oligo ID list using Gene Ontology database + http://bioconductor.org/packages/2.4/bioc/html/goTools.html + Nandini Badarinarayan + goTools - + - - rsbml - - - - - - - - - - - - - - + + - - + + - - + + - + - - + + - + - - + + - Nandini Badarinarayan - R support for SBML, using libsbml - http://bioconductor.org/packages/2.4/bioc/html/rsbml.html + + + + + + + Classification using generalized partial least squares for two-group and multi-group (more than 2 group) classification. + http://bioconductor.org/packages/2.4/bioc/html/gpls.html + Nandini Badarinarayan + gpls - + + + + + GenePix Pro Results file format + gpr format + + + + + - - rtracklayer - + + - - - - - - - - - - - - - - + + + + + + + + - + - - + + - - + + - - + + + + + + + + + - - + + - Nandini Badarinarayan - R interface to genome browsers and their annotation tracks - http://bioconductor.org/packages/2.4/bioc/html/rtracklayer.html + A package that implements some simple graph handling capabilities. + http://bioconductor.org/packages/2.4/bioc/html/graph.html + Nandini Badarinarayan + graph - + + + + + gtr + + + + + - - safe - + + + gxl format + + + + + + + + + Marked as obsolete by Allyson Lister. + Obsoleted after the 0.4 release. + Equivalence with EDAM data_1636. + obsolete_Heatmap + true + + + + + + + + - - - 3 + + - + + + + + + + - - - - - - - - + + + + - - + + - + - - - - - + + @@ -72041,154 +72137,178 @@ tiple samples - - - - - - - - + + - Nandini Badarinarayan - SAFE is a resampling-based method for testing functional categories is gene expression experiments. SAFE can be applied to 2-sample and multi-class comparisons, or simple linear regressions. Other experimental designs can also be accommodated through user-defined functions. - http://bioconductor.org/packages/2.4/bioc/html/safe.html + Binning and plotting functions for hexagonal bins. Now uses and relies on grid graphics and formal (S4) classes and methods. + http://bioconductor.org/packages/2.4/bioc/html/hexbin.html + Nandini Badarinarayan + hexbin - + - - sagenhaft - - - - - - - + + + Hierarchical clustering + + + + + + + + - - + + - - - - - - - + + - - + + - - + + + + + + + + + - + - - + + + + + - Nandini Badarinarayan - This package implements several functions useful for analysis of SAGE (Serial Analysis of Gene Expressen) data, i.e. extraction of a SAGE library from sequence files, sequence error correction, library comparison - http://bioconductor.org/packages/2.4/bioc/html/sagenhaft.html + The HOPACH clustering algorithm builds a hierarchical tree of clusters by recursively partitioning a data set, while ordering and possibly collapsing clusters at each level. The algorithm uses the Mean/Median Split Silhouette (MSS) criteria to identify the level of the tree with maximally homogeneous clusters. It also runs the tree down to produce a final ordered list of the elements. The non-parametric bootstrap allows one to estimate the probability that each element belongs to each cluster (fuzzy clustering). + http://bioconductor.org/packages/2.4/bioc/html/hopach.html + Nandini Badarinarayan + hopach - + - - seqLogo - + + - - + + + HTML report + + + + + + + + + Hypergeometric enrichment + + + + + + + + - - + + - - + + - + - - + + - - - - - - - + + - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/seqLogo.html - seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo + + + + + + + A package that implements some simple capabilities for representing and manipulating hypergraphs. + http://bioconductor.org/packages/2.4/bioc/html/hypergraph.html + Nandini Badarinarayan + hypergraph - + - - sigPathway - + + - - + + - + - - + + + + + @@ -72196,49 +72316,57 @@ tiple samples - - + + + + + + + + + + + + - Conducts pathway analysis by calculating the NT_k and NE_k statistics - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/sigPathway.html + Many functions for computing the NPMLE for censored and truncated data. + http://bioconductor.org/packages/2.4/bioc/html/Icens.html + Nandini Badarinarayan + Icens - + - - siggenes - - - - - - - + + - - + + - - + + + + + + + - + - - - + + @@ -72246,287 +72374,292 @@ tiple samples - - + + - Identification of differentially expressed genes and estimation of the False Discovery Rate (FDR) using both the Significance Analysis of Microarrays (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM). - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/siggenes.html + A package for plotting genomic data by chromosomal location + http://bioconductor.org/packages/2.4/bioc/html/idiogram.html + Nandini Badarinarayan + idiogram - + - - Sim method - + + + Marked as obsolete by Allyson Lister. + Obsoleted after the 0.4 release. + Equivalence with EDAM data_2968 + obsolete_Image + true - + - - simpleaffy - - - - - - - - - - - - - - - - - - - - - + + - - - - - - - - - - + + - - - - - - - - - + + - - - - - - - - - - - - - - + + - - + + - Nandini Badarinarayan - Provides high level functions for reading Affy .CEL files, phenotypic data, and then computing simple things with it, such as t-tests, fold changes and the like. Makes heavy use of the affy library. Also has some basic scatter plot functions and mechanisms for generating high resolution journal figures - http://bioconductor.org/packages/2.4/bioc/html/simpleaffy.html + Imputation for microarray data (currently KNN only) + http://bioconductor.org/packages/2.4/bioc/html/impute.html + Nandini Badarinarayan + impute - + - - simulatorAPMS - + + - - + + - - + + - - + + - + - - + + - - - - - - - Functions to computationally simulate the AP-MS technology based on wet-lab data. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/simulatorAPMS.html + The iterative Bayesian Model Averaging (BMA) algorithm is a variable selection and classification algorithm with an application of classifying 2-class microarray samples, as described in Yeung, Bumgarner and Raftery (Bioinformatics 2005, 21: 2394-2402). + http://bioconductor.org/packages/2.4/bioc/html/iterativeBMA.html + Nandini Badarinarayan + iterativeBMA - + - - sizepower - + + - - - - - - - - - - + + - - - - - - - + + - + - - + + - - + + - - + + - Nandini Badarinarayan - This package has been prepared to assist users in computing either a sample size or power value for a microarray experimental study. The user is referred to the cited references for technical background on the methodology underpinning these calculations. This package provides support for five types of sample size and power calculations. - http://bioconductor.org/packages/2.4/bioc/html/sizepower.html + The iterative Bayesian Model Averaging (BMA) algorithm for survival analysis is a variable selection method for applying survival analysis to microarray data. + http://bioconductor.org/packages/2.4/bioc/html/iterativeBMAsurv.html + Nandini Badarinarayan + iterativeBMAsurv - + + + + + Iterative local regression and model selection + + + + + + + + + Marked as obsolete by Allyson Lister. + 0.4 + The original label for this class, .java file, was used in two separate class URIs. The first was SWO_0000585, initially created within the originalsoftwareontology.owl. The second URI is stored within swo_data.owl and is SWO_3000034. As SWO_3000034 is properly modelled as a child of 'Programming language format' this class was retained and SWO_0000585 deemed obsolete. The usages of SWO_0000585 were refactored to reference 3. SWO_3000034, and SWO_0000585 was marked as obsolete. Please use SWO_3000034 instead. + obsolete_.java file + true + + + + + + + + + Marked as obsolete by Allyson Lister. + 0.4 + SWO_0000586 (jpeg) was initially created within the originalsoftwareontology.owl and later moved to swo_data.owl. SWO_3000017, with the label 'JPEG', is also present, and stored within swo_data.owl. SWO_3000017 was retained and SWO_ 0000586 deemed obsolete, as SWO_3000017 has a better location in the hierarchy. All axioms belonging to SWO_0000586 were transferred to SWO_3000017. Please use SWO_3000017 instead. + obsolete_jpeg + true + + + + + + + + + k-cores + + + + + - - xmapbridge - + + + k-means + + + + + + + + + k-nearest neighbour classification + + + + + + + + - - + + - - - - - - - + + - - + + + + + + + - - + + - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/xmapbridge.html - xmapBridge can plot graphs in the X:Map genome browser. This package exports plotting files in a suitable format. + Test package for a pathway 'ontology' + http://bioconductor.org/packages/2.4/bioc/html/keggorth.html + Nandini Badarinarayan + keggorth - + - - snapCGH - + + - - - - - - - - - + + + + + + + + - + + + + + + + - + - - + + @@ -72535,56 +72668,66 @@ tiple samples - - + + - - + + + lapmix is a software package for the identification of differentially expressed genes. A hierarchical Bayesian approach is used, and the hyperparameters are estimated using empirical Bayes. + http://bioconductor.org/packages/2.4/bioc/html/lapmix.html + Allyson Lister + Nandini Badarinarayan + lapmix + + + + + + + + + Likelihood method + + + + + + + + - - + + - - + + - Methods for segmenting, normalising and processing aCGH data; including plotting functions for visualising raw and segmented data for individual and multiple arrays. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/snapCGH.html - - - - - - - - snpMatrix - - - + + - + - + - - + + @@ -72593,66 +72736,57 @@ tiple samples - - - - - - - + + - - + + + Data analysis, linear models and differential expression for microarray data. + http://bioconductor.org/packages/2.4/bioc/html/limma.html + Nandini Badarinarayan + limma + + + + + + + + - - - - - - - - - + + - - + + - Implements classes and methods for large-scale SNP association studies - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/snpMatrix.html - - - - - - - - spikeLI - - - + + - + - - + + + + + @@ -72660,105 +72794,91 @@ tiple samples - - + + - - - - - - - - - - - - - Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/spikeLI.html + A Graphical User Interface for the limma Microarray package + http://bioconductor.org/packages/2.4/bioc/html/limmaGUI.html + Nandini Badarinarayan + limmaGUI - + - - spkTools - - - - - - - - - - - - - - - - - - - - + + + Linear modelling + + + + + + + + + lma + + + + + + + + + Local-pooled-error + + + + + + + + + log file + + + + + + + + - - - - - - - - - + + - - + + - Nandini Badarinarayan - The package contains functions that can be used to compare expression measures on different array platforms. - http://bioconductor.org/packages/2.4/bioc/html/spkTools.html - - - - - - - - splicegear - - + - - + + - + - + - - + + @@ -72767,264 +72887,244 @@ tiple samples - - - - - - - - + + - A set of tools to work with alternative splicing - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/splicegear.html + Identification of interactions between binary variables using Logic Regression. Can, e.g., be used to find interesting SNP interactions. Contains also a bagging version of logic regression for classification. + http://bioconductor.org/packages/2.4/bioc/html/logicFS.html + Nandini Badarinarayan + logicFS - + - - splots - - - - - - - - - - - - - + + + logicFS dataset + + + + + + + + - - + + + + + + + + + - - + + - + - - + + + + + + + + + - Nandini Badarinarayan - The splots package provides the plotScreen function for the visualization of for high-throughput assays in microtitre plate or chamber slide format. - http://bioconductor.org/packages/2.4/bioc/html/splots.html - - - - - - - - spotSegmentation - - + - - + + - - - - - - - - - - - - - - - - - - - - + + - - + + - Nandini Badarinarayan - Spot segmentation via model-based clustering and gridding for blocks within microarray slides - http://bioconductor.org/packages/2.4/bioc/html/spotSegmentation.html - - - - - - - - sproc - + The logitT library implements the Logit-t algorithm introduced in --A high performance test of differential gene expression for oligonucleotide arrays-- by William J Lemon, Sandya Liyanarachchi and Ming You for use with Affymetrix data stored in an AffyBatch object in R. + http://bioconductor.org/packages/2.4/bioc/html/logitT.html + Nandini Badarinarayan + logitT - + - - sqlite - + + + Logit-t algorithm - + - - sscore - + + - - + + - - + + - - - - - - - + + - - + + + + + + + - - + + - Nandini Badarinarayan - This package contains an implementation of the S-Score algorithm - http://bioconductor.org/packages/2.4/bioc/html/sscore.html + The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. + http://bioconductor.org/packages/2.4/bioc/html/lumi.html + Nandini Badarinarayan + lumi - + - - ssize - + + - - - - - - - - - - - - + + - + - - + + + + + + + + + - - + + - - - - - - - - + + + + + + + + + + - - + + - Functions for computing and displaying sample size information for gene expression arrays. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/ssize.html + Graphically displays correlation in microarray data that is due to insufficient normalization + http://bioconductor.org/packages/2.4/bioc/html/maCorrPlot.html + Nandini Badarinarayan + maCorrPlot - + - - stam - + + + + + + + + - + + + + + + + - - + + + + + @@ -73032,12 +73132,12 @@ tiple samples - + - - + + @@ -73045,104 +73145,89 @@ tiple samples - - - - - - - - + + - Nandini Badarinarayan - The stam package performs a biologically structured classification of microarray profiles according to clinical phenotypes. GO terms are used to link classification results to biological aspects. - http://bioconductor.org/packages/2.4/bioc/html/stam.html - - - - - - - - Statistical tests - - A statistical test is an algorithm for making quantitative decisions to determine which outcomes of a study would lead to a rejection of the null hypothesis for a pre-specified level of significance. - Modified from http://en.wikipedia.org/wiki/Statistical_test, accessed 9 May 2013; http://www.itl.nist.gov/div898/handbook/prc/section1/prc13.htm, accessed 9 May 2013. + maDB allows to create a simple microarray database to store microarray experiments and annotation data into it. Affymetrix GeneChip expression values as well as values from two color microarrays can be stored into the database. Whole experiments or subsets from a experiment (or also values for a subset of genes in a subset of microarrays) can be fetched back to R. Additionally maDB provides different utility functions for the microarray data analysis like functions to draw MA plots or volcano plots with the data points color coded according to the local point density or functions that allow a replicate handling of miroarrays. + http://bioconductor.org/packages/2.4/bioc/html/maDB.html + Nandini Badarinarayan + maDB - + - - stepNorm - + + - - + + + + + + + + + - - + + - - + + - - + + + + + + + + + + - Nandini Badarinarayan - Stepwise normalization functions for cDNA microarray data. - http://bioconductor.org/packages/2.4/bioc/html/stepNorm.html - - - - - - - - 't-test' - + + + + + + + maSigPro is a regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray experiments. + http://bioconductor.org/packages/2.4/bioc/html/maSigPro.html + Nandini Badarinarayan + maSigPro - + - - tilingArray - - - - - - - - - - - - + + - + - - - + + + + @@ -73150,173 +73235,177 @@ tiple samples - - + + - - + + + + + + + + + - + - - - - - + + + + + + + + + + + + + + + - Nandini Badarinarayan - Transcript mapping with high-density oligonucleotide tiling arrays - http://bioconductor.org/packages/2.4/bioc/html/tilingArray.html + Analysis of N-dye Micro Array experiment using mixed model effect. Containing anlysis of variance, permutation and bootstrap, cluster and consensus tree. + http://bioconductor.org/packages/2.4/bioc/html/maanova.html + Nandini Badarinarayan + maanova - + - - timecourse - + + - - + + + + + + + + + + - - + + - - + + - - + + + + + + + + + - + - - - - + + + + + + + + - Functions for data analysis and graphical displays for developmental microarray time course data. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/timecourse.html + This library contains functions to investigate links between differential gene expression and the chromosomal localization of the genes. MACAT is motivated by the common observation of phenomena involving large chromosomal regions in tumor cells. MACAT is the implementation of a statistical approach for identifying significantly differentially expressed chromosome regions. The functions have been tested on a publicly available data set about acute lymphoblastic leukemia (Yeoh et al.Cancer Cell 2002), which is provided in the library 'stjudem'. + Nandini Badarinarayan + macat - + - - tkWidgets - + + - - + + - Nandini Badarinarayan - Widgets to provide user interfaces. tcltk should have been installed for the widgets to run. - http://bioconductor.org/packages/2.4/bioc/html/tkWidgets.html - - - - - - - - topGO - - - + + - - + + - + - - - - + + + + + + - - - - - - - - - - - - - - - - - - - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/topGO.html - topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied. + Multivariate data analysis and graphical display of microarray data. Functions include between group analysis and coinertia analysis. It contains functions that require ADE4. + http://bioconductor.org/packages/2.4/bioc/html/made4.html + Nandini Badarinarayan + made4 - + - - tspair - + + - + - - - - - + + @@ -73324,410 +73413,308 @@ tiple samples - - - - - - - - - - - - - - + + - + - - + + + + - Nandini Badarinarayan - Top Scoring Pairs for Microarray Classification - http://bioconductor.org/packages/2.4/bioc/html/tspair.html - - - - - - - - twilight - - + - - - - - + + + + This package uses functions of various other packages together with other functions in a coordinated way to handle and analyse cDNA microarray data + http://bioconductor.org/packages/2.4/bioc/html/maigesPack.html + Nandini Badarinarayan + maigesPack + + + + + + + + - - - - - - - - + + - + - - - - - - + + + + + + + + + + + + - - + + + + + + + - - + + - Estimation of local false discovery rate - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/twilight.html - - - - - - - - Two-stage measurement error model - + makePlatformDesign creates the Platform Design environments (PDenvs) required by oligo. + http://bioconductor.org/packages/2.4/bioc/html/makePlatformDesign.html + Nandini Badarinarayan + makePlatformDesign - + - - vbmp - + + - - + + - + - - + + + + + + + + + - + - - - - - - - - - + + + + - - - - - - - - - - - - - - + + - Nandini Badarinarayan - Variational Bayesian Multinomial Probit Regression with Gaussian Process Priors. It estimates class membership posterior probability employing variational and sparse approximation to the full posterior. This software also incorporates feature weighting by means of Automatic Relevance Determination. - http://bioconductor.org/packages/2.4/bioc/html/vbmp.html - - - - - - - - data visualization - + This package has two functions. One reads a Affymetrix chip description file (CDF) and creates a hash table environment containing the location/probe set membership mapping. The other creates a package that automatically loads that environment. + http://bioconductor.org/packages/2.4/bioc/html/makecdfenv.html + Nandini Badarinarayan + makecdfenv - + - - vsn - + + - - + + - - + + - + - - - + + - Nandini Badarinarayan - The package implements a method for normalising microarray intensities, both between colours within array, and between arrays. The method uses a robust variant of the maximum-likelihood estimator for the stochastic model of microarray data described in the references - http://bioconductor.org/packages/2.4/bioc/html/vsn.html - - - - - - - - weaver - - - - - - - - + - - - - + + + + + + + + + + + + + + - - + + - - - - - - - + + - Nandini Badarinarayan - This package provides enhancements on the Sweave() function in the base package. In particular a facility for caching code chunk results is included. - http://bioconductor.org/packages/2.4/bioc/html/weaver.html + Class definitions for two-color spotted microarray data. Fuctions for data input, diagnostic plots, normalization and quality checking. + http://bioconductor.org/packages/2.4/bioc/html/marray.html + Nandini Badarinarayan + marray - + - - webbioc - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - An integrated web interface for doing microarray analysis using several of the Bioconductor packages. It is intended to be deployed as a centralized bioinformatics resource for use by many users. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/webbioc.html + + + 'MAS5' - + - - widgetTools - - - - - - - - - - - - - - Nandini Badarinarayan - This packages contains tools to support the construction of tcltk widgets - http://bioconductor.org/packages/2.4/bioc/html/widgetTools.html + + + mas5 format - + - - xcms - + + - - + + - + - - + + + + + + + + + + - - + + + + + + + - - + + - Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, and mzData files. Preprocesses data for high-throughput, untargeted analyte profiling. - Nandini Badarinarayan - http://bioconductor.org/packages/2.4/bioc/html/xcms.html + Basic infrastructure for using oligonucleotide microarray reporter sequence information for preprocessing and quality assessment. For general work with genomic sequences, this package is inadequate. Please refer to the Biostrings package for that. + http://bioconductor.org/packages/2.4/bioc/html/matchprobes.html + Nandini Badarinarayan + matchprobes - + - - xps - - - - - - - - - - - - + + - + - - - - + + @@ -73735,18 +73722,18 @@ tiple samples - - + + - + - - + + @@ -73754,139 +73741,120 @@ tiple samples - - + + - Nandini Badarinarayan - Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays - http://bioconductor.org/packages/2.4/bioc/html/xps.html + MDQC is a multivariate quality assessment method for microarrays based on quality control (QC) reports. The Mahalanobis distance of an array's quality attributes is used to measure the similarity of the quality of that array against the quality of the other arrays. Then, arrays with unusually high distances can be flagged as potentially low-quality. + http://bioconductor.org/packages/2.4/bioc/html/mdqc.html + Nandini Badarinarayan + mdqc - + + + + + M-estimation regression + + - - yaqcaffy - + + + + + - - + + - - + + - - + + + + + + + + + + + + + + + + + + - Nandini Badarinarayan - Quality control of Affymetrix GeneChip expression data and reproducibility analysis of human whole genome chips with the MAQC reference datasets. - http://bioconductor.org/packages/2.4/bioc/html/yaqcaffy.html - - - - - - - - software - - - + + - Computer software, or generally just software, is any set of machine-readable instructions (most often in the form of a computer program) that conform to a given syntax (sometimes referred to as a language) that is interpretable by a given processor and that directs a computer's processor to perform specific operations. - Modified in parts from https://en.wikipedia.org/wiki/Software - Robert Stevens - James Malone - - - - - - - - software license - software license - - http://en.wikipedia.org/wiki/Software_license - A software license is a legal instrument (usually by way of contract law, with or without printed material) governing the use or redistribution of software. - James Malone + 1) Data transformation for meta-analysis of microarray Data: Transformation of gene expression data to signed probability scale (MCMC/EM methods) 2) Combined differential expression on raw scale: Weighted Z-score after stabilizing mean-variance relation within platform + http://bioconductor.org/packages/2.4/bioc/html/metaArray.html + Nandini Badarinarayan + metaArray - + - - information processing - information processing - - - Information processing is a process in which input information is analysed or transformed in order to produce information as output. - James Malone + + + Meta data - + - - Microsoft Excel 2007 - + + - - - - - - - - - - - - + + - - - - - - - - - - - - + + + + + + + + - + - + - - + + @@ -73895,32 +73863,50 @@ tiple samples - - 2007-01-30T0:00:00 + + + + + Tools for meta-analysis in the presence of hierarchical (and/or sampling) dependence, including with gene expression studies + http://bioconductor.org/packages/2.4/bioc/html/metahdep.html + Nandini Badarinarayan + metahdep + + + + + + + + + + + + - - http://office.microsoft.com/ + + - - + + - + - + - - + + @@ -73929,85 +73915,97 @@ tiple samples - - + + - - - - - - - - - - - - + + - Microsoft Excel 2007 is a spreadsheet editing and viewing tool. + This package provides pathway enrichment techniques for miRNA expression data. Specifically, the set of methods handles the many-to-many relationship between miRNAs and the multiple genes they are predicted to target (and thus affect.) It also handles the gene-to-pathway relationships separately. Both steps are designed to preserve the additive effects of miRNAs on genes, many miRNAs affecting one gene, one miRNA affecting multiple genes, or many miRNAs affecting many genes. + http://bioconductor.org/packages/2.4/bioc/html/miRNApath.html + Nandini Badarinarayan + miRNApath - + - - MATLAB - + + + + + + + + - + - - - - - - - - - + + + + - + - - - - - - - - - + + + + - - + + + microRNA is a software package which provides data resources for microRNAs and various functions for manipulating them. + http://bioconductor.org/packages/2.4/bioc/html/microRNA.html, accessed 28 May 2013. + Allyson Lister + Nandini Badarinarayan + microRNA + + + + + + + + + Marked as obsolete by Allyson Lister. + Obsoleted after the 0.4 release. + Equivalent to EDAM class data_2603. + obsolete_Microarray data + true + + + + + + + + - + - - - - - + + + @@ -74015,21 +74013,24 @@ tiple samples - - + + - + + + + + + + - - - - - + + @@ -74037,302 +74038,370 @@ tiple samples - - http://www.mathworks.com/products/matlab/ + + - MATLAB® is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran - Nandini Badarinarayan - http://www.mathworks.com/products/matlab/?s_cid=SA_trafrefpai_MLipspot_Doc_bioinfo_MATLAB + This package implements various algorithms for inferring mutual information networks from data. All the algorithms compute the mutual information matrix in order to infer a network. Several mutual information estimators are implemented. + http://bioconductor.org/packages/2.4/bioc/html/minet.html + Nandini Badarinarayan + minet - + - - Protege 4 - + + + mrnet algorithm + + + + + + + + + Multinomial probit regression with Gaussian Process priors + + + + + + + + + multiple testing which includes controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). Tests based on a variety of t- and F-statistics (including t-statistics based on regression parameters from linear and survival models as well as those based on correlation parameters) are included. + Multiple testing + + + + + + + + + Multivariate t mixture models + + + + + + + + - - - - - - - - - - - - + + - - - - - - - - - - - - + + - - + + - + - - - - - - - - - + + + + - - http://protege.stanford.edu/ + + - - - - - - - - - - - - + + + Resampling-based multiple hypothesis testing + http://bioconductor.org/packages/2.4/bioc/html/multtest.html + Nandini Badarinarayan + multtest + + + + + + + + + Negative binomial distribution + + + + + + + + - - + + - - - - - - - - - - - - + + - - - - - - - - - - - - + + + + + + + + - + - - - - - + + + + Nested Effects Models to reconstruct phenotypic hierarchies + http://bioconductor.org/packages/2.4/bioc/html/nem.html + Nandini Badarinarayan + nem + + + + + + + + + Neural networks models + + + + + + + + + Marked as obsolete by Allyson Lister + Obsoleted after the 0.4 release. + Equivalence with EDAM format_1910. + obsolete_newick + true + + + + + + + + + + + + + + + + + + + + + + + + + + - + - - + + + - - + + - + - - + + + + + + + + + This package allows to detect and correct for spatial and intensity biases with two-channel microarray data. The normalization method implemented in this package is based on robust neural networks fitting. + http://bioconductor.org/packages/2.4/bioc/html/nnNorm.html + Nandini Badarinarayan + nnNorm - + - - OmniOutliner - + + - - - - - - - - - - - - + + - - + + - + - - - - - - - - - + + + + - - http://www.omnigroup.com/products/omnioutliner/ + + + + + + + - - + + - - - - - - - - - - - - + + - OmniOutliner is commercial outlining software for Mac OS X produced by The Omni Group + Package for normalizing microarray data in single and multiple replicate experiments and fitting a normal-uniform mixture to detect differentially expressed genes in the cases where the two samples are being compared directly or indirectly (via a common reference sample) + http://bioconductor.org/packages/2.4/bioc/html/nudge.html + Nandini Badarinarayan + nudge - + - - Racket - + + + + + + + + - - + + - + - - - - - - - - - + + + + - Racket is a Scheme-based language interpreter and programming environment + + + + + + + + + + + + + + + + + + Statistical tools for building random mutagenesis libraries for prokaryotes. The package has functions for handling the occupancy distribution for a multinomial and for estimating the number of essential genes in random transposon mutagenesis libraries. + http://bioconductor.org/packages/2.4/bioc/html/occugene.html + Nandini Badarinarayan + occugene - + - - Kakadu - + + - + - - - - - + + @@ -74340,79 +74409,141 @@ tiple samples - - + + - - + + + + + + + + + + + + + + - + - - - - - - - - - + + + + - - http://www.kakadusoftware.com + + + A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. + http://bioconductor.org/packages/2.4/bioc/html/oligo.html + Nandini Badarinarayan + oligo - + - - WordStar - + + - - + + + This package contains class definitions, validity checks, and initialization methods for classes used by the oligo package. + http://bioconductor.org/packages/2.4/bioc/html/oligoClasses.html + Nandini Badarinarayan + oligoClasses + + + + + + + + + OMICS data + + + + + + + + - + - + + + + + + + + + + + + + + + + + + + + + + + - - + + + + + + + + + + - + - + - + + - - + + @@ -74421,15 +74552,16 @@ tiple samples - + - - - - - + + + + + + @@ -74437,86 +74569,100 @@ tiple samples - - + + + This package was developed to simplify the use of Bioconductor tools for beginners having limited or no experience in writing R code. This library provides a graphical interface allowing QC, filtering, statistical validation, and alternative splicing analysis. + http://bioconductor.org/packages/2.4/bioc/html/oneChannelGUI.html + Nandini Badarinarayan + oneChannelGUI - + - - IntelliJ IDEA - + + - - http://www.jetbrains.com/idea/ + + - + - - - - - - - - - + + + + - - - - - - - - - + + + + + + + + + tools for working with ontologies and graphs + http://bioconductor.org/packages/2.4/bioc/html/ontoTools.html + Nandini Badarinarayan + ontoTools + + + + + + + + + pair file + + + + + + + + - - + + - - - - - - - - - - - - + + + + + + + + - + - + - - + + @@ -74525,52 +74671,57 @@ tiple samples - - + + - IntelliJ IDEA is a commercial Java IDE for developing software. - IntelliJ - - - - - - - - Java - - - http://www.java.com + + + Some functions for sample classification in microarrays + http://bioconductor.org/packages/2.4/bioc/html/pamr.html + Nandini Badarinarayan + pamr - + - - COPASI - + + - - http://www.copasi.org + + + + + + + + - + - + - - + + + + + + + + + @@ -74579,45 +74730,75 @@ tiple samples - - + + + + + + + + + - + - - - - - + + + + + + + + + A function to make gene presence/absence calls based on distance from negative strand matching probesets (NSMP) which are derived from Affymetrix annotation. PANP is applied after gene expression values are created, and therefore can be used after any preprocessing method such as MAS5 or GCRMA, or PM-only methods like RMA. NSMP sets have been established for the HGU133A and HGU133-Plus-2.0 chipsets to date. + http://bioconductor.org/packages/2.4/bioc/html/panp.html + Nandini Badarinarayan + panp - + - - Microsoft Excel 2003 - + + + + + + + + + + + + + + + + + + + - + - + - - + + @@ -74626,210 +74807,171 @@ tiple samples - - + + - Microsoft Excel 2003 is a spreadsheet editing and viewing tool. + Routines for univariate and multivariate outlier detection with a focus on parametric methods, but support for some methods based on resistant statistics + http://bioconductor.org/packages/2.4/bioc/html/parody.html + Nandini Badarinarayan + parody - + - - Microsoft Excel 2002 - - - - - - - + + + parse - + - - MATLAB 7 - + + - - + + - - - - - - - - MATLAB 6 - - - + + - - - - - - - - MATLAB 7.12 - - - + + - - - - - - - - STARLIMS - - - + + + + + + + + + + build graphs from pathway databases, render them by Rgraphviz + http://bioconductor.org/packages/2.4/bioc/html/pathRender.html + Nandini Badarinarayan + pathRender - + - - Unix - + + + + + + + + + + + + + + + + + - - + + - - + + + + + + + - - - - - - - - operating system - + - - + + - - - An operating system is a piece of software which is responsible for managing software that runs on a computer and the interactions of that software with the hardware and system resources. - - - - - - - - Linux - + - - + + + + + + + + + - - + + + A cluster based method for missing value estimationn is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA on incomplete data as well as for accurate missing value estimation. A set of methods for printing and plotting the results is also provided. + http://bioconductor.org/packages/2.4/bioc/html/pcaMethods.html + Nandini Badarinarayan + pcaMethods - - - - Microsoft Word 2001 - - - - - - + - - Adobe Illustrator 10 - + + - - + + - - - - - - - - - - - - + + - - - - - - - - - - - - + + - + - + - - + + @@ -74838,46 +74980,59 @@ tiple samples - - - - - - - - - - - - + + + PCOT2 is a permutation-based method for investigating changes in the activity of multi-gene networks. It utilizes inter-gene correlation information to detect significant