From ad057c09098b1e1145ded114f9a40c0faec98a00 Mon Sep 17 00:00:00 2001 From: Colleen Xu Date: Mon, 5 Feb 2024 19:09:36 -0800 Subject: [PATCH] monarch api: switch endpoints, add operations see https://github.com/biothings/biothings_explorer/issues/774\#issuecomment-1923328949 for reasons to use association endpoint now covering all the operations written for old api (that are still available) --- biolink/openapi.yml | 242 ++++++++++++++++++++++++++++++++++---------- 1 file changed, 190 insertions(+), 52 deletions(-) diff --git a/biolink/openapi.yml b/biolink/openapi.yml index 25a32675..93c3eadf 100644 --- a/biolink/openapi.yml +++ b/biolink/openapi.yml @@ -29,6 +29,19 @@ tags: paths: /v3/api/association: get: + x-bte-kgs-operations: + - "$ref": "#/components/x-bte-kgs-operations/disease-pheno" + - "$ref": "#/components/x-bte-kgs-operations/pheno-disease" + - "$ref": "#/components/x-bte-kgs-operations/gene-disease-causal" + - "$ref": "#/components/x-bte-kgs-operations/disease-gene-causal" + - "$ref": "#/components/x-bte-kgs-operations/gene-disease-contributesTo" + - "$ref": "#/components/x-bte-kgs-operations/disease-gene-contributesTo" + - "$ref": "#/components/x-bte-kgs-operations/gene-disease-associatedCondition" + - "$ref": "#/components/x-bte-kgs-operations/disease-gene-associatedCondition" + - "$ref": "#/components/x-bte-kgs-operations/gene-pheno" + - "$ref": "#/components/x-bte-kgs-operations/pheno-gene" + - "$ref": "#/components/x-bte-kgs-operations/gene-gene-interaction-forward" + - "$ref": "#/components/x-bte-kgs-operations/gene-gene-interaction-backward" tags: - association summary: ' Get Associations' @@ -298,15 +311,6 @@ paths: application/json: schema: $ref: '#/components/schemas/HTTPValidationError' - x-bte-kgs-operations: - - "$ref": "#/components/x-bte-kgs-operations/disease-pheno" - - "$ref": "#/components/x-bte-kgs-operations/pheno-disease" - - "$ref": "#/components/x-bte-kgs-operations/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" - - "$ref": "#/components/x-bte-kgs-operations/pheno-gene" '/v3/api/histopheno/{id}': get: tags: @@ -2637,6 +2641,11 @@ components: output_name: items.object_label input_name: items.subject_label ref_pmid: items.publications + object-gene-hgnc: + HGNC: items.object + output_name: items.object_label + input_name: items.subject_label + ref_pmid: items.publications object-pheno-hp: HP: items.object output_name: items.object_label @@ -2657,69 +2666,77 @@ components: ## - `liimt`: max seems to be 500 ## - `download`: not specifying it seems to work best (setting to false sometimes doesn't seem to work) disease-pheno: - ## items.direction will be "outgoing" + ## 242154 items: https://api-v3.monarchinitiative.org/v3/api/association?category=biolink:DiseaseToPhenotypicFeatureAssociation&direct=true&format=json&limit=10&offset=0 + ## all have predicate has_phenotype, since the record count is the same https://api-v3.monarchinitiative.org/v3/api/association?category=biolink:DiseaseToPhenotypicFeatureAssociation&predicate=biolink:has_phenotype&direct=true&format=json&limit=10&offset=0 - supportBatch: false useTemplating: true inputs: - id: MONDO semantic: Disease parameters: - id: "{{ queryInputs | replPrefix('MONDO') }}" ## has prefix category: "biolink:DiseaseToPhenotypicFeatureAssociation" + subject: "{{ queryInputs | replPrefix('MONDO') }}" ## has prefix + predicate: "biolink:has_phenotype" + direct: true format: json limit: 500 outputs: - id: HP semantic: PhenotypicFeature predicate: has_phenotype - source: "infores:monarchinitiative" ## but the response has more information + ## the primary_knowledge_source field values I've encountered: `infores:hpo-annotations` + source: "infores:monarchinitiative" response_mapping: "$ref": "#/components/x-bte-response-mapping/object-pheno-hp" ## Examples have publication pmids, involves merging multiple hits where some don't have pmids # testExamples: - ## link https://api-v3.monarchinitiative.org/v3/api/entity/MONDO:0007298/biolink:DiseaseToPhenotypicFeatureAssociation?format=json&limit=500&offset=0 + ## link