From 39984a0b1c87dcc55ab0f191136248038edfd7df Mon Sep 17 00:00:00 2001 From: Colleen Xu Date: Mon, 16 Oct 2023 16:48:05 -0700 Subject: [PATCH 1/6] ctd: adjust operations for batch-query --- CTD/smartapi.yaml | 68 +++++++++++++++++++++++------------------------ 1 file changed, 34 insertions(+), 34 deletions(-) diff --git a/CTD/smartapi.yaml b/CTD/smartapi.yaml index 9ad6c153..377096b4 100644 --- a/CTD/smartapi.yaml +++ b/CTD/smartapi.yaml @@ -166,7 +166,7 @@ components: ## - gene <-> go: currently we get this info from MyGene. ## We could also try getting this info from Biolink/Monarch chemical2gene: - - supportBatch: false + - supportBatch: true useTemplating: true inputs: - id: MESH @@ -176,7 +176,7 @@ components: semantic: Gene parameters: inputType: chem - inputTerms: "{{ queryInputs }}" ## no prefix + inputTerms: "{{ queryInputs | joinSafe('|') }}" inputTermSearchType: directAssociations report: genes_curated format: json @@ -187,7 +187,7 @@ components: # - qInput: "MESH:C006303" ## acivicin # oneOutput: "NCBIGene:1080" ## CFTR gene2chemical: - - supportBatch: false + - supportBatch: true useTemplating: true inputs: - id: NCBIGene @@ -197,7 +197,7 @@ components: semantic: SmallMolecule parameters: inputType: gene - inputTerms: "{{ queryInputs | rmPrefix() }}" ## no prefix + inputTerms: "{{ queryInputs | rmPrefix() | joinSafe('|') }}" ## no prefix inputTermSearchType: directAssociations report: chems_curated format: json @@ -209,7 +209,7 @@ components: # oneOutput: "MESH:C010395" ## acetylsalicylic acid lysinate / Aspirin DL-lysine ## commenting out chemical2disease operations because BTE isn't recognizing MESH vs OMIM Disease IDs # chemical2disease_1: - # - supportBatch: false + # - supportBatch: true # useTemplating: true # inputs: # - id: MESH @@ -219,7 +219,7 @@ components: # semantic: Disease # parameters: # inputType: chem - # inputTerms: "{{ queryInputs }}" ## no prefix + # inputTerms: "{{ queryInputs | joinSafe('|') }}" ## no prefix # inputTermSearchType: directAssociations # report: diseases_curated # format: json @@ -230,7 +230,7 @@ components: # # - qInput: "MESH:D005492" ## Folic Acid # # oneOutput: "MESH:D000748" ## Anemia, Macrocytic disease2chemical_1: - - supportBatch: false + - supportBatch: true useTemplating: true inputs: - id: MESH @@ -240,7 +240,7 @@ components: semantic: SmallMolecule parameters: inputType: disease - inputTerms: "{{ queryInputs | replPrefix('MESH') }}" ## HAS PREFIX + inputTerms: "{{ queryInputs | replPrefix('MESH') | joinSafe('|') }}" ## HAS PREFIX inputTermSearchType: directAssociations report: chems_curated format: json @@ -251,7 +251,7 @@ components: # - qInput: "MESH:D020138" ## Hyperhomocysteinemia # oneOutput: "MESH:D016291" ## Dizocilpine Maleate / Neurogard # chemical2disease_2: - # - supportBatch: false + # - supportBatch: true # useTemplating: true # inputs: # - id: MESH @@ -261,7 +261,7 @@ components: # semantic: Disease # parameters: # inputType: chem - # inputTerms: "{{ queryInputs }}" ## no prefix + # inputTerms: "{{ queryInputs | joinSafe('|') }}" ## no prefix # inputTermSearchType: directAssociations # report: diseases_curated # format: json @@ -272,7 +272,7 @@ components: # # - qInput: "MESH:D004317" ## Doxorubicin # # oneOutput: "OMIM:610141" ## QT INTERVAL, VARIATION IN disease2chemical_2: - - supportBatch: false + - supportBatch: true useTemplating: true inputs: - id: OMIM @@ -282,7 +282,7 @@ components: semantic: SmallMolecule parameters: inputType: disease - inputTerms: "{{ queryInputs | replPrefix('OMIM') }}" ## HAS PREFIX + inputTerms: "{{ queryInputs | replPrefix('OMIM') | joinSafe('|') }}" ## HAS PREFIX inputTermSearchType: directAssociations report: chems_curated format: json @@ -295,7 +295,7 @@ components: chemical2bp: ## only one way (no GO terms -> chemicals) ## goes through gene intermediates, not the same as the "enriched" dataset - - supportBatch: false + - supportBatch: true useTemplating: true inputs: - id: MESH @@ -305,7 +305,7 @@ components: semantic: BiologicalProcess parameters: inputType: chem - inputTerms: "{{ queryInputs }}" ## no prefix + inputTerms: "{{ queryInputs | joinSafe('|') }}" ## no prefix inputTermSearchType: directAssociations report: go ontology: go_bp @@ -319,7 +319,7 @@ components: chemical2cc: ## only one way (no GO terms -> chemicals) ## goes through gene intermediates, not the same as the "enriched" dataset - - supportBatch: false + - supportBatch: true useTemplating: true inputs: - id: MESH @@ -329,7 +329,7 @@ components: semantic: CellularComponent parameters: inputType: chem - inputTerms: "{{ queryInputs }}" ## no prefix + inputTerms: "{{ queryInputs | joinSafe('|') }}" ## no prefix inputTermSearchType: directAssociations report: go ontology: go_cc @@ -343,7 +343,7 @@ components: chemical2mf: ## only one way (no GO terms -> chemicals) ## goes through gene intermediates, not the same as the "enriched" dataset - - supportBatch: false + - supportBatch: true useTemplating: true inputs: - id: MESH @@ -353,7 +353,7 @@ components: semantic: MolecularActivity parameters: inputType: chem - inputTerms: "{{ queryInputs }}" ## no prefix + inputTerms: "{{ queryInputs | joinSafe('|') }}" ## no prefix inputTermSearchType: directAssociations report: go ontology: go_mf @@ -366,7 +366,7 @@ components: # oneOutput: "GO:0070742" ## C2H2 zinc finger domain binding ## commenting out gene2disease operations because BTE isn't recognizing MESH vs OMIM Disease IDs disease2gene_1: - - supportBatch: false + - supportBatch: true useTemplating: true inputs: - id: MESH @@ -376,7 +376,7 @@ components: semantic: Gene parameters: inputType: disease - inputTerms: "{{ queryInputs | replPrefix('MESH') }}" ## HAS PREFIX + inputTerms: "{{ queryInputs | replPrefix('MESH') | joinSafe('|') }}" ## HAS PREFIX inputTermSearchType: directAssociations report: genes_curated format: json @@ -387,7 +387,7 @@ components: # - qInput: "MESH:D020138" ## Hyperhomocysteinemia # oneOutput: "NCBIGene:4524" ## MTHFR # gene2disease_1: - # - supportBatch: false + # - supportBatch: true # useTemplating: true # inputs: # - id: NCBIGene @@ -397,7 +397,7 @@ components: # semantic: Disease # parameters: # inputType: gene - # inputTerms: "{{ queryInputs | rmPrefix() }}" ## no prefix + # inputTerms: "{{ queryInputs | rmPrefix() | joinSafe('|') }}" ## no prefix # inputTermSearchType: directAssociations # report: diseases_curated # format: json @@ -408,7 +408,7 @@ components: # # - qInput: "NCBIGene:4868" ## NPHS1 # # oneOutput: "MESH:C535761" ## Nephrosis, congenital / familial nephrotic syndrome disease2gene_2: - - supportBatch: false + - supportBatch: true useTemplating: true inputs: - id: OMIM @@ -418,7 +418,7 @@ components: semantic: Gene parameters: inputType: disease - inputTerms: "{{ queryInputs | replPrefix('OMIM') }}" ## HAS PREFIX + inputTerms: "{{ queryInputs | replPrefix('OMIM') | joinSafe('|') }}" ## HAS PREFIX inputTermSearchType: directAssociations report: genes_curated format: json @@ -429,7 +429,7 @@ components: # - qInput: "OMIM:615075" ## NEURODEVELOPMENTAL DISORDER WITH SPASTIC DIPLEGIA AND VISUAL DEFECTS # oneOutput: "NCBIGene:1499" ## CTNNB1 # gene2disease_2: - # - supportBatch: false + # - supportBatch: true # useTemplating: true # inputs: # - id: NCBIGene @@ -439,7 +439,7 @@ components: # semantic: Disease # parameters: # inputType: gene - # inputTerms: "{{ queryInputs | rmPrefix() }}" ## no prefix + # inputTerms: "{{ queryInputs | rmPrefix() | joinSafe('|') }}" ## no prefix # inputTermSearchType: directAssociations # report: diseases_curated # format: json @@ -451,7 +451,7 @@ components: # # oneOutput: "OMIM:259710" ## OSTEOPETROSIS, AUTOSOMAL RECESSIVE 2 ## commenting out gene2pathway operations because BTE isn't recognizing REACT vs KEGG Pathway IDs # gene2pathway_1: - # - supportBatch: false + # - supportBatch: true # useTemplating: true # inputs: # - id: NCBIGene @@ -461,7 +461,7 @@ components: # semantic: Pathway # parameters: # inputType: gene - # inputTerms: "{{ queryInputs | rmPrefix() }}" ## no prefix + # inputTerms: "{{ queryInputs | rmPrefix() | joinSafe('|') }}" ## no prefix # inputTermSearchType: directAssociations # report: pathways_curated # format: json @@ -472,7 +472,7 @@ components: # # - qInput: "NCBIGene:8600" ## TNFSF11 # # oneOutput: "REACT:R-HSA-5668541" ## TNFR2 non-canonical NF-kB pathway pathway2gene_1: - - supportBatch: false + - supportBatch: true useTemplating: true inputs: - id: REACT @@ -482,7 +482,7 @@ components: semantic: Gene parameters: inputType: pathway - inputTerms: "{{ queryInputs | replPrefix('REACT') }}" ## HAS PREFIX + inputTerms: "{{ queryInputs | replPrefix('REACT') | joinSafe('|') }}" ## HAS PREFIX inputTermSearchType: directAssociations report: genes_curated format: json @@ -493,7 +493,7 @@ components: # - qInput: "REACT:R-HSA-5669034" ## TNFs bind their physiological receptors # oneOutput: "NCBIGene:939" ## CD27 # gene2pathway_2: - # - supportBatch: false + # - supportBatch: true # useTemplating: true # inputs: # - id: NCBIGene @@ -503,7 +503,7 @@ components: # semantic: Pathway # parameters: # inputType: gene - # inputTerms: "{{ queryInputs | rmPrefix() }}" ## no prefix + # inputTerms: "{{ queryInputs | rmPrefix() | joinSafe('|') }}" ## no prefix # inputTermSearchType: directAssociations # report: pathways_curated # format: json @@ -514,7 +514,7 @@ components: # # - qInput: "NCBIGene:8600" ## TNFSF11 # # oneOutput: "KEGG.PATHWAY:hsa04917" ## Prolactin signaling pathway pathway2gene_2: - - supportBatch: false + - supportBatch: true useTemplating: true inputs: - id: KEGG.PATHWAY @@ -524,7 +524,7 @@ components: semantic: Gene parameters: inputType: pathway - inputTerms: "{{ queryInputs | replPrefix('KEGG') }}" ## HAS PREFIX (not biolink-model spelling) + inputTerms: "{{ queryInputs | replPrefix('KEGG') | joinSafe('|') }}" ## HAS PREFIX (not biolink-model spelling) inputTermSearchType: directAssociations report: genes_curated format: json From 9fdd0582cb4d78706ad77863270f688a4ffc8c8d Mon Sep 17 00:00:00 2001 From: Colleen Xu Date: Mon, 4 Dec 2023 22:48:02 -0800 Subject: [PATCH 2/6] mydisease, biothings rare source: update ORPHANET -> orphanet --- mydisease.info/smartapi.yaml | 10 +++++----- ncats_rare_source/smartapi.yaml | 10 +++++----- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/mydisease.info/smartapi.yaml b/mydisease.info/smartapi.yaml index f7a6dd82..440e0d39 100644 --- a/mydisease.info/smartapi.yaml +++ b/mydisease.info/smartapi.yaml @@ -661,7 +661,7 @@ components: omim: OMIM: hpo.omim ## no prefix orphanet: - ORPHANET: hpo.orphanet ## no prefix + orphanet: hpo.orphanet ## no prefix mondo: ## added for a bunch of operations MONDO: mondo.mondo ## HAS PREFIX (MONDO) ctd-mesh-disease: ## added for chemical-disease operation @@ -827,7 +827,7 @@ components: - supportBatch: true useTemplating: true inputs: - - id: ORPHANET + - id: orphanet semantic: Disease requestBody: body: @@ -870,7 +870,7 @@ components: response_mapping: "$ref": "#/components/x-bte-response-mapping/disease-phenotype" # testExamples: - # - qInput: "ORPHANET:881" ## Turner Syndrome + # - qInput: "orphanet:881" ## Turner Syndrome # oneOutput: "HP:0000137" ## Abnormality of the ovary ## for ctd-based operations: ## - when the mydisease parser maps the resources' IDs to MONDO, are there situations where a MESH and a OMIM ID map to the same MONDO? @@ -1038,7 +1038,7 @@ components: q: "{{ queryInputs }}" scopes: hpo.phenotype_related_to_disease.hpo_id outputs: - - id: ORPHANET + - id: orphanet semantic: Disease parameters: fields: hpo.orphanet @@ -1049,7 +1049,7 @@ components: "$ref": "#/components/x-bte-response-mapping/orphanet" # testExamples: # - qInput: "HP:0000224" ## Hypogeusia - # oneOutput: "ORPHANET:99857" ## Secondary Syringomyelia + # oneOutput: "orphanet:99857" ## Secondary Syringomyelia chemical-disease: - supportBatch: true useTemplating: true diff --git a/ncats_rare_source/smartapi.yaml b/ncats_rare_source/smartapi.yaml index 5133ff61..2f279ddc 100644 --- a/ncats_rare_source/smartapi.yaml +++ b/ncats_rare_source/smartapi.yaml @@ -599,7 +599,7 @@ components: q: "{{ queryInputs }}" ## no prefix scopes: entrezgene outputs: - - id: ORPHANET + - id: orphanet semantic: Disease parameters: ## orphanet ID has no prefix @@ -611,12 +611,12 @@ components: "$ref": "#/components/x-bte-response-mapping/diseaseOrphanet-object" # testExamples: # - qInput: "NCBIGene:100" ## ADA - # oneOutput: "ORPHANET:39041" ## Omenn syndrome + # oneOutput: "orphanet:39041" ## Omenn syndrome diseaseOrphanet-gene: - supportBatch: true useTemplating: true inputs: - - id: ORPHANET + - id: orphanet semantic: Disease requestBody: body: @@ -635,7 +635,7 @@ components: response_mapping: "$ref": "#/components/x-bte-response-mapping/gene-object" # testExamples: - # - qInput: "ORPHANET:110" ## Bardet-Biedl syndrome + # - qInput: "orphanet:110" ## Bardet-Biedl syndrome # oneOutput: "NCBIGene:10806" ## SDCCAG8 gene-diseaseUMLS: - supportBatch: true @@ -692,7 +692,7 @@ components: ## didn't add names for gene -> disease. when I tried, the co-occurrence urls would appear on every Edge, ## when they're supposed to show up only on the edge they correspond to diseaseOrphanet-object: - ORPHANET: raresource.disease.orphanet ## no prefix + orphanet: raresource.disease.orphanet ## no prefix ref_url: raresource.disease.cooccurrence_url ## this url leads to a webpage with literature supporting the gene-disease relationship diseaseUMLS-object: From 62cf47f7dd8e7a74ab346ea10ab8ba856e61678c Mon Sep 17 00:00:00 2001 From: Colleen Xu Date: Thu, 7 Dec 2023 22:26:50 -0800 Subject: [PATCH 3/6] mychem: edit fda-orphan-data operations --- mychem.info/openapi_full.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/mychem.info/openapi_full.yml b/mychem.info/openapi_full.yml index b8ebeed9..81852c7b 100644 --- a/mychem.info/openapi_full.yml +++ b/mychem.info/openapi_full.yml @@ -1907,8 +1907,8 @@ components: # fda_orphan_drug.orphan_designation.original_text fields: fda_orphan_drug.orphan_designation.umls predicate: treats ## current biolink predicate - ## through drugcentral, FDA Orphan Drug Designations and Approvals database... - source: "infores:drugcentral" + ## FDA Orphan Drug Designations and Approvals database + source: "infores:fda-orphan-drug-db" response_mapping: "$ref": "#/components/x-bte-response-mapping/fdaOrphanDrug" # testExamples: @@ -1931,8 +1931,8 @@ components: fields: fda_orphan_drug.pubchem_cid size: 1000 ## note size limit predicate: treated_by ## current biolink predicate - ## through drugcentral, FDA Orphan Drug Designations and Approvals database... - source: "infores:drugcentral" + ## FDA Orphan Drug Designations and Approvals database + source: "infores:fda-orphan-drug-db" response_mapping: "$ref": "#/components/x-bte-response-mapping/fdaOrphanDrug-pubchemCompound" # testExamples: From 727b9c272f88415bae38394089394a45c5c1b3db Mon Sep 17 00:00:00 2001 From: Colleen Xu Date: Tue, 12 Dec 2023 23:48:45 -0800 Subject: [PATCH 4/6] complex portal: ORPHANET->orphanet change --- complexportal/smartapi.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/complexportal/smartapi.yaml b/complexportal/smartapi.yaml index feb55505..1ea83f0e 100644 --- a/complexportal/smartapi.yaml +++ b/complexportal/smartapi.yaml @@ -109,7 +109,7 @@ components: - supportBatch: false useTemplating: true inputs: - - id: ORPHANET + - id: orphanet semantic: Disease outputs: - id: ComplexPortal @@ -122,7 +122,7 @@ components: response_mapping: "$ref": "#/components/x-bte-response-mapping/complex-output" # testExamples: - # - qInput: "ORPHANET:848" ## Beta-thalassemia + # - qInput: "orphanet:848" ## Beta-thalassemia # oneOutput: "ComplexPortal:CPX-2158" ## Hemoglobin HbA complex ## Complex -> entity x-bte operations use JQ post-processing # complex2protein: @@ -172,7 +172,7 @@ components: # - id: ComplexPortal # semantic: MacromolecularComplex # outputs: - # - id: ORPHANET + # - id: orphanet # semantic: Disease # parameters: # id: "{{ queryInputs }}" ## no prefix @@ -187,7 +187,7 @@ components: # "$ref": "#/components/x-bte-response-mapping/complex2disease" # # testExamples: # # - qInput: "ComplexPortal:CPX-2158" ## Hemoglobin HbA complex - # # oneOutput: "ORPHANET:848" ## Beta-thalassemia + # # oneOutput: "orphanet:848" ## Beta-thalassemia x-bte-response-mapping: complex-output: ComplexPortal: elements.complexAC @@ -203,5 +203,5 @@ components: CHEBI: participants.identifier complex2disease: ## this is a field made with JQ-post-processing - ORPHANET: disease_ids + orphanet: disease_ids \ No newline at end of file From 68c869b4adecbecda1faa7d144f84270e5218f14 Mon Sep 17 00:00:00 2001 From: Colleen Xu Date: Wed, 31 Jan 2024 12:51:01 -0800 Subject: [PATCH 5/6] biothings fooddata central: edit examples in comments for FOODON ID adjustment in https://github.com/biothings/pending.api/issues/170 only in CI at the moment but will rollout to all instances --- fooddata_central/smartapi.yaml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/fooddata_central/smartapi.yaml b/fooddata_central/smartapi.yaml index 70d13047..855c28e7 100644 --- a/fooddata_central/smartapi.yaml +++ b/fooddata_central/smartapi.yaml @@ -611,8 +611,8 @@ components: response_mapping: "$ref": "#/components/x-bte-response-mapping/compound" # testExamples: - # - qInput: "FOODON:FOODON_03302578" ## Oil, canola - # oneOutput: "CHEBI:27693" ## Beta-sitosterol + # - qInput: "FOODON:03302578" ## Oil, canola (was FOODON_03302578) + # oneOutput: "CHEBI:27693" ## Beta-sitosterol food-compound-rev: - supportBatch: true useTemplating: true @@ -638,8 +638,8 @@ components: response_mapping: "$ref": "#/components/x-bte-response-mapping/food" # testExamples: - # - qInput: "CHEBI:27693" ## Beta-sitosterol - # oneOutput: "FOODON:FOODON_03309857" ## Oil, peanut + # - qInput: "CHEBI:27693" ## Beta-sitosterol + # oneOutput: "FOODON:03309857" ## Oil, peanut (was FOODON_03309857) x-bte-response-mapping: compound: CHEBI: object.chebiId From e03295bdfccf14d930fdc49af16ba269176de3c4 Mon Sep 17 00:00:00 2001 From: Colleen Xu Date: Thu, 8 Feb 2024 15:47:25 -0800 Subject: [PATCH 6/6] multiple apis: uncomment testExamples also some minor comment edits for some apis --- AGR/agr.yaml | 294 +++++++++++------------ CTD/smartapi.yaml | 102 ++++---- DISEASES/smartapi.yaml | 12 +- EBIgene2phenotype/smartapi.yaml | 12 +- LINCS/smartapi.yml | 6 +- MGIgene2phenotype/smartapi.yaml | 24 +- bindingdb/smartapi.yaml | 12 +- biolink/openapi.yml | 278 ++++++++++----------- bioplanet/bioplanet-pathway-disease.yaml | 12 +- bioplanet/bioplanet-pathway-gene.yaml | 12 +- biothings_foodb/smartapi.yaml | 12 +- complexportal/smartapi.yaml | 48 ++-- ddinter/ddinter.yaml | 12 +- dgidb/openapi.yml | 216 ++++++++--------- ebi_proteins/openapi.yml | 6 +- fooddata_central/smartapi.yaml | 12 +- go_bp/smartapi.yaml | 60 ++--- go_cc/smartapi.yaml | 24 +- go_mf/smartapi.yaml | 24 +- gtrx/gtrx.yaml | 12 +- hpo/smartapi.yaml | 24 +- iPTMnet/smartapi.yaml | 12 +- idisk/smartapi.yaml | 48 ++-- innatedb/smartapi.yaml | 72 +++--- litvar/smartapi.yaml | 6 +- mychem.info/openapi_full.yml | 227 +++++++++-------- mydisease.info/smartapi.yaml | 156 ++++++------ mygene.info/openapi_full.yml | 109 +++++---- myvariant.info/openapi_full.yml | 168 ++++++------- ncats_rare_source/smartapi.yaml | 24 +- ols/smartapi.yaml | 6 +- pfocr/smartapi.yaml | 36 +-- pharmgkb/smartapi.yaml | 186 +++++++------- quickgo/smartapi.yaml | 6 +- repodb/smartapi.yaml | 31 +-- rhea/smartapi.yaml | 30 +-- suppkg/suppkg.yaml | 12 +- ttd/smartapi.yaml | 192 +++++++-------- uberon/smartapi.yaml | 96 ++++---- 39 files changed, 1315 insertions(+), 1316 deletions(-) diff --git a/AGR/agr.yaml b/AGR/agr.yaml index 211417a8..e61aff92 100644 --- a/AGR/agr.yaml +++ b/AGR/agr.yaml @@ -674,9 +674,9 @@ components: source: "infores:agrkb" response_mapping: "$ref": "#/components/x-bte-response-mapping/isMarkerFor-doid" - # testExamples: - # - qInput: "HGNC:10615" ## CCL17 - # oneOutput: "DOID:3082" ## interstitial lung disease + testExamples: + - qInput: "HGNC:10615" ## CCL17 + oneOutput: "DOID:3082" ## interstitial lung disease doid-to-hgnc-bothBiomarker: - supportBatch: true useTemplating: true @@ -700,13 +700,13 @@ components: source: "infores:agrkb" response_mapping: "$ref": "#/components/x-bte-response-mapping/hgnc" - # testExamples: - ## for biomarker_via_orthology - # - qInput: "DOID:0080322" ## polycystic kidney disease - # oneOutput: "HGNC:1043" ## BGLAP - ## for is_marker_for - # - qInput: "DOID:0080600" ## COVID-19 - # oneOutput: "HGNC:10626" ## CCL27 + testExamples: + # for biomarker_via_orthology + - qInput: "DOID:0080322" ## polycystic kidney disease + oneOutput: "HGNC:1043" ## BGLAP + # for is_marker_for + - qInput: "DOID:0080600" ## COVID-19 + oneOutput: "HGNC:10626" ## CCL27 rgd-to-doid-isMarkerFor: ## 1534 records - supportBatch: true @@ -732,9 +732,9 @@ components: source: "infores:agrkb" response_mapping: "$ref": "#/components/x-bte-response-mapping/isMarkerFor-doid" - # testExamples: - # - qInput: "RGD:1303018" ## Mcm7 - # oneOutput: "DOID:684" ## hepatocellular carcinoma + testExamples: + - qInput: "RGD:1303018" ## Mcm7 + oneOutput: "DOID:684" ## hepatocellular carcinoma doid-to-rgd-bothBiomarker: - supportBatch: true useTemplating: true @@ -758,13 +758,13 @@ components: source: "infores:agrkb" response_mapping: "$ref": "#/components/x-bte-response-mapping/rgd" - # testExamples: - ## for biomarker_via_orthology - # - qInput: "DOID:3587" ## pancreatic ductal carcinoma - # oneOutput: "RGD:1303018" ## Mcm7 - ## for is_marker_for - # - qInput: "DOID:10325" ## silicosis - # oneOutput: "RGD:1303058" ## Chia + testExamples: + # for biomarker_via_orthology + - qInput: "DOID:3587" ## pancreatic ductal carcinoma + oneOutput: "RGD:1303018" ## Mcm7 + # for is_marker_for + - qInput: "DOID:10325" ## silicosis + oneOutput: "RGD:1303058" ## Chia hgnc-to-doid-biomarkerViaOrthology: ## 1581 records - supportBatch: true @@ -794,9 +794,9 @@ components: source: "infores:agrkb" response_mapping: "$ref": "#/components/x-bte-response-mapping/biomarkerViaOrthology-doid" - # testExamples: - # - qInput: "HGNC:1037" ## CFB - # oneOutput: "DOID:0080322" ## polycystic kidney disease + testExamples: + - qInput: "HGNC:1037" ## CFB + oneOutput: "DOID:0080322" ## polycystic kidney disease mgi-to-doid-biomarkerViaOrthology: ## 2590 records - supportBatch: true @@ -822,9 +822,9 @@ components: source: "infores:agrkb" response_mapping: "$ref": "#/components/x-bte-response-mapping/biomarkerViaOrthology-doid" - # testExamples: - # - qInput: "MGI:109384" ## Atf3 - # oneOutput: "DOID:10283" ## prostate cancer + testExamples: + - qInput: "MGI:109384" ## Atf3 + oneOutput: "DOID:10283" ## prostate cancer doid-to-mgi-biomarkerViaOrthology: - supportBatch: true useTemplating: true @@ -848,9 +848,9 @@ components: source: "infores:agrkb" response_mapping: "$ref": "#/components/x-bte-response-mapping/mgi" - # testExamples: - # - qInput: "DOID:0050758" ## metabolic acidosis - # oneOutput: "MGI:109393" ## Slc4a1 + testExamples: + - qInput: "DOID:0050758" ## metabolic acidosis + oneOutput: "MGI:109393" ## Slc4a1 rgd-to-doid-biomarkerViaOrthology: ## 1879 records - supportBatch: true @@ -876,9 +876,9 @@ components: source: "infores:agrkb" response_mapping: "$ref": "#/components/x-bte-response-mapping/biomarkerViaOrthology-doid" - # testExamples: - # - qInput: "RGD:1302977" ## Slpil3 - # oneOutput: "DOID:2945" ## severe acute respiratory syndrome + testExamples: + - qInput: "RGD:1302977" ## Slpil3 + oneOutput: "DOID:2945" ## severe acute respiratory syndrome zfin-to-doid-biomarkerViaOrthology: ## 2800 records - supportBatch: true @@ -904,9 +904,9 @@ components: source: "infores:agrkb" response_mapping: "$ref": "#/components/x-bte-response-mapping/biomarkerViaOrthology-doid" - # testExamples: - # - qInput: "ZFIN:ZDB-GENE-011205-17" ## mt-cyb - # oneOutput: "DOID:9352" ## type 2 diabetes mellitus + testExamples: + - qInput: "ZFIN:ZDB-GENE-011205-17" ## mt-cyb + oneOutput: "DOID:9352" ## type 2 diabetes mellitus doid-to-zfin-biomarkerViaOrthology: - supportBatch: true useTemplating: true @@ -930,9 +930,9 @@ components: source: "infores:agrkb" response_mapping: "$ref": "#/components/x-bte-response-mapping/zfin" - # testExamples: - # - qInput: "DOID:7997" ## thyrotoxicosis - # oneOutput: "ZFIN:ZDB-GENE-011205-17" ## mt-cyb + testExamples: + - qInput: "DOID:7997" ## thyrotoxicosis + oneOutput: "ZFIN:ZDB-GENE-011205-17" ## mt-cyb fb-to-doid-biomarkerViaOrthology: ## 1630 records - supportBatch: true @@ -958,9 +958,9 @@ components: source: "infores:agrkb" response_mapping: "$ref": "#/components/x-bte-response-mapping/biomarkerViaOrthology-doid" - # testExamples: - # - qInput: "FB:FBgn0023518" ## trr - # oneOutput: "DOID:5517" ## stomach carcinoma + testExamples: + - qInput: "FB:FBgn0023518" ## trr + oneOutput: "DOID:5517" ## stomach carcinoma doid-to-fb-biomarkerViaOrthology: - supportBatch: true useTemplating: true @@ -984,9 +984,9 @@ components: source: "infores:agrkb" response_mapping: "$ref": "#/components/x-bte-response-mapping/fb" - # testExamples: - # - qInput: "DOID:8634" ## prostate carcinoma in situ - # oneOutput: "FB:FBgn0024227" ## aurB + testExamples: + - qInput: "DOID:8634" ## prostate carcinoma in situ + oneOutput: "FB:FBgn0024227" ## aurB wb-to-doid-biomarkerViaOrthology: ## 1670 records - supportBatch: true @@ -1012,9 +1012,9 @@ components: source: "infores:agrkb" response_mapping: "$ref": "#/components/x-bte-response-mapping/biomarkerViaOrthology-doid" - # testExamples: - # - qInput: "WB:WBGene00000149" ## apl-1 - # oneOutput: "DOID:11758" ## iron deficiency anemia + testExamples: + - qInput: "WB:WBGene00000149" ## apl-1 + oneOutput: "DOID:11758" ## iron deficiency anemia doid-to-wb-biomarkerViaOrthology: - supportBatch: true useTemplating: true @@ -1038,9 +1038,9 @@ components: source: "infores:agrkb" response_mapping: "$ref": "#/components/x-bte-response-mapping/wb" - # testExamples: - # - qInput: "DOID:824" ## periodontitis - # oneOutput: "WB:WBGene00000149" ## apl-1 + testExamples: + - qInput: "DOID:824" ## periodontitis + oneOutput: "WB:WBGene00000149" ## apl-1 sgd-to-doid-biomarkerViaOrthology: ## 622 records - supportBatch: true @@ -1066,9 +1066,9 @@ components: source: "infores:agrkb" response_mapping: "$ref": "#/components/x-bte-response-mapping/biomarkerViaOrthology-doid" - # testExamples: - # - qInput: "SGD:S000000030" ## PRP45 - # oneOutput: "DOID:684" ## hepatocellular carcinoma + testExamples: + - qInput: "SGD:S000000030" ## PRP45 + oneOutput: "DOID:684" ## hepatocellular carcinoma doid-to-sgd-biomarkerViaOrthology: - supportBatch: true useTemplating: true @@ -1092,9 +1092,9 @@ components: source: "infores:agrkb" response_mapping: "$ref": "#/components/x-bte-response-mapping/sgd" - # testExamples: - # - qInput: "DOID:3008" ## invasive ductal carcinoma - # oneOutput: "SGD:S000000011" ## DEP1 + testExamples: + - qInput: "DOID:3008" ## invasive ductal carcinoma + oneOutput: "SGD:S000000011" ## DEP1 hgnc-to-doid-isImplicatedIn: ## 4543 records - supportBatch: true @@ -1126,9 +1126,9 @@ components: source: "infores:agrkb" response_mapping: "$ref": "#/components/x-bte-response-mapping/isImplicatedIn-doid" - # testExamples: - # - qInput: "HGNC:1043" ## BGLAP - # oneOutput: "DOID:11249" ## vitamin K deficiency bleeding + testExamples: + - qInput: "HGNC:1043" ## BGLAP + oneOutput: "DOID:11249" ## vitamin K deficiency bleeding doid-to-hgnc-bothImplicated: - supportBatch: true useTemplating: true @@ -1152,13 +1152,13 @@ components: source: "infores:agrkb" response_mapping: "$ref": "#/components/x-bte-response-mapping/hgnc" - # testExamples: - ## for implicated_via_orthology - # - qInput: "DOID:11476" ## osteoporosis - # oneOutput: "HGNC:1043" ## BGLAP - ## for is_implicated_in - # - qInput: "DOID:13564" ## aspergillosis - # oneOutput: "HGNC:10500" ## S100B + testExamples: + # for implicated_via_orthology + - qInput: "DOID:11476" ## osteoporosis + oneOutput: "HGNC:1043" ## BGLAP + # for is_implicated_in + - qInput: "DOID:13564" ## aspergillosis + oneOutput: "HGNC:10500" ## S100B mgi-to-doid-isImplicatedIn: ## 2010 records - supportBatch: true @@ -1184,9 +1184,9 @@ components: source: "infores:agrkb" response_mapping: "$ref": "#/components/x-bte-response-mapping/isImplicatedIn-doid" - # testExamples: - # - qInput: "MGI:109393" ## Slc4a1 - # oneOutput: "DOID:0110919" ## hereditary spherocytosis type 4 + testExamples: + - qInput: "MGI:109393" ## Slc4a1 + oneOutput: "DOID:0110919" ## hereditary spherocytosis type 4 doid-to-mgi-bothImplicated: - supportBatch: true useTemplating: true @@ -1210,13 +1210,13 @@ components: source: "infores:agrkb" response_mapping: "$ref": "#/components/x-bte-response-mapping/mgi" - # testExamples: - ## for implicated_via_orthology - # - qInput: "DOID:589" ## congenital hemolytic anemia - # oneOutput: "MGI:109393" ## Slc4a1 - ## for is_implicated_in - # - qInput: "DOID:0110354" ## retinitis pigmentosa 19 - # oneOutput: "MGI:109424" ## Abca4 + testExamples: + # for implicated_via_orthology + - qInput: "DOID:589" ## congenital hemolytic anemia + oneOutput: "MGI:109393" ## Slc4a1 + # for is_implicated_in + - qInput: "DOID:0110354" ## retinitis pigmentosa 19 + oneOutput: "MGI:109424" ## Abca4 rgd-to-doid-isImplicatedIn: ## 881 records - supportBatch: true @@ -1242,9 +1242,9 @@ components: source: "infores:agrkb" response_mapping: "$ref": "#/components/x-bte-response-mapping/isImplicatedIn-doid" - # testExamples: - # - qInput: "RGD:1305332" ## Mdm2 - # oneOutput: "DOID:2055" ## post-traumatic stress disorder + testExamples: + - qInput: "RGD:1305332" ## Mdm2 + oneOutput: "DOID:2055" ## post-traumatic stress disorder doid-to-rgd-bothImplicated: - supportBatch: true useTemplating: true @@ -1268,13 +1268,13 @@ components: source: "infores:agrkb" response_mapping: "$ref": "#/components/x-bte-response-mapping/rgd" - # testExamples: - ## for implicated_via_orthology - # - qInput: "DOID:0050682" ## Athabaskan brainstem dysgenesis syndrome - # oneOutput: "RGD:11414885" ## Hoxa1 - ## for is_implicated_in - # - qInput: "DOID:224" ## transient cerebral ischemia - # oneOutput: "RGD:1305332" ## Mdm2 + testExamples: + # for implicated_via_orthology + - qInput: "DOID:0050682" ## Athabaskan brainstem dysgenesis syndrome + oneOutput: "RGD:11414885" ## Hoxa1 + # for is_implicated_in + - qInput: "DOID:224" ## transient cerebral ischemia + oneOutput: "RGD:1305332" ## Mdm2 zfin-to-doid-isImplicatedIn: ## 401 records - supportBatch: true @@ -1300,9 +1300,9 @@ components: source: "infores:agrkb" response_mapping: "$ref": "#/components/x-bte-response-mapping/isImplicatedIn-doid" - # testExamples: - # - qInput: "ZFIN:ZDB-GENE-000208-18" ## urod - # oneOutput: "DOID:5230" ## hepatoerythropoietic porphyria + testExamples: + - qInput: "ZFIN:ZDB-GENE-000208-18" ## urod + oneOutput: "DOID:5230" ## hepatoerythropoietic porphyria doid-to-zfin-bothImplicated: - supportBatch: true useTemplating: true @@ -1326,13 +1326,13 @@ components: source: "infores:agrkb" response_mapping: "$ref": "#/components/x-bte-response-mapping/zfin" - # testExamples: - ## for implicated_via_orthology - # - qInput: "DOID:0050709" ## early infantile epileptic encephalopathy - # oneOutput: "ZFIN:ZDB-GENE-010608-3" ## neurod2 - ## for is_implicated_in - # - qInput: "DOID:3191" ## nemaline myopathy - # oneOutput: "ZFIN:ZDB-GENE-000322-1" ## actc1b + testExamples: + # for implicated_via_orthology + - qInput: "DOID:0050709" ## early infantile epileptic encephalopathy + oneOutput: "ZFIN:ZDB-GENE-010608-3" ## neurod2 + # for is_implicated_in + - qInput: "DOID:3191" ## nemaline myopathy + oneOutput: "ZFIN:ZDB-GENE-000322-1" ## actc1b fb-to-doid-isImplicatedIn: ## 640 records - supportBatch: true @@ -1358,9 +1358,9 @@ components: source: "infores:agrkb" response_mapping: "$ref": "#/components/x-bte-response-mapping/isImplicatedIn-doid" - # testExamples: - # - qInput: "FB:FBgn0024320" ## Npc1a - # oneOutput: "DOID:14504" ## Niemann-Pick disease + testExamples: + - qInput: "FB:FBgn0024320" ## Npc1a + oneOutput: "DOID:14504" ## Niemann-Pick disease doid-to-fb-bothImplicated: - supportBatch: true useTemplating: true @@ -1384,13 +1384,13 @@ components: source: "infores:agrkb" response_mapping: "$ref": "#/components/x-bte-response-mapping/fb" - # testExamples: - ## for implicated_via_orthology - # - qInput: "DOID:0050699" ## Dent disease - # oneOutput: "FB:FBgn0023508" ## Ocrl - ## for is_implicated_in - # - qInput: "DOID:0080598" ## Kleefstra syndrome 2 - # oneOutput: "FB:FBgn0023518" ## trr + testExamples: + # for implicated_via_orthology + - qInput: "DOID:0050699" ## Dent disease + oneOutput: "FB:FBgn0023508" ## Ocrl + # for is_implicated_in + - qInput: "DOID:0080598" ## Kleefstra syndrome 2 + oneOutput: "FB:FBgn0023518" ## trr wb-to-doid-isImplicatedIn: ## 275 records - supportBatch: true @@ -1416,9 +1416,9 @@ components: source: "infores:agrkb" response_mapping: "$ref": "#/components/x-bte-response-mapping/isImplicatedIn-doid" - # testExamples: - # - qInput: "WB:WBGene00000227" ## atm-1 - # oneOutput: "DOID:12704" ## ataxia telangiectasia + testExamples: + - qInput: "WB:WBGene00000227" ## atm-1 + oneOutput: "DOID:12704" ## ataxia telangiectasia doid-to-wb-bothImplicated: - supportBatch: true useTemplating: true @@ -1442,13 +1442,13 @@ components: source: "infores:agrkb" response_mapping: "$ref": "#/components/x-bte-response-mapping/wb" - # testExamples: - ## for implicated_via_orthology - # - qInput: "DOID:12387" ## nephrogenic diabetes insipidus - # oneOutput: "WB:WBGene00000170" ## aqp-2 - ## for is_implicated_in - # - qInput: "DOID:14503" ## neuronal ceroid lipofuscinosis - # oneOutput: "WB:WBGene00000539" ## cln-3.1 + testExamples: + # for implicated_via_orthology + - qInput: "DOID:12387" ## nephrogenic diabetes insipidus + oneOutput: "WB:WBGene00000170" ## aqp-2 + # for is_implicated_in + - qInput: "DOID:14503" ## neuronal ceroid lipofuscinosis + oneOutput: "WB:WBGene00000539" ## cln-3.1 sgd-to-doid-isImplicatedIn: ## 307 records - supportBatch: true @@ -1474,9 +1474,9 @@ components: source: "infores:agrkb" response_mapping: "$ref": "#/components/x-bte-response-mapping/isImplicatedIn-doid" - # testExamples: - # - qInput: "SGD:S000000027" ## MYO4 - # oneOutput: "DOID:1909" ## melanoma + testExamples: + - qInput: "SGD:S000000027" ## MYO4 + oneOutput: "DOID:1909" ## melanoma doid-to-sgd-bothImplicated: - supportBatch: true useTemplating: true @@ -1500,13 +1500,13 @@ components: source: "infores:agrkb" response_mapping: "$ref": "#/components/x-bte-response-mapping/sgd" - # testExamples: - ## for implicated_via_orthology - # - qInput: "DOID:0080411" ## familial adenomatous polyposis 3 - # oneOutput: "SGD:S000000013" ## NTG1 - ## for is_implicated_in - # - qInput: "DOID:10629" ## microphthalmia - # oneOutput: "SGD:S000000037" ## CYC3 + testExamples: + # for implicated_via_orthology + - qInput: "DOID:0080411" ## familial adenomatous polyposis 3 + oneOutput: "SGD:S000000013" ## NTG1 + # for is_implicated_in + - qInput: "DOID:10629" ## microphthalmia + oneOutput: "SGD:S000000037" ## CYC3 hgnc-to-doid-implicatedViaOrthology: ## 4012 records - supportBatch: true @@ -1539,9 +1539,9 @@ components: source: "infores:agrkb" response_mapping: "$ref": "#/components/x-bte-response-mapping/implicatedViaOrthology-doid" - # testExamples: - # - qInput: "HGNC:1043" ## BGLAP - # oneOutput: "DOID:0050328" ## congenital hypothyroidism + testExamples: + - qInput: "HGNC:1043" ## BGLAP + oneOutput: "DOID:0050328" ## congenital hypothyroidism mgi-to-doid-implicatedViaOrthology: ## 5953 records - supportBatch: true @@ -1567,9 +1567,9 @@ components: source: "infores:agrkb" response_mapping: "$ref": "#/components/x-bte-response-mapping/implicatedViaOrthology-doid" - # testExamples: - # - qInput: "MGI:109393" ## Slc4a1 - # oneOutput: "DOID:14219" ## renal tubular acidosis + testExamples: + - qInput: "MGI:109393" ## Slc4a1 + oneOutput: "DOID:14219" ## renal tubular acidosis rgd-to-doid-implicatedViaOrthology: ## 5862 records - supportBatch: true @@ -1595,9 +1595,9 @@ components: source: "infores:agrkb" response_mapping: "$ref": "#/components/x-bte-response-mapping/implicatedViaOrthology-doid" - # testExamples: - # - qInput: "RGD:11414885" ## Hoxa1 - # oneOutput: "DOID:12849" ## autistic disorder + testExamples: + - qInput: "RGD:11414885" ## Hoxa1 + oneOutput: "DOID:12849" ## autistic disorder zfin-to-doid-implicatedViaOrthology: ## 6865 records - supportBatch: true @@ -1623,9 +1623,9 @@ components: source: "infores:agrkb" response_mapping: "$ref": "#/components/x-bte-response-mapping/implicatedViaOrthology-doid" - # testExamples: - # - qInput: "ZFIN:ZDB-GENE-010801-1" ## tnfsf10l - # oneOutput: "DOID:0050685" ## small cell carcinoma + testExamples: + - qInput: "ZFIN:ZDB-GENE-010801-1" ## tnfsf10l + oneOutput: "DOID:0050685" ## small cell carcinoma fb-to-doid-implicatedViaOrthology: ## 3744 records - supportBatch: true @@ -1651,9 +1651,9 @@ components: source: "infores:agrkb" response_mapping: "$ref": "#/components/x-bte-response-mapping/implicatedViaOrthology-doid" - # testExamples: - # - qInput: "FB:FBgn0023508" ## Ocrl - # oneOutput: "DOID:1056" ## oculocerebrorenal syndrome + testExamples: + - qInput: "FB:FBgn0023508" ## Ocrl + oneOutput: "DOID:1056" ## oculocerebrorenal syndrome wb-to-doid-implicatedViaOrthology: ## 3739 records - supportBatch: true @@ -1679,9 +1679,9 @@ components: source: "infores:agrkb" response_mapping: "$ref": "#/components/x-bte-response-mapping/implicatedViaOrthology-doid" - # testExamples: - # - qInput: "WB:WBGene00000148" ## aph-2 - # oneOutput: "DOID:11054" ## urinary bladder cancer + testExamples: + - qInput: "WB:WBGene00000148" ## aph-2 + oneOutput: "DOID:11054" ## urinary bladder cancer sgd-to-doid-implicatedViaOrthology: ## 622 records - supportBatch: true @@ -1707,9 +1707,9 @@ components: source: "infores:agrkb" response_mapping: "$ref": "#/components/x-bte-response-mapping/implicatedViaOrthology-doid" - # testExamples: - # - qInput: "SGD:S000000010" ## CYS3 - # oneOutput: "DOID:0090142" ## cystathioninuria + testExamples: + - qInput: "SGD:S000000010" ## CYS3 + oneOutput: "DOID:0090142" ## cystathioninuria x-bte-response-mapping: isMarkerFor-doid: DOID: agr.is_marker_for.doid diff --git a/CTD/smartapi.yaml b/CTD/smartapi.yaml index 24127f31..d88b8387 100644 --- a/CTD/smartapi.yaml +++ b/CTD/smartapi.yaml @@ -183,9 +183,9 @@ components: predicate: related_to response_mapping: "$ref": "#/components/x-bte-response-mapping/chemical2gene" - # testExamples: - # - qInput: "MESH:C006303" ## acivicin - # oneOutput: "NCBIGene:1080" ## CFTR + testExamples: + - qInput: "MESH:C006303" ## acivicin + oneOutput: "NCBIGene:1080" ## CFTR gene2chemical: - supportBatch: false useTemplating: true @@ -204,9 +204,9 @@ components: predicate: related_to response_mapping: "$ref": "#/components/x-bte-response-mapping/gene2chemical" - # testExamples: - # - qInput: "NCBIGene:10800" ## CYSLTR1 - # oneOutput: "MESH:C010395" ## acetylsalicylic acid lysinate / Aspirin DL-lysine + testExamples: + - qInput: "NCBIGene:10800" ## CYSLTR1 + oneOutput: "MESH:C010395" ## acetylsalicylic acid lysinate / Aspirin DL-lysine ## commenting out chemical2disease operations because BTE isn't recognizing MESH vs OMIM Disease IDs # chemical2disease_1: # - supportBatch: false @@ -226,9 +226,9 @@ components: # predicate: related_to # response_mapping: # "$ref": "#/components/x-bte-response-mapping/chemical2disease_1" - # # testExamples: - # # - qInput: "MESH:D005492" ## Folic Acid - # # oneOutput: "MESH:D000748" ## Anemia, Macrocytic + # testExamples: + # - qInput: "MESH:D005492" ## Folic Acid + # oneOutput: "MESH:D000748" ## Anemia, Macrocytic disease2chemical_1: - supportBatch: false useTemplating: true @@ -247,9 +247,9 @@ components: predicate: related_to response_mapping: "$ref": "#/components/x-bte-response-mapping/disease2chemical" - # testExamples: - # - qInput: "MESH:D020138" ## Hyperhomocysteinemia - # oneOutput: "MESH:D016291" ## Dizocilpine Maleate / Neurogard + testExamples: + - qInput: "MESH:D020138" ## Hyperhomocysteinemia + oneOutput: "MESH:D016291" ## Dizocilpine Maleate / Neurogard # chemical2disease_2: # - supportBatch: false # useTemplating: true @@ -268,9 +268,9 @@ components: # predicate: related_to # response_mapping: # "$ref": "#/components/x-bte-response-mapping/chemical2disease_2" - # # testExamples: - # # - qInput: "MESH:D004317" ## Doxorubicin - # # oneOutput: "OMIM:610141" ## QT INTERVAL, VARIATION IN + # testExamples: + # - qInput: "MESH:D004317" ## Doxorubicin + # oneOutput: "OMIM:610141" ## QT INTERVAL, VARIATION IN disease2chemical_2: - supportBatch: false useTemplating: true @@ -289,9 +289,9 @@ components: predicate: related_to response_mapping: "$ref": "#/components/x-bte-response-mapping/disease2chemical" - # testExamples: - # - qInput: "OMIM:613290" ## HEARING LOSS, CISPLATIN-INDUCED, SUSCEPTIBILITY TO - # oneOutput: "MESH:D002945" ## Cisplatin + testExamples: + - qInput: "OMIM:613290" ## HEARING LOSS, CISPLATIN-INDUCED, SUSCEPTIBILITY TO + oneOutput: "MESH:D002945" ## Cisplatin chemical2bp: ## only one way (no GO terms -> chemicals) ## goes through gene intermediates, not the same as the "enriched" dataset @@ -313,9 +313,9 @@ components: predicate: related_to response_mapping: "$ref": "#/components/x-bte-response-mapping/chemical2go" - # testExamples: - # - qInput: "MESH:D015250" ## Aclarubicin - # oneOutput: "GO:0019226" ## transmission of nerve impulse + testExamples: + - qInput: "MESH:D015250" ## Aclarubicin + oneOutput: "GO:0019226" ## transmission of nerve impulse chemical2cc: ## only one way (no GO terms -> chemicals) ## goes through gene intermediates, not the same as the "enriched" dataset @@ -337,9 +337,9 @@ components: predicate: related_to response_mapping: "$ref": "#/components/x-bte-response-mapping/chemical2go" - # testExamples: - # - qInput: "MESH:D015250" ## Aclarubicin - # oneOutput: "GO:0097169" ## AIM2 inflammasome complex + testExamples: + - qInput: "MESH:D015250" ## Aclarubicin + oneOutput: "GO:0097169" ## AIM2 inflammasome complex chemical2mf: ## only one way (no GO terms -> chemicals) ## goes through gene intermediates, not the same as the "enriched" dataset @@ -361,9 +361,9 @@ components: predicate: related_to response_mapping: "$ref": "#/components/x-bte-response-mapping/chemical2go" - # testExamples: - # - qInput: "MESH:D015250" ## Aclarubicin - # oneOutput: "GO:0070742" ## C2H2 zinc finger domain binding + testExamples: + - qInput: "MESH:D015250" ## Aclarubicin + oneOutput: "GO:0070742" ## C2H2 zinc finger domain binding ## commenting out gene2disease operations because BTE isn't recognizing MESH vs OMIM Disease IDs disease2gene_1: - supportBatch: false @@ -383,9 +383,9 @@ components: predicate: related_to response_mapping: "$ref": "#/components/x-bte-response-mapping/disease2gene" - # testExamples: - # - qInput: "MESH:D020138" ## Hyperhomocysteinemia - # oneOutput: "NCBIGene:4524" ## MTHFR + testExamples: + - qInput: "MESH:D020138" ## Hyperhomocysteinemia + oneOutput: "NCBIGene:4524" ## MTHFR # gene2disease_1: # - supportBatch: false # useTemplating: true @@ -404,9 +404,9 @@ components: # predicate: related_to # response_mapping: # "$ref": "#/components/x-bte-response-mapping/gene2disease_1" - # # testExamples: - # # - qInput: "NCBIGene:4868" ## NPHS1 - # # oneOutput: "MESH:C535761" ## Nephrosis, congenital / familial nephrotic syndrome + # testExamples: + # - qInput: "NCBIGene:4868" ## NPHS1 + # oneOutput: "MESH:C535761" ## Nephrosis, congenital / familial nephrotic syndrome disease2gene_2: - supportBatch: false useTemplating: true @@ -425,9 +425,9 @@ components: predicate: related_to response_mapping: "$ref": "#/components/x-bte-response-mapping/disease2gene" - # testExamples: - # - qInput: "OMIM:615075" ## NEURODEVELOPMENTAL DISORDER WITH SPASTIC DIPLEGIA AND VISUAL DEFECTS - # oneOutput: "NCBIGene:1499" ## CTNNB1 + testExamples: + - qInput: "OMIM:615075" ## NEURODEVELOPMENTAL DISORDER WITH SPASTIC DIPLEGIA AND VISUAL DEFECTS + oneOutput: "NCBIGene:1499" ## CTNNB1 # gene2disease_2: # - supportBatch: false # useTemplating: true @@ -446,9 +446,9 @@ components: # predicate: related_to # response_mapping: # "$ref": "#/components/x-bte-response-mapping/gene2disease_2" - # # testExamples: - # # - qInput: "NCBIGene:8600" ## TNFSF11 - # # oneOutput: "OMIM:259710" ## OSTEOPETROSIS, AUTOSOMAL RECESSIVE 2 + # testExamples: + # - qInput: "NCBIGene:8600" ## TNFSF11 + # oneOutput: "OMIM:259710" ## OSTEOPETROSIS, AUTOSOMAL RECESSIVE 2 ## commenting out gene2pathway operations because BTE isn't recognizing REACT vs KEGG Pathway IDs # gene2pathway_1: # - supportBatch: false @@ -468,9 +468,9 @@ components: # predicate: participates_in # response_mapping: # "$ref": "#/components/x-bte-response-mapping/gene2pathway_1" - # # testExamples: - # # - qInput: "NCBIGene:8600" ## TNFSF11 - # # oneOutput: "REACT:R-HSA-5668541" ## TNFR2 non-canonical NF-kB pathway + # testExamples: + # - qInput: "NCBIGene:8600" ## TNFSF11 + # oneOutput: "REACT:R-HSA-5668541" ## TNFR2 non-canonical NF-kB pathway pathway2gene_1: - supportBatch: false useTemplating: true @@ -489,9 +489,9 @@ components: predicate: has_participant response_mapping: "$ref": "#/components/x-bte-response-mapping/pathway2gene" - # testExamples: - # - qInput: "REACT:R-HSA-5669034" ## TNFs bind their physiological receptors - # oneOutput: "NCBIGene:939" ## CD27 + testExamples: + - qInput: "REACT:R-HSA-5669034" ## TNFs bind their physiological receptors + oneOutput: "NCBIGene:939" ## CD27 # gene2pathway_2: # - supportBatch: false # useTemplating: true @@ -510,9 +510,9 @@ components: # predicate: participates_in # response_mapping: # "$ref": "#/components/x-bte-response-mapping/gene2pathway_2" - # # testExamples: - # # - qInput: "NCBIGene:8600" ## TNFSF11 - # # oneOutput: "KEGG.PATHWAY:hsa04917" ## Prolactin signaling pathway + # testExamples: + # - qInput: "NCBIGene:8600" ## TNFSF11 + # oneOutput: "KEGG.PATHWAY:hsa04917" ## Prolactin signaling pathway pathway2gene_2: - supportBatch: false useTemplating: true @@ -531,9 +531,9 @@ components: predicate: has_participant response_mapping: "$ref": "#/components/x-bte-response-mapping/pathway2gene" - # testExamples: - # - qInput: "KEGG.PATHWAY:hsa05323" ## Rheumatoid arthritis - # oneOutput: "NCBIGene:54" ## ACP5 + testExamples: + - qInput: "KEGG.PATHWAY:hsa05323" ## Rheumatoid arthritis + oneOutput: "NCBIGene:54" ## ACP5 x-bte-response-mapping: chemical2gene: NCBIGene: data.GeneId ## no prefix diff --git a/DISEASES/smartapi.yaml b/DISEASES/smartapi.yaml index 11e58741..8560ee2b 100644 --- a/DISEASES/smartapi.yaml +++ b/DISEASES/smartapi.yaml @@ -601,9 +601,9 @@ components: source: "infores:diseases" response_mapping: "$ref": "#/components/x-bte-response-mapping/disease-gene" - # testExamples: - # - qInput: "DOID:0060041" ## Autism spectrum disorder - # oneOutput: "ENSEMBL:ENSP00000482335" ## MAP7 + testExamples: + - qInput: "DOID:0060041" ## Autism spectrum disorder + oneOutput: "ENSEMBL:ENSP00000482335" ## MAP7 ## should be able to see results with all 3 methods/combos of edge attributes gene-disease: - supportBatch: true @@ -627,9 +627,9 @@ components: source: "infores:diseases" response_mapping: "$ref": "#/components/x-bte-response-mapping/gene-disease" - # testExamples: - # - qInput: "ENSEMBL:ENSP00000298910" ## LRRK2 - # oneOutput: "DOID:1926" ## Gaucher disease + testExamples: + - qInput: "ENSEMBL:ENSP00000298910" ## LRRK2 + oneOutput: "DOID:1926" ## Gaucher disease x-bte-response-mapping: disease-gene: ENSEMBL: DISEASES.associatedWith.ensembl ## no prefix diff --git a/EBIgene2phenotype/smartapi.yaml b/EBIgene2phenotype/smartapi.yaml index 6a32bbb4..69fd39e0 100644 --- a/EBIgene2phenotype/smartapi.yaml +++ b/EBIgene2phenotype/smartapi.yaml @@ -619,9 +619,9 @@ components: source: "infores:ebi-gene2phenotype" response_mapping: "$ref": "#/components/x-bte-response-mapping/disease-object" - # testExamples: - # - qInput: "HGNC:1020" ## BCS1L - # oneOutput: "OMIM:603358" ## GRACILE SYNDROME + testExamples: + - qInput: "HGNC:1020" ## BCS1L + oneOutput: "OMIM:603358" ## GRACILE SYNDROME disease_to_gene: - supportBatch: true useTemplating: true @@ -644,9 +644,9 @@ components: source: "infores:ebi-gene2phenotype" response_mapping: "$ref": "#/components/x-bte-response-mapping/gene-object" - # testExamples: - # - qInput: "OMIM:615355" ## NOONAN SYNDROME 8 - # oneOutput: "HGNC:10023" ## RIT1 + testExamples: + - qInput: "OMIM:615355" ## NOONAN SYNDROME 8 + oneOutput: "HGNC:10023" ## RIT1 x-bte-response-mapping: ## data: ## - allelic_requirement seems similar to "inheritance" but focused on the affected individual diff --git a/LINCS/smartapi.yml b/LINCS/smartapi.yml index 6ed89fb5..17c63a2b 100644 --- a/LINCS/smartapi.yml +++ b/LINCS/smartapi.yml @@ -409,9 +409,9 @@ components: response_mapping: $ref: '#/components/x-bte-response-mapping/drug-indication' supportBatch: false ## no batch support (get operation) - # testExamples: - # - qInput: "LINCS:LSM-1023" ## Imatinib - # oneOutput: "MESH:D046152" ## GASTROINTESTINAL STROMAL TUMORS + testExamples: + - qInput: "LINCS:LSM-1023" ## Imatinib + oneOutput: "MESH:D046152" ## GASTROINTESTINAL STROMAL TUMORS ## example raw query: http://lincsportal.ccs.miami.edu/dcic/api/drugindication?id=LSM-1008 x-bte-response-mapping: drug-indication: diff --git a/MGIgene2phenotype/smartapi.yaml b/MGIgene2phenotype/smartapi.yaml index 4ef39adb..22ee4f95 100644 --- a/MGIgene2phenotype/smartapi.yaml +++ b/MGIgene2phenotype/smartapi.yaml @@ -594,9 +594,9 @@ components: source: "infores:mgi" response_mapping: "$ref": "#/components/x-bte-response-mapping/gene_related_to_disease" - # testExamples: - # - qInput: "MGI:104511" ## Tnfsf4 - # oneOutput: "DOID:14557" ## primary pulmonary hypertension + testExamples: + - qInput: "MGI:104511" ## Tnfsf4 + oneOutput: "DOID:14557" ## primary pulmonary hypertension disease_related_to_gene: ## "reverse-type" operation - supportBatch: true @@ -618,9 +618,9 @@ components: source: "infores:mgi" response_mapping: "$ref": "#/components/x-bte-response-mapping/mgi" - # testExamples: - # - qInput: "DOID:0110731" ## neuronal ceroid lipofuscinosis 3 - # oneOutput: "MGI:103555" ## Clcn3 + testExamples: + - qInput: "DOID:0110731" ## neuronal ceroid lipofuscinosis 3 + oneOutput: "MGI:103555" ## Clcn3 gene_related_to_phenotype: ## there are 1447 records with mgi.associated_with_phenotype field ## 1359 of these records also have mgi.has_homolog field (NCBIGene ID for mouse gene) @@ -645,9 +645,9 @@ components: source: "infores:mgi" response_mapping: "$ref": "#/components/x-bte-response-mapping/gene_related_to_phenotype" - # testExamples: - # - qInput: "MGI:102539" ## Tbx6 - # oneOutput: "MP:0002151" ## abnormal neural tube morphology + testExamples: + - qInput: "MGI:102539" ## Tbx6 + oneOutput: "MP:0002151" ## abnormal neural tube morphology phenotype_related_to_gene: ## "reverse-type" operation - supportBatch: true @@ -669,9 +669,9 @@ components: source: "infores:mgi" response_mapping: "$ref": "#/components/x-bte-response-mapping/mgi" - # testExamples: - # - qInput: "MP:0000623" ## decreased salivation - # oneOutput: "MGI:88398" ## Chrm3 + testExamples: + - qInput: "MP:0000623" ## decreased salivation + oneOutput: "MGI:88398" ## Chrm3 x-bte-response-mapping: gene_related_to_disease: DOID: mgi.associated_with_disease.doid ## has prefix diff --git a/bindingdb/smartapi.yaml b/bindingdb/smartapi.yaml index 5e590b29..2f005a98 100644 --- a/bindingdb/smartapi.yaml +++ b/bindingdb/smartapi.yaml @@ -602,9 +602,9 @@ components: source: "infores:bindingdb" response_mapping: "$ref": "#/components/x-bte-response-mapping/pubchem-object" - # testExamples: - # - qInput: "UniProtKB:Q08722" ## Leukocyte surface antigen CD47 - # oneOutput: "INCHIKEY:CLTVCCLZSPKLRB-NRGGWPRRSA-N" ## CHEMBL4474790 / H-D-Lys-N(Me)Arg-Phe-Tyr-Val-Val-Nle-Trp-Lys-D-Lys-OH + testExamples: + - qInput: "UniProtKB:Q08722" ## Leukocyte surface antigen CD47 + oneOutput: "INCHIKEY:CLTVCCLZSPKLRB-NRGGWPRRSA-N" ## CHEMBL4474790 / H-D-Lys-N(Me)Arg-Phe-Tyr-Val-Val-Nle-Trp-Lys-D-Lys-OH ligand-protein: - supportBatch: true useTemplating: true @@ -632,9 +632,9 @@ components: source: "infores:bindingdb" response_mapping: "$ref": "#/components/x-bte-response-mapping/uniprot-subject" - # testExamples: - # - qInput: "INCHIKEY:NZLXOECMDRNZDN-GUYCJALGSA-N" ## US10736883, Example 387.0 - # oneOutput: "UniProtKB:P35414" ## Apelin receptor / APLNR + testExamples: + - qInput: "INCHIKEY:NZLXOECMDRNZDN-GUYCJALGSA-N" ## US10736883, Example 387.0 + oneOutput: "UniProtKB:P35414" ## Apelin receptor / APLNR x-bte-response-mapping: ## note on references: ## sometimes the doi + pmid will refer to the same publication (so..."duplicate" references) diff --git a/biolink/openapi.yml b/biolink/openapi.yml index 5b3ea9cf..7e98a1b1 100644 --- a/biolink/openapi.yml +++ b/biolink/openapi.yml @@ -956,11 +956,11 @@ components: source: "infores:monarchinitiative" response_mapping: "$ref": "#/components/x-bte-response-mapping/gene-hgnc" - # testExamples: - # - qInput: "UBERON:0001817" ## lacrimal gland - # oneOutput: "HGNC:8548" ## P4HB aka NCBIGene:5034 - # - qInput: "UBERON:0002110" ## gall bladder - # oneOutput: "HGNC:8548" ## P4HB aka NCBIGene:5034 + testExamples: + - qInput: "UBERON:0001817" ## lacrimal gland + oneOutput: "HGNC:8548" ## P4HB aka NCBIGene:5034 + - qInput: "UBERON:0002110" ## gall bladder + oneOutput: "HGNC:8548" ## P4HB aka NCBIGene:5034 disease-gene-1: ## put multiple causal relations here by using association_type parameter ## to find examples with /association/find, set relation @@ -984,25 +984,25 @@ components: source: "infores:monarchinitiative" response_mapping: "$ref": "#/components/x-bte-response-mapping/gene-hgnc" - # testExamples: - ## for "causes condition" / RO:0003303 - # - qInput: "MONDO:0011562" ## autosomal dominant Parkinson disease 4 - # oneOutput: "HGNC:11138" ## SNCA aka NCBIGene:6622 - ## for "causal germline mutation in" / RO:0004013 - # - qInput: "MONDO:0019600" ## Xeroderma pigmentosum - # oneOutput: "HGNC:3434" ## ERCC2 aka NCBIGene:2068 - ## for "causal loss of function germline mutation of in" / RO:0004012 - # - qInput: "MONDO:0009889" ## autosomal recessive polycystic kidney disease - # oneOutput: "HGNC:9016" ## PKHD1 aka NCBIGene:5314 - ## for "is marker for" / RO:0002607 - # - qInput: "MONDO:0009861" ## phenylketonuria - # oneOutput: "HGNC:8582" ## PAH aka NCBIGene:5053 - ## for "is causal somatic mutation in" / RO:0004014 - # - qInput: "MONDO:0004948" ## B-cell chronic lymphocytic leukemia - # oneOutput: "HGNC:17284" ## POT1 aka NCBIGene:25913 - ## for "causal gain of function germline mutation of in" / RO:0004011 - # - qInput: "MONDO:0013648" ## familial progressive hyperpigmentation - # oneOutput: "HGNC:6343" ## KITLG aka NCBIGene:4254 + testExamples: + # for "causes condition" / RO:0003303 + - qInput: "MONDO:0011562" ## autosomal dominant Parkinson disease 4 + oneOutput: "HGNC:11138" ## SNCA aka NCBIGene:6622 + # for "causal germline mutation in" / RO:0004013 + - qInput: "MONDO:0019600" ## Xeroderma pigmentosum + oneOutput: "HGNC:3434" ## ERCC2 aka NCBIGene:2068 + # for "causal loss of function germline mutation of in" / RO:0004012 + - qInput: "MONDO:0009889" ## autosomal recessive polycystic kidney disease + oneOutput: "HGNC:9016" ## PKHD1 aka NCBIGene:5314 + # for "is marker for" / RO:0002607 + - qInput: "MONDO:0009861" ## phenylketonuria + oneOutput: "HGNC:8582" ## PAH aka NCBIGene:5053 + # for "is causal somatic mutation in" / RO:0004014 + - qInput: "MONDO:0004948" ## B-cell chronic lymphocytic leukemia + oneOutput: "HGNC:17284" ## POT1 aka NCBIGene:25913 + # for "causal gain of function germline mutation of in" / RO:0004011 + - qInput: "MONDO:0013648" ## familial progressive hyperpigmentation + oneOutput: "HGNC:6343" ## KITLG aka NCBIGene:4254 disease-gene-2: ## put non-causal relations together here ## to find examples with /association/find, set relation @@ -1027,28 +1027,28 @@ components: source: "infores:monarchinitiative" response_mapping: "$ref": "#/components/x-bte-response-mapping/gene-hgnc" - # testExamples: - ## for "contributes to condition" / RO:0003304 - # - qInput: "MONDO:0019171" ## familial long QT syndrome - # oneOutput: "HGNC:6294" ## KCNQ1 aka NCBIGene:3784 - ## for "contributes to" / RO:0002326 - # - qInput: "MONDO:0007915" ## systemic lupus erythematosus (disease) - # oneOutput: "HGNC:9652" ## PTPN22 aka NCBIGene:26191 - ## for "has phenotype" / RO:0002200 - # - qInput: "MONDO:0009131" ## Riley-Day syndrome - # oneOutput: "HGNC:4878" ## HEXA aka NCBIGene:3073 - ## for "is causal susceptibility factor for" / RO:0004015 - # - qInput: "MONDO:0018961" ## familial melanoma - # oneOutput: "HGNC:1787" ## CDKN2A aka NCBIGene:1029 - ## for "pathogenic_for_condition" / GENO:0000840 - # - qInput: "MONDO:0008647" ## hypertrophic cardiomyopathy 1 - # oneOutput: "HGNC:7551" ## MYBPC3 aka NCBIGene:4607 - ## for "is causal germline mutation partially giving rise to" / RO:0004016 - # - qInput: "MONDO:0018875" ## Li-Fraumeni syndrome - # oneOutput: "HGNC:6973" ## MDM2 aka NCBIGene:4193 - ## for "likely_pathogenic_for_condition" / GENO:0000841 - # - qInput: "MONDO:0019497" ## nonsyndromic genetic deafness - # oneOutput: "HGNC:7605" ## MYO6 aka NCBIGene:4646 + testExamples: + # for "contributes to condition" / RO:0003304 + - qInput: "MONDO:0019171" ## familial long QT syndrome + oneOutput: "HGNC:6294" ## KCNQ1 aka NCBIGene:3784 + # for "contributes to" / RO:0002326 + - qInput: "MONDO:0007915" ## systemic lupus erythematosus (disease) + oneOutput: "HGNC:9652" ## PTPN22 aka NCBIGene:26191 + # for "has phenotype" / RO:0002200 + - qInput: "MONDO:0009131" ## Riley-Day syndrome + oneOutput: "HGNC:4878" ## HEXA aka NCBIGene:3073 + # for "is causal susceptibility factor for" / RO:0004015 + - qInput: "MONDO:0018961" ## familial melanoma + oneOutput: "HGNC:1787" ## CDKN2A aka NCBIGene:1029 + # for "pathogenic_for_condition" / GENO:0000840 + - qInput: "MONDO:0008647" ## hypertrophic cardiomyopathy 1 + oneOutput: "HGNC:7551" ## MYBPC3 aka NCBIGene:4607 + # for "is causal germline mutation partially giving rise to" / RO:0004016 + - qInput: "MONDO:0018875" ## Li-Fraumeni syndrome + oneOutput: "HGNC:6973" ## MDM2 aka NCBIGene:4193 + # for "likely_pathogenic_for_condition" / GENO:0000841 + - qInput: "MONDO:0019497" ## nonsyndromic genetic deafness + oneOutput: "HGNC:7605" ## MYO6 aka NCBIGene:4646 disease-pathway: ## will include non-human pathways because Monarch doesn't include the taxon for pathways ## but REACT prefixes show the species (MMU = mouse) @@ -1073,11 +1073,11 @@ components: source: "infores:monarchinitiative" response_mapping: "$ref": "#/components/x-bte-response-mapping/pathway-react" - # testExamples: - # - qInput: "MONDO:0010524" ## X-linked sideroblastic anemia with ataxia - # oneOutput: "REACT:R-HSA-1369007" ## Mitochondrial ABC transporters - # - qInput: "MONDO:0010665" ## Wilson-Turner syndrome - # oneOutput: "REACT:R-HSA-2467813" ## Separation of Sister Chromatids + testExamples: + - qInput: "MONDO:0010524" ## X-linked sideroblastic anemia with ataxia + oneOutput: "REACT:R-HSA-1369007" ## Mitochondrial ABC transporters + - qInput: "MONDO:0010665" ## Wilson-Turner syndrome + oneOutput: "REACT:R-HSA-2467813" ## Separation of Sister Chromatids disease-phenotype: ## will include non-human phenotypes because Monarch doesn't include the taxon for phenotypes ## but prefixes show the species (MP = mouse) @@ -1099,11 +1099,11 @@ components: source: "infores:monarchinitiative" response_mapping: "$ref": "#/components/x-bte-response-mapping/phenotype-hp" - # testExamples: - # - qInput: "MONDO:0008974" ## Greenberg dysplasia - # oneOutput: "HP:0000272" ## Malar flattening - # - qInput: "MONDO:0010524" ## X-linked sideroblastic anemia with ataxia - # oneOutput: "HP:0002470" ## Nonprogressive cerebellar ataxia + testExamples: + - qInput: "MONDO:0008974" ## Greenberg dysplasia + oneOutput: "HP:0000272" ## Malar flattening + - qInput: "MONDO:0010524" ## X-linked sideroblastic anemia with ataxia + oneOutput: "HP:0002470" ## Nonprogressive cerebellar ataxia disease-variant: ## not using: ## - GENO:0000840 (pathogenic_for_condition). seems to use ClinVarVariant (ClinVarVariant:13417) @@ -1129,11 +1129,11 @@ components: source: "infores:monarchinitiative" response_mapping: "$ref": "#/components/x-bte-response-mapping/variant-dbsnp" - # testExamples: - # - qInput: "MONDO:0004747" ## cleft lip (disease) - # oneOutput: "DBSNP:rs227731" - # - qInput: "MONDO:0005150" ## age-related macular degeneration - # oneOutput: "DBSNP:rs2230199" + testExamples: + - qInput: "MONDO:0004747" ## cleft lip (disease) + oneOutput: "DBSNP:rs227731" + - qInput: "MONDO:0005150" ## age-related macular degeneration + oneOutput: "DBSNP:rs2230199" gene-anatomy: ## see anatomy-gene operation for more details - supportBatch: false @@ -1155,11 +1155,11 @@ components: source: "infores:monarchinitiative" response_mapping: "$ref": "#/components/x-bte-response-mapping/anatomy-uberon" - # testExamples: - # - qInput: "HGNC:8548" ## P4HB aka NCBIGene:5034 - # oneOutput: "UBERON:0000970" ## eye - # - qInput: "HGNC:11138" ## SNCA aka NCBIGene:6622 - # oneOutput: "UBERON:0001017" ## central nervous system + testExamples: + - qInput: "HGNC:8548" ## P4HB aka NCBIGene:5034 + oneOutput: "UBERON:0000970" ## eye + - qInput: "HGNC:11138" ## SNCA aka NCBIGene:6622 + oneOutput: "UBERON:0001017" ## central nervous system gene-disease-1: ## see disease-gene-1 for details - supportBatch: false @@ -1182,13 +1182,13 @@ components: source: "infores:monarchinitiative" response_mapping: "$ref": "#/components/x-bte-response-mapping/disease-mondo" - # testExamples: - ## for "causes condition" / RO:0003303 - # - qInput: "HGNC:11138" ## SNCA aka NCBIGene:6622 - # oneOutput: "MONDO:0011562" ## autosomal dominant Parkinson disease 4 - ## for "causal gain of function germline mutation of in" / RO:0004011 - # - qInput: "HGNC:6343" ## KITLG aka NCBIGene:4254 - # oneOutput: "MONDO:0013648" ## familial progressive hyperpigmentation + testExamples: + # for "causes condition" / RO:0003303 + - qInput: "HGNC:11138" ## SNCA aka NCBIGene:6622 + oneOutput: "MONDO:0011562" ## autosomal dominant Parkinson disease 4 + # for "causal gain of function germline mutation of in" / RO:0004011 + - qInput: "HGNC:6343" ## KITLG aka NCBIGene:4254 + oneOutput: "MONDO:0013648" ## familial progressive hyperpigmentation gene-disease-2: ## see disease-gene-2 for details - supportBatch: false @@ -1211,13 +1211,13 @@ components: source: "infores:monarchinitiative" response_mapping: "$ref": "#/components/x-bte-response-mapping/disease-mondo" - # testExamples: - ## for "contributes to condition" / RO:0003304 - # - qInput: "HGNC:6294" ## KCNQ1 aka NCBIGene:3784 - # oneOutput: "MONDO:0019171" ## familial long QT syndrome - ## for "pathogenic_for_condition" / GENO:0000840 - # - qInput: "HGNC:7551" ## MYBPC3 aka NCBIGene:4607 - # oneOutput: "MONDO:0008647" ## hypertrophic cardiomyopathy 1 + testExamples: + # for "contributes to condition" / RO:0003304 + - qInput: "HGNC:6294" ## KCNQ1 aka NCBIGene:3784 + oneOutput: "MONDO:0019171" ## familial long QT syndrome + # for "pathogenic_for_condition" / GENO:0000840 + - qInput: "HGNC:7551" ## MYBPC3 aka NCBIGene:4607 + oneOutput: "MONDO:0008647" ## hypertrophic cardiomyopathy 1 gene-interaction: - supportBatch: false useTemplating: true @@ -1239,11 +1239,11 @@ components: source: "infores:monarchinitiative" response_mapping: "$ref": "#/components/x-bte-response-mapping/gene-hgnc" - # testExamples: - # - qInput: "HGNC:2950" ## DNAH5 aka NCBIGene:1767 - # oneOutput: "HGNC:9069" ## PLEC aka NCBIGene:5339 - # - qInput: "HGNC:7551" ## MYBPC3 aka NCBIGene:4607 - # oneOutput: "HGNC:16007" ## TRIM63 aka NCBIGene:84676 + testExamples: + - qInput: "HGNC:2950" ## DNAH5 aka NCBIGene:1767 + oneOutput: "HGNC:9069" ## PLEC aka NCBIGene:5339 + - qInput: "HGNC:7551" ## MYBPC3 aka NCBIGene:4607 + oneOutput: "HGNC:16007" ## TRIM63 aka NCBIGene:84676 geneOrtholog-disease: ## - starting with HGNC = starting with human gene, getting non-human gene orthologs ## then finding directly-related diseases @@ -1272,9 +1272,9 @@ components: source: "infores:monarchinitiative" response_mapping: "$ref": "#/components/x-bte-response-mapping/orthologGene2diseaseMondo" - # testExamples: - # - qInput: "HGNC:9508" ## PSEN1 aka NCBIGene:5663 - # oneOutput: "MONDO:0006559" ## hidradenitis suppurativa, not found through gene-disease endpoints + testExamples: + - qInput: "HGNC:9508" ## PSEN1 aka NCBIGene:5663 + oneOutput: "MONDO:0006559" ## hidradenitis suppurativa, not found through gene-disease endpoints geneOrtholog-phenotype: ## - starting with HGNC = starting with human gene, getting non-human gene orthologs ## then finding directly-related phenotypes @@ -1302,11 +1302,11 @@ components: source: "infores:monarchinitiative" response_mapping: "$ref": "#/components/x-bte-response-mapping/orthologGene2phenoHP" - # testExamples: - # - qInput: "HGNC:8548" ## P4HB aka NCBIGene:5034 - # oneOutput: "HP:0003540" ## Impaired platelet aggregation, not found from gene-phenotype operation - # - qInput: "HGNC:9508" ## PSEN1 aka NCBIGene:5663 - # oneOutput: "HP:0009121" ## Abnormal axial skeleton morphology + testExamples: + - qInput: "HGNC:8548" ## P4HB aka NCBIGene:5034 + oneOutput: "HP:0003540" ## Impaired platelet aggregation, not found from gene-phenotype operation + - qInput: "HGNC:9508" ## PSEN1 aka NCBIGene:5663 + oneOutput: "HP:0009121" ## Abnormal axial skeleton morphology gene-phenotype: ## will include non-human phenotypes because Monarch doesn't include the taxon for phenotypes ## but prefixes show the species (MP = mouse) @@ -1328,12 +1328,12 @@ components: source: "infores:monarchinitiative" response_mapping: "$ref": "#/components/x-bte-response-mapping/phenotype-hp" - # testExamples: - # - qInput: "HGNC:8548" ## P4HB aka NCBIGene:5034 - # oneOutput: "HP:0000944" ## Abnormal metaphysis morphology - # - qInput: "HGNC:9508" ## PSEN1 aka NCBIGene:5663 - # oneOutput: HP:0000751" ## Personality changes - ## other possible inputs: HGNC:7551 / MYBPC3, HGNC:9508 / DNAH5 + testExamples: + - qInput: "HGNC:8548" ## P4HB aka NCBIGene:5034 + oneOutput: "HP:0000944" ## Abnormal metaphysis morphology + - qInput: "HGNC:9508" ## PSEN1 aka NCBIGene:5663 + oneOutput: HP:0000751" ## Personality changes + # other possible inputs: HGNC:7551 / MYBPC3, HGNC:9508 / DNAH5 gene-variant: ## can take human or non-human genes as input... ## to find examples with /association/find, set subject_category as "variant" and object category as "gene" @@ -1354,11 +1354,11 @@ components: source: "infores:monarchinitiative" response_mapping: "$ref": "#/components/x-bte-response-mapping/variant-dbsnp" - # testExamples: - # - qInput: "HGNC:2950" ## DNAH5 aka NCBIGene:1767 - # oneOutput: "dbSNP:rs795544" - # - qInput: "HGNC:7551" ## MYBPC3 aka NCBIGene:4607 - # oneOutput: "dbSNP:rs2071305" + testExamples: + - qInput: "HGNC:2950" ## DNAH5 aka NCBIGene:1767 + oneOutput: "dbSNP:rs795544" + - qInput: "HGNC:7551" ## MYBPC3 aka NCBIGene:4607 + oneOutput: "dbSNP:rs2071305" pathway-disease: ## see disease-pathway for details - supportBatch: false @@ -1380,11 +1380,11 @@ components: source: "infores:monarchinitiative" response_mapping: "$ref": "#/components/x-bte-response-mapping/disease-mondo" - # testExamples: - # - qInput: "REACT:R-HSA-2644606" ## Constitutive Signaling by NOTCH1 PEST Domain Mutants - # oneOutput: "MONDO:0010665" ## Wilson-Turner syndrome - # - qInput: "REACT:R-HSA-1369007" ## Mitochondrial ABC transporters - # oneOutput: "MONDO:0012204" ## familial pseudohyperkalemia + testExamples: + - qInput: "REACT:R-HSA-2644606" ## Constitutive Signaling by NOTCH1 PEST Domain Mutants + oneOutput: "MONDO:0010665" ## Wilson-Turner syndrome + - qInput: "REACT:R-HSA-1369007" ## Mitochondrial ABC transporters + oneOutput: "MONDO:0012204" ## familial pseudohyperkalemia phenotype-disease: ## see disease-phenotype for details - supportBatch: false @@ -1404,11 +1404,11 @@ components: source: "infores:monarchinitiative" response_mapping: "$ref": "#/components/x-bte-response-mapping/disease-mondo" - # testExamples: - # - qInput: "HP:0000272" ## Malar flattening - # oneOutput: "MONDO:0008974" ## Greenberg dysplasia - # - qInput: "HP:0032543" ## Lithoptysis - # oneOutput: "MONDO:0016575" ## primary ciliary dyskinesia + testExamples: + - qInput: "HP:0000272" ## Malar flattening + oneOutput: "MONDO:0008974" ## Greenberg dysplasia + - qInput: "HP:0032543" ## Lithoptysis + oneOutput: "MONDO:0016575" ## primary ciliary dyskinesia phenotype-gene: ## see gene-phenotype for details - supportBatch: false @@ -1429,11 +1429,11 @@ components: source: "infores:monarchinitiative" response_mapping: "$ref": "#/components/x-bte-response-mapping/gene-hgnc" - # testExamples: - # - qInput: "HP:0000183" ## Difficulty in tongue movements - # oneOutput: "HGNC:4065" ## GAA - # - qInput: "HP:0032543" ## Lithoptysis - # oneOutput: "HGNC:2950" ## DNAH5 aka NCBIGene:1767 + testExamples: + - qInput: "HP:0000183" ## Difficulty in tongue movements + oneOutput: "HGNC:4065" ## GAA + - qInput: "HP:0032543" ## Lithoptysis + oneOutput: "HGNC:2950" ## DNAH5 aka NCBIGene:1767 phenotype-variant: ## could also use OMIM IDs... ## note: relation RO:0003304 (contributes to condition) seems to use EFO terms, rather than HP... @@ -1457,11 +1457,11 @@ components: source: "infores:monarchinitiative" response_mapping: "$ref": "#/components/x-bte-response-mapping/variant-dbsnp" - # testExamples: - # - qInput: "HP:0002944" ## Thoracolumbar scoliosis - # oneOutput: "DBSNP:rs115165302" - # - qInput: "HP:0000183" ## Difficulty in tongue movements - # oneOutput: "DBSNP:rs771684665" + testExamples: + - qInput: "HP:0002944" ## Thoracolumbar scoliosis + oneOutput: "DBSNP:rs115165302" + - qInput: "HP:0000183" ## Difficulty in tongue movements + oneOutput: "DBSNP:rs771684665" variant-disease: ## see disease-variant for details - supportBatch: false @@ -1485,11 +1485,11 @@ components: response_mapping: "$ref": "#/components/x-bte-response-mapping/disease-mondo-dbsnp-start" ## examples have publications!!! - # testExamples: - # - qInput: "DBSNP:rs227731" - # oneOutput: "MONDO:0004747" ## cleft lip (disease) - # - qInput: "DBSNP:rs2230199" - # oneOutput: "MONDO:0005150" ## age-related macular degeneration + testExamples: + - qInput: "DBSNP:rs227731" + oneOutput: "MONDO:0004747" ## cleft lip (disease) + - qInput: "DBSNP:rs2230199" + oneOutput: "MONDO:0005150" ## age-related macular degeneration variant-gene: ## see gene-variant for details - supportBatch: false @@ -1510,11 +1510,11 @@ components: source: "infores:monarchinitiative" response_mapping: "$ref": "#/components/x-bte-response-mapping/gene-hgnc-dbsnp-start" - # testExamples: - # - qInput: "DBSNP:rs11879191" - # oneOutput: "HGNC:1735" ## CDC37 aka NCBIGene:11140 - # - qInput: "DBSNP:rs2230199" - # oneOutput: "HGNC:1318" ## C3 aka NCBIGene:718 + testExamples: + - qInput: "DBSNP:rs11879191" + oneOutput: "HGNC:1735" ## CDC37 aka NCBIGene:11140 + - qInput: "DBSNP:rs2230199" + oneOutput: "HGNC:1318" ## C3 aka NCBIGene:718 variant-phenotype: ## see phenotype-variant for details - supportBatch: false @@ -1537,9 +1537,9 @@ components: source: "infores:monarchinitiative" response_mapping: "$ref": "#/components/x-bte-response-mapping/phenotype-hp-dbsnp-start" - # testExamples: - # - qInput: "DBSNP:rs115165302" - # oneOutput: "HP:0002944" ## Thoracolumbar scoliosis - # - qInput: "DBSNP:rs771684665" - # oneOutput: "HP:0200055" ## Small hand + testExamples: + - qInput: "DBSNP:rs115165302" + oneOutput: "HP:0002944" ## Thoracolumbar scoliosis + - qInput: "DBSNP:rs771684665" + oneOutput: "HP:0200055" ## Small hand \ No newline at end of file diff --git a/bioplanet/bioplanet-pathway-disease.yaml b/bioplanet/bioplanet-pathway-disease.yaml index 2ca76d42..1d7e3cbf 100644 --- a/bioplanet/bioplanet-pathway-disease.yaml +++ b/bioplanet/bioplanet-pathway-disease.yaml @@ -606,9 +606,9 @@ components: source: "infores:bioplanet" response_mapping: "$ref": "#/components/x-bte-response-mapping/disease" - # testExamples: - # - qInput: "ncats.bioplanet:bioplanet_276" ## Alpha-hemoglobin stabilizing enzyme (AHSP) pathway - # oneOutput: "OMIM:300751" ## Anemia, sideroblastic, X-linked, 300751 (3) + testExamples: + - qInput: "ncats.bioplanet:bioplanet_276" ## Alpha-hemoglobin stabilizing enzyme (AHSP) pathway + oneOutput: "OMIM:300751" ## Anemia, sideroblastic, X-linked, 300751 (3) disease-pathway: - supportBatch: true useTemplating: true ## flag to say templating is being used below @@ -641,9 +641,9 @@ components: source: "infores:bioplanet" response_mapping: "$ref": "#/components/x-bte-response-mapping/pathway" - # testExamples: - # - qInput: "OMIM:603909" ## Autoimmune lymphoproliferative syndrome, type II, 603909 (3) - # oneOutput: "ncats.bioplanet:bioplanet_26" ## D4-GDI signaling pathway + testExamples: + - qInput: "OMIM:603909" ## Autoimmune lymphoproliferative syndrome, type II, 603909 (3) + oneOutput: "ncats.bioplanet:bioplanet_26" ## D4-GDI signaling pathway x-bte-response-mapping: disease: OMIM: subject.PHENO_TYPE ## no prefix diff --git a/bioplanet/bioplanet-pathway-gene.yaml b/bioplanet/bioplanet-pathway-gene.yaml index d4331755..9ab51ada 100644 --- a/bioplanet/bioplanet-pathway-gene.yaml +++ b/bioplanet/bioplanet-pathway-gene.yaml @@ -595,9 +595,9 @@ components: source: "infores:bioplanet" response_mapping: "$ref": "#/components/x-bte-response-mapping/gene" - # testExamples: - # - qInput: "ncats.bioplanet:bioplanet_869" ## Chondroitin sulfate/dermatan sulfate metabolism - # oneOutput: "NCBIGene:9672" ## SDC3 + testExamples: + - qInput: "ncats.bioplanet:bioplanet_869" ## Chondroitin sulfate/dermatan sulfate metabolism + oneOutput: "NCBIGene:9672" ## SDC3 gene-pathway: - supportBatch: true useTemplating: true ## flag to say templating is being used below @@ -622,9 +622,9 @@ components: source: "infores:bioplanet" response_mapping: "$ref": "#/components/x-bte-response-mapping/pathway" - # testExamples: - # - qInput: "NCBIGene:1463" ## NCAN - # oneOutput: "ncats.bioplanet:bioplanet_789" ## Dermatan sulfate biosynthesis + testExamples: + - qInput: "NCBIGene:1463" ## NCAN + oneOutput: "ncats.bioplanet:bioplanet_789" ## Dermatan sulfate biosynthesis x-bte-response-mapping: gene: NCBIGene: subject.GENE_ID ## no prefix diff --git a/biothings_foodb/smartapi.yaml b/biothings_foodb/smartapi.yaml index 0569f11a..8e8b0a6d 100644 --- a/biothings_foodb/smartapi.yaml +++ b/biothings_foodb/smartapi.yaml @@ -597,9 +597,9 @@ components: source: "infores:fooddb" response_mapping: "$ref": "#/components/x-bte-response-mapping/compound" - # testExamples: - # - qInput: "foodb.food:FOOD00914" ## Soybean oil - # oneOutput: "INCHIKEY:KZJWDPNRJALLNS-VJSFXXLFSA-N" ## beta-Sitosterol + testExamples: + - qInput: "foodb.food:FOOD00914" ## Soybean oil + oneOutput: "INCHIKEY:KZJWDPNRJALLNS-VJSFXXLFSA-N" ## beta-Sitosterol food-compound-rev: ## not including compound name because getting this nested info from reverse queries is tricky - supportBatch: true @@ -622,9 +622,9 @@ components: source: "infores:fooddb" response_mapping: "$ref": "#/components/x-bte-response-mapping/food" - # testExamples: - # - qInput: "INCHIKEY:QZAYGJVTTNCVMB-UHFFFAOYSA-N" ## Serotonin - # oneOutput: "foodb.food:FOOD00022" ## Oat + testExamples: + - qInput: "INCHIKEY:QZAYGJVTTNCVMB-UHFFFAOYSA-N" ## Serotonin + oneOutput: "foodb.food:FOOD00022" ## Oat x-bte-response-mapping: compound: INCHIKEY: compounds.moldb_inchikey diff --git a/complexportal/smartapi.yaml b/complexportal/smartapi.yaml index 517ee8f2..82f506f5 100644 --- a/complexportal/smartapi.yaml +++ b/complexportal/smartapi.yaml @@ -88,9 +88,9 @@ components: predicate: part_of response_mapping: "$ref": "#/components/x-bte-response-mapping/complex-output" - # testExamples: - # - qInput: "UniProtKB:P69905" ## Hemoglobin subunit alpha - # oneOutput: "ComplexPortal:CPX-2158" ## Hemoglobin HbA complex + testExamples: + - qInput: "UniProtKB:P69905" ## Hemoglobin subunit alpha + oneOutput: "ComplexPortal:CPX-2158" ## Hemoglobin HbA complex chemical2complex: - supportBatch: false useTemplating: true @@ -105,9 +105,9 @@ components: predicate: part_of response_mapping: "$ref": "#/components/x-bte-response-mapping/complex-output" - # testExamples: - # - qInput: "CHEBI:30413" ## heme - # oneOutput: "ComplexPortal:CPX-2158" ## Hemoglobin HbA complex + testExamples: + - qInput: "CHEBI:30413" ## heme + oneOutput: "ComplexPortal:CPX-2158" ## Hemoglobin HbA complex disease2complex: - supportBatch: false useTemplating: true @@ -124,9 +124,9 @@ components: ## https://www.ebi.ac.uk/complexportal/documentation response_mapping: "$ref": "#/components/x-bte-response-mapping/complex-output" - # testExamples: - # - qInput: "ORPHANET:848" ## Beta-thalassemia - # oneOutput: "ComplexPortal:CPX-2158" ## Hemoglobin HbA complex + testExamples: + - qInput: "ORPHANET:848" ## Beta-thalassemia + oneOutput: "ComplexPortal:CPX-2158" ## Hemoglobin HbA complex bp2complex: - supportBatch: false useTemplating: true @@ -143,9 +143,9 @@ components: ## not sure if a different predicate should be used... response_mapping: "$ref": "#/components/x-bte-response-mapping/complex-output" - # testExamples: - # - qInput: "GO:0015670" ## carbon dioxide transport - # oneOutput: "ComplexPortal:CPX-2936" ## Hemoglobin HbH complex + testExamples: + - qInput: "GO:0015670" ## carbon dioxide transport + oneOutput: "ComplexPortal:CPX-2936" ## Hemoglobin HbH complex mf2complex: - supportBatch: false useTemplating: true @@ -162,9 +162,9 @@ components: ## not sure if a different predicate should be used... response_mapping: "$ref": "#/components/x-bte-response-mapping/complex-output" - # testExamples: - # - qInput: "GO:0070026" ## nitric oxide binding - # oneOutput: "ComplexPortal:CPX-52" ## iNOS-S100A8/A9 complex + testExamples: + - qInput: "GO:0070026" ## nitric oxide binding + oneOutput: "ComplexPortal:CPX-52" ## iNOS-S100A8/A9 complex ## Commenting out for now ## Complex -> entity x-bte operations use JQ post-processing ## MISSING: Complex -> BP, Complex -> MF operations. Will need different custom JQ post-processing @@ -185,9 +185,9 @@ components: # .participants |= map(if (.identifier | contains(":") | not) then . else empty end) # response_mapping: # "$ref": "#/components/x-bte-response-mapping/complex2protein" - # # testExamples: - # # - qInput: "ComplexPortal:CPX-2158" ## Hemoglobin HbA complex - # # oneOutput: "UniProtKB:P69905" ## Hemoglobin subunit alpha + # testExamples: + # - qInput: "ComplexPortal:CPX-2158" ## Hemoglobin HbA complex + # oneOutput: "UniProtKB:P69905" ## Hemoglobin subunit alpha # complex2chemical: # - supportBatch: false # useTemplating: true @@ -205,9 +205,9 @@ components: # .participants |= map(if (.identifier | contains(":")) then .identifier = (.identifier | split(":") | last) else empty end) # response_mapping: # "$ref": "#/components/x-bte-response-mapping/complex2chemical" - # # testExamples: - # # - qInput: "ComplexPortal:CPX-2158" ## Hemoglobin HbA complex - # # oneOutput: "CHEBI:30413" ## heme + # testExamples: + # - qInput: "ComplexPortal:CPX-2158" ## Hemoglobin HbA complex + # oneOutput: "CHEBI:30413" ## heme # complex2disease: # - supportBatch: false # useTemplating: true @@ -228,9 +228,9 @@ components: # .disease_ids = (.diseases | map([ . | match("\\[(\\S*)\\]"; "g") | .captures | .[0] | .string | split(":") | last ]) | flatten) # response_mapping: # "$ref": "#/components/x-bte-response-mapping/complex2disease" - # # testExamples: - # # - qInput: "ComplexPortal:CPX-2158" ## Hemoglobin HbA complex - # # oneOutput: "ORPHANET:848" ## Beta-thalassemia + # testExamples: + # - qInput: "ComplexPortal:CPX-2158" ## Hemoglobin HbA complex + # oneOutput: "ORPHANET:848" ## Beta-thalassemia x-bte-response-mapping: complex-output: ComplexPortal: elements.complexAC diff --git a/ddinter/ddinter.yaml b/ddinter/ddinter.yaml index ef9144e6..0ab1539e 100644 --- a/ddinter/ddinter.yaml +++ b/ddinter/ddinter.yaml @@ -601,9 +601,9 @@ components: response_mapping: "$ref": "#/components/x-bte-response-mapping/drugB" ## compare to http://ddinter.scbdd.com/ddinter/interact/977140/ - # testExamples: - # - qInput: "DRUGBANK:DB00244" ## Mesalazine - # oneOutput: "DRUGBANK:DB00414" ## Acetohexamide + testExamples: + - qInput: "DRUGBANK:DB00244" ## Mesalazine + oneOutput: "DRUGBANK:DB00414" ## Acetohexamide drugB-to-drugA: - supportBatch: true useTemplating: true @@ -627,9 +627,9 @@ components: response_mapping: "$ref": "#/components/x-bte-response-mapping/drugA" ## compare to http://ddinter.scbdd.com/ddinter/interact/1047482/ - # testExamples: - # - qInput: "DRUGBANK:DB00540" ## Nortriptyline - # oneOutput: "DRUGBANK:DB00451" ## Levothyroxine + testExamples: + - qInput: "DRUGBANK:DB00540" ## Nortriptyline + oneOutput: "DRUGBANK:DB00451" ## Levothyroxine x-bte-response-mapping: drugB: DRUGBANK: drug_b.drugbank diff --git a/dgidb/openapi.yml b/dgidb/openapi.yml index 0c9dae5d..98b439c9 100644 --- a/dgidb/openapi.yml +++ b/dgidb/openapi.yml @@ -657,9 +657,9 @@ components: source: "infores:dgidb" response_mapping: "$ref": "#/components/x-bte-response-mapping/forward" - # testExamples: - # - qInput: "CHEMBL.COMPOUND:CHEMBL266510" ## FLINDOKALNER - # oneOutput: "NCBIGene:9132" ## KCNQ4 + testExamples: + - qInput: "CHEMBL.COMPOUND:CHEMBL266510" ## FLINDOKALNER + oneOutput: "NCBIGene:9132" ## KCNQ4 activator-rev: - supportBatch: true useTemplating: true ## flag to say templating is being used below @@ -692,9 +692,9 @@ components: source: "infores:dgidb" response_mapping: "$ref": "#/components/x-bte-response-mapping/reverse" - # testExamples: - # - qInput: "NCBIGene:2983" ## GUCY1B1 - # oneOutput: "CHEMBL.COMPOUND:CHEMBL730 ## NITROGLYCERIN + testExamples: + - qInput: "NCBIGene:2983" ## GUCY1B1 + oneOutput: "CHEMBL.COMPOUND:CHEMBL730" ## NITROGLYCERIN agonist: ## https://biothings.ncats.io/dgidb/query?q=association.interaction_types:agonist ## 2234 records @@ -729,9 +729,9 @@ components: source: "infores:dgidb" response_mapping: "$ref": "#/components/x-bte-response-mapping/forward" - # testExamples: - # - qInput: "CHEMBL.COMPOUND:CHEMBL1200833" ## DIPIVEFRIN HYDROCHLORIDE - # oneOutput: "NCBIGene:155" ## ADRB3 + testExamples: + - qInput: "CHEMBL.COMPOUND:CHEMBL1200833" ## DIPIVEFRIN HYDROCHLORIDE + oneOutput: "NCBIGene:155" ## ADRB3 ## some records have multiple interaction_types ## 1 record, agonist + allosteric_modulator: https://biothings.ncats.io/dgidb/query?q=association.interaction_types:agonist%20AND%20association.interaction_types:allosteric_modulator ## 17 records, agonist + antagonist: https://biothings.ncats.io/dgidb/query?q=association.interaction_types:agonist%20AND%20association.interaction_types:antagonist @@ -767,9 +767,9 @@ components: source: "infores:dgidb" response_mapping: "$ref": "#/components/x-bte-response-mapping/reverse" - # testExamples: - # - qInput: "NCBIGene:1814" ## DRD3 - # oneOutput: "CHEMBL.COMPOUND:CHEMBL2146110 ## SARIZOTAN HYDROCHLORIDE + testExamples: + - qInput: "NCBIGene:1814" ## DRD3 + oneOutput: "CHEMBL.COMPOUND:CHEMBL2146110" ## SARIZOTAN HYDROCHLORIDE allosteric_modulator: ## https://biothings.ncats.io/dgidb/query?q=association.interaction_types:allosteric_modulator ## 170 records @@ -802,9 +802,9 @@ components: source: "infores:dgidb" response_mapping: "$ref": "#/components/x-bte-response-mapping/forward" - # testExamples: - # - qInput: "CHEMBL.COMPOUND:CHEMBL3305985" ## ALCURONIUM - # oneOutput: "NCBIGene:1132" ## CHRM4 + testExamples: + - qInput: "CHEMBL.COMPOUND:CHEMBL3305985" ## ALCURONIUM + oneOutput: "NCBIGene:1132" ## CHRM4 allosteric_modulator-rev: - supportBatch: true useTemplating: true ## flag to say templating is being used below @@ -835,9 +835,9 @@ components: source: "infores:dgidb" response_mapping: "$ref": "#/components/x-bte-response-mapping/reverse" - # testExamples: - # - qInput: "NCBIGene:207" ## AKT1 - # oneOutput: "CHEMBL.COMPOUND:CHEMBL1079175 ## MK-2206 + testExamples: + - qInput: "NCBIGene:207" ## AKT1 + oneOutput: "CHEMBL.COMPOUND:CHEMBL1079175" ## MK-2206 antagonist: ## https://biothings.ncats.io/dgidb/query?q=association.interaction_types:antagonist ## 2330 records @@ -872,9 +872,9 @@ components: source: "infores:dgidb" response_mapping: "$ref": "#/components/x-bte-response-mapping/forward" - # testExamples: - # - qInput: "CHEMBL.COMPOUND:CHEMBL3545038" ## S-237648 - # oneOutput: "NCBIGene:4889" ## NPY5R + testExamples: + - qInput: "CHEMBL.COMPOUND:CHEMBL3545038" ## S-237648 + oneOutput: "NCBIGene:4889" ## NPY5R ## some records have multiple interaction_types ## 1 record, antagonist + allosteric_modulator: https://biothings.ncats.io/dgidb/query?q=association.interaction_types:allosteric_modulator%20AND%20association.interaction_types:antagonist antagonist-rev: @@ -909,9 +909,9 @@ components: source: "infores:dgidb" response_mapping: "$ref": "#/components/x-bte-response-mapping/reverse" - # testExamples: - # - qInput: "NCBIGene:185" ## AGTR1 - # oneOutput: "CHEMBL.COMPOUND:CHEMBL1017 ## TELMISARTAN + testExamples: + - qInput: "NCBIGene:185" ## AGTR1 + oneOutput: "CHEMBL.COMPOUND:CHEMBL1017" ## TELMISARTAN antibody: ## https://biothings.ncats.io/dgidb/query?q=association.interaction_types:antibody ## 222 records @@ -943,9 +943,9 @@ components: source: "infores:dgidb" response_mapping: "$ref": "#/components/x-bte-response-mapping/forward" - # testExamples: - # - qInput: "CHEMBL.COMPOUND:CHEMBL4297570" ## AMP-224 - # oneOutput: "NCBIGene:80380" ## PDCD1LG2 + testExamples: + - qInput: "CHEMBL.COMPOUND:CHEMBL4297570" ## AMP-224 + oneOutput: "NCBIGene:80380" ## PDCD1LG2 antibody-rev: - supportBatch: true useTemplating: true ## flag to say templating is being used below @@ -975,9 +975,9 @@ components: source: "infores:dgidb" response_mapping: "$ref": "#/components/x-bte-response-mapping/reverse" - # testExamples: - # - qInput: "NCBIGene:56963" ## RGMA - # oneOutput: "CHEMBL.COMPOUND:CHEMBL4297743 ## ELEZANUMAB + testExamples: + - qInput: "NCBIGene:56963" ## RGMA + oneOutput: "CHEMBL.COMPOUND:CHEMBL4297743" ## ELEZANUMAB ## commenting out because there's only 4 records for this set of operations # antisense_oligonucleotide: # ## https://biothings.ncats.io/dgidb/query?q=association.interaction_types:antisense_oligonucleotide @@ -1013,9 +1013,9 @@ components: # source: "infores:dgidb" # response_mapping: # "$ref": "#/components/x-bte-response-mapping/forward" - # # testExamples: - # # - qInput: "CHEMBL.COMPOUND:CHEMBL2108309" ## CUSTIRSEN - # # oneOutput: "NCBIGene:1191" ## CLU + # testExamples: + # - qInput: "CHEMBL.COMPOUND:CHEMBL2108309" ## CUSTIRSEN + # oneOutput: "NCBIGene:1191" ## CLU # antisense_oligonucleotide-rev: # - supportBatch: true # useTemplating: true ## flag to say templating is being used below @@ -1048,9 +1048,9 @@ components: # source: "infores:dgidb" # response_mapping: # "$ref": "#/components/x-bte-response-mapping/reverse" - # # testExamples: - # # - qInput: "NCBIGene:332" ## BIRC5 - # # oneOutput: "CHEMBL.COMPOUND:CHEMBL2219774 ## GATAPARSEN + # testExamples: + # - qInput: "NCBIGene:332" ## BIRC5 + # oneOutput: "CHEMBL.COMPOUND:CHEMBL2219774" ## GATAPARSEN blocker: ## https://biothings.ncats.io/dgidb/query?q=association.interaction_types:blocker ## 1134 records @@ -1086,9 +1086,9 @@ components: source: "infores:dgidb" response_mapping: "$ref": "#/components/x-bte-response-mapping/forward" - # testExamples: - # - qInput: "CHEMBL.COMPOUND:CHEMBL91" ## MICONAZOLE - # oneOutput: "NCBIGene:7226" ## TRPM2 + testExamples: + - qInput: "CHEMBL.COMPOUND:CHEMBL91" ## MICONAZOLE + oneOutput: "NCBIGene:7226" ## TRPM2 ## some records have multiple interaction_types ## 2 records, blocker + activator: https://biothings.ncats.io/dgidb/query?q=association.interaction_types:blocker%20AND%20association.interaction_types:activator ## 1 record, blocker + inhibitor: https://biothings.ncats.io/dgidb/query?q=association.interaction_types:blocker%20AND%20association.interaction_types:inhibitor @@ -1124,9 +1124,9 @@ components: source: "infores:dgidb" response_mapping: "$ref": "#/components/x-bte-response-mapping/reverse" - # testExamples: - # - qInput: "NCBIGene:775" ## CACNA1C - # oneOutput: "CHEMBL.COMPOUND:CHEMBL1648 ## ISRADIPINE + testExamples: + - qInput: "NCBIGene:775" ## CACNA1C + oneOutput: "CHEMBL.COMPOUND:CHEMBL1648" ## ISRADIPINE ## commenting out because there's only 1 record for this set of operations # inducer: # ## https://biothings.ncats.io/dgidb/query?q=association.interaction_types:inducer @@ -1163,9 +1163,9 @@ components: # source: "infores:dgidb" # response_mapping: # "$ref": "#/components/x-bte-response-mapping/forward" - # # testExamples: - # # - qInput: "CHEMBL.COMPOUND:CHEMBL71263" ## VADIMEZAN - # # oneOutput: "NCBIGene:7124" ## TNF + # testExamples: + # - qInput: "CHEMBL.COMPOUND:CHEMBL71263" ## VADIMEZAN + # oneOutput: "NCBIGene:7124" ## TNF # inducer-rev: # - supportBatch: true # useTemplating: true ## flag to say templating is being used below @@ -1197,9 +1197,9 @@ components: # source: "infores:dgidb" # response_mapping: # "$ref": "#/components/x-bte-response-mapping/reverse" - # # testExamples: - # # - qInput: "NCBIGene:7124" ## TNF - # # oneOutput: "CHEMBL.COMPOUND:CHEMBL71263" ## VADIMEZAN + # testExamples: + # - qInput: "NCBIGene:7124" ## TNF + # oneOutput: "CHEMBL.COMPOUND:CHEMBL71263" ## VADIMEZAN inhibitor: ## https://biothings.ncats.io/dgidb/query?q=association.interaction_types:inhibitor ## 6928 records @@ -1235,9 +1235,9 @@ components: source: "infores:dgidb" response_mapping: "$ref": "#/components/x-bte-response-mapping/forward" - # testExamples: - # - qInput: "CHEMBL.COMPOUND:CHEMBL1229517" ## VEMURAFENIB - # oneOutput: "NCBIGene:673" ## BRAF + testExamples: + - qInput: "CHEMBL.COMPOUND:CHEMBL1229517" ## VEMURAFENIB + oneOutput: "NCBIGene:673" ## BRAF inhibitor-rev: - supportBatch: true useTemplating: true ## flag to say templating is being used below @@ -1271,9 +1271,9 @@ components: source: "infores:dgidb" response_mapping: "$ref": "#/components/x-bte-response-mapping/reverse" - # testExamples: - # - qInput: "NCBIGene:3481" ## IGF2 - # oneOutput: "CHEMBL.COMPOUND:CHEMBL2109355" ## DUSIGITUMAB + testExamples: + - qInput: "NCBIGene:3481" ## IGF2 + oneOutput: "CHEMBL.COMPOUND:CHEMBL2109355" ## DUSIGITUMAB ## commenting out because there's only 1 record for this set of operations # inhibitory_allosteric_modulator: # ## https://biothings.ncats.io/dgidb/query?q=association.interaction_types:inhibitory_allosteric_modulator @@ -1309,9 +1309,9 @@ components: # source: "infores:dgidb" # response_mapping: # "$ref": "#/components/x-bte-response-mapping/forward" - # # testExamples: - # # - qInput: "CHEMBL.COMPOUND:CHEMBL1079175" ## MK-2206 - # # oneOutput: "NCBIGene:207" ## AKT1 + # testExamples: + # - qInput: "CHEMBL.COMPOUND:CHEMBL1079175" ## MK-2206 + # oneOutput: "NCBIGene:207" ## AKT1 # inhibitory_allosteric_modulator-rev: # - supportBatch: true # useTemplating: true ## flag to say templating is being used below @@ -1344,9 +1344,9 @@ components: # source: "infores:dgidb" # response_mapping: # "$ref": "#/components/x-bte-response-mapping/reverse" - # # testExamples: - # # - qInput: "NCBIGene:207" ## AKT1 - # # oneOutput: "CHEMBL.COMPOUND:CHEMBL1079175" ## MK-2206 + # testExamples: + # - qInput: "NCBIGene:207" ## AKT1 + # oneOutput: "CHEMBL.COMPOUND:CHEMBL1079175" ## MK-2206 inverse_agonist: ## https://biothings.ncats.io/dgidb/query?q=association.interaction_types:inverse_agonist ## 24 records @@ -1381,9 +1381,9 @@ components: source: "infores:dgidb" response_mapping: "$ref": "#/components/x-bte-response-mapping/forward" - # testExamples: - # - qInput: "CHEMBL.COMPOUND:CHEMBL1200986" ## HALOPERIDOL DECANOATE - # oneOutput: "NCBIGene:1814" ## DRD3 + testExamples: + - qInput: "CHEMBL.COMPOUND:CHEMBL1200986" ## HALOPERIDOL DECANOATE + oneOutput: "NCBIGene:1814" ## DRD3 inverse_agonist-rev: - supportBatch: true useTemplating: true ## flag to say templating is being used below @@ -1416,9 +1416,9 @@ components: source: "infores:dgidb" response_mapping: "$ref": "#/components/x-bte-response-mapping/reverse" - # testExamples: - # - qInput: "NCBIGene:3356" ## HTR2A - # oneOutput: "CHEMBL.COMPOUND:CHEMBL1084617" ## TEMANOGREL + testExamples: + - qInput: "NCBIGene:3356" ## HTR2A + oneOutput: "CHEMBL.COMPOUND:CHEMBL1084617" ## TEMANOGREL modulator: ## https://biothings.ncats.io/dgidb/query?q=association.interaction_types:modulator ## 222 records @@ -1453,9 +1453,9 @@ components: source: "infores:dgidb" response_mapping: "$ref": "#/components/x-bte-response-mapping/forward" - # testExamples: - # - qInput: "CHEMBL.COMPOUND:CHEMBL3301626" ## BASIMGLURANT - # oneOutput: "NCBIGene:2915" ## GRM5 + testExamples: + - qInput: "CHEMBL.COMPOUND:CHEMBL3301626" ## BASIMGLURANT + oneOutput: "NCBIGene:2915" ## GRM5 modulator-rev: - supportBatch: true useTemplating: true ## flag to say templating is being used below @@ -1486,9 +1486,9 @@ components: source: "infores:dgidb" response_mapping: "$ref": "#/components/x-bte-response-mapping/reverse" - # testExamples: - # - qInput: "NCBIGene:5241" ## PGR - # oneOutput: "CHEMBL.COMPOUND:CHEMBL2105694" ## TELAPRISTONE ACETATE + testExamples: + - qInput: "NCBIGene:5241" ## PGR + oneOutput: "CHEMBL.COMPOUND:CHEMBL2105694" ## TELAPRISTONE ACETATE ## commenting out because there's only 5 records for this set of operations # negative_modulator: # ## https://biothings.ncats.io/dgidb/query?q=association.interaction_types:negative_modulator @@ -1525,9 +1525,9 @@ components: # source: "infores:dgidb" # response_mapping: # "$ref": "#/components/x-bte-response-mapping/forward" - # # testExamples: - # # - qInput: "CHEMBL.COMPOUND:CHEMBL2109095" ## ERLIZUMAB - # # oneOutput: "NCBIGene:3689" ## ITGB2 + # testExamples: + # - qInput: "CHEMBL.COMPOUND:CHEMBL2109095" ## ERLIZUMAB + # oneOutput: "NCBIGene:3689" ## ITGB2 # negative_modulator-rev: # - supportBatch: true # useTemplating: true ## flag to say templating is being used below @@ -1560,9 +1560,9 @@ components: # source: "infores:dgidb" # response_mapping: # "$ref": "#/components/x-bte-response-mapping/reverse" - # # testExamples: - # # - qInput: "NCBIGene:920" ## CD4 - # # oneOutput: "CHEMBL.COMPOUND:CHEMBL2108475" ## PRILIXIMAB + # testExamples: + # - qInput: "NCBIGene:920" ## CD4 + # oneOutput: "CHEMBL.COMPOUND:CHEMBL2108475" ## PRILIXIMAB no_dgidb_relationship: ## 44557 records ## Most records did not have a value for that column. We put the value to "not_applicable" in those cases... @@ -1592,9 +1592,9 @@ components: source: "infores:dgidb" response_mapping: "$ref": "#/components/x-bte-response-mapping/forward" - # testExamples: - # - qInput: "CHEMBL.COMPOUND:CHEMBL3989914" ## GLESATINIB - # oneOutput: "NCBIGene:7010" ## TEK + testExamples: + - qInput: "CHEMBL.COMPOUND:CHEMBL3989914" ## GLESATINIB + oneOutput: "NCBIGene:7010" ## TEK no_dgidb_relationship-rev: - supportBatch: true useTemplating: true ## flag to say templating is being used below @@ -1621,9 +1621,9 @@ components: source: "infores:dgidb" response_mapping: "$ref": "#/components/x-bte-response-mapping/reverse" - # testExamples: - # - qInput: "NCBIGene:4985" ## OPRD1 - # oneOutput: "CHEMBL.COMPOUND:CHEMBL2159122" ## ELUXADOLINE + testExamples: + - qInput: "NCBIGene:4985" ## OPRD1 + oneOutput: "CHEMBL.COMPOUND:CHEMBL2159122" ## ELUXADOLINE partial_agonist: ## https://biothings.ncats.io/dgidb/query?q=association.interaction_types:partial_agonist ## 74 records @@ -1658,9 +1658,9 @@ components: source: "infores:dgidb" response_mapping: "$ref": "#/components/x-bte-response-mapping/forward" - # testExamples: - # - qInput: "CHEMBL.COMPOUND:CHEMBL3544917" ## RAPASTINEL - # oneOutput: "NCBIGene:2903" ## GRIN2A + testExamples: + - qInput: "CHEMBL.COMPOUND:CHEMBL3544917" ## RAPASTINEL + oneOutput: "NCBIGene:2903" ## GRIN2A partial_agonist-rev: - supportBatch: true useTemplating: true ## flag to say templating is being used below @@ -1693,9 +1693,9 @@ components: source: "infores:dgidb" response_mapping: "$ref": "#/components/x-bte-response-mapping/reverse" - # testExamples: - # - qInput: "NCBIGene:1137" ## CHRNA4 - # oneOutput: "CHEMBL.COMPOUND:CHEMBL3707250" ## CP-601927 + testExamples: + - qInput: "NCBIGene:1137" ## CHRNA4 + oneOutput: "CHEMBL.COMPOUND:CHEMBL3707250" ## CP-601927 positive_modulator: ## https://biothings.ncats.io/dgidb/query?q=association.interaction_types:positive_modulator ## 602 records @@ -1731,9 +1731,9 @@ components: source: "infores:dgidb" response_mapping: "$ref": "#/components/x-bte-response-mapping/forward" - # testExamples: - # - qInput: "CHEMBL.COMPOUND:CHEMBL30219" ## METHOHEXITAL SODIUM - # oneOutput: "NCBIGene:2565" ## GABRG1 + testExamples: + - qInput: "CHEMBL.COMPOUND:CHEMBL30219" ## METHOHEXITAL SODIUM + oneOutput: "NCBIGene:2565" ## GABRG1 positive_modulator-rev: - supportBatch: true useTemplating: true ## flag to say templating is being used below @@ -1766,9 +1766,9 @@ components: source: "infores:dgidb" response_mapping: "$ref": "#/components/x-bte-response-mapping/reverse" - # testExamples: - # - qInput: "NCBIGene:2557" ## GABRA4 - # oneOutput: "CHEMBL.COMPOUND:CHEMBL969" ## PRAZEPAM + testExamples: + - qInput: "NCBIGene:2557" ## GABRA4 + oneOutput: "CHEMBL.COMPOUND:CHEMBL969" ## PRAZEPAM ## commenting out because there's only 1 record for this set of operations # suppressor: # ## https://biothings.ncats.io/dgidb/query?q=association.interaction_types:suppressor @@ -1805,9 +1805,9 @@ components: # source: "infores:dgidb" # response_mapping: # "$ref": "#/components/x-bte-response-mapping/forward" - # # testExamples: - # # - qInput: "CHEMBL.COMPOUND:CHEMBL4297755" ## FP-1039 - # # oneOutput: "NCBIGene:2247" ## FGF2 + # testExamples: + # - qInput: "CHEMBL.COMPOUND:CHEMBL4297755" ## FP-1039 + # oneOutput: "NCBIGene:2247" ## FGF2 # suppressor-rev: # - supportBatch: true # useTemplating: true ## flag to say templating is being used below @@ -1840,9 +1840,9 @@ components: # source: "infores:dgidb" # response_mapping: # "$ref": "#/components/x-bte-response-mapping/reverse" - # # testExamples: - # # - qInput: "NCBIGene:2247" ## FGF2 - # # oneOutput: "CHEMBL.COMPOUND:CHEMBL4297755" ## FP-1039 + # testExamples: + # - qInput: "NCBIGene:2247" ## FGF2 + # oneOutput: "CHEMBL.COMPOUND:CHEMBL4297755" ## FP-1039 ## commenting out because there's only 8 records for this set of operations # vaccine: # ## https://biothings.ncats.io/dgidb/query?q=association.interaction_types:vaccine @@ -1874,9 +1874,9 @@ components: # source: "infores:dgidb" # response_mapping: # "$ref": "#/components/x-bte-response-mapping/forward" - # # testExamples: - # # - qInput: "CHEMBL.COMPOUND:CHEMBL75094" ## PRINOMASTAT - # # oneOutput: "NCBIGene:4323" ## MMP14 + # testExamples: + # - qInput: "CHEMBL.COMPOUND:CHEMBL75094" ## PRINOMASTAT + # oneOutput: "NCBIGene:4323" ## MMP14 # vaccine-rev: # - supportBatch: true # useTemplating: true ## flag to say templating is being used below @@ -1903,9 +1903,9 @@ components: # source: "infores:dgidb" # response_mapping: # "$ref": "#/components/x-bte-response-mapping/reverse" - # # testExamples: - # # - qInput: "NCBIGene:4313" ## MMP2 - # # oneOutput: "CHEMBL.COMPOUND:CHEMBL297792" ## S-3304 + # testExamples: + # - qInput: "NCBIGene:4313" ## MMP2 + # oneOutput: "CHEMBL.COMPOUND:CHEMBL297792" ## S-3304 x-bte-response-mapping: forward: NCBIGene: object.NCBIGene diff --git a/ebi_proteins/openapi.yml b/ebi_proteins/openapi.yml index d11b40d1..974d684b 100644 --- a/ebi_proteins/openapi.yml +++ b/ebi_proteins/openapi.yml @@ -3258,9 +3258,9 @@ components: source: "infores:uniprot" response_mapping: "$ref": "#/components/x-bte-response-mapping/rheaReaction" - # testExamples: - # - qInput: "UniProtKB:Q93099" ## Homogentisate 1,2-dioxygenase (HGD, human) - # oneOutput: "RHEA:15449" ## Under the comment with type (CATALYTIC_ACTIVTY), homogentisate + O2 = 4-maleylacetoacetate + H(+) + testExamples: + - qInput: "UniProtKB:Q93099" ## Homogentisate 1,2-dioxygenase (HGD, human) + oneOutput: "RHEA:15449" ## Under the comment with type (CATALYTIC_ACTIVTY), homogentisate + O2 = 4-maleylacetoacetate + H(+) ## another possible input: "UniProtKB:Q9Y6P5" ## SESN1 / SESN1_HUMAN Sestrin-1 (sprot) x-bte-response-mapping: rheaReaction: diff --git a/fooddata_central/smartapi.yaml b/fooddata_central/smartapi.yaml index 855c28e7..795691f4 100644 --- a/fooddata_central/smartapi.yaml +++ b/fooddata_central/smartapi.yaml @@ -610,9 +610,9 @@ components: source: "infores:fooddata-central" response_mapping: "$ref": "#/components/x-bte-response-mapping/compound" - # testExamples: - # - qInput: "FOODON:03302578" ## Oil, canola (was FOODON_03302578) - # oneOutput: "CHEBI:27693" ## Beta-sitosterol + testExamples: + - qInput: "FOODON:03302578" ## Oil, canola (was FOODON_03302578) + oneOutput: "CHEBI:27693" ## Beta-sitosterol food-compound-rev: - supportBatch: true useTemplating: true @@ -637,9 +637,9 @@ components: source: "infores:fooddata-central" response_mapping: "$ref": "#/components/x-bte-response-mapping/food" - # testExamples: - # - qInput: "CHEBI:27693" ## Beta-sitosterol - # oneOutput: "FOODON:03309857" ## Oil, peanut (was FOODON_03309857) + testExamples: + - qInput: "CHEBI:27693" ## Beta-sitosterol + oneOutput: "FOODON:03309857" ## Oil, peanut (was FOODON_03309857) x-bte-response-mapping: compound: CHEBI: object.chebiId diff --git a/go_bp/smartapi.yaml b/go_bp/smartapi.yaml index 5417c831..b87a7544 100644 --- a/go_bp/smartapi.yaml +++ b/go_bp/smartapi.yaml @@ -594,9 +594,9 @@ components: source: "infores:go" response_mapping: $ref: '#/components/x-bte-response-mapping/has_subclass' - # testExamples: - # - qInput: "GO:0089722" ## phosphoenolpyruvate transmembrane transport - # oneOutput: "GO:1990536" ## phosphoenolpyruvate transmembrane import into Golgi lumen + testExamples: + - qInput: "GO:0089722" ## phosphoenolpyruvate transmembrane transport + oneOutput: "GO:1990536" ## phosphoenolpyruvate transmembrane import into Golgi lumen subclass_of: ## all records but one have a "parents" field - supportBatch: true @@ -617,9 +617,9 @@ components: source: "infores:go" response_mapping: $ref: '#/components/x-bte-response-mapping/subclass_of' - # testExamples: - # - qInput: "GO:0150068" ## positive regulation of tubulin deacetylase activity - # oneOutput: "GO:0090044" ## positive regulation of tubulin deacetylation + testExamples: + - qInput: "GO:0150068" ## positive regulation of tubulin deacetylase activity + oneOutput: "GO:0090044" ## positive regulation of tubulin deacetylation negatively_regulates: ## 2774 records https://biothings.ncats.io/go_bp/query?q=_exists_:negatively_regulates - supportBatch: true @@ -645,9 +645,9 @@ components: source: "infores:go" response_mapping: $ref: '#/components/x-bte-response-mapping/negatively_regulates' - # testExamples: - # - qInput: "GO:0090272" ## negative regulation of fibroblast growth factor production - # oneOutput: "GO:0090269" ## fibroblast growth factor production + testExamples: + - qInput: "GO:0090272" ## negative regulation of fibroblast growth factor production + oneOutput: "GO:0090269" ## fibroblast growth factor production negatively_regulated_by: - supportBatch: true useTemplating: true @@ -672,9 +672,9 @@ components: source: "infores:go" response_mapping: $ref: '#/components/x-bte-response-mapping/negatively_regulated_by' - # testExamples: - # - qInput: "GO:0016126" ## sterol biosynthetic process - # oneOutput: "GO:0106119" ## negative regulation of sterol biosynthetic process + testExamples: + - qInput: "GO:0016126" ## sterol biosynthetic process + oneOutput: "GO:0106119" ## negative regulation of sterol biosynthetic process positively_regulates: ## 2761 records https://biothings.ncats.io/go_bp/query?q=_exists_:positively_regulates - supportBatch: true @@ -700,9 +700,9 @@ components: source: "infores:go" response_mapping: $ref: '#/components/x-bte-response-mapping/positively_regulates' - # testExamples: - # - qInput: "GO:0090129" ## positive regulation of synapse maturation - # oneOutput: "GO:0060074" ## synapse maturation + testExamples: + - qInput: "GO:0090129" ## positive regulation of synapse maturation + oneOutput: "GO:0060074" ## synapse maturation positively_regulated_by: - supportBatch: true useTemplating: true @@ -727,9 +727,9 @@ components: source: "infores:go" response_mapping: $ref: '#/components/x-bte-response-mapping/positively_regulated_by' - # testExamples: - # - qInput: "GO:0006641" ## triglyceride metabolic process - # oneOutput: "GO:0090208" ## positive regulation of triglyceride metabolic process + testExamples: + - qInput: "GO:0006641" ## triglyceride metabolic process + oneOutput: "GO:0090208" ## positive regulation of triglyceride metabolic process regulates: ## 3207 records https://biothings.ncats.io/go_bp/query?q=_exists_:regulates - supportBatch: true @@ -752,9 +752,9 @@ components: source: "infores:go" response_mapping: $ref: '#/components/x-bte-response-mapping/regulates' - # testExamples: - # - qInput: "GO:0090016" ## regulation of leaflet formation - # oneOutput: "GO:0090014" ## leaflet formation + testExamples: + - qInput: "GO:0090016" ## regulation of leaflet formation + oneOutput: "GO:0090014" ## leaflet formation regulated_by: - supportBatch: true useTemplating: true @@ -776,9 +776,9 @@ components: source: "infores:go" response_mapping: $ref: '#/components/x-bte-response-mapping/regulated_by' - # testExamples: - # - qInput: "GO:0001822" ## kidney development - # oneOutput: "GO:0090183" ## regulation of kidney development + testExamples: + - qInput: "GO:0001822" ## kidney development + oneOutput: "GO:0090183" ## regulation of kidney development part_of: ## 4928 records https://biothings.ncats.io/go_bp/query?q=_exists_:part_of - supportBatch: true @@ -799,9 +799,9 @@ components: source: "infores:go" response_mapping: $ref: '#/components/x-bte-response-mapping/part_of' - # testExamples: - # - qInput: "GO:0090010" ## transforming growth factor beta receptor signaling pathway involved in primitive streak formation - # oneOutput: "GO:0090009" ## primitive streak formation + testExamples: + - qInput: "GO:0090010" ## transforming growth factor beta receptor signaling pathway involved in primitive streak formation + oneOutput: "GO:0090009" ## primitive streak formation has_part: - supportBatch: true useTemplating: true @@ -821,9 +821,9 @@ components: source: "infores:go" response_mapping: $ref: '#/components/x-bte-response-mapping/has_part' - # testExamples: - # - qInput: "GO:0048313" ## Golgi inheritance - # oneOutput: "GO:0090168" ## Golgi reassembly + testExamples: + - qInput: "GO:0048313" ## Golgi inheritance + oneOutput: "GO:0090168" ## Golgi reassembly x-bte-response-mapping: has_subclass: GO: children diff --git a/go_cc/smartapi.yaml b/go_cc/smartapi.yaml index 1888558a..c0d8ce5f 100644 --- a/go_cc/smartapi.yaml +++ b/go_cc/smartapi.yaml @@ -588,9 +588,9 @@ components: source: "infores:go" response_mapping: $ref: '#/components/x-bte-response-mapping/has_subclass' - # testExamples: - # - qInput: "GO:0000136" ## mannan polymerase complex - # oneOutput: "GO:0140497" ## mannan polymerase II complex + testExamples: + - qInput: "GO:0000136" ## mannan polymerase complex + oneOutput: "GO:0140497" ## mannan polymerase II complex subclass_of: - supportBatch: true useTemplating: true @@ -610,9 +610,9 @@ components: source: "infores:go" response_mapping: $ref: '#/components/x-bte-response-mapping/subclass_of' - # testExamples: - # - qInput: "GO:0000835" ## ER ubiquitin ligase complex - # oneOutput: "GO:0000153" ## cytoplasmic ubiquitin ligase complex + testExamples: + - qInput: "GO:0000835" ## ER ubiquitin ligase complex + oneOutput: "GO:0000153" ## cytoplasmic ubiquitin ligase complex part_of: ## 2056 records https://biothings.ncats.io/go_cc/query?q=_exists_:part_of - supportBatch: true @@ -633,9 +633,9 @@ components: source: "infores:go" response_mapping: $ref: '#/components/x-bte-response-mapping/part_of' - # testExamples: - # - qInput: "GO:0000136" ## mannan polymerase complex - # oneOutput: "GO:0000137" ## Golgi cis cisterna + testExamples: + - qInput: "GO:0000136" ## mannan polymerase complex + oneOutput: "GO:0000137" ## Golgi cis cisterna has_part: - supportBatch: true useTemplating: true @@ -655,9 +655,9 @@ components: source: "infores:go" response_mapping: $ref: '#/components/x-bte-response-mapping/has_part' - # testExamples: - # - qInput: "GO:0005753" ## mitochondrial proton-transporting ATP synthase complex - # oneOutput: "GO:0000275" ## mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) + testExamples: + - qInput: "GO:0005753" ## mitochondrial proton-transporting ATP synthase complex + oneOutput: "GO:0000275" ## mitochondrial proton-transporting ATP synthase complex, catalytic sector F(1) x-bte-response-mapping: has_subclass: GO: children diff --git a/go_mf/smartapi.yaml b/go_mf/smartapi.yaml index bcba9a02..8c8f1a4d 100644 --- a/go_mf/smartapi.yaml +++ b/go_mf/smartapi.yaml @@ -588,9 +588,9 @@ components: source: "infores:go" response_mapping: $ref: '#/components/x-bte-response-mapping/has_subclass' - # testExamples: - # - qInput: "GO:0120013" ## lipid transfer activity - # oneOutput: "GO:0017089" ## glycolipid transfer activity + testExamples: + - qInput: "GO:0120013" ## lipid transfer activity + oneOutput: "GO:0017089" ## glycolipid transfer activity subclass_of: - supportBatch: true useTemplating: true @@ -610,9 +610,9 @@ components: source: "infores:go" response_mapping: $ref: '#/components/x-bte-response-mapping/subclass_of' - # testExamples: - # - qInput: "GO:0102505" ## apigeninidin 5-O-glucosyltransferase activity - # oneOutput: "GO:0016758" ## hexosyltransferase activity + testExamples: + - qInput: "GO:0102505" ## apigeninidin 5-O-glucosyltransferase activity + oneOutput: "GO:0016758" ## hexosyltransferase activity part_of: ## 11 records https://biothings.ncats.io/go_mf/query?q=_exists_:part_of - supportBatch: true @@ -633,9 +633,9 @@ components: source: "infores:go" response_mapping: $ref: '#/components/x-bte-response-mapping/part_of' - # testExamples: - # - qInput: "GO:0000332" ## template for synthesis of G-rich strand of telomere DNA activity - # oneOutput: "GO:0003720" ## telomerase activity + testExamples: + - qInput: "GO:0000332" ## template for synthesis of G-rich strand of telomere DNA activity + oneOutput: "GO:0003720" ## telomerase activity has_part: - supportBatch: true useTemplating: true @@ -655,9 +655,9 @@ components: source: "infores:go" response_mapping: $ref: '#/components/x-bte-response-mapping/has_part' - # testExamples: - # - qInput: "GO:0044823" ## retroviral integrase activity - # oneOutput: "GO:0044824" ## retroviral 3' processing activity + testExamples: + - qInput: "GO:0044823" ## retroviral integrase activity + oneOutput: "GO:0044824" ## retroviral 3' processing activity x-bte-response-mapping: has_subclass: GO: children diff --git a/gtrx/gtrx.yaml b/gtrx/gtrx.yaml index f460fe3f..d6eefa08 100644 --- a/gtrx/gtrx.yaml +++ b/gtrx/gtrx.yaml @@ -620,9 +620,9 @@ components: response_mapping: "$ref": "#/components/x-bte-response-mapping/drug" ## compare to hhttps://gtrx.rbsapp.net/?q=1&i=true - # testExamples: - # - qInput: "OMIM:250250" ## CARTILAGE-HAIR HYPOPLASIA; - # oneOutput: "UNII:MZ1IW7Q79D" ## Valaciclovir + testExamples: + - qInput: "OMIM:250250" ## CARTILAGE-HAIR HYPOPLASIA; + oneOutput: "UNII:MZ1IW7Q79D" ## Valaciclovir drug-disease: - supportBatch: true useTemplating: true ## flag to say templating is being used below @@ -659,9 +659,9 @@ components: response_mapping: "$ref": "#/components/x-bte-response-mapping/disease" ## compare to https://gtrx.rbsapp.net/?q=MALIGNANT%20HYPERTHERMIA,%20SUSCEPTIBILITY%20TO,%201 - # testExamples: - # - qInput: "UNII:F64QU97QCR" ## Dantrolene - # oneOutput: "OMIM:145600" ## MALIGNANT HYPERTHERMIA, SUSCEPTIBILITY TO, 1 + testExamples: + - qInput: "UNII:F64QU97QCR" ## Dantrolene + oneOutput: "OMIM:145600" ## MALIGNANT HYPERTHERMIA, SUSCEPTIBILITY TO, 1 x-bte-response-mapping: drug: ## using order and language from gtrx website for these fields diff --git a/hpo/smartapi.yaml b/hpo/smartapi.yaml index 08aadcf3..fa966026 100644 --- a/hpo/smartapi.yaml +++ b/hpo/smartapi.yaml @@ -591,9 +591,9 @@ components: source: "infores:hpo-annotations" response_mapping: $ref: '#/components/x-bte-response-mapping/annotated-genes' - # testExamples: - # - qInput: "HP:0031445" ## Oral mucosa nodule - # oneOutput: "NCBIGene:11146" ## GLMN + testExamples: + - qInput: "HP:0031445" ## Oral mucosa nodule + oneOutput: "NCBIGene:11146" ## GLMN pheno_gene-rev: - supportBatch: true useTemplating: true @@ -614,9 +614,9 @@ components: source: "infores:hpo-annotations" response_mapping: $ref: '#/components/x-bte-response-mapping/hp-id' - # testExamples: - # - qInput: "NCBIGene:3909" ## LAMA3 - # oneOutput: "HP:0031446" ## Erosion of oral mucosa + testExamples: + - qInput: "NCBIGene:3909" ## LAMA3 + oneOutput: "HP:0031446" ## Erosion of oral mucosa has_subclass: ## 5607 records: https://biothings.ncats.io/hpo/query?q=_exists_:descendants - supportBatch: true @@ -637,9 +637,9 @@ components: source: "infores:hpo" response_mapping: $ref: '#/components/x-bte-response-mapping/has_subclass' - # testExamples: - # - qInput: "HP:0025598" ## Inferior oblique muscle weakness - # oneOutput: "HP:0025597" ## Inferior oblique muscle restriction + testExamples: + - qInput: "HP:0025598" ## Inferior oblique muscle weakness + oneOutput: "HP:0025597" ## Inferior oblique muscle restriction subclass_of: - supportBatch: true useTemplating: true @@ -659,9 +659,9 @@ components: source: "infores:hpo" response_mapping: $ref: '#/components/x-bte-response-mapping/subclass_of' - # testExamples: - # - qInput: "HP:0025532" ## Positive pathergy test - # oneOutput: "HP:0011122" ## Abnormality of skin physiology + testExamples: + - qInput: "HP:0025532" ## Positive pathergy test + oneOutput: "HP:0011122" ## Abnormality of skin physiology x-bte-response-mapping: annotated-genes: NCBIGene: annotations.gene.id diff --git a/iPTMnet/smartapi.yaml b/iPTMnet/smartapi.yaml index 987c9b0f..b7e38a73 100644 --- a/iPTMnet/smartapi.yaml +++ b/iPTMnet/smartapi.yaml @@ -135,9 +135,9 @@ components: ## not sure what all the possible values are though... response_mapping: "$ref": "#/components/x-bte-response-mapping/is_substrate_of" - # testExamples: - # - qInput: "UniProtKB:P24941" ## CDK2 - # oneOutput: "UniProtKB:P50613" ## CDK7 + testExamples: + - qInput: "UniProtKB:P24941" ## CDK2 + oneOutput: "UniProtKB:P50613" ## CDK7 has_substrate: ## response: an object where the keys are the protein IDs and the values are an array of objects. ## the objects have fields like substrate, substrate_symbol, site, score, sources, pmids @@ -157,9 +157,9 @@ components: ## see notes on is_substrate_of response_mapping: "$ref": "#/components/x-bte-response-mapping/has_substrate" - # testExamples: - # - qInput: "UniProtKB:P24941" ## CDK2 - # oneOutput: "UniProtKB:P33991" ## MCM4 + testExamples: + - qInput: "UniProtKB:P24941" ## CDK2 + oneOutput: "UniProtKB:P33991" ## MCM4 x-bte-response-mapping: is_substrate_of: UniProtKB: enzymes.id diff --git a/idisk/smartapi.yaml b/idisk/smartapi.yaml index 87be5a2c..905b692f 100644 --- a/idisk/smartapi.yaml +++ b/idisk/smartapi.yaml @@ -610,9 +610,9 @@ components: source: "infores:idisk" response_mapping: $ref: '#/components/x-bte-response-mapping/has_adverse_effect_on' - # testExamples: - # - qInput: "UMLS:C0000392" ## beta-Alanine - # oneOutput: "MEDDRA:10017947" ## gastrointestinal disorders + testExamples: + - qInput: "UMLS:C0000392" ## beta-Alanine + oneOutput: "MEDDRA:10017947" ## gastrointestinal disorders has_adverse_effect_on-rev: - supportBatch: true useTemplating: true ## flag to say templating is being used below @@ -635,9 +635,9 @@ components: source: "infores:idisk" response_mapping: $ref: '#/components/x-bte-response-mapping/rev' - # testExamples: - # - qInput: "MEDDRA:10017947" ## gastrointestinal disorders - # oneOutput: "UMLS:C0000392" ## beta-Alanine + testExamples: + - qInput: "MEDDRA:10017947" ## gastrointestinal disorders + oneOutput: "UMLS:C0000392" ## beta-Alanine has_adverse_reaction: ## there are 204 records with the has_adverse_reaction field ## the dietary supplement has an adverse effect/reaction (specific sign/symptom) @@ -672,9 +672,9 @@ components: source: "infores:idisk" response_mapping: $ref: '#/components/x-bte-response-mapping/has_adverse_reaction' - # testExamples: - # - qInput: "UMLS:C0000578" ## 5-Hydroxytryptophan - # oneOutput: "UMLS:C0027497" ## nausea + testExamples: + - qInput: "UMLS:C0000578" ## 5-Hydroxytryptophan + oneOutput: "UMLS:C0027497" ## nausea has_adverse_reaction-rev: - supportBatch: true useTemplating: true ## flag to say templating is being used below @@ -697,9 +697,9 @@ components: source: "infores:idisk" response_mapping: $ref: '#/components/x-bte-response-mapping/rev' - # testExamples: - # - qInput: "UMLS:C0027497" ## nausea - # oneOutput: "UMLS:C0000578" ## 5-Hydroxytryptophan + testExamples: + - qInput: "UMLS:C0027497" ## nausea + oneOutput: "UMLS:C0000578" ## 5-Hydroxytryptophan interacts_with: ## there are 673 records with the interacts_with field ## most use NMCD (604), but some use MSKCC (178). Some records must have both? @@ -728,9 +728,9 @@ components: source: "infores:idisk" response_mapping: $ref: '#/components/x-bte-response-mapping/interacts_with' - # testExamples: - # - qInput: "UMLS:C0000473" ## 4-Aminobenzoic Acid - # oneOutput: "UMLS:C0010137" ## Cortisone + testExamples: + - qInput: "UMLS:C0000473" ## 4-Aminobenzoic Acid + oneOutput: "UMLS:C0010137" ## Cortisone interacts_with-rev: - supportBatch: true useTemplating: true ## flag to say templating is being used below @@ -753,9 +753,9 @@ components: source: "infores:idisk" response_mapping: $ref: '#/components/x-bte-response-mapping/rev' - # testExamples: - # - qInput: "UMLS:C0010137" ## Cortisone - # oneOutput: "UMLS:C0000473" ## 4-Aminobenzoic Acid + testExamples: + - qInput: "UMLS:C0010137" ## Cortisone + oneOutput: "UMLS:C0000473" ## 4-Aminobenzoic Acid is_effective_for: ## there are 654 records with the is_effective_for field ## most use NMCD (552), but some use MSKCC (238). Some records must have both? @@ -785,9 +785,9 @@ components: source: "infores:idisk" response_mapping: $ref: '#/components/x-bte-response-mapping/is_effective_for' - # testExamples: - # - qInput: "UMLS:C0000503" ## gamma hydroxybutyrate - # oneOutput: "UMLS:C0016053" ## Fibromyalgias + testExamples: + - qInput: "UMLS:C0000503" ## gamma hydroxybutyrate + oneOutput: "UMLS:C0016053" ## Fibromyalgias is_effective_for-rev: - supportBatch: true useTemplating: true ## flag to say templating is being used below @@ -810,9 +810,9 @@ components: source: "infores:idisk" response_mapping: $ref: '#/components/x-bte-response-mapping/rev' - # testExamples: - # - qInput: "UMLS:C0016053" ## Fibromyalgias - # oneOutput: "UMLS:C0000503" ## gamma hydroxybutyrate + testExamples: + - qInput: "UMLS:C0016053" ## Fibromyalgias + oneOutput: "UMLS:C0000503" ## gamma hydroxybutyrate x-bte-response-mapping: ## name not included since BTE doesn't ingest it right now... has_adverse_effect_on: diff --git a/innatedb/smartapi.yaml b/innatedb/smartapi.yaml index 76d7e956..9af4994d 100644 --- a/innatedb/smartapi.yaml +++ b/innatedb/smartapi.yaml @@ -655,9 +655,9 @@ components: source: "infores:innatedb" response_mapping: "$ref": "#/components/x-bte-response-mapping/object" - # testExamples: - # - qInput: "ENSEMBL:ENSG00000078142" ## PIK3C3 - # oneOutput: "ENSEMBL:ENSG00000126775" ## ATG14 + testExamples: + - qInput: "ENSEMBL:ENSG00000078142" ## PIK3C3 + oneOutput: "ENSEMBL:ENSG00000126775" ## ATG14 physical_association-rev: - supportBatch: true useTemplating: true @@ -683,9 +683,9 @@ components: source: "infores:innatedb" response_mapping: "$ref": "#/components/x-bte-response-mapping/subject" - # testExamples: - # - qInput: "ENSEMBL:ENSG00000113558" ## SKP1 - # oneOutput: "ENSEMBL:ENSG00000100906" ## NFKBIA + testExamples: + - qInput: "ENSEMBL:ENSG00000113558" ## SKP1 + oneOutput: "ENSEMBL:ENSG00000100906" ## NFKBIA phosphorylation: ## 1201 records ## all have subject/object as "protein" @@ -725,9 +725,9 @@ components: source: "infores:innatedb" response_mapping: "$ref": "#/components/x-bte-response-mapping/object" - # testExamples: - # - qInput: "ENSEMBL:ENSG00000109339" ## MAPK10 (enzyme) - # oneOutput: "ENSEMBL:ENSG00000196793" ## ZNF239 (enzyme target) + testExamples: + - qInput: "ENSEMBL:ENSG00000109339" ## MAPK10 (enzyme) + oneOutput: "ENSEMBL:ENSG00000196793" ## ZNF239 (enzyme target) phosphorylation-rev: - supportBatch: true useTemplating: true @@ -753,9 +753,9 @@ components: source: "infores:innatedb" response_mapping: "$ref": "#/components/x-bte-response-mapping/subject" - # testExamples: - # - qInput: "ENSEMBL:ENSG00000213341" ## CHUK (enzyme target) - # oneOutput: "ENSEMBL:ENSG00000105221" ## AKT2 (enzyme) + testExamples: + - qInput: "ENSEMBL:ENSG00000213341" ## CHUK (enzyme target) + oneOutput: "ENSEMBL:ENSG00000105221" ## AKT2 (enzyme) ubiquitination: ## 423 records ## all have subject/object as "protein" @@ -789,9 +789,9 @@ components: source: "infores:innatedb" response_mapping: "$ref": "#/components/x-bte-response-mapping/object" - # testExamples: - # - qInput: "ENSEMBL:ENSG00000100906" ## NFKBIA (enzyme target) - # oneOutput: "ENSEMBL:ENSG00000131508" ## UBE2D2 (enzyme) + testExamples: + - qInput: "ENSEMBL:ENSG00000100906" ## NFKBIA (enzyme target) + oneOutput: "ENSEMBL:ENSG00000131508" ## UBE2D2 (enzyme) ubiquitination-rev: - supportBatch: true useTemplating: true @@ -817,9 +817,9 @@ components: source: "infores:innatedb" response_mapping: "$ref": "#/components/x-bte-response-mapping/subject" - # testExamples: - # - qInput: "ENSEMBL:ENSG00000173039" ## RELA (unspecified role) - # oneOutput: "ENSEMBL:ENSG00000100906" ## NFKBIA (enzyme target) + testExamples: + - qInput: "ENSEMBL:ENSG00000173039" ## RELA (unspecified role) + oneOutput: "ENSEMBL:ENSG00000100906" ## NFKBIA (enzyme target) protein_cleavage: ## 324 records ## all have subject/object as "protein" @@ -859,9 +859,9 @@ components: source: "infores:innatedb" response_mapping: "$ref": "#/components/x-bte-response-mapping/object" - # testExamples: - # - qInput: "ENSEMBL:ENSG00000092009" ## CMA1 (enzyme) - # oneOutput: "ENSEMBL:ENSMUSG00000024810" ## mgi:Il33 (enzyme target) + testExamples: + - qInput: "ENSEMBL:ENSG00000092009" ## CMA1 (enzyme) + oneOutput: "ENSEMBL:ENSMUSG00000024810" ## mgi:Il33 (enzyme target) protein_cleavage-rev: - supportBatch: true useTemplating: true @@ -887,9 +887,9 @@ components: source: "infores:innatedb" response_mapping: "$ref": "#/components/x-bte-response-mapping/subject" - # testExamples: - # - qInput: "ENSEMBL:ENSG00000108700" ## CCL8 (enzyme target) - # oneOutput: "ENSEMBL:ENSG00000262406" ## MMP12 (enzyme) + testExamples: + - qInput: "ENSEMBL:ENSG00000108700" ## CCL8 (enzyme target) + oneOutput: "ENSEMBL:ENSG00000262406" ## MMP12 (enzyme) cleavage_reaction: ## 147 records ## not sure how this differs from the "protein cleavage" label @@ -930,9 +930,9 @@ components: source: "infores:innatedb" response_mapping: "$ref": "#/components/x-bte-response-mapping/object" - # testExamples: - # - qInput: "ENSEMBL:ENSG00000014216" ## CAPN1 (enzyme) - # oneOutput: "ENSEMBL:ENSG00000196396" ## PTPN1 (enzyme target) + testExamples: + - qInput: "ENSEMBL:ENSG00000014216" ## CAPN1 (enzyme) + oneOutput: "ENSEMBL:ENSG00000196396" ## PTPN1 (enzyme target) cleavage_reaction-rev: - supportBatch: true useTemplating: true @@ -958,9 +958,9 @@ components: source: "infores:innatedb" response_mapping: "$ref": "#/components/x-bte-response-mapping/subject" - # testExamples: - # - qInput: "ENSEMBL:ENSG00000150782" ## IL18 (enzyme target) - # oneOutput: "ENSEMBL:ENSG00000137752" ## CASP1 (enzyme) + testExamples: + - qInput: "ENSEMBL:ENSG00000150782" ## IL18 (enzyme target) + oneOutput: "ENSEMBL:ENSG00000137752" ## CASP1 (enzyme) dephosphorylation: ## 40 records ## all have subject/object as "protein" @@ -1000,9 +1000,9 @@ components: source: "infores:innatedb" response_mapping: "$ref": "#/components/x-bte-response-mapping/object" - # testExamples: - # - qInput: "ENSEMBL:ENSG00000127329" ## PTPRB (enzyme) - # oneOutput: "ENSEMBL:ENSG00000120156" ## TEK (enzyme target) + testExamples: + - qInput: "ENSEMBL:ENSG00000127329" ## PTPRB (enzyme) + oneOutput: "ENSEMBL:ENSG00000120156" ## TEK (enzyme target) dephosphorylation-rev: - supportBatch: true useTemplating: true @@ -1028,9 +1028,9 @@ components: source: "infores:innatedb" response_mapping: "$ref": "#/components/x-bte-response-mapping/subject" - # testExamples: - # - qInput: "ENSEMBL:ENSG00000135341" ## MAP3K7 (enzyme target) - # oneOutput: "ENSEMBL:ENSG00000138032" ## PPM1B (enzyme) + testExamples: + - qInput: "ENSEMBL:ENSG00000135341" ## MAP3K7 (enzyme target) + oneOutput: "ENSEMBL:ENSG00000138032" ## PPM1B (enzyme) x-bte-response-mapping: object: ENSEMBL: object.alt_identifier.ensembl diff --git a/litvar/smartapi.yaml b/litvar/smartapi.yaml index 53293991..03acc737 100644 --- a/litvar/smartapi.yaml +++ b/litvar/smartapi.yaml @@ -61,9 +61,9 @@ components: source: "infores:dbsnp" response_mapping: "$ref": "#/components/x-bte-response-mapping/variant_located_in_gene" - # testExamples: - # - qInput: "DBSNP:rs121913527" - # oneOutput: "NCBIGene:3845" ## KRAS + testExamples: + - qInput: "DBSNP:rs121913527" + oneOutput: "NCBIGene:3845" ## KRAS ## another example input is rs1193171808 ## raw query example: https://www.ncbi.nlm.nih.gov/research/bionlp/litvar/api/v1/entity/litvar/rs121913527%23%23 x-bte-response-mapping: diff --git a/mychem.info/openapi_full.yml b/mychem.info/openapi_full.yml index bd98e17e..47da03ee 100644 --- a/mychem.info/openapi_full.yml +++ b/mychem.info/openapi_full.yml @@ -742,9 +742,9 @@ components: source: "infores:aeolus" response_mapping: "$ref": "#/components/x-bte-response-mapping/aeolusIndication-meddra" - # testExamples: - # - qInput: "UNII:90347YTW5F" ## alfuzosin - # oneOutput: "MEDDRA:10004446" ## Benign prostatic hyperplasia + testExamples: + - qInput: "UNII:90347YTW5F" ## alfuzosin + oneOutput: "MEDDRA:10004446" ## Benign prostatic hyperplasia aeolusTreats-rev: - supportBatch: true useTemplating: true @@ -765,9 +765,9 @@ components: source: "infores:aeolus" response_mapping: "$ref": "#/components/x-bte-response-mapping/aeolus-unii" - # testExamples: - # - qInput: "MEDDRA:10012378" ## Depression - # oneOutput: "UNII:OGG85SX4E4" ## Imipramine + testExamples: + - qInput: "MEDDRA:10012378" ## Depression + oneOutput: "UNII:OGG85SX4E4" ## Imipramine ## chebi xrefs actually include relationships to other bioentities... ## - note that truncation was done by MyChem for rhea... ## see https://docs.mychem.info/en/latest/doc/data_source.html @@ -800,9 +800,9 @@ components: source: "infores:chebi" response_mapping: "$ref": "#/components/x-bte-response-mapping/chebiXrefs-reactome" - # testExamples: - # - qInput: "CHEBI:15724" ## trimethylamine N-oxide - # oneOutput: "REACT:R-HSA-139970" ## FMO3:FAD N-oxidises TMA to TMAO + testExamples: + - qInput: "CHEBI:15724" ## trimethylamine N-oxide + oneOutput: "REACT:R-HSA-139970" ## FMO3:FAD N-oxidises TMA to TMAO chebiToReactome-rev: - supportBatch: true useTemplating: true @@ -823,9 +823,9 @@ components: source: "infores:chebi" response_mapping: "$ref": "#/components/x-bte-response-mapping/chebi" - # testExamples: - # - qInput: "REACT:R-HSA-1855166" ## PP-IP4 is dephosphorylated to I(1,3,4,5,6)P5 by NUDT4 in the cytosol - # oneOutput: "CHEBI:62926" ## 1-Diphospho-1D-myo-inositol 3,4,5,6-tetrakisphosphate + testExamples: + - qInput: "REACT:R-HSA-1855166" ## PP-IP4 is dephosphorylated to I(1,3,4,5,6)P5 by NUDT4 in the cytosol + oneOutput: "CHEBI:62926" ## 1-Diphospho-1D-myo-inositol 3,4,5,6-tetrakisphosphate chebiToRhea: ## there are 11079 records with chebi.xrefs.rhea - supportBatch: true @@ -847,9 +847,9 @@ components: source: "infores:chebi" response_mapping: "$ref": "#/components/x-bte-response-mapping/chebiXrefs-rhea" - # testExamples: - # - qInput: "CHEBI:4885" ## ethionamide - # oneOutput: "RHEA:47616" ## ethionamide + H(+) + NADPH + O2 = ethionamide S-oxide + H2O + NADP(+) + testExamples: + - qInput: "CHEBI:4885" ## ethionamide + oneOutput: "RHEA:47616" ## ethionamide + H(+) + NADPH + O2 = ethionamide S-oxide + H2O + NADP(+) chebiToRhea-rev: - supportBatch: true useTemplating: true @@ -870,9 +870,9 @@ components: source: "infores:chebi" response_mapping: "$ref": "#/components/x-bte-response-mapping/chebi" - # testExamples: - # - qInput: "RHEA:23312" ## 2 sucrose = 1(F)-beta-D-fructosylsucrose + D-glucose - # oneOutput: "CHEBI:16885" ## 1-kestose / 1(F)-beta-D-fructosylsucrose + testExamples: + - qInput: "RHEA:23312" ## 2 sucrose = 1(F)-beta-D-fructosylsucrose + D-glucose + oneOutput: "CHEBI:16885" ## 1-kestose / 1(F)-beta-D-fructosylsucrose ## chembl ## - drug_mechanisms: ## - can filter for human vs non-human targets and by target-type @@ -921,9 +921,9 @@ components: source: "infores:chembl" response_mapping: "$ref": "#/components/x-bte-response-mapping/drugMechChembl_EnsemblOutput" - # testExamples: - # - qInput: "CHEMBL.COMPOUND:CHEMBL4298198" ## VUPANORSEN SODIUM - # oneOutput: "ENSEMBL:ENSG00000132855" ## ANGPTL3 / Angiopoietin like 3 (ANGPTL3) mRNA + testExamples: + - qInput: "CHEMBL.COMPOUND:CHEMBL4298198" ## VUPANORSEN SODIUM + oneOutput: "ENSEMBL:ENSG00000132855" ## ANGPTL3 / Angiopoietin like 3 (ANGPTL3) mRNA drugMechChemblEnsembl-rev: - supportBatch: true useTemplating: true @@ -944,9 +944,9 @@ components: source: "infores:chembl" response_mapping: "$ref": "#/components/x-bte-response-mapping/drugMechChembl-rev" - # testExamples: - # - qInput: "ENSEMBL:ENSG00000276536" ## H-Ras mRNA 5'UTR - # oneOutput: "CHEMBL.COMPOUND:CHEMBL4594562" ## ISIS-2503 + testExamples: + - qInput: "ENSEMBL:ENSG00000276536" ## H-Ras mRNA 5'UTR + oneOutput: "CHEMBL.COMPOUND:CHEMBL4594562" ## ISIS-2503 drugMechChemblUniprot: ## 4553 chem/records have chembl.drug_mechanisms.target_components.uniprot - supportBatch: true @@ -988,9 +988,9 @@ components: source: "infores:chembl" response_mapping: "$ref": "#/components/x-bte-response-mapping/drugMechChembl_UniprotOutput" - # testExamples: - # - qInput: "CHEMBL.COMPOUND:CHEMBL3989919" ## FOSNETUPITANT CHLORIDE HYDROCHLORIDE - # oneOutput: "UniProtKB:P25103" ## TACR1 / Neurokinin 1 receptor + testExamples: + - qInput: "CHEMBL.COMPOUND:CHEMBL3989919" ## FOSNETUPITANT CHLORIDE HYDROCHLORIDE + oneOutput: "UniProtKB:P25103" ## TACR1 / Neurokinin 1 receptor drugMechChemblUniprot-rev: - supportBatch: true useTemplating: true @@ -1011,9 +1011,9 @@ components: source: "infores:chembl" response_mapping: "$ref": "#/components/x-bte-response-mapping/drugMechChembl-rev" - # testExamples: - # - qInput: "UniProtKB:Q16539" ## MAP kinase p38 alpha - # oneOutput: "CHEMBL.COMPOUND:CHEMBL585902" ## AMG-548 / 4(3H)-Pyrimidinone, 2-(((2S)-2-amino-3-phenylpropyl)amino)-3-methyl-5-(2-naphthalenyl)-6-(4-pyridinyl)- + testExamples: + - qInput: "UniProtKB:Q16539" ## MAP kinase p38 alpha + oneOutput: "CHEMBL.COMPOUND:CHEMBL585902" ## AMG-548 / 4(3H)-Pyrimidinone, 2-(((2S)-2-amino-3-phenylpropyl)amino)-3-methyl-5-(2-naphthalenyl)-6-(4-pyridinyl)- treatsChembl: ## all drug_indication records have a mesh ID for the indication... - supportBatch: true @@ -1046,9 +1046,9 @@ components: source: "infores:chembl" response_mapping: "$ref": "#/components/x-bte-response-mapping/chembl-treats" - # testExamples: - # - qInput: "CHEMBL.COMPOUND:CHEMBL471737" ## IVABRADINE - # oneOutput: "MESH:D000072658" ## Non-ST Elevated Myocardial Infarction + testExamples: + - qInput: "CHEMBL.COMPOUND:CHEMBL471737" ## IVABRADINE + oneOutput: "MESH:D000072658" ## Non-ST Elevated Myocardial Infarction treatsChembl-rev: - supportBatch: true useTemplating: true @@ -1069,9 +1069,9 @@ components: source: "infores:chembl" response_mapping: "$ref": "#/components/x-bte-response-mapping/chembl" - # testExamples: - # - qInput: "MESH:D014376" ## Tuberculosis - # oneOutput: "CHEMBL.COMPOUND:CHEMBL1441" ## ETHIONAMIDE + testExamples: + - qInput: "MESH:D014376" ## Tuberculosis + oneOutput: "CHEMBL.COMPOUND:CHEMBL1441" ## ETHIONAMIDE ## DrugCentral source ## Not annotating: ## - drugcentral.approval (node properties?) @@ -1155,9 +1155,9 @@ components: source: "infores:drugcentral" response_mapping: "$ref": "#/components/x-bte-response-mapping/drugcentral-bioactivity" - # testExamples: - # - qInput: "UMLS:C1452152" ## ingenol mebutate - # oneOutput: "UniProtKB:Q05655" ## PRKCD + testExamples: + - qInput: "UMLS:C1452152" ## ingenol mebutate + oneOutput: "UniProtKB:Q05655" ## PRKCD drugcentral-bioactivity-agonist: ## right now "PARTIAL AGONIST" (14 records) is also included because of partial matching, see https://github.com/biothings/mychem.info/issues/153 ## 563 records: https://mychem.info/v1/query?q=%20_exists_:%22drugcentral.bioactivity.uniprot.uniprot_id%22%20AND%20_exists_:%22drugcentral.xrefs.umlscui%22%20AND%20drugcentral.bioactivity.action_type:%22AGONIST%22&fields=drugcentral @@ -1198,9 +1198,9 @@ components: source: "infores:drugcentral" response_mapping: "$ref": "#/components/x-bte-response-mapping/drugcentral-bioactivity" - # testExamples: - # - qInput: "UMLS:C0030071" ## oxymetazoline - # oneOutput: "UniProtKB:P35348" ## ADRA1A + testExamples: + - qInput: "UMLS:C0030071" ## oxymetazoline + oneOutput: "UniProtKB:P35348" ## ADRA1A drugcentral-bioactivity-antagonist: ## right now "ALLOSTERIC ANTAGONIST" (1 chem / 6+ genes) is also included because of partial matching, see https://github.com/biothings/mychem.info/issues/153 ## 382 records: https://mychem.info/v1/query?q=%20_exists_:%22drugcentral.bioactivity.uniprot.uniprot_id%22%20AND%20_exists_:%22drugcentral.xrefs.umlscui%22%20AND%20drugcentral.bioactivity.action_type:%22ANTAGONIST%22&fields=drugcentral @@ -1241,9 +1241,9 @@ components: source: "infores:drugcentral" response_mapping: "$ref": "#/components/x-bte-response-mapping/drugcentral-bioactivity" - # testExamples: - # - qInput: "UMLS:C0724441" ## yohimbine - # oneOutput: "UniProtKB:P41595" ## HTR2B + testExamples: + - qInput: "UMLS:C0724441" ## yohimbine + oneOutput: "UniProtKB:P41595" ## HTR2B drugcentral-bioactivity-antibody: ## 121 records: https://mychem.info/v1/query?q=%20_exists_:%22drugcentral.bioactivity.uniprot.uniprot_id%22%20AND%20_exists_:%22drugcentral.xrefs.umlscui%22%20AND%20drugcentral.bioactivity.action_type:%22ANTIBODY%20BINDING%22&fields=drugcentral - supportBatch: true @@ -1283,9 +1283,9 @@ components: source: "infores:drugcentral" response_mapping: "$ref": "#/components/x-bte-response-mapping/drugcentral-bioactivity" - # testExamples: - # - qInput: "UMLS:C1172734" ## natalizumab - # oneOutput: "UniProtKB:P05556" ## ITGA4 + testExamples: + - qInput: "UMLS:C1172734" ## natalizumab + oneOutput: "UniProtKB:P05556" ## ITGA4 drugcentral-bioactivity-antisense-inhibitor: ## 9 records: https://mychem.info/v1/query?q=%20_exists_:%22drugcentral.bioactivity.uniprot.uniprot_id%22%20AND%20_exists_:%22drugcentral.xrefs.umlscui%22%20AND%20drugcentral.bioactivity.action_type:%22ANTISENSE%20INHIBITOR%22&fields=drugcentral - supportBatch: true @@ -1324,9 +1324,9 @@ components: source: "infores:drugcentral" response_mapping: "$ref": "#/components/x-bte-response-mapping/drugcentral-bioactivity" - # testExamples: - # - qInput: "UMLS:C4726970" ## volanesorsen - # oneOutput: "UniProtKB:P02656" ## APOC3 + testExamples: + - qInput: "UMLS:C4726970" ## volanesorsen + oneOutput: "UniProtKB:P02656" ## APOC3 drugcentral-bioactivity-binding-agent: ## 22 records: https://mychem.info/v1/query?q=%20_exists_:%22drugcentral.bioactivity.uniprot.uniprot_id%22%20AND%20_exists_:%22drugcentral.xrefs.umlscui%22%20AND%20drugcentral.bioactivity.action_type:%22BINDING%20AGENT%22&fields=drugcentral - supportBatch: true @@ -1360,9 +1360,9 @@ components: source: "infores:drugcentral" response_mapping: "$ref": "#/components/x-bte-response-mapping/drugcentral-bioactivity" - # testExamples: - # - qInput: "UMLS:C2346797" ## moxetumomab pasudotox - # oneOutput: "UniProtKB:P20273" ## CD22 + testExamples: + - qInput: "UMLS:C2346797" ## moxetumomab pasudotox + oneOutput: "UniProtKB:P20273" ## CD22 drugcentral-bioactivity-blockage: ## includes action_type = ## - "BLOCKER", 152 records: https://mychem.info/v1/query?q=%20_exists_:%22drugcentral.bioactivity.uniprot.uniprot_id%22%20AND%20_exists_:%22drugcentral.xrefs.umlscui%22%20AND%20drugcentral.bioactivity.action_type:%22BLOCKER%22&fields=drugcentral @@ -1401,13 +1401,13 @@ components: source: "infores:drugcentral" response_mapping: "$ref": "#/components/x-bte-response-mapping/drugcentral-bioactivity" - # testExamples: - ## for BLOCKER - # - qInput: "UMLS:C0242375" ## lidocaine - # oneOutput: "UniProtKB:Q99250" ## SCN2A - ## for GATING INHIBITOR - # - qInput: "UMLS:C0028066" ## nifedipine - # oneOutput: "UniProtKB:Q01668" ## CACNA1D + testExamples: + # for BLOCKER + - qInput: "UMLS:C0242375" ## lidocaine + oneOutput: "UniProtKB:Q99250" ## SCN2A + # for GATING INHIBITOR + - qInput: "UMLS:C0028066" ## nifedipine + oneOutput: "UniProtKB:Q01668" ## CACNA1D drugcentral-bioactivity-inhibitor: ## 793 records: https://mychem.info/v1/query?q=%20_exists_:%22drugcentral.bioactivity.uniprot.uniprot_id%22%20AND%20_exists_:%22drugcentral.xrefs.umlscui%22%20AND%20drugcentral.bioactivity.action_type:%22INHIBITOR%22&fields=drugcentral - supportBatch: true @@ -1447,9 +1447,9 @@ components: source: "infores:drugcentral" response_mapping: "$ref": "#/components/x-bte-response-mapping/drugcentral-bioactivity" - # testExamples: - # - qInput: "UMLS:C2703109" ## ponatinib - # oneOutput: "UniProtKB:P35968" ## KDR + testExamples: + - qInput: "UMLS:C2703109" ## ponatinib + oneOutput: "UniProtKB:P35968" ## KDR drugcentral-bioactivity-modulator: ## includes action_type = ## - ALLOSTERIC MODULATOR: <= 61 chem/records @@ -1486,13 +1486,13 @@ components: source: "infores:drugcentral" response_mapping: "$ref": "#/components/x-bte-response-mapping/drugcentral-bioactivity" - # testExamples: - ## for ALLOSTERIC MODULATOR - # - qInput: "UMLS:C0109102" ## cervoxan - # oneOutput: "UniProtKB:P20309" ## CHRM3 - ## for MODULATOR - # - qInput: "UMLS:C4548896" ## siponimod - # oneOutput: "UniProtKB:P21453" ## S1PR1 + testExamples: + # for ALLOSTERIC MODULATOR + - qInput: "UMLS:C0109102" ## cervoxan + oneOutput: "UniProtKB:P20309" ## CHRM3 + # for MODULATOR + - qInput: "UMLS:C4548896" ## siponimod + oneOutput: "UniProtKB:P21453" ## S1PR1 drugcentral-bioactivity-opener: ## 15 records: https://mychem.info/v1/query?q=%20_exists_:%22drugcentral.bioactivity.uniprot.uniprot_id%22%20AND%20_exists_:%22drugcentral.xrefs.umlscui%22%20AND%20drugcentral.bioactivity.action_type:%22OPENER%22&fields=drugcentral - supportBatch: true @@ -1531,9 +1531,9 @@ components: source: "infores:drugcentral" response_mapping: "$ref": "#/components/x-bte-response-mapping/drugcentral-bioactivity" - # testExamples: - # - qInput: "UMLS:C3265565" ## sevoflurane - # oneOutput: "UniProtKB:O95069" ## KCNK2 + testExamples: + - qInput: "UMLS:C3265565" ## sevoflurane + oneOutput: "UniProtKB:O95069" ## KCNK2 drugcentral-bioactivity-positive-allosteric-modulator: ## 44 records: https://mychem.info/v1/query?q=%20_exists_:%22drugcentral.bioactivity.uniprot.uniprot_id%22%20AND%20_exists_:%22drugcentral.xrefs.umlscui%22%20AND%20drugcentral.bioactivity.action_type:%22POSITIVE%20ALLOSTERIC%20MODULATOR%22&fields=drugcentral - supportBatch: true @@ -1573,9 +1573,9 @@ components: source: "infores:drugcentral" response_mapping: "$ref": "#/components/x-bte-response-mapping/drugcentral-bioactivity" - # testExamples: - # - qInput: "UMLS:C0072828" ## quazepam - # oneOutput: "UniProtKB:P18505" ## GABRA3 + testExamples: + - qInput: "UMLS:C0072828" ## quazepam + oneOutput: "UniProtKB:P18505" ## GABRA3 drugcentral-bioactivity-positive-modulator: ## 14 records: https://mychem.info/v1/query?q=%20_exists_:%22drugcentral.bioactivity.uniprot.uniprot_id%22%20AND%20_exists_:%22drugcentral.xrefs.umlscui%22%20AND%20drugcentral.bioactivity.action_type:%22POSITIVE%20MODULATOR%22&fields=drugcentral - supportBatch: true @@ -1615,9 +1615,9 @@ components: source: "infores:drugcentral" response_mapping: "$ref": "#/components/x-bte-response-mapping/drugcentral-bioactivity" - # testExamples: - # - qInput: "UMLS:C4256131" ## enflurane - # oneOutput: "UniProtKB:P23415" ## GLRA1 + testExamples: + - qInput: "UMLS:C4256131" ## enflurane + oneOutput: "UniProtKB:P23415" ## GLRA1 drugcentral-bioactivity-rev: - supportBatch: true useTemplating: true @@ -1641,9 +1641,9 @@ components: source: "infores:drugcentral" response_mapping: "$ref": "#/components/x-bte-response-mapping/drugcentral-umls" - # testExamples: - # - qInput: "UniProtKB:Q07912" ## TNK2 - # oneOutput: "UMLS:C4086264" ## entrectinib + testExamples: + - qInput: "UniProtKB:Q07912" ## TNK2 + oneOutput: "UMLS:C4086264" ## entrectinib drugcentral-contraindication: - supportBatch: true useTemplating: true @@ -1669,9 +1669,9 @@ components: source: "infores:drugcentral" response_mapping: "$ref": "#/components/x-bte-response-mapping/drugcentral-contraindication" - # testExamples: - # - qInput: "CHEMBL.COMPOUND:CHEMBL1441" ## ethioniamide - # oneOutput: "UMLS:C0001973" ## Alcoholism + testExamples: + - qInput: "CHEMBL.COMPOUND:CHEMBL1441" ## ethioniamide + oneOutput: "UMLS:C0001973" ## Alcoholism drugcentral-contraindication-rev: - supportBatch: true useTemplating: true @@ -1692,9 +1692,9 @@ components: source: "infores:drugcentral" response_mapping: "$ref": "#/components/x-bte-response-mapping/drugcentral-chembl" - # testExamples: - # - qInput: "UMLS:C0020621" ## Hypokalemia - # oneOutput: "CHEMBL.COMPOUND:CHEMBL471" ## sotalol + testExamples: + - qInput: "UMLS:C0020621" ## Hypokalemia + oneOutput: "CHEMBL.COMPOUND:CHEMBL471" ## sotalol drugcentral-indication: ## note: some records don't have the needed output IDs...only a concept name... - supportBatch: true @@ -1723,9 +1723,9 @@ components: source: "infores:drugcentral" response_mapping: "$ref": "#/components/x-bte-response-mapping/drugcentral-indication" - # testExamples: - # - qInput: "UNII:17VGG92R23" ## pemafibrate - # oneOutput: "UMLS:C0242339" ## Dyslipidemia + testExamples: + - qInput: "UNII:17VGG92R23" ## pemafibrate + oneOutput: "UMLS:C0242339" ## Dyslipidemia drugcentral-indication-rev: - supportBatch: true useTemplating: true @@ -1748,10 +1748,9 @@ components: source: "infores:drugcentral" response_mapping: "$ref": "#/components/x-bte-response-mapping/drugcentral-unii" - # testExamples: - # - qInput: "UMLS:C0234974" ## Simple partial seizure - # oneOutput: "UNII:44YRR34555" ## keppra / Levetiracetam - ## edit, try this out once spaces in fields are fixed (next MyChem release) + testExamples: + - qInput: "UMLS:C0234974" ## Simple partial seizure + oneOutput: "UNII:44YRR34555" ## keppra / Levetiracetam drugcentral-offlabel: - supportBatch: true useTemplating: true @@ -1778,9 +1777,9 @@ components: source: "infores:drugcentral" response_mapping: "$ref": "#/components/x-bte-response-mapping/drugcentral-offlabel" - # testExamples: - # - qInput: "CHEMBL.COMPOUND:CHEMBL11" ## imipramine - # oneOutput: "UMLS:C0027796" ## Neuropathic pain / neuralgia + testExamples: + - qInput: "CHEMBL.COMPOUND:CHEMBL11" ## imipramine + oneOutput: "UMLS:C0027796" ## Neuropathic pain / neuralgia drugcentral-offlabel-rev: - supportBatch: true useTemplating: true @@ -1801,9 +1800,9 @@ components: source: "infores:drugcentral" response_mapping: "$ref": "#/components/x-bte-response-mapping/drugcentral-chembl" - # testExamples: - # - qInput: "UMLS:C0149931" ## Migraine - # oneOutput: "CHEMBL.COMPOUND:CHEMBL2105833" ## octodrine + testExamples: + - qInput: "UMLS:C0149931" ## Migraine + oneOutput: "CHEMBL.COMPOUND:CHEMBL2105833" ## octodrine drugcentral-adverseEvent: ## - chose to map to Disease semantic type since I saw SRI map some MEDDRA IDs to Disease... ## https://nodenormalization-sri.renci.org/1.2/get_normalized_nodes?curie=MEDDRA%3A10035528&conflate=true @@ -1841,9 +1840,9 @@ components: source: "infores:drugcentral" response_mapping: "$ref": "#/components/x-bte-response-mapping/drugcentral-adverseEvent" - # testExamples: - # - qInput: "CHEMBL.COMPOUND:CHEMBL440" ## thiamylal sodium - # oneOutput: "MEDDRA:10006093" ## Bradycardia + testExamples: + - qInput: "CHEMBL.COMPOUND:CHEMBL440" ## thiamylal sodium + oneOutput: "MEDDRA:10006093" ## Bradycardia drugcentral-adverseEvent-rev: - supportBatch: true useTemplating: true @@ -1865,9 +1864,9 @@ components: source: "infores:drugcentral" response_mapping: "$ref": "#/components/x-bte-response-mapping/drugcentral-chembl" - # testExamples: - # - qInput: "MEDDRA:10040108" ## Serotonin syndrome - # oneOutput: "CHEMBL.COMPOUND:CHEMBL395091" ## esketamine HCl + testExamples: + - qInput: "MEDDRA:10040108" ## Serotonin syndrome + oneOutput: "CHEMBL.COMPOUND:CHEMBL395091" ## esketamine HCl fdaOrphanData: - supportBatch: true useTemplating: true @@ -1908,9 +1907,9 @@ components: source: "infores:drugcentral" response_mapping: "$ref": "#/components/x-bte-response-mapping/fdaOrphanDrug" - # testExamples: - # - qInput: "PUBCHEM.COMPOUND:24889392" ## quizartinib - # oneOutput: "UMLS:C0023467" ## Acute myeloid leukemia + testExamples: + - qInput: "PUBCHEM.COMPOUND:24889392" ## quizartinib + oneOutput: "UMLS:C0023467" ## Acute myeloid leukemia fdaOrphanData-rev: - supportBatch: true useTemplating: true @@ -1932,6 +1931,6 @@ components: source: "infores:drugcentral" response_mapping: "$ref": "#/components/x-bte-response-mapping/fdaOrphanDrug-pubchemCompound" - # testExamples: - # - qInput: "UMLS:C1412063" ## Stargardt disease - # oneOutput: "PUBCHEM.COMPOUND:25221720" ## emixustat + testExamples: + - qInput: "UMLS:C1412063" ## Stargardt disease + oneOutput: "PUBCHEM.COMPOUND:25221720" ## emixustat diff --git a/mydisease.info/smartapi.yaml b/mydisease.info/smartapi.yaml index 5fe58113..2dee7ac0 100644 --- a/mydisease.info/smartapi.yaml +++ b/mydisease.info/smartapi.yaml @@ -722,9 +722,9 @@ components: source: "infores:disgenet" response_mapping: "$ref": "#/components/x-bte-response-mapping/disease-gene" - # testExamples: - # - qInput: "UMLS:C0023264" ## Leigh Disease - # oneOutput: "NCBIGene:4694" ## NDUFA1 + testExamples: + - qInput: "UMLS:C0023264" ## Leigh Disease + oneOutput: "NCBIGene:4694" ## NDUFA1 disease-variant: ## 11200 / 12605 disgenet.variants_related_to_disease records have disgenet.xrefs.umls - supportBatch: true @@ -759,9 +759,9 @@ components: source: "infores:disgenet" response_mapping: "$ref": "#/components/x-bte-response-mapping/disease-variant" - # testExamples: - # - qInput: "UMLS:C0023264" ## Leigh Disease - # oneOutput: "DBSNP:rs1161932777" + testExamples: + - qInput: "UMLS:C0023264" ## Leigh Disease + oneOutput: "DBSNP:rs1161932777" ## for hpo-annotation-based operations: ## - currently, the mydisease parser for hpo maps the resources' IDs (OMIM or orphanet) to MONDO. ## If two IDs (ex: OMIM:218340 and orphanet:1777 for Temtamy syndrome) map to the same MONDO ID, it looks like only the OMIM data was kept. @@ -817,9 +817,9 @@ components: source: "infores:hpo-annotations" response_mapping: "$ref": "#/components/x-bte-response-mapping/disease-phenotype" - # testExamples: - # - qInput: "OMIM:246900" ## Dihydrolipoamide Dehydrogenase Deficiency - # oneOutput: "HP:0001254" ## Lethargy + testExamples: + - qInput: "OMIM:246900" ## Dihydrolipoamide Dehydrogenase Deficiency + oneOutput: "HP:0001254" ## Lethargy disease-phenotype2: - supportBatch: true useTemplating: true @@ -866,9 +866,9 @@ components: source: "infores:hpo-annotations" response_mapping: "$ref": "#/components/x-bte-response-mapping/disease-phenotype" - # testExamples: - # - qInput: "ORPHANET:881" ## Turner Syndrome - # oneOutput: "HP:0000137" ## Abnormality of the ovary + testExamples: + - qInput: "ORPHANET:881" ## Turner Syndrome + oneOutput: "HP:0000137" ## Abnormality of the ovary ## for ctd-based operations: ## - when the mydisease parser maps the resources' IDs to MONDO, are there situations where a MESH and a OMIM ID map to the same MONDO? ## If so, 1) Is only one of them kept?, @@ -910,9 +910,9 @@ components: source: "infores:ctd" response_mapping: "$ref": "#/components/x-bte-response-mapping/disease-chemical" - # testExamples: - # - qInput: "MESH:D009102" ## Multiple Organ Failure - # oneOutput: "MESH:C448659" ## Geldanamycin, monohydrochloride + testExamples: + - qInput: "MESH:D009102" ## Multiple Organ Failure + oneOutput: "MESH:C448659" ## Geldanamycin, monohydrochloride disease-chemical2: - supportBatch: true useTemplating: true @@ -941,9 +941,9 @@ components: source: "infores:ctd" response_mapping: "$ref": "#/components/x-bte-response-mapping/disease-chemical" - # testExamples: - # - qInput: "OMIM:613290" ## hearing loss, cisplatin-induced, susceptibility to - # oneOutput: "MESH:D002945" ## Cisplatin + testExamples: + - qInput: "OMIM:613290" ## hearing loss, cisplatin-induced, susceptibility to + oneOutput: "MESH:D002945" ## Cisplatin ########################################################################## ## with "reverse" querying, we will pull up ALL info under the disease, rather than under a specific record... ## so we can't retrieve the subset of data for the specific gene / variant / etc's record @@ -969,9 +969,9 @@ components: source: "infores:disgenet" response_mapping: "$ref": "#/components/x-bte-response-mapping/umls" - # testExamples: - # - qInput: "NCBIGene:1629" ## DBT - # oneOutput: "UMLS:C3658290" ## Drug-Induced Acute Liver Injury + testExamples: + - qInput: "NCBIGene:1629" ## DBT + oneOutput: "UMLS:C3658290" ## Drug-Induced Acute Liver Injury variant-disease: - supportBatch: true useTemplating: true @@ -994,9 +994,9 @@ components: source: "infores:disgenet" response_mapping: "$ref": "#/components/x-bte-response-mapping/umls" - # testExamples: - # - qInput: "DBSNP:rs78655421" - # oneOutput: "UMLS:C4021107" ## Non-obstructive azoospermia + testExamples: + - qInput: "DBSNP:rs78655421" + oneOutput: "UMLS:C4021107" ## Non-obstructive azoospermia phenotype-disease: - supportBatch: true useTemplating: true @@ -1019,9 +1019,9 @@ components: source: "infores:hpo-annotations" response_mapping: "$ref": "#/components/x-bte-response-mapping/omim" - # testExamples: - # - qInput: "HP:0000224" ## Hypogeusia - # oneOutput: "OMIM:201300" ## Neuropathy, hereditary sensory and autonomic, type II + testExamples: + - qInput: "HP:0000224" ## Hypogeusia + oneOutput: "OMIM:201300" ## Neuropathy, hereditary sensory and autonomic, type II phenotype-disease2: - supportBatch: true useTemplating: true @@ -1044,9 +1044,9 @@ components: source: "infores:hpo-annotations" response_mapping: "$ref": "#/components/x-bte-response-mapping/orphanet" - # testExamples: - # - qInput: "HP:0000224" ## Hypogeusia - # oneOutput: "ORPHANET:99857" ## Secondary Syringomyelia + testExamples: + - qInput: "HP:0000224" ## Hypogeusia + oneOutput: "ORPHANET:99857" ## Secondary Syringomyelia chemical-disease: - supportBatch: true useTemplating: true @@ -1069,9 +1069,9 @@ components: source: "infores:ctd" response_mapping: "$ref": "#/components/x-bte-response-mapping/ctd-mesh-disease" - # testExamples: - # - qInput: "MESH:D000655" ## Amodiaquine - # oneOutput: "MESH:D008288" ## Malaria (maps to MONDO:0005136) + testExamples: + - qInput: "MESH:D000655" ## Amodiaquine + oneOutput: "MESH:D008288" ## Malaria (maps to MONDO:0005136) chemical-disease2: - supportBatch: true useTemplating: true @@ -1094,9 +1094,9 @@ components: source: "infores:ctd" response_mapping: "$ref": "#/components/x-bte-response-mapping/ctd-omim-disease" - # testExamples: - # - qInput: "MESH:D000655" ## Amodiaquine - # oneOutput: "OMIM:248310" ## PLASMODIUM FALCIPARUM BLOOD INFECTION LEVEL (maps to MONDO:0009553) + testExamples: + - qInput: "MESH:D000655" ## Amodiaquine + oneOutput: "OMIM:248310" ## PLASMODIUM FALCIPARUM BLOOD INFECTION LEVEL (maps to MONDO:0009553) ############################################################################ ## - there's also disease_ontology info (ancestors, children, descendants, parents) ## - there's also mondo info (ancestors, descendants) @@ -1129,9 +1129,9 @@ components: source: "infores:mondo" response_mapping: "$ref": "#/components/x-bte-response-mapping/has_subclass" - # testExamples: - # - qInput: "MONDO:0002494" ## substance-related disorder - # oneOutput: "MONDO:0021698" ## alcohol-related disorders + testExamples: + - qInput: "MONDO:0002494" ## substance-related disorder + oneOutput: "MONDO:0021698" ## alcohol-related disorders subclass_of: - supportBatch: true useTemplating: true @@ -1155,9 +1155,9 @@ components: source: "infores:mondo" response_mapping: "$ref": "#/components/x-bte-response-mapping/subclass_of" - # testExamples: - # - qInput: "MONDO:0002494" ## substance-related disorder - # oneOutput: "MONDO:0002025" ## psychiatric disorder + testExamples: + - qInput: "MONDO:0002494" ## substance-related disorder + oneOutput: "MONDO:0002025" ## psychiatric disorder predisposes_towards: - supportBatch: true useTemplating: true @@ -1181,9 +1181,9 @@ components: source: "infores:mondo" response_mapping: "$ref": "#/components/x-bte-response-mapping/predisposes_towards" - # testExamples: - # - qInput: "MONDO:0010940" ## inherited susceptibility to asthma - # oneOutput: "MONDO:0004979" ## asthma + testExamples: + - qInput: "MONDO:0010940" ## inherited susceptibility to asthma + oneOutput: "MONDO:0004979" ## asthma predisposes_towards-rev: - supportBatch: true useTemplating: true @@ -1208,9 +1208,9 @@ components: source: "infores:mondo" response_mapping: "$ref": "#/components/x-bte-response-mapping/mondo" - # testExamples: - # - qInput: "MONDO:0004979" ## asthma - # oneOutput: "MONDO:0010940" ## inherited susceptibility to asthma + testExamples: + - qInput: "MONDO:0004979" ## asthma + oneOutput: "MONDO:0010940" ## inherited susceptibility to asthma disease_shares_features_of: - supportBatch: true useTemplating: true @@ -1234,9 +1234,9 @@ components: source: "infores:mondo" response_mapping: "$ref": "#/components/x-bte-response-mapping/disease_shares_features_of" - # testExamples: - # - qInput: "MONDO:0008711" ## Goodman syndrome - # oneOutput: "MONDO:0019012" ## Carpenter syndrome + testExamples: + - qInput: "MONDO:0008711" ## Goodman syndrome + oneOutput: "MONDO:0019012" ## Carpenter syndrome disease_shares_features_of-rev: ## checked and inverse relationship doesn't exist already in the data ## for example, the record for Carpenter syndrome doesn't have disease_shares_features_of @@ -1261,9 +1261,9 @@ components: source: "infores:mondo" response_mapping: "$ref": "#/components/x-bte-response-mapping/mondo" - # testExamples: - # - qInput: "MONDO:0019012" ## Carpenter syndrome - # oneOutput: "MONDO:0008711" ## Goodman syndrome + testExamples: + - qInput: "MONDO:0019012" ## Carpenter syndrome + oneOutput: "MONDO:0008711" ## Goodman syndrome disease_has_major_feature: - supportBatch: true useTemplating: true @@ -1286,9 +1286,9 @@ components: source: "infores:mondo" response_mapping: "$ref": "#/components/x-bte-response-mapping/disease_has_major_feature" - # testExamples: - # - qInput: "MONDO:0015140" ## early-onset autosomal dominant Alzheimer disease - # oneOutput: "MONDO:0001627" ## dementia (disease) + testExamples: + - qInput: "MONDO:0015140" ## early-onset autosomal dominant Alzheimer disease + oneOutput: "MONDO:0001627" ## dementia (disease) disease_has_major_feature-rev: - supportBatch: true useTemplating: true @@ -1311,9 +1311,9 @@ components: source: "infores:mondo" response_mapping: "$ref": "#/components/x-bte-response-mapping/mondo" - # testExamples: - # - qInput: "MONDO:0001627" ## dementia (disease) - # oneOutput: "MONDO:0015140" ## early-onset autosomal dominant Alzheimer disease + testExamples: + - qInput: "MONDO:0001627" ## dementia (disease) + oneOutput: "MONDO:0015140" ## early-onset autosomal dominant Alzheimer disease disease_has_feature: - supportBatch: true useTemplating: true @@ -1336,9 +1336,9 @@ components: source: "infores:mondo" response_mapping: "$ref": "#/components/x-bte-response-mapping/disease_has_feature" - # testExamples: - # - qInput: "MONDO:0005796" ## HIV enteropathy - # oneOutput: "MONDO:0005020" ## intestinal disease + testExamples: + - qInput: "MONDO:0005796" ## HIV enteropathy + oneOutput: "MONDO:0005020" ## intestinal disease disease_has_feature-rev: - supportBatch: true useTemplating: true @@ -1361,9 +1361,9 @@ components: source: "infores:mondo" response_mapping: "$ref": "#/components/x-bte-response-mapping/mondo" - # testExamples: - # - qInput: "MONDO:0005020" ## intestinal disease - # oneOutput: "MONDO:0005796" ## HIV enteropathy + testExamples: + - qInput: "MONDO:0005020" ## intestinal disease + oneOutput: "MONDO:0005796" ## HIV enteropathy disease_causes_feature: - supportBatch: true useTemplating: true @@ -1386,9 +1386,9 @@ components: source: "infores:mondo" response_mapping: "$ref": "#/components/x-bte-response-mapping/disease_causes_feature" - # testExamples: - # - qInput: "MONDO:0000490" ## glomerulosclerosis - # oneOutput: "MONDO:0001106" ## kidney failure + testExamples: + - qInput: "MONDO:0000490" ## glomerulosclerosis + oneOutput: "MONDO:0001106" ## kidney failure disease_causes_feature-rev: - supportBatch: true useTemplating: true @@ -1411,9 +1411,9 @@ components: source: "infores:mondo" response_mapping: "$ref": "#/components/x-bte-response-mapping/mondo" - # testExamples: - # - qInput: "MONDO:0001106" ## kidney failure - # oneOutput: "MONDO:0000490" ## glomerulosclerosis + testExamples: + - qInput: "MONDO:0001106" ## kidney failure + oneOutput: "MONDO:0000490" ## glomerulosclerosis disease_arises_from_feature: - supportBatch: true useTemplating: true @@ -1436,9 +1436,9 @@ components: source: "infores:mondo" response_mapping: "$ref": "#/components/x-bte-response-mapping/disease_arises_from_feature" - # testExamples: - # - qInput: "MONDO:0009346" ## histidinuria due to a renal tubular defect - # oneOutput: "MONDO:0021568" ## renal tubule disease + testExamples: + - qInput: "MONDO:0009346" ## histidinuria due to a renal tubular defect + oneOutput: "MONDO:0021568" ## renal tubule disease disease_arises_from_feature-rev: - supportBatch: true useTemplating: true @@ -1459,6 +1459,6 @@ components: source: "infores:mondo" response_mapping: "$ref": "#/components/x-bte-response-mapping/mondo" - # testExamples: - # - qInput: "MONDO:0021568" ## renal tubule disease - # oneOutput: "MONDO:0009346" ## histidinuria due to a renal tubular defect + testExamples: + - qInput: "MONDO:0021568" ## renal tubule disease + oneOutput: "MONDO:0009346" ## histidinuria due to a renal tubular defect diff --git a/mygene.info/openapi_full.yml b/mygene.info/openapi_full.yml index e589842c..d87fc4e0 100644 --- a/mygene.info/openapi_full.yml +++ b/mygene.info/openapi_full.yml @@ -734,9 +734,9 @@ components: source: "infores:reactome" response_mapping: $ref: "#/components/x-bte-response-mapping/entrezgene" - # testExamples: - # - qInput: "REACT:R-HSA-70895" ## Branched-chain amino acid catabolism - # oneOutput: "NCBIGene:10295" ## BCKDK + testExamples: + - qInput: "REACT:R-HSA-70895" ## Branched-chain amino acid catabolism + oneOutput: "NCBIGene:10295" ## BCKDK PathwayHasGene2: - supportBatch: true useTemplating: true @@ -759,9 +759,9 @@ components: source: "infores:cpdb" ## ConsensusPathDB response_mapping: $ref: "#/components/x-bte-response-mapping/entrezgene-keggname" - # testExamples: - # - qInput: "KEGG.PATHWAY:hsa00120" ## Primary bile acid biosynthesis - Homo sapiens (human) - # oneOutput: "NCBIGene:8309" ## ACOX2 + testExamples: + - qInput: "KEGG.PATHWAY:hsa00120" ## Primary bile acid biosynthesis - Homo sapiens (human) + oneOutput: "NCBIGene:8309" ## ACOX2 PathwayHasGene3: - supportBatch: true useTemplating: true @@ -784,9 +784,9 @@ components: source: "infores:cpdb" ## ConsensusPathDB response_mapping: $ref: "#/components/x-bte-response-mapping/entrezgene-wikiname" - # testExamples: - # - qInput: "WIKIPATHWAYS:WP2034" ## Leptin signaling pathway - # oneOutput: "NCBIGene:3953" ## LEPR + testExamples: + - qInput: "WIKIPATHWAYS:WP2034" ## Leptin signaling pathway + oneOutput: "NCBIGene:3953" ## LEPR PathwayHasGene4: - supportBatch: true useTemplating: true @@ -809,9 +809,9 @@ components: source: "infores:cpdb" ## ConsensusPathDB response_mapping: $ref: "#/components/x-bte-response-mapping/entrezgene-biocartaname" - # testExamples: - # - qInput: "BIOCARTA:raspathway" - # oneOutput: "NCBIGene:3265" ## HRAS + testExamples: + - qInput: "BIOCARTA:raspathway" + oneOutput: "NCBIGene:3265" ## HRAS involvedInPathway1: ## using Reactome, KEGG, Wikipathways, Biocarta - supportBatch: true useTemplating: true @@ -835,9 +835,9 @@ components: source: "infores:reactome" response_mapping: $ref: "#/components/x-bte-response-mapping/reactomePathway" - # testExamples: - # - qInput: "NCBIGene:1629" ## DBT - # oneOutput: "REACT:R-HSA-70895" ## Branched-chain amino acid catabolism + testExamples: + - qInput: "NCBIGene:1629" ## DBT + oneOutput: "REACT:R-HSA-70895" ## Branched-chain amino acid catabolism involvedInPathway2: - supportBatch: true useTemplating: true @@ -861,9 +861,9 @@ components: source: "infores:cpdb" ## ConsensusPathDB response_mapping: $ref: "#/components/x-bte-response-mapping/keggPathway" - # testExamples: - # - qInput: "NCBIGene:1629" ## DBT - # oneOutput: "KEGG.PATHWAY:hsa00280" ## Valine, leucine and isoleucine degradation - Homo sapiens (human) + testExamples: + - qInput: "NCBIGene:1629" ## DBT + oneOutput: "KEGG.PATHWAY:hsa00280" ## Valine, leucine and isoleucine degradation - Homo sapiens (human) involvedInPathway3: - supportBatch: true useTemplating: true @@ -887,9 +887,9 @@ components: source: "infores:cpdb" ## ConsensusPathDB response_mapping: $ref: "#/components/x-bte-response-mapping/wikipathway" - # testExamples: - # - qInput: "NCBIGene:8309" ## ACOX2 - # oneOutput: "WIKIPATHWAYS:WP3942" ## PPAR signaling pathway + testExamples: + - qInput: "NCBIGene:8309" ## ACOX2 + oneOutput: "WIKIPATHWAYS:WP3942" ## PPAR signaling pathway involvedInPathway4: - supportBatch: true useTemplating: true @@ -913,9 +913,9 @@ components: source: "infores:cpdb" ## ConsensusPathDB response_mapping: $ref: "#/components/x-bte-response-mapping/biocarta" - # testExamples: - # - qInput: "NCBIGene:5608" ## MAP2K6 - # oneOutput: "BIOCARTA:p38mapkpathway" ## p38 mapk signaling pathway + testExamples: + - qInput: "NCBIGene:5608" ## MAP2K6 + oneOutput: "BIOCARTA:p38mapkpathway" ## p38 mapk signaling pathway involvedInBP: - supportBatch: true useTemplating: true @@ -945,9 +945,9 @@ components: source: "infores:ncbi-gene" ## which got from GO Annotations... response_mapping: $ref: "#/components/x-bte-response-mapping/biologicalProcess" - # testExamples: - # - qInput: "NCBIGene:632" ## BGLAP - # oneOutput: "GO:0001501" ## skeletal system development + testExamples: + - qInput: "NCBIGene:632" ## BGLAP + oneOutput: "GO:0001501" ## skeletal system development BPToGene: - supportBatch: true useTemplating: true @@ -970,9 +970,9 @@ components: source: "infores:ncbi-gene" ## which got from GO Annotations... response_mapping: $ref: "#/components/x-bte-response-mapping/entrezgene" - # testExamples: - # - qInput: "GO:0001501" ## skeletal system development - # oneOutput: "NCBIGene:5741" ## PTH + testExamples: + - qInput: "GO:0001501" ## skeletal system development + oneOutput: "NCBIGene:5741" ## PTH enablesMF: - supportBatch: true useTemplating: true @@ -1002,9 +1002,9 @@ components: source: "infores:ncbi-gene" ## which got from GO Annotations... response_mapping: $ref: "#/components/x-bte-response-mapping/molecularFunction" - # testExamples: - # - qInput: "NCBIGene:1629" ## DBT - # oneOutput: "GO:0031405" ## lipoic acid binding + testExamples: + - qInput: "NCBIGene:1629" ## DBT + oneOutput: "GO:0031405" ## lipoic acid binding MFToGene: - supportBatch: true useTemplating: true @@ -1027,9 +1027,9 @@ components: source: "infores:ncbi-gene" ## which got from GO Annotations... response_mapping: $ref: "#/components/x-bte-response-mapping/entrezgene" - # testExamples: - # - qInput: "GO:0008147" ## structural constituent of bone - # oneOutput: "NCBIGene:632" ## BGLAP + testExamples: + - qInput: "GO:0008147" ## structural constituent of bone + oneOutput: "NCBIGene:632" ## BGLAP involvedInCC: - supportBatch: true useTemplating: true @@ -1059,9 +1059,9 @@ components: source: "infores:ncbi-gene" ## which got from GO Annotations... response_mapping: $ref: "#/components/x-bte-response-mapping/cellularComponent" - # testExamples: - # - qInput: "NCBIGene:5741" ## PTH - # oneOutput: "GO:0005576" ## extracellular region + testExamples: + - qInput: "NCBIGene:5741" ## PTH + oneOutput: "GO:0005576" ## extracellular region CCToGene: - supportBatch: true useTemplating: true @@ -1084,9 +1084,9 @@ components: source: "infores:ncbi-gene" ## which got from GO Annotations... response_mapping: $ref: "#/components/x-bte-response-mapping/entrezgene" - # testExamples: - # - qInput: "GO:0033268" ## node of Ranvier - # oneOutput: "NCBIGene:6326" ## SCN2A + testExamples: + - qInput: "GO:0033268" ## node of Ranvier + oneOutput: "NCBIGene:6326" ## SCN2A geneToDisease: - supportBatch: true useTemplating: true @@ -1121,9 +1121,9 @@ components: source: "infores:clingen" response_mapping: $ref: "#/components/x-bte-response-mapping/clingen" - # testExamples: - # - qInput: "NCBIGene:23126" ## POGZ - # oneOutput: "MONDO:0014606" ## intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome + testExamples: + - qInput: "NCBIGene:23126" ## POGZ + oneOutput: "MONDO:0014606" ## intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome diseaseToGene: - supportBatch: true useTemplating: true @@ -1146,9 +1146,9 @@ components: source: "infores:clingen" response_mapping: $ref: "#/components/x-bte-response-mapping/entrezgene" - # testExamples: - # - qInput: "MONDO:0014606" ## intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome - # oneOutput: "NCBIGene:23126" ## POGZ + testExamples: + - qInput: "MONDO:0014606" ## intellectual disability-microcephaly-strabismus-behavioral abnormalities syndrome + oneOutput: "NCBIGene:23126" ## POGZ ## pantherdb gives orthologs and paralogs, which are both homologs. Hence we use homolog ## currently written: MGI ## Also have Ensembl (for specific non-human species) and UniprotKB (for all orthologs) @@ -1178,11 +1178,10 @@ components: source: "infores:panther" response_mapping: $ref: "#/components/x-bte-response-mapping/pantherMGI" - # testExamples: - # - qInput: "HGNC:20589" ## KCMF1 - # oneOutput: "MGI:1921537" ## Kcmf1 + testExamples: + - qInput: "HGNC:20589" ## KCMF1 + oneOutput: "MGI:1921537" ## Kcmf1 hasHomolog-MGI-rev: - ## UPDATED TO USE TEMPLATING - supportBatch: true useTemplating: true inputs: @@ -1204,9 +1203,9 @@ components: source: "infores:panther" response_mapping: $ref: "#/components/x-bte-response-mapping/pantherHGNC" - # testExamples: - # - qInput: "MGI:1916384" ## Fam25c - # oneOutput: "HGNC:23586" ## FAM25C + testExamples: + - qInput: "MGI:1916384" ## Fam25c + oneOutput: "HGNC:23586" ## FAM25C x-bte-response-mapping: entrezgene: NCBIGene: entrezgene ## no prefix diff --git a/myvariant.info/openapi_full.yml b/myvariant.info/openapi_full.yml index 67abfd69..3729edc3 100644 --- a/myvariant.info/openapi_full.yml +++ b/myvariant.info/openapi_full.yml @@ -782,9 +782,9 @@ components: response_mapping: "$ref": "#/components/x-bte-response-mapping/civic-geneDisease" ## this record has drug interaction: https://myvariant.info/v1/query?q=_exists_:%22civic.evidence_items.drug_interaction_type%22 - # testExamples: - # - qInput: "NCBIGene:1956" ## EGFR - # oneOutput: "DOID:3910" ## Lung Adenocarcinoma aka MONDO:0005061 + testExamples: + - qInput: "NCBIGene:1956" ## EGFR + oneOutput: "DOID:3910" ## Lung Adenocarcinoma aka MONDO:0005061 civic-geneDisease-rev: - supportBatch: true useTemplating: true @@ -807,9 +807,9 @@ components: response_mapping: "$ref": "#/components/x-bte-response-mapping/civic-geneOnly" ## this record has drug interaction: https://myvariant.info/v1/query?q=_exists_:%22civic.evidence_items.drug_interaction_type%22 - # testExamples: - # - qInput: "DOID:9256" ## Colorectal Cancer aka MONDO:0005575 - # oneOutput: "NCBIGene:5290" ## PIK3CA + testExamples: + - qInput: "DOID:9256" ## Colorectal Cancer aka MONDO:0005575 + oneOutput: "NCBIGene:5290" ## PIK3CA civic-variantDisease: ## out of 2648 civic records, only some (653) have the doid disease field... - supportBatch: true @@ -846,9 +846,9 @@ components: response_mapping: "$ref": "#/components/x-bte-response-mapping/civic-variantDisease" ## this record has drug interaction: https://myvariant.info/v1/query?q=_exists_:%22civic.evidence_items.drug_interaction_type%22%20AND%20_exists_:%22dbsnp.rsid%22 - # testExamples: - # - qInput: "DBSNP:rs121913521" ## chr4:g.55593613T>G in KIT - # oneOutput: "DOID:9253" ## Gastrointestinal Stromal Tumor aka MONDO:0011719 + testExamples: + - qInput: "DBSNP:rs121913521" ## chr4:g.55593613T>G in KIT + oneOutput: "DOID:9253" ## Gastrointestinal Stromal Tumor aka MONDO:0011719 civic-variantDisease-rev: - supportBatch: true useTemplating: true @@ -871,9 +871,9 @@ components: response_mapping: "$ref": "#/components/x-bte-response-mapping/dbsnp-rsid" ## this record has drug interaction: https://myvariant.info/v1/query?q=_exists_:%22civic.evidence_items.drug_interaction_type%22%20AND%20_exists_:%22dbsnp.rsid%22 - # testExamples: - # - qInput: "DOID:2671" ## Transitional Cell Carcinoma aka MONDO:0006474 - # oneOutput: "DBSNP:rs1057519803" ## chr12:g.56481922G>A in ERBB3 + testExamples: + - qInput: "DOID:2671" ## Transitional Cell Carcinoma aka MONDO:0006474 + oneOutput: "DBSNP:rs1057519803" ## chr12:g.56481922G>A in ERBB3 dbsnp-variantGene: ## note: there may be redundant results in the response ## there are 741 million records for hg38 @@ -898,9 +898,9 @@ components: response_mapping: "$ref": "#/components/x-bte-response-mapping/dbsnp-gene" ## https://myvariant.info/v1/query?q=_exists_:%22dbsnp.rsid%22%20AND%20_exists_:%22dbsnp.gene.geneid%22&fields=dbsnp&assembly=hg38 - # testExamples: - # - qInput: "DBSNP:rs770112667" ## chr10:g.14218676G>A (diff for hg19) - # oneOutput: "NCBIGene:55691" ## FRMD4A + testExamples: + - qInput: "DBSNP:rs770112667" ## chr10:g.14218676G>A (diff for hg19) + oneOutput: "NCBIGene:55691" ## FRMD4A dbsnp-variantGene-rev: - supportBatch: true useTemplating: true @@ -923,9 +923,9 @@ components: response_mapping: "$ref": "#/components/x-bte-response-mapping/dbsnp-rsid" ## https://myvariant.info/v1/query?q=_exists_:%22dbsnp.rsid%22%20AND%20_exists_:%22dbsnp.gene.geneid%22 - # testExamples: - # - qInput: "NCBIGene:102724392" ## LINC02197 - # oneOutput: "DBSNP:rs188861200" ## chr5:g.71414410C>T (diff for hg19) + testExamples: + - qInput: "NCBIGene:102724392" ## LINC02197 + oneOutput: "DBSNP:rs188861200" ## chr5:g.71414410C>T (diff for hg19) clinvar-variantGene: ## possibly redundant, with all hg38 clinvar data already covered by hg38 dbsnp.rsid <-> gene... ## > 822k records for hg38 @@ -949,9 +949,9 @@ components: source: "infores:clinvar" response_mapping: "$ref": "#/components/x-bte-response-mapping/clinvar-gene-variant-start" - # testExamples: - # - qInput: "DBSNP:rs794727661" ## chrX:g.32343175_32343176dup (diff for hg19) - # oneOutput: "NCBIGene:1756" ## DMD + testExamples: + - qInput: "DBSNP:rs794727661" ## chrX:g.32343175_32343176dup (diff for hg19) + oneOutput: "NCBIGene:1756" ## DMD clinvar-variantGene-rev: - supportBatch: true useTemplating: true @@ -973,9 +973,9 @@ components: source: "infores:clinvar" response_mapping: "$ref": "#/components/x-bte-response-mapping/clinvar-rsid" - # testExamples: - # - qInput: "NCBIGene:9231" ## DLG5 - # oneOutput: "DBSNP:rs200237878" ## chr10:g.77811216G>A + testExamples: + - qInput: "NCBIGene:9231" ## DLG5 + oneOutput: "DBSNP:rs200237878" ## chr10:g.77811216G>A ## clinvar disease ID info: ## - some conditions have no IDs, some have multiple IDs (not all have OMIM). ## - omim: 987390 (no prefix) @@ -1019,9 +1019,9 @@ components: source: "infores:clinvar" response_mapping: "$ref": "#/components/x-bte-response-mapping/clinvar-diseaseOMIM" - # testExamples: - # - qInput: "NCBIGene:55806" ## HR - # oneOutput: "OMIM:209500" ## Atrichia with papular lesions (APL) aka MONDO:0008847 + testExamples: + - qInput: "NCBIGene:55806" ## HR + oneOutput: "OMIM:209500" ## Atrichia with papular lesions (APL) aka MONDO:0008847 clinvar-gene-diseaseORPHANET: ## see original operation clinvar-gene-diseaseOMIM notes ## 826439 records for hg38 @@ -1046,9 +1046,9 @@ components: source: "infores:clinvar" response_mapping: "$ref": "#/components/x-bte-response-mapping/clinvar-diseaseORPHANET" - # testExamples: - # - qInput: "NCBIGene:106099062" ## LOC106099062 - # oneOutput: "ORPHANET:848" ## beta Thalassemia (BTHAL) aka MONDO:0019402 + testExamples: + - qInput: "NCBIGene:106099062" ## LOC106099062 + oneOutput: "ORPHANET:848" ## beta Thalassemia (BTHAL) aka MONDO:0019402 clinvar-gene-diseaseMONDO: ## see original operation clinvar-gene-diseaseOMIM notes ## 1133095 records @@ -1074,9 +1074,9 @@ components: response_mapping: "$ref": "#/components/x-bte-response-mapping/clinvar-diseaseMONDO" ## https://myvariant.info/v1/query?q=_exists_:clinvar.rcv.conditions.identifiers.mondo%20AND%20NOT%20(_exists_:clinvar.rcv.conditions.identifiers.mesh%20OR%20_exists_:clinvar.rcv.conditions.identifiers.omim%20%20OR%20_exists_:clinvar.rcv.conditions.identifiers.orphanet)%20AND%20_exists_:clinvar.gene%20AND%20clinvar.rcv.clinical_significance:Pathogenic&fields=clinvar,dbsnp.rsid - # testExamples: - # - qInput: "NCBIGene:3897" ## L1CAM - # oneOutput: "MONDO:0017140" ## L1 syndrome + testExamples: + - qInput: "NCBIGene:3897" ## L1CAM + oneOutput: "MONDO:0017140" ## L1 syndrome clinvar-gene-diseaseMESH: ## see original operation clinvar-gene-diseaseOMIM notes ## 558108 records for hg38 @@ -1101,9 +1101,9 @@ components: source: "infores:clinvar" response_mapping: "$ref": "#/components/x-bte-response-mapping/clinvar-diseaseMESH" - # testExamples: - # - qInput: "NCBIGene:4359" ## MPZ - # oneOutput: "MESH:D030342" ## Inborn genetic diseases, aka MONDO:0003847 hereditary disease + testExamples: + - qInput: "NCBIGene:4359" ## MPZ + oneOutput: "MESH:D030342" ## Inborn genetic diseases, aka MONDO:0003847 hereditary disease clinvar-gene-phenoHP: ## see original operation clinvar-gene-diseaseOMIM notes ## 141412 records @@ -1128,9 +1128,9 @@ components: source: "infores:clinvar" response_mapping: "$ref": "#/components/x-bte-response-mapping/clinvar-phenoHP" - # testExamples: - # - qInput: "NCBIGene:5314" ## PKHD1 - # oneOutput: "HP:0004719" ## Hyperechogenic kidneys + testExamples: + - qInput: "NCBIGene:5314" ## PKHD1 + oneOutput: "HP:0004719" ## Hyperechogenic kidneys clinvar-gene-diseaseOMIM-rev: - supportBatch: true useTemplating: true @@ -1152,9 +1152,9 @@ components: source: "infores:clinvar" response_mapping: "$ref": "#/components/x-bte-response-mapping/clinvar-gene" - # testExamples: - # - qInput: "OMIM:615592" ## Immunodeficiency 15 (IMD15B) - # oneOutput: "NCBIGene:3551" ## IKBKB + testExamples: + - qInput: "OMIM:615592" ## Immunodeficiency 15 (IMD15B) + oneOutput: "NCBIGene:3551" ## IKBKB clinvar-gene-diseaseORPHANET-rev: - supportBatch: true useTemplating: true @@ -1176,9 +1176,9 @@ components: source: "infores:clinvar" response_mapping: "$ref": "#/components/x-bte-response-mapping/clinvar-gene" - # testExamples: - # - qInput: "ORPHANET:827" ## Stargardt disease (FFM) - # oneOutput: "NCBIGene:5961" ## PRPH2 + testExamples: + - qInput: "ORPHANET:827" ## Stargardt disease (FFM) + oneOutput: "NCBIGene:5961" ## PRPH2 clinvar-gene-diseaseMONDO-rev: - supportBatch: true useTemplating: true @@ -1200,9 +1200,9 @@ components: source: "infores:clinvar" response_mapping: "$ref": "#/components/x-bte-response-mapping/clinvar-gene" - # testExamples: - # - qInput: "MONDO:0001464" ## Sigmoid colon cancer - # oneOutput: "NCBIGene:4436" ## MSH2 + testExamples: + - qInput: "MONDO:0001464" ## Sigmoid colon cancer + oneOutput: "NCBIGene:4436" ## MSH2 clinvar-gene-diseaseMESH-rev: - supportBatch: true useTemplating: true @@ -1224,9 +1224,9 @@ components: source: "infores:clinvar" response_mapping: "$ref": "#/components/x-bte-response-mapping/clinvar-gene" - # testExamples: - # - qInput: "MESH:D003123" ## Hereditary nonpolyposis colorectal neoplasms / Lynch syndrome - # oneOutput: "NCBIGene:4292" ## MLH1 + testExamples: + - qInput: "MESH:D003123" ## Hereditary nonpolyposis colorectal neoplasms / Lynch syndrome + oneOutput: "NCBIGene:4292" ## MLH1 clinvar-gene-phenoHP-rev: - supportBatch: true useTemplating: true @@ -1248,9 +1248,9 @@ components: source: "infores:clinvar" response_mapping: "$ref": "#/components/x-bte-response-mapping/clinvar-gene" - # testExamples: - # - qInput: "HP:0000105" ## Enlarged kidney - # oneOutput: "NCBIGene:5314" ## PKHD1 + testExamples: + - qInput: "HP:0000105" ## Enlarged kidney + oneOutput: "NCBIGene:5314" ## PKHD1 clinvar-variant-diseaseOMIM: ## using dbsnp.rsid rather than clinvar.rsid field, because more records have dbsnp.rsid... ## 858244 records @@ -1289,9 +1289,9 @@ components: response_mapping: "$ref": "#/components/x-bte-response-mapping/clinvar-variantDiseaseOMIM" ## https://myvariant.info/v1/query?q=_exists_:%22clinvar.rcv.conditions.identifiers.omim%22%20AND%20_exists_:%22dbsnp.rsid%22 - # testExamples: - # - qInput: "DBSNP:rs1193171808" ## chr8:g.42314329A>G - # oneOutput: "OMIM:615592" ## MONDO:0014267 / severe combined immunodeficiency due to IKK2 deficiency + testExamples: + - qInput: "DBSNP:rs1193171808" ## chr8:g.42314329A>G + oneOutput: "OMIM:615592" ## MONDO:0014267 / severe combined immunodeficiency due to IKK2 deficiency clinvar-variant-diseaseORPHANET: ## see original operation clinvar-variant-diseaseOMIM notes ## 719970 records @@ -1316,9 +1316,9 @@ components: source: "infores:clinvar" response_mapping: "$ref": "#/components/x-bte-response-mapping/clinvar-variantDiseaseORPHANET" - # testExamples: - # - qInput: "DBSNP:rs1554270834" ## chr6:g.42722069_42722076del - # oneOutput: "ORPHANET:827" ## Stargardt disease (FFM) / MONDO:0019353 + testExamples: + - qInput: "DBSNP:rs1554270834" ## chr6:g.42722069_42722076del + oneOutput: "ORPHANET:827" ## Stargardt disease (FFM) / MONDO:0019353 clinvar-variant-diseaseMONDO: ## see