alterations in gene network activities. Currently it can be applied to two-sample comparisons. + http://bioconductor.org/packages/2.4/bioc/html/pcot2.html + Nandini Badarinarayan + pcot2 + + + + + + + + + Marked as obsolete by Allyson Lister. + 0.4 + SWO_0000652 was initially created within the originalsoftwareontology.owl and later moved to swo_data.owl. SWO_3000015 is also present and stored within swo_data.owl. SWO_3000015 was retained and SWO_0000652 deemed obsolete, as SWO_3000015 has a better location in the hierarchy. All axioms belonging to SWO_0000652 were transferred to SWO_3000015. Please use SWO_3000015 instead. + obsolete_pdf + true + + + + + + + + - - - - - - - - - - - - + + - + - + + - - + + + + + + + + + @@ -74886,110 +75041,62 @@ tiple samples - - - - - - - - - - - - + + - - - - - - - - - - - - + + - - - - - - - - - - - - + + + Builds platform design information packages. These consist of a SQLite database containing feature-level data such as x, y position on chip and featureSet ID. The database also incorporates featureSet-level annotation data. The products of this packages are used by the oligo pkg. + http://bioconductor.org/packages/2.4/bioc/html/pdInfoBuilder.html + Nandini Badarinarayan + pdInfoBuilder + + + + + + + + - - - - - - - - - - - - + + - - - - - - - - - - - - + + - - - - - - - - - - - - + + - + - + - - + + @@ -74998,154 +75105,92 @@ tiple samples - - - - - - - - - - - - + + - - - - - - - - - - - - + + + This package can be used to classify microarray data using one of three penalized regression methods; partial least squares, principal components regression, or ridge regression. + http://bioconductor.org/packages/2.4/bioc/html/pdmclass.html + Nandini Badarinarayan + pdmclass + + + + + + + + + pedigree data file + + + + + + + + - - - - - - - - - - - - + + - - - - - - - - - - - - + + - + - - - - - - - - - + + + + - - - - - - - - - - - - + + - - - - - - - - - - - - + + - James Malone - Adobe Illustrator is a graphics editor for creating and editing vector graphics. + Functions for creating PostgreSQL database tables, with auto incrementing primary keys, selection of foreign keys to allow referencial integrity and a logging mechanism. + http://bioconductor.org/packages/2.4/bioc/html/pgUtils.html + Nandini Badarinarayan + pgUtils - + - - Microsoft Word - - - - - - - - - - - - - - - - - + + - + - - - - - + + @@ -75153,258 +75198,218 @@ tiple samples - - - - - - - - - - - - + + - - + + - - + + + + + + + - + - - - - - + + + - - - - - - - - software with image input - + - - - - - - - - - - - - + + - - + + Functions to Analyze Microarray (Gene Expression) Data. + http://bioconductor.org/packages/2.4/bioc/html/pickgene.html + Nandini Badarinarayan + pickgene - + - - OBO-Edit - + + - - - - - - - - - - - - + + - + - - - - - - - - - + + + + - - - - - - - - + + - - http://oboedit.org/ + + - OBO-Edit is an open source ontology editor optimized for the OBO biological ontology file format. It features an easy to use editing interface, a simple but fast reasoner, and powerful search capabilities. - OBO edit + This package provides tools for computing and analyzing dependency relationships among R packages. It provides tools for building a graph-based representation of the dependencies among all packages in a list of CRAN-style package repositories. There are also utilities for computing installation order of a given package. If the RCurl package is available, an estimate of the download size required to install a given package and its dependencies can be obtained. + http://bioconductor.org/packages/2.4/bioc/html/pkgDepTools.html + Nandini Badarinarayan + pkgDepTools - + - - ontology engineering software - + + + - - + + - - - - - - - - - - Microsoft developed software - + + + + + + + + + + + + + + - + - + - - + + - - - - - - - - - - software with command line interface - + + + + + + + + + + + + + + + - - + + - - + + PLGEM is useful for detecting differential expression in microarray and proteomics datasets. + http://bioconductor.org/packages/2.4/bioc/html/plgem.html + Nandini Badarinarayan + plgem - + - - Smultron - - - - - - - + + - - + + - - - - - - - - - - - - + + - - + + - - http://www.peterborgapps.com/smultron/ + + + The PLIER (Probe Logarithmic Error Intensity Estimate) method produces an improved signal by accounting for experimentally observed patterns in probe behavior and handling error at the appropriately at low and high signal values. + http://bioconductor.org/packages/2.4/bioc/html/plier.html + Nandini Badarinarayan + plier - + - - BLAST+ 2.2.26 - + + + Graph plot + + + + + + + + - + - - - - - + + @@ -75412,32 +75417,38 @@ tiple samples - - - - - - - - + + - - + + + + + + + + + + + + + + - + - + - - + + @@ -75446,96 +75457,80 @@ tiple samples - - ftp://ftp.ncbi.nih.gov/blast/executables/ + + + + + + + + + + - The C++ version of the command line BLAST+ tool made by the NCBI. (See also http://www.ncbi.nlm.nih.gov/books/NBK1763) - Allyson Lister - - - - - - - - Ensembl - - - - - - - - - Clustal - - - + + - http://www.clustal.org/, Accessed 13 June 2012. - Allyson Lister - Multiple alignment program for nucleic acid or protein sequences. - - - - - - - - Clustal Omega - - Allyson Lister - Clustal Omega provides improved scalability over previous Clustal versions, allowing hundreds of thousands of sequences to be aligned in a few hours. It will also make use of multiple processors, where present. In addition, the quality of alignments is superior to previous versions, as measured by a range of popular benchmarks. - http://www.clustal.org/omega/, Accessed 13 June 2012 + Probe level Locally moderated Weighted median-t (PLW) and Locally Moderated Weighted-t (LMW). + http://bioconductor.org/packages/2.4/bioc/html/plw.html + Nandini Badarinarayan + plw - + - - ClustalW - - Allyson Lister + + + Marked as obsolete by Allyson Lister. + 0.4 + SWO_0000663 was initially created within the originalsoftwareontology.owl and later moved to swo_data.owl. SWO_3000018 is also present and stored within swo_data.owl. SWO_3000018 was retained and SWO_0000663 deemed obsolete, as SWO_3000018 has a better location in the hierarchy. All axioms belonging to SWO_0000663 were transferred to SWO_3000018 . Please use SWO_3000018 instead. + obsolete_png + true - + - - ClustalX - - Allyson Lister + + + Position weight matrix (PWM ) - + - - Clustal Omega 1.1 - + + - - http://dx.doi.org/10.1038/msb.2011.75 + + + + + + + + - + - + - - + + @@ -75544,42 +75539,42 @@ tiple samples - - - - - - - - + + - Allyson Lister + Tools for the analysis of protein interaction data. + http://bioconductor.org/packages/2.4/bioc/html/ppiStats.html + Nandini Badarinarayan + ppiStats - + - - ClustalW 2.1 - + + - - http://dx.doi.org/10.1093/bioinformatics/btm404 + + - + - + + + + + - - + + @@ -75588,81 +75583,111 @@ tiple samples - - + + + + + + + + + + + + - - + + - Allyson Lister + Tools for analysing and navigating data from high-throughput phenotyping experiments based on cellular assays and fluorescent detection (flow cytometry (FACS), high-content screening microscopy). + http://bioconductor.org/packages/2.4/bioc/html/prada.html + Nandini Badarinarayan + prada - + - - ClustalX 2.1 - + + - - + + - - + + - + - - - - - - - - - + + + + - - http://dx.doi.org/10.1093/bioinformatics/btm404 + + + + + + + - Allyson Lister + + + + + + + A library of core preprocessing routines + http://bioconductor.org/packages/2.4/bioc/html/preprocessCore.html + Nandini Badarinarayan + preprocessCore - + - - EBI Clustal W2 Web Tool - + + + Marked as obsolete by Allyson Lister. + 0.4 + An equivalence statement is already marked for these two classes. Removed equivalence statement as the location of the obsoleted class has been changed. SWO_0000668 was initially created within the originalsoftwareontology.owl and later moved to swo_data.owl. SWO_3000024 is also present and stored within swo_data.owl. SWO_3000018 was retained and SWO_0000668 deemed obsolete, as SWO_3000024 has a better location in the hierarchy. All axioms belonging to SWO_0000668 were transferred to SWO_3000024. Please use SWO_3000024 instead. + obsolete_ps + true + + + + + + + + - + - - - - - + + @@ -75670,37 +75695,36 @@ tiple samples - - + + - - + + + + + + + + + + + + + + - Allyson Lister - - - - - - - - EBI Clustal Omega Web Tool - - + - - - - - + + @@ -75708,53 +75732,52 @@ tiple samples - - + + + + + + + + + - - + + - Allyson Lister + Most analyses of Affymetrix GeneChip data are based on point estimates of expression levels and ignore the uncertainty of such estimates. By propagating uncertainty to downstream analyses we can improve results from microarray analyses. For the first time, the puma package makes a suite of uncertainty propagation methods available to a general audience. puma also offers improvements in terms of scope and speed of execution over previously available uncertainty propagation methods. + http://bioconductor.org/packages/2.4/bioc/html/puma.html + Nandini Badarinarayan + puma - + - - MUSCLE - - - - - - - - Allyson Lister + + + qPCR data - + - - EBI Muscle Web Tool - + + - + - - - - - + + @@ -75762,239 +75785,309 @@ tiple samples - - + + - - + + - Allyson Lister - - - - - - - - MUSCLE 3.8.31 - - - http://www.drive5.com/muscle/downloads.htm + + - - + + + The package contains functions to perform normalization of high-throughput qPCR data. Basic functions for processing raw Ct data plus functions to generate diagnostic plots are also available. + http://bioconductor.org/packages/2.4/bioc/html/qpcrNorm.html + Nandini Badarinarayan + qpcrNorm + + + + + + + + - - http://www.drive5.com/muscle/muscle_userguide3.8.html + + + + + + + + + - - + + - - http://dx.doi.org/10.1093/nar/gkh340 + + - Allyson Lister - - - - - - - - Drive5 MUSCLE - - + - + - - + + - Allyson Lister - - - - - - - - TCoffee - - - + + - Allyson Lister + + + + + + + Reverse engineering of molecular regulatory networks with qp-graphs + http://bioconductor.org/packages/2.4/bioc/html/qpgraph.html + Nandini Badarinarayan + qpgraph - + - - CRG TCoffee - + + + Quantile normalization + + + + + + + + + Quantile regression techniques + + + + + + + + - - http://dx.doi.org/10.1006/jmbi.2000.4042 + + - Allyson Lister - TCoffee is a multiple sequence alignment program with a number of different modes. + + + + + + + + + + + + + + + + + + + + + + + + + + Quantile smoothing and genomic visualization of array data + http://bioconductor.org/packages/2.4/bioc/html/quantsmooth.html + Nandini Badarinarayan + quantsmooth - + - - EBI TCoffee Web Tool - + + + + + + + + - - + + - - + + - + - - - - - + + - - - - - - - Allyson Lister - Performs an alignment of DNA, RNA or Proteins with the standard TCoffee mode. This Web tool provides both interactive access via a Web browser and programmatic SOAP Web service access. Currently only the Web service interface is modelled in OWL. + This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values. The q-value of a test measures the proportion of false positives incurred (called the false discovery rate) when that particular test is called significant. + http://bioconductor.org/packages/2.4/bioc/html/qvalue.html + Nandini Badarinarayan + qvalue - + - - CRG RCoffee Web Tool - + + + + + + + + + + + + + + - - + + - - + + - + - - - - - + + - - - - http://dx.doi.org/10.1093/nar/gkn278 - - - Allyson Lister - Aligns RNA sequences using predicted secondary structures by accessing the RCoffee mode of the underlying TCoffee software. - http://tcoffee.crg.cat/apps/tcoffee/index.html, Accessed 19 June 2012 + Hidden Variable Dynamic Modeling + http://bioconductor.org/packages/2.4/bioc/html/rHVDM.html + Nandini Badarinarayan + rHVDM - + - - CRG TCoffee Web Tool - + + - - + + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - - - - - + + + @@ -76002,183 +76095,246 @@ tiple samples - - http://dx.doi.org/10.1093/nar/gkr245 + + - http://tcoffee.crg.cat/apps/tcoffee/index.html, Accessed 19 June 2012 - Allyson Lister - Performs an alignment of DNA, RNA or Proteins with the standard TCoffee mode. + R implementation from MAT program to normalize and analyze tiling arrays and ChIP-chip data. + http://bioconductor.org/packages/2.4/bioc/html/rMAT.html + Nandini Badarinarayan + rMAT - + - - CRG MCoffee Web Tool - + + - - + + + + + + + + + - - http://dx.doi.org/10.1093/nar/gkm333 + + - - + + - + - + - - + + - Aligns DNA, RNA or Proteins by combining the output of popular aligners and by accessing the MCoffee mode of the underlying TCoffee software. - Allyson Lister - http://tcoffee.crg.cat/apps/tcoffee/index.html, Accessed 19 June 2012 + + + + + + + + + + + + + + + + + + + + + + + 2 + + + + The rama package consists of several functions for robust estimation of two color microarray intensities with replicates + http://bioconductor.org/packages/2.4/bioc/html/rama.html + Nandini Badarinarayan + rama - + - - CRG Expresso Web Tool - + + + Rank-invariant set normalization + + + + + + + + + Rank product non-parametric method + + + + + + + + + .raw files + + + + + + + + - - http://dx.doi.org/10.1093/nar/gkl092 + + - - + + - - + + - + - - - - - - - - - + + + + - Aligns protein sequences using structural information by accessing the 3DCoffee/Expresso mode of the underlying TCoffee software. - http://tcoffee.crg.cat/apps/tcoffee/index.html, Accessed 19 June 2012 - Allyson Lister + + + + + + + This package selects genes associated with survival. + http://bioconductor.org/packages/2.4/bioc/html/rbsurv.html + Nandini Badarinarayan + rbsurv - + - - CRG PSICoffee Web Tool - + + + rda + + + + + + + + + + + + + + - - + + - + - - - - - + + - - - - - - - - - - http://dx.doi.org/10.1093/nar/gkr245 - - - Allyson Lister - http://tcoffee.crg.cat/apps/tcoffee/index.html, Accessed 19 June 2012 - Aligns distantly related proteins using homology extension (slow and accurate) by accessing the PSICoffee mode of the underlying TCoffee software. + A set of functions to dentify regional expression biases + http://bioconductor.org/packages/2.4/bioc/html/reb.html + Nandini Badarinarayan + reb - + - - CRG TCoffee 9.02.r1228 - + + - - + + - - + + + + + + + - + - - - - - + + @@ -76186,61 +76342,67 @@ tiple samples - - + + - The initial interface is via the command line. Depending on the options and inputs provided at the command line, an appropriate alignment takes place and is then presented to the user via a Graphical User Interface. - Allyson Lister + Statistical tools and data structures for analytic flow cytometry + http://bioconductor.org/packages/2.4/bioc/html/rflowcyt.html + Nandini Badarinarayan + rflowcyt - + - - Q - + + + .rma format + + + + + + + + - - + + - - + + + + + + + - - + + + + + + + - Allyson Lister - Data analysis software which performs a variety of statistical, summarising, analytical and visualization tasks. - - - - - - - - Q 4.2 - - + - - - - - + + @@ -76248,59 +76410,91 @@ tiple samples - - http://www.q-researchsoftware.com + + + R support for SBML, using libsbml + http://bioconductor.org/packages/2.4/bioc/html/rsbml.html + Nandini Badarinarayan + rsbml - + - - SPSS - + + - - + + - - + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - Allyson Lister - Data analysis software which performs a variety of statistical, summarising, analytical and visualization tasks. + + + + + + + R interface to genome browsers and their annotation tracks + http://bioconductor.org/packages/2.4/bioc/html/rtracklayer.html + Nandini Badarinarayan + rtracklayer - + - - SPSS 20.0 - + + - + - - - - - + + + + @@ -76308,49 +76502,26 @@ tiple samples - - http://www-01.ibm.com/software/uk/analytics/spss/downloads.html + + - Allyson Lister - - - - - - - - Sequence Alignment and Modeling System - - - + + - Sequence Alignment and Modeling System, a collection of flexible software tools for creating, refining, and using linear hidden Markov models for biological sequence analysis. - Allyson Lister - SAM - http://bioinformatics.org/wiki/SAM, Accessed 19 June 2012. - - - - - - - - SAM 3.5 - - + - + - - + + @@ -76359,570 +76530,498 @@ tiple samples - - + + + + + + + + 3 + + SAFE is a resampling-based method for testing functional categories is gene expression experiments. SAFE can be applied to 2-sample and multi-class comparisons, or simple linear regressions. Other experimental designs can also be accommodated through user-defined functions. + http://bioconductor.org/packages/2.4/bioc/html/safe.html + Nandini Badarinarayan + safe - + - - Cytoscape - + + - - + + - - http://dx.doi.org/10.1101/gr.1239303 + + - - + + + + + + + - http://www.cytoscape.org/what_is_cytoscape.html, Accessed June 20, 2012. - Allyson Lister - Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. - - - - - - - - Cytoscape 2.8 - - - http://www.cytoscape.org/download.html + + - + - - - - - - - - - - - - - - - - + + + + + + + + + This package implements several functions useful for analysis of SAGE (Serial Analysis of Gene Expressen) data, i.e. extraction of a SAGE library from sequence files, sequence error correction, library comparison + http://bioconductor.org/packages/2.4/bioc/html/sagenhaft.html + Nandini Badarinarayan + sagenhaft - - - - Plugin - - Allyson Lister - This role can be borne by any software which is a plugin for another piece of software. It can be used, for example, with an axiom such as "ParentSoftware 'uses software' some (PluginSoftware has_role some Plugin)" - - - - - + - - Gene Expression Atlas at EBI R statistics package - + + - - https://github.com/gxa/gxa/blob/develop/atlas-analytics/src/main/resources/R/analytics.R + + - R package for producing statistics that populate the Gene Expression Atlas. https://github.com/gxa/gxa/blob/develop/atlas-analytics/src/main/resources/R/analytics.R + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo + http://bioconductor.org/packages/2.4/bioc/html/seqLogo.html + Nandini Badarinarayan + seqLogo - + - - ActionScript - - http://dbpedia.org/resource/ActionScript + + + + + + + + + + + + + + + + + + + + + + + + + + + + Conducts pathway analysis by calculating the NT_k and NE_k statistics + http://bioconductor.org/packages/2.4/bioc/html/sigPathway.html + Nandini Badarinarayan + sigPathway - + - - Ada - - http://dbpedia.org/resource/Ada_(programming_language) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Identification of differentially expressed genes and estimation of the False Discovery Rate (FDR) using both the Significance Analysis of Microarrays (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM). + http://bioconductor.org/packages/2.4/bioc/html/siggenes.html + Nandini Badarinarayan + siggenes - + - - AppleScript - - http://dbpedia.org/resource/AppleScript + + + Sim method - + - - Assembly - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Provides high level functions for reading Affy .CEL files, phenotypic data, and then computing simple things with it, such as t-tests, fold changes and the like. Makes heavy use of the affy library. Also has some basic scatter plot functions and mechanisms for generating high resolution journal figures + http://bioconductor.org/packages/2.4/bioc/html/simpleaffy.html + Nandini Badarinarayan + simpleaffy - + - - C - - http://dbpedia.org/resource/C_(programming_language) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Functions to computationally simulate the AP-MS technology based on wet-lab data. + http://bioconductor.org/packages/2.4/bioc/html/simulatorAPMS.html + Nandini Badarinarayan + simulatorAPMS - + - - C Sharp - - http://dbpedia.org/resource/C_Sharp_(programming_language) - - - - - - - - C++ - - http://dbpedia.org/resource/C++ - - - - - - - - COBOL - - http://dbpedia.org/resource/COBOL - - - - - - - - ColdFusion - - http://dbpedia.org/resource/ColdFusion_Markup_Language - - - - - - - - D - - http://dbpedia.org/resource/D_(programming_language) - - - - - - - - Delphi - - - - - - - - - Dylan - - http://dbpedia.org/resource/Dylan_(programming_language) - - - - - - - - Eiffel - - http://dbpedia.org/resource/Eiffel_(programming_language) - - - - - - - - Forth - - http://dbpedia.org/resource/Forth_(programming_language) - - - - - - - - Fortran - - http://dbpedia.org/resource/Fortran - - - - - - - - Groovy - - http://dbpedia.org/resource/Groovy_(programming_language) - - - - - - - - Haskell - - http://dbpedia.org/resource/Haskell_(programming_language) - - - - - - - - JavaScript - - http://dbpedia.org/resource/JavaScript - - - - - - - - LabVIEW - - - - - - - - - Lisp - - http://dbpedia.org/resource/Lisp_(programming_language) - - - - - - - - Lua - - http://dbpedia.org/resource/Lua_(programming_language) - - - - - - - - Maple - - - - - - - - - Mathematica - - - - - - - - - Pascal - - http://dbpedia.org/resource/Pascal_(programming_language) - - - - - - - - Perl - - http://dbpedia.org/resource/Perl - - - - - - - - PHP - - http://dbpedia.org/resource/PHP - - - - - - - - Prolog - - http://dbpedia.org/resource/Prolog - - - - - - - - Python - - Python is a widely used general-purpose, high-level programming language. Its design philosophy emphasizes code readability, and its syntax allows programmers to express concepts in fewer lines of code than would be possible in languages such as C. The language provides constructs intended to enable clear programs on both a small and large scale.Python supports multiple programming paradigms, including object-oriented, imperative and functional programming or procedural styles. - http://dbpedia.org/resource/Python_(programming_language), accessed 27 November 2014. - - - - - - - - REXX - - http://dbpedia.org/resource/REXX - - - - - - - - Ruby - - http://dbpedia.org/resource/Ruby_(programming_language) - - - - - - - - SAS - - - - - - - - - Scala - - http://dbpedia.org/resource/Scala_(programming_language) - - - - - - - - Scheme - - http://dbpedia.org/resource/Scheme_(programming_language) - - - - - - - - Shell - - - - - - - - - Smalltalk - - http://dbpedia.org/resource/Smalltalk - - - - - - - - SQL - - http://dbpedia.org/resource/SQL - - - - - - - - Turing - - http://dbpedia.org/resource/Turing_(programming_language) - - - - - - - - Verilog - - http://dbpedia.org/resource/Verilog - - - - - - - - VHDL - - http://dbpedia.org/resource/VHDL - - - - - - - - Visual Basic - - http://dbpedia.org/resource/Visual_Basic - - - - - - - - DAVID - + + - - http://david.abcc.ncifcrf.gov/ + + + + + + + + + + + + + - - + + + + + + + - - + + + + + + + + + + - - + + - DAVID Bioinformatics resource - http://david.abcc.ncifcrf.gov/ - James Malone - DAVID (the Database for Annotation, Visualization and Integrated Discovery) is a free online bioinformatics resource developed by the Laboratory of Immunopathogenesis and Bioinformatics (LIB). All tools in the DAVID Bioinformatics Resources aim to provide functional interpretation of large lists of genes derived from genomic studies, e.g. microarray and proteomics studies. - Database for Annotation, Visualization and Integrated Discovery + This package has been prepared to assist users in computing either a sample size or power value for a microarray experimental study. The user is referred to the cited references for technical background on the methodology underpinning these calculations. This package provides support for five types of sample size and power calculations. + http://bioconductor.org/packages/2.4/bioc/html/sizepower.html + Nandini Badarinarayan + sizepower - + - - MLXTRAN - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + xmapBridge can plot graphs in the X:Map genome browser. This package exports plotting files in a suitable format. + http://bioconductor.org/packages/2.4/bioc/html/xmapbridge.html + Nandini Badarinarayan + xmapbridge - + - - PSI-BLAST - - + + + + + + + + + + + + + + + + + + + + - + - + - - + + @@ -76931,14 +77030,68 @@ tiple samples - + + + + + + + + + + + + + + + + + + Methods for segmenting, normalising and processing aCGH data; including plotting functions for visualising raw and segmented data for individual and multiple arrays. + http://bioconductor.org/packages/2.4/bioc/html/snapCGH.html + Nandini Badarinarayan + snapCGH + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - + - - + + @@ -76947,264 +77100,383 @@ tiple samples - - + + + + + + + + + - - + + - Position-Specific Iterative - Position-Specific Iterated (PSI)-BLAST is the most sensitive BLAST program, making it useful for finding very distantly related proteins or new members of a protein family. Use PSI-BLAST when your standard protein-protein BLAST search either failed to find significant hits, or returned hits with descriptions such as "hypothetical protein" or "similar to...". - NIH BLAST homepage - - - - - - - - NMTRAN - + Implements classes and methods for large-scale SNP association studies + http://bioconductor.org/packages/2.4/bioc/html/snpMatrix.html + Nandini Badarinarayan + snpMatrix - + - - NONMEM - + + - - + + - - + + - - + + - - + + - - + + + + + + + + + + Affymetrix Spike-in Langmuir Isotherm Data Analysis Tool + http://bioconductor.org/packages/2.4/bioc/html/spikeLI.html + Nandini Badarinarayan + spikeLI - + - - Entrez - + + - - + + + + + + + + + - - + + - Ncbi Resource, C. (2012). "Database resources of the National Center for Biotechnology Information". Nucleic Acids Research 41 (Database issue): D8–D20. doi:10.1093/nar/gks1189. PMC 3531099. - The Entrez Global Query Cross-Database Search System is a powerful federated search engine, or web portal that allows users to search many discrete health sciences databases at the National Center for Biotechnology Information (NCBI) website. - Entrez Global Query Cross-Database Search System - - - - - - - - web content search - - Web content search is the searching for information on the World Wide Web. - website content search + + + + + + + + + + + + + + + + + + + + The package contains functions that can be used to compare expression measures on different array platforms. + http://bioconductor.org/packages/2.4/bioc/html/spkTools.html + Nandini Badarinarayan + spkTools - + - - search engine - - - - + + + + + + + + + + + + - - + + - - - - - web search engine - A search engine is a software system that is designed to search for information on the World Wide Web. + + + + + + + + + + + + + + + + + + + + + + + + + + A set of tools to work with alternative splicing + http://bioconductor.org/packages/2.4/bioc/html/splicegear.html + Nandini Badarinarayan + splicegear - + - - Weka - + + - - + + - - + + + + + + + - - http://www.cs.waikato.ac.nz/~ml/weka/ + + - - + + - Weka (Waikato Environment for Knowledge Analysis) is a suite of machine learning software, originally intended for data mining tasks, written in Java and developed at the University of Waikato, New Zealand. - Waikato Environment for Knowledge Analysis + + + + + + + The splots package provides the plotScreen function for the visualization of for high-throughput assays in microtitre plate or chamber slide format. + http://bioconductor.org/packages/2.4/bioc/html/splots.html + Nandini Badarinarayan + splots - + - - PostgreSQL - + + - - + + - - http://www.postgresql.org/ + + - PostgreSQL, often simply Postgres, is an open source object-relational database management system (ORDBMS) with an emphasis on extensibility and standards compliance. - Postgres + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Spot segmentation via model-based clustering and gridding for blocks within microarray slides + http://bioconductor.org/packages/2.4/bioc/html/spotSegmentation.html + Nandini Badarinarayan + spotSegmentation - + - - data storage - - The storing of digital information. Often this is done for archiving and retrieval purposes. + + + sproc - + - - Segway 1.2 - + + + sqlite + + + + + + + + - - - - - - - - - - - - + + - - + + - - + + - - + + + + + + + - - - - - - - - - + + + + + This package contains an implementation of the S-Score algorithm + http://bioconductor.org/packages/2.4/bioc/html/sscore.html + Nandini Badarinarayan + sscore + + + + + + + + + + + + + + + + + + - - + + + + + + + - + - + - - + + @@ -77213,443 +77485,48 @@ tiple samples - - + + - The free Segway software package contains a novel method for analyzing multiple tracks of functional genomics data. Our method uses a dynamic Bayesian network (DBN) model, which enables it to analyze the entire genome at 1-bp resolution even in the face of heterogeneous patterns of missing data. This method is the first application of DBN techniques to genome-scale data and the first genomic segmentation method designed for use with the maximum resolution data available from ChIP-seq experiments without downsampling. - http://pmgenomics.ca/hoffmanlab/proj/segway/, accessed 27 November 2014. - - - - - - - - Python 2.6 - - - + + - Allyson Lister - Allyson Lister - Version 2.6 of the Python programming language. + Functions for computing and displaying sample size information for gene expression arrays. + http://bioconductor.org/packages/2.4/bioc/html/ssize.html + Nandini Badarinarayan + ssize - + - - Python 2.7 - + + - - - - - Allyson Lister - Allyson Lister - Version 2.7 of the Python programming language. - - - - - - - - clause - license clause - - A licence clause is a component of a license which defines some aspect of a restriction or conversely permission in how something corresponding to a license may be legally redistributed, partially redistrubed, extended, modified or otherwise used in some way. - James Malone - - - - - - - - Attribution clause - - An Attribution clause is a license clause intended to provide a specified level of recognition of the licensor as the copyright holder of the work. This can take many forms, including the requirement to preserve any copyright notice, attribution statements and the URL (link) to the original work. The attribution requirement thus serves the dual purpose of ensuring that the publisher receives appropriate credit, and that provenance information is kept intact. There are varying strengths of these clauses, from licensors requesting not to be attributed at all to requiring attribution for all uses of the software. - Modified by Allyson Lister from http://creativecommons.org/tag/attribution - - - - - - - - Derivatives clause - - Allyson Lister - Derivatives clauses are license clauses which state what requirements on derivative software, if any, are attached to a software license. The license for a piece of software may or may not allow the creation of new software derived from it. If it is allowed, such usage may be restricted in a variety of ways. - - - - - - - - Source code clause - - A source code clause is a license clause which states the restrictions placed on the source code for the licensed software, if any. The license for a piece of software may or may not allow access to the source code. If such access is allowed, usage may be restricted in a variety of ways. - Allyson Lister - - - - - - - - Platform clause - - A Platform clause is a license clause which states the platform restrictions for the licensed software, if any. The license for a piece of software may or may not allow the use of any software platform. If it is allowed, such usage may be restricted in a variety of ways. - Allyson Lister - - - - - - - - Number of installations clause - - A Number of installations clause is a license clause which may limit the number of installations a particular licensee may peform. - Allyson Lister - - - - - - - - Number of users clause - - A Number of users clause is a license clause which may limit the number of users a particular licensee may allow to use the product. - Allyson Lister - - - - - - - - Time clause - - A time clause is a license clause which states the restrictions placed on the length of time the licensed software may be used, if any. The license for a piece of software may or may not allow access to the software for an unlimited time. If such access is allowed, usage may be restricted in a variety of ways. - Allyson Lister - - - - - - - - Usage clause - - A usage clause is a license clause which states the restrictions placed on how the licensed software may be used. The license for a piece of software may restrict how the licensee may use the software. If such access is allowed, usage may be restricted in a variety of ways. - Allyson Lister - - - - - - - - No restrictions on derivatives - - - Allyson Lister - No restrictions on derivatives is a derivatives clause which places no rules or restrictions on how derivative software is created. - - - - - - - - Restrictions on derivative software - - Allyson Lister - Restrictions on derivative software is a derivatives clause which allows the creation of derivatives but which also places some kind of restriction on how derivative software may be created. - - - - - - - - derivative software not allowed - - - Allyson Lister - Derivative software not allowed clauses are derivatives clauses which state that derivative software is never allowed using the licensed software. - - - - - - - - derivative code same license - - Allyson Lister - Derivative code same license is a restrictive derivatives clause where derivative software must be released under the same license. - - - - - - - - Source code available - - - A source code available clause is a source code clause which states that the source code for the licensed software is available to the licensee. However, usage of the source code may or may not be restricted in a variety of ways. - Allyson Lister - - - - - - - - Source code unavailable - - A source code unavailable clause is a source code clause which states that the source code for the licensed software is not available to the licensee. - Allyson Lister - - - - - - - - Platform restricted - - - Allyson Lister - Platform restricted is a platform clause which places restrictions on which