https://api-v3.monarchinitiative.org/v3/api/association?category=biolink:DiseaseToPhenotypicFeatureAssociation&subject=MONDO:0007298&predicate=biolink:has_phenotype&direct=true&format=json&limit=500&offset=0 # - qInput: "MONDO:0007298" ## spinocerebellar ataxia type 29 # oneOutput: "HP:0006855" ## Cerebellar vermis atrophy - ## link https://api-v3.monarchinitiative.org/v3/api/entity/MONDO:0008974/biolink:DiseaseToPhenotypicFeatureAssociation?format=json&limit=500&offset=0 + ## link https://api-v3.monarchinitiative.org/v3/api/association?category=biolink:DiseaseToPhenotypicFeatureAssociation&subject=MONDO:0008974&predicate=biolink:has_phenotype&direct=true&format=json&limit=500&offset=0 # - qInput: "MONDO:0008974" ## Greenberg dysplasia # oneOutput: "HP:0000926" ## Platyspondyly pheno-disease: - ## items.direction will be "incoming" - supportBatch: false useTemplating: true inputs: - id: HP semantic: PhenotypicFeature parameters: - id: "{{ queryInputs | replPrefix('HP') }}" ## has prefix category: "biolink:DiseaseToPhenotypicFeatureAssociation" + object: "{{ queryInputs | replPrefix('HP') }}" ## has prefix + predicate: "biolink:has_phenotype" + direct: true format: json limit: 500 outputs: - id: MONDO semantic: Disease predicate: phenotype_of - source: "infores:monarchinitiative" ## but the response has more information + source: "infores:monarchinitiative" response_mapping: "$ref": "#/components/x-bte-response-mapping/subject-disease-mondo" - ## Example has publication pmids + ## Examples have publication pmids # testExamples: - ## link https://api-v3.monarchinitiative.org/v3/api/entity/HP:0031629/biolink:DiseaseToPhenotypicFeatureAssociation?format=json&limit=500&offset=0 + ## link https://api-v3.monarchinitiative.org/v3/api/association?category=biolink:DiseaseToPhenotypicFeatureAssociation&predicate=biolink:has_phenotype&object=HP:0031629&direct=true&format=json&limit=100&offset=0 # - qInput: "HP:0031629" ## Impaired tandem gait # oneOutput: "MONDO:0030458" ## Charcot-Marie-Tooth disease, axonal, Type 2HH" - ## link https://api-v3.monarchinitiative.org/v3/api/entity/HP:0006855/biolink:DiseaseToPhenotypicFeatureAssociation?format=json&limit=500&offset=0 + ## link https://api-v3.monarchinitiative.org/v3/api/association?category=biolink:DiseaseToPhenotypicFeatureAssociation&predicate=biolink:has_phenotype&object=HP:0006855&direct=true&format=json&limit=100&offset=0 # - qInput: "HP:0006855" ## Cerebellar vermis atrophy # oneOutput: "MONDO:0010041" ## Charlevoix-Saguenay spastic ataxia gene-disease-causal: - ## - items.direction will be "outgoing" + ## 6573 items: https://api-v3.monarchinitiative.org/v3/api/association?category=biolink:CausalGeneToDiseaseAssociation&direct=true&format=json&limit=10&offset=0 + ## all have predicate causes, since the record count is the same https://api-v3.monarchinitiative.org/v3/api/association?category=biolink:CausalGeneToDiseaseAssociation&predicate=biolink:causes&direct=true&format=json&limit=10&offset=0 - supportBatch: false useTemplating: true inputs: - id: HGNC semantic: Gene parameters: - id: "{{ queryInputs | replPrefix('HGNC') }}" ## has prefix category: "biolink:CausalGeneToDiseaseAssociation" + subject: "{{ queryInputs | replPrefix('HGNC') }}" ## has prefix + predicate: "biolink:causes" + direct: true format: json limit: 500 outputs: @@ -2731,147 +2748,268 @@ components: "$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:11138/biolink:CausalGeneToDiseaseAssociation?format=json&limit=20&offset=0 + ## link https://api-v3.monarchinitiative.org/v3/api/association?category=biolink:CausalGeneToDiseaseAssociation&subject=HGNC:11138&predicate=biolink:causes&direct=true&format=json&limit=10&offset=0 # - qInput: "HGNC:11138" ## SNCA aka NCBIGene:6622 # oneOutput: "MONDO:0007488" ## Lewy body dementia - ## link https://api-v3.monarchinitiative.org/v3/api/entity/HGNC:3434/biolink:CausalGeneToDiseaseAssociation?format=json&limit=20&offset=0 + ## link https://api-v3.monarchinitiative.org/v3/api/association?category=biolink:CausalGeneToDiseaseAssociation&subject=HGNC:3434&predicate=biolink:causes&direct=true&format=json&limit=10&offset=0 # - qInput: "HGNC:3434" ## ERCC2 aka NCBIGene:2068 # oneOutput: "MONDO:0012553" ## cerebrooculofacioskeletal syndrome 2 disease-gene-causal: - ## - items.direction will be "incoming" - supportBatch: false useTemplating: true inputs: - id: MONDO semantic: Disease parameters: - id: "{{ queryInputs | replPrefix('MONDO') }}" ## has prefix category: "biolink:CausalGeneToDiseaseAssociation" + object: "{{ queryInputs | replPrefix('MONDO') }}" ## has prefix + predicate: "biolink:has_phenotype" + direct: true format: json limit: 500 outputs: - id: HGNC semantic: Gene predicate: caused_by - source: "infores:monarchinitiative" ## but the response has more information + source: "infores:monarchinitiative" 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:0011562/biolink:CausalGeneToDiseaseAssociation?format=json&limit=20&offset=0 + ## link https://api-v3.monarchinitiative.org/v3/api/association?category=biolink:CausalGeneToDiseaseAssociation&predicate=biolink:causes&object=MONDO:0011562&direct=true&format=json&limit=10&offset=0 # - qInput: "MONDO:0011562" ## autosomal dominant Parkinson disease 4 # oneOutput: "HGNC:11138" ## SNCA aka NCBIGene:6622 - ## link https://api-v3.monarchinitiative.org/v3/api/entity/MONDO:0009861/biolink:CausalGeneToDiseaseAssociation?format=json&limit=20&offset=0 + ## link https://api-v3.monarchinitiative.org/v3/api/association?category=biolink:CausalGeneToDiseaseAssociation&predicate=biolink:causes&object=MONDO:0009861&direct=true&format=json&limit=10&offset=0 # - qInput: "MONDO:0009861" ## phenylketonuria # oneOutput: "HGNC:8582" ## PAH aka NCBIGene:5053 - gene-disease-correlated: - ## - items.direction will be "outgoing" + gene-disease-contributesTo: + ## 589 items: https://api-v3.monarchinitiative.org/v3/api/association?category=biolink:CorrelatedGeneToDiseaseAssociation&predicate=biolink:contributes_to&direct=true&format=json&limit=10&offset=0 - supportBatch: false useTemplating: true inputs: - id: HGNC semantic: Gene parameters: - id: "{{ queryInputs | replPrefix('HGNC') }}" ## has prefix category: "biolink:CorrelatedGeneToDiseaseAssociation" + subject: "{{ queryInputs | replPrefix('HGNC') }}" ## has prefix + predicate: "biolink:contributes_to" + direct: true 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 + ## link https://api-v3.monarchinitiative.org/v3/api/association?category=biolink:CorrelatedGeneToDiseaseAssociation&subject=HGNC:6294&predicate=biolink:contributes_to&direct=true&format=json&limit=10&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 + # oneOutput: "MONDO:0100316" ## long QT syndrome 1 + ## link https://api-v3.monarchinitiative.org/v3/api/association?category=biolink:CorrelatedGeneToDiseaseAssociation&subject=HGNC:9652&predicate=biolink:contributes_to&direct=true&format=json&limit=10&offset=0 # - qInput: "HGNC:9652" ## PTPN22 aka NCBIGene:26191 # oneOutput: "MONDO:0007915" ## systemic lupus erythematosus - disease-gene-correlated: - ## - items.direction will be "incoming" + disease-gene-contributesTo: - supportBatch: false useTemplating: true inputs: - id: MONDO semantic: Disease parameters: - id: "{{ queryInputs | replPrefix('MONDO') }}" ## has prefix category: "biolink:CorrelatedGeneToDiseaseAssociation" + object: "{{ queryInputs | replPrefix('MONDO') }}" ## has prefix + predicate: "biolink:contributes_to" + direct: true format: json limit: 500 outputs: - id: HGNC semantic: Gene predicate: contribution_from + source: "infores:monarchinitiative" + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-gene-hgnc" + ## Examples don't have publication info + # testExamples: + ## link https://api-v3.monarchinitiative.org/v3/api/association?category=biolink:CorrelatedGeneToDiseaseAssociation&predicate=biolink:contributes_to&object=MONDO:0014629&direct=true&format=json&limit=10&offset=0 + # - qInput: "MONDO:0014629" ## autoimmune interstitial lung disease-arthritis syndrome + # oneOutput: "HGNC:2230" ## COPA aka NCBIGene:1314 + ## link