original operation clinvar-variant-diseaseOMIM notes ## 973693 records @@ -1343,9 +1343,9 @@ components: source: "infores:clinvar" response_mapping: "$ref": "#/components/x-bte-response-mapping/clinvar-variantDiseaseMONDO" - # testExamples: - # - qInput: "DBSNP:rs1860418734" ## chr10:g.87952157T>G - # oneOutput: "MONDO:0017623" ## PTEN hamartoma tumor syndrome (PHTS) + testExamples: + - qInput: "DBSNP:rs1860418734" ## chr10:g.87952157T>G + oneOutput: "MONDO:0017623" ## PTEN hamartoma tumor syndrome (PHTS) clinvar-variant-diseaseMESH: ## see original operation clinvar-variant-diseaseOMIM notes ## 472287 records @@ -1370,9 +1370,9 @@ components: source: "infores:clinvar" response_mapping: "$ref": "#/components/x-bte-response-mapping/clinvar-variantDiseaseMESH" - # testExamples: - # - qInput: "DBSNP:rs1554897280" ## chr10:g.87925558G>A - # oneOutput: "MESH:D009386" ## MONDO:0015356 / Hereditary cancer-predisposing syndrome / hereditary neoplastic syndrome + testExamples: + - qInput: "DBSNP:rs1554897280" ## chr10:g.87925558G>A + oneOutput: "MESH:D009386" ## MONDO:0015356 / Hereditary cancer-predisposing syndrome / hereditary neoplastic syndrome clinvar-variant-phenoHP: ## see original operation clinvar-variant-diseaseOMIM notes ## 125085 records @@ -1397,9 +1397,9 @@ components: source: "infores:clinvar" response_mapping: "$ref": "#/components/x-bte-response-mapping/clinvar-variantPhenoHP" - # testExamples: - # - qInput: "DBSNP:rs367947846" ## chr11:g.47346298G>T - # oneOutput: "HP:0001638" ## Cardiomyopathy (CMYO) / MONDO:0004994 + testExamples: + - qInput: "DBSNP:rs367947846" ## chr11:g.47346298G>T + oneOutput: "HP:0001638" ## Cardiomyopathy (CMYO) / MONDO:0004994 clinvar-variant-diseaseOMIM-rev: - supportBatch: true useTemplating: true @@ -1421,9 +1421,9 @@ components: source: "infores:clinvar" response_mapping: "$ref": "#/components/x-bte-response-mapping/dbsnp-rsid" - # testExamples: - # - qInput: "OMIM:602629" ## Torsion dystonia 6 (DYT6) - # oneOutput: "DBSNP:rs1480200060" ## chr8:g.42837127T>C + testExamples: + - qInput: "OMIM:602629" ## Torsion dystonia 6 (DYT6) + oneOutput: "DBSNP:rs1480200060" ## chr8:g.42837127T>C clinvar-variant-diseaseORPHANET-rev: - supportBatch: true useTemplating: true @@ -1445,9 +1445,9 @@ components: source: "infores:clinvar" response_mapping: "$ref": "#/components/x-bte-response-mapping/dbsnp-rsid" - # testExamples: - # - qInput: "ORPHANET:848" ## beta Thalassemia (BTHAL) - # oneOutput: "DBSNP:rs33956879" ## chr11:g.5226928A>C + testExamples: + - qInput: "ORPHANET:848" ## beta Thalassemia (BTHAL) + oneOutput: "DBSNP:rs33956879" ## chr11:g.5226928A>C clinvar-variant-diseaseMONDO-rev: - supportBatch: true useTemplating: true @@ -1469,9 +1469,9 @@ components: source: "infores:clinvar" response_mapping: "$ref": "#/components/x-bte-response-mapping/dbsnp-rsid" - # testExamples: - # - qInput: "MONDO:0016268" ## Papillary carcinoma of the corpus uteri - # oneOutput: "DBSNP:rs398123231" ## chr2:g.47804948C>G + testExamples: + - qInput: "MONDO:0016268" ## Papillary carcinoma of the corpus uteri + oneOutput: "DBSNP:rs398123231" ## chr2:g.47804948C>G clinvar-variant-diseaseMESH-rev: - supportBatch: true useTemplating: true @@ -1493,9 +1493,9 @@ components: source: "infores:clinvar" response_mapping: "$ref": "#/components/x-bte-response-mapping/dbsnp-rsid" - # testExamples: - # - qInput: "MESH:D003123" ## Hereditary nonpolyposis colorectal neoplasms / Lynch syndrome - # oneOutput: "DBSNP:rs398123231" ## chr2:g.47804948C>A + testExamples: + - qInput: "MESH:D003123" ## Hereditary nonpolyposis colorectal neoplasms / Lynch syndrome + oneOutput: "DBSNP:rs398123231" ## chr2:g.47804948C>A clinvar-variant-phenoHP-rev: - supportBatch: true useTemplating: true @@ -1517,6 +1517,6 @@ components: source: "infores:clinvar" response_mapping: "$ref": "#/components/x-bte-response-mapping/dbsnp-rsid" - # testExamples: - # - qInput: "HP:0011040" ## Abnormal intrahepatic bile duct morphology - # oneOutput: "DBSNP:rs727504096" ## chr6:g.52079920G>A + testExamples: + - qInput: "HP:0011040" ## Abnormal intrahepatic bile duct morphology + oneOutput: "DBSNP:rs727504096" ## chr6:g.52079920G>A diff --git a/ncats_rare_source/smartapi.yaml b/ncats_rare_source/smartapi.yaml index 220a7889..fef7d485 100644 --- a/ncats_rare_source/smartapi.yaml +++ b/ncats_rare_source/smartapi.yaml @@ -606,9 +606,9 @@ components: source: "infores:rare-source" response_mapping: "$ref": "#/components/x-bte-response-mapping/diseaseOrphanet-object" - # testExamples: - # - qInput: "NCBIGene:100" ## ADA - # oneOutput: "ORPHANET:39041" ## Omenn syndrome + testExamples: + - qInput: "NCBIGene:100" ## ADA + oneOutput: "ORPHANET:39041" ## Omenn syndrome diseaseOrphanet-gene: - supportBatch: true useTemplating: true @@ -631,9 +631,9 @@ components: source: "infores:rare-source" response_mapping: "$ref": "#/components/x-bte-response-mapping/gene-object" - # testExamples: - # - qInput: "ORPHANET:110" ## Bardet-Biedl syndrome - # oneOutput: "NCBIGene:10806" ## SDCCAG8 + testExamples: + - qInput: "ORPHANET:110" ## Bardet-Biedl syndrome + oneOutput: "NCBIGene:10806" ## SDCCAG8 gene-diseaseUMLS: - supportBatch: true useTemplating: true @@ -655,9 +655,9 @@ components: source: "infores:rare-source" response_mapping: "$ref": "#/components/x-bte-response-mapping/diseaseUMLS-object" - # testExamples: - # - qInput: "NCBIGene:10075" ## HUWE1 - # oneOutput: "UMLS:C0796003" ## Intellectual developmental disorder, x-linked, syndromic, turner type + testExamples: + - qInput: "NCBIGene:10075" ## HUWE1 + oneOutput: "UMLS:C0796003" ## Intellectual developmental disorder, x-linked, syndromic, turner type diseaseUMLS-gene: - supportBatch: true useTemplating: true @@ -680,9 +680,9 @@ components: source: "infores:rare-source" response_mapping: "$ref": "#/components/x-bte-response-mapping/gene-object" - # testExamples: - # - qInput: "UMLS:C3887743" ## Wilms tumor 2 - # oneOutput: "NCBIGene:105259599" ## H19-ICR (will use output_name) + testExamples: + - qInput: "UMLS:C3887743" ## Wilms tumor 2 + oneOutput: "NCBIGene:105259599" ## H19-ICR (will use output_name) ## testing with "UMLS:C2675767" (Epiphyseal dysplasia, multiple, 6) -> ## "NCBIGene:1297" (COL9A1) will use SRI-Node-Norm-retrieved name x-bte-response-mapping: diff --git a/ols/smartapi.yaml b/ols/smartapi.yaml index ed29279a..5043f7ad 100644 --- a/ols/smartapi.yaml +++ b/ols/smartapi.yaml @@ -62,9 +62,9 @@ components: source: "infores:disease-ontology" response_mapping: "$ref": "#/components/x-bte-response-mapping/disease_has_subclass_disease" - # testExamples: - # - qInput: "DOID:10123" ## skin pigmentation disorder - # oneOutput: "MONDO:0007483" ## dyschromatosis symmetrica hereditaria + testExamples: + - qInput: "DOID:10123" ## skin pigmentation disorder + oneOutput: "MONDO:0007483" ## dyschromatosis symmetrica hereditaria x-bte-response-mapping: disease_has_subclass_disease: DOID: _embedded.terms.obo_id ## HAS PREFIX (DOID) diff --git a/pfocr/smartapi.yaml b/pfocr/smartapi.yaml index 8f081e9b..5c105261 100644 --- a/pfocr/smartapi.yaml +++ b/pfocr/smartapi.yaml @@ -599,9 +599,9 @@ components: source: "infores:pfocr" response_mapping: "$ref": "#/components/x-bte-response-mapping/chem" - # testExamples: - # - qInput: "NCBIGene:3620" ## IDO1 - # oneOutput: "MESH:D004958" ## Estradiol + testExamples: + - qInput: "NCBIGene:3620" ## IDO1 + oneOutput: "MESH:D004958" ## Estradiol ## should have 2 figures: https://biothings.ncats.io/pfocr/query?q=associatedWith.mentions.chemicals.mesh:D004958%20AND%20associatedWith.mentions.genes.ncbigene:3620 chem-gene: - supportBatch: true @@ -627,9 +627,9 @@ components: source: "infores:pfocr" response_mapping: "$ref": "#/components/x-bte-response-mapping/gene" - # testExamples: - # - qInput: "MESH:C000541" ## cyclopamine - # oneOutput: "NCBIGene:208" ## AKT2 + testExamples: + - qInput: "MESH:C000541" ## cyclopamine + oneOutput: "NCBIGene:208" ## AKT2 ## should have 9 figures: https://biothings.ncats.io/pfocr/query?q=associatedWith.mentions.chemicals.mesh:C000541%20AND%20associatedWith.mentions.genes.ncbigene:208 disease-chem: ## https://biothings.ncats.io/pfocr/query?q=_exists_:associatedWith.mentions.diseases%20AND%20_exists_:associatedWith.mentions.chemicals @@ -657,9 +657,9 @@ components: source: "infores:pfocr" response_mapping: "$ref": "#/components/x-bte-response-mapping/chem" - # testExamples: - # - qInput: "MESH:D006623" ## von Hippel-Lindau Disease - # oneOutput: "MESH:C516667" ## pazopanib + testExamples: + - qInput: "MESH:D006623" ## von Hippel-Lindau Disease + oneOutput: "MESH:C516667" ## pazopanib ## should have 9 figures: https://biothings.ncats.io/pfocr/query?q=associatedWith.mentions.chemicals.mesh:C516667%20AND%20associatedWith.mentions.diseases.mesh:D006623 chem-disease: - supportBatch: true @@ -685,9 +685,9 @@ components: source: "infores:pfocr" response_mapping: "$ref": "#/components/x-bte-response-mapping/disease" - # testExamples: - # - qInput: "MESH:D002945" ## Cisplatin - # oneOutput: "MESH:D009369" ## Neoplasms + testExamples: + - qInput: "MESH:D002945" ## Cisplatin + oneOutput: "MESH:D009369" ## Neoplasms ## should have 18 figures: https://biothings.ncats.io/pfocr/query?q=associatedWith.mentions.chemicals.mesh:D002945%20AND%20associatedWith.mentions.diseases.mesh:D009369 disease-gene: ## https://biothings.ncats.io/pfocr/query?q=_exists_:associatedWith.mentions.diseases%20AND%20_exists_:associatedWith.mentions.genes @@ -715,9 +715,9 @@ components: source: "infores:pfocr" response_mapping: "$ref": "#/components/x-bte-response-mapping/gene" - # testExamples: - # - qInput: "MESH:D005199" ## Fanconi Anemia - # oneOutput: "NCBIGene:672" ## BRCA1 + testExamples: + - qInput: "MESH:D005199" ## Fanconi Anemia + oneOutput: "NCBIGene:672" ## BRCA1 ## should have 7 figures: https://biothings.ncats.io/pfocr/query?q=associatedWith.mentions.genes.ncbigene:672%20AND%20associatedWith.mentions.diseases.mesh:D005199 gene-disease: - supportBatch: true @@ -743,9 +743,9 @@ components: source: "infores:pfocr" response_mapping: "$ref": "#/components/x-bte-response-mapping/disease" - # testExamples: - # - qInput: "NCBIGene:3791" ## KDR - # oneOutput: "MESH:D002318" ## Cardiovascular Diseases + testExamples: + - qInput: "NCBIGene:3791" ## KDR + oneOutput: "MESH:D002318" ## Cardiovascular Diseases ## should have 1 figure: https://biothings.ncats.io/pfocr/query?q=associatedWith.mentions.genes.ncbigene:3791%20AND%20associatedWith.mentions.diseases.mesh:D002318 x-bte-response-mapping: ## not including because because data-processing / biolink-modeling issues diff --git a/pharmgkb/smartapi.yaml b/pharmgkb/smartapi.yaml index 835d1b16..d28d6be4 100644 --- a/pharmgkb/smartapi.yaml +++ b/pharmgkb/smartapi.yaml @@ -1343,9 +1343,9 @@ components: predicate: has_participant response_mapping: "$ref": "#/components/x-bte-response-mapping/connection-obj-chem" - # testExamples: - # - qInput: "PHARMGKB.PATHWAYS:PA154426155" ## Taxane Pathway, Pharmacokinetics - # oneOutput: "PHARMGKB.CHEMICAL:PA449383" ## docetaxel + testExamples: + - qInput: "PHARMGKB.PATHWAYS:PA154426155" ## Taxane Pathway, Pharmacokinetics + oneOutput: "PHARMGKB.CHEMICAL:PA449383" ## docetaxel connect-chemical-pathway: - supportBatch: false useTemplating: true @@ -1361,9 +1361,9 @@ components: predicate: participates_in response_mapping: "$ref": "#/components/x-bte-response-mapping/connection-obj-pathway" - # testExamples: - # - qInput: "PHARMGKB.CHEMICAL:PA166131458" ## doxorubicin semiquinone - # oneOutput: "PHARMGKB.PATHWAYS:PA165292163" ## Doxorubicin Pathway (Cancer Cell), Pharmacodynamics + testExamples: + - qInput: "PHARMGKB.CHEMICAL:PA166131458" ## doxorubicin semiquinone + oneOutput: "PHARMGKB.PATHWAYS:PA165292163" ## Doxorubicin Pathway (Cancer Cell), Pharmacodynamics connect-pathway-disease: - supportBatch: false useTemplating: true @@ -1379,9 +1379,9 @@ components: predicate: related_to response_mapping: "$ref": "#/components/x-bte-response-mapping/connection-obj-disease" - # testExamples: - # - qInput: "PHARMGKB.PATHWAYS:PA166163705" ## Diclofenac Pathway, Pharmacokinetics - # oneOutput: "PHARMGKB.DISEASE:PA164925725" ## Toxic liver disease + testExamples: + - qInput: "PHARMGKB.PATHWAYS:PA166163705" ## Diclofenac Pathway, Pharmacokinetics + oneOutput: "PHARMGKB.DISEASE:PA164925725" ## Toxic liver disease connect-disease-pathway: - supportBatch: false useTemplating: true @@ -1397,9 +1397,9 @@ components: predicate: related_to response_mapping: "$ref": "#/components/x-bte-response-mapping/connection-obj-pathway" - # testExamples: - # - qInput: "PHARMGKB.DISEASE:PA445876" ## Tobacco Use Disorder - # oneOutput: "PHARMGKB.PATHWAYS:PA166163828" ## Haloperidol Pathway, Pharmacokinetics + testExamples: + - qInput: "PHARMGKB.DISEASE:PA445876" ## Tobacco Use Disorder + oneOutput: "PHARMGKB.PATHWAYS:PA166163828" ## Haloperidol Pathway, Pharmacokinetics connect-pathway-gene: - supportBatch: false useTemplating: true @@ -1415,9 +1415,9 @@ components: predicate: has_participant response_mapping: "$ref": "#/components/x-bte-response-mapping/connection-obj-gene" - # testExamples: - # - qInput: "PHARMGKB.PATHWAYS:PA166247041" ## Acenocoumarol Pathway, Pharmacokinetics - # oneOutput: "PHARMGKB.GENE:PA126" ## CYP2C9 + testExamples: + - qInput: "PHARMGKB.PATHWAYS:PA166247041" ## Acenocoumarol Pathway, Pharmacokinetics + oneOutput: "PHARMGKB.GENE:PA126" ## CYP2C9 connect-gene-pathway: - supportBatch: false useTemplating: true @@ -1433,9 +1433,9 @@ components: predicate: participates_in response_mapping: "$ref": "#/components/x-bte-response-mapping/connection-obj-pathway" - # testExamples: - # - qInput: "PHARMGKB.GENE:PA236" ## MAOA - # oneOutput: "PHARMGKB.PATHWAYS:PA166183426" ## Propranolol Pathway, Pharmacokinetics + testExamples: + - qInput: "PHARMGKB.GENE:PA236" ## MAOA + oneOutput: "PHARMGKB.PATHWAYS:PA166183426" ## Propranolol Pathway, Pharmacokinetics connect-chemical-chemical: ## seems to be different from the chemical components/metabolites in other operations - supportBatch: false @@ -1452,9 +1452,9 @@ components: predicate: related_to response_mapping: "$ref": "#/components/x-bte-response-mapping/connection-obj-chem" - # testExamples: - # - qInput: "PHARMGKB.CHEMICAL:PA164888966" ## raltegravir - # oneOutput: "PHARMGKB.CHEMICAL:PA10251" ## atazanavir + testExamples: + - qInput: "PHARMGKB.CHEMICAL:PA164888966" ## raltegravir + oneOutput: "PHARMGKB.CHEMICAL:PA10251" ## atazanavir connect-chemical-disease: - supportBatch: false useTemplating: true @@ -1470,9 +1470,9 @@ components: predicate: related_to response_mapping: "$ref": "#/components/x-bte-response-mapping/connection-obj-disease" - # testExamples: - # - qInput: "PHARMGKB.CHEMICAL:PA164888966" ## raltegravir - # oneOutput: "PHARMGKB.DISEASE:PA447230" ## HIV Infections + testExamples: + - qInput: "PHARMGKB.CHEMICAL:PA164888966" ## raltegravir + oneOutput: "PHARMGKB.DISEASE:PA447230" ## HIV Infections connect-disease-chemical: - supportBatch: false useTemplating: true @@ -1488,9 +1488,9 @@ components: predicate: related_to response_mapping: "$ref": "#/components/x-bte-response-mapping/connection-obj-chem" - # testExamples: - # - qInput: "PHARMGKB.DISEASE:PA444418" ## Gastrointestinal Hemorrhage - # oneOutput: "PHARMGKB.CHEMICAL:PA165958395" ## lornoxicam + testExamples: + - qInput: "PHARMGKB.DISEASE:PA444418" ## Gastrointestinal Hemorrhage + oneOutput: "PHARMGKB.CHEMICAL:PA165958395" ## lornoxicam connect-disease-disease: - supportBatch: false useTemplating: true @@ -1506,9 +1506,9 @@ components: predicate: related_to response_mapping: "$ref": "#/components/x-bte-response-mapping/connection-obj-disease" - # testExamples: - # - qInput: "PHARMGKB.DISEASE:PA447054" ## Stroke - # oneOutput: "PHARMGKB.DISEASE:PA443459" ## Atrial Fibrillation + testExamples: + - qInput: "PHARMGKB.DISEASE:PA447054" ## Stroke + oneOutput: "PHARMGKB.DISEASE:PA443459" ## Atrial Fibrillation connect-disease-gene: - supportBatch: false useTemplating: true @@ -1524,9 +1524,9 @@ components: predicate: related_to response_mapping: "$ref": "#/components/x-bte-response-mapping/connection-obj-gene" - # testExamples: - # - qInput: "PHARMGKB.DISEASE:PA447054" ## Stroke - # oneOutput: "PHARMGKB.GENE:PA107" ## CES1 + testExamples: + - qInput: "PHARMGKB.DISEASE:PA447054" ## Stroke + oneOutput: "PHARMGKB.GENE:PA107" ## CES1 connect-gene-disease: - supportBatch: false useTemplating: true @@ -1542,9 +1542,9 @@ components: predicate: related_to response_mapping: "$ref": "#/components/x-bte-response-mapping/connection-obj-disease" - # testExamples: - # - qInput: "PHARMGKB.GENE:PA133787052" ## VKORC1 - # oneOutput: "PHARMGKB.DISEASE:PA166123298" ## over-anticoagulation + testExamples: + - qInput: "PHARMGKB.GENE:PA133787052" ## VKORC1 + oneOutput: "PHARMGKB.DISEASE:PA166123298" ## over-anticoagulation connect-disease-variant: - supportBatch: false useTemplating: true @@ -1560,9 +1560,9 @@ components: predicate: related_to response_mapping: "$ref": "#/components/x-bte-response-mapping/connection-obj-dbsnp" - # testExamples: - # - qInput: "PHARMGKB.DISEASE:PA443459" ## Atrial Fibrillation - # oneOutput: "DBSNP:rs2260863" + testExamples: + - qInput: "PHARMGKB.DISEASE:PA443459" ## Atrial Fibrillation + oneOutput: "DBSNP:rs2260863" connect-variant-disease: - supportBatch: false useTemplating: true @@ -1578,9 +1578,9 @@ components: predicate: related_to response_mapping: "$ref": "#/components/x-bte-response-mapping/connection-obj-disease" - # testExamples: - # - qInput: "DBSNP:rs1057910" - # oneOutput: "PHARMGKB.DISEASE:PA443915" ## Diplopia + testExamples: + - qInput: "DBSNP:rs1057910" + oneOutput: "PHARMGKB.DISEASE:PA443915" ## Diplopia connect-gene-gene: ## 2023-07-06: test not completed, seemed to have endpoint issues (404) - supportBatch: false @@ -1597,9 +1597,9 @@ components: predicate: related_to response_mapping: "$ref": "#/components/x-bte-response-mapping/connection-obj-gene" - # testExamples: - # - qInput: "PHARMGKB.GENE:PA126" ## CYP2C9 - # oneOutput: "PHARMGKB.GENE:PA133787052" ## VKORC1 + testExamples: + - qInput: "PHARMGKB.GENE:PA126" ## CYP2C9 + oneOutput: "PHARMGKB.GENE:PA133787052" ## VKORC1 connect-gene-chemical: ## complements clinicalAnnot-chemical-gene operation, since that /data/clinicalAnnotation endpoint ## doesn't allow querying using gene ID @@ -1617,9 +1617,9 @@ components: predicate: related_to response_mapping: "$ref": "#/components/x-bte-response-mapping/connection-obj-chem" - # testExamples: - # - qInput: "PHARMGKB.GENE:PA27829" ## EPHX1 - # oneOutput: "PHARMGKB.CHEMICAL:PA448785" ## carbamazepine + testExamples: + - qInput: "PHARMGKB.GENE:PA27829" ## EPHX1 + oneOutput: "PHARMGKB.CHEMICAL:PA448785" ## carbamazepine ############################################################### ## uses /pathway/{id} endpoint ## annotates data.relatedChemicals, data.relatedDiseases, data.relatedGenes, data.relatedPathways @@ -1643,9 +1643,9 @@ components: predicate: related_to response_mapping: "$ref": "#/components/x-bte-response-mapping/pathEnd-chem" - # testExamples: - # - qInput: "PHARMGKB.PATHWAYS:PA2023" ## ACE Inhibitor Pathway, Pharmacodynamics - # oneOutput: "PHARMGKB.CHEMICAL:PA448780" ## captopril + testExamples: + - qInput: "PHARMGKB.PATHWAYS:PA2023" ## ACE Inhibitor Pathway, Pharmacodynamics + oneOutput: "PHARMGKB.CHEMICAL:PA448780" ## captopril pathwayEndpoint-disease: ## info maybe only retrievable in this direction (no relatedPathways in /disease response) - supportBatch: false @@ -1662,9 +1662,9 @@ components: predicate: related_to response_mapping: "$ref": "#/components/x-bte-response-mapping/pathEnd-disease" - # testExamples: - # - qInput: "PHARMGKB.PATHWAYS:PA2023" ## ACE Inhibitor Pathway, Pharmacodynamics - # oneOutput: "PHARMGKB.DISEASE:PA444552" ## Hypertension + testExamples: + - qInput: "PHARMGKB.PATHWAYS:PA2023" ## ACE Inhibitor Pathway, Pharmacodynamics + oneOutput: "PHARMGKB.DISEASE:PA444552" ## Hypertension pathwayEndpoint-gene: ## info maybe only retrievable in this direction (no relatedPathways in /gene response) - supportBatch: false @@ -1681,9 +1681,9 @@ components: predicate: related_to response_mapping: "$ref": "#/components/x-bte-response-mapping/pathEnd-gene" - # testExamples: - # - qInput: "PHARMGKB.PATHWAYS:PA166114721" ## Uricosurics Pathway, Pharmacodynamics - # oneOutput: "PHARMGKB.GENE:PA397" ## ABCC4 + testExamples: + - qInput: "PHARMGKB.PATHWAYS:PA166114721" ## Uricosurics Pathway, Pharmacodynamics + oneOutput: "PHARMGKB.GENE:PA397" ## ABCC4 pathwayEndpoint-pathway: ## relationships seem retrievable in both directions: PathwayA -> PathwayB and PathwayB -> PathwayA - supportBatch: false @@ -1700,9 +1700,9 @@ components: predicate: related_to response_mapping: "$ref": "#/components/x-bte-response-mapping/pathEnd-path" - # testExamples: - # - qInput: "PHARMGKB.PATHWAYS:PA2023" ## ACE Inhibitor Pathway, Pharmacodynamics - # oneOutput: "PHARMGKB.PATHWAYS:PA166165076" ## Verapamil Pathway, Pharmacokinetics + testExamples: + - qInput: "PHARMGKB.PATHWAYS:PA2023" ## ACE Inhibitor Pathway, Pharmacodynamics + oneOutput: "PHARMGKB.PATHWAYS:PA166165076" ## Verapamil Pathway, Pharmacokinetics ############################################################### ## uses /chemical/{id} endpoint ## x-bte annotation for data.components, data.metabolites @@ -1722,9 +1722,9 @@ components: predicate: has_active_ingredient response_mapping: "$ref": "#/components/x-bte-response-mapping/chemComponents" - # testExamples: - # - qInput: "PHARMGKB.CHEMICAL:PA166182864" ## XELOX - # oneOutput: "PHARMGKB.CHEMICAL:PA448771" ## capecitabine + testExamples: + - qInput: "PHARMGKB.CHEMICAL:PA166182864" ## XELOX + oneOutput: "PHARMGKB.CHEMICAL:PA448771" ## capecitabine chemical-metabolites: ## info maybe only retrievable in this direction - supportBatch: false @@ -1741,9 +1741,9 @@ components: predicate: has_metabolite response_mapping: "$ref": "#/components/x-bte-response-mapping/chemMetabolites" - # testExamples: - # - qInput: "PHARMGKB.CHEMICAL:PA451241" ## ribavirin - # oneOutput: "PHARMGKB.CHEMICAL:PA166271901" ## 1,2,4-triazole-3-carboxamide + testExamples: + - qInput: "PHARMGKB.CHEMICAL:PA451241" ## ribavirin + oneOutput: "PHARMGKB.CHEMICAL:PA166271901" ## 1,2,4-triazole-3-carboxamide ############################################################### ## uses /guidelineAnnotation endpoint ## view=base is enough to get useful info, I think... @@ -1764,9 +1764,9 @@ components: predicate: related_to response_mapping: "$ref": "#/components/x-bte-response-mapping/guidelineEnd-gene" - # testExamples: - # - qInput: "PHARMGKB.CHEMICAL:PA448004" ## abacavir - # oneOutput: "PHARMGKB.GENE:PA35056" ## HLA-B + testExamples: + - qInput: "PHARMGKB.CHEMICAL:PA448004" ## abacavir + oneOutput: "PHARMGKB.GENE:PA35056" ## HLA-B guideline-gene-chemical: - supportBatch: false useTemplating: true @@ -1782,9 +1782,9 @@ components: predicate: related_to response_mapping: "$ref": "#/components/x-bte-response-mapping/guidelineEnd-chem" - # testExamples: - # - qInput: "PHARMGKB.GENE:PA189" ## HMGCR - # oneOutput: "PHARMGKB.CHEMICAL:PA449688" ## fluvastatin + testExamples: + - qInput: "PHARMGKB.GENE:PA189" ## HMGCR + oneOutput: "PHARMGKB.CHEMICAL:PA449688" ## fluvastatin ############################################################### ## uses /label endpoint ## can query for a chemical -> get drug label info on whether to give/how to give this chemical, @@ -1804,9 +1804,9 @@ components: predicate: related_to response_mapping: "$ref": "#/components/x-bte-response-mapping/labelEnd-gene" - # testExamples: - # - qInput: "PHARMGKB.CHEMICAL:PA166153471" ## abemaciclib - # oneOutput: "PHARMGKB.GENE:PA27886" ## ESR2 + testExamples: + - qInput: "PHARMGKB.CHEMICAL:PA166153471" ## abemaciclib + oneOutput: "PHARMGKB.GENE:PA27886" ## ESR2 label-gene-chemical: - supportBatch: false useTemplating: true @@ -1822,9 +1822,9 @@ components: predicate: related_to response_mapping: "$ref": "#/components/x-bte-response-mapping/labelEnd-chem" - # testExamples: - # - qInput: "PHARMGKB.GENE:PA31111" ## MS4A1 - # oneOutput: "PHARMGKB.CHEMICAL:PA165291493" ## ofatumumab + testExamples: + - qInput: "PHARMGKB.GENE:PA31111" ## MS4A1 + oneOutput: "PHARMGKB.CHEMICAL:PA165291493" ## ofatumumab ############################################################### ## uses /clinicalAnnotation endpoint, pharmgkb says this is variant-drug info ## - can query for a chemical -> get clinical-supported info on whether to give/how to give this chemical, @@ -1847,9 +1847,9 @@ components: predicate: related_to response_mapping: "$ref": "#/components/x-bte-response-mapping/clinicalAnnotEnd-variant" - # testExamples: - # - qInput: "PHARMGKB.CHEMICAL:PA134308647" ## rosuvastatin - # oneOutput: "DBSNP:rs4693075" + testExamples: + - qInput: "PHARMGKB.CHEMICAL:PA134308647" ## rosuvastatin + oneOutput: "DBSNP:rs4693075" clinicalAnnot-variant-chem: - supportBatch: false useTemplating: true @@ -1865,9 +1865,9 @@ components: predicate: related_to response_mapping: "$ref": "#/components/x-bte-response-mapping/clinicalAnnotEnd-chem" - # testExamples: - # - qInput: "DBSNP:rs45445694" - # oneOutput: "PHARMGKB.CHEMICAL:PA450428" ## methotrexate + testExamples: + - qInput: "DBSNP:rs45445694" + oneOutput: "PHARMGKB.CHEMICAL:PA450428" ## methotrexate clinicalAnnot-chemical-gene: ## using connect-gene-chemical operation to retrieve info in gene -> chem direction ## since this endpoint doesn't allow querying using gene ID @@ -1885,9 +1885,9 @@ components: predicate: related_to response_mapping: "$ref": "#/components/x-bte-response-mapping/clinicalAnnotEnd-gene" - # testExamples: - # - qInput: "PHARMGKB.CHEMICAL:PA451250" ## rifampin - # oneOutput: "PHARMGKB.GENE:PA18" ## NAT2 + testExamples: + - qInput: "PHARMGKB.CHEMICAL:PA451250" ## rifampin + oneOutput: "PHARMGKB.GENE:PA18" ## NAT2 ############################################################### ## uses /variantAnnotation endpoint ## - can query for a chemical -> get publication-supported info on whether to give/how to give this chemical, @@ -1908,9 +1908,9 @@ components: predicate: related_to response_mapping: "$ref": "#/components/x-bte-response-mapping/variantAnnotEnd-chem" - # testExamples: - # - qInput: "DBSNP:rs319952" - # oneOutput: "PHARMGKB.CHEMICAL:PA451250" ## rifampin + testExamples: + - qInput: "DBSNP:rs319952" + oneOutput: "PHARMGKB.CHEMICAL:PA451250" ## rifampin variantAnnot-chem-variant: ## not documented in swagger, but you can query with chemicals using parameter: relatedChemicals.accessionId - supportBatch: false @@ -1927,9 +1927,9 @@ components: predicate: related_to response_mapping: "$ref": "#/components/x-bte-response-mapping/variantAnnotEnd-variant" - # testExamples: - # - qInput: "PHARMGKB.CHEMICAL:PA166123407" ## abiraterone - # oneOutput: "DBSNP:rs10493112" + testExamples: + - qInput: "PHARMGKB.CHEMICAL:PA166123407" ## abiraterone + oneOutput: "DBSNP:rs10493112" x-bte-response-mapping: ## not annotating name fields in some cases because the fields will have multiple values that we aren't keeping separate connection-obj-chem: diff --git a/quickgo/smartapi.yaml b/quickgo/smartapi.yaml index 7d912bb1..589a89d6 100644 --- a/quickgo/smartapi.yaml +++ b/quickgo/smartapi.yaml @@ -62,9 +62,9 @@ components: source: "infores:go" response_mapping: "$ref": "#/components/x-bte-response-mapping/ma_has_subclass_ma" - # testExamples: - # - qInput: "GO:0000082" ## G1/S transition of mitotic cell cycle - # oneOutput: "GO:2000045" ## regulation of G1/S transition of mitotic cell cycle + testExamples: + - qInput: "GO:0000082" ## G1/S transition of mitotic cell cycle + oneOutput: "GO:2000045" ## regulation of G1/S transition of mitotic cell cycle x-bte-response-mapping: ma_has_subclass_ma: GO: results.children.id ## has prefix (GO) diff --git a/repodb/smartapi.yaml b/repodb/smartapi.yaml index 9a2a25b7..9aad9a4e 100644 --- a/repodb/smartapi.yaml +++ b/repodb/smartapi.yaml @@ -611,9 +611,9 @@ components: source: "infores:repodb" response_mapping: "$ref": "#/components/x-bte-response-mapping/disease" - # testExamples: - # - qInput: "DRUGBANK:DB00002" ## Cetuximab - # oneOutput: "UMLS:C0007102" ## Malignant tumor of colon + testExamples: + - qInput: "DRUGBANK:DB00002" ## Cetuximab + oneOutput: "UMLS:C0007102" ## Malignant tumor of colon drug-disease-not-approved: ## 518 records with Terminated ## 336 with Withdrawn @@ -641,15 +641,16 @@ components: source: "infores:repodb" response_mapping: "$ref": "#/components/x-bte-response-mapping/disease" - # ## for Terminated - # - qInput: "DRUGBANK:DB00043" ## Omalizumab - # oneOutput: "UMLS:C0004096" ## Asthma - # ## for Withdrawn - # - qInput: "DRUGBANK:DB00007" ## Leuprolide - # oneOutput: "UMLS:C0042133" ## Uterine Fibroids / uterine corpus leiomyoma - # ## for Suspended - # - qInput: "DRUGBANK:DB00104" ## Octreotide - # oneOutput: "UMLS:C0001206" ## Acromegaly + testExamples: + ## for Terminated + - qInput: "DRUGBANK:DB00043" ## Omalizumab + oneOutput: "UMLS:C0004096" ## Asthma + ## for Withdrawn + - qInput: "DRUGBANK:DB00007" ## Leuprolide + oneOutput: "UMLS:C0042133" ## Uterine Fibroids / uterine corpus leiomyoma + ## for Suspended + - qInput: "DRUGBANK:DB00104" ## Octreotide + oneOutput: "UMLS:C0001206" ## Acromegaly rev-disease-drug: - supportBatch: true useTemplating: true @@ -672,9 +673,9 @@ components: source: "infores:repodb" response_mapping: "$ref": "#/components/x-bte-response-mapping/drug" - # testExamples: - # - qInput: "UMLS:C0032797" ## Postpartum Hemorrhage - # oneOutput: "DRUGBANK:DB00107" ## Oxytocin + testExamples: + - qInput: "UMLS:C0032797" ## Postpartum Hemorrhage + oneOutput: "DRUGBANK:DB00107" ## Oxytocin x-bte-response-mapping: disease: UMLS: repodb.indications.umls diff --git a/rhea/smartapi.yaml b/rhea/smartapi.yaml