feat: Define JSON Schemas for ontology data release artifacts

artifact-schemas/all_ontology_schema.json

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+{
+  "$schema": "http://json-schema.org/draft-07/schema#",
+  "title": "Valid Ontology Term JSON Schema",
+  "description": "Schema for file containing metadata for Ontology Terms accepted in dataset submissions to CZ CellXGene Data Portal.",
+  "type": "object",
+  "properties": {
+    "EFO": { "$ref": "#/definitions/ontologyCategory" },
+    "UBERON": { "$ref": "#/definitions/ontologyCategory" },
+    "CL": { "$ref": "#/definitions/ontologyCategory" },
+    "HANCESTRO": { "$ref": "#/definitions/ontologyCategory" },
+    "HsapDv": { "$ref": "#/definitions/ontologyCategory" },
+    "MmusDv": { "$ref": "#/definitions/ontologyCategory" },
+    "PATO": { "$ref": "#/definitions/ontologyCategory" },
+    "NCBITaxon": { "$ref": "#/definitions/ontologyCategory" },
+    "MONDO": { "$ref": "#/definitions/ontologyCategory" }
+  },
+  "additionalProperties": false,
+  "definitions": {
+    "ontologyCategory": {
+      "type": "object",
+      "patternProperties": {
+        "^(EFO|UBERON|CL|HANCESTRO|HsapDv|MmusDv|PATO|NCBITaxon|MONDO):[0-9]{7}$": {
+          "type": "object",
+          "properties": {
+            "label": {
+              "type": "string",
+              "description": "human-readable name for the ontology entry."
+            },
+            "deprecated": {
+              "type": "boolean",
+              "description": "Indicates whether the ontology entry is deprecated."
+            },
+            "ancestors": {
+              "type": "array",
+              "items": {
+                "type": "string",
+                "pattern": "^(EFO|UBERON|CL|HANCESTRO|HsapDv|MmusDv|PATO|NCBITaxon|MONDO):[0-9]{7}$",
+                "description": "List of ancestor IDs for the ontology entry."
+              },
+              "description": "An array of ancestor ontology terms that this term is a subclass of."
+            },
+            "comments": {
+              "type": "array",
+              "items": {
+                "type": "string"
+              },
+              "minItems": 0,
+              "description": "Optional comments regarding the ontology entry from ontology curators."
+            },
+            "term_tracker": {
+              "type": "string",
+              "format": "uri",
+              "description": "Optional URL to track discussion around the term's history and changes."
+            },
+            "consider": {
+              "type": "array",
+              "items": {
+                "type": "string"
+              },
+              "minItems": 0,
+              "description": "Suggests alternative IDs to consider in place of this ontology entry."
+            },
+            "replaced_by": {
+              "type": "string",
+              "pattern": "^(EFO|UBERON|CL|HANCESTRO|HsapDv|MmusDv|PATO|NCBITaxon|MONDO):[0-9]{7}$",
+              "description": "If deprecated, the ID of the ontology entry that should canonically replace this one."
+            }
+          },
+          "required": ["label", "deprecated", "ancestors"],
+          "additionalProperties": false,
+        }
+      },
+      "additionalProperties": false
+    }
+  }
+}

artifact-schemas/cell_class_list_schema.json

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+{
+  "$schema": "http://json-schema.org/draft-07/schema#",
+  "title": "Curated 'Cell Class' Ontology Terms Schema",
+  "description": "A schema for validating an array of CL ontology term IDs representing high-level 'Cell Classes', curated for CZ CellxGene use.",
+  "type": "array",
+  "items": {
+    "type": "string",
+    "pattern": "^CL:[0-9]{7}$"
+  },
+  "minItems": 1,
+  "uniqueItems": true
+}

artifact-schemas/cell_subclass_list_schema.json

@@ -0,0 +1,12 @@
+{
+  "$schema": "http://json-schema.org/draft-07/schema#",
+  "title": "Curated 'Cell Subclass' Ontology Terms Schema",
+  "description": "A schema for validating an array of CL ontology term IDs representing high-level 'Cell Subclasses', curated for CZ CellxGene use.",
+  "type": "array",
+  "items": {
+    "type": "string",
+    "pattern": "^CL:[0-9]{7}$"
+  },
+  "minItems": 1,
+  "uniqueItems": true
+}

artifact-schemas/cell_type_descendants_schema.json

@@ -0,0 +1,17 @@
+{
+  "$schema": "http://json-schema.org/draft-07/schema#",
+  "title": "Cell Type Ontology Descendants Schema",
+  "description": "Schema for Mapping Cell Type Ontology Terms to its Descendant Cell Type Ontology Terms",
+  "type": "object",
+  "patternProperties": {
+    "^CL:[0-9]{7}$": {
+      "type": "array",
+      "items": {
+        "type": "string",
+        "pattern": "^CL:[0-9]{7}$"
+      },
+      "description": "An array of CL ontology term IDs that are subclasses of the key CL ontology term ID."
+    }
+  },
+  "additionalProperties": false
+}

artifact-schemas/organ_list_schema.json

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+{
+  "$schema": "http://json-schema.org/draft-07/schema#",
+  "title": "Curated 'Organ' Ontology Terms Schema",
+  "description": "A schema for validating an array of UBERON ontology term IDs representing 'Organ' ontology terms, curated for CZ CellxGene use.",
+  "type": "array",
+  "items": {
+    "type": "string",
+    "pattern": "^UBERON:[0-9]{7}$"
+  },
+  "minItems": 1,
+  "uniqueItems": true
+}

artifact-schemas/system_list_schema_.json

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+{
+  "$schema": "http://json-schema.org/draft-07/schema#",
+  "title": "Curated 'System' Ontology Terms Schema",
+  "description": "A schema for validating an array of UBERON ontology term IDs representing organ 'System' ontology terms, curated for CZ CellxGene use.",
+  "type": "array",
+  "items": {
+    "type": "string",
+    "pattern": "^UBERON:[0-9]{7}$"
+  },
+  "minItems": 1,
+  "uniqueItems": true
+}

artifact-schemas/tissue_descendants_schema.json

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+{
+  "$schema": "http://json-schema.org/draft-07/schema#",
+  "title": "Tissue Ontology Descendants Schema",
+  "description": "Schema for Mapping Tissue Ontology Terms to its Descendant Tissue Ontology Terms",
+  "type": "object",
+  "patternProperties": {
+    "^UBERON:[0-9]{7}$": {
+      "type": "array",
+      "items": {
+        "type": "string",
+        "pattern": "^UBERON:[0-9]{7}$"
+      },
+      "description": "An array of UBERON ontology term IDs that are subclasses of the key UBERON ontology term ID."
+    }
+  },
+  "additionalProperties": false
+}

artifact-schemas/tissue_general_list_schema.json

@@ -0,0 +1,12 @@
+{
+  "$schema": "http://json-schema.org/draft-07/schema#",
+  "title": "Curated 'Tissue General' Ontology Terms Schema",
+  "description": "A schema for validating an array of high-level UBERON ontology term IDs representing 'general tissue' ontology terms, curated for CZ CellxGene use.",
+  "type": "array",
+  "items": {
+    "type": "string",
+    "pattern": "^UBERON:[0-9]{7}$"
+  },
+  "minItems": 1,
+  "uniqueItems": true
+}