Merge pull request #91 from HumanCellAtlas/v4.3.0_minorRelease

V4.3.0 minor release
HumanCellAtlas · Dec 6, 2017 · 15dac04 · 15dac04
2 parents afe2cc0 + f95cb68
commit 15dac04
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Showing 22 changed files with 109 additions and 102 deletions.
diff --git a/json_schema/analysis.json b/json_schema/analysis.json
@@ -76,7 +76,7 @@
         "inputs": {
             "items": {
                 "type": {
-                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/analysis.json#/definitions/parameter"
+                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/analysis.json#/definitions/parameter"
                 }
             }, 
             "type": "array", 
@@ -89,7 +89,7 @@
         "tasks": {
             "items": {
                 "type": {
-                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/analysis.json#/definitions/task"
+                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/analysis.json#/definitions/task"
                 }
             }, 
             "type": "array", 
@@ -113,7 +113,7 @@
         "outputs": {
             "items": {
                 "type": {
-                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/analysis.json#/definitions/file"
+                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/analysis.json#/definitions/file"
                 }
             }, 
             "type": "array", 
@@ -133,7 +133,7 @@
         }, 
         "core": {
             "description": "Type and schema for this object.", 
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/core.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/core.json"
         }, 
         "analysis_run_type": {
             "enum": [

diff --git a/json_schema/assay.json b/json_schema/assay.json
@@ -12,27 +12,27 @@
     "properties": {
         "core": {
             "description": "Type and schema for this object.", 
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/core.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/core.json"
         }, 
         "name": {
             "type": "string", 
             "description": "A short, descriptive name for the assay that need not be unique."
         }, 
         "seq": {
             "description": "Information about how a cDNA sample was sequenced.", 
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/seq.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/seq.json"
         }, 
         "rna": {
             "description": "Information about how RNA was converted to cDNA.", 
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/rna.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/rna.json"
         }, 
         "single_cell": {
             "description": "Information on single-cell aspects of an assay.", 
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/single_cell.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/single_cell.json"
         }, 
         "imaging": {
             "description": "Information on image based RNA quantification assays", 
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/imaging.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/imaging.json"
         }, 
         "assay_id": {
             "type": "string", 

diff --git a/json_schema/assay_bundle.json b/json_schema/assay_bundle.json
@@ -10,19 +10,19 @@
                 "content": {
                     "type": "object", 
                     "description": "Assay content", 
-                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/assay.json"
+                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/assay.json"
                 }, 
                 "derivation_protocols": {
                     "items": {
                         "description": "An array of protocols used in derivation of this sample.", 
-                        "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/protocol.json"
+                        "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/protocol.json"
                     }, 
                     "type": "array"
                 }, 
                 "hca_ingest": {
                     "type": "object", 
                     "description": "core fields added by HCA ingest service", 
-                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/ingest.json"
+                    "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/ingest.json"
                 }
             }
         }
@@ -31,6 +31,6 @@
     "type": "array", 
     "description": "A schema for an assay bundle", 
     "items": {
-        "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/assay_bundle.json#/definitions/assay_ingest"
+        "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/assay_bundle.json#/definitions/assay_ingest"
     }
 }
diff --git a/json_schema/cell_suspension.json b/json_schema/cell_suspension.json
@@ -1,15 +1,14 @@
 {
     "$schema": "http://json-schema.org/draft-04/schema#", 
     "title": "cell_suspension", 
-    "description": "Information about the cell suspension derived from the collected or cultured specimen", 
     "properties": {
         "well": {
             "description": "Information about wells in a plate or chip used for single-cell isolation.", 
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/well.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/well.json"
         }, 
         "target_cell_type": {
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/ontology_json/cell_type_ontology.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/ontology_json/cell_type_ontology.json"
             }, 
             "type": "array", 
             "description": "Cell types present in the suspension."
@@ -22,10 +21,11 @@
         }, 
         "enrichment": {
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/enrichment.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/enrichment.json"
             }, 
             "type": "array", 
             "description": "How sample was enriched for specific cell type(s)."
         }
-    }
+    }, 
+    "description": "Information about the cell suspension derived from the collected or cultured specimen"
 }
diff --git a/json_schema/contact.json b/json_schema/contact.json
@@ -64,7 +64,8 @@
                 "XY", 
                 "FU", 
                 "PR", 
-                "VI"
+                "VI", 
+                "Cambridgeshire"
             ], 
             "description": "Name of state, province, canton, or other country subdivision."
         }, 