platform the licensed software may be installed on. - - - - - - - - Platform unrestricted - - Allyson Lister - Platform unrestrictred is a platform clause which does not place any restrictions on which type of platform the software may be licensed for. - - - - - - - - Number of installations restricted - - - A Number of installations restricted clause is a number of installations clause which restricts the number of times the software may be installed by any given licensee. - Allyson Lister - - - - - - - - Number of installations unrestricted - - A Number of installations unrestricted clause is a number of installations clause which does not restrict the number of times the software may be installed by any given licensee. - Allyson Lister - - - - - - - - Number of users restricted - - - A Number of users restricted clause is a number of users clause which restricts the number of users the software may have for a particular licensee. This may be number of total users, or number of concurrent users. - Allyson Lister - - - - - - - - Number of users unrestricted - - A Number of users unrestricted clause is a number of users clause which does not restrict the number of users of the licensed software. - Allyson Lister - - - - - - - - Time for use restricted - - - Allyson Lister - Time for use restricted is a time clause which places restrictions on the length of time the licensed software may be used. - - - - - - - - Time for use unrestricted - - Time for use unrestrictred is a time clause which does not place any restrictions on the length of time the software may be licensed for. - - - - - - - - Usage unrestricted - - - Allyson Lister - Usage unrestricted is a usage clause which places no restrictions on how the licensed software may be used. - - - - - - - - Usage restricted - - Allyson Lister - Usage restricted is a usage clause which places restrictions on how the licensed software may be used. These restrictions will vary according to the individual license. - - - - - - - - usage non commercial only - - Usage non commercial only is a usage restricted clause which restricts the use of the licensed software only to licensees who are not commercial entites. - - - - - - - - usage academic only - - Allyson Lister - Usage academic only is a usage restricted clause which restricts the use of the licensed software to academic licensees only. - - - - - - - - derivative code linked same license - - Allyson Lister - Derivative code linked same license is a restrictive derivatives clause where code may only be linked to in derivative software that is released under the same license. - - - - - - - - software interface - - The mode of interaction with a piece of software. - - - - - - - - Microsoft Excel - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + + - - + + - + - - - - - + + @@ -77657,84 +77534,112 @@ tiple samples - + - - - - - + + + The stam package performs a biologically structured classification of microarray profiles according to clinical phenotypes. GO terms are used to link classification results to biological aspects. + http://bioconductor.org/packages/2.4/bioc/html/stam.html + Nandini Badarinarayan + stam - + - - Microsoft Excel for Windows 2010 - - - - - - - + + + A statistical test is an algorithm for making quantitative decisions to determine which outcomes of a study would lead to a rejection of the null hypothesis for a pre-specified level of significance. + Modified from http://en.wikipedia.org/wiki/Statistical_test, accessed 9 May 2013; http://www.itl.nist.gov/div898/handbook/prc/section1/prc13.htm, accessed 9 May 2013. + Statistical tests + + + + + + + + - - + + - - 2010-06-15T0:00:00 + + - - + + - - + + + Stepwise normalization functions for cDNA microarray data. + http://bioconductor.org/packages/2.4/bioc/html/stepNorm.html + Nandini Badarinarayan + stepNorm - + + + + + 't-test' + + + + + - - Microsoft Windows - + + - - + + - + + + + + + + + + + + + - + - - + + @@ -77743,15 +77648,13 @@ tiple samples - + - - - - - + + + @@ -77759,228 +77662,207 @@ tiple samples - - + + - The Windows Operating System + Transcript mapping with high-density oligonucleotide tiling arrays + http://bioconductor.org/packages/2.4/bioc/html/tilingArray.html + Nandini Badarinarayan + tilingArray - + - - Windows Vista - - - - - 2006-11-08T0:00:00 - - - - - - - - + + - - + + - - - - - - - - Windows XP - - - + + - - + + - - 2001-10-25T0:00:00 + + + + + + + - - + + + Functions for data analysis and graphical displays for developmental microarray time course data. + http://bioconductor.org/packages/2.4/bioc/html/timecourse.html + Nandini Badarinarayan + timecourse - + - - Microsoft Office 2001 - - - - - - - + + - - + + + Widgets to provide user interfaces. tcltk should have been installed for the widgets to run. + http://bioconductor.org/packages/2.4/bioc/html/tkWidgets.html + Nandini Badarinarayan + tkWidgets - - - - software suite - - - - - - - - - - - - - - - - - + - - Adobe Acrobat Reader - + + - - - - - - - - - - - - + + + + + + + + - - http://get.adobe.com/reader/ + + - - + + + + + + + - - + + - - + + + topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied. + http://bioconductor.org/packages/2.4/bioc/html/topGO.html + Nandini Badarinarayan + topGO + + + + + + + + - - + + - - + + - + - + - - + + - Andy Brown - - - - - - - - Annotare - - - - - - - - - http://code.google.com/p/annotare/ + + + + + + + + + - - + + + Top Scoring Pairs for Microarray Classification + http://bioconductor.org/packages/2.4/bioc/html/tspair.html + Nandini Badarinarayan + tspair + + + + + + + + - + - - - - - + + @@ -77988,36 +77870,26 @@ tiple samples - - + + - - - - - - - - - - - - + + - + - + - - + + @@ -78026,279 +77898,315 @@ tiple samples - - + + - - + + - Andy Brown + Estimation of local false discovery rate + http://bioconductor.org/packages/2.4/bioc/html/twilight.html + Nandini Badarinarayan + twilight - + - - BioJava - + + + Two-stage measurement error model + + + + + + + + + + + + + + + + + + + + - - + + + + + + + - - + + + + + + + + + + + + - - + + - - http://biojava.org + + + Variational Bayesian Multinomial Probit Regression with Gaussian Process Priors. It estimates class membership posterior probability employing variational and sparse approximation to the full posterior. This software also incorporates feature weighting by means of Automatic Relevance Determination. + http://bioconductor.org/packages/2.4/bioc/html/vbmp.html + Nandini Badarinarayan + vbmp + + + + + + + + + data visualization + + + + + + + + - - + + - - + + - + - - - - - + + + + The package implements a method for normalising microarray intensities, both between colours within array, and between arrays. The method uses a robust variant of the maximum-likelihood estimator for the stochastic model of microarray data described in the references + http://bioconductor.org/packages/2.4/bioc/html/vsn.html + Nandini Badarinarayan + vsn - + - - BioPerl - - - - - - - - - - - - - + + - - + + - - + + + + + + + - - + + + + + + + - - http://www.bioperl.org + + - Andy Brown + This package provides enhancements on the Sweave() function in the base package. In particular a facility for caching code chunk results is included. + http://bioconductor.org/packages/2.4/bioc/html/weaver.html + Nandini Badarinarayan + weaver - + - - DNDC - + + - - + + - - http://ecobas.org/www-server/rem/mdb/dndc.html + + - + - - - - - - - - - + + + + - - - - - - - - - - - - + + - - + + + An integrated web interface for doing microarray analysis using several of the Bioconductor packages. It is intended to be deployed as a centralized bioinformatics resource for use by many users. + http://bioconductor.org/packages/2.4/bioc/html/webbioc.html + Nandini Badarinarayan + webbioc + + + + + + + + - - + + - - http://www.dndc.sr.unh.edu/ + + - Soil Chemistry Model - Andy Brown + This packages contains tools to support the construction of tcltk widgets + http://bioconductor.org/packages/2.4/bioc/html/widgetTools.html + Nandini Badarinarayan + widgetTools - + - - DROID - - - - - http://sourceforge.net/projects/droid/ - - + + - - + + - - + + - + - - - - - - - - - + + + + - - - - - - - - + + - Digital Record Object Identification + Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, and mzData files. Preprocesses data for high-throughput, untargeted analyte profiling. + http://bioconductor.org/packages/2.4/bioc/html/xcms.html + Nandini Badarinarayan + xcms - + - - Dropbox - - - - - www.dropbox.com - - + + - + - - - - - + + + + @@ -78306,57 +78214,145 @@ tiple samples - - + + - + - - - - - - - - - + + + + - - + + + + + + + + + - - + + + Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays + http://bioconductor.org/packages/2.4/bioc/html/xps.html + Nandini Badarinarayan + xps - + - - Eclipse - + + - - - - - + + + + + + + + + + + + + + + + + Quality control of Affymetrix GeneChip expression data and reproducibility analysis of human whole genome chips with the MAQC reference datasets. + http://bioconductor.org/packages/2.4/bioc/html/yaqcaffy.html + Nandini Badarinarayan + yaqcaffy + + + + + + + + + + + + + + + Computer software, or generally just software, is any set of machine-readable instructions (most often in the form of a computer program) that conform to a given syntax (sometimes referred to as a language) that is interpretable by a given processor and that directs a computer's processor to perform specific operations. + James Malone + Modified in parts from https://en.wikipedia.org/wiki/Software + Robert Stevens + software + + + + + + + + + + + + + + + + + + + A license is a legal instrument (usually by way of contract law, with or without printed material) governing the use or redistribution of the resource containing the license. + Modified from http://en.wikipedia.org/wiki/Software_license + James Malone + license + software license + + + + + + + + + Information processing is a process in which input information is analysed or transformed in order to produce information as output. + James Malone + information processing + + + + + + + + + + + + + + + - - + + @@ -78365,32 +78361,62 @@ tiple samples - - + + + + + + + + + + + + - - + + + + + + + + + + + + - - + + + + + + + + + + + + - + - + - - + + @@ -78399,49 +78425,80 @@ tiple samples - - http://www.eclipse.org + + - - + + - The Eclipse IDE - Andy Brown + + + + http://office.microsoft.com/ + + + + + + 2007-01-30T0:00:00 + + + Microsoft Excel 2007 is a spreadsheet editing and viewing tool. + Microsoft Excel 2007 - + - - EMBOSS package - + + - - + + + + + + + + + + + + - - + + + + + + + + + + + + - + - + - - + + @@ -78450,122 +78507,253 @@ tiple samples - - + + + + + + + + + + + + - - + + - - + + - - + + http://www.mathworks.com/products/matlab/ + MATLAB® is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran + http://www.mathworks.com/products/matlab/?s_cid=SA_trafrefpai_MLipspot_Doc_bioinfo_MATLAB + Nandini Badarinarayan + MATLAB - + - - Endnote - + + + + + + + + + + + + + + + + + + - - + + + + + + + + + + + + - - + + + + + + + + + + + + - - + + + + + + + + + + + + - - http://www.endnote.com/ + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + + + + + + + + + + + - + - + - - + + - Andy Brown - Citation management software + + + + + + + + + + + + + + + + + + + + + + http://protege.stanford.edu/ + + + Protege 4 - + - - Grimoires - - - - - - - + + - - + + + + + + + + + + + + - - http://sf.net/projects/grimoires + + + + + + + + + + + + - + - + - - + + @@ -78574,32 +78762,42 @@ tiple samples - - + + - - + + - - + + http://www.omnigroup.com/products/omnioutliner/ + OmniOutliner is commercial outlining software for Mac OS X produced by The Omni Group + OmniOutliner + + + + + + + + - + - + - - + + @@ -78608,1895 +78806,11805 @@ tiple samples - - + + - Andy Brown + Racket is a Scheme-based language interpreter and programming environment + Racket - + - - obsolete_ontology - - true - Equivalence with EDAM data_0582. - Marked as obsolete by Allyson Lister. - Obsoleted after the 0.4 release. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://www.kakadusoftware.com + + + Kakadu - + - - software before Microsoft 2007 - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + WordStar - + - - clustering algorithm - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://www.jetbrains.com/idea/ + + + IntelliJ IDEA is a commercial Java IDE for developing software. + IntelliJ + IntelliJ IDEA - + - - pattern discovery algorithm - + + + + + + http://www.java.com + + + Java - + - - predictive modeling algorithm - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://www.copasi.org + + + COPASI is a software application for simulation and analysis of biochemical networks and their dynamics. COPASI is a stand-alone program that supports models in the SBML standard and can simulate their behavior using ODEs or Gillespie's stochastic simulation algorithm; arbitrary discrete events can be included in such simulations. COPASI provides an C++ API with language bindings for Perl, python, R, Java, and Octave and is able to communicate with the Systems Biology Workbench COPASI carries out several analyses of the network and its dynamics and has extensive support for parameter estimation and optimization. COPASI provides means to visualize data in customizable plots, histograms and animations of network diagrams. + http://sbml.org/SBML_Software_Guide/SBML_Software_Summary, accessed 24 March 2015. + COPASI - + - - clustering specification - - Clustering specification is a single generalization specification is a generalization specification and denotes a type of generalization that models the mapping of a set of objects S of type T from S to a set of natural numbers {1,...K}. This generalization is obtained by appliing a clustering algorithm on a set of data. - OntoDM - - + + + + + + + + + + + + + + + + + + + + + + + + + Microsoft Excel 2003 is a spreadsheet editing and viewing tool. + Microsoft Excel 2003 + + - + - - SAEM - - http://www.math.u-bordeaux1.fr/MAS10/DOC/PDF-PRES/Lavielle.pdf - A stochastic algorithm for population pharmacology modeling + + + + + + + + + Microsoft Excel 2002 - + - - dynamic Bayesian network model - - A Dynamic Bayesian Network model is a Bayesian Network which relates variables to each other over adjacent time steps. - http://en.wikipedia.org/wiki/Dynamic_Bayesian_network, accessed 27 November 2014. + + + + + + + + + MATLAB 7 - + - - spreadsheet format - - A spreadsheet data format is one in which data is organised into a matrix (or matrices) of columns and rows to form cells in which values are entered. - James Malone + + + + + + + + + MATLAB 6 - + - - XLS spreadsheet - - A spreadsheet data format designed for Microsoft Excel. - James Malone + + + + + + + + + MATLAB 7.12 - + - - XML spreadsheet - - A spreadsheet data format in which the structure of the data is described using XML, such as column and row headers and cell identity. - James Malone + + + + + + + + + STARLIMS - + - - Matlab .m file - - James Malone + + + + + + + + + + + + + + + Unix - + - - obsolete_XML - - 1.5 - Equivalence with EDAM http://edamontology.org/format_2332, please use that instead. - Marked as obsolete by Allyson Lister. - true + + + + + + + + + An operating system is a piece of software which is responsible for managing software that runs on a computer and the interactions of that software with the hardware and system resources. + operating system - + - - RDF - - http://www.w3.org/TR/REC-rdf-syntax/ - formats - bioinformatics - Jon Ison - format - Data in RDF format can be serialised into XML, textual, or binary format. - James Malone - "Resource Description Framework (RDF) format." [http://edamontology.org] - Merged with now-obsolete EDAM class 'RDF' http://edamontology.org/format_2376 by Allyson Lister. - edam - The Resource Description Framework (RDF) is a general-purpose language for representing information in the Web. + + + + + + + + + + + + + + + Linux - + - - RDF-XML - - - James Malone - A serialisation of RDF into an XML format. + + + Microsoft Word 2001 - + - - image format - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Adobe Illustrator is a graphics editor for creating and editing vector graphics. + James Malone + Adobe Illustrator 10 - + - - DWG - - James Malone - DWG ("drawing") is a binary file format used for storing two and three dimensional design data and metadata - http://en.wikipedia.org/wiki/.dwg + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Microsoft Word - + - - DXF - - DXF (Drawing Interchange Format, or Drawing Exchange Format) is a CAD data file format developed by Autodesk for enabling data interoperability between AutoCAD and other programs. - http://en.wikipedia.org/wiki/AutoCAD_DXF - James Malone + + + + + + + + + + + + + + + + + + + software with image input - + - - BMP - - James Malone - The BMP File Format is a Raster graphics image file format used to store bitmap digital images, independently of the display device (such as a graphics adapter). - http://www.fileformat.info/format/bmp/egff.htm + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://oboedit.org/ + + + OBO-Edit is an open source ontology editor optimized for the OBO biological ontology file format. It features an easy to use editing interface, a simple but fast reasoner, and powerful search capabilities. + OBO edit + OBO-Edit - + - - CGM - - http://en.wikipedia.org/wiki/Computer_Graphics_Metafile - Computer Graphics Metafile (CGM) is a free and open international standard file format for 2D vector graphics, raster graphics, and text, and is defined by ISO/IEC 8632. - James Malone + + + + + + + + + ontology engineering software - + - - web page specification - + + + + + + + + + + + + + + + + + + + Microsoft developed software - - - - document exchange format - - - - - - - - - pdf - - PDF is an open standard for document exchange. - Portable Document Format - - - - - - - - TIFF - - TIFF is a flexible, adaptable file format for handling images and data within a single file, by including the header tags (size, definition, image-data arrangement, applied image compression) defining the image's geometry. - Tagged Image File Format - - - - - + - - JPEG - - JPG - JPEG is a lossy file format for storing images + + + + + + + + + software with command line interface - + - - PNG - - PNG is a bitmapped image format and video codec that employs lossless data compression. - Portable Network Graphics + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://www.peterborgapps.com/smultron/ + + + Smultron - + - - GIF - - Graphics Interchange Format - The Graphics Interchange Format (GIF) is a bitmap image format. The format supports up to 8 bits per pixel thus allowing a single image to reference a palette of up to 256 distinct colors. The colors are chosen from the 24-bit RGB color space. It also supports animations and allows a separate palette of 256 colors for each frame. The color limitation makes the GIF format unsuitable for reproducing color photographs and other images with continuous color, but it is well-suited for simpler images such as graphics or logos with solid areas of color. [wikipedia] + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ftp://ftp.ncbi.nih.gov/blast/executables/ + + + The C++ version of the command line BLAST+ tool made by the NCBI. (See also http://www.ncbi.nlm.nih.gov/books/NBK1763) + Allyson Lister + BLAST+ 2.2.26 - + - - raster image format - - A raster image is a format for representing a rectangular grid of dots (pixels) which contains information on the specific colour of each pixel. + + + Ensembl - + - - vector image format - - A vector image is a collection of connected lines and curves that produce objects. This geometric description enables the image to be displayed without loss at any size rendering. + + + + + + + + + Multiple alignment program for nucleic acid or protein sequences. + http://www.clustal.org/, Accessed 13 June 2012. + Allyson Lister + Clustal - + - - SVG - - Scalable Vector Graphics + + + Clustal Omega provides improved scalability over previous Clustal versions, allowing hundreds of thousands of sequences to be aligned in a few hours. It will also make use of multiple processors, where present. In addition, the quality of alignments is superior to previous versions, as measured by a range of popular benchmarks. + http://www.clustal.org/omega/, Accessed 13 June 2012 + Allyson Lister + Clustal Omega - + - - AI - - Adobe Illustrator format + + + Allyson Lister + ClustalW - + - - PostScript - - PostScript is a format used for describing documents. + + + Allyson Lister + ClustalX - + - - tex - - tex is a format for documents written in the document markup language and document preparation system LaTeX. - LaTeX format + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://dx.doi.org/10.1038/msb.2011.75 + + + Allyson Lister + Clustal Omega 1.1 - + - - outline document format - - A format specification for data used or produced by outliner software + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://dx.doi.org/10.1093/bioinformatics/btm404 + + + Allyson Lister + ClustalW 2.1 - + - - OmniOutline format - - A proprietary format for documents created and edited using OmniOutliner outliner software, + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://dx.doi.org/10.1093/bioinformatics/btm404 + + + Allyson Lister + ClustalX 2.1 - + - - OPML - - Outline Processor Markup Language - OPML (Outline Processor Markup Language) is an XML format for outlines + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Allyson Lister + EBI Clustal W2 Web Tool - + - - JPEG 2000 - - JPEG 2000 is a compression standard enabling both lossless and lossy storage. The compression methods used are different from the ones in standard JFIF/JPEG; they improve quality and compression ratios, but also require more computational power to process. [wikipedia] + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Allyson Lister + EBI Clustal Omega Web Tool - + - - word processing document format - + + + + + + + + + Allyson Lister + MUSCLE - + - - WordStar format - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Allyson Lister + EBI Muscle Web Tool - + - - Microsoft Word doc - - A file format for word processing documents for Microsoft Word. + + + + + + + + + + + + + + + + + + http://dx.doi.org/10.1093/nar/gkh340 + + + + + + http://www.drive5.com/muscle/muscle_userguide3.8.html + + + + + + http://www.drive5.com/muscle/downloads.htm + + + Allyson Lister + MUSCLE 3.8.31 - + - - programming language format - + + + + + + + + + + + + + + + + + + + Allyson Lister + Drive5 MUSCLE - + - - .java file - - A source code file format which is specified to be used with the Java programming language. - James Malone + + + + + + + + + Allyson Lister + TCoffee - + - - .class file - - James Malone - A format in which a .java file has been compiled into bytecode using a Java compiler and which is specified to be executed using the Java virtual machine. + + + + + + http://dx.doi.org/10.1006/jmbi.2000.4042 + + + TCoffee is a multiple sequence alignment program with a number of different modes. + Allyson Lister + CRG TCoffee - + - - CopasiML - - An XML-based file format for use with the COPASI software. - .cps + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Performs an alignment of DNA, RNA or Proteins with the standard TCoffee mode. This Web tool provides both interactive access via a Web browser and programmatic SOAP Web service access. Currently only the Web service interface is modelled in OWL. + Allyson Lister + EBI TCoffee Web Tool - + - - obsolete_SBML - - true - Marked as obsolete by Allyson Lister. - Obsoleted after the 0.4 release. - Equivalence with the EDAM SBML class format_2585. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://dx.doi.org/10.1093/nar/gkn278 + + + Aligns RNA sequences using predicted secondary structures by accessing the RCoffee mode of the underlying TCoffee software. + http://tcoffee.crg.cat/apps/tcoffee/index.html, Accessed 19 June 2012 + Allyson Lister + CRG RCoffee Web Tool - + - - OWL-XML - - The Web Ontology Language (OWL) in XML serialization + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://dx.doi.org/10.1093/nar/gkr245 + + + Performs an alignment of DNA, RNA or Proteins with the standard TCoffee mode. + http://tcoffee.crg.cat/apps/tcoffee/index.html, Accessed 19 June 2012 + Allyson Lister + CRG TCoffee Web Tool - + - - OWL2-XML - - Web Ontology Language version 2 in XML Serialization - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://dx.doi.org/10.1093/nar/gkm333 + + + Aligns DNA, RNA or Proteins by combining the output of popular aligners and by accessing the MCoffee mode of the underlying TCoffee software. + http://tcoffee.crg.cat/apps/tcoffee/index.html, Accessed 19 June 2012 + Allyson Lister + CRG MCoffee Web Tool + - + - - obsolete_OBO flat file format - - true - Equivalence with EDAM term format_2549. - Marked as obsolete by Allyson Lister. - Obsoleted after the 0.4 release. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://dx.doi.org/10.1093/nar/gkl092 + + + Aligns protein sequences using structural information by accessing the 3DCoffee/Expresso mode of the underlying TCoffee software. + http://tcoffee.crg.cat/apps/tcoffee/index.html, Accessed 19 June 2012 + Allyson Lister + CRG Expresso Web Tool - + - - obsolete_text file format - - 1.5 - Equivalence with EDAM http://edamontology.org/format_2330, please use that class instead. - Marked as obsolete by Allyson Lister. - false - true + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://dx.doi.org/10.1093/nar/gkr245 + + + Aligns distantly related proteins using homology extension (slow and accurate) by accessing the PSICoffee mode of the underlying TCoffee software. + http://tcoffee.crg.cat/apps/tcoffee/index.html, Accessed 19 June 2012 + Allyson Lister + CRG PSICoffee Web Tool - + - - ASCII format - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The initial interface is via the command line. Depending on the options and inputs provided at the command line, an appropriate alignment takes place and is then presented to the user via a Graphical User Interface. + Allyson Lister + CRG TCoffee 9.02.r1228 - + - - plain text file format - + + + + + + + + + + + + + + + + + + + + + Data analysis software which performs a variety of statistical, summarising, analytical and visualization tasks. + Allyson Lister + Q - + - - obsolete_MAGE tab format - - true - Equivalent with EDAM format_3162. - Obsoleted after release 0.4 - Marked as obsolete by Allyson Lister. + + + + + + + + + + + + + + + + + + + + + + http://www.q-researchsoftware.com + + + Q 4.2 - + - - tab delimited file format - - Tab delimited file format is a plain text file format where each field value of a record is separated from the next by a tab stop character. + + + + + + + + + + + + + + + + + + + + + Data analysis software which performs a variety of statistical, summarising, analytical and visualization tasks. Allyson Lister - http://en.wikipedia.org/wiki/Tab-separated_values, accessed 6 June 2013. + SPSS - + - - obsolete_PSI-MI format - - true - Marked as obsolete by Allyson Lister. - Obsoleted after the version 0.4 release. - Equivalence with EDAM format_3158. + + + + + + + + + + + + + + + + + + + + + + http://www-01.ibm.com/software/uk/analytics/spss/downloads.html + + + Allyson Lister + SPSS 20.0 - + - - SIF - - SIF stands for Simple Interaction Format, and is a text format invented for Cytoscape. If the file contains any tab characters, then tabs are used to delimit the fields and spaces are considered part of the name. If the file contains no tabs, then any spaces are delimiters that separate names (and names cannot contain spaces). + + + + + + + + + Sequence Alignment and Modeling System, a collection of flexible software tools for creating, refining, and using linear hidden Markov models for biological sequence analysis. + SAM + http://bioinformatics.org/wiki/SAM, Accessed 19 June 2012. Allyson Lister - http://wiki.cytoscape.org/GettingStarted and http://wiki.cytoscape.org/Cytoscape_User_Manual/Network_Formats, accessed 20 June 2012 + Sequence Alignment and Modeling System - + - - GML - - http://wiki.cytoscape.org/GettingStarted, accessed 20 June 2012 - GML stands for Graph Markup Language, and is a standard network file format; supported by multiple generic network software packages + + + + + + + + + + + + + + + + + + + + + + + + + SAM 3.5 - + - - XGMML - - XGMML stands for eXtensible Graph Markup and Modelling Language, and it is a XML standard; similar to but preferred over GML. - http://wiki.cytoscape.org/GettingStarted, accessed 20 June 2012 + + + + + + + + + + + + + + + + + + http://dx.doi.org/10.1101/gr.1239303 + + + Cytoscape is an open source bioinformatics software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. + http://www.cytoscape.org/what_is_cytoscape.html, Accessed June 20, 2012. + Allyson Lister + Cytoscape - + - - Interaction data - - A type of data which defines interactions between items in the file. This can be simple pairwise interactions or more complex ones. Used to provide a class of data for software requiring specific types of interaction data as input. - Allyson Lister + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://www.cytoscape.org/download.html + + + Cytoscape 2.8 - + - - Knowledge representation role + - Modified from http://en.wikipedia.org/wiki/Knowledge_representation, accessed 10 February 2014 - A knowledge representation role is a role borne by a data format which utilizes formalisms to make complex systems easier to design and build. Knowledge representation is the field of artificial intelligence devoted to representing information about the world in a form that a computer system can utilize to solve complex tasks. + This role can be borne by any software which is a plugin for another piece of software. It can be used, for example, with an axiom such as "ParentSoftware 'uses software' some (PluginSoftware has_role some Plugin)" + Allyson Lister + Plugin - + - - BioPAX RDF/XML format - + + + + + + https://github.com/gxa/gxa/blob/develop/atlas-analytics/src/main/resources/R/analytics.R + + + R package for producing statistics that populate the Gene Expression Atlas. https://github.com/gxa/gxa/blob/develop/atlas-analytics/src/main/resources/R/analytics.R + Gene Expression Atlas at EBI R statistics package + + + + + + + + + http://dbpedia.org/resource/ActionScript + ActionScript + + + + + + + + + http://dbpedia.org/resource/Ada_(programming_language) + Ada + + + + + + + + + http://dbpedia.org/resource/AppleScript + AppleScript + + + + + + + + + Assembly + + + + + + + + + http://dbpedia.org/resource/C_(programming_language) + C + + + + + + + + + http://dbpedia.org/resource/C_Sharp_(programming_language) + C Sharp + + + + + + + + + http://dbpedia.org/resource/C++ + C++ + + + + + + + + + http://dbpedia.org/resource/COBOL + COBOL + + + + + + + + + http://dbpedia.org/resource/ColdFusion_Markup_Language + ColdFusion + + + + + + + + + http://dbpedia.org/resource/D_(programming_language) + D + + + + + + + + + Delphi + + + + + + + + + http://dbpedia.org/resource/Dylan_(programming_language) + Dylan + + + + + + + + + http://dbpedia.org/resource/Eiffel_(programming_language) + Eiffel + + + + + + + + + http://dbpedia.org/resource/Forth_(programming_language) + Forth + + + + + + + + + http://dbpedia.org/resource/Fortran + Fortran + + + + + + + + + http://dbpedia.org/resource/Groovy_(programming_language) + Groovy + + + + + + + + + http://dbpedia.org/resource/Haskell_(programming_language) + Haskell + + + + + + + + + http://dbpedia.org/resource/JavaScript + JavaScript + + + + + + + + + LabVIEW + + + + + + + + + http://dbpedia.org/resource/Lisp_(programming_language) + Lisp + + + + + + + + + http://dbpedia.org/resource/Lua_(programming_language) + Lua + + + + + + + + + Maple + + + + + + + + + Mathematica + + + + + + + + + http://dbpedia.org/resource/Pascal_(programming_language) + Pascal + + + + + + + + + http://dbpedia.org/resource/Perl + Perl + + + + + + + + + http://dbpedia.org/resource/PHP + PHP + + + + + + + + + http://dbpedia.org/resource/Prolog + Prolog + + + + + + + + + Python is a widely used general-purpose, high-level programming language. Its design philosophy emphasizes code readability, and its syntax allows programmers to express concepts in fewer lines of code than would be possible in languages such as C. The language provides constructs intended to enable clear programs on both a small and large scale.Python supports multiple programming paradigms, including object-oriented, imperative and functional programming or procedural styles. + http://dbpedia.org/resource/Python_(programming_language), accessed 27 November 2014. + Python + + + + + + + + + http://dbpedia.org/resource/REXX + REXX + + + + + + + + + http://dbpedia.org/resource/Ruby_(programming_language) + Ruby + + + + + + + + + SAS + + + + + + + + + http://dbpedia.org/resource/Scala_(programming_language) + Scala + + + + + + + + + http://dbpedia.org/resource/Scheme_(programming_language) + Scheme + + + + + + + + + Shell + + + + + + + + + http://dbpedia.org/resource/Smalltalk + Smalltalk + + + + + + + + + http://dbpedia.org/resource/SQL + SQL + + + + + + + + + http://dbpedia.org/resource/Turing_(programming_language) + Turing + + + + + + + + + http://dbpedia.org/resource/Verilog + Verilog + + + + + + + + + http://dbpedia.org/resource/VHDL + VHDL + + + + + + + + + http://dbpedia.org/resource/Visual_Basic + Visual Basic + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://david.abcc.ncifcrf.gov/ + + + DAVID (the Database for Annotation, Visualization and Integrated Discovery) is a free online bioinformatics