diff --git a/biolink/openapi.yml b/biolink/openapi.yml index 48a48afd..4cbf5f72 100644 --- a/biolink/openapi.yml +++ b/biolink/openapi.yml @@ -30,6 +30,8 @@ paths: /v3/api/association: get: x-bte-kgs-operations: + - "$ref": "#/components/x-bte-kgs-operations/gene-anatomy" + - "$ref": "#/components/x-bte-kgs-operations/anatomy-gene" - "$ref": "#/components/x-bte-kgs-operations/disease-pheno" - "$ref": "#/components/x-bte-kgs-operations/pheno-disease" - "$ref": "#/components/x-bte-kgs-operations/gene-disease-causal" @@ -2898,6 +2900,12 @@ components: ## - has_evidence: ECO codes for where this edge came from / how?, list of curies ## - provided_by: strangely, this can differ from the knowledge source fields ## - qualifier fields + object-anatomy-uberon: + UBERON: items.object + output_name: items.object_label + input_name: items.subject_label + ref_pmid: items.publications + trapi_sources: items.sources object-disease-mondo: MONDO: items.object output_name: items.object_label @@ -2931,7 +2939,73 @@ components: x-bte-kgs-operations: ## commenting out the x-bte source field: replaced with the post-processed trapi_sources info ## Parameters - ## - `liimt`: max seems to be 500 + ## - `limit`: max seems to be 500 + gene-anatomy: + ## 161069 items: https://api-v3.monarchinitiative.org/v3/api/association?category=biolink:GeneToExpressionSiteAssociation&subject_namespace=HGNC&subject_taxon=NCBITaxon:9606&predicate=biolink:expressed_in&object_namespace=UBERON&direct=true&format=json&limit=10 + - supportBatch: false + useTemplating: true + inputs: + - id: HGNC + semantic: Gene + parameters: + subject: "{{ queryInputs | replPrefix('HGNC') }}" ## has prefix + category: "biolink:GeneToExpressionSiteAssociation" + subject_namespace: HGNC + subject_taxon: "NCBITaxon:9606" + predicate: "biolink:expressed_in" + object_namespace: UBERON + direct: true + format: json + limit: 500 + outputs: + - id: UBERON + semantic: GrossAnatomicalStructure + predicate: expressed_in + ## knowledge_source info encountered: + ## - primary: "infores:bgee" + ## - aggregator: ["infores:monarchinitiative"] + # source: "infores:monarchinitiative" + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-anatomy-uberon" + # Examples don't have publication info + testExamples: + # link https://api-v3.monarchinitiative.org/v3/api/association?subject=HGNC:28264&category=biolink:GeneToExpressionSiteAssociation&subject_namespace=HGNC&subject_taxon=NCBITaxon:9606&predicate=biolink:expressed_in&object_namespace=UBERON&direct=true&format=json&limit=500 + - qInput: "HGNC:28264" ## PCGF5 aka NCBIGene:84333 + oneOutput: "UBERON:0006566" ## left ventricle myocardium + # link https://api-v3.monarchinitiative.org/v3/api/association?subject=HGNC:9360&category=biolink:GeneToExpressionSiteAssociation&subject_namespace=HGNC&subject_taxon=NCBITaxon:9606&predicate=biolink:expressed_in&object_namespace=UBERON&direct=true&format=json&limit=500 + - qInput: "HGNC:9360" ## PRF1 aka NCBIGene:5551 + oneOutput: "UBERON:0002450" ## decidua + anatomy-gene: + - supportBatch: false + useTemplating: true + inputs: + - id: UBERON + semantic: GrossAnatomicalStructure + parameters: + object: "{{ queryInputs | replPrefix('UBERON') }}" ## has prefix + category: "biolink:GeneToExpressionSiteAssociation" + subject_namespace: HGNC + subject_taxon: "NCBITaxon:9606" + predicate: "biolink:expressed_in" + object_namespace: UBERON + direct: true + format: json + limit: 500 + outputs: + - id: HGNC + semantic: Gene + predicate: expresses + # source: "infores:monarchinitiative" + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-gene-hgnc" + # Examples have publication pmids + testExamples: + # link https://api-v3.monarchinitiative.org/v3/api/association?object=UBERON:0001817&category=biolink:GeneToExpressionSiteAssociation&subject_taxon=NCBITaxon:9606&predicate=biolink:expressed_in&object_namespace=UBERON&direct=true&format=json&limit=500 + - qInput: "UBERON:0001817" ## lacrimal gland + oneOutput: "HGNC:16430" ## LACRT aka NCBIGene:90070 + # link https://api-v3.monarchinitiative.org/v3/api/association?object=UBERON:0002073&category=biolink:GeneToExpressionSiteAssociation&subject_taxon=NCBITaxon:9606&predicate=biolink:expressed_in&object_namespace=UBERON&direct=true&format=json&limit=500 + - qInput: "UBERON:0002073" ## hair follicle + oneOutput: "HGNC:25851" ## GINS3 aka NCBIGene:64785 disease-pheno: ## 242009 items: https://api-v3.monarchinitiative.org/v3/api/association?category=biolink:DiseaseToPhenotypicFeatureAssociation&subject_namespace=MONDO&predicate=biolink:has_phenotype&object_namespace=HP&direct=true&format=json&limit=10 - supportBatch: false