index 1394c93f..3acbd1f9 100644 --- a/rhea/smartapi.yaml +++ b/rhea/smartapi.yaml @@ -611,9 +611,9 @@ components: source: "infores:rhea" response_mapping: $ref: '#/components/x-bte-response-mapping/side_l-object' - # testExamples: - # - qInput: "RHEA:21429" ## child-id for (R)-3-sulfolactate = H(+) + pyruvate + sulfite - # oneOutput: "CHEBI:58738" ## (R)-3-sulfolactate + testExamples: + - qInput: "RHEA:21429" ## child-id for (R)-3-sulfolactate = H(+) + pyruvate + sulfite + oneOutput: "CHEBI:58738" ## (R)-3-sulfolactate reaction-to-chem-2: - supportBatch: true useTemplating: true ## flag to say templating is being used below @@ -646,9 +646,9 @@ components: source: "infores:rhea" response_mapping: $ref: '#/components/x-bte-response-mapping/side_r-object' - # testExamples: - # - qInput: "RHEA:15533" ## main-id for (R)-3-sulfolactate + NAD(+) = 3-sulfopyruvate + H(+) + NADH - # oneOutput: "CHEBI:57940" ## 3-sulfopyruvate + testExamples: + - qInput: "RHEA:15533" ## main-id for (R)-3-sulfolactate + NAD(+) = 3-sulfopyruvate + H(+) + NADH + oneOutput: "CHEBI:57940" ## 3-sulfopyruvate reaction-to-chem-3: - supportBatch: true useTemplating: true ## flag to say templating is being used below @@ -681,9 +681,9 @@ components: source: "infores:rhea" response_mapping: $ref: '#/components/x-bte-response-mapping/side_l_reactive-object' - # testExamples: - # - qInput: "RHEA:10024" ## main-id for L-lysyl-[histone] + S-adenosyl-L-methionine = H(+) + N(6)-methyl-L-lysyl-[histone] + S-adenosyl-L-homocysteine - # oneOutput: "CHEBI:29969" ## L-lysine residue + testExamples: + - qInput: "RHEA:10024" ## main-id for L-lysyl-[histone] + S-adenosyl-L-methionine = H(+) + N(6)-methyl-L-lysyl-[histone] + S-adenosyl-L-homocysteine + oneOutput: "CHEBI:29969" ## L-lysine residue reaction-to-chem-4: - supportBatch: true useTemplating: true ## flag to say templating is being used below @@ -716,9 +716,9 @@ components: source: "infores:rhea" response_mapping: $ref: '#/components/x-bte-response-mapping/side_r_reactive-object' - # testExamples: - # - qInput: "RHEA:10032" ## main-id for [protein]-C-terminal-L-glutamine + H2O = [protein]-C-terminal-L-glutamate + NH4(+) - # oneOutput: "CHEBI:88115" ## C-terminal L-glutaminyl residue + testExamples: + - qInput: "RHEA:10032" ## main-id for [protein]-C-terminal-L-glutamine + H2O = [protein]-C-terminal-L-glutamate + NH4(+) + oneOutput: "CHEBI:88115" ## C-terminal L-glutaminyl residue ## going to try doing chemicals -> main RHEA ID first. ## If we need the children rheas, we'll just write another copy of the operation below chem-to-reaction: @@ -757,9 +757,9 @@ components: source: "infores:rhea" response_mapping: $ref: '#/components/x-bte-response-mapping/reaction-object' - # testExamples: - # - qInput: "CHEBI:88115" ## C-terminal L-glutaminyl residue - # oneOutput: "RHEA:10032" ## main-id for [protein]-C-terminal-L-glutamine + H2O = [protein]-C-terminal-L-glutamate + NH4(+) + testExamples: + - qInput: "CHEBI:88115" ## C-terminal L-glutaminyl residue + oneOutput: "RHEA:10032" ## main-id for [protein]-C-terminal-L-glutamine + H2O = [protein]-C-terminal-L-glutamate + NH4(+) x-bte-response-mapping: side_l-object: CHEBI: side_l.chebi_id ## has CHEBI prefix diff --git a/suppkg/suppkg.yaml b/suppkg/suppkg.yaml index 66234d9c..01f8ef71 100644 --- a/suppkg/suppkg.yaml +++ b/suppkg/suppkg.yaml @@ -604,9 +604,9 @@ components: source: "infores:suppkg" # no infores for suppkg yet response_mapping: "$ref": "#/components/x-bte-response-mapping/object" - # testExamples: - # - qInput: "UMLS:C0016277" ## Fluconazole - # oneOutput: "UMLS:C0009324" ## ulcerative colitis + testExamples: + - qInput: "UMLS:C0016277" ## Fluconazole + oneOutput: "UMLS:C0009324" ## ulcerative colitis disease-treated_by-supplement: - supportBatch: true useTemplating: true @@ -632,9 +632,9 @@ components: source: "infores:suppkg" # no infores for suppkg yet response_mapping: "$ref": "#/components/x-bte-response-mapping/subject" - # testExamples: - # - qInput: "UMLS:C0009324" ## ulcerative colitis - # oneOutput: "UMLS:DC0023791" ## (r)-dithiolane-3-pentanoic acid + testExamples: + - qInput: "UMLS:C0009324" ## ulcerative colitis + oneOutput: "UMLS:DC0023791" ## (r)-dithiolane-3-pentanoic acid x-bte-response-mapping: object: UMLS: object.umls diff --git a/ttd/smartapi.yaml b/ttd/smartapi.yaml index be2f14f4..2daf6d90 100644 --- a/ttd/smartapi.yaml +++ b/ttd/smartapi.yaml @@ -632,9 +632,9 @@ components: # source: "infores:ttd" # response_mapping: # "$ref": "#/components/x-bte-response-mapping/mondo-object" - # # testExamples: - # # - qInput: "CHEBI:6960" ## Moexipril - # # oneOutput: "MONDO:0001134" ## Hypertension + # testExamples: + # - qInput: "CHEBI:6960" ## Moexipril + # oneOutput: "MONDO:0001134" ## Hypertension # chebi_treats_mondo-rev: # - supportBatch: true # useTemplating: true @@ -661,9 +661,9 @@ components: # source: "infores:ttd" # response_mapping: # "$ref": "#/components/x-bte-response-mapping/chebi-subject" - # # testExamples: - # # - qInput: "MONDO:0005180" ## Parkinson disease - # # oneOutput: "CHEBI:134699" ## Opicapone + # testExamples: + # - qInput: "MONDO:0005180" ## Parkinson disease + # oneOutput: "CHEBI:134699" ## Opicapone # chebi_treats_icd11: # ## url: https://biothings.transltr.io/ttd/query?q=\_exists_:subject.chebi%20AND%20association.predicate:%22biolink:treats%22%20AND%20_exists_:object.icd11 # ## 3806 records @@ -695,9 +695,9 @@ components: # source: "infores:ttd" # response_mapping: # "$ref": "#/components/x-bte-response-mapping/icd11-object" - # # testExamples: - # # - qInput: "CHEBI:107601" ## Savirin - # # oneOutput: "ICD11:1B5Y" ## Staphylococcus infection + # testExamples: + # - qInput: "CHEBI:107601" ## Savirin + # oneOutput: "ICD11:1B5Y" ## Staphylococcus infection # chebi_treats_icd11-rev: # - supportBatch: true # useTemplating: true @@ -726,9 +726,9 @@ components: # source: "infores:ttd" # response_mapping: # "$ref": "#/components/x-bte-response-mapping/chebi-subject" - # # testExamples: - # # - qInput: "ICD11:CB03.4" ## Pulmonary fibrosis - # # oneOutput: "CHEBI:144367" ## 3PO + # testExamples: + # - qInput: "ICD11:CB03.4" ## Pulmonary fibrosis + # oneOutput: "CHEBI:144367" ## 3PO pubchem_treats_mondo: ## https://biothings.transltr.io/ttd/query?q=_exists_:subject.pubchem_compound%20AND%20_exists_:object.mondo%20AND%20association.predicate:%22biolink:treats%22 ## 1604 records @@ -757,9 +757,9 @@ components: source: "infores:ttd" response_mapping: "$ref": "#/components/x-bte-response-mapping/mondo-object" - # testExamples: - # - qInput: "PUBCHEM.COMPOUND:118063735" ## LMB763 (Nidufexor) - # oneOutput: "MONDO:0004790" ## fatty liver disease + testExamples: + - qInput: "PUBCHEM.COMPOUND:118063735" ## LMB763 (Nidufexor) + oneOutput: "MONDO:0004790" ## fatty liver disease pubchem_treats_mondo-rev: - supportBatch: true useTemplating: true @@ -784,9 +784,9 @@ components: source: "infores:ttd" response_mapping: "$ref": "#/components/x-bte-response-mapping/pubchem-subject" - # testExamples: - # - qInput: "MONDO:0021094" ## Human immunodeficiency virus infection / immunodeficiency disease?? - # oneOutput: "PUBCHEM.COMPOUND:103596027" ## GS-1156 (8-(3-Chloro-5-(trifluoromethyl)pyridin-2-yl)-8-azabicyclo[3.2.1]octan-3-one) + testExamples: + - qInput: "MONDO:0021094" ## Human immunodeficiency virus infection / immunodeficiency disease?? + oneOutput: "PUBCHEM.COMPOUND:103596027" ## GS-1156 (8-(3-Chloro-5-(trifluoromethyl)pyridin-2-yl)-8-azabicyclo[3.2.1]octan-3-one) pubchem_treats_icd11: ## url: https://biothings.transltr.io/ttd/query?q=_exists_:subject.pubchem_compound%20AND%20_exists_:object.icd11%20AND%20(NOT%20_exists_:object.mondo)%20AND%20association.predicate:%22biolink:treats%22 ## 9985 records @@ -817,9 +817,9 @@ components: source: "infores:ttd" response_mapping: "$ref": "#/components/x-bte-response-mapping/icd11-object" - # testExamples: - # - qInput: "PUBCHEM.COMPOUND:126843189" ## AVN-101 (AVN-101 HCl) - # oneOutput: "ICD11:6D71" ## Cognitive impairment + testExamples: + - qInput: "PUBCHEM.COMPOUND:126843189" ## AVN-101 (AVN-101 HCl) + oneOutput: "ICD11:6D71" ## Cognitive impairment pubchem_treats_icd11-rev: - supportBatch: true useTemplating: true @@ -844,9 +844,9 @@ components: source: "infores:ttd" response_mapping: "$ref": "#/components/x-bte-response-mapping/pubchem-subject" - # testExamples: - # - qInput: "ICD11:MG51" ## Multidrug resistant infection - # oneOutput: "PUBCHEM.COMPOUND:139600308" ## SPR206 + testExamples: + - qInput: "ICD11:MG51" ## Multidrug resistant infection + oneOutput: "PUBCHEM.COMPOUND:139600308" ## SPR206 ttd_drug_id_treats_mondo: ## url: https://biothings.transltr.io/ttd/query?q=_exists_:subject.ttd_drug_id%20AND%20(NOT%20_exists_:subject.pubchem_compound)%20AND%20_exists_:object.mondo%20AND%20association.predicate:%22biolink:treats%22 ## 2240 records @@ -877,9 +877,9 @@ components: source: "infores:ttd" response_mapping: "$ref": "#/components/x-bte-response-mapping/mondo-object" - # testExamples: - # - qInput: "TTD.DRUG:DZJ3D5" ## PF-07220060 - # oneOutput: "MONDO:0008315" ## Prostate cancer + testExamples: + - qInput: "TTD.DRUG:DZJ3D5" ## PF-07220060 + oneOutput: "MONDO:0008315" ## Prostate cancer ttd_drug_id_treats_mondo-rev: - supportBatch: true useTemplating: true @@ -904,9 +904,9 @@ components: source: "infores:ttd" response_mapping: "$ref": "#/components/x-bte-response-mapping/ttd_drug_id-subject" - # testExamples: - # - qInput: "MONDO:0019056" ## Myasthenia gravis / neuromuscular disease?? - # oneOutput: "TTD.DRUG:DZA98D" ## ARGX-113 + testExamples: + - qInput: "MONDO:0019056" ## Myasthenia gravis / neuromuscular disease?? + oneOutput: "TTD.DRUG:DZA98D" ## ARGX-113 ttd_drug_id_treats_icd11: ## url: https://biothings.transltr.io/ttd/query?q=_exists_:subject.ttd_drug_id%20AND%20association.predicate:%22biolink:treats%22%20AND%20_exists_:object.icd11%20AND%20NOT%20_exists_:object.mondoAND%20NOT%20_exists_:subject.pubchem_compound ## 16,956 records @@ -941,9 +941,9 @@ components: source: "infores:ttd" response_mapping: "$ref": "#/components/x-bte-response-mapping/icd11-object" - # testExamples: - # - qInput: "TTD.DRUG:DZW53X" ## GSK4069889 - # oneOutput: "ICD11:2C25" ## Non-small cell lung cancer + testExamples: + - qInput: "TTD.DRUG:DZW53X" ## GSK4069889 + oneOutput: "ICD11:2C25" ## Non-small cell lung cancer ttd_drug_id_treats_icd11-rev: - supportBatch: true useTemplating: true @@ -973,9 +973,9 @@ components: source: "infores:ttd" response_mapping: "$ref": "#/components/x-bte-response-mapping/ttd_drug_id-subject" - # testExamples: - # - qInput: "ICD11:1D48" ## Zika virus infection - # oneOutput: "TTD.DRUG:DZTL59" ## INO-A002 + testExamples: + - qInput: "ICD11:1D48" ## Zika virus infection + oneOutput: "TTD.DRUG:DZTL59" ## INO-A002 uniprotkb_target_for_mondo: ## url: https://biothings.transltr.io/ttd/query?q=_exists_:subject.uniprotkb%20AND%20association.predicate:%22biolink:target_for%22%20AND%20_exists_:object.mondo ## 601 records @@ -1006,9 +1006,9 @@ components: source: "infores:ttd" response_mapping: "$ref": "#/components/x-bte-response-mapping/mondo-object" - # testExamples: - # - qInput: "UniProtKB:Q08722" ## Leukocyte surface antigen CD47 - # oneOutput: "MONDO:0001351" ## Ovarian cancer (uterine adnexa cancer) + testExamples: + - qInput: "UniProtKB:Q08722" ## Leukocyte surface antigen CD47 + oneOutput: "MONDO:0001351" ## Ovarian cancer (uterine adnexa cancer) uniprotkb_target_for_mondo-rev: - supportBatch: true useTemplating: true @@ -1037,9 +1037,9 @@ components: source: "infores:ttd" response_mapping: "$ref": "#/components/x-bte-response-mapping/uniprotkb-subject" - # testExamples: - # - qInput: "MONDO:0005083" ## Psoriasis - # oneOutput: "UniProtKB:P01270" ## Parathyroid hormone (PTH) + testExamples: + - qInput: "MONDO:0005083" ## Psoriasis + oneOutput: "UniProtKB:P01270" ## Parathyroid hormone (PTH) uniprotkb_target_for_icd11: ## url: https://biothings.transltr.io/ttd/query?q=_exists_:subject.uniprotkb%20AND%20association.predicate:%22biolink:target_for%22%20AND%20_exists_:object.icd11%20AND%20NOT%20_exists_:object.mondo ## 5,564 records @@ -1072,9 +1072,9 @@ components: source: "infores:ttd" response_mapping: "$ref": "#/components/x-bte-response-mapping/icd11-object" - # testExamples: - # - qInput: "UniProtKB:P49674" ## Casein kinase I epsilon (CSNK1E) - # oneOutput: "ICD11:2C10" ## Pancreatic cancer + testExamples: + - qInput: "UniProtKB:P49674" ## Casein kinase I epsilon (CSNK1E) + oneOutput: "ICD11:2C10" ## Pancreatic cancer uniprotkb_target_for_icd11-rev: - supportBatch: true useTemplating: true @@ -1103,9 +1103,9 @@ components: source: "infores:ttd" response_mapping: "$ref": "#/components/x-bte-response-mapping/uniprotkb-subject" - # testExamples: - # - qInput: "ICD11:6D71" ## Mild neurocognitive disorder - # oneOutput: "UniProtKB:Q92542" ## Gamma-secretase (GS) NCSTN -> checked uniprotkb that NCSTN is an essential subunit of the gamma-secretase complex + testExamples: + - qInput: "ICD11:6D71" ## Mild neurocognitive disorder + oneOutput: "UniProtKB:Q92542" ## Gamma-secretase (GS) NCSTN -> checked uniprotkb that NCSTN is an essential subunit of the gamma-secretase complex ttd_target_id_target_for_mondo: ## url: https://biothings.transltr.io/ttd/query?q=_exists_:subject.ttd_target_id%20AND%20association.predicate:%22biolink:target_for%22%20AND%20_exists_:object.mondo%20AND%20NOT%20_exists_:subject.uniprotkb ## 417 records @@ -1138,9 +1138,9 @@ components: source: "infores:ttd" response_mapping: "$ref": "#/components/x-bte-response-mapping/mondo-object" - # testExamples: - # - qInput: "TTD.TARGET:T99948" ## Programmed cell death 1 ligand 1 (PD-L1) - # oneOutput: "MONDO:0005447" ## Testicular cancer + testExamples: + - qInput: "TTD.TARGET:T99948" ## Programmed cell death 1 ligand 1 (PD-L1) + oneOutput: "MONDO:0005447" ## Testicular cancer ttd_target_id_target_for_mondo-rev: - supportBatch: true useTemplating: true @@ -1169,9 +1169,9 @@ components: source: "infores:ttd" response_mapping: "$ref": "#/components/x-bte-response-mapping/ttd_target_id-subject" - # testExamples: - # - qInput: "MONDO:0001351" ## Ovarian cancer (uterine adnexa cancer) - # oneOutput: "TTD.TARGET:T99948" ## Programmed cell death 1 ligand 1 (PD-L1) + testExamples: + - qInput: "MONDO:0001351" ## Ovarian cancer (uterine adnexa cancer) + oneOutput: "TTD.TARGET:T99948" ## Programmed cell death 1 ligand 1 (PD-L1) ttd_target_id_target_for_icd11: ## url: https://biothings.transltr.io/ttd/query?q=_exists_:subject.ttd_target_id%20AND%20association.predicate:%22biolink:target_for%22%20AND%20_exists_:object.icd11%20AND%20NOT%20_exists_:subject.uniprotkb%20AND%20NOT%20_exists_object.mondo ## 4,209 records @@ -1207,9 +1207,9 @@ components: source: "infores:ttd" response_mapping: "$ref": "#/components/x-bte-response-mapping/icd11-object" - # testExamples: - # - qInput: "TTD.TARGET:T99948" ## Programmed cell death 1 ligand 1 (PD-L1) - # oneOutput: "ICD11:2B54" ## Pleomorphic sarcoma + testExamples: + - qInput: "TTD.TARGET:T99948" ## Programmed cell death 1 ligand 1 (PD-L1) + oneOutput: "ICD11:2B54" ## Pleomorphic sarcoma ttd_target_id_target_for_icd11-rev: - supportBatch: true useTemplating: true @@ -1241,9 +1241,9 @@ components: source: "infores:ttd" response_mapping: "$ref": "#/components/x-bte-response-mapping/ttd_target_id-subject" - # testExamples: - # - qInput: "ICD11:1D6Y" ## COVID-19 - # oneOutput: "TTD.TARGET:T99041" ## HUMAN dipeptidyl peptidase 4 (DPP-4) + testExamples: + - qInput: "ICD11:1D6Y" ## COVID-19 + oneOutput: "TTD.TARGET:T99041" ## HUMAN dipeptidyl peptidase 4 (DPP-4) # chebi_interacts_with_uniprotkb: # ## url: https://biothings.transltr.io/ttd/query?q=_exists_:subject.chebi%20AND%20association.predicate:%22biolink:interacts_with%22%20AND%20_exists_:object.uniprotkb%20AND%20_exists_:subject.name%20AND%20_exists_:object.name # ## 13,020 records @@ -1275,9 +1275,9 @@ components: # source: "infores:ttd" # response_mapping: # "$ref": "#/components/x-bte-response-mapping/uniprotkb-object" - # # testExamples: - # # - qInput: "CHEBI:2696" - # # oneOutput: "UniProtKB:Q8WYB5" + # testExamples: + # - qInput: "CHEBI:2696" + # oneOutput: "UniProtKB:Q8WYB5" # chebi_interacts_with_uniprotkb-rev: # - supportBatch: true # useTemplating: true @@ -1307,9 +1307,9 @@ components: # source: "infores:ttd" # response_mapping: # "$ref": "#/components/x-bte-response-mapping/chebi-subject" - # # testExamples: - # # - qInput: "UniProtKB:P47870" - # # oneOutput: "CHEBI:2631" + # testExamples: + # - qInput: "UniProtKB:P47870" + # oneOutput: "CHEBI:2631" # chebi_interacts_with_ttd_target_id: # ## url: https://biothings.transltr.io/ttd/query?q=_exists_:subject.chebi%20AND%20association.predicate:%22biolink:interacts_with%22%20AND%20_exists_:object.ttd_target_id%20AND%20NOT%20_exists_:object.uniprotkb%20AND%20_exists_:subject.name%20AND%20_exists_:object.name # ## 5788 records @@ -1341,9 +1341,9 @@ components: # source: "infores:ttd" # response_mapping: # "$ref": "#/components/x-bte-response-mapping/ttd_target_id-object" - # # testExamples: - # # - qInput: "CHEBI:9953" - # # oneOutput: "TTD.TARGET:T12808" + # testExamples: + # - qInput: "CHEBI:9953" + # oneOutput: "TTD.TARGET:T12808" # chebi_interacts_with_ttd_target_id-rev: # - supportBatch: true # useTemplating: true @@ -1373,9 +1373,9 @@ components: # source: "infores:ttd" # response_mapping: # "$ref": "#/components/x-bte-response-mapping/chebi-subject" - # # testExamples: - # # - qInput: "TTD.TARGET:T31204" - # # oneOutput: "CHEBI:9711" + # testExamples: + # - qInput: "TTD.TARGET:T31204" + # oneOutput: "CHEBI:9711" pubchem_interacts_with_uniprotkb: ## url: https://biothings.transltr.io/ttd/query?q=_exists_:subject.pubchem_compound%20AND%20association.predicate:%22biolink:interacts_with%22%20AND%20_exists_:object.uniprotkb ## 38,914 records @@ -1408,9 +1408,9 @@ components: source: "infores:ttd" response_mapping: "$ref": "#/components/x-bte-response-mapping/uniprotkb-object" - # testExamples: - # - qInput: "PUBCHEM.COMPOUND:12795894" ## Procyanidin B-2 3,3'-di-O-gallate - # oneOutput: "UniProtKB:Q14534" ## Squalene monooxygenase (SQLE) + testExamples: + - qInput: "PUBCHEM.COMPOUND:12795894" ## Procyanidin B-2 3,3'-di-O-gallate + oneOutput: "UniProtKB:Q14534" ## Squalene monooxygenase (SQLE) pubchem_interacts_with_uniprotkb-rev: - supportBatch: true useTemplating: true @@ -1440,9 +1440,9 @@ components: source: "infores:ttd" response_mapping: "$ref": "#/components/x-bte-response-mapping/pubchem-subject" - # testExamples: - # - qInput: "UniProtKB:P29371" ## Neuromedin-K receptor (TACR3) - # oneOutput: "PUBCHEM.COMPOUND:132846" ## L-733060 + testExamples: + - qInput: "UniProtKB:P29371" ## Neuromedin-K receptor (TACR3) + oneOutput: "PUBCHEM.COMPOUND:132846" ## L-733060 pubchem_interacts_with_ttd_target_id: ## url: https://biothings.transltr.io/ttd/query?q=_exists_:subject.pubchem_compound%20AND%20association.predicate:%22biolink:interacts_with%22%20AND%20_exists_:object.ttd_target_id%20AND%20NOT%20_exists_:object.uniprotkb%20AND%20_exists_:object.name ## 18,714 records @@ -1480,9 +1480,9 @@ components: source: "infores:ttd" response_mapping: "$ref": "#/components/x-bte-response-mapping/ttd_target_id-object" - # testExamples: - # - qInput: "PUBCHEM.COMPOUND:128354" ## FR-62765 - # oneOutput: "TTD.TARGET:T26623" ## Aldose reductase (AKR1B1) + testExamples: + - qInput: "PUBCHEM.COMPOUND:128354" ## FR-62765 + oneOutput: "TTD.TARGET:T26623" ## Aldose reductase (AKR1B1) pubchem_interacts_with_ttd_target_id-rev: - supportBatch: true useTemplating: true @@ -1515,9 +1515,9 @@ components: source: "infores:ttd" response_mapping: "$ref": "#/components/x-bte-response-mapping/pubchem-subject" - # testExamples: - # - qInput: "TTD.TARGET:T60529" ## Prostaglandin G/H synthase 1 (COX-1) - # oneOutput: "PUBCHEM.COMPOUND:128861" ## CYANIDIN + testExamples: + - qInput: "TTD.TARGET:T60529" ## Prostaglandin G/H synthase 1 (COX-1) + oneOutput: "PUBCHEM.COMPOUND:128861" ## CYANIDIN ttd_drug_id_interacts_with_uniprotkb: ## url: https://biothings.transltr.io/ttd/query?q=_exists_:subject.ttd_drug_id%20AND%20association.predicate:%22biolink:interacts_with%22%20AND%20_exists_:object.uniprotkb%20AND%20NOT%20_exists_:subject.pubchem_compound ## 130 records @@ -1555,9 +1555,9 @@ components: source: "infores:ttd" response_mapping: "$ref": "#/components/x-bte-response-mapping/uniprotkb-object" - # testExamples: - # - qInput: "TTD.DRUG:D01ZYG" ## Alemtuzumab - # oneOutput: "UniProtKB:P31358" ## Cambridge pathology 1 antigen (CD52) + testExamples: + - qInput: "TTD.DRUG:D01ZYG" ## Alemtuzumab + oneOutput: "UniProtKB:P31358" ## Cambridge pathology 1 antigen (CD52) ttd_drug_id_interacts_with_uniprotkb-rev: - supportBatch: true useTemplating: true @@ -1590,9 +1590,9 @@ components: source: "infores:ttd" response_mapping: "$ref": "#/components/x-bte-response-mapping/ttd_drug_id-subject" - # testExamples: - # - qInput: "UniProtKB:P48551" ## Interferon alpha/beta receptor 2 (IFNAR2) - # oneOutput: "TTD.DRUG:D0GA0A" ## Interferon alfacon-1 + testExamples: + - qInput: "UniProtKB:P48551" ## Interferon alpha/beta receptor 2 (IFNAR2) + oneOutput: "TTD.DRUG:D0GA0A" ## Interferon alfacon-1 ttd_drug_id_interacts_with_ttd_target_id: ## url: https://biothings.transltr.io/ttd/query?q=_exists_:subject.ttd_drug_id%20AND%20association.predicate:%22biolink:interacts_with%22%20AND%20_exists_:object.ttd_target_id%20AND%20NOT%20_exists_:subject.pubchem_compound%20AND%20NOT%20_exists_:object.uniprotkb%20AND%20_exists_:subject.name%20AND%20_exists_:object.name ## 57 records @@ -1630,9 +1630,9 @@ components: source: "infores:ttd" response_mapping: "$ref": "#/components/x-bte-response-mapping/ttd_target_id-object" - # testExamples: - # - qInput: "TTD.DRUG:D02DES" ## Anakinra - # oneOutput: "TTD.TARGET:T72515" ## Interleukin 1 receptor type 1 (IL1R1) + testExamples: + - qInput: "TTD.DRUG:D02DES" ## Anakinra + oneOutput: "TTD.TARGET:T72515" ## Interleukin 1 receptor type 1 (IL1R1) ttd_drug_id_interacts_with_ttd_target_id-rev: - supportBatch: true useTemplating: true @@ -1665,9 +1665,9 @@ components: source: "infores:ttd" response_mapping: "$ref": "#/components/x-bte-response-mapping/ttd_drug_id-subject" - # testExamples: - # - qInput: "TTD.TARGET:T65414" ## Human immunodeficiency virus Envelope messenger RNA (HIV env mRNA) - # oneOutput: "TTD.DRUG:D0L3MP" ## VRX496 + testExamples: + - qInput: "TTD.TARGET:T65414" ## Human immunodeficiency virus Envelope messenger RNA (HIV env mRNA) + oneOutput: "TTD.DRUG:D0L3MP" ## VRX496 x-bte-response-mapping: # chebi-subject: # CHEBI: subject.chebi # no prefix diff --git a/uberon/smartapi.yaml b/uberon/smartapi.yaml index 86c5414a..dd501935 100644 --- a/uberon/smartapi.yaml +++ b/uberon/smartapi.yaml @@ -615,9 +615,9 @@ components: source: "infores:uberon" response_mapping: $ref: '#/components/x-bte-response-mapping/adjacent_to' - # testExamples: - # - qInput: "UBERON:0000319" ## cytotrophoblast - # oneOutput: "UBERON:0000371" ## syncytiotrophoblast + testExamples: + - qInput: "UBERON:0000319" ## cytotrophoblast + oneOutput: "UBERON:0000371" ## syncytiotrophoblast adjacent_to-rev: - supportBatch: true useTemplating: true @@ -637,9 +637,9 @@ components: source: "infores:uberon" response_mapping: $ref: '#/components/x-bte-response-mapping/id' - # testExamples: - # - qInput: "UBERON:0004367" ## Descemet's membrane - # oneOutput: "UBERON:0001777" ## substantia propria of cornea + testExamples: + - qInput: "UBERON:0004367" ## Descemet's membrane + oneOutput: "UBERON:0001777" ## substantia propria of cornea attaches_to: ## 125 records - supportBatch: true @@ -660,9 +660,9 @@ components: source: "infores:uberon" response_mapping: $ref: '#/components/x-bte-response-mapping/attaches_to' - # testExamples: - # - qInput: "UBERON:0011312" ## hyoepiglottic muscle - # oneOutput: "UBERON:0000388" ## epiglottis + testExamples: + - qInput: "UBERON:0011312" ## hyoepiglottic muscle + oneOutput: "UBERON:0000388" ## epiglottis attaches_to-rev: - supportBatch: true useTemplating: true @@ -682,9 +682,9 @@ components: source: "infores:uberon" response_mapping: $ref: '#/components/x-bte-response-mapping/id' - # testExamples: - # - qInput: "UBERON:0001075" ## bony vertebral centrum - # oneOutput: "UBERON:0011136" ## vertebral column ligament / ligament of vertebral column + testExamples: + - qInput: "UBERON:0001075" ## bony vertebral centrum + oneOutput: "UBERON:0011136" ## vertebral column ligament / ligament of vertebral column has_subclass: ## 6741 records - supportBatch: true @@ -705,9 +705,9 @@ components: source: "infores:uberon" response_mapping: $ref: '#/components/x-bte-response-mapping/has_subclass' - # testExamples: - # - qInput: "UBERON:0034709" ## hindbrain marginal layer - # oneOutput: "UBERON:0034708" ## cerebellum marginal layer + testExamples: + - qInput: "UBERON:0034709" ## hindbrain marginal layer + oneOutput: "UBERON:0034708" ## cerebellum marginal layer subclass_of: - supportBatch: true useTemplating: true @@ -727,9 +727,9 @@ components: source: "infores:uberon" response_mapping: $ref: '#/components/x-bte-response-mapping/subclass_of' - # testExamples: - # - qInput: "UBERON:0034704" ## inflow tract of left ventricle - # oneOutput: "UBERON:0034698" ## inflow tract of ventricle + testExamples: + - qInput: "UBERON:0034704" ## inflow tract of left ventricle + oneOutput: "UBERON:0034698" ## inflow tract of ventricle develops_from: ## 1354 records - supportBatch: true @@ -750,9 +750,9 @@ components: source: "infores:uberon" response_mapping: $ref: '#/components/x-bte-response-mapping/develops_from' - # testExamples: - # - qInput: "UBERON:2000088" ## yolk syncytial layer - # oneOutput: "UBERON:2000084" ## yolk + testExamples: + - qInput: "UBERON:2000088" ## yolk syncytial layer + oneOutput: "UBERON:2000084" ## yolk develops_from-rev: - supportBatch: true useTemplating: true @@ -772,9 +772,9 @@ components: source: "infores:uberon" response_mapping: $ref: '#/components/x-bte-response-mapping/id' - # testExamples: - # - qInput: "UBERON:0006604" ## lamina orbitonasalis - # oneOutput: "UBERON:2000226" ## lateral ethmoid bone + testExamples: + - qInput: "UBERON:0006604" ## lamina orbitonasalis + oneOutput: "UBERON:2000226" ## lateral ethmoid bone extends_fibers_into: ## 109 records - supportBatch: true @@ -795,9 +795,9 @@ components: source: "infores:uberon" response_mapping: $ref: '#/components/x-bte-response-mapping/extends_fibers_into' - # testExamples: - # - qInput: "UBERON:0000959" ## optic chiasma - # oneOutput: "UBERON:0000941" ## cranial nerve II + testExamples: + - qInput: "UBERON:0000959" ## optic chiasma + oneOutput: "UBERON:0000941" ## cranial nerve II extends_fibers_into-rev: - supportBatch: true useTemplating: true @@ -817,9 +817,9 @@ components: source: "infores:uberon" response_mapping: $ref: '#/components/x-bte-response-mapping/id' - # testExamples: - # - qInput: "UBERON:0002925" ## trigeminal nucleus - # oneOutput: "UBERON:0001645" ## trigeminal nerve + testExamples: + - qInput: "UBERON:0002925" ## trigeminal nucleus + oneOutput: "UBERON:0001645" ## trigeminal nerve has_part: ## 263 records - supportBatch: true @@ -840,9 +840,9 @@ components: source: "infores:uberon" response_mapping: $ref: '#/components/x-bte-response-mapping/has_part' - # testExamples: - # - qInput: "UBERON:0002364" ## tympanic membrane - # oneOutput: "UBERON:0005042" ## inner epithelial layer of tympanic membrane + testExamples: + - qInput: "UBERON:0002364" ## tympanic membrane + oneOutput: "UBERON:0005042" ## inner epithelial layer of tympanic membrane has_part-rev: - supportBatch: true useTemplating: true @@ -862,9 +862,9 @@ components: source: "infores:uberon" response_mapping: $ref: '#/components/x-bte-response-mapping/id' - # testExamples: - # - qInput: "UBERON:0001751" ## dentine - # oneOutput: "UBERON:0001091" ## calcareous tooth + testExamples: + - qInput: "UBERON:0001751" ## dentine + oneOutput: "UBERON:0001091" ## calcareous tooth located_in: ## 151 records - supportBatch: true @@ -885,9 +885,9 @@ components: source: "infores:uberon" response_mapping: $ref: '#/components/x-bte-response-mapping/located_in' - # testExamples: - # - qInput: "UBERON:4000030" ## oropharyngeal papilla - # oneOutput: "UBERON:0001729" ## oropharynx + testExamples: + - qInput: "UBERON:4000030" ## oropharyngeal papilla + oneOutput: "UBERON:0001729" ## oropharynx located_in-rev: - supportBatch: true useTemplating: true @@ -907,9 +907,9 @@ components: source: "infores:uberon" response_mapping: $ref: '#/components/x-bte-response-mapping/id' - # testExamples: - # - qInput: "UBERON:0002224" ## thoracic cavity - # oneOutput: "UBERON:0000170" ## pair of lungs + testExamples: + - qInput: "UBERON:0002224" ## thoracic cavity + oneOutput: "UBERON:0000170" ## pair of lungs part_of: ## 8248 records - supportBatch: true @@ -930,9 +930,9 @@ components: source: "infores:uberon" response_mapping: $ref: '#/components/x-bte-response-mapping/part_of' - # testExamples: - # - qInput: "UBERON:0034754" ## occipitofrontal fasciculus - # oneOutput: "UBERON:0011299" ## white matter of telencephalon + testExamples: + - qInput: "UBERON:0034754" ## occipitofrontal fasciculus + oneOutput: "UBERON:0011299" ## white matter of telencephalon part_of-rev: - supportBatch: true useTemplating: true @@ -952,9 +952,9 @@ components: source: "infores:uberon" response_mapping: $ref: '#/components/x-bte-response-mapping/id' - # testExamples: - # - qInput: "UBERON:0002084" ## heart left ventricle - # oneOutput: "UBERON:0036285" ## wall of left ventricle + testExamples: + - qInput: "UBERON:0002084" ## heart left ventricle + oneOutput: "UBERON:0036285" ## wall of left ventricle x-bte-response-mapping: adjacent_to: UBERON: adjacent_to.uberon