resource developed by the Laboratory of Immunopathogenesis and Bioinformatics (LIB). All tools in the DAVID Bioinformatics Resources aim to provide functional interpretation of large lists of genes derived from genomic studies, e.g. microarray and proteomics studies. + DAVID Bioinformatics resource + Database for Annotation, Visualization and Integrated Discovery + http://david.abcc.ncifcrf.gov/ + James Malone + DAVID + + + + + + + + + MLXTRAN + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Position-Specific Iterated (PSI)-BLAST is the most sensitive BLAST program, making it useful for finding very distantly related proteins or new members of a protein family. Use PSI-BLAST when your standard protein-protein BLAST search either failed to find significant hits, or returned hits with descriptions such as "hypothetical protein" or "similar to...". + Position-Specific Iterative + NIH BLAST homepage + PSI-BLAST + + + + + + + + + NMTRAN + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + NONMEM + + + + + + + + + + + + + + + + + + + + + The Entrez Global Query Cross-Database Search System is a powerful federated search engine, or web portal that allows users to search many discrete health sciences databases at the National Center for Biotechnology Information (NCBI) website. + Entrez Global Query Cross-Database Search System + Ncbi Resource, C. (2012). "Database resources of the National Center for Biotechnology Information". Nucleic Acids Research 41 (Database issue): D8–D20. doi:10.1093/nar/gks1189. PMC 3531099. + Entrez + + + + + + + + + Web content search is the searching for information on the World Wide Web. + website content search + web content search + + + + + + + + + + + + + + + + + + + + A search engine is a software system that is designed to search for information on the World Wide Web. + web search engine + search engine + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://www.cs.waikato.ac.nz/~ml/weka/ + + + Weka (Waikato Environment for Knowledge Analysis) is a suite of machine learning software, originally intended for data mining tasks, written in Java and developed at the University of Waikato, New Zealand. + Waikato Environment for Knowledge Analysis + Weka + + + + + + + + + + + + + + + + + + http://www.postgresql.org/ + + + PostgreSQL, often simply Postgres, is an open source object-relational database management system (ORDBMS) with an emphasis on extensibility and standards compliance. + Postgres + PostgreSQL + + + + + + + + + The storing of digital information. Often this is done for archiving and retrieval purposes. + data storage + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The free Segway software package contains a novel method for analyzing multiple tracks of functional genomics data. Our method uses a dynamic Bayesian network (DBN) model, which enables it to analyze the entire genome at 1-bp resolution even in the face of heterogeneous patterns of missing data. This method is the first application of DBN techniques to genome-scale data and the first genomic segmentation method designed for use with the maximum resolution data available from ChIP-seq experiments without downsampling. + http://pmgenomics.ca/hoffmanlab/proj/segway/, accessed 27 November 2014. + Segway 1.2 + + + + + + + + + + + + + + + Version 2.6 of the Python programming language. + Allyson Lister + Allyson Lister + Python 2.6 + + + + + + + + + + + + + + + Version 2.7 of the Python programming language. + Allyson Lister + Allyson Lister + Python 2.7 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Mac OS is software which is used as the operating system for the Macintosh personal computer created by Apple Inc. + http://en.wikipedia.org/wiki/History_of_Mac_OS, accessed 25 March 2015. + Allyson Lister + Mac OS + + + + + + + + + OS X is a Mac OS operating system which succeeds the original Mac OS, which had been Apple's primary operating system since 1984. Unlike the earlier Macintosh operating system, OS X is a Unix-based operating system. + http://en.wikipedia.org/wiki/History_of_Mac_OS#OS_X, accessed 25 March 2015. + Allyson Lister + OS X + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + iBioSim has been developed for the modeling, analysis, and design of genetic circuits. While iBioSim primarily targets models of genetic circuits, models representing metabolic networks, cell-signaling pathways, and other biological and chemical systems can also be analyzed. iBioSim also includes modeling and visualization support for multi-cellular and spatial models as well. + http://www.async.ece.utah.edu/iBioSim/, accessed 25 March 2015. + Allyson Lister + iBioSim + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + VCell is a complete model building, editing and simulation environment. Includes spatial modeling capabilites, deterministic, stochastic, and hybrid algorithms. Parameter sensitivity analysis and parameter optimization. Desktop application and web-based environment. Bio- and math-based interfaces. Database and model sharing/publishing. + Virtual Cell + http://sbml.org/SBML_Software_Guide/SBML_Software_Summary, accessed 26 March 2015. + Allyson Lister + The licensing issue is not clear. On the VCell wikipedia page, the source is described as having an MIT license (see http://en.wikipedia.org/wiki/Virtual_Cell, accessed 26 March 2015). However, the exact type of license is not mentioned on the VCell homepage (http://www.vcell.org), therefore I have not added the statement that the MIT license is the *only* license for VCell. + VCell + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + COBRA (COnstraint-Based Reconstruction and Analysis Toolbox) includes implementations of many of the commonly used forms of constraint-based analysis such as FBA, gene deletions, flux variability analysis, sampling, and batch simulations together with tools to read in and manipulate constraint-based models. + COnstraints Based Reconstruction and Analysis + Allyson Lister + COBRA + + + + + + + + + + + + + + + + + + + + + COBRA Toolbox is the version of the COBRA software for Python. + COnstraints Based Reconstruction and Analysis for Python + Allyson Lister + COBRApy + + + + + + + + + + + + + + + + + + + + + COBRA Toolbox is the version of the COBRA software for Matlab. + COnstraints Based Reconstruction and Analysis Toolbox for MATLAB + Allyson Lister + COBRA Toolbox + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + LibSBML is a free, open-source programming library to help you read, write, manipulate, translate, and validate SBML files and data streams. It provides interfaces for C, C++, C#(.NET), Java, MATLAB, Octave, Perl, Python R and Ruby. LibSBML is available for free under LGPL terms in both source-code form and precompiled binaries for Windows, Mac OS X, and Linux. + http://sbml.org/SBML_Software_Guide/SBML_Software_Summary, accessed 27 March 2015. + Allyson Lister + libSBML + + + + + + + + + GNU Octave is a high-level interpreted language, primarily intended for numerical computations. It provides capabilities for the numerical solution of linear and nonlinear problems, and for performing other numerical experiments. It also provides extensive graphics capabilities for data visualization and manipulation. Octave is normally used through its interactive command line interface, but it can also be used to write non-interactive programs. The Octave language is quite similar to Matlab so that most programs are easily portable. + https://www.gnu.org/software/octave/, accessed 27 March 2015. + Allyson Lister + GNU Octave + + + + + + + + + GWT + + + + + + + + + S language + + + + + + + + + Excel + + + + + + + + + A licence clause is a component of a license which defines some aspect of a restriction or conversely permission in how something corresponding to a license may be legally redistributed, partially redistrubed, extended, modified or otherwise used in some way. + James Malone + clause + license clause + + + + + + + + + An Attribution clause is a license clause intended to provide a specified level of recognition of the licensor as the copyright holder of the work. This can take many forms, including the requirement to preserve any copyright notice, attribution statements and the URL (link) to the original work. The attribution requirement thus serves the dual purpose of ensuring that the publisher receives appropriate credit, and that provenance information is kept intact. There are varying strengths of these clauses, from licensors requesting not to be attributed at all to requiring attribution for all uses of the resource. + Modified by Allyson Lister from http://creativecommons.org/tag/attribution + Attribution clause + + + + + + + + + Derivatives clauses are license clauses which state what requirements on derivative resource, if any, are attached to a license. The license for a resource may or may not allow the creation of new resources derived from it. If it is allowed, such usage may be restricted in a variety of ways. + Allyson Lister + Derivatives clause + + + + + + + + + A source code clause is a license clause which states the restrictions placed on the source code for the licensed software, if any. The license for a piece of software may or may not allow access to the source code. If such access is allowed, usage may be restricted in a variety of ways. + Allyson Lister + Source code clause + + + + + + + + + A Platform clause is a license clause which states the platform restrictions for the licensed resource, if any. The license for a resource may or may not allow the use of any platform. If it is allowed, such usage may be restricted in a variety of ways. + Allyson Lister + Platform clause + + + + + + + + + A Number of installations clause is a license clause which may limit the number of installations a particular licensee may peform. + Allyson Lister + Number of installations clause + + + + + + + + + A Number of users clause is a license clause which may limit the number of users a particular licensee may allow to use the resource. + Allyson Lister + Number of users clause + + + + + + + + + A time clause is a license clause which states the restrictions placed on the length of time the licensed resource may be used, if any. The license for a resource may or may not allow access to the resource for an unlimited time. If such access is allowed, usage may be restricted in a variety of ways. + Allyson Lister + Time clause + + + + + + + + + A usage clause is a license clause which states the restrictions placed on how the licensed resource may be used. The license for a resource may restrict how the licensee may use the software. If such access is allowed, usage may be restricted in a variety of ways. + Allyson Lister + Usage clause + + + + + + + + + + No restrictions on derivatives is a derivatives clause which places no rules or restrictions on how derivative software is created. + Allyson Lister + No restrictions on derivatives + + + + + + + + + Restrictions on derivative software is a derivatives clause which allows the creation of derivatives but which also places some kind of restriction on how derivative software may be created. + Allyson Lister + Restrictions on derivative software + + + + + + + + + + Derivatives not allowed clauses are derivatives clauses which state that derivative resources are never allowed using the licensed resource. + Allyson Lister + Derivatives not allowed + + + + + + + + + Derivative code same license is a restrictive derivatives clause where derivative software must be released under the same license. + Allyson Lister + derivative code same license + + + + + + + + + + A source code available clause is a source code clause which states that the source code for the licensed software is available to the licensee. However, usage of the source code may or may not be restricted in a variety of ways. + Allyson Lister + Source code available + + + + + + + + + A source code unavailable clause is a source code clause which states that the source code for the licensed software is not available to the licensee. + Allyson Lister + Source code unavailable + + + + + + + + + + Platform restricted is a platform clause which places restrictions on which platform the licensed resource may be installed on. + Allyson Lister + Platform restricted + + + + + + + + + Platform unrestrictred is a platform clause which does not place any restrictions on which type of platform the resource may be licensed for. + Allyson Lister + Platform unrestricted + + + + + + + + + + A Number of installations restricted clause is a number of installations clause which restricts the number of times the resource may be installed by any given licensee. + Allyson Lister + Number of installations restricted + + + + + + + + + A Number of installations unrestricted clause is a number of installations clause which does not restrict the number of times the resource may be installed by any given licensee. + Allyson Lister + Number of installations unrestricted + + + + + + + + + + A Number of users restricted clause is a number of users clause which restricts the number of users the resource may have for a particular licensee. This may be number of total users, or number of concurrent users. + Allyson Lister + Number of users restricted + + + + + + + + + A Number of users unrestricted clause is a number of users clause which does not restrict the number of users of the licensed resource. + Allyson Lister + Number of users unrestricted + + + + + + + + + + Time for use restricted is a time clause which places restrictions on the length of time the licensed resource may be used. + Allyson Lister + Time for use restricted + + + + + + + + + Time for use unrestrictred is a time clause which does not place any restrictions on the length of time the resource may be licensed for. + Time for use unrestricted + + + + + + + + + + Usage unrestricted is a usage clause which places no restrictions on how the licensed resource may be used. + Allyson Lister + Usage unrestricted + + + + + + + + + Usage restricted is a usage clause which places restrictions on how the licensed resource may be used. These restrictions will vary according to the individual license. + Allyson Lister + Usage restricted + + + + + + + + + Non-commercial use only is a usage restricted clause which restricts the use of the licensed resource only to licensees who are not commercial entites. + Non-commercial use only + + + + + + + + + Academic use only is a usage restricted clause which restricts the use of the licensed resource to academic licensees only. + Allyson Lister + Academic use only + + + + + + + + + Derivative code linked same license is a restrictive derivatives clause where code may only be linked to in derivative software that is released under the same license. + Allyson Lister + derivative code linked same license + + + + + + + + + The mode of interaction with a piece of software. + software interface + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Microsoft Excel + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2010-06-15T0:00:00 + + + Microsoft Excel for Windows 2010 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + The Windows Operating System + Microsoft Windows + + + + + + + + + + + + + + + + + + + + + + + + 2006-11-08T0:00:00 + + + Windows Vista + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 2001-10-25T0:00:00 + + + Windows XP + + + + + + + + + + + + + + + + + + + + + Microsoft Office 2001 + + + + + + + + + + + + + + + + + + + + software suite + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://get.adobe.com/reader/ + + + Andy Brown + Adobe Acrobat Reader + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://code.google.com/p/annotare/ + + + Andy Brown + Annotare + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://biojava.org + + + BioJava + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://www.bioperl.org + + + Andy Brown + BioPerl + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://ecobas.org/www-server/rem/mdb/dndc.html + + + + + + http://www.dndc.sr.unh.edu/ + + + Andy Brown + Soil Chemistry Model + DNDC + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://sourceforge.net/projects/droid/ + + + Digital Record Object Identification + DROID + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + www.dropbox.com + + + Dropbox + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://www.eclipse.org + + + Andy Brown + The Eclipse IDE + Eclipse + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + EMBOSS package + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://www.endnote.com/ + + + Andy Brown + Citation management software + Endnote + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://sf.net/projects/grimoires + + + Andy Brown + Grimoires + + + + + + + + + Marked as obsolete by Allyson Lister. + Obsoleted after the 0.4 release. + Equivalence with EDAM data_0582. + obsolete_ontology + true + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + software before Microsoft 2007 + + + + + + + + + clustering algorithm + + + + + + + + + pattern discovery algorithm + + + + + + + + + predictive modeling algorithm + + + + + + + + + Clustering specification is a single generalization specification is a generalization specification and denotes a type of generalization that models the mapping of a set of objects S of type T from S to a set of natural numbers {1,...K}. This generalization is obtained by appliing a clustering algorithm on a set of data. + OntoDM + clustering specification + + + + + + + + + A stochastic algorithm for population pharmacology modeling + http://www.math.u-bordeaux1.fr/MAS10/DOC/PDF-PRES/Lavielle.pdf + SAEM + + + + + + + + + A Dynamic Bayesian Network model is a Bayesian Network which relates variables to each other over adjacent time steps. + http://en.wikipedia.org/wiki/Dynamic_Bayesian_network, accessed 27 November 2014. + dynamic Bayesian network model + + + + + + + + + In mathematics, an ordinary differential equation or ODE is an equation containing a function of one independent variable and its derivatives. The term "ordinary" is used in contrast with the term partial differential equation which may be with respect to more than one independent variable. + Ordinary Differential Equation Algorithm + http://en.wikipedia.org/wiki/Ordinary_differential_equation, accessed 25 March 2015. + Allyson Lister + ODE Algorithm + + + + + + + + + Gillespie's Stochastic Simulation Algorithm is an algorithm which generates a statistically correct trajectory (possible solution) of a stochastic equation. It can be used to simulate chemical or biochemical systems of reactions efficiently and accurately using limited computational power. The algorithm is particularly useful for simulating reactions within cells where the number of reagents typically number in the tens of molecules (or less). Mathematically, it is a variety of a dynamic Monte Carlo method and similar to the kinetic Monte Carlo methods. It is used heavily in computational systems biology + http://en.wikipedia.org/wiki/Gillespie_algorithm, accessed 25 March 2015. + Allyson Lister + Gillespie's Stochastic Simulation Algorithm + + + + + + + + + Monte Carlo is a discrete stochastic simulation algorithm and an estimation procedure algorithm. If it is necessary to know the average value of some random variable and its distribution can not be stated, and if it is possible to take samples from the distribution, we can estimate it by taking the samples, independently, and averaging them. If there are sufficiently enough samples, then the law of large numbers says the average must be close to the true value. The central limit theorem says that the average has a Gaussian distribution around the true value. + http://en.wikipedia.org/wiki/Stochastic_simulation#Monte_Carlo_simulation, accessed 25 March 2015, and http://www.async.ece.utah.edu/iBioSim/docs/iBioSim.html, accessed 25 March 2015. + Allyson Lister + Monte Carlo + + + + + + + + + Differential Algebraic equations (DAEs) are a general form of (systems of) differential equations for vector–valued functions in one independent variable. In practical terms, the distinction between DAEs and ODEs is often that the solution of a DAE system depends on the derivatives of the input signal and not just the signal itself as in the case of ODEs. + Differential Algebraic Equation Algorithm + http://en.wikipedia.org/wiki/Differential_algebraic_equation, accessed 26 March 2015. + Allyson Lister + DAE Algorithm + + + + + + + + + A partial differential equation (PDE) is a differential equation that contains unknown multivariable functions and their partial derivatives. This is in contrast to ordinary differential equations, which deal with functions of a single variable and their derivatives. + Partial Differential Equation Algorithm + http://en.wikipedia.org/wiki/Partial_differential_equation, accessed 26 March 2015. + Allyson Lister + PDE Algorithm + + + + + + + + + A spreadsheet data format is one in which data is organised into a matrix (or matrices) of columns and rows to form cells in which values are entered. + James Malone + spreadsheet format + + + + + + + + + A spreadsheet data format designed for Microsoft Excel. + James Malone + XLS spreadsheet + + + + + + + + + A spreadsheet data format in which the structure of the data is described using XML, such as column and row headers and cell identity. + James Malone + XML spreadsheet + + + + + + + + + James Malone + Matlab .m file + + + + + + + + + Marked as obsolete by Allyson Lister. + 1.5 + Equivalence with EDAM http://edamontology.org/format_2332, please use that instead. + obsolete_XML + true + + + + + + + + + "Resource Description Framework (RDF) format." [http://edamontology.org] + format + bioinformatics + edam + formats + The Resource Description Framework (RDF) is a general-purpose language for representing information in the Web. + http://www.w3.org/TR/REC-rdf-syntax/ + James Malone + Jon Ison + Data in RDF format can be serialised into XML, textual, or binary format. + Merged with now-obsolete EDAM class 'RDF' http://edamontology.org/format_2376 by Allyson Lister. + RDF + + + + + + + + + + A serialisation of RDF into an XML format. + James Malone + RDF-XML + + + + + + + + + image format + + + + + + + + + DWG ("drawing") is a binary file format used for storing two and three dimensional design data and metadata + http://en.wikipedia.org/wiki/.dwg + James Malone + DWG + + + + + + + + + DXF (Drawing Interchange Format, or Drawing Exchange Format) is a CAD data file format developed by Autodesk for enabling data interoperability between AutoCAD and other programs. + http://en.wikipedia.org/wiki/AutoCAD_DXF + James Malone + DXF + + + + + + + + + The BMP File Format is a Raster graphics image file format used to store bitmap digital images, independently of the display device (such as a graphics adapter). + http://www.fileformat.info/format/bmp/egff.htm + James Malone + BMP + + + + + + + + + Computer Graphics Metafile (CGM) is a free and open international standard file format for 2D vector graphics, raster graphics, and text, and is defined by ISO/IEC 8632. + http://en.wikipedia.org/wiki/Computer_Graphics_Metafile + James Malone + CGM + + + + + + + + + web page specification + + + + + + + + + document exchange format + + + + + + + + + PDF is an open standard for document exchange. + Portable Document Format + pdf + + + + + + + + + TIFF is a flexible, adaptable file format for handling images and data within a single file, by including the header tags (size, definition, image-data arrangement, applied image compression) defining the image's geometry. + Tagged Image File Format + TIFF + + + + + + + + + JPEG is a lossy file format for storing images + JPG + JPEG + + + + + + + + + PNG is a bitmapped image format and video codec that employs lossless data compression. + Portable Network Graphics + PNG + + + + + + + + + The Graphics Interchange Format (GIF) is a bitmap image format. The format supports up to 8 bits per pixel thus allowing a single image to reference a palette of up to 256 distinct colors. The colors are chosen from the 24-bit RGB color space. It also supports animations and allows a separate palette of 256 colors for each frame. The color limitation makes the GIF format unsuitable for reproducing color photographs and other images with continuous color, but it is well-suited for simpler images such as graphics or logos with solid areas of color. [wikipedia] + Graphics Interchange Format + GIF + + + + + + + + + A raster image is a format for representing a rectangular grid of dots (pixels) which contains information on the specific colour of each pixel. + raster image format + + + + + + + + + A vector image is a collection of connected lines and curves that produce objects. This geometric description enables the image to be displayed without loss at any size rendering. + vector image format + + + + + + + + + Scalable Vector Graphics + SVG + + + + + + + + + Adobe Illustrator format + AI + + + + + + + + + PostScript is a format used for describing documents. + PostScript + + + + + + + + + tex is a format for documents written in the document markup language and document preparation system LaTeX. + LaTeX format + tex + + + + + + + + + A format specification for data used or produced by outliner software + outline document format + + + + + + + + + A proprietary format for documents created and edited using OmniOutliner outliner software, + OmniOutline format + + + + + + + + + OPML (Outline Processor Markup Language) is an XML format for outlines + Outline Processor Markup Language + OPML + + + + + + + + + JPEG 2000 is a compression standard enabling both lossless and lossy storage. The compression methods used are different from the ones in standard JFIF/JPEG; they improve quality and compression ratios, but also require more computational power to process. [wikipedia] + JPEG 2000 + + + + + + + + + word processing document format + + + + + + + + + WordStar format + + + + + + + + + A file format for word processing documents for Microsoft Word. + Microsoft Word doc + + + + + + + + + programming language format + + + + + + + + + A source code file format which is specified to be used with the Java programming language. + James Malone + .java file + + + + + + + + + A format in which a .java file has been compiled into bytecode using a Java compiler and which is specified to be executed using the Java virtual machine. + James Malone + .class file + + + + + + + + + An XML-based file format for use with the COPASI software. + .cps + CopasiML + + + + + + + + + Marked as obsolete by Allyson Lister. + Obsoleted after the 0.4 release. + Equivalence with the EDAM SBML class format_2585. + obsolete_SBML + true + + + + + + + + + The Web Ontology Language (OWL) in XML serialization + OWL-XML + + + + + + + + + Web Ontology Language version 2 in XML Serialization + OWL2-XML + + + + + + + + + Marked as obsolete by Allyson Lister. + Obsoleted after the 0.4 release. + Equivalence with EDAM term format_2549. + obsolete_OBO flat file format + true + + + + + + + + + Marked as obsolete by Allyson Lister. + 1.5 + Equivalence with EDAM http://edamontology.org/format_2330, please use that class instead. + obsolete_text file format + false + true + + + + + + + + + ASCII format + + + + + + + + + plain text file format + + + + + + + + + Marked as obsolete by Allyson Lister. + Obsoleted after release 0.4 + Equivalent with EDAM format_3162. + obsolete_MAGE tab format + true + + + + + + + + + Tab delimited file format is a plain text file format where each field value of a record is separated from the next by a tab stop character. + http://en.wikipedia.org/wiki/Tab-separated_values, accessed 6 June 2013. + Allyson Lister + tab delimited file format + + + + + + + + + Marked as obsolete by Allyson Lister. + Obsoleted after the version 0.4 release. + Equivalence with EDAM format_3158. + obsolete_PSI-MI format + true + + + + + + + + + SIF stands for Simple Interaction Format, and is a text format invented for Cytoscape. If the file contains any tab characters, then tabs are used to delimit the fields and spaces are considered part of the name. If the file contains no tabs, then any spaces are delimiters that separate names (and names cannot contain spaces). + http://wiki.cytoscape.org/GettingStarted and http://wiki.cytoscape.org/Cytoscape_User_Manual/Network_Formats, accessed 20 June 2012 + Allyson Lister + SIF + + + + + + + + + GML stands for Graph Markup Language, and is a standard network file format; supported by multiple generic network software packages + http://wiki.cytoscape.org/GettingStarted, accessed 20 June 2012 + GML + + + + + + + + + XGMML stands for eXtensible Graph Markup and Modelling Language, and it is a XML standard; similar to but preferred over GML. + http://wiki.cytoscape.org/GettingStarted, accessed 20 June 2012 + XGMML + + + + + + + + + A type of data which defines interactions between items in the file. This can be simple pairwise interactions or more complex ones. Used to provide a class of data for software requiring specific types of interaction data as input. + Allyson Lister + Interaction data + + + + + + + + + A knowledge representation role is a role borne by a data format which utilizes formalisms to make complex systems easier to design and build. Knowledge representation is the field of artificial intelligence devoted to representing information about the world in a form that a computer system can utilize to solve complex tasks. + Modified from http://en.wikipedia.org/wiki/Knowledge_representation, accessed 10 February 2014 + Knowledge representation role + + + + + + + + + + + + + + + BioPAX RDF/XML format + + + + + + + + + + + + + + + + + + + + + BioPAX Manchester OWL Syntax format + + + + + + + + + + + + + + + The CDF ASCII format is an ASCII data format specification created by Affymetrix similar to the Windows INI format. This format describes the layout for an Affymetrix GeneChip array. An array may contain Expression, Genotyping, CustomSeq, Copy Number and/or Tag probe sets. All probe set names within an array are unique. Multiple copies of a probe set may exist on a single array as long as each copy has a unique name. + http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/cdf.html, accessed 22 May 2013 + Allyson Lister + CDF ASCII format + + + + + + + + + + + + + + + BAR is a binary data format specification created by Affymetrix where the data is stored in big-endian format. The format of the file is a header section followed by sequences sections (one section per sequence defined). The BAR file contains one and two sample analysis results (signal and p-values) from the tiling array software. + http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/bar.html, accessed 22 May 2013. + Allyson Lister + BAR + + + + + + + + + + + + + + + CEL ASCII format is ASCII data format specification created by Affymetrix similar to the Windows INI format. The CEL format stores the results of the intensity calculations on the pixel values of the DAT file. This includes an intensity value, standard deviation of the intensity, the number of pixels used to calculate the intensity value, a flag to indicate an outlier as calculated by the algorithm and a user defined flag indicating the feature should be excluded from future analysis. The file stores the previously stated data for each feature on the probe array. + http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/cel.html, accessed 22 May 2013. + Allyson Lister + CEL ASCII format + + + + + + + + + + + + + + + + + + + + + + + + + Affymetrix-compliant data is data produced in a format compatible with Affymetrix software. This is a defined class where other data classes will be inferred to be members if they have a data format specification which has been published by Affymetrix. + Allyson Lister + Affymetrix-compliant data + + + + + + + + + The flow cytometry data file standard provides the specifications needed to completely describe flow cytometry data sets within the confines of the file containing the experimental data. The principal goal of the Standard is to provide a uniform file format allowing files created by one type of acquisition hardware and software to be analyzed by another type. + FCS + http://www.bioconductor.org/packages/2.12/bioc/vignettes/prada/inst/doc/fcs3.html, accessed May 29. 2013. + Allyson Lister + Data File Standard for Flow Cytometry + + + + + + + + + + + + + + + FCS3.0 is version 3.0 of the Data File Standard for Flow Cytometry. It contains a mechanism for handling data sets of 100 megabytes and larger, support for UNICODE text for keyword values, support for cyclic redundancy check (CRC) validation for each data set, a requirement for the inclusion of information describing the method of signal amplification and increased support for the inclusion of time as a measurement parameter. + http://www.bioconductor.org/packages/2.12/bioc/vignettes/prada/inst/doc/fcs3.html, accessed May 29. 