diff --git a/json_schema/death.json b/json_schema/death.json
@@ -11,7 +11,7 @@
     "properties": {
         "cause_of_death": {
             "description": "Cause of death from death report for human donor, from research lab for mouse.", 
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/ontology.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/ontology.json"
         }, 
         "hardy_scale": {
             "minimum": 0, 

diff --git a/json_schema/donor.json b/json_schema/donor.json
@@ -22,7 +22,7 @@
         }, 
         "death": {
             "description": "Information about conditions of death (or info that donor was living at time of collection).", 
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/death.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/death.json"
         }, 
         "genotype": {
             "type": "string", 
@@ -35,10 +35,10 @@
         }, 
         "strain": {
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/ontology.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/ontology.json"
             }, 
             "type": "array", 
-            "description": "The name of th mouse inbred strain. e.g. C57BL/6."
+            "description": "The name of the mouse inbred strain. e.g. C57BL/6."
         }, 
         "alcohol_history": {
             "type": "string", 
@@ -60,7 +60,7 @@
         }, 
         "disease": {
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/ontology_json/disease_ontology.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/ontology_json/disease_ontology.json"
             }, 
             "type": "array", 
             "description": "Short description of disease status of individual."
@@ -91,7 +91,7 @@
         }, 
         "ancestry": {
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/ontology.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/ontology.json"
             }, 
             "type": "array", 
             "description": "An array of ontology terms from EMBL-EBI's Ancestry Ontology describing ancestral groups, uncategorised ancestral groups, and population isolates."
@@ -111,14 +111,14 @@
         }, 
         "medication": {
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/ontology.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/ontology.json"
             }, 
             "type": "array", 
             "description": "List of medications the donor was currently taking at time of sample donation."
         }, 
         "development_stage": {
             "description": "More detailed (especially for embryos) version of life_stage. e.g. \"E9\" or \"P17\" for mouse.", 
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/ontology.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/ontology.json"
         }
     }
 }
diff --git a/json_schema/file.json b/json_schema/file.json
@@ -10,7 +10,7 @@
     "properties": {
         "core": {
             "description": "Type and schema for this object.", 
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/core.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/core.json"
         }, 
         "file_format": {
             "enum": [

