From e95474d1afa410db726cf99ba6e77f0b797e83ec Mon Sep 17 00:00:00 2001
From: tokebe <43009413+tokebe@users.noreply.github.com>
Date: Mon, 11 Dec 2023 13:18:12 -0500
Subject: [PATCH 1/2] chore: update cached smartapi

---
 data/predicates.json     | 2 +-
 data/smartapi_specs.json | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/data/predicates.json b/data/predicates.json
index 4ed249f4..edc4b43f 100644
--- a/data/predicates.json
+++ b/data/predicates.json
@@ -1 +1 @@
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diff --git a/data/smartapi_specs.json b/data/smartapi_specs.json
index 471b2d04..e62efd67 100644
--- a/data/smartapi_specs.json
+++ b/data/smartapi_specs.json
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If the CURIE is from the Relation Ontology, the service will check its superproperties until an exact match is found.","tags":["lookup"]}},"/versions":{"get":{"description":"","responses":{"200":{"content":{"application/json":{"schema":{"items":{"type":"string"},"type":"array"}}},"description":"successful operation"}},"summary":"Get available BioLink Model versions. These values can be used to parameterize other function calls.","tags":["meta"]}}},"servers":[{"description":"Default server","url":"https://biolink-lookup.ci.transltr.io","x-location":"ITRB","x-maturity":"staging"},{"description":"Default server","url":"https://biolink-lookup.test.transltr.io","x-location":"ITRB","x-maturity":"testing"},{"description":"Default server","url":"https://biolink-lookup.transltr.io","x-location":"ITRB","x-maturity":"production"}],"tags":[{"name":"translator"},{"name":"lookup"},{"name":"meta"}]},{"_id":"1c056ffc7ed0dd1229e71c4752239465","_meta":{"date_created":"2020-12-07T23:02:21.623909+00:00","last_updated":"2023-05-22T07:00:55.858690+00:00","url":"https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/ols/smartapi.yaml","username":"newgene"},"components":{"x-bte-kgs-operations":{"disease_has_subclass_disease":[{"inputs":[{"id":"DOID","semantic":"Disease"}],"outputs":[{"id":"DOID","semantic":"Disease"}],"parameters":{"id":"{{ queryInputs }}"},"predicate":"superclass_of","response_mapping":{"$ref":"#/components/x-bte-response-mapping/disease_has_subclass_disease"},"source":"infores:disease-ontology","supportBatch":false,"useTemplating":true}]},"x-bte-response-mapping":{"disease_has_subclass_disease":{"DOID":"_embedded.terms.obo_id"}}},"info":{"contact":{"email":"help@pharmgkb.org","name":"pharmgkb help desk","x-role":"responsible developer"},"description":"The OLS REST API provides access to key biological data from OLS. The services provide a unified interface to query information about ontology terms from GO (the Gene Ontology) and ECO (the Evidence & Conclusion Ontology), Gene Ontology annotations from the EBI's GOA database, and gene products (proteins from UniProt, RNA from RNAcentral and complexes from ComplexPortal). 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}}\n}"},"requestBodyType":"object","response_mapping":{"$ref":"#/components/x-bte-response-mapping/reactome"},"supportBatch":false,"useTemplating":true}],"gene2pathway_1":[{"inputs":[{"id":"NCBIGene","semantic":"Gene"}],"outputs":[{"id":"REACT","semantic":"Pathway"}],"parameters":{},"predicate":"participates_in","requestBody":{"body":"{ \n  \"analytes\":\n    {{ queryInputs \n       | replPrefix('entrez') \n       | dump }}\n}"},"requestBodyType":"object","response_mapping":{"$ref":"#/components/x-bte-response-mapping/reactome"},"supportBatch":false,"useTemplating":true}]},"x-bte-response-mapping":{"reactome":{"REACT":"data.pathwayId","output_name":"data.pathwayName"}}},"info":{"contact":{"email":"NCATSRaMP@nih.gov","name":"RaMP","x-id":"https://github.com/tsheils","x-role":"responsible developer"},"description":"Relational Database of Metabolic Pathways (RaMP) API","termsOfService":"https://rampdb.nih.gov","title":"RaMP API 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types"}},"/api/entity_counts":{"get":{"parameters":[],"responses":{"200":{"content":{"application/json":{"schema":{"type":"object"}}},"description":"OK"},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal Server Error"},"default":{"content":{"application/json":{"schema":{"type":"object"}}},"description":"Default response."}},"summary":"Return counts on entities and their associations"}},"/api/analyte_intersects":{"get":{"parameters":[{"description":"specifies type of analyte intersects to return, 'metabolites' or 'genes'","in":"query","name":"analytetype","required":true,"schema":{"enum":["metabolites","genes"],"type":"string"}},{"description":"specifies 'global' or 'mapped-to-pathway'","in":"query","name":"query_scope","required":true,"schema":{"enum":["global","mapped-to-pathway"],"type":"string"}}],"responses":{"200":{"description":"OK"},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal Server 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ClassyFire)"}},"/api/pathways-from-analytes":{"post":{"requestBody":{"content":{"application/json":{"schema":{"example":{"analytes":["ensembl:ENSG00000135679","hmdb:HMDB0000064","hmdb:HMDB0000148","ensembl:ENSG00000141510"]},"properties":{"analytes":{"items":{"type":"string"},"type":"array"}},"type":"object"}}},"description":"Retrieve pathway(s) for a given analyte(s). IDs should be prepended by ID source (e.g. **hmdb**:C00412).","required":true},"responses":{"200":{"description":"OK"},"500":{"description":"Internal Server Error"}},"summary":"Return pathways from given list of analytes","x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/chemical2pathway_1"},{"$ref":"#/components/x-bte-kgs-operations/gene2pathway_1"}]}},"/api/analytes-from-pathways":{"post":{"requestBody":{"content":{"application/json":{"schema":{"example":{"analyte_type":"both","pathway":["De Novo Triacylglycerol Biosynthesis","sphingolipid metabolism"]},"properties":{"analyte_type":{"enum":["gene","metabolite","both"],"type":"string"},"pathway":{"items":{"type":"string"},"type":"array"}},"type":"object"}}},"description":"Enter exact pathway name(s). `analyte_type` should be `\"gene\"`, `\"metabolite\"`, or `\"both\"` *(default)*","required":true},"responses":{"200":{"description":"OK"},"500":{"description":"Internal Server Error"}},"summary":"Retrieve analytes (genes/proteins, metabolites) by pathway."}},"/api/ontologies-from-metabolites":{"post":{"requestBody":{"content":{"application/json":{"schema":{"example":{"NameOrIds":"ids","metabolite":["ensembl:ENSG00000135679","hmdb:HMDB0000064","hmdb:HMDB0000148","ensembl:ENSG00000141510"]},"properties":{"NameOrIds":{"enum":["name","ids"],"type":"string"},"metabolite":{"items":{"type":"string"},"type":"array"}},"type":"object"}}},"description":"Enter a list of metabolites. IDs should be prepended by ID source (e.g. **kegg**:C00412).","required":true},"responses":{"200":{"description":"OK"},"500":{"description":"Internal Server Error"}},"summary":"Return ontologies from list of metabolites"}},"/api/metabolites-from-ontologies":{"post":{"requestBody":{"content":{"application/json":{"schema":{"example":{"format":"json","ontology":["Colon","Liver","Lung"]},"properties":{"format":{"enum":["json","tsv"],"type":"string"},"ontology":{"items":{"type":"string"},"type":"array"}},"type":"object"}}},"description":"Enter ontology(ies) and retrieve corresponding analytes (metabolites).","required":true},"responses":{"200":{"description":"OK"},"500":{"description":"Internal Server Error"}},"summary":"Return metabolites from ontology"}},"/api/chemical-classes":{"post":{"requestBody":{"content":{"application/json":{"schema":{"example":{"metabolites":["hmdb:HMDB0000056","hmdb:HMDB0000439","hmdb:HMDB0000479","hmdb:HMDB0000532","hmdb:HMDB0001015","hmdb:HMDB0001138","hmdb:HMDB0029159","hmdb:HMDB0029412","hmdb:HMDB0034365","hmdb:HMDB0035227","hmdb:HMDB0007973","hmdb:HMDB0008057","hmdb:HMDB0011211"]},"properties":{"biospecimen":{"enum":["Blood","Adipose","Heart","Urine","Brain","Liver","Kidney","Saliva","Feces"],"type":"string"},"metabolites":{"items":{"type":"string"},"type":"array"}},"type":"object"}}},"description":"Retrieve chemical class information (from ClassyFire and LIPID MAPS) for input metabolite IDs. 