2013. + Allyson Lister + FCS3.0 + + + + + + + + + NONMEM data format + + + + + + + + + A nucleic acid sequence that indicate the order of nucleotides within some DNA. + DNA nucleotide sequence + + + + + + + + + Data about primary biological sequence information, such as DNA neucleotide sequences. + biological sequence data + + + + + + + + + Data which contains information about amino acid sequences of proteins. + amino acid protein sequence data + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Nucleotide-nucleotide BLAST (blastn) is a type of BLAST software that takes a given DNA query and returns the most similar DNA sequences from the DNA database that the user specifies. + Nucleotide-nucleotide BLAST + BLASTN + + + + + + + + + Tabix indexes a TAB-delimited genome position file and creates an index file when region is absent from the command-line. The input data file must be position sorted and compressed by bgzip which has a gzip like interface. After indexing, tabix is able to quickly retrieve data lines overlapping regions specified in the format "chr:beginPos-endPos". Fast data retrieval also works over network if URI is given as a file name and in this case the index file will be downloaded if it is not present locally. + http://samtools.sourceforge.net/tabix.shtml + tabix file format + + + + + + + + + Genomedata provides a way to store and access large-scale functional genomics data in a format which is both space-efficient and allows efficient random-access. Genomedata archives are implemented as one or more HDF5 files, either as single files or as directory archives. HDF5 archives are self describing, like XML, but may also contain more complex structures such contain binary data. + http://pmgenomics.ca/hoffmanlab/proj/genomedata/doc/1.3.5/genomedata.html and http://www.hdfgroup.org/why_hdf/, accessed 27 November 2014. + Allyson Lister + genomedata format + + + + + + + + + The bedGraph format is a line-oriented text file format. Bedgraph data are preceeded by a track definition line, which adds a number of options for controlling the default display of this track. Following the track definition line are the track data in four column BED format. The bedGraph format allows display of continuous-valued data in track format. This display type is useful for probability scores and transcriptome data. This track type is similar to the wiggle (WIG) format, but unlike the wiggle format, data exported in the bedGraph format are preserved in their original state. + http://genome.ucsc.edu/goldenpath/help/bedgraph.html, accessed December 3, 2014. + Allyson Lister + BedGraph + + + + + + + + + GMTK parameter data is a type of data which contains the various parameter files required by GMTK to define a dynamic Bayesian network. + These parameter files come in multiple types (e.g. structure files and master files), and therefore this is a data type rather than a single format. + Graphical Models Toolkit parameter data + Allyson Lister + http://noble.gs.washington.edu/proj/philius/README, accessed 3 December 2014. + Allyson Lister + GMTK parameter data + + + + + These parameter files come in multiple types (e.g. structure files and master files), and therefore this is a data type rather than a single format. + + + + + + + + + + MathML 2.0 is an XML format which is a low-level specification for describing mathematics as a basis for machine to machine communication. It is a W3C Recommendation and was released on 21 Feb 2001. A product of the W3C Math working group, it provides a much needed foundation for the inclusion of mathematical expressions in Web pages. + http://www.w3.org/Math/ + Allyson Lister + James Malone + MathML 2.0 + + + + + + + + + FieldML is an XML-based language for describing time-varying and +spatially-varying fields. The aims of the language design process are to +keep the language concise, consistent, intuitive and flexible. + http://www.physiomeproject.org/xml_languages/fieldml + James Malone + FieldML + + + + + + + + + WKn is a collective name for a spreadsheet format created for Lotus 1-2-3. + http://support.sas.com/documentation/cdl/en/acpcref/63184/HTML/default/viewer.htm#a003103772.htm and http://en.wikipedia.org/wiki/Lotus_1-2-3, accessed 3 December 2014. + Allyson Lister + Please note that this is a collective class for all versions of the WKn format, and the specific version required should be created as necessary and placed as a child of this class. + WKn + + + + + + + + + GZipped format + .gz + + + + + + + + + Zipped format + .zip + + + + + + + + + audio format + + + + + + + + + Resource Interchange File Format + RIFF + + + + + + + + + BigWig format + .bw + + + + + + + + + Comma-separated value format + .csv + + + + + + + + + MASCOT generic format + .mgf + + + + + + + + + MySQL format + .mysql + + + + + + + + + SQL format + .sql + + + + + + + + + A Web User interface is a Graphical User Interface which is loaded and run via a Web browser rather than within the user's operating system. + WUI + Web UI + Allyson Lister + web user interface + + + + + + + + + A Desktop Graphical User interface is a Graphical User Interface which is loaded and run within the user's operating system rather than via a Web browser. + Desktop GUI + Allyson Lister + desktop graphical user interface + + + + + + + + + A SOAP service is a Web service which provides a standard, extensible, composable framework for packaging and exchanging XML messages. The service may expose an arbitrary, application-specific set of operations. + SOAP Service + Modified from http://en.wikipedia.org/wiki/SOAP, accessed 6 June 2013; modified from http://www.w3.org/TR/ws-arch, accessed 6 June 2013. + Allyson Lister + SOAP service + + + + + + + + + A REST service is a Web service in which the primary purpose of the service is to manipulate XML representations of Web resources using a uniform set of "stateless" operations. RESTful APIs do not require XML-based web service protocols (SOAP and WSDL) to support their light-weight interfaces. + REST Service + Modified from http://www.w3.org/TR/ws-arch, accessed 6 June 2013, Modified from http://en.wikipedia.org/wiki/Web_service, accessed 6 June 2013. + Allyson Lister + REST service + + + + + + + + + A web service in which calls invoked return JSON. + JSON web service + + + + + + + + + A web service is a software interface which works as a method of communication between two electronic devices over the World Wide Web and which is provided at a particular network address. There are two major classes of Web services: REST-compliant Web services, and arbitrary (or application-specific) Web services. + Web Service + Modified from http://www.w3.org/TR/ws-arch/, accessed 6 June 2013; Modified from http://en.wikipedia.org/wiki/Web_service, accessed 6 June 2013. + Allyson Lister + web service + + + + + + + + + A Graphical user interface is a type of software interface that allows users to interact with electronic devices using images rather than text commands. A GUI represents the information and actions available to a user through graphical icons and visual indicators such as secondary notation, as opposed to text-based interfaces, typed command labels or text navigation. + https://en.wikipedia.org/wiki/Graphical_user_interface, accessed 6 June 2013. + GUI + Allyson Lister + graphical user interface + + + + + + + + + A command-line interface is a means of interacting with a computer program where the user (or client) issues commands to the program in the form of successive lines of text (command lines). + Command line + Command line interface + Command-line + http://en.wikipedia.org/wiki/Command-line_interface, accessed 25 November 2014. + command-line interface + + + + + + + + + An application programming interface is a set of routines, protocols, and tools for building software applications. An API expresses a software component in terms of its operations, inputs, outputs, and underlying types. An API defines functionalities that are independent of their respective implementations, which allows definitions and implementations to vary without compromising each other. The API specifies how software components should interact. + API + http://en.wikipedia.org/wiki/Application_programming_interface, accessed 25 November 2014. + application programming interface + + + + + + + + + CC + Creative Commons + + + + + + + + + Proprietary commercial software license + + + + + + + + + + + + + + + + + + + + + + + + + + + Mozilla Public License Version 1.1 + MPL v1.1 + + + + + + + + + Distribution clauses are license clauses which state the requirements on how the licensed resource is redistributed. The license for a resource may or may not allow the redistribution of that resource. If it is allowed, such usage may be restricted in a variety of ways. + Allyson Lister + Distribution clause + + + + + + + + + + Distribution restricted is a distribution clause which places restrictions on how the licensed resource may be distributed by third parties. These restrictions may be complete, e.g. no further redistribution, or partial. + Allyson Lister + Distribution restricted + + + + + + + + + Distribution unrestricted is a distribution clause which states that the licensed resource can be redistributed by a third party in whatever manner that party wishes. + Allyson Lister + Distribution unrestricted + + + + + + + + + Derivatives allowed clauses are derivatives clauses which state that derivative resources are allowed using the licensed resource. Even when allowed, such a clause may or may not restrict the usage of the licensed resource in a variety of ways. + Allyson Lister + Derivatives allowed + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + GNU General Public License + GNU GPL + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://www.apache.org/licenses/LICENSE-2.0 + + + This is a free software license under the definition of "free" by the GNU Project, and is compatible with version 3 of the GNU GPL. + http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013. + Allyson Lister + Apache License Version 2.0 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://www.opensource.org/licenses/afl-3.0.php + + + + + + https://opensource.org/licenses/AFL-3.0 + + + The Academic Free License is a free software license under the definition of "free" by the GNU Project, is not copyleft, and is incompatible with the GNU GPL. + AFL + http://directory.fsf.org/wiki/License:AFLv3, accessed 12 June 2013; http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013 + Allyson Lister + Andy Brown + Academic Free License version 3 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://www.freebsd.org/copyright/freebsd-license.html + + + This is the original BSD license with the advertising clause and another clause removed. (It is also sometimes called the “2-clause BSD license”.) It is a lax, permissive non-copyleft free software license, compatible with the GNU GPL. + 2-clause BSD License + http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013. + Allyson Lister + Andy Brown + FreeBSD + + + + + + + + + + + + + + + Open source software license + + + + + + + + + + + + + + + License without restrictions on derivatives + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + A licensed is a free license according to GNU if the users have the four essential freedoms: + + The freedom to run the program, for any purpose (freedom 0). + The freedom to study how the program works, and change it so it does your computing as you wish (freedom 1). Access to the source code is a precondition for this. + The freedom to redistribute copies so you can help your neighbor (freedom 2). + The freedom to distribute copies of your modified versions to others (freedom 3). By doing this you can give the whole community a chance to benefit from your changes. Access to the source code is a precondition for this. + +A program is free software if users have all of these freedoms. Thus, you should be free to redistribute copies, either with or without modifications, either gratis or charging a fee for distribution, to anyone anywhere. Being free to do these things means (among other things) that you do not have to ask or pay for permission to do so. + +“Free software” does not mean “noncommercial”. A free program must be available for commercial use, commercial development, and commercial distribution. Commercial development of free software is no longer unusual; such free commercial software is very important. You may have paid money to get copies of free software, or you may have obtained copies at no charge. But regardless of how you got your copies, you always have the freedom to copy and change the software, even to sell copies. + http://www.gnu.org/philosophy/free-sw.html, accessed 12 June 2013. + Allyson Lister + Allyson Lister: This class defines those licenses which are free licenses, but which may or may not be compatible with any version of the GNU GPL. + GNU Project Free License Type + + + + + + + + + + + + + + + + + + + + + + + + + + + GNU GPL Compatible License Type is a GNU Project Free License Type which is also compatible with one or more versions of the GNU GPL + Modified from http://www.gnu.org/copyleft/copyleft.html, accessed 12 June 2013. + Allyson Lister + GNU GPL Compatible License Type + + + + + + + + + Copyleft is a derivative code same license clause which says that anyone who redistributes the software, with or without changes, must pass along the freedom to further copy and change it. In other words, it requires that all derivative code uses the same license, but further limits the type of license to one which gives everyone the rights to use, modify, and redistribute the program's code, or any program derived from it, but only if the distribution terms are unchanged. To copyleft a program, you first state that it is copyrighted; then the distribution terms described above are added. This makes copyleft a legal instrument ensuring that the code and the freedoms become legally inseparable. + Modified from http://www.gnu.org/copyleft/copyleft.html, accessed 12 June 2013. + Allyson Lister + Copyleft + + + + + + + + + The GNU GPL v3 is the latest version of the GNU GPL: a free software license, and a copyleft license. Please note that GPLv3 is not compatible with GPLv2 by itself. However, most software released under GPLv2 allows you to use the terms of later versions of the GPL as well. When this is the case, you can use the code under GPLv3 to make the desired combination. + GNU General Public License Version 3 + https://www.gnu.org/licenses/license-list.html, accessed on 23 June 2016. + Allyson Lister + GNU GPL v3 + + + + + + + + + The GNU GPL v2 is an earlier version of the GNU GPL: a free software license, and a copyleft license. Please note that GPLv2 is, by itself, not compatible with GPLv3. However, most software released under GPLv2 allows you to use the terms of later versions of the GPL as well. When this is the case, you can use the code under GPLv3 to make the desired combination. + GNU General Public License Version 2 + https://www.gnu.org/licenses/license-list.html, accessed 23 June 2016. + GNU GPL v2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + https://creativecommons.org/publicdomain/zero/1.0/ + + + CC0 is a public domain dedication from Creative Commons. A work released under CC0 is dedicated to the public domain to the fullest extent permitted by law. If that is not possible for any reason, CC0 also provides a lax, permissive license as a fallback. Both public domain works and the lax license provided by CC0 are compatible with the GNU GPL. + CC0 1.0 Universal (CC0 1.0) Public Domain Dedication + http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013. + Allyson Lister + CC0 1.0 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://creativecommons.org/licenses/by/2.0/ + + + CC BY 2.0 is a non-copyleft free (free by the definition of the GNU Project) license which lets others distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you for the original creation. This is the most accommodating of Creative Commons licenses offered. Recommended for maximum dissemination and use of licensed materials. The GNU Project recommend it for art, entertainment works, and educational works. It is compatible with all versions of the GNU GPL; however, like all CC licenses, it should not be used on software. + Creative Commons Attribution 2.0 Generic (CC BY 2.0) + Modified from http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013 and 28 June 2016; Modified from http://creativecommons.org/licenses/, accessed 12 June 2013. + Allyson Lister + CC BY 2.0 + + + + + + + + + Attribution required is an attribution clause which states that attribution of the type specified in the license must be provided whenever the resource is used. + Allyson Lister + Attribution required + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + https://creativecommons.org/licenses/by-sa/2.0/ + + + CC BY-SA 2.0 is a copyleft free (free by the definition of the GNU Project) license which lets others remix, tweak, and build upon your work even for commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project recommend this license for art, entertainment and educational works, but also recommend that it is not used for software or documentation, since it is tricky as to how exactly this license is compatible with the GNU GPL. + Creative Commons Attribution-Sharealike 2.0 Generic + Modified from http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013; Modified from http://creativecommons.org/licenses/, accessed 12 June 2013. + Allyson Lister + CC BY-SA 2.0 + + + + + + + + + + + + + + + + + + + + + + + + + + + https://latex-project.org/lppl/lppl-1-3c.html + + + LPPL v1.3 is a free software license (by the defintion of the GNU Project), with less stringent requirements on distribution than LPPL 1.2. It is still incompatible with the GPL because some modified versions must include a copy of or pointer to an unmodified version.Software projects other than LaTeX rarely use it. + Latex Project Public License v1.3c + Modified from http://en.wikipedia.org/wiki/LaTeX_Project_Public_License, accessed 12 June 2013; modified from http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013. + LPPL v1.3c + + + + + + + + + + + + + + + + + + + + + + + + + + + https://latex-project.org/lppl/lppl-1-2.html + + + LPPL v1.2 is a free software license (by the defintion of the GNU Project), This license is an incomplete statement of the distribution terms for LaTeX. While it is a free software license, it is incompatible with the GPL because it has many requirements that are not in the GPL. Software projects other than LaTeX rarely use it. + Latex Project Public License v1.2 + Modified from http://en.wikipedia.org/wiki/LaTeX_Project_Public_License, accessed 12 June 2013; modified from http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013. + LPPL v1.2 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + MPL v2.0 a free software license as defined by the GNU Project. Section 3.3 provides indirect compatibility between this license and the GNU GPL version 2.0, the GNU LGPL version 2.1, the GNU AGPL version 3.0, and all later versions of those licenses. The MPL allows covered source code to be mixed with other files under a different, even proprietary license. However, code files licensed under the MPL must remain under the MPL and freely available in source form. + http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013; http://en.wikipedia.org/wiki/Mozilla_Public_License, accessed 12 June 2013. + MPL v2.0 + Mozilla Public License Version 2.0 + + + + + + + + + Allyson Lister + Artistic License + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + https://opensource.org/licenses/Artistic-2.0 + + + The Artistic License v 2.0 is a free software license by the definition of the GNU Project and compatible with the GPL thanks to the relicensing option in section 4(c)(ii) (as compared with the Artistic License 1.0). + http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013. + Allyson Lister + Artistic License 2.0 + + + + + + + + + Purchase cost is a license clause which states whether there is a cost involved with a particular usage or licensing of a resource. + Allyson Lister + Allyson Lister + In some ways, purchase cost is similar to the already-extant usage clause hierarchy, which includes restricted and unrestricted usage. However, a usage limitation is not necessarily due to whether or not something costs money: even if the usage is academic only, it could still be either free or non-free. A license could have multiple usage clauses, e.g. academic only when free, and unrestricted if a fee is paid. Purchase cost was created which, together with a usage clause, defines both limitations and cost. + Purchase cost + + + + + + + + + Free is a type of purchase cost clause which, when applied, means that there is no cost for the users of the resource to which the license is attached. This clause can be combined with other clauses (such as usage clauses) to specify that only certain usages are free. + Allyson Lister + Allyson Lister + This class refers only to the cost of the resource, not to the definition of "free software" as provided by the GNU Project and which is commonly used to describe software that respects users' freedom and community (http://www.gnu.org/philosophy/free-sw.html). + Free + + + + + + + + + Not Free is a type of purchase cost clause which, when applied, means that there is a cost for the users of the resource to which the license is attached. This clause can be combined with other clauses (such as usage clauses) to specify that only certain usages incur a purchase cost. + Allyson Lister + Allyson Lister + This class refers only to the cost of the resource, not to the definition of "free software" as provided by the GNU Project and which is commonly used to describe software that respects users' freedom and community (http://www.gnu.org/philosophy/free-sw.html). + Not Free + + + + + + + + + + + + + + + A license which allows any form of usage of the artifact. + free to use license + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://creativecommons.org/licenses/by/4.0/ + + + The CC BY 4.0 license is a Creative Commons license. This is a non-copyleft free license that is good for art and entertainment works, and educational works. It is compatible with all versions of the GNU GPL; however, like all CC licenses, it should not be used on software. People are free to: +Share — copy and redistribute the material in any medium or format; +Adapt — remix, transform, and build upon the material for any purpose, even commercially. +The licensor cannot revoke these freedoms as long as you follow the license terms. +But they must conform to the following terms: +Attribution — You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. +No additional restrictions — You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. + Creative Commons Attribution 4.0 International (CC BY 4.0) + http://creativecommons.org/licenses/by/4.0/ accessed June 22, 2016; https://www.gnu.org/licenses/license-list.html, accessed on June 28, 2016. + Allyson Lister + Allyson Lister: The only restriction on derivatives is that of the attribution requirement. + CC BY 4.0 + + + + + + + + + Attribution not required is an attribution clause which states that no attribution need be provided whenever the resource is used. + Allyson Lister + Allyson Lister + Attribution not required + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + https://creativecommons.org/licenses/by/2.0/uk/ + + + CC BY 2.0 UK is a UK-specific non-copyleft free (free by the definition of the GNU Project) license which lets others distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you for the original creation. This is the most accommodating of Creative Commons licenses offered. Recommended for maximum dissemination and use of licensed materials. The GNU Project recommend it for art, entertainment works, and educational works. It is compatible with all versions of the GNU GPL; however, like all CC licenses, it should not be used on software. + Creative Commons Attribution 2.0 UK: England & Wales (CC BY 2.0 UK) + Modified from the definition of http://www.ebi.ac.uk/swo/license/SWO_1000050. + Allyson Lister + CC BY 2.0 UK + + + + + + + + + + + + + + + + + + + + + + + + + + + + This is the latest version of the LGPL: a free software license, but not a strong copyleft license, because it permits linking with nonfree modules. It is compatible with GPLv3. It is therefore recommend for special circumstances only. + +Please note that LGPLv3 is not compatible with GPLv2 by itself. However, most software released under GPLv2 allows you to use the terms of later versions of the GPL as well. When this is the case, you can use the code under GPLv3 to make the desired combination. + GNU Lesser General Public License (LGPL) version 3 + https://www.gnu.org/licenses/license-list.html, accessed 23 June 2016. + GNU LGPL v3 + + + + + + + + + GNU AGPL + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + This is a free software, copyleft license. Its terms effectively consist of the terms of GPLv3, with an additional paragraph in section 13 to allow users who interact with the licensed software over a network to receive the source for that program. It is recommended that developers consider using the GNU AGPL for any software which will commonly be run over a network. + GNU Affero General Public License (AGPL) version 3 + https://www.gnu.org/licenses/license-list.html, accessed on 23 June 2016. + Allyson Lister + GNU AGPL v3 + + + + + + + + + + + + + + + + + + + + + This is the previous version of the LGPL: a free software license, but not a strong copyleft license, because it permits linking with nonfree modules. It is compatible with GPLv2 and GPLv3. We generally recommend the latest version of the LGPL, for special circumstances only. + GNU Lesser General Public License (LGPL) version 2.1 + https://www.gnu.org/licenses/license-list.html, accessed 28 June 2016. + GNU LGPL v2.1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://creativecommons.org/licenses/by/2.1/jp/deed.en + + + CC BY 2.1 JP is a Japan-specific non-copyleft free (free by the definition of the GNU Project) license which lets others distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you for the original creation. This is the most accommodating of Creative Commons licenses offered. Recommended for maximum dissemination and use of licensed materials. The GNU Project recommend it for art, entertainment works, and educational works. It is compatible with all versions of the GNU GPL; however, like all CC licenses, it should not be used on software. + Creative Commons Attribution 2.1 Japan (CC BY 2.1 JP) + Modified from the definition of http://www.ebi.ac.uk/swo/license/SWO_1000050. + Allyson Lister + CC BY 2.1 JP + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + https://creativecommons.org/licenses/by/2.5/ + + + CC BY 2.5 is a non-copyleft free (free by the definition of the GNU Project) license which lets others distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you for the original creation. This is the most accommodating of Creative Commons licenses offered. Recommended for maximum dissemination and use of licensed materials. The GNU Project recommend it for art, entertainment works, and educational works. It is compatible with all versions of the GNU GPL; however, like all CC licenses, it should not be used on software. + Creative Commons Attribution 2.5 Generic (CC BY 2.5) + Modified from the definition of http://www.ebi.ac.uk/swo/license/SWO_1000050. + Allyson Lister + CC BY 2.5 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + https://creativecommons.org/licenses/by/3.0/au/ + + + CC BY 3.0 AU is an Australia-specific non-copyleft free (free by the definition of the GNU Project) license which lets others distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you for the original creation. This is the most accommodating of Creative Commons licenses offered. Recommended for maximum dissemination and use of licensed materials. The GNU Project recommend it for art, entertainment works, and educational works. It is compatible with all versions of the GNU GPL; however, like all CC licenses, it should not be used on software. + Creative Commons Attribution 3.0 Australia (CC BY 3.0 AU) + Modified from the definition of http://www.ebi.ac.uk/swo/license/SWO_1000050. + Allyson Lister + CC BY 3.0 AU + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + https://creativecommons.org/licenses/by/3.0/ + + + CC BY 3.0 is a non-copyleft free (free by the definition of the GNU Project) license which lets others distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you for the original creation. This is the most accommodating of Creative Commons licenses offered. Recommended for maximum dissemination and use of licensed materials. The GNU Project recommend it for art, entertainment works, and educational works. It is compatible with all versions of the GNU GPL; however, like all CC licenses, it should not be used on software. + Creative Commons Attribution 3.0 Unported (CC BY 3.0) + Modified from the definition of http://www.ebi.ac.uk/swo/license/SWO_1000050. + Allyson Lister + CC BY 3.0 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + https://creativecommons.org/licenses/by/3.0/us/ + + + CC BY 3.0 US is a US-specific non-copyleft free (free by the definition of the GNU Project) license which lets others distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you for the original creation. This is the most accommodating of Creative Commons licenses offered. Recommended for maximum dissemination and use of licensed materials. The GNU Project recommend it for art, entertainment works, and educational works. It is compatible with all versions of the GNU GPL; however, like all CC licenses, it should not be used on software. + Creative Commons Attribution 3.0 United States (CC BY 3.0 US) + Modified from the definition of http://www.ebi.ac.uk/swo/license/SWO_1000050. + Allyson Lister + CC BY 3.0 US + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + https://creativecommons.org/licenses/by-nd/3.0/ + + + CC BY-ND 3.0 is a nonfree license, as there are restrictions on distributing modified versions. You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. If you remix, transform, or build upon the material, you may not distribute the modified material. This license is generally used for documentation. + Creative Commons Attribution-NoDerivs 3.0 Unported (CC BY-ND 3.0) + https://www.gnu.org/licenses/license-list.html accessed 29 June 2016; https://creativecommons.org/licenses/by-nd/3.0/ accessed 29 June 2016. + Allyson Lister + CC BY-ND 3.0 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + https://creativecommons.org/licenses/by-nd/4.0/ + + + CC BY-ND 4.0 is a nonfree license, as there are restrictions on distributing modified versions. You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. If you remix, transform, or build upon the material, you may not distribute the modified material. This license is generally used for documentation. + Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0) + https://www.gnu.org/licenses/license-list.html accessed 29 June 2016; https://creativecommons.org/licenses/by-nd/3.0/ accessed 29 June 2016. + Allyson Lister + CC BY-ND 4.0 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + https://creativecommons.org/licenses/by-nc/3.0/ + + + CC BY-NC 3.0 is a nonfree license, as there are restrictions on charging money for copies. You must give appropriate credit, provide a link to the license, use the work for non-commercial purposes, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. The GNU Project does not recommend that you use this license for documentation. In addition, it has a drawback for any sort of work: when a modified version has many authors, in practice getting permission for commercial use from all of them would become infeasible. + + + Creative Commons Attribution-NonCommercial 3.0 Unported (CC BY-NC 3.0) + https://www.gnu.org/licenses/license-list.html accessed 29 June 2016. + Allyson Lister + CC BY-NC 3.0 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + https://creativecommons.org/licenses/by-nc/4.0/ + + + CC BY-NC 4.0 is a nonfree license, as there are restrictions on charging money for copies. You must give appropriate credit, provide a link to the license, use the work for non-commercial purposes, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. The GNU Project does not recommend that you use this license for documentation. In addition, it has a drawback for any sort of work: when a modified version has many authors, in practice getting permission for commercial use from all of them would become infeasible. + + + Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) + https://www.gnu.org/licenses/license-list.html accessed 29 June 2016. + Allyson Lister + CC BY-NC 4.0 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + https://creativecommons.org/licenses/by-nc-nd/3.0/ + + + CC BY-NC-ND 3.0 is a nonfree license, as there are restrictions on distributing modified versions and on charging money for copies. You must give appropriate credit, provide a link to the license, and use the work for non-commercial purposes. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. If you remix, transform, or build upon the material, you may not distribute the modified material. + Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported (CC BY-NC-ND 3.0) + https://www.gnu.org/licenses/license-list.html accessed 29 June 2016. + Allyson Lister + CC BY-NC-ND 3.0 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + https://creativecommons.org/licenses/by-nc-nd/2.5/ + + + CC BY-NC-ND 2.5 is a nonfree license, as there are restrictions on distributing modified versions and on charging money for copies. You must give appropriate credit, provide a link to the license, and use the work for non-commercial purposes. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. If you remix, transform, or build upon the material, you may not distribute the modified material. + Creative Commons Attribution-NonCommercial-NoDerivs 2.5 Generic (CC BY-NC-ND 2.5) + https://www.gnu.org/licenses/license-list.html accessed 29 June 2016. + Allyson Lister + CC BY-NC-ND 2.5 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://creativecommons.org/licenses/by-nc-nd/2.5/ch/deed.en + + + CC BY-NC-ND 2.5 CH is a nonfree license, as there are restrictions on distributing modified versions and on charging money for copies. You must give appropriate credit, provide a link to the license, and use the work for non-commercial purposes. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. If you remix, transform, or build upon the material, you may not distribute the modified material. + Creative Commons Attribution-NonCommercial-NoDerivs 2.5 Switzerland (CC BY-NC-ND 2.5 CH) + https://www.gnu.org/licenses/license-list.html accessed 29 June 2016. + Allyson Lister + CC BY-NC-ND 2.5 CH + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + https://creativecommons.org/licenses/by-nc-nd/4.0/ + + + CC BY-NC-ND 4.0 is a nonfree license, as there are restrictions on distributing modified versions and on charging money for copies. You must give appropriate credit, provide a link to the license, and use the work for non-commercial purposes. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. If you remix, transform, or build upon the material, you may not distribute the modified material. + Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International (CC BY-NC-ND 4.0) + https://www.gnu.org/licenses/license-list.html accessed 29 June 2016. + Allyson Lister + CC BY-NC-ND 4.0 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + https://creativecommons.org/licenses/by-nc-sa/2.5/ + + + CC BY-NC-SA 2.5 is a nonfree license, as there are restrictions on charging money for copies. You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. This license also lets others build upon the original work for non-commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project does not recommend that you use this license for documentation. In addition, it has a drawback for any sort of work: when a modified version has many authors, in practice getting permission for commercial use from all of them would become infeasible. + + + Creative Commons Attribution-NonCommercial-ShareAlike 2.5 Generic (CC BY-NC-SA 2.5) + https://www.gnu.org/licenses/license-list.html accessed 29 June 2016. + Allyson Lister + CC BY-NC-SA 2.5 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + https://creativecommons.org/licenses/by-nc-sa/3.0/ + + + CC BY-NC-SA 3.0 is a nonfree license, as there are restrictions on charging money for copies. You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. This license also lets others build upon the original work for non-commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project does not recommend that you use this license for documentation. In addition, it has a drawback for any sort of work: when a modified version has many authors, in practice getting permission for commercial use from all of them would become infeasible. + + + Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported (CC BY-NC-SA 3.0) + https://www.gnu.org/licenses/license-list.html accessed 29 June 2016. + Allyson Lister + CC BY-NC-SA 3.0 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + https://creativecommons.org/licenses/by-nc-sa/3.0/us/ + + + CC BY-NC-SA 3.0 US is a nonfree license, as there are restrictions on charging money for copies. You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. This license also lets others build upon the original work for non-commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project does not recommend that you use this license for documentation. In addition, it has a drawback for any sort of work: when a modified version has many authors, in practice getting permission for commercial use from all of them would become infeasible. + + + Creative Commons Attribution-NonCommercial-ShareAlike 3.0 United States (CC BY-NC-SA 3.0 US) + https://www.gnu.org/licenses/license-list.html accessed 29 June 2016. + Allyson Lister + CC BY-NC-SA 3.0 US + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + https://creativecommons.org/licenses/by-nc-sa/2.5/in/ + + + CC BY-NC-SA 2.5 IN is a nonfree license, as there are restrictions on charging money for copies. You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. This license also lets others build upon the original work for non-commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project does not recommend that you use this license for documentation. In addition, it has a drawback for any sort of work: when a modified version has many authors, in practice getting permission for commercial use from all of them would become infeasible. + + + Creative Commons Attribution-NonCommercial-ShareAlike 2.5 India (CC BY-NC-SA 2.5 IN) + https://www.gnu.org/licenses/license-list.html accessed 29 June 2016. + Allyson Lister + CC BY-NC-SA 2.5 IN + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + https://creativecommons.org/licenses/by-nc-sa/4.0/ + + + CC BY-NC-SA 4.0 is a nonfree license, as there are restrictions on charging money for copies. You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use. This license also lets others build upon the original work for non-commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project does not recommend that you use this license for documentation. In addition, it has a drawback for any sort of work: when a modified version has many authors, in practice getting permission for commercial use from all of them would become infeasible. + + + Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) + https://www.gnu.org/licenses/license-list.html accessed 29 June 2016. + Allyson Lister + CC BY-NC-SA 4.0 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + https://creativecommons.org/licenses/by-sa/2.1/jp/deed.en + + + CC BY-SA 2.1 JP is a copyleft free (free by the definition of the GNU Project) license which lets others remix, tweak, and build upon your work even for commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project recommend this license for art, entertainment and educational works, but also recommend that it is not used for software or documentation, since it is tricky as to how exactly this license is compatible with the GNU GPL. + Creative Commons Attribution-Sharealike 2.1 Japan + Modified from http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013; Modified from http://creativecommons.org/licenses/, accessed 12 June 2013. + Allyson Lister + CC BY-SA 2.1 JP + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://creativecommons.org/licenses/by-sa/3.0/ + + + CC BY-SA 3.0 is a copyleft free (free by the definition of the GNU Project) license which lets others remix, tweak, and build upon your work even for commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project recommend this license for art, entertainment and educational works, but also recommend that it is not used for software or documentation, since it is tricky as to how exactly this license is compatible with the GNU GPL. + Creative Commons Attribution-Sharealike 3.0 Unported + Modified from http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013; Modified from http://creativecommons.org/licenses/, accessed 12 June 2013. + Allyson Lister + CC BY-SA 3.0 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://creativecommons.org/licenses/by-sa/3.0/us/ + + + CC BY-SA 3.0 US is a copyleft free (free by the definition of the GNU Project) license which lets others remix, tweak, and build upon your work even for commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project recommend this license for art, entertainment and educational works, but also recommend that it is not used for software or documentation, since it is tricky as to how exactly this license is compatible with the GNU GPL. + Creative Commons Attribution-Sharealike 3.0 United States + Modified from http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013; Modified from http://creativecommons.org/licenses/, accessed 12 June 2013. + Allyson Lister + CC BY-SA 3.0 US + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://creativecommons.org/licenses/by-sa/4.0/ + + + CC BY-SA 4.0 is a copyleft free (free by the definition of the GNU Project) license which lets others remix, tweak, and build upon your work even for commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project recommend this license for art, entertainment and educational works, but also recommend that it is not used for software or documentation, since it is tricky as to how exactly this license is compatible with the GNU GPL. + Creative Commons Attribution-Sharealike 4.0 International + Modified from http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013; Modified from http://creativecommons.org/licenses/, accessed 12 June 2013. + Allyson Lister + CC BY-SA 4.0 + + + + + + + + + Open Data Commons + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://www.opendatacommons.org/licenses/odbl/1.0/ + + + The ODbL v1.0 allows a user of the databases to share, create and adapt the database. You must attribute any public use of the database, or works produced from the database. For redistribution of the database or derivative works, you must make the use of this license clear to others, and you must keep intact any notices on the original database. If you publicly use any adapted version of this database, or works produced from an adapted database, you must also offer that adapted database under the ODbL. If you redistribute the database, or an adapted version of it, then you may use technological measures that restrict the work (such as DRM) as long as you also redistribute a version without such measures. + Open Database License (ODbL) v1.0 + http://opendatacommons.org/licenses/odbl/summary/, accessed 5 July 2016. + Allyson Lister + ODbL v1.0 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://opendatacommons.org/licenses/dbcl/1.0/ + + + The DbCL v1.0 allows a user of the database contents to share, create and adapt the contents. You must attribute any public use of the contents, or works produced from them. For redistribution or derivative works, you must make the use of this license clear to others, and you must keep intact any notices on the original. If you publicly use any adapted version, or works produced from an adapted version, you must also offer it under the DbCL. If you redistribute the contents, or an adapted version of them, then you may use technological measures that restrict the work (such as DRM) as long as you also redistribute a version without such measures. Users of the DbCL must comply with the ODbL v1.0. + ODC Database Contents License (DbCL) v1.0 + http://opendatacommons.org/licenses/odbl/summary/, accessed 5 July 2016; http://opendatacommons.org/licenses/dbcl/1.0/, accessed 5 July 2016. + Allyson Lister + DbCL v1.0 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://elm.eu.org/media/Elm_academic_license.pdf + + + The EMBLEM ELM Academic LIcense was developed as the license for the ELM (Eukaryotic Linear Motif) resource. Non-commerical use is allowed under this license, an additional commercial license is also available. This license makes the Licensed Software available free of charge for the licensee, +which is a non-profit educational, academic and/or research institution. The software can only be used for academic research projects. This explicitly excludes projects which charge a fee, or projects that are done in +collaboration with a third party that is funding the research in whole or in part in exchange for commercial rights on the results and/or possible delay in publication of any relevant results to the academic community. The user and any research assistants, co-workers or other workers who may use the Software agree to not grant licenses on any software that includes the Licensed Software, alone or integrated into other software, to third parties. Modification of the Licensed Software code is prohibited without the prior written consent of EMBLEM. + ELM Software License Agreement + http://elm.eu.org/media/Elm_academic_license.pdf, accessed 6 July 2017; http://elm.eu.org/infos/about.html accessed 6 July 2016. + Allyson Lister + EMBLEM ELM Academic License + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + + + + + http://flowrepository.org/terms_of_service + + + The FlowRepository Open Access Terms of Use license allows any individual to access the licensed product (originally the Flow Cytometry Data Repository) for any purpose. There are no restrictions on the use or redistribution of the data associated with this license, though it makes the statement that some data covered may also be included under more restrictive licensing. + http://flowrepository.org/terms_of_service, accessed 6 July 2016. + Allyson Lister + FlowRepository Open Access Terms of Use - + - - BioPAX Manchester OWL Syntax format - + + - - + + - - + + - - - - - - - - CDF ASCII format - - - + + - Allyson Lister - http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/cdf.html, accessed 22 May 2013 - The CDF ASCII format is an ASCII data format specification created by Affymetrix similar to the Windows INI format. This format describes the layout for an Affymetrix GeneChip array. An array may contain Expression, Genotyping, CustomSeq, Copy Number and/or Tag probe sets. All probe set names within an array are unique. Multiple copies of a probe set may exist on a single array as long as each copy has a unique name. - - - - - - - - BAR - - - + + - http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/bar.html, accessed 22 May 2013. - Allyson Lister - BAR is a binary data format specification created by Affymetrix where the data is stored in big-endian format. The format of the file is a header section followed by sequences sections (one section per sequence defined). The BAR file contains one and two sample analysis results (signal and p-values) from the tiling array software. + + + + + + + + + + http://opendatacommons.org/licenses/by/1.0/ + + + The ODbL v1.0 allows a user of the databases to share, create and adapt the database. You must attribute any public use of the database, or works produced from the database. For redistribution of the database or derivative works, you must make the use of this license clear to others, and you must keep intact any notices on the original database. If you redistribute the database, or an adapted version of it, then you may use technological measures that restrict the work (such as DRM) as long as you also redistribute a version without such measures. + Open Data Commons Attribution License (ODC-By) v1.0 + http://opendatacommons.org/licenses/by/summary/, accessed 6 July 2016. + Allyson Lister + ODC-By v1.0 - + - - CEL ASCII format - + + - - + + - http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/cel.html, accessed 22 May 2013. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + https://creativecommons.org/publicdomain/zero/1.0/ + + + The ODC Public Domain Dedication and Licence is a document intended to allow you to freely share, modify, and use this work for any purpose and without any restrictions. This licence is intended for use on databases or their contents (“data”), either together or individually. The goal is to eliminate restrictions held by the original creator of the data and database on the use of it by others. Rightsholders will not be able to “dual license” their work by releasing the same work under different licences. This is because they have allowed anyone to use the work in whatever way they choose. Rightsholders therefore can’t re-license it under copyright or database rights on different terms because they have nothing left to license. + ODC Public Domain Dedication and Licence + http://opendatacommons.org/licenses/pddl/1.0/, accessed 7 July 2016. Allyson Lister - CEL ASCII format is ASCII data format specification created by Affymetrix similar to the Windows INI format. The CEL format stores the results of the intensity calculations on the pixel values of the DAT file. This includes an intensity value, standard deviation of the intensity, the number of pixels used to calculate the intensity value, a flag to indicate an outlier as calculated by the algorithm and a user defined flag indicating the feature should be excluded from future analysis. The file stores the previously stated data for each feature on the probe array. + PDDL v1.0 - + - - Affymetrix-compliant data - - - - - - - - - - - - - - - - - - Affymetrix-compliant data is data produced in a format compatible with Affymetrix software. This is a defined class where other data classes will be inferred to be members if they have a data format specification which has been published by Affymetrix. + + + This is the original BSD license, modified by removal of the advertising clause. It is a lax, permissive non-copyleft free software license, compatible with the GNU GPL. + +This license is sometimes referred to as the 3-clause BSD license. + +According to the GNU Project, the modified BSD license is not bad, as lax permissive licenses go, though the Apache 2.0 license is preferable. However, it is risky to recommend use of “the BSD license”, even for special cases such as small programs, because confusion could easily occur and lead to use of the flawed original BSD license. To avoid this risk, you can suggest the X11 license instead. The X11 license and the modified BSD license are more or less equivalent. + +According to the GNU project, the Apache 2.0 license is better for substantial programs, since it prevents patent treachery. + obsolete_3-clause BSD License + http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013. + Marked as obsolete by Allyson Lister Allyson Lister + Andy Brown + 1.6 (expected version number, after 1.5) + This class is a duplicate of http://www.ebi.ac.uk/swo/license/SWO_9000085. + obsolete_Modified BSD License + true - + - - Data File Standard for Flow Cytometry - - FCS - http://www.bioconductor.org/packages/2.12/bioc/vignettes/prada/inst/doc/fcs3.html, accessed May 29. 2013. - The flow cytometry data file standard provides the specifications needed to completely describe flow cytometry data sets within the confines of the file containing the experimental data. The principal goal of the Standard is to provide a uniform file format allowing files created by one type of acquisition hardware and software to be analyzed by another type. - Allyson Lister + + + A vendor-specific license is a license which was, at least originally, created by a specific organization to be used just on the resources created within that organization. This is a hierarchy of convenience rather than of shared philosophy. Many of the licenses have since been taken up by other groups whose licensing requirements matched those of the originating organization. + Allyson Lister + Allyson Lister + Vendor-specific License - + - - FCS3.0 - + + - - + + - Allyson Lister - http://www.bioconductor.org/packages/2.12/bioc/vignettes/prada/inst/doc/fcs3.html, accessed May 29. 2013. - FCS3.0 is version 3.0 of the Data File Standard for Flow Cytometry. It contains a mechanism for handling data sets of 100 megabytes and larger, support for UNICODE text for keyword values, support for cyclic redundancy check (CRC) validation for each data set, a requirement for the inclusion of information describing the method of signal amplification and increased support for the inclusion of time as a measurement parameter. - - - - - - - - NONMEM data format - + + + + https://www.drugabuse.gov/researchers/research-resources/genetics-research-resources/distribution-genetic-data-biomaterials-nida-center-gene + + + The NIDA NIH Data Access Policy specifies under what legal requirements NIDA NIH data may be accessed. Researchers may gain access to clinical data, genetic analysis data, and DNA by obtaining formal approval from the NIDA Genetic Data Access Request Committee. + Allyson Lister + Allyson Lister + NIDA NIH Data Access Policy - + - - DNA nucleotide sequence - - A nucleic acid sequence that indicate the order of nucleotides within some DNA. + + + + + + + + + + + + + + + + + + + + + + + + https://www.addgene.org/terms-of-use/ + + + The Addgene Terms of Use specifies under what legal requirements Addgene data may be accessed. Data is available for use for non-commercial purposes, but users must get express written consent of Addgene to exploit the data for commercial purposes. All copyright, trademark and other proprietary notices must be retained on the data. As consent must be aquired for commercial use, this license only allows non-commercial use (a separate agreement must be entered into for commercial use). + https://www.addgene.org/terms-of-use/, accessed 7 July 2016 + Allyson Lister + Addgene Terms of Use - + - - biological sequence data - - Data about primary biological sequence information, such as DNA neucleotide sequences. + + + + + + + + + + + + + + + + + + + + + + + + http://www.cas.org/legal/infopolicy + + + The CAS Information Use Policy specifies under what legal requirements CAS Information may be accessed. Attribution to ACS must be included whenever creating derivatives or redistributing data covered under this license.Each User is permitted to download and retain a maximum of 5,000 Records and a maximum of 5,000 Molfiles at any given time for personal use or to share within a Project team for the life of the Project. There are also limits on how long records may be stored with the licensee, and how records may be linked. + http://www.cas.org/legal/infopolicy accessed 7 July 2016. + Allyson Lister + CAS Information Use Policy - + - - amino acid protein sequence data - - Data which contains information about amino acid sequences of proteins. + + + + + + + + + + + + + + + + + + + + + + + + http://cellfinder.de/contact/disclaimer/ + + + The created contents and works provided under this license by CellFinder are subject to the German copyright law. Third-party contributions are marked as such. Reproduction, adaptation, dissemination and any kind of exploitation outside the limits of the copyright require the written consent of the author or creator. Downloads and copies of these pages are only permitted for private, non-commercial use. The operators of these pages aim to observe the copyright of others or will refer to their own or license-free works. + http://cellfinder.de/contact/disclaimer/, accessed 7 July 2016. + Allyson Lister + CellFinder Copyright - + - - BLASTN - + + - - - - - - - - - - - - + + - - - - - - - - - - - - + + - Nucleotide-nucleotide BLAST (blastn) is a type of BLAST software that takes a given DNA query and returns the most similar DNA sequences from the DNA database that the user specifies. - Nucleotide-nucleotide BLAST + + + + + + + + + + + + + + + + http://www.lincsproject.org/data/data-release-policy/ + + + The LINCS Data Policy is a license which allows redistribution and derivative works as long as the original data is attributed correctly. All investigators are encouraged, to publish results based on LINCS data. These results may include, but would not be limited to, integrating LINCS data with data from other sources. LINCS data are released with the sole restriction that they must be correctly cited so that others can establish provenance and access the original data; the correct citation will be released with each data set and will comprise either a PMID/PMCID reference or a unique LINCS identifier. + http://www.lincsproject.org/data/data-release-policy/, accessed 7 July 2016. + Allyson Lister + LINCS Data Policy - + - - tabix file format - - Tabix indexes a TAB-delimited genome position file and creates an index file when region is absent from the command-line. The input data file must be position sorted and compressed by bgzip which has a gzip like interface. After indexing, tabix is able to quickly retrieve data lines overlapping regions specified in the format "chr:beginPos-endPos". Fast data retrieval also works over network if URI is given as a file name and in this case the index file will be downloaded if it is not present locally. - http://samtools.sourceforge.net/tabix.shtml + + + + + + + + + + + + http://www.genenetwork.org/conditionsofUse.html + + + The GeneNetwork Conditions of Use describes the data licensing for the resource covered. Commercial and non-commercial use is allowed, though attribution is requested via either acknowledgement or co-authorship. Further restrictions on the bulk download of as-yet unpublished data is also described. (While mentioned in the document, software licensing is not the focus of this conditions of use and therefore is not modelled here.) + http://www.genenetwork.org/conditionsofUse.html, accessed 7 July 2016. + Allyson Lister + GeneNetwork Conditions of Use - + - - genomedata format - - Allyson Lister - Genomedata provides a way to store and access large-scale functional genomics data in a format which is both space-efficient and allows efficient random-access. Genomedata archives are implemented as one or more HDF5 files, either as single files or as directory archives. HDF5 archives are self describing, like XML, but may also contain more complex structures such contain binary data. - http://pmgenomics.ca/hoffmanlab/proj/genomedata/doc/1.3.5/genomedata.html and http://www.hdfgroup.org/why_hdf/, accessed 27 November 2014. + + + + + + + + + + + + + + + + + + + + + + + + http://gmd.mpimp-golm.mpg.de/termsconditions.aspx + + + The GMD Academic License is a vendor-specific license which allows the access and use of the licensed data for non-commercial purposes, as long as the appropriate attribution is used and copyright notices retained. A separate license agreement is required for commercial users and as such, they are not covered by this license. Without written consent by the GMD, no part of the GMD - in its original or in any way processed or reformatted form - may be re-distributed in any way. + Golm Metabolome Database Academic License + http://gmd.mpimp-golm.mpg.de/termsconditions.aspx, accessed 7 July 2016. + GMD Academic License - + - - BedGraph - - Allyson Lister - The bedGraph format is a line-oriented text file format. Bedgraph data are preceeded by a track definition line, which adds a number of options for controlling the default display of this track. Following the track definition line are the track data in four column BED format. The bedGraph format allows display of continuous-valued data in track format. This display type is useful for probability scores and transcriptome data. This track type is similar to the wiggle (WIG) format, but unlike the wiggle format, data exported in the bedGraph format are preserved in their original state. - http://genome.ucsc.edu/goldenpath/help/bedgraph.html, accessed December 3, 2014. + + + + + + + + + + + + http://www.geneprof.org/GeneProf/terms_and_conditions.jsp + + + The GeneProf Academic License is a vendor-specific license which allows the access and use of the licensed resource for non-commercial purposes. + http://www.geneprof.org/GeneProf/terms_and_conditions.jsp, accessed 7 July 2016. + GeneProf Academic License - + - - GMTK parameter data - - Allyson Lister - Allyson Lister - GMTK parameter data is a type of data which contains the various parameter files required by GMTK to define a dynamic Bayesian network. - Graphical Models Toolkit parameter data - These parameter files come in multiple types (e.g. structure files and master files), and therefore this is a data type rather than a single format. - http://noble.gs.washington.edu/proj/philius/README, accessed 3 December 2014. - - - These parameter files come in multiple types (e.g. structure files and master files), and therefore this is a data type rather than a single format. - - - - - + + + + + + + + + + + + + + + + + + + + + + + + http://www.ema.europa.eu/ema/index.jsp?curl=pages/regulation/general/general_content_000178.jsp + + + The European Medicines Agency Copyright states that the Agency is the owner of copyright and other intellectual property rights for documents and other content published on their website. +Information and documents made available on the Agency's webpages are public and may be reproduced and/or distributed, totally or in part, irrespective of the means and/or the formats used, for non-commercial and commercial purposes, provided that the Agency is always acknowledged as the source of the material. Such acknowledgement must be included in each copy of the material. - +Citations may be made from such material without prior permission, provided the source is always acknowledged. - - MathML 2.0 - - Allyson Lister - James Malone - MathML 2.0 is an XML format which is a low-level specification for describing mathematics as a basis for machine to machine communication. It is a W3C Recommendation and was released on 21 Feb 2001. A product of the W3C Math working group, it provides a much needed foundation for the inclusion of mathematical expressions in Web pages. - http://www.w3.org/Math/ +The above-mentioned permissions do not apply to content supplied by third parties. Therefore, for documents where the copyright vests in a third party, permission for reproduction must be obtained from this copyright holder. + http://www.ema.europa.eu/ema/index.jsp?curl=pages/regulation/general/general_content_000178.jsp, accessed 12 July 2016. + Allyson Lister + European Medicines Agency Copyright - + - - FieldML - - FieldML is an XML-based language for describing time-varying and -spatially-varying fields. The aims of the language design process are to -keep the language concise, consistent, intuitive and flexible. - James Malone - http://www.physiomeproject.org/xml_languages/fieldml + + + + + + + + + + + + + + + + + + http://mirtarbase.mbc.nctu.edu.tw/cache/download/LICENSE + + + miRTaBase Data License is a simple vendor license which allows academic users to make use of the data for free. + http://mirtarbase.mbc.nctu.edu.tw/cache/download/LICENSE, accessed 12 July 2016 + Allyson Lister + miRTaBase Data License - + - - WKn - - Allyson Lister - Please note that this is a collective class for all versions of the WKn format, and the specific version required should be created as necessary and placed as a child of this class. - WKn is a collective name for a spreadsheet format created for Lotus 1-2-3. - http://support.sas.com/documentation/cdl/en/acpcref/63184/HTML/default/viewer.htm#a003103772.htm and http://en.wikipedia.org/wiki/Lotus_1-2-3, accessed 3 December 2014. + + + + + + + + + + + + + + + + + + + + + + + + http://www.gbif.org/terms/licences/data-sharing + + + GBIF Data Sharing Agreement is a simple vendor license which allows all users to make use of the data for free, as long as the source of the data is properly attributed. + http://www.gbif.org/terms/licences/data-sharing, accessed 12 July 2016 + Allyson Lister + GBIF Data Sharing Agreement - + - - web user interface - - WUI - Web UI - A Web User interface is a Graphical User Interface which is loaded and run via a Web browser rather than within the user's operating system. - Allyson Lister + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://www.inchi-trust.org/wp/wp-content/uploads/2014/06/LICENCE.pdf + + + IUPAC/InChI-Trust InChI Licence No. 1.0 is a vendor license which allows all users to make use of the resource, including the source code, for free, as long as its source is properly attributed. It is broadly compatible with the GNU GPL v3 and v2 in that it states in the license that you can change the license from this one to the GNU GPL if you wish. + IUPAC/InChI-Trust Licence for the International Chemical Identifier (InChI) +Software version 1.04 + http://www.inchi-trust.org/wp/wp-content/uploads/2014/06/LICENCE.pdf, accessed 12 July 2016 + Allyson Lister + IUPAC/InChI-Trust InChI Licence No. 1.0 - + - - desktop graphical user interface - - A Desktop Graphical User interface is a Graphical User Interface which is loaded and run within the user's operating system rather than via a Web browser. - Allyson Lister - Desktop GUI + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://www.labome.com/about/copyright.html + + + The Labome copyright makes the contents of their resource freely available for browsing. Any redistribution or reproduction of part or all of the contents in any form is prohibited other than the following: you may print or download to a local hard disk extracts for your use only, with a daily limit of 50 webpages; and you may copy the content to individual third parties for their use, but only if you acknowledge the website as the source of the material. +You may not, except with our express written permission, distribute or commercially exploit the content. + http://www.labome.com/about/copyright.html, accessed 12 July 2016. + Allyson Lister + Labome Copyright - + - - SOAP service - - SOAP Service - A SOAP service is a Web service which provides a standard, extensible, composable framework for packaging and exchanging XML messages. The service may expose an arbitrary, application-specific set of operations. - Allyson Lister - Modified from http://en.wikipedia.org/wiki/SOAP, accessed 6 June 2013; modified from http://www.w3.org/TR/ws-arch, accessed 6 June 2013. + + + + + + + + + + + + + + + + + + + + + + + + http://ctdbase.org/about/legal.jsp + + + The CTD Legal Notice and Terms of Data Use specifies under what legal requirements the CTD data may be accessed. Data is available for use for non-commercial purposes as long as the data is properly attributed, but users must get express written consent of CTD to exploit the data for commercial purposes. As consent must be aquired for commercial use, this license only allows non-commercial use (a separate agreement must be entered into for commercial use). Additionally,You must notify CTD and describe your use of their data. For quality control purposes, you must provide CTD with periodic access to your publication of their data. + Comparative Toxicogenomics Database Legal Notice and Terms of Use + http://ctdbase.org/about/legal.jsp, accessed 12 July 2016 + Allyson Lister + CTD Legal Notice and Terms of Data Use - + - - REST service - - REST Service - A REST service is a Web service in which the primary purpose of the service is to manipulate XML representations of Web resources using a uniform set of "stateless" operations. RESTful APIs do not require XML-based web service protocols (SOAP and WSDL) to support their light-weight interfaces. - Allyson Lister - Modified from http://www.w3.org/TR/ws-arch, accessed 6 June 2013, Modified from http://en.wikipedia.org/wiki/Web_service, accessed 6 June 2013. