From 4d5f3154b1f8c3011179a92074cbf2a845b93a32 Mon Sep 17 00:00:00 2001 From: Colleen Xu Date: Mon, 5 Feb 2024 16:53:34 -0800 Subject: [PATCH] monarch api: add operations --- biolink/openapi.yml | 117 +++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 116 insertions(+), 1 deletion(-) diff --git a/biolink/openapi.yml b/biolink/openapi.yml index d05038b9..25a32675 100644 --- a/biolink/openapi.yml +++ b/biolink/openapi.yml @@ -301,8 +301,12 @@ paths: x-bte-kgs-operations: - "$ref": "#/components/x-bte-kgs-operations/disease-pheno" - "$ref": "#/components/x-bte-kgs-operations/pheno-disease" - - "$ref": "#/components/x-bte-kgs-operations/disease-gene-causal" - "$ref": "#/components/x-bte-kgs-operations/gene-disease-causal" + - "$ref": "#/components/x-bte-kgs-operations/disease-gene-causal" + - "$ref": "#/components/x-bte-kgs-operations/gene-disease-correlated" + - "$ref": "#/components/x-bte-kgs-operations/disease-gene-correlated" + - "$ref": "#/components/x-bte-kgs-operations/gene-pheno" + - "$ref": "#/components/x-bte-kgs-operations/pheno-gene" '/v3/api/histopheno/{id}': get: tags: @@ -2760,3 +2764,114 @@ components: ## link https://api-v3.monarchinitiative.org/v3/api/entity/MONDO:0009861/biolink:CausalGeneToDiseaseAssociation?format=json&limit=20&offset=0 # - qInput: "MONDO:0009861" ## phenylketonuria # oneOutput: "HGNC:8582" ## PAH aka NCBIGene:5053 + gene-disease-correlated: + ## - items.direction will be "outgoing" + - supportBatch: false + useTemplating: true + inputs: + - id: HGNC + semantic: Gene + parameters: + id: "{{ queryInputs | replPrefix('HGNC') }}" ## has prefix + category: "biolink:CorrelatedGeneToDiseaseAssociation" + format: json + limit: 500 + outputs: + - id: MONDO + semantic: Disease + ## sometimes the raw response's predicate is "biolink:contributes_to", other times it's the child term "biolink:gene_associated_with_condition" + ## we can put these terms in the "query" parameter to get only the matching records + predicate: contributes_to + source: "infores:monarchinitiative" ## but the response has more information + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-disease-mondo" + ## Examples don't have publication info + # testExamples: + ## link https://api-v3.monarchinitiative.org/v3/api/entity/HGNC:6294/biolink:CorrelatedGeneToDiseaseAssociation?format=json&limit=20&offset=0 + # - qInput: "HGNC:6294" ## KCNQ1 aka NCBIGene:3784 + # oneOutput: "MONDO:0019171" ## familial long QT syndrome + ## link https://api-v3.monarchinitiative.org/v3/api/entity/HGNC:9652/biolink:CorrelatedGeneToDiseaseAssociation?format=json&limit=20&offset=0 + # - qInput: "HGNC:9652" ## PTPN22 aka NCBIGene:26191 + # oneOutput: "MONDO:0007915" ## systemic lupus erythematosus + disease-gene-correlated: + ## - items.direction will be "incoming" + - supportBatch: false + useTemplating: true + inputs: + - id: MONDO + semantic: Disease + parameters: + id: "{{ queryInputs | replPrefix('MONDO') }}" ## has prefix + category: "biolink:CorrelatedGeneToDiseaseAssociation" + format: json + limit: 500 + outputs: + - id: HGNC + semantic: Gene + predicate: contribution_from + source: "infores:monarchinitiative" ## but the response has more information + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-gene-hgnc" + ## Examples don't have publication info + # testExamples: + ## link https://api-v3.monarchinitiative.org/v3/api/entity/MONDO:0018961/biolink:CorrelatedGeneToDiseaseAssociation?format=json&limit=20&offset=0 + # - qInput: "MONDO:0018961" ## familial melanoma + # oneOutput: "HGNC:1787" ## CDKN2A aka NCBIGene:1029 + ## link https://api-v3.monarchinitiative.org/v3/api/entity/MONDO:0018875/biolink:CorrelatedGeneToDiseaseAssociation?format=json&limit=20&offset=0 + # - qInput: "MONDO:0018875" ## Li-Fraumeni syndrome + # oneOutput: "HGNC:6973" ## MDM2 aka NCBIGene:4193 + gene-pheno: + ## - items.direction will be "outgoing" + - supportBatch: false + useTemplating: true + inputs: + - id: HGNC + semantic: Gene + parameters: + id: "{{ queryInputs | replPrefix('HGNC') }}" ## has prefix + category: "biolink:GeneToPhenotypicFeatureAssociation" + format: json + limit: 500 + outputs: + - id: HP + semantic: PhenotypicFeature + ## a little odd: I used to use gene_associated_with_condition + predicate: has_phenotype + source: "infores:monarchinitiative" ## but the response has more information + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-pheno-hp" + ## Examples don't have publication info + # testExamples: + ## link https://api-v3.monarchinitiative.org/v3/api/entity/HGNC:8548/biolink:GeneToPhenotypicFeatureAssociation?format=json&limit=20&offset=0 + # - qInput: "HGNC:8548" ## P4HB aka NCBIGene:5034 + # oneOutput: "HP:0000944" ## Abnormal metaphysis morphology + ## link https://api-v3.monarchinitiative.org/v3/api/entity/HGNC:7551/biolink:GeneToPhenotypicFeatureAssociation?format=json&limit=20&offset=0 + # - qInput: "HGNC:7551" ## MYBPC3 aka NCBIGene:4607 + # oneOutput: "HP:0011675" ## Arrhythmia + pheno-gene: + ## - items.direction will be "incoming" + - supportBatch: false + useTemplating: true + inputs: + - id: HP + semantic: PhenotypicFeature + parameters: + id: "{{ queryInputs | replPrefix('HP') }}" ## has prefix + category: "biolink:GeneToPhenotypicFeatureAssociation" + format: json + limit: 500 + outputs: + - id: HGNC + semantic: Gene + predicate: phenotype_of + source: "infores:monarchinitiative" ## but the response has more information + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-gene-hgnc" + ## Examples don't have publication info + # testExamples: + ## link https://api-v3.monarchinitiative.org/v3/api/entity/HP:0000183/biolink:GeneToPhenotypicFeatureAssociation?format=json&limit=20&offset=0 + # - qInput: "HP:0000183" ## Difficulty in tongue movements + # oneOutput: "HGNC:4065" ## GAA + ## link https://api-v3.monarchinitiative.org/v3/api/entity/HP:0032543/biolink:GeneToPhenotypicFeatureAssociation?format=json&limit=20&offset=0 + # - qInput: "HP:0032543" ## Lithoptysis + # oneOutput: "HGNC:2950" ## DNAH5 aka NCBIGene:1767