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IDs should be prepended by ID source (e.g. **hmdb**:C00412).","required":true},"responses":{"200":{"description":"OK"},"500":{"description":"Internal Server Error"}},"summary":"Return chemical properties of given metabolites"}},"/api/common-reaction-analytes":{"post":{"requestBody":{"content":{"application/json":{"schema":{"example":{"analyte":["ensembl:ENSG00000135679","hmdb:HMDB0000064","hmdb:HMDB0000148","ensembl:ENSG00000141510"]},"properties":{"NameOrIds":{"enum":["name","ids"],"type":"string"},"analyte":{"items":{"type":"string"},"type":"array"}},"type":"object"}}},"description":"Retrieve Analytes Involved in the Same Reaction. 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This is a newer version where each record is a unique combination of subjectID-predicate- objectID and contains a count of the unique pmids and predications supporting it.","termsOfService":"https://biothings.io/about","title":"BioThings SEMMEDDB v2 API","version":"43","x-translator":{"biolink-version":"3.1.1","component":"KP","infores":"infores:biothings-semmeddb-2","team":["Service Provider"]}},"paths":{"/association/{id}":{"get":{"description":"By default, this will return the complete association in JSON format. If the input is not valid, 404 (NOT FOUND) will be returned.\n\nOptionally, you can pass a \"fields\" parameter to return only the annotation you want  (by filtering returned object fields). \"fields\" accepts any attributes (a.k.a fields) available  from the association. Multiple attributes should be separated by commas. If an attribute is not  available for a specific association, it will be ignored. 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RUPTS-orgf-rev"},{"$ref":"#/components/x-bte-kgs-operations/orch-PREDISPOSES-inpo"},{"$ref":"#/components/x-bte-kgs-operations/eico-INHIBITS-gngm-rev"},{"$ref":"#/components/x-bte-kgs-operations/gngm-INTERACTS_WITH-imft"},{"$ref":"#/components/x-bte-kgs-operations/gngm-INTERACTS_WITH-imft-rev"},{"$ref":"#/components/x-bte-kgs-operations/lipd-ASSOCIATED_WITH-patf-rev"},{"$ref":"#/components/x-bte-kgs-operations/antb-COEXISTS_WITH-aapp-rev"},{"$ref":"#/components/x-bte-kgs-operations/aapp-PREVENTS-dsyn"},{"$ref":"#/components/x-bte-kgs-operations/cgab-LOCATION_OF-neop-rev"},{"$ref":"#/components/x-bte-kgs-operations/gngm-INTERACTS_WITH-carb"},{"$ref":"#/components/x-bte-kgs-operations/phsf-PRODUCES-bacs-rev"},{"$ref":"#/components/x-bte-kgs-operations/eico-ASSOCIATED_WITH-dsyn-rev"},{"$ref":"#/components/x-bte-kgs-operations/topp-TREATS-comd"},{"$ref":"#/components/x-bte-kgs-operations/hops-ASSOCIATED_WITH-patf-rev"},{"$ref":"#/components/x-bte-kgs-operations/cell-PRODUCES-horm"},{"$ref":"#/components/x-bte-kgs-operations/inch-AUGMENTS-bpoc-rev"},{"$ref":"#/components/x-bte-kgs-operations/gngm-PREDISPOSES-mobd"},{"$ref":"#/components/x-bte-kgs-operations/lipd-INTERACTS_WITH-gngm-rev"},{"$ref":"#/components/x-bte-kgs-operations/celc-AFFECTS-phsf"},{"$ref":"#/components/x-bte-kgs-operations/gngm-AFFECTS-sosy"},{"$ref":"#/components/x-bte-kgs-operations/gngm-AFFECTS-sosy-rev"},{"$ref":"#/components/x-bte-kgs-operations/bacs-AFFECTS-sosy-rev"},{"$ref":"#/components/x-bte-kgs-operations/gngm-STIMULATES-moft"},{"$ref":"#/components/x-bte-kgs-operations/gngm-STIMULATES-moft-rev"},{"$ref":"#/components/x-bte-kgs-operations/phsu-PREDISPOSES-patf-rev"},{"$ref":"#/components/x-bte-kgs-operations/imft-COEXISTS_WITH-imft"},{"$ref":"#/components/x-bte-kgs-operations/imft-COEXISTS_WITH-imft-rev"},{"$ref":"#/components/x-bte-kgs-operations/aapp-PRODUCES-hops"},{"$ref":"#/components/x-bte-kgs-operations/orch-PREVENTS-sosy-rev"},{"$ref":"#/components/x-bte-kgs-operations/horm-DISRUPTS-celf-rev"},{"$ref":"#/components/x-bte-kgs-operations/inch-COEXISTS_WITH-gngm-rev"},{"$ref":"#/components/x-bte-kgs-operations/hops-COEXISTS_WITH-gngm-rev"},{"$ref":"#/components/x-bte-kgs-operations/bpoc-PRODUCES-orch"},{"$ref":"#/components/x-bte-kgs-operations/dsyn-AFFECTS-comd"},{"$ref":"#/components/x-bte-kgs-operations/carb-AUGMENTS-bpoc-rev"},{"$ref":"#/components/x-bte-kgs-operations/hops-PREDISPOSES-neop-rev"},{"$ref":"#/components/x-bte-kgs-operations/aapp-DISRUPTS-inpo"},{"$ref":"#/components/x-bte-kgs-operations/lipd-DISRUPTS-celf-rev"},{"$ref":"#/components/x-bte-kgs-operations/gngm-PRODUCES-gngm"},{"$ref":"#/components/x-bte-kgs-operations/gngm-PRODUCES-gngm-rev"},{"$ref":"#/components/x-bte-kgs-operations/food-AFFECTS-ortf"},{"$ref":"#/components/x-bte-kgs-operations/orch-AUGMENTS-sosy"},{"$ref":"#/components/x-bte-kgs-operations/orch-AUGMENTS-sosy-rev"},{"$ref":"#/components/x-bte-kgs-operations/comd-PRODUCES-bacs-rev"},{"$ref":"#/components/x-bte-kgs-operations/aapp-PREDISPOSES-sosy"},{"$ref":"#/components/x-bte-kgs-operations/aapp-PREDISPOSES-sosy-rev"},{"$ref":"#/components/x-bte-kgs-operations/gngm-PRODUCES-imft"},{"$ref":"#/components/x-bte-kgs-operations/gngm-PRODUCES-imft-rev"},{"$ref":"#/components/x-bte-kgs-operations/gngm-COEXISTS_WITH-hops"},{"$ref":"#/components/x-bte-kgs-operations/imft-INTERACTS_WITH-gngm"},{"$ref":"#/components/x-bte-kgs-operations/imft-INTERACTS_WITH-gngm-rev"},{"$ref":"#/components/x-bte-kgs-operations/dsyn-COMPLICATES-neop"},{"$ref":"#/components/x-bte-kgs-operations/nsba-COEXISTS_WITH-aapp-rev"},{"$ref":"#/components/x-bte-kgs-operations/phsu-DISRUPTS-cell-rev"},{"$ref":"#/components/x-bte-kgs-operations/gngm-AUGMENTS-cell"},{"$ref":"#/components/x-bte-kgs-operations/gngm-AUGMENTS-cell-rev"},{"$ref":"#/components/x-bte-kgs-operations/strd-INHIBITS-gngm-rev"},{"$ref":"#/components/x-bte-kgs-operations/aapp-INHIBITS-antb"},{"$ref":"#/components/x-bte-kgs-operations/orch-CAUSES-cgab"},{"$ref":"#/components/x-bte-kgs-operations/cgab-COEXISTS_WITH-patf-rev"},{"$ref":"#/components/x-bte-kgs-operations/horm-AUGMENTS-ortf-rev"},{"$ref":"#/components/x-bte-kgs-operations/bacs-DISRUPTS-celc-rev"},{"$ref":"#/components/x-bte-kgs-operations/antb-TREATS-sosy-rev"},{"$ref":"#/components/x-bte-kgs-operations/phsu-DISRUPTS-dsyn-rev"},{"$ref":"#/components/x-bte-kgs-operations/topp-PREDISPOSES-sosy"},{"$ref":"#/components/x-bte-kgs-operations/topp-PREDISPOSES-sosy-rev"},{"$ref":"#/components/x-bte-kgs-operations/inch-CAUSES-sosy-rev"},{"$ref":"#/components/x-bte-kgs-operations/orch-DISRUPTS-inpo"},{"$ref":"#/components/x-bte-kgs-operations/strd-STIMULATES-gngm-rev"},{"$ref":"#/components/x-bte-kgs-operations/gngm-INTERACTS_WITH-antb"},{"$ref":"#/components/x-bte-kgs-operations/aapp-PREVENTS-acab"},{"$ref":"#/components/x-bte-kgs-operations/diap-DIAGNOSES-comd"},{"$ref":"#/components/x-bte-kgs-operations/inch-AFFECTS-bpoc-rev"},{"$ref":"#/components/x-bte-kgs-operations/gngm-CONVERTS_TO-gngm"},{"$ref":"#/componen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RUPTS-orgf-rev"},{"$ref":"#/components/x-bte-kgs-operations/orch-PREDISPOSES-inpo"},{"$ref":"#/components/x-bte-kgs-operations/eico-INHIBITS-gngm-rev"},{"$ref":"#/components/x-bte-kgs-operations/gngm-INTERACTS_WITH-imft"},{"$ref":"#/components/x-bte-kgs-operations/gngm-INTERACTS_WITH-imft-rev"},{"$ref":"#/components/x-bte-kgs-operations/lipd-ASSOCIATED_WITH-patf-rev"},{"$ref":"#/components/x-bte-kgs-operations/antb-COEXISTS_WITH-aapp-rev"},{"$ref":"#/components/x-bte-kgs-operations/aapp-PREVENTS-dsyn"},{"$ref":"#/components/x-bte-kgs-operations/cgab-LOCATION_OF-neop-rev"},{"$ref":"#/components/x-bte-kgs-operations/gngm-INTERACTS_WITH-carb"},{"$ref":"#/components/x-bte-kgs-operations/phsf-PRODUCES-bacs-rev"},{"$ref":"#/components/x-bte-kgs-operations/eico-ASSOCIATED_WITH-dsyn-rev"},{"$ref":"#/components/x-bte-kgs-operations/topp-TREATS-comd"},{"$ref":"#/components/x-bte-kgs-operations/hops-ASSOCIATED_WITH-patf-rev"},{"$ref":"#/components/x-bte-kgs-operations/cell-PRODUCES-horm"},{"$ref":"#/components/x-bte-kgs-operations/inch-AUGMENTS-bpoc-rev"},{"$ref":"#/components/x-bte-kgs-operations/gngm-PREDISPOSES-mobd"},{"$ref":"#/components/x-bte-kgs-operations/lipd-INTERACTS_WITH-gngm-rev"},{"$ref":"#/components/x-bte-kgs-operations/celc-AFFECTS-phsf"},{"$ref":"#/components/x-bte-kgs-operations/gngm-AFFECTS-sosy"},{"$ref":"#/components/x-bte-kgs-operations/gngm-AFFECTS-sosy-rev"},{"$ref":"#/components/x-bte-kgs-operations/bacs-AFFECTS-sosy-rev"},{"$ref":"#/components/x-bte-kgs-operations/gngm-STIMULATES-moft"},{"$ref":"#/components/x-bte-kgs-operations/gngm-STIMULATES-moft-rev"},{"$ref":"#/components/x-bte-kgs-operations/phsu-PREDISPOSES-patf-rev"},{"$ref":"#/components/x-bte-kgs-operations/imft-COEXISTS_WITH-imft"},{"$ref":"#/components/x-bte-kgs-operations/imft-COEXISTS_WITH-imft-rev"},{"$ref":"#/components/x-bte-kgs-operations/aapp-PRODUCES-hops"},{"$ref":"#/components/x-bte-kgs-operations/orch-PREVENTS-sosy-rev"},{"$ref":"#/components/x-bte-kgs-operations/horm-DISRUPTS-celf-rev"},{"$ref":"#/components/x-bte-kgs-operations/inch-COEXISTS_WITH-gngm-rev"},{"$ref":"#/components/x-bte-kgs-operations/hops-COEXISTS_WITH-gngm-rev"},{"$ref":"#/components/x-bte-kgs-operations/bpoc-PRODUCES-orch"},{"$ref":"#/components/x-bte-kgs-operations/dsyn-AFFECTS-comd"},{"$ref":"#/components/x-bte-kgs-operations/carb-AUGMENTS-bpoc-rev"},{"$ref":"#/components/x-bte-kgs-operations/hops-PREDISPOSES-neop-rev"},{"$ref":"#/components/x-bte-kgs-operations/aapp-DISRUPTS-inpo"},{"$ref":"#/components/x-bte-kgs-operations/lipd-DISRUPTS-celf-rev"},{"$ref":"#/components/x-bte-kgs-operations/gngm-PRODUCES-gngm"},{"$ref":"#/components/x-bte-kgs-operations/gngm-PRODUCES-gngm-rev"},{"$ref":"#/components/x-bte-kgs-operations/food-AFFECTS-ortf"},{"$ref":"#/components/x-bte-kgs-operations/orch-AUGMENTS-sosy"},{"$ref":"#/components/x-bte-kgs-operations/orch-AUGMENTS-sosy-rev"},{"$ref":"#/components/x-bte-kgs-operations/comd-PRODUCES-bacs-rev"},{"$ref":"#/components/x-bte-kgs-operations/aapp-PREDISPOSES-sosy"},{"$ref":"#/components/x-bte-kgs-operations/aapp-PREDISPOSES-sosy-rev"},{"$ref":"#/components/x-bte-kgs-operations/gngm-PRODUCES-imft"},{"$ref":"#/components/x-bte-kgs-operations/gngm-PRODUCES-imft-rev"},{"$ref":"#/components/x-bte-kgs-operations/gngm-COEXISTS_WITH-hops"},{"$ref":"#/components/x-bte-kgs-operations/imft-INTERACTS_WITH-gngm"},{"$ref":"#/components/x-bte-kgs-operations/imft-INTERACTS_WITH-gngm-rev"},{"$ref":"#/components/x-bte-kgs-operations/dsyn-COMPLICATES-neop"},{"$ref":"#/components/x-bte-kgs-operations/nsba-COEXISTS_WITH-aapp-rev"},{"$ref":"#/components/x-bte-kgs-operations/phsu-DISRUPTS-cell-rev"},{"$ref":"#/components/x-bte-kgs-operations/gngm-AUGMENTS-cell"},{"$ref":"#/components/x-bte-kgs-operations/gngm-AUGMENTS-cell-rev"},{"$ref":"#/components/x-bte-kgs-operations/strd-INHIBITS-gngm-rev"},{"$ref":"#/components/x-bte-kgs-operations/aapp-INHIBITS-antb"},{"$ref":"#/components/x-bte-kgs-operations/orch-CAUSES-cgab"},{"$ref":"#/components/x-bte-kgs-operations/cgab-COEXISTS_WITH-patf-rev"},{"$ref":"#/components/x-bte-kgs-operations/horm-AUGMENTS-ortf-rev"},{"$ref":"#/components/x-bte-kgs-operations/bacs-DISRUPTS-celc-rev"},{"$ref":"#/components/x-bte-kgs-operations/antb-TREATS-sosy-rev"},{"$ref":"#/components/x-bte-kgs-operations/phsu-DISRUPTS-dsyn-rev"},{"$ref":"#/components/x-bte-kgs-operations/topp-PREDISPOSES-sosy"},{"$ref":"#/components/x-bte-kgs-operations/topp-PREDISPOSES-sosy-rev"},{"$ref":"#/components/x-bte-kgs-operations/inch-CAUSES-sosy-rev"},{"$ref":"#/components/x-bte-kgs-operations/orch-DISRUPTS-inpo"},{"$ref":"#/components/x-bte-kgs-operations/strd-STIMULATES-gngm-rev"},{"$ref":"#/components/x-bte-kgs-operations/gngm-INTERACTS_WITH-antb"},{"$ref":"#/components/x-bte-kgs-operations/aapp-PREVENTS-acab"},{"$ref":"#/components/x-bte-kgs-operations/diap-DIAGNOSES-comd"},{"$ref":"#/components/x-bte-kgs-operations/inch-AFFECTS-bpoc-rev"},{"$ref":"#/components/x-bte-kgs-operations/gngm-CONVERTS_TO-gngm"},{"$ref":"#/componen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payload."}},"tags":["query"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/gene-sensitivity-chem"},{"$ref":"#/components/x-bte-kgs-operations/gene-sensitivity-chem-rev"},{"$ref":"#/components/x-bte-kgs-operations/gene-resistance-chem"},{"$ref":"#/components/x-bte-kgs-operations/gene-resistance-chem-rev"},{"$ref":"#/components/x-bte-kgs-operations/gene-associated-disease"},{"$ref":"#/components/x-bte-kgs-operations/gene-associated-disease-rev"},{"$ref":"#/components/x-bte-kgs-operations/disease-biomarker-gene"},{"$ref":"#/components/x-bte-kgs-operations/disease-biomarker-gene-rev"},{"$ref":"#/components/x-bte-kgs-operations/chem-targets-gene"},{"$ref":"#/components/x-bte-kgs-operations/chem-targets-gene-rev"},{"$ref":"#/components/x-bte-kgs-operations/gene-physicallyInteracts-gene"},{"$ref":"#/components/x-bte-kgs-operations/gene-physicallyInteracts-gene-rev"},{"$ref":"#/components/x-bte-kgs-operations/gene-geneticallyInteracts-gene"},{"$ref":"#/components/x-bte-kgs-operations/gene-geneticallyInteracts-gene-rev"},{"$ref":"#/components/x-bte-kgs-operations/gene-negativelyCorrelated-gene"},{"$ref":"#/components/x-bte-kgs-operations/gene-negativelyCorrelated-gene-rev"},{"$ref":"#/components/x-bte-kgs-operations/gene-positivelyCorrelated-gene"},{"$ref":"#/components/x-bte-kgs-operations/gene-positivelyCorrelated-gene-rev"}]}}},"servers":[{"description":"Encrypted Production server","url":"https://biothings.ncats.io/biggim_drugresponse_kp","x-maturity":"production"},{"description":"Production server","url":"http://biothings.ncats.io/biggim_drugresponse_kp","x-maturity":"production"}],"tags":[{"name":"gene"},{"name":"disease"},{"name":"chemical"},{"name":"association"},{"name":"annotation"},{"name":"query"},{"name":"translator"},{"name":"biothings"},{"name":"biothings_graph"}]},{"_id":"3d41210995d6cf1c97f355e678b9b09f","_meta":{"date_created":"2022-09-06T19:39:04.108979+00:00","last_updated":"2023-05-05T07:05:12.376510+00:00","url":"https://cam-kp-api.transltr.io/1.3.0/docs/docs.yaml","username":"gaurav"},"info":{"contact":{"email":"balhoff@renci.org","name":"Jim Balhoff"},"description":"TRAPI interface to database of Causal Activity Models","license":{"name":"MIT License","url":"https://opensource.org/licenses/MIT"},"termsOfService":"https://opensource.org/licenses/MIT","title":"CAM-KP 