diff --git a/json_schema/immortalized_cell_line.json b/json_schema/immortalized_cell_line.json
@@ -11,7 +11,7 @@
         }, 
         "cell_type": {
             "description": "What cell type the line was derived from. CLO ontology.", 
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/ontology_json/cell_type_ontology.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/ontology_json/cell_type_ontology.json"
         }, 
         "date_established": {
             "type": "string", 
@@ -24,7 +24,7 @@
         }, 
         "disease": {
             "description": "A disease associated with the cell line. EFO ontology.", 
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/ontology_json/disease_ontology.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/ontology_json/disease_ontology.json"
         }, 
         "passage_number": {
             "minimum": 0, 
@@ -34,15 +34,15 @@
         }, 
         "cell_cycle": {
             "description": "The cell cycle phase, if known.", 
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/ontology.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/ontology.json"
         }, 
         "karyotype": {
             "type": "string", 
             "description": "The karyotype of the cell line."
         }, 
         "publication": {
             "description": "The publication in which the cell line creation was cited.", 
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/publication.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/publication.json"
         }
     }
 }
diff --git a/json_schema/organoid.json b/json_schema/organoid.json
@@ -1,14 +1,14 @@
 {
+    "title": "organoid", 
+    "$schema": "http://json-schema.org/draft-04/schema#", 
     "required": [
         "model_for_organ"
     ], 
-    "$schema": "http://json-schema.org/draft-04/schema#", 
-    "title": "organoid", 
-    "description": "A description of an organoid sample.", 
     "properties": {
         "model_for_organ": {
             "description": "Organ that this organoid is a model system for.", 
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/ontology.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/ontology.json"
         }
-    }
+    }, 
+    "description": "A description of an organoid sample."
 }
diff --git a/json_schema/primary_cell_line.json b/json_schema/primary_cell_line.json
@@ -7,7 +7,7 @@
     "properties": {
         "cell_type": {
             "description": "The cell type that the cell line was derived from. Should be a CLO ontology.", 
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/ontology_json/cell_type_ontology.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/ontology_json/cell_type_ontology.json"
         }, 
         "date_established": {
             "type": "string", 
@@ -16,7 +16,7 @@
         }, 
         "disease": {
             "description": "Free text describing any disease association to the cell type. Should be found in EFO ontology.", 
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/ontology_json/disease_ontology.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/ontology_json/disease_ontology.json"
         }, 
         "passage_number": {
             "minimum": 0, 
@@ -26,7 +26,7 @@
         }, 
         "cell_cycle": {
             "description": "The cell cycle phase if the cell line is synchronized growing cells or the phase is known.", 
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/ontology.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/ontology.json"
         }
     }
 }
diff --git a/json_schema/project.json b/json_schema/project.json
@@ -19,7 +19,7 @@
     "properties": {
         "core": {
             "description": "type and schema for this object", 
-            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/core.json"
+            "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/core.json"
         }, 
         "related_projects": {
             "items": {
@@ -34,21 +34,14 @@
         }, 
         "contributors": {
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/contact.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/contact.json"
             }, 
             "type": "array", 
             "description": "List of people contributing to the project."
         }, 
-        "experimental_factor_name": {
-            "items": {
-                "type": "string"
-            }, 
-            "type": "array", 
-            "description": "A list of the factors that vary between samples in the experiment. e.g. \"time since collection\", \"preservation method\""
-        }, 
         "submitters": {
             "items": {
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/contact.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/contact.json"
             }, 
             "type": "array", 
             "description": "List of people submitting data to the project."
@@ -73,26 +66,33 @@
         "experimental_design": {
             "items": {
                 "description": "A short description of overall experiment type. e.g. \"single cell RNA sequencing.\"", 
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/ontology.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/ontology.json"
             }, 
             "type": "array"
         }, 
         "publications": {
             "items": {
                 "description": "An array of publication modules.", 
-                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.2.0/json_schema/publication.json"
+                "$ref": "https://raw.githubusercontent.com/HumanCellAtlas/metadata-schema/4.3.0/json_schema/publication.json"
             }, 
             "type": "array"
         }, 
-        "array_express_investigation": {
-            "pattern": "^E-....-.*$", 
-            "type": "string", 
-            "description": "An EBI ArrayExpress investigation accession."
+        "experimental_factor_name": {
+            "items": {
+                "type": "string"
+            }, 
+            "type": "array", 
+            "description": "A list of the factors that vary between samples in the experiment. e.g. \"time since collection\", \"preservation method\""
         }, 
         "project_id": {
             "type": "string", 
             "description": "A unique ID for this project."
         }, 
+        "array_express_investigation": {
+            "pattern": "^E-....-.*$", 
+            "type": "string", 
+            "description": "An EBI ArrayExpress investigation accession."
+        }, 
         "insdc_study": {
             "pattern": "^PRJ[E|N|D][a-zA-Z][0-9]+$", 
             "type": "string",
-Original file line number
+Diff line change
@@ Expand Up / @@ -64,7 +64,8 @@ @@
                     "XY",
                     "FU",
                     "PR",
-                    "VI"
+                    "VI",
+                    "Cambridgeshire"
                 ],
                 "description": "Name of state, province, canton, or other country subdivision."
             },
@@ Expand Down @@