https://api-v3.monarchinitiative.org/v3/api/entity/MONDO:0018875/biolink:CorrelatedGeneToDiseaseAssociation?format=json&limit=20&offset=0 + # - qInput: "MONDO:0013416" ## age related macular degeneration 8 + # oneOutput: "HGNC:32685" ## ARMS2 aka NCBIGene:387715 + gene-disease-associatedCondition: + ## 7995 items: https://api-v3.monarchinitiative.org/v3/api/association?category=biolink:CorrelatedGeneToDiseaseAssociation&predicate=biolink:gene_associated_with_condition&direct=true&format=json&limit=10&offset=0 + - supportBatch: false + useTemplating: true + inputs: + - id: HGNC + semantic: Gene + parameters: + category: "biolink:CorrelatedGeneToDiseaseAssociation" + subject: "{{ queryInputs | replPrefix('HGNC') }}" ## has prefix + predicate: "biolink:gene_associated_with_condition" + direct: true + format: json + limit: 500 + outputs: + - id: MONDO + semantic: Disease + predicate: gene_associated_with_condition source: "infores:monarchinitiative" ## but the response has more information + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-disease-mondo" + ## Examples don't have publication info + # testExamples: + ## link https://api-v3.monarchinitiative.org/v3/api/association?category=biolink:CorrelatedGeneToDiseaseAssociation&subject=HGNC:6493&predicate=biolink:gene_associated_with_condition&direct=true&format=json&limit=10&offset=0 + # - qInput: "HGNC:6493" ## LAMC2 aka NCBIGene:3918 + # oneOutput: "MONDO:0009182" ## junctional epidermolysis bullosa Herlitz type + ## link https://api-v3.monarchinitiative.org/v3/api/association?category=biolink:CorrelatedGeneToDiseaseAssociation&subject=HGNC:9652&predicate=biolink:contributes_to&direct=true&format=json&limit=10&offset=0 + # - qInput: "HGNC:9462" ## PRPS1 aka NCBIGene:5631 + # oneOutput: "MONDO:0010699" ## Charcot-Marie-Tooth disease X-linked recessive 5 + disease-gene-associatedCondition: + - supportBatch: false + useTemplating: true + inputs: + - id: MONDO + semantic: Disease + parameters: + category: "biolink:CorrelatedGeneToDiseaseAssociation" + object: "{{ queryInputs | replPrefix('MONDO') }}" ## has prefix + predicate: "biolink:gene_associated_with_condition" + direct: true + format: json + limit: 500 + outputs: + - id: HGNC + semantic: Gene + predicate: condition_associated_with_gene + source: "infores:monarchinitiative" 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 + ## link https://api-v3.monarchinitiative.org/v3/api/association?category=biolink:CorrelatedGeneToDiseaseAssociation&predicate=biolink:gene_associated_with_condition&object=MONDO:0018961&direct=true&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 + ## link https://api-v3.monarchinitiative.org/v3/api/association?category=biolink:CorrelatedGeneToDiseaseAssociation&predicate=biolink:gene_associated_with_condition&object=MONDO:0018875&direct=true&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" + ## 922268 items: https://api-v3.monarchinitiative.org/v3/api/association?category=biolink:GeneToPhenotypicFeatureAssociation&direct=true&format=json&limit=10&offset=0 + ## all have predicate causes, since the record count is the same https://api-v3.monarchinitiative.org/v3/api/association?category=biolink:GeneToPhenotypicFeatureAssociation&predicate=biolink:has_phenotype&direct=true&format=json&limit=10&offset=0 - supportBatch: false useTemplating: true inputs: - id: HGNC semantic: Gene parameters: - id: "{{ queryInputs | replPrefix('HGNC') }}" ## has prefix category: "biolink:GeneToPhenotypicFeatureAssociation" + subject: "{{ queryInputs | replPrefix('HGNC') }}" ## has prefix + predicate: "biolink:has_phenotype" + direct: true format: json limit: 500 outputs: - id: HP semantic: PhenotypicFeature - ## a little odd: I used to use gene_associated_with_condition + ## I previously used 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 + ## link https://api-v3.monarchinitiative.org/v3/api/association?category=biolink:GeneToPhenotypicFeatureAssociation&subject=HGNC:8548&predicate=biolink:has_phenotype&direct=true&format=json&limit=100&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 + ## link