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body"},"default":{"content":{"text/plain":{"schema":{"type":"string"}}},"description":""}},"summary":"Submit a TRAPI question graph and retrieve matching solutions"}},"/meta_knowledge_graph":{"get":{"operationId":"getMeta_knowledge_graph","responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/MetaKnowledgeGraph"}}},"description":""},"default":{"content":{"text/plain":{"schema":{"type":"string"}}},"description":""}},"summary":"Get MetaKnowledgeGraph used at this service"}},"/lookup":{"get":{"operationId":"getLookup","parameters":[{"in":"query","name":"subject","required":false,"schema":{"default":"NCBIGene:478","type":"string"}},{"description":"The number of hops to recurse in objRelations","example":10,"in":"query","name":"hopLimit","required":false,"schema":{"default":10,"type":"integer"}},{"description":"The URL where the Translator NodeNormalizer can be found -- if blank or missing, no node normalization will occur","example":"https://nodenorm.transltr.io/1.3/get_normalized_nodes","in":"query","name":"nodeNormURL","required":false,"schema":{"type":"string"}},{"description":"Whether or not to use conflation (should be 'true' or 'false')","example":true,"in":"query","name":"conflate","required":false,"schema":{"default":true,"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Result"}}},"description":""},"400":{"content":{"text/plain":{"schema":{"type":"string"}}},"description":"Invalid value for: query parameter hopLimit, Invalid value for: query parameter nodeNormURL"},"default":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Error"}}},"description":""}},"summary":"Look up relationships within CAM-KP-API by identifier."}}},"servers":[{"description":"Default server","url":"https://cam-kp-api.transltr.io/1.3.0","x-location":"RENCI","x-maturity":"production"}],"tags":[{"name":"maturity"},{"name":"translator"},{"name":"trapi"}]},{"_id":"dc91716f44207d2e1287c727f281d339","_ignored":["paths.pathitem.post.summary.raw"],"_meta":{"date_created":"2021-03-11T18:52:08.763346+00:00","last_updated":"2023-05-22T07:05:46.676193+00:00","url":"https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/biothings_explorer/smartapi.yaml","username":"andrewsu"},"info":{"contact":{"email":"asu@scripps.edu","name":"Andrew Su","url":"https://github.com/andrewsu"},"description":"A TRAPI/Reasoner Standard API for BioThings Explorer (BTE)","termsOfService":"https://biothings.io/about","title":"BioThings Explorer (BTE) TRAPI","version":"2.8.1","x-translator":{"biolink-version":"3.1.1","component":"ARA","infores":"infores:biothings-explorer","team":["Exploring 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The easiest way to find these is to read the list of APIs BTE uses https://github.com/biothings/biothings_explorer/blob/main/src/config/apis.js","example":"09c8782d9f4027712e65b95424adba79","in":"path","name":"smartapi_id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/MetaKnowledgeGraph"}}},"description":"Returns a TRAPI-compliant meta-knowledge-graph representation for an individual SmartAPI KP API (that has x-bte annotation)"}},"summary":"TRAPI-compliant meta-knowledge-graph representation for an individual SmartAPI KP API (that has x-bte annotation)","tags":["meta_knowledge_graph"]}},"/team/{team_name}/meta_knowledge_graph":{"get":{"parameters":[{"description":"Translator Team Name. Current options: Service Provider, Multiomics Provider, Text Mining Provider. The easiest way to find what KP APIs would be included under these teams is to read the list of APIs BTE uses https://github.com/biothings/biothings_explorer/blob/main/src/config/apis.js. Note that Service Provider endpoints are also advertised separately as a KP  http://smart-api.info/registry?q=36f82f05705c317bac17ddae3a0ea2f0 ","example":"Service Provider","in":"path","name":"team_name","required":true,"schema":{"enum":["Multiomics Provider","Text Mining Provider","Service Provider"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/MetaKnowledgeGraph"}}},"description":"Returns a TRAPI-compliant meta-knowledge-graph representation for one KP team's SmartAPI KP APIs (that have x-bte annotation)"}},"summary":"TRAPI-compliant meta-knowledge-graph representation for one KP team's SmartAPI KP APIs (that have x-bte annotation)","tags":["meta_knowledge_graph"]}},"/query":{"post":{"parameters":[{"description":"option to choose whether or not to enable caching","in":"query","name":"caching","required":false,"schema":{"type":"boolean"}},{"description":"dryrun a query (logs the queries BTE will make)","in":"query","name":"dryrun","required":false,"schema":{"type":"boolean"}}],"requestBody":{"content":{"application/json":{"example":{"message":{"query_graph":{"edges":{"e1":{"object":"n1","subject":"n0"}},"nodes":{"n0":{"categories":["biolink:SequenceVariant"],"ids":["DBSNP:rs121913521"]},"n1":{"categories":["biolink:Disease"]}}}}},"schema":{"$ref":"#/components/schemas/Query"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Response"}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"413":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Payload too large. Indicates that batch size was over the limit specified in x-trapi."},"429":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Too many requests. Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"Initiate a TRAPI-format query to BTE (operating as an ARA) and wait to receive a Response","tags":["query"]}},"/smartapi/{smartapi_id}/query":{"post":{"parameters":[{"description":"SmartAPI ID of an API with x-bte annotation. 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There may or may not be results. Note that some of the provided identifiers may not have been recognized."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"413":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Payload too large. Indicates that batch size was over the limit specified in x-trapi."},"429":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Too many requests. Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"Query individual SmartAPI KP API (that has x-bte annotation) as a TRAPI KP API","tags":["query"]}},"/team/{team_name}/query":{"post":{"parameters":[{"description":"Translator Team Name. Current options: Service Provider, Multiomics Provider, Text Mining Provider. The easiest way to find what KP APIs would be included under these teams is to read the list of APIs BTE uses https://github.com/biothings/biothings_explorer/blob/main/src/config/apis.js. Note that Service Provider endpoints are also advertised separately as a KP  http://smart-api.info/registry?q=36f82f05705c317bac17ddae3a0ea2f0 ","example":"Service Provider","in":"path","name":"team_name","required":true,"schema":{"enum":["Multiomics Provider","Text Mining Provider","Service Provider"],"type":"string"}},{"description":"option to choose whether or not to enable caching","in":"query","name":"caching","required":false,"schema":{"type":"boolean"}},{"description":"dryrun a query (logs the queries BTE will make)","in":"query","name":"dryrun","required":false,"schema":{"type":"boolean"}}],"requestBody":{"content":{"application/json":{"example":{"message":{"query_graph":{"edges":{"e1":{"object":"n1","subject":"n0"}},"nodes":{"n0":{"categories":["biolink:SequenceVariant"],"ids":["DBSNP:rs121913521"]},"n1":{"categories":["biolink:Disease"]}}}}},"schema":{"$ref":"#/components/schemas/Query"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Response"}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"413":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Payload too large. Indicates that batch size was over the limit specified in x-trapi."