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + https://loinc.org/terms-of-use/ + + + LOINC RELMA Terms of Use is a vendor license which allows all users to make use of the data for free, as long as the source of the data is properly attributed. An unlimited number of copies of the licensed material may be used. + https://loinc.org/terms-of-use/, accessed 12 July 2016 + Allyson Lister + LOINC RELMA Terms of Use - + - - JSON web service - - A web service in which calls invoked return JSON. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://miaca.sourceforge.net/copyrightNotice.txt + + + MIACA Full Copyright is a vendor-specific license which allows the document it references to be copied and furnished to others, and derivative works that comment on or otherwise explain it or assist in its implementation may be prepared, copied, published and distributed, in whole or in part, without restriction of any kind, provided that the above copyright notice and this paragraph are included on all such copies and derivative works. However, this document itself may not be modified in any way, such as by removing the copyright notice or references to the MIACA Standards Initiative or other organizations, except as needed for the purpose of developing MIACA Standards Initiative Recommendations in which case the procedures for copyrights defined in the MIACA Document process must be followed, or as required to translate it into languages other than English. + http://miaca.sourceforge.net/copyrightNotice.txt, accessed 12 July 2016 + Allyson Lister + MIACA Full Copyright - + - - web service - - Allyson Lister - Web Service - Modified from http://www.w3.org/TR/ws-arch/, accessed 6 June 2013; Modified from http://en.wikipedia.org/wiki/Web_service, accessed 6 June 2013. - A web service is a software interface which works as a method of communication between two electronic devices over the World Wide Web and which is provided at a particular network address. There are two major classes of Web services: REST-compliant Web services, and arbitrary (or application-specific) Web services. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + https://github.com/ORCID/ORCID-Source/blob/master/LICENSE.md + + + The ORCID MIT-style license is identical to the MIT License, except for the addition of the following two clauses: 1. "The above license does not apply to the branding or the "look and feel" of the websites located at the orcid.org URL even if elements thereof are contained in the Software."; 2. "Except to provide the copyright notice required above or as allowed under ORCID Inc.'s Trademark Use Policy (available at http://orcid.org, under "Policies"), you may not use the name of ORCID, Inc., ORCID, its marks and logo, to advertise, promote or suggest any affiliation with or endorsement by ORCID, Inc. in connection with your use of the Software.". The MIT License is is a lax, permissive non-copyleft free software license, compatible with the GNU GPL. + https://github.com/ORCID/ORCID-Source/blob/master/LICENSE.md, accessed 12 July 2016; https://www.gnu.org/licenses/license-list.html, accessed 28 June 2016. + ORCID MIT-Style License (MIT) - + - - graphical user interface - - GUI - Allyson Lister - https://en.wikipedia.org/wiki/Graphical_user_interface, accessed 6 June 2013. - A Graphical user interface is a type of software interface that allows users to interact with electronic devices using images rather than text commands. A GUI represents the information and actions available to a user through graphical icons and visual indicators such as secondary notation, as opposed to text-based interfaces, typed command labels or text navigation. + + + + + + + + + + + + + + + + + + https://gds.nih.gov/03policy2.html + + + The NIH Genomic Data Sharing Policy specifies under what legal requirements NIH genomic data may be accessed. Access to human data is through a tiered model involving unrestricted- and controlled-data +access mechanisms. Requests for controlled-access data are reviewed by NIH Data Access Committees (DACs). + https://gds.nih.gov/PDF/NIH_GDS_Policy.pdf + Allyson Lister + NIH Genomic Data Sharing Policy - + - - command-line interface - - A command-line interface is a means of interacting with a computer program where the user (or client) issues commands to the program in the form of successive lines of text (command lines). - http://en.wikipedia.org/wiki/Command-line_interface, accessed 25 November 2014. - Command line - Command line interface - Command-line + + + + + + + + + + + + + + + + + + + + + + + + https://www.facebase.org/methods/policies/ + + + The Facebase Data Access Policy specifies under what legal requirements Facebase data may be accessed. Non-sensitive data is available for use for all purposes and usages. As consent must be aquired for sensitive (or closed) data, this license only covers the use of the open data (a separate agreement must be entered into for restricted access data). + https://www.facebase.org/methods/policies/, accessed 12 July 2016 + Allyson Lister + Facebase Data Access Policy - + - - application programming interface - - An application programming interface is a set of routines, protocols, and tools for building software applications. An API expresses a software component in terms of its operations, inputs, outputs, and underlying types. An API defines functionalities that are independent of their respective implementations, which allows definitions and implementations to vary without compromising each other. The API specifies how software components should interact. - http://en.wikipedia.org/wiki/Application_programming_interface, accessed 25 November 2014. - API + + + + + + + + + + + + + + + + + + http://orcid.org/content/orcid-terms-use + + + The ORCID Terms of Use is a vendor-specific license for describing how the data in the ORCID resource may be used. ORCID data can be sublicensed, reproduced, stored, transmitted, distributed, publicly performed and publicly displayed for non-commercial and commercial uses. + http://orcid.org/content/orcid-terms-use, accessed 12 July 2016 + Allyson Lister + ORCID Terms of Use - + - - Creative Commons - - CC + + + + + + + + + + + + + + + + + + + + + + + + http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/license.cgi + + + The PPDB Academic Licens specifies under what legal requirements PPDB data may be accessed. Data is available for use for non-commercial purposes, but users must get express written consent of PPDB to exploit the data for commercial purposes. The resource will be used for teaching or not-for-profit research purposes only. The resource will not be further distributed to others. The recipient agrees to acknowledge the source of the material in any publication reporting its use. As consent must be aquired for commercial use, this license only allows non-commercial use (a separate agreement must be entered into for commercial use). + Plant Promoter Database Academic License + http://ppdb.agr.gifu-u.ac.jp/ppdb/cgi-bin/license.cgi, accessed 12 July 2016 + Allyson Lister + PPDB Academic License - + - - Proprietary commercial software license - + + + + + + + + + + + + + + + + + + https://neuinfo.org/page/terms + + + The SciCrunch Terms and Conditions specifies under what legal requirements SciCrunch data may be accessed. Broadly speaking, the site conforms, both for data and for the site documents themselves, to the CC BY 3.0 license. However, particular details for this resource (other than attribution requirements) are unclear. + https://neuinfo.org/page/terms, accessed 12 July 2016. + Allyson Lister + SciCrunch Terms and Conditions - + - - MPL v1.1 - - Mozilla Public License Version 1.1 + + + + + + + + + + + + + + + + + + + + + + + + http://prodom.prabi.fr/prodom/current/html/downcom.php + + + The ProDom Commercial License is a vendor-specific license which allows the access and use of the licensed data for commercial purposes for a fee. Non-commercial use does not require licensing or a fee, and is covered by a separate license. + http://prodom.prabi.fr/prodom/current/html/downcom.php, accessed 12 July 2016. + ProDom Commercial License - + - - Distribution clause - - Allyson Lister - Distribution clauses are license clauses which state the requirements on how the licensed software is redistributed. The license for a piece of software may or may not allow the redistribution of that software. If it is allowed, such usage may be restricted in a variety of ways. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://www.sbgn.org/About + + + The SBGN Open License with Attribution is a very simple statement of openness for the SBGN standard and related resources available on its website. No one—not the principal investigators, nor the SBGN Editors, nor the members of the SBGN Scientific Committee, nor the funding agencies or anyone else—owns SBGN; it is a free and open community effort that extends beyond any single group, and they view themselves only as organizers and fellow developers. + Systems Biology Graphical Notation Open License with Attribution + http://www.sbgn.org/About, accessed 12July 2016. + Allyson Lister + SBGN Open License with Attribution - + - - Distribution restricted - - - Allyson Lister - Distribution restricted is a distribution clause which places restrictions on how the licensed software may be distributed by third parties. These restrictions may be complete, e.g. no further redistribution, or partial. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + https://www.nlm.nih.gov/copyright.html + + + The NLM Open License with Attribution is a vendor-specific license which is similar to public domain, but which requests attribution. Government information at NLM Web sites is in the public domain. Public domain information may be freely distributed and copied, but it is requested that in any subsequent use the National Library of Medicine (NLM) be given appropriate acknowledgement. When using NLM Web sites, you may encounter documents, illustrations, photographs, or other information resources contributed or licensed by private individuals, companies, or organizations that may be protected by U.S. and foreign copyright laws. Transmission or reproduction of protected items beyond that allowed by fair use as defined in the copyright laws requires the written permission of the copyright owners. Specific NLM Web sites containing protected information provide additional notification of conditions associated with its use. + National Library of Medicine Open License with Attribution + https://www.nlm.nih.gov/copyright.html, accessed 12 July 2016. + Allyson Lister + NLM Open License with Attribution - + - - Distribution unrestricted - - Allyson Lister - Distribution unrestricted is a distribution clause which states that the licensed software can be redistributed by a third party in whatever manner that party wishes. + + + + + + + + + + + + http://regenbase.org/terms-of-use.html + + + The RegenBase Terms of Use is a vendor-specific license which requires attribution and which does not meet the requirements for open source code, as there is a statement saying that the user will NOT translate, reverse engineer, decompile or disassemble the SYSTEM, or disclose the SYSTEM or any underlying information or technology to any third party. + http://regenbase.org/terms-of-use.html, accessed 12 July 2016 + Allyson Lister + RegenBase Terms of Use - + - - derivative software allowed - - Allyson Lister - Derivative software allowed clauses are derivatives clauses which state that derivative software is allowed using the licensed software. Even when allowed, such a clause may or may not restrict the usage of the licensed software in a variety of ways. + + + + + + + + + + + + + + + + + + http://sabiork.h-its.org/layouts/content/termscondition.gsp + + + The SABIO-RK Non-Commercial Purpose License covers use of the Database for Non-Commercial Purpose only, and appropriate attribution must be given. Non-Commercial Purpose means the use of the Database solely for internal non-commercial research and academic purposes. As consent must be aquired for commercial use, a separate agreement must be entered into for commercial use and is not covered here. + http://sabiork.h-its.org/layouts/content/termscondition.gsp, accessed 13 July 2016 + Allyson Lister + SABIO-RK Non-Commercial Purpose License - + - - GNU GPL - + + - - - - - - - - - - - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - GNU General Public License + + + + + + + + + + http://www.ebi.ac.uk/about/terms-of-use + + + The Terms of Use for EMBL-EBI Services reflect EMBL-EBI’s commitment to OpenScience through its mission to provide freely available online services, databases and software relating to data contributed from life science experiments to the largest possible community. They impose no additional constraints on the use of the contributed data than those provided by the data owner. 
EMBL-EBI expects attribution (e.g. in publications, services or products) for any of its online services, databases or software in accordance with good scientific practice. The expected attribution will be indicated on the appropriate web page. 
 + http://www.ebi.ac.uk/about/terms-of-use, accessed 13 July 2016. + Allyson Lister + Terms of Use for EMBL-EBI Services - + - - Apache license v2 - + + - - + + - - + + - - + + - - + + - http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013. - Allyson Lister - This is a free software license under the definition of "free" by the GNU Project, and is compatible with version 3 of the GNU GPL. + + + + + + + + + + http://unitsofmeasure.org/trac/wiki/TermsOfUse + + + The UCUM Terms of Use is a vendor-specific license which allows the resource it references to be used for commercial or non-commercial purposes without restriction of any kind, provided that appropriate attribution is given. However, the resource itself may not be modified in any way. Users may make and distribute an unlimited number of copies of the Licensed Materials. Each copy thereof must include the Copyright Notice and License. + The Unified Code for Units of Measure Terms of Use + http://unitsofmeasure.org/trac/wiki/TermsOfUse, accessed 13 July 2016 + Allyson Lister + UCUM Terms of Use - + - - Academic Free License version 3 - + + - - http://www.opensource.org/licenses/afl-3.0.php + + - - + + - - + + - - + + - Andy Brown - Allyson Lister - The Academic Free License is a free software license under the definition of "free" by the GNU Project, is not copyleft, and is incompatible with the GNU GPL. - http://directory.fsf.org/wiki/License:AFLv3, accessed 12 June 2013; http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013 - AFL + + + + + + + + + + https://uts.nlm.nih.gov/license.html + + + The UMLS Metathesaurus License is a vendor-specific license which allows redistribution (as part of a larger computer application) as long as the original data is attributed correctly and a summary of data use provided each year. There is no cost to use the service, and may be used both commercially and non-commercially. Users must inform the resource if it is redistributed within a computer application. + https://uts.nlm.nih.gov/license.html, accessed 13 July 2016. + Allyson Lister + UMLS Metathesaurus License - + - - FreeBSD - + + - - + + - - + + - - + + - - + + - - + + http://www.mhasweb.org/Data.aspx - Andy Brown - Allyson Lister - http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013. - This is the original BSD license with the advertising clause and another clause removed. (It is also sometimes called the “2-clause BSD license”.) It is a lax, permissive non-copyleft free software license, compatible with the GNU GPL. - 2 clause BSD License + The MHAS Data Policy is a vendor-specific license which requires that users attribute the data properly. The data is accessible free of charge to all commercial and non-commercial users. + http://www.mhasweb.org/Data.aspx, accessed 13 July 2016. + Allyson Lister + MHAS Data Policy - + - - Open source software license - + + + - - + + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + hhttps://alfred.med.yale.edu/alfred/fullcopyrightpage.asp + + + The ALFRED Copyright is a vendor-specific license which states that the resource is freely available to the scientific community for statistical analysis, the only condition being that attribution is required. + The ALlele FREquency Database Copyright + https://alfred.med.yale.edu/alfred/fullcopyrightpage.asp, accessed 13 July 2016. + Allyson Lister + ALFRED Copyright - + - - License without restrictions on derivatives + + + Commercial use only is a usage restricted clause which restricts the use of the licensed resource only to licensees who are commercial entites. + Allyson Lister + Allyson Lister + Allyson Lister: Some licenses are expressly written for their commercial users. In such cases, a vendor will normally have multiple licenses, one for non-commercial use and one for commercial use. + Commercial use only + + + + + + + + + + + + + - - + + - + + Fee-Based Commercial License is a license which, among its license clauses, states that commercial entities may use the resource for a fee. + Allyson Lister + Allyson Lister + Allyson Lister: This is a convenience class which combines multiple license clauses to create a defined class, such that any license type which meets the requirements will be inferred to fall into this category. + Fee-Based Commercial License - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://www.brenda-enzymes.org/copy.php + + + The BRENDA License is a vendor-specific license which allows access to the official website and its data free of charge. Any inclusion of BRENDA components into other data bases, or redistribution of BRENDA requires a license. To obtain commercial in-house versions please contact our distributor Biobase GmbH ( http://www.biobase-international.com). In-house versions for academic users are available from Enzymeta GmbH (http://www.enzymeta.de). The copyright of the printed version is held by Springer publishers. Users of the website may retrieve a copy of the data but must not alter the BRENDA data or charge money for a copy of it, and must not distribute any BRENDA data without prior permission of the copyright holder. As there are separate licenses for in-house versions of BRENDA, please note that this license only describes the website-accessible version of BRENDA. + http://www.brenda-enzymes.org/copy.php, accessed 13 July 2016. + Allyson Lister + BRENDA License + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://cancergenome.nih.gov/pdfs/Data_Use_Certv082014 + + + The TCGA Data Use Certification is a vendor-specific license which specifies the certification which must be officially agreed to before data may be accessed. There are a number of requirements in this license including attribution, non-transferability, annual progress updates, and a number of security measures. + The Cancer Genome Atlas Data Use Certification + http://cancergenome.nih.gov/pdfs/Data_Use_Certv082014, accessed 13 July 2016 + Allyson Lister + TCGA Data Use Certification + + + - - GNU Project Free Software License Type + + + - - - + + - - - - - - - - - + + - - http://www.gnu.org/philosophy/free-sw.html, accessed 12 June 2013. - A program is free software if the program's users have the four essential freedoms: + + Non-Commercial No-Fee License is a license which, among its license clauses, states that non-commercial entities may use the resource without a purchase or usage cost. + Allyson Lister + Allyson Lister + Allyson Lister: This is a convenience class which combines multiple license clauses to create a defined class, such that any license type which meets the requirements will be inferred to fall into this category. + Non-Commercial No-Fee License + + - The freedom to run the program, for any purpose (freedom 0). - The freedom to study how the program works, and change it so it does your computing as you wish (freedom 1). Access to the source code is a precondition for this. - The freedom to redistribute copies so you can help your neighbor (freedom 2). - The freedom to distribute copies of your modified versions to others (freedom 3). By doing this you can give the whole community a chance to benefit from your changes. Access to the source code is a precondition for this. -A program is free software if users have all of these freedoms. Thus, you should be free to redistribute copies, either with or without modifications, either gratis or charging a fee for distribution, to anyone anywhere. Being free to do these things means (among other things) that you do not have to ask or pay for permission to do so. + -“Free software” does not mean “noncommercial”. A free program must be available for commercial use, commercial development, and commercial distribution. Commercial development of free software is no longer unusual; such free commercial software is very important. You may have paid money to get copies of free software, or you may have obtained copies at no charge. But regardless of how you got your copies, you always have the freedom to copy and change the software, even to sell copies. - Allyson Lister + + + + + + + + + + + + + + + + + + + + + + + + http://www.drugbank.ca/about + + + DrugBank is offered to the public as a freely available resource. Use and re-distribution of the data, in whole or in part, for commercial purposes (including internal use) requires a license. We ask that users who download significant portions of the database cite the DrugBank paper in any resulting publications. As consent must be aquired for commercial use, this license only describes the non-commercial aspects of data usage (a separate agreement must be entered into for commercial use). + http://www.drugbank.ca/about, accessed 13 July 2016 + Allyson Lister + DrugBank Academic License - + - - GNU Copyleft Software License Type - - - - - - - - - - - - - Allyson Lister - Modified from http://www.gnu.org/copyleft/copyleft.html, accessed 12 June 2013. - GNU Copyleft Software License is a GNU Project Free Software License which requires that all modified and extended versions of the program be free as well. Copyleft says that anyone who redistributes the software, with or without changes, must pass along the freedom to further copy and change it. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + http://genome.cse.ucsc.edu/license/ + + + The UCSC Genome Browser Commercial Software License is a vendor-specific license which allows the access and use of the licensed data for commercial purposes under specific restrictions for a fee. The licensee shall not have the right to create Derivative Works of the Licensed Products, and the Licensee shall not have the right to sublicense, sell, transfer, or assign the Licensed Products. Non-commercial use does not require licensing or a fee, and is covered by a separate license. + http://genome.cse.ucsc.edu/license/gblicense.pdf, accessed 13 July 2016. + UCSC Genome Browser Commercial Software License - + - - Copyleft - - Copyleft is a derivative code same license clause which requires that all derivative code uses the same license, but further limits the type of license to one which gives everyone the rights to use, modify, and redistribute the program's code, or any program derived from it, but only if the distribution terms are unchanged. To copyleft a program, we first state that it is copyrighted; then we add the distribution terms described above. This makes copyleft a legal instrument ensuring that the code and the freedoms become legally inseparable. - Allyson Lister - Modified from http://www.gnu.org/copyleft/copyleft.html, accessed 12 June 2013. + + + Permission required for commercial use is a clause which restricts the use of the licensed resource only to licensees who are commercial entites which have received explicit permission in the manner stipulated by the resource. + Allyson Lister + Allyson Lister + Allyson Lister: Some licenses are expressly written for their commercial users. In such cases, a vendor will normally have multiple licenses, one for non-commercial use and one for commercial use. + Permission required for commercial use - + - - GNU GPL v3 - - GNU General Public License Version 3 + + + Permission required for derivative work is a clause which restricts the production of derivative work based on the licensed resource only to licensees who have received explicit permission in the manner stipulated by the resource. + Allyson Lister + Allyson Lister + Permission required for derivative work - + - - GNU GPL v2 - - GNU General Public License Version 2 + + + + + + + + + + + + + + + + + + http://www.xenbase.org/other/static/aboutXenbase.jsp + + + Data are to be used only for purposes of research and education. Commercial use is prohibited without written permission from Xenbase. +The contributor(s) of unpublished data should be explicitly acknowledged in any publication that incorporates, or is based in part or entirely on these data. Xenbase should be explicitly acknowledged when data used in any publication, has been in part or solely derived from analysis of data from this website. As consent must be aquired for commercial use, this license only describes the non-commercial aspects of data usage (a separate agreement must be entered into for commercial use). + http://www.xenbase.org/other/static/aboutXenbase.jsp, accessed 13 July 2016 + Allyson Lister + Xenbase Academic Conditions of Use - + + + + + + + + + + + + + + http://www.riken.jp/en/terms/ + + + The RIKEN copyright is a vendor-specific license which states that all text, photographs, diagrams, and other materials on their website are copyrighted by RIKEN unless explicitly specified otherwise on the website. It is prohibited to use, reproduce, or modify any of the material without RIKEN's permission. + http://www.riken.jp/en/terms/, accessed 14 July 2016 + Allyson Lister + RIKEN Copyright + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + https://www.gnu.org/licenses/dsl.html + + + The Design Science License is a license intended to be a general "copyleft" that can be applied to any kind of work that has protection under copyright. This license states those certain conditions under which a work published under its terms may be copied, distributed, and modified. Unlike other open source licenses, the DSL was intended to be used on any type of copyrightable work, including documentation and source code. It was the first "generalized copyleft" license. This is a free and copyleft license meant for general data. THe GNU Project does not recommend it for software or documentation, since it is incompatible with the GNU GPL and with the GNU FDL; however, they consider it appropriate for other kinds of data. The DSL was written by Michael Stutz. The DSL came out in the 1990s, before the formation of the Creative Commons. According to Wikipedia, once the Creative Commons arrived, Stutz considered the DSL experiment "over" and no longer recommended its use. + https://www.gnu.org/licenses/dsl.html, accessed 13 July 2016; https://www.gnu.org/licenses/license-list.html, accessed 13 July 2016; https://en.wikipedia.org/wiki/Design_science_license, accessed 13 July 2016. + Allyson Lister + Design Science License + + + + + + + + + + + + + + + + + + http://www.concordia.ca/web/terms.html + + + The University of Concordia Terms of Use is a vendor-specific license which states that no document appearing on this website or any other website owned, operated or controlled by Concordia may be copied, sold, reproduced, republished, downloaded, posted, transmitted or distributed by any means with the exception of downloading or printing the contents of the site for personal, non-commercial use. This use must bear in mind that Concordia reserves its copyright and its rights to exclusivity over the material. + http://www.concordia.ca/web/terms.html, accessed 14 July 2016 + Allyson Lister + University of Concordia Terms of Use + + + + + - - CC0 - + + + + + + + + + + + + + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - Allyson Lister - Creative Commons 0 - CC0 is a public domain dedication from Creative Commons. A work released under CC0 is dedicated to the public domain to the fullest extent permitted by law. If that is not possible for any reason, CC0 also provides a lax, permissive license as a fallback. Both public domain works and the lax license provided by CC0 are compatible with the GNU GPL. - http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013. + All OME formats and software are freely available, and all OMERO and Bio-Formats source code is available under GNU public "copyleft" licenses or through commercial license from Glencoe Software. FLIMfit is also now available under a GNU public "copyleft" license. + +For questions about the GNU license refer to the Frequently Asked Questions about the GNU Licenses page. + +Bio-Formats - under the terms of the GNU public "copyleft" license, any software package linking to Bio-Formats, either directly or indirectly, cannot be distributed unless its source code is also made available under the terms of the GPL. Some components which provide reader and writer implementations for open file formats, are released under a more permissive BSD-2 license which enables non-GPL third party software. For a complete list of which file formats are included in the BSD license, see the BSD column of the supported formats table. Developers of non-GPL software wishing to leverage Bio-Formats components not covered by the BSD license may purchase a commercial license from Glencoe Software; please contact them at bioformats@glencoesoftware.com to discuss your requirements. + +The core OME Model Schema files (.XSD) use the Creative Commons Attribution 4.0 International License, and as such you are free to share or adapt them as long as you attribute the OME consortium as follows; "This work is derived in part from the OME specification. Copyright (C) 2002-2016 Open Microscopy Environment". See further information about using OME-XML in your work. + +This website is also covered by the Creative Commons Attribution 4.0 International License - you are free to share or adapt content as long as you credit the Open Microscopy Environment. The exception to this is the screenshots and videos which can only be used for non-commercial purposes, see Attributions below. + + + http://www.openmicroscopy.org/site/about/licensing-attribution/licensing, accessed on 23 June 2016. + Allyson Lister + OME Software Conditons of Use - + - - CC BY 2.0 - + + - - + + - - + + - - + + https://aspera-immport.niaid.nih.gov:9443/displayAgreement - - - - - - - CC BY 2.0 is a non-copyleft free (free by the definition of the GNU Project) license which lets others distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you for the original creation. This is the most accommodating of Creative Commons licenses offered. Recommended for maximum dissemination and use of licensed materials. The GNU Project recommend this license for art, entertainment and educational works, but also recommend that it is not used for software or documentation, since it is incompatible with the GNU GPL and with the GNU FDL. - Allyson Lister - Modified from http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013; Modified from http://creativecommons.org/licenses/, accessed 12 June 2013. - Creative Commons Attribution 2.0 license + The ImmPort Conditions of Use is a vendor-specific license which allows the use of ImmPort data for any legal purpose except for those prohibited elsewhere in this agreement. There are very few prohibitions, and no requirement for attribution. + https://aspera-immport.niaid.nih.gov:9443/displayAgreement, accessed 14 July 2016 + Allyson Lister + ImmPort Conditions of Use - + - - Attribution required - - Allyson Lister - Attribution required is an attribution clause which states that attribution of the type specified in the license must be provided whenever the software is used. + + + + + + + + + Distribution with notices is a distribution clause in which distribution is unrestricted, except that all distributions must retain certain licence information (e.g., copyright notices). + Andy Brown + Andy Brown + Distribution with notices - + - - CC BY-SA 2.0 - + + - - + + - - + + - - + + - - + + - Modified from http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013; Modified from http://creativecommons.org/licenses/, accessed 12 June 2013. - Allyson Lister - CC BY-SA 2.0 is a copyleft free (free by the definition of the GNU Project) license which lets others remix, tweak, and build upon your work even for commercial purposes, as long as they credit you and license their new creations under the identical terms. The GNU Project recommend this license for art, entertainment and educational works, but also recommend that it is not used for software or documentation, since it is incompatible with the GNU GPL and with the GNU FDL. - Creative Commons Attribution-Sharealike 2.0 license - - - - - - - - LPPL v1.3 - - Modified from http://en.wikipedia.org/wiki/LaTeX_Project_Public_License, accessed 12 June 2013; modified from http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013. - LPPL v1.3 is a free software license (by the defintion of the GNU Project), with less stringent requirements on distribution than LPPL 1.2. It is still incompatible with the GPL because some modified versions must include a copy of or pointer to an unmodified version.Software projects other than LaTeX rarely use it. - Latex Project Public License v1.3 - - - - - - - - LPPL v1.2 - - Modified from http://en.wikipedia.org/wiki/LaTeX_Project_Public_License, accessed 12 June 2013; modified from http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013. - LPPL v1.2 is a free software license (by the defintion of the GNU Project), This license is an incomplete statement of the distribution terms for LaTeX. While it is a free software license, it is incompatible with the GPL because it has many requirements that are not in the GPL. Software projects other than LaTeX rarely use it. - Latex Project Public License v1.2 - - - - - - - - Mozilla Public License Version 2.0 - MPL v2.0 - - - + + - - + + - MPL v2.0 a free software license as defined by the GNU Project. Section 3.3 provides indirect compatibility between this license and the GNU GPL version 2.0, the GNU LGPL version 2.1, the GNU AGPL version 3.0, and all later versions of those licenses. The MPL allows covered source code to be mixed with other files under a different, even proprietary license. However, code files licensed under the MPL must remain under the MPL and freely available in source form. - http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013; http://en.wikipedia.org/wiki/Mozilla_Public_License, accessed 12 June 2013. - - - - - - - - Artistic License - - Allyson Lister - - - - - - - - Artistic License v2.0 - - - + + - - - - - - - - + + + + + + + + + - - + + https://opensource.org/licenses/MIT - http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013. - Allyson Lister - The Artistic License v 2.0 is a free software license by the definition of the GNU Project and compatible with the GPL thanks to the relicensing option in section 4(c)(ii) (as compared with the Artistic License 1.0). - - - - - - - - Purchase cost - - Allyson Lister - Allyson Lister - Purchase cost is a license clause which states whether there is a cost involved with a particular usage or licensing of a piece of software. - In some ways, purchase cost is similar to the already-extant usage clause hierarchy, which includes restricted and unrestricted usage. However, a usage limitation is not necessarily due to whether or not something costs money: even if the usage is academic only, it could still be either free or non-free. A license could have multiple usage clauses, e.g. academic only when free, and unrestricted if a fee is paid. Purchase cost was created which, together with a usage clause, defines both limitations and cost. - - + This is a lax, permissive non-copyleft free software license, compatible with the GNU GPL. It is sometimes ambiguously referred to as the MIT License. - - - - - Free - - Allyson Lister - Allyson Lister - Free is a type of purchase cost clause which, when applied, means that there is no cost for the users of the software to which the license is attached. This clause can be combined with other clauses (such as usage clauses) to specify that only certain usages are free. - This class refers only to the cost of the software, not to the definition of "free software" as provided by the GNU Project and which is commonly used to describe software that respects users' freedom and community (http://www.gnu.org/philosophy/free-sw.html). - - - - - - - - Not Free - - This class refers only to the cost of the software, not to the definition of "free software" as provided by the GNU Project and which is commonly used to describe software that respects users' freedom and community (http://www.gnu.org/philosophy/free-sw.html). - Not Free is a type of purchase cost clause which, when applied, means that there is a cost for the users of the software to which the license is attached. This clause can be combined with other clauses (such as usage clauses) to specify that only certain usages incur a purchase cost. - Allyson Lister - Allyson Lister +For substantial programs it is better to use the Apache 2.0 license since it blocks patent treachery. + Expat License + https://www.gnu.org/licenses/license-list.html, accessed 28 June 2016. + MIT License - + - - free to use license - + + - - + + - A license which allows any form of usage of the artifact. - - - - - - - - Distribution with notices - - Andy Brown - Andy Brown - Distribution with notices is a distribution clause in which distribution is unrestricted, except that all distributions must retain certain licence information (e.g., copyright notices). - - - - - - - - MIT License - - - + + - - + + - - + + - - + + - - + + + The GNU Lesser General Public License (LGPL) is a free software license published by the Free Software Foundation (FSF). The license allows developers and companies to use and integrate LGPL software into their own (even proprietary) software without being required by the terms of a strong copyleft license to release the source code of their own software-parts. The license requires that only the LGPL software-parts be modifiable by end-users via source code availability. + GNU Lesser General Public License + http://en.wikipedia.org/wiki/GNU_Lesser_General_Public_License, accessed 27 March 2015. + Allyson Lister + GNU LGPL + + + + + + + + - - + + - - + + https://opensource.org/licenses/Artistic-1.0 - - - - - - - - lGPL - - Lesser GNU Public License - - - - - - - - Artistic License v1.0 - - Allyson Lister The Artistic License v1.0 is not considered a free software license by the definition of the GNU Project because it is too vague; some passages are &quot;too clever for their own good&quot;, and their meaning is not clear. The GNU Project recommends that it is not used except as part of the disjunctive license of Perl. - Andy Brown http://www.gnu.org/licenses/license-list.html, accessed 13 June 2013. + Allyson Lister + Andy Brown + Artistic License 1.0 - - EPL v1 - + + - + + + + + + + + + + + + + + + + + + + - - + + @@ -80504,638 +90612,706 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + + + + + + + + + + + + - - + + https://www.eclipse.org/legal/epl-v10.html + The Eclipse Public License is similar to the Common Public License. This is a free software license. Unfortunately, its weak copyleft and choice of law clause make it incompatible with the GNU GPL. The only change is that the EPL removes the broader patent retaliation language regarding patent infringement suits specifically against Contributors to the EPL'd program. Eclipse Public License Version 1.0 + https://www.gnu.org/licenses/license-list.html, accessed 28 June 2016. + EPL v1 - - Modified BSD - + + + + + + + + - - + + - - + + - - + + - - + + + + + + + + + + + + https://opensource.org/licenses/BSD-3-Clause + + + The Modified BSD is a software license based on he original FreeBSD license, modified by removal of the advertising clause. It is a lax, permissive non-copyleft free software license, compatible with the GNU GPL. + +This license is sometimes referred to as the 3-clause BSD license. + +According to the GNU Project, the modified BSD license is not bad, as lax permissive licenses go, though the Apache 2.0 license is preferable. However, it is risky to recommend use of “the BSD license”, even for special cases such as small programs, because confusion could easily occur and lead to use of the flawed original BSD license. To avoid this risk, you can suggest the X11 license instead. The X11 license and the modified BSD license are more or less equivalent. + +According to the GNU project, the Apache 2.0 license is better for substantial programs, since it prevents patent treachery. 3 clause BSD License - The Modified BSD is a software license based on he original FreeBSD license, modified by removal of the advertising clause. It is a lax, permissive non-copyleft free software license, compatible with the GNU GPL. - Allyson Lister http://www.gnu.org/licenses/license-list.html, accessed June 12, 2013. + Allyson Lister + Andy Jones + Modified BSD - - LPPL - + + + + + + + + - - + + - - + + - - + + Latex Project Public License + LPPL - - OPL v1.0 - + + - - + + - - + + - - + + + + + + + + + + + + + + + + + + + - http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013. - Open Public License Version 1.0 OPL v1.0 is not a free software license according to the definition of the GNU Project because it requires sending every published modified version to a specific initial developer. + Open Public License Version 1.0 + http://www.gnu.org/licenses/license-list.html, accessed 12 June 2013. + OPL v1.0 - - MPL - + + + + + + + + - - + + - - + + Mozilla Public License + MPL - - Development status - - Allyson Lister - Andy Brown - Development status is an information content entity which indicates the maturity of a sofrware entity within the context of the software life cycle. + + + Development status is an information content entity which indicates the maturity of a sofrware entity within the context of the software life cycle. + Allyson Lister + Andy Brown + Development status - - alpha - - Alpha is a development status which is applied to software by the developer/publisher during initial development and testing. Software designated alpha is commonly unstable and prone to crashing. It may or may not be released publicly. - Allyson Lister + + + Alpha is a development status which is applied to software by the developer/publisher during initial development and testing. Software designated alpha is commonly unstable and prone to crashing. It may or may not be released publicly. Modified from http://en.wikipedia.org/wiki/Software_release_life_cycle, accessed 11 June 2013. + Allyson Lister + alpha - - beta - - Beta is a development status which is generally applied to software by the developer/publisher once the majority of features have been implemented, but when the software may still contain bugs or cause crashes or data loss. Software designated beta is often released publicly, either on a general release or to a specific subset of users called beta testers. - Allyson Lister + + + Beta is a development status which is generally applied to software by the developer/publisher once the majority of features have been implemented, but when the software may still contain bugs or cause crashes or data loss. Software designated beta is often released publicly, either on a general release or to a specific subset of users called beta testers. Modified from http://en.wikipedia.org/wiki/Software_release_life_cycle, accessed 11 June 2013. + Allyson Lister + beta - + + + A release candidate (RC) is a beta version with potential to be a final product, which is ready to release unless significant bugs emerge. + http://en.wikipedia.org/wiki/Software_release_life_cycle#Release_candidate, accessed 22 October 2014. Release candidate - - A release candidate (RC) is a beta version with potential to be a final product, which is ready to release unless significant bugs emerge. - http://en.wikipedia.org/wiki/Software_release_life_cycle#Release_candidate, accessed 22 October 2014. - - Live - - Live is a development status which is applied to software that has been designated as suitable for production environments by the developer/publisher. If a non-free product, software at this stage is available for purchase + + + Live is a development status which is applied to software that has been designated as suitable for production environments by the developer/publisher. If a non-free product, software at this stage is available for purchase Production - Allyson Lister Allyson Lister, Jon Ison, and Modified from http://en.wikipedia.org/wiki/Software_release_life_cycle, accessed 11 June 2013. + Allyson Lister + Live - + + + + Sofware is no longer being supplied by the developers/publishers Obsolete - - - Sofware is no longer being supplied by the developers/publishers - + + + An updated version of the software is available. + Andy Brown Superseded - - An updated version of the software is available. - Andy Brown - - First release - + + The first release of a piece of software. A first release does not imply any particular levels of maturity other than is this is the first instance of this software to be considered released. James Malone + First release - - Latest release - - James Malone + + The latest release of a piece of software. This does not imply any levels of maturity other than indicating this is the most recent release. + James Malone + Latest release - - Maintained - - Andy Brown - Software has developers actively maintaining it (fixing bugs) + + + Software has developers actively maintaining it (fixing bugs) + Andy Brown + Maintained - - matrix manipulation - + + + matrix manipulation - - spreadsheet editing - + + + spreadsheet editing - + + document outlining - - + + image compression - - + + ontology engineering - - + + word processing - - + + software development - - + + simulation and analysis of biochemical networks - - - laboratory information management - + + Manage Laboratory information such is commonly performed by LIMS software. + laboratory information management - - manage computer operations - + + the objective of performing the actions of an operation system such as managing the software running a computer and the interactions with the system resources and hardware. + manage computer operations - - text editing - + + Text editing is the objective of editing plain text files. + text editing - - file rendering - + + Renders a file in such a way that its contents can be understood by users. + file rendering - + + annotation editing - - + + biological data processing - - + + modelling - - + + molecular sequence analysis - - - citation management - + + Andy Brown + citation management - - sequence alignment + Allyson Lister + sequence alignment - - multiple sequence alignment - + + Allyson Lister + multiple sequence alignment - - pairwise sequence alignment - + + Allyson Lister + pairwise sequence alignment - - averaging - - An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation. - James Malone + + + An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation. + James Malone + averaging - - center calculation - - A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set. - James Malone + + + A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set. + James Malone + center calculation - - class discovery - - A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic. - James Malone + + + A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input data (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic. + James Malone + class discovery - - class prediction - - A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and class labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data. - PERSON: Elisabetta Manduchi - PERSON: James Malone + + + A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning technique. The training data consist of pairs of objects (typically vectors of attributes) and class labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data. + PERSON: Elisabetta Manduchi + PERSON: James Malone + class prediction - - correction - - A correction is where the aim is to correct for error, noise or other impairments to the input of the data transformation or derived from the data transformation itself. - PERSON: James Malone - PERSON: Melanie Courtot + + + A correction is where the aim is to correct for error, noise or other impairments to the input of the data transformation or derived from the data transformation itself. + PERSON: James Malone + PERSON: Melanie Courtot + correction - - background correction - - A background correction is where the aim is to remove irrelevant contributions from the measured signal, e.g. those due to instrument noise or sample preparation. - James Malone - PERSON: Elisabetta Manduchi + + + A background correction is where the aim is to remove irrelevant contributions from the measured signal, e.g. those due to instrument noise or sample preparation. + PERSON: Elisabetta Manduchi + James Malone + background correction - - error correction - - An error correction is a data transformation objective where the aim is to remove (correct for) erroneous contributions arising from the input data, or the transformation itself. - James Malone - PERSON: James Malone + + + An error correction is a data transformation objective where the aim is to remove (correct for) erroneous contributions arising from the input data, or the transformation itself. + PERSON: James Malone + James Malone + error correction - - cross validation - + + + cross validation - - curve fitting - - Elisabetta Manduchi - James Malone - PERSON: Elisabetta Manduchi - curve fitting is a data transformation in which the aim is to find a curve which matches a series of data points and possibly other constraints. + + + curve fitting is a data transformation in which the aim is to find a curve which matches a series of data points and possibly other constraints. + PERSON: Elisabetta Manduchi + Elisabetta Manduchi + James Malone + curve fitting - - data normalization - - A normalization is a data transformation objective where the aim is to remove systematic sources of variation to put the data on equal footing in order to create a common base for comparisons. - James Malone - PERSON: Elisabetta Manduchi - PERSON: Helen Parkinson - PERSON: James Malone + + + A normalization is a data transformation objective where the aim is to remove systematic sources of variation to put the data on equal footing in order to create a common base for comparisons. + PERSON: Elisabetta Manduchi + PERSON: Helen Parkinson + PERSON: James Malone + James Malone + data normalization - - decision tree induction - - A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made. - James Malone - PERSON: James Malone + + + A decision tree induction objective is a data transformation objective in which a tree-like graph of edges and nodes is created and from which the selection of each branch requires that some type of logical decision is made. + PERSON: James Malone + James Malone + decision tree induction - - descriptive statistical calculation - - A descriptive statistical calculation objective is a data transformation objective which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability. - James Malone - PERSON: Elisabetta Manduchi - PERSON: James Malone - PERSON: Melanie Courtot - PERSON: Monnie McGee - mean calculation + + + mean calculation + A descriptive statistical calculation objective is a data transformation objective which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability. + James Malone + PERSON: Elisabetta Manduchi + PERSON: James Malone + PERSON: Melanie Courtot + PERSON: Monnie McGee + descriptive statistical calculation - - differential expression analysis - + + + differential expression analysis - - feature extraction - - A feature extraction objective is a data transformation objective where the aim of the data transformation is to generate quantified values from a scanned image. + + + A feature extraction objective is a data transformation objective where the aim of the data transformation is to generate quantified values from a scanned image. + feature extraction - - software publishing process - - Andy Brown + + The process of publishing software. Typically this process involves a software publisher performing acts such as licensing, marketing, publicising and/or providing support for a product. + Andy Brown + software publishing process - - software development process - - Andy Brown + + The process of developing software, typically involving the design, implementation and testing of software. + Andy Brown + software development process - - obsolete SWO class - Obsolete concept (EDAM) - - + + - 1.2 - Needed for conversion to the OBO format. + 1.2 An obsolete concept (redefined in EDAM). + + Needed for conversion to the OBO format. + Obsolete concept (EDAM) + obsolete SWO class true @@ -81144,31 +91320,31 @@ A program is free software if users have all of these freedoms. Thus, you should - role - role - A role is an entity which is borne in a material entity in some kinds of natural, social or institutional contexts, but which is not essential to the fundamental definition of that material entity (i.e. the material entity exists with or without the role). For example, the role of a person as a surgeon, the role of an artificial heart in pumping blood, the role of a chemical compound in an experiment, the role of a drug in the treatment of a disease. - BFO - the role of a person as a surgeon, the role of a chemical compound in an experiment, the role of a patient relative as defined by a hospital administrative form, the role of a woman as a legal mother in the context of system of laws, the role of a biological grandfather as legal guardian in the context of a system of laws, the role of ingested matter in digestion, the role of a student in a university + the role of a person as a surgeon, the role of a chemical compound in an experiment, the role of a patient relative as defined by a hospital administrative form, the role of a woman as a legal mother in the context of system of laws, the role of a biological grandfather as legal guardian in the context of a system of laws, the role of ingested matter in digestion, the role of a student in a university A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. + A role is an entity which is borne in a material entity in some kinds of natural, social or institutional contexts, but which is not essential to the fundamental definition of that material entity (i.e. the material entity exists with or without the role). For example, the role of a person as a surgeon, the role of an artificial heart in pumping blood, the role of a chemical compound in an experiment, the role of a drug in the treatment of a disease. + BFO + role + role - A role is an entity which is borne in a material entity in some kinds of natural, social or institutional contexts, but which is not essential to the fundamental definition of that material entity (i.e. the material entity exists with or without the role). For example, the role of a person as a surgeon, the role of an artificial heart in pumping blood, the role of a chemical compound in an experiment, the role of a drug in the treatment of a disease. - - + + A role is an entity which is borne in a material entity in some kinds of natural, social or institutional contexts, but which is not essential to the fundamental definition of that material entity (i.e. the material entity exists with or without the role). For example, the role of a person as a surgeon, the role of an artificial heart in pumping blood, the role of a chemical compound in an experiment, the role of a drug in the treatment of a disease. + - + - + @@ -81185,447 +91361,447 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + - - + + - - + + - - + + - Affymetrix + Affymetrix - - - Agilent Technologies + + + Agilent Technologies - - - Applied Biosystems + + + Applied Biosystems - - - Applied Precision Life Science + + + Applied Precision Life Science - - - Bahler Lab + + + Bahler Lab - - - Bio-Rad Laboratories, Inc. + + + Bio-Rad Laboratories, Inc. - - - Bio Discovery + + + Bio Discovery - - - Bioconductor + + + Bioconductor - - - Biometric Research Branch - + + + + Biometric Research Branch - - - COSE, France + + + COSE, France - - - Clontech Laboratories, Inc + + + Clontech Laboratories, Inc - - - Dana-Farber Cancer Institute and Harvard School of Public Health + + + Dana-Farber Cancer Institute and Harvard School of Public Health - - - EMBL - European Molecular Biology Laboratory + + + European Molecular Biology Laboratory + EMBL - - - Fujifilm + + + Fujifilm - - - GE Healthcare Life Sciences + + + GE Healthcare Life Sciences - - - Genedata + + + Genedata - - - Genicon Sciences + + + Genicon Sciences - - - Grid grinder + + + Grid grinder - - - Havard School of Public Health + + + Havard School of Public Health - - - Illumina + + + Illumina - - - Incyte Genomics + + + Incyte Genomics - - - Institute for Genomics and Bioinformatics Graz University of Technology + + + Institute for Genomics and Bioinformatics Graz University of Technology - - - J. Craig Venter Institute + + + J. Craig Venter Institute - - - MWG Biotech + + + MWG Biotech - - + + - - + + - Matforsk + Matforsk - - - obsolete_MathWorks - 0.3 + + Marked as obsolete by Allyson Lister. + 0.3 MathWorks (SWO_0000291 and SWO_9000002), SWO_9000002 was retained, whileSWO_0000291 became an instance of obsolete class. Please use SWO_9000002 instead. + obsolete_MathWorks - - - Molecular Devices + + + Molecular Devices - - - Molecular Neuroscience Core, Center for Behavioral Neuroscience, Atlanta + + + Molecular Neuroscience Core, Center for Behavioral Neuroscience, Atlanta - - - Molecular Dynamics + + + Molecular Dynamics - - - Motorola Life Sciences + + + Motorola Life Sciences - - - NIH + + + NIH - - - PerkinElmer + + + PerkinElmer - - - Raytest + + + Raytest - - - Research Genetics + + + Research Genetics - - - Rosetta Biosoftware + + + Rosetta Biosoftware - - - SAS Institute Inc. + + + SAS Institute Inc. - - - Speed Berkeley Research Group + + + Speed Berkeley Research Group - - - obsolete_Stanford University - Stanford University (SWO_0000431 and SWO_9000003). SWO_9000003 was retained, while SWO_0000431 became an instance of obsolete class. Please use SWO_9000003 instead. - 0.3 + + Marked as obsolete by Allyson Lister. + 0.3 + Stanford University (SWO_0000431 and SWO_9000003). SWO_9000003 was retained, while SWO_0000431 became an instance of obsolete class. Please use SWO_9000003 instead. + obsolete_Stanford University - - - TIBCO Software Inc + + + TIBCO Software Inc - - - Technological Advances for Genomics and Clinics, France + + + Technological Advances for Genomics and Clinics, France - - - UC Irvine + + + UC Irvine - - - University Of California, Berkeley + + + University Of California, Berkeley - - - Walter and Eliza Hall Institute + + + Walter and Eliza Hall Institute - - - Cambridge Bluegnome + + + Cambridge Bluegnome - - - Strand Life Sciences + + + Strand Life Sciences - - + + FCS Data Standard Version 3.0 @@ -81633,26 +91809,26 @@ A program is free software if users have all of these freedoms. Thus, you should - - - Microsoft + + + Microsoft - - - MathWorks + + + MathWorks - - + + Stanford University @@ -81660,8 +91836,8 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + Omni @@ -81669,8 +91845,8 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + PLT Scheme Inc @@ -81678,8 +91854,8 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + MicroPro International @@ -81687,8 +91863,8 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + JetBrains @@ -81696,8 +91872,8 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + Free Software Foundation @@ -81705,8 +91881,8 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + Adobe Systems @@ -81714,19 +91890,19 @@ A program is free software if users have all of these freedoms. Thus, you should - - - The Community + + Andy Brown An undefined, or ill-defined, group of people. May be used, for example, to denote software development as being done by 'the community', with contributions by many individuals, but no over-arching organisation. + The Community - - + + University of New Hampshire @@ -81734,8 +91910,8 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + The National Archives @@ -81743,8 +91919,8 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + Eclipse Foundation @@ -81752,8 +91928,8 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + Dropbox @@ -81761,8 +91937,8 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + Thompson Reuters @@ -81770,8 +91946,8 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + OMII-UK @@ -81779,17 +91955,17 @@ A program is free software if users have all of these freedoms. Thus, you should - - - Apple + + + Apple Inc. - - + + The University of Manchester @@ -81797,8 +91973,8 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + European Bioinformatics Institute @@ -81806,8 +91982,8 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + EPCC @@ -81815,8 +91991,8 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + The National Archives, Tessella @@ -81824,8 +92000,8 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + Spotify Ltd. @@ -81833,8 +92009,8 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + Mozilla Foundation @@ -81842,8 +92018,8 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + Altova @@ -81851,8 +92027,8 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + The GIMP Development Team @@ -81860,8 +92036,8 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + Canonical Ltd @@ -81869,8 +92045,8 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + Apache Software Foundation @@ -81878,8 +92054,8 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + European Patent Office @@ -81887,8 +92063,8 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + National Cancer Institute @@ -81896,8 +92072,8 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + Drive5 @@ -81905,8 +92081,8 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + Conway Institute UCD Dublin @@ -81914,8 +92090,8 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + Centre for Genomic Regulation (CRG) of Barcelona @@ -81923,8 +92099,8 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + IBM @@ -81932,8 +92108,8 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + Numbers International Pty Ltd @@ -81941,26 +92117,17 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + UC Santa Cruz Computational Biology Group - - - - - Windows 6.0 - - - - - - + + beta @@ -81968,8 +92135,8 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + alpha @@ -81977,72 +92144,72 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + + + Microsoft 98 version - - - - + + + + Microsoft 2002 version - - - - + + + + Microsoft 2003 version - - - - + + + Microsoft 95 version - - - + + + + Microsoft 2007 version - - - - + + + Microsoft 2010 version - - - + + version 3 @@ -82050,8 +92217,8 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + version 4 @@ -82059,39 +92226,39 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + + + Matlab R14 - - - - + + + Matlab R12 - - - + + + R2011a - - - + + Microsoft XP @@ -82099,8 +92266,8 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + Excel 14 @@ -82108,8 +92275,8 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + Windows 5.1 @@ -82117,8 +92284,8 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + 3.5.1 @@ -82126,8 +92293,8 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + Adobe Acrobat 10.1 @@ -82135,8 +92302,8 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + 1 @@ -82144,8 +92311,8 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + 3.0.1 @@ -82153,8 +92320,8 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + 1.6.9 @@ -82162,8 +92329,8 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + 6.02 @@ -82171,8 +92338,8 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + Helios Service Release 2 @@ -82180,8 +92347,8 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + 6.3.0 @@ -82189,8 +92356,8 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + 2.0.0 @@ -82198,58 +92365,58 @@ A program is free software if users have all of these freedoms. Thus, you should - - - BLAST+ version 2.2.26 + + Allyson Lister + BLAST+ version 2.2.26 - - - ClustalW version 2.1 + + Allyson Lister + ClustalW version 2.1 - - - ClustalX version 2.1 + + Allyson Lister + ClustalX version 2.1 - - - Clustal Omega version 1.1 + + Allyson Lister + Clustal Omega version 1.1 - - - MUSCLE version 3.8.31 + + Allyson Lister + MUSCLE version 3.8.31 - - + + CRG TCoffee version 9.02.r1228 @@ -82257,7 +92424,7 @@ A program is free software if users have all of these freedoms. Thus, you should - + Python version 2.6 @@ -82265,7 +92432,7 @@ A program is free software if users have all of these freedoms. Thus, you should - + Python version 2.7 @@ -82273,8 +92440,8 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + 4.2.2 @@ -82282,8 +92449,8 @@ A program is free software if users have all of these freedoms. Thus, you should - - + + 7.2.0 @@ -82291,11 +92458,20 @@ A program is free software if users have all of these freedoms. Thus, you should - + Segway version 1.2 + + + + + + + + Windows 6.0 + - + @@ -82309,35 +92485,35 @@ A program is free software if users have all of these freedoms. Thus, you should --> - + - - - - - + + + + - + - - - + + + - + - - - - + + + + + - +