https://api-v3.monarchinitiative.org/v3/api/association?category=biolink:GeneToPhenotypicFeatureAssociation&subject=HGNC:7551&predicate=biolink:has_phenotype&direct=true&format=json&limit=100&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" + object: "{{ queryInputs | replPrefix('HP') }}" ## has prefix + predicate: "biolink:gene_associated_with_condition" + direct: true format: json limit: 500 outputs: - id: HGNC semantic: Gene predicate: phenotype_of - source: "infores:monarchinitiative" ## but the response has more information + source: "infores:monarchinitiative" 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 + ## link https://api-v3.monarchinitiative.org/v3/api/association?category=biolink:GeneToPhenotypicFeatureAssociation&predicate=biolink:has_phenotype&object=HP:0000183&direct=true&format=json&limit=100&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 + ## link https://api-v3.monarchinitiative.org/v3/api/association?category=biolink:GeneToPhenotypicFeatureAssociation&predicate=biolink:has_phenotype&object=HP:0032543&direct=true&format=json&limit=100&offset=0 # - qInput: "HP:0032543" ## Lithoptysis # oneOutput: "HGNC:2950" ## DNAH5 aka NCBIGene:1767 + gene-gene-interaction-forward: + ## 4096781 items: https://api-v3.monarchinitiative.org/v3/api/association?category=biolink:PairwiseGeneToGeneInteraction&direct=true&format=json&limit=10&offset=0 + ## all have predicate causes, since the record count is the same https://api-v3.monarchinitiative.org/v3/api/association?category=biolink:PairwiseGeneToGeneInteraction&predicate=biolink:interacts_with&direct=true&format=json&limit=10&offset=0 + - supportBatch: false + useTemplating: true + inputs: + - id: HGNC + semantic: Gene + parameters: + category: "biolink:PairwiseGeneToGeneInteraction" + subject: "{{ queryInputs | replPrefix('HGNC') }}" ## has prefix + predicate: "biolink:interacts_with" + direct: true + format: json + limit: 500 + outputs: + - id: HGNC + semantic: Gene + ## could this predicate be more specific? like genetically_interacts_with? + predicate: interacts_with + source: "infores:monarchinitiative" ## but the response has more information + response_mapping: + "$ref": "#/components/x-bte-response-mapping/object-gene-hgnc" + ## Examples have publication pmids + # testExamples: + ## link https://api-v3.monarchinitiative.org/v3/api/association?category=biolink:PairwiseGeneToGeneInteraction&subject=HGNC:2950&predicate=biolink:interacts_with&direct=true&format=json&limit=100&offset=0 + # - qInput: "HGNC:2950" ## DNAH5 aka NCBIGene:1767 + # oneOutput: "HGNC:13671" ## H2AC12 aka NCBIGene:85235 + ## link https://api-v3.monarchinitiative.org/v3/api/association?category=biolink:PairwiseGeneToGeneInteraction&subject=HGNC:7551&predicate=biolink:interacts_with&direct=true&format=json&limit=100&offset=0 + # - qInput: "HGNC:7551" ## MYBPC3 aka NCBIGene:4607 + # oneOutput: "HGNC:16007" ## TRIM63 aka NCBIGene:84676 + gene-gene-interaction-backward: + - supportBatch: false + useTemplating: true + inputs: + - id: HGNC + semantic: Gene + parameters: + category: "biolink:PairwiseGeneToGeneInteraction" + object: "{{ queryInputs | replPrefix('HGNC') }}" ## has prefix + predicate: "biolink:interacts_with" + direct: true + format: json + limit: 500 + outputs: + - id: HGNC + semantic: Gene + predicate: interacts_with + source: "infores:monarchinitiative" + response_mapping: + "$ref": "#/components/x-bte-response-mapping/subject-gene-hgnc" + # testExamples: + ## link https://api-v3.monarchinitiative.org/v3/api/association?category=biolink:PairwiseGeneToGeneInteraction&predicate=biolink:interacts_with&object=HGNC:2950&direct=true&format=json&limit=100&offset=0 + # - qInput: "HGNC:2950" ## DNAH5 aka NCBIGene:1767 + # oneOutput: "HGNC:8607" ## PRKN aka NCBIGene:5071 + ## link https://api-v3.monarchinitiative.org/v3/api/association?category=biolink:PairwiseGeneToGeneInteraction&predicate=biolink:interacts_with&object=HGNC:7551&direct=true&format=json&limit=100&offset=0 + # - qInput: "HGNC:7551" ## MYBPC3 aka NCBIGene:4607 + # oneOutput: "HGNC:1476" ## CAPN1 aka NCBIGene:823