},"429":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Too many requests. Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"Query an individual Translator team's SMARTAPI KP APIs (that have x-bte annotation) as an individual TRAPI service by specifying the team name","tags":["query"]}},"/check_query_status/{id}":{"get":{"parameters":[{"description":"option to override original query log level","in":"query","name":"log_level","required":false,"schema":{"description":"Logging level. The order of priority is ERROR, WARNING, INFO, DEBUG. BTE will return all logs at the  specified level and those at higher priority levels","enum":["ERROR","WARNING","INFO","DEBUG"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"properties":{"id":{"description":"the job-id","type":"string"},"reason":{"description":"when the state is 'failed', this field states a reason for the failure","type":"string"},"returnvalue":{"description":"When the state is 'completed', this will contain the TRAPI Response object. Note that BTE might return an error, no results, etc as a Response...","properties":{"response":{"$ref":"#/components/schemas/Response"}},"type":"object"},"state":{"description":"the status of the job"}},"required":["id","state"],"type":"object"}}},"description":"Returns status. If successfully completed, it will return a TRAPI Response object under the field returnvalue"}},"summary":"This endpoint should be used when a Query was sent to BTE through an /asyncquery endpoint without a callback property: BTE then handled it in a polling manner and provided a job id. The job id can be used here to check the status or retrieve the Response.","tags":["asyncquery"]},"parameters":[{"description":"job-id","in":"path","name":"id","required":true,"schema":{"type":"string"}}]},"/asyncquery":{"post":{"parameters":[{"description":"option to choose whether or not to enable caching","in":"query","name":"caching","required":false,"schema":{"type":"boolean"}},{"description":"dryrun a query (logs the queries BTE will make)","in":"query","name":"dryrun","required":false,"schema":{"type":"boolean"}}],"requestBody":{"content":{"application/json":{"example":{"message":{"query_graph":{"edges":{"e1":{"object":"n1","subject":"n0"}},"nodes":{"n0":{"categories":["biolink:SequenceVariant"],"ids":["DBSNP:rs121913521"]},"n1":{"categories":["biolink:Disease"]}}}}},"schema":{"$ref":"#/components/schemas/AsyncQuery"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"The query is accepted for processing. The behavior will depend on whether the callback property is included. If the callback property is included, the Response will be sent to the callback url when complete. If the callback property is not included, BTE will handle the query in a polling manner: it will provide a job-id that can be used to check the status or retrieve the Response using BTE's /v1/check_query_status/{id} endpoint."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"413":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Payload too large. Indicates that batch size was over the limit specified in x-trapi."},"429":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Too many requests. Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"Initiate a query that will be handled in an asynchronous manner (there is a queue and queries will be executed in the order that they enter the queue). For BTE, it is optional to have a callback property in the request-body. If the callback property is not included, BTE will handle the query in a polling manner: it will provide a job-id that can be used to check the status or retrieve the Response using BTE's /v1/check_query_status/{id} endpoint.","tags":["asyncquery"]}},"/smartapi/{smartapi_id}/asyncquery":{"post":{"parameters":[{"description":"SmartAPI ID of an API with x-bte annotation. The easiest way to find these is to read the list of APIs BTE uses https://github.com/biothings/biothings_explorer/blob/main/src/config/apis.js","example":"09c8782d9f4027712e65b95424adba79","in":"path","name":"smartapi_id","required":true,"schema":{"type":"string"}},{"description":"option to choose whether or not to enable caching","in":"query","name":"caching","required":false,"schema":{"type":"boolean"}},{"description":"dryrun a query (logs the queries BTE will make)","in":"query","name":"dryrun","required":false,"schema":{"type":"boolean"}}],"requestBody":{"content":{"application/json":{"example":{"message":{"query_graph":{"edges":{"e1":{"object":"n1","subject":"n0"}},"nodes":{"n0":{"categories":["biolink:SequenceVariant"],"ids":["DBSNP:rs121913521"]},"n1":{"categories":["biolink:Disease"]}}}}},"schema":{"$ref":"#/components/schemas/AsyncQuery"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"The query is accepted for processing. The behavior will depend on whether the callback property is included. If the callback property is included, the Response will be sent to the callback url when complete. If the callback property is not included, BTE will handle the query in a polling manner: it will provide a job-id that can be used to check the status or retrieve the Response using BTE's /v1/check_query_status/{id} endpoint."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"413":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Payload too large. Indicates that batch size was over the limit specified in x-trapi."},"429":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Too many requests. Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"This endpoint is for asynchronously querying an individual SmartAPI KP API (that has x-bte annotation)  as a TRAPI KP API.\nInitiate a query that will be handled in an asynchronous manner (there is a queue and queries will be executed in the order that they enter the queue). For BTE, it is optional to have a callback property in the request-body. If the callback property is not included, BTE will handle the query in a polling manner: it will provide a job-id that can be used to check the status or retrieve the Response using BTE's /v1/check_query_status/{id} endpoint.","tags":["asyncquery"]}},"/team/{team_name}/asyncquery":{"post":{"parameters":[{"description":"Translator Team Name. Current options: Service Provider, Multiomics Provider, Text Mining Provider. The easiest way to find what KP APIs would be included under these teams is to read the list of APIs BTE uses https://github.com/biothings/biothings_explorer/blob/main/src/config/apis.js. Note that Service Provider endpoints are also advertised separately as a KP  http://smart-api.info/registry?q=36f82f05705c317bac17ddae3a0ea2f0 ","example":"Service Provider","in":"path","name":"team_name","required":true,"schema":{"enum":["Multiomics Provider","Text Mining Provider","Service Provider"],"type":"string"}},{"description":"option to choose whether or not to enable caching","in":"query","name":"caching","required":false,"schema":{"type":"boolean"}},{"description":"dryrun a query (logs the queries BTE will make)","in":"query","name":"dryrun","required":false,"schema":{"type":"boolean"}}],"requestBody":{"content":{"application/json":{"example":{"message":{"query_graph":{"edges":{"e1":{"object":"n1","subject":"n0"}},"nodes":{"n0":{"categories":["biolink:SequenceVariant"],"ids":["DBSNP:rs121913521"]},"n1":{"categories":["biolink:Disease"]}}}}},"schema":{"$ref":"#/components/schemas/AsyncQuery"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"The query is accepted for processing. 