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feat: Define JSON Schemas for ontology data release artifacts (#32)
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,76 @@ | ||
| { | ||
| "$schema": "http://json-schema.org/draft-07/schema#", | ||
| "title": "Valid Ontology Term JSON Schema", | ||
| "description": "Schema for file containing metadata for Ontology Terms accepted in dataset submissions to CZ CellXGene Data Portal.", | ||
| "type": "object", | ||
| "properties": { | ||
| "EFO": { "$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}$", | ||
| "description": "If deprecated, the ID of the ontology entry that should canonically replace this one." | ||
| } | ||
| }, | ||
| "required": ["label", "deprecated", "ancestors"], | ||
| "additionalProperties": false, | ||
| } | ||
| }, | ||
| "additionalProperties": false | ||
| } | ||
| } | ||
| } |
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| { | ||
| "$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}$" | ||
| }, | ||
| "minItems": 1, | ||
| "uniqueItems": true | ||
| } |
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| { | ||
| "$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}$" | ||
| }, | ||
| "minItems": 1, | ||
| "uniqueItems": true | ||
| } |
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| { | ||
| "$schema": "http://json-schema.org/draft-07/schema#", | ||
| "title": "Cell Type Ontology Descendants Schema", | ||
| "description": "A 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 | ||
| } |
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| { | ||
| "$schema": "http://json-schema.org/draft-07/schema#", | ||
| "title": "Ontology Version and Source Schema", | ||
| "description": "A schema for the set of valid ontology reference files mapping to a CZ CellXGene Dataset Schema Version", | ||
| "type": "object", | ||
| "properties": { | ||
| "CL": { "$ref": "#/definitions/ontologyEntry" }, | ||
| "EFO": { "$ref": "#/definitions/ontologyEntry" }, | ||
| "HANCESTRO": { "$ref": "#/definitions/ontologyEntry" }, | ||
| "HsapDv": { "$ref": "#/definitions/ontologyEntry" }, | ||
| "MONDO": { "$ref": "#/definitions/ontologyEntry" }, | ||
| "MmusDv": { "$ref": "#/definitions/ontologyEntry" }, | ||
| "NCBITaxon": { "$ref": "#/definitions/ontologyEntry" }, | ||
| "UBERON": { "$ref": "#/definitions/ontologyEntry" }, | ||
| "PATO": { "$ref": "#/definitions/ontologyEntry" } | ||
| }, | ||
| "additionalProperties": false, | ||
| "definitions": { | ||
| "ontologyEntry": { | ||
| "type": "object", | ||
| "properties": { | ||
| "version": { | ||
| "type": "string", | ||
| "description": "version of ontology canonical to this data release, as defined in its source repo" | ||
| }, | ||
| "source": { | ||
| "type": "string", | ||
| "format": "uri", | ||
| "description": "Source to find and download canonical ontology version for this data release" | ||
| }, | ||
| "filetype": { | ||
| "type": "string", | ||
| "description": "filetype used to build generated artifacts for this ontology data release" | ||
| } | ||
| }, | ||
| "required": ["version", "source", "filetype"], | ||
| "additionalProperties": false | ||
| } | ||
| } | ||
| } |
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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 | ||
| } |
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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 | ||
| } |
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| { | ||
| "$schema": "http://json-schema.org/draft-07/schema#", | ||
| "title": "Tissue Ontology Descendants Schema", | ||
| "description": "A schema for mapping Tissue ontology terms to its descendant Tissue ontology terms", | ||
| "type": "object", | ||
| "patternProperties": { | ||
| "^UBERON:[0-9]{7}$": { | ||
| "type": "array", | ||
| "items": { | ||
| "type": "string", | ||
| "pattern": "^UBERON:[0-9]{7}$" | ||
| }, | ||
| "description": "An array of UBERON ontology term IDs that are subclasses of the key UBERON ontology term ID." | ||
| } | ||
| }, | ||
| "additionalProperties": false | ||
| } |
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| { | ||
| "$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 | ||
| } |