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Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"This endpoint is for asynchronously querying an individual Translator team's SMARTAPI KP APIs (that have x-bte annotation)  as an individual TRAPI service by specifying the team name.\nInitiate a query that will be handled in an asynchronous manner (there is a queue and queries will be executed in the order that they enter the queue). For BTE, it is optional to have a callback property in the request-body. 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}}","rows":-1,"taxon":"NCBITaxon:9606","unselect_evidence":true},"predicate":"related_to","response_mapping":{"$ref":"#/components/x-bte-response-mapping/phenotype-hp-dbsnp-start"},"source":"infores:monarchinitiative","supportBatch":false,"useTemplating":true}]},"x-bte-response-mapping":{"anatomy-uberon":{"UBERON":"associations.object.UBERON","biolink:original_predicate":"associations.relation.label","monarch_source_database":"associations.provided_by","pubmed":"associations.publications.id"},"disease-mondo":{"MONDO":"associations.object.MONDO","biolink:original_predicate":"associations.relation.label","monarch_source_database":"associations.provided_by","pubmed":"associations.publications.id"},"disease-mondo-dbsnp-start":{"MONDO":"associations.object.MONDO","biolink:original_predicate":"associations.relation.label","input_name":"associations.subject.label","monarch_source_database":"associations.provided_by","pubmed":"associations.publications.id"},"gene-hgnc":{"HGNC":"associations.object.HGNC","biolink:original_predicate":"associations.relation.label","monarch_source_database":"associations.provided_by","pubmed":"associations.publications.id"},"gene-hgnc-dbsnp-start":{"HGNC":"associations.object.HGNC","biolink:original_predicate":"associations.relation.label","input_name":"associations.subject.label","monarch_source_database":"associations.provided_by","pubmed":"associations.publications.id"},"orthologGene2diseaseMondo":{"MONDO":"associations.object.MONDO","biolink:original_predicate":"associations.relation.label","homologous_gene_model_id":"associations.subject.id","homologous_gene_model_name":"associations.subject.label","monarch_source_database":"associations.provided_by","pubmed":"associations.publications.id"},"orthologGene2phenoHP":{"HP":"associations.object.HP","biolink:original_predicate":"associations.relation.label","homologous_gene_model_id":"associations.subject.id","homologous_gene_model_name":"associations.subject.label","monarch_source_database":"associations.provided_by","pubmed":"associations.publications.id"},"pathway-react":{"REACT":"associations.object.REACT","biolink:original_predicate":"associations.relation.label","monarch_source_database":"associations.provided_by","pubmed":"associations.publications.id"},"phenotype-hp":{"HP":"associations.object.HP","biolink:original_predicate":"associations.relation.label","monarch_source_database":"associations.provided_by","pubmed":"associations.publications.id"},"phenotype-hp-dbsnp-start":{"HP":"associations.object.HP","biolink:original_predicate":"associations.relation.label","input_name":"associations.subject.label","monarch_source_database":"associations.provided_by","pubmed":"associations.publications.id"},"variant-dbsnp":{"DBSNP":"associations.object.dbSNP","biolink:original_predicate":"associations.relation.label","monarch_source_database":"associations.provided_by","output_name":"associations.object.label","pubmed":"associations.publications.id"}}},"info":{"contact":{"email":"cjm@berkeleybop.org","name":"Chris Mungall","x-id":"https://github.com/cmungall","x-role":"responsible developer"},"description":"API integration layer for linked biological objects.","termsOfService":"https://github.com/monarch-initiative/biolink-api/","title":"BioLink API","version":"1.1.14","x-translator":{"biolink-version":"3.1.1","component":"KP","infores":"infores:biolink-api","team":["Service Provider","Standards Reference Implementation Team"]}},"paths":{"/bioentity/anatomy/{id}/genes":{"get":{"parameters":[{"description":"CURIE identifier of anatomical entity, e.g. GO:0005634 (nucleus), UBERON:0002037 (cerebellum), CL:0000540 (neuron). Equivalent IDs can be used with same results","example":"UBERON:0001817","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns genes associated with a given anatomy","tags":["anatomy"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/anatomy-gene"}]}},"/bioentity/disease/{id}/genes":{"get":{"parameters":[{"description":"CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results","example":"MONDO:0011562","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"description":"Additional filters: causal, non_causal, both","example":"causal","in":"query","name":"association_type","required":false,"schema":{"default":"both","enum":["causal","non_causal","both"],"type":"string"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns genes associated with a disease","tags":["disease"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/disease-gene-1"},{"$ref":"#/components/x-bte-kgs-operations/disease-gene-2"}]}},"/bioentity/disease/{id}/pathways":{"get":{"parameters":[{"description":"CURIE identifier of disease, e.g. DOID:4450. Equivalent IDs can be used with same results","example":"MONDO:0010524","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns pathways associated with a disease","tags":["disease"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/disease-pathway"}]}},"/bioentity/disease/{id}/phenotypes":{"get":{"parameters":[{"description":"CURIE identifier of disease, e.g. OMIM:605543, Orphanet:1934, DOID:678. Equivalent IDs can be used with same results","example":"MONDO:0008974","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns phenotypes associated with a disease","tags":["disease"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/disease-phenotype"}]}},"/bioentity/disease/{id}/variants":{"get":{"parameters":[{"description":"CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results","example":"MONDO:0004747","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns variants associated with a disease","tags":["disease"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/disease-variant"}]}},"/bioentity/gene/{id}/anatomy":{"get":{"parameters":[{"description":"CURIE identifier of gene, e.g. NCBIGene:13434","example":"HGNC:8548","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns anatomies associated with a gene","tags":["gene"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/gene-anatomy"}]}},"/bioentity/gene/{id}/diseases":{"get":{"parameters":[{"description":"CURIE identifier of gene, e.g. NCBIGene:4750. Equivalent IDs can be used with same results","example":"HGNC:11138","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"description":"Additional filters: causal, non_causal, both","example":"causal","in":"query","name":"association_type","required":false,"schema":{"default":"both","enum":["causal","non_causal","both"],"type":"string"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns diseases associated with a gene","tags":["gene"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/gene-disease-1"},{"$ref":"#/components/x-bte-kgs-operations/gene-disease-2"}]}},"/bioentity/gene/{id}/interactions":{"get":{"parameters":[{"description":"id, e.g. NCBIGene:3630. Equivalent IDs can be used with same results","example":"HGNC:2950","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns gene interaction","tags":["gene"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/gene-interaction"}]}},"/bioentity/gene/{id}/ortholog/diseases":{"get":{"parameters":[{"description":"CURIE identifier of gene, e.g. NCBIGene:4750","example":"HGNC:8548","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns diseases associated with orthologs of a gene","tags":["gene"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/geneOrtholog-disease"}]}},"/bioentity/gene/{id}/ortholog/phenotypes":{"get":{"parameters":[{"description":"CURIE identifier of gene, e.g. NCBIGene:4750","example":"HGNC:8548","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns phenotypes associated with orthologs for a gene","tags":["gene"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/geneOrtholog-phenotype"}]}},"/bioentity/gene/{id}/phenotypes":{"get":{"parameters":[{"description":"CURIE identifier of gene, e.g. NCBIGene:4750. Equivalent IDs can be used with same results","example":"HGNC:2950","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns phenotypes associated with a gene","tags":["gene"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/gene-phenotype"}]}},"/bioentity/gene/{id}/variants":{"get":{"parameters":[{"description":"CURIE identifier of gene, e.g. HGNC:10896","example":"HGNC:2950","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns variants associated with a gene","tags":["gene"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/gene-variant"}]}},"/bioentity/pathway/{id}/diseases":{"get":{"parameters":[{"description":"CURIE any pathway element. E.g. REACT:R-HSA-5387390","example":"REACT:R-HSA-2644606","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns diseases associated with a pathway","tags":["pathway"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/pathway-disease"}]}},"/bioentity/phenotype/{id}/diseases":{"get":{"parameters":[{"description":"CURIE identifier of phenotype, e.g. HP:0007359. Equivalent IDs can be used with same results","example":"HP:0000272","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns diseases associated with a phenotype","tags":["phenotype"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/phenotype-disease"}]}},"/bioentity/phenotype/{id}/genes":{"get":{"parameters":[{"description":"Pheno class CURIE identifier, e.g  WBPhenotype:0000180 (axon morphology variant), MP:0001569 (abnormal circulating bilirubin level)","example":"HP:0000183","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns genes associated with a phenotype","tags":["phenotype"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/phenotype-gene"}]}},"/bioentity/phenotype/{id}/variants":{"get":{"parameters":[{"description":"Pheno class CURIE identifier, e.g  WBPhenotype:0000180 (axon morphology variant), MP:0001569 (abnormal circulating bilirubin level)","example":"HP:0002944","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns variants associated with a phenotype","tags":["phenotype"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/phenotype-variant"}]}},"/bioentity/variant/{id}/diseases":{"get":{"parameters":[{"description":"CURIE identifier of variant, e.g. ClinVarVariant:14925","example":"dbSNP:rs227731","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"$ref":"#/components/parameters/rows"},{"$ref":"#/components/parameters/start"},{"$ref":"#/components/parameters/facet"},{"$ref":"#/components/parameters/facet_fields"},{"$ref":"#/components/parameters/unselect_evidence"},{"$ref":"#/components/parameters/exclude_automatic_assertions"},{"$ref":"#/components/parameters/fetch_objects"},{"$ref":"#/components/parameters/use_compact_associations"},{"$ref":"#/components/parameters/slim"},{"$ref":"#/components/parameters/evidence"},{"$ref":"#/components/parameters/direct"},{"$ref":"#/components/parameters/taxon"},{"$ref":"#/components/parameters/direct_taxon"},{"$ref":"#/components/parameters/relation"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns diseases associated with a 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Learn more about [MyChem.info](https://docs.mychem.info/en/latest/index.html)","termsOfService":"http://MyChem.info/terms","title":"MyChem.info API","version":"1.0","x-translator":{"biolink-version":"3.1.1","component":"KP","infores":"infores:mychem-info","team":["Service Provider"]}},"paths":{"/chem/{id}":{"get":{"description":"By default, this will return the complete chemical annotation object in JSON format.  See [here](https://docs.mychem.info/en/latest/doc/chem_annotation_service.html#returned-object)  for an example and [here](https://docs.mychem.info/en/latest/doc/data.html#chemical-object) for more details. If the input chemical ID is not valid, 404 (NOT FOUND) will be returned.\n\nOptionally, you can pass a \"fields\" parameter to return only the annotation you want  (by filtering returned object fields). \"fields\" accepts any attributes (a.k.a fields) available  from the object. Multiple attributes should be separated by commas. 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The easiest way to find these is to read the list of APIs BTE uses https://github.com/biothings/biothings_explorer/blob/main/src/config/apis.js","example":"09c8782d9f4027712e65b95424adba79","in":"path","name":"smartapi_id","required":true,"schema":{"type":"string"}},{"description":"option to choose whether or not to enable caching","in":"query","name":"caching","required":false,"schema":{"type":"boolean"}},{"description":"dryrun a query (logs the queries BTE will make)","in":"query","name":"dryrun","required":false,"schema":{"type":"boolean"}}],"requestBody":{"content":{"application/json":{"example":{"message":{"query_graph":{"edges":{"e1":{"object":"n1","subject":"n0"}},"nodes":{"n0":{"categories":["biolink:SequenceVariant"],"ids":["DBSNP:rs121913521"]},"n1":{"categories":["biolink:Disease"]}}}}},"schema":{"$ref":"#/components/schemas/AsyncQuery"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AsyncQueryResponse"}}},"description":"The query is accepted for processing. 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Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"This endpoint is for asynchronously querying an individual SmartAPI KP API (that has x-bte annotation)  as a TRAPI KP API.\nInitiate a query that will be handled in an asynchronous manner (there is a queue and queries will be executed in the order that they enter the queue). For BTE, it is optional to have a callback property in the request-body. If the callback property is not included, BTE will handle the query in a polling manner: it will provide a job-id that can be used to check the status or retrieve the Response.","tags":["asyncquery"]}},"/team/{team_name}/asyncquery":{"post":{"parameters":[{"description":"Translator Team Name. Current options: Service Provider, Multiomics Provider, Text Mining Provider. The easiest way to find what KP APIs would be included under these teams is to read the list of APIs BTE uses https://github.com/biothings/biothings_explorer/blob/main/src/config/apis.js. Note that Service Provider endpoints are also registered separately as a KP in the SmartAPI Registry","example":"Service Provider","in":"path","name":"team_name","required":true,"schema":{"enum":["Multiomics Provider","Text Mining Provider","Service Provider"],"type":"string"}},{"description":"option to choose whether or not to enable caching","in":"query","name":"caching","required":false,"schema":{"type":"boolean"}},{"description":"dryrun a query (logs the queries BTE will make)","in":"query","name":"dryrun","required":false,"schema":{"type":"boolean"}}],"requestBody":{"content":{"application/json":{"example":{"message":{"query_graph":{"edges":{"e1":{"object":"n1","subject":"n0"}},"nodes":{"n0":{"categories":["biolink:SequenceVariant"],"ids":["DBSNP:rs121913521"]},"n1":{"categories":["biolink:Disease"]}}}}},"schema":{"$ref":"#/components/schemas/AsyncQuery"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AsyncQueryResponse"}}},"description":"The query is accepted for processing. 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Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"This endpoint is for asynchronously querying an individual Translator team's SMARTAPI KP APIs (that have x-bte annotation)  as an individual TRAPI service by specifying the team name.\nInitiate a query that will be handled in an asynchronous manner (there is a queue and queries will be executed in the order that they enter the queue). For BTE, it is optional to have a callback property in the request-body. 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If the input is not valid, 404 (NOT FOUND) will be returned.\n\nOptionally, you can pass a \"fields\" parameter to return only the annotation you want  (by filtering returned object fields). \"fields\" accepts any attributes (a.k.a fields) available  from the association. Multiple attributes should be separated by commas. If an attribute is not  available for a specific ontology term, it will be ignored. Note that the attribute names are  case-sensitive.\n\nJust like the query service, you can also pass a \"callback\" parameter to make a JSONP call.","parameters":[{"example":"GO:0008613","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"$ref":"#/components/parameters/fields"},{"$ref":"#/components/parameters/callback"},{"$ref":"#/components/parameters/email"},{"$ref":"#/components/parameters/size"}],"responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["ontology"]}},"/geneset":{"post":{"description":"Although making simple GET requests above to our service is sufficient in most use cases,  there are some times you might find it easier to batch query (e.g., retrieving multiple ontology terms).  Fortunately, you can also make batch queries via POST requests when you need to.","parameters":[{"description":"Accepts multiple ontology term ids separated by commas. 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Note that currently we only take the input ids  up to 1000 maximum, the rest will be omitted.","items":{"type":"string"},"type":"array"}},"type":"object"}}}},"responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["ontology"]}},"/metadata":{"get":{"description":"Get metadata about the data available from the API","responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["metadata"]}},"/metadata/fields":{"get":{"description":"Get metadata about the data fields available from the API","responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["metadata"]}},"/query":{"get":{"description":"Query service. In the output, \"total\" in the output gives the total number  of matching hits, while the actual hits are returned under \"hits\" field.","parameters":[{"description":"Required, passing user query. The detailed query syntax for parameter is explained  [here for a core BioThings  API](https://docs.mychem.info/en/latest/doc/chem_query_service.html#query-syntax).","example":"go:\"GO:0008613\"","in":"query","name":"q","required":true,"schema":{"type":"string"}},{"$ref":"#/components/parameters/fields"},{"$ref":"#/components/parameters/size"},{"$ref":"#/components/parameters/from"},{"$ref":"#/components/parameters/fetch_all"},{"$ref":"#/components/parameters/scroll_id"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/facets"},{"$ref":"#/components/parameters/facet_size"},{"$ref":"#/components/parameters/callback"},{"$ref":"#/components/parameters/dotfield"},{"$ref":"#/components/parameters/email"}],"responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["query"]},"post":{"description":"Although making simple GET requests above to our query service is sufficient for most use cases,  there are times you might find it more efficient to make batch queries (e.g., retrieving data  for multiple inputs). 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Default: _id\n\nThe request body can also be used to provide this information.","in":"query","name":"scopes","required":false,"schema":{"type":"string"}},{"$ref":"#/components/parameters/fields"},{"$ref":"#/components/parameters/email"},{"$ref":"#/components/parameters/size"},{"$ref":"#/components/parameters/from"},{"$ref":"#/components/parameters/fetch_all"},{"$ref":"#/components/parameters/scroll_id"}],"requestBody":{"content":{"application/json":{"example":{"q":["GO:0008613","GO:0008510"],"scopes":["go"]},"schema":{"properties":{"q":{"description":"Accepts multiple values separated by commas. Note that currently we only take the input values  up to 1000 maximum, the rest will be omitted.","items":{"type":"string"},"type":"array"},"scopes":{"description":"Specify one or more fields (separated by commas) to search. Default: _id","items":{"type":"string"},"type":"array"}},"type":"object"}}}},"responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["query"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/has_subclass"},{"$ref":"#/components/x-bte-kgs-operations/subclass_of"},{"$ref":"#/components/x-bte-kgs-operations/part_of"},{"$ref":"#/components/x-bte-kgs-operations/has_part"}]}}},"servers":[{"description":"Encrypted Production server","url":"https://biothings.ncats.io/go_mf","x-maturity":"production"},{"description":"Production server","url":"http://biothings.ncats.io/go_mf","x-maturity":"production"}],"tags":[{"name":"ontology"},{"name":"molecular activity"},{"name":"query"},{"name":"translator"},{"name":"biothings"}]},{"_id":"7f70cdfaeb801501da08dacc294e8b9f","_meta":{"date_created":"2023-05-08T23:59:06.007881+00:00","last_updated":"2023-05-22T07:06:12.952126+00:00","url":"https://raw.githubusercontent.com/suihuanglab/spoke-kp/main/spoke-kp.yaml","username":"brettasmi"},"info":{"contact":{"email":"brett.smith@isbscience.org"},"description":"SPOKE KP for TRAPI 1.4 - an NIH NCATS Knowledge Provider exposing UCSF's SPOKE","license":{"name":"Apache 2.0","url":"http://www.apache.org/licenses/LICENSE-2.0.html"},"termsOfService":"https://spoke.rbvi.ucsf.edu/license.html","title":"SPOKE KP for TRAPI 1.4","version":"1.4.0","x-translator":{"biolink-version":"3.2.5","component":"KP","externalDocs":{"description":"Repository","url":"https://github.com/suihuanglab/spoke-kp"},"infores":"infores:spoke","team":["imProving Agent"]},"x-trapi":{"asyncquery":false,"batch_size_limit":200,"operations":["lookup"],"rate_limit":20,"test_data_location":{"default":{"url":"https://github.com/suihuanglab/spoke-kp/tree/main/test-data"}},"version":"1.4.0-beta2"}},"paths":{"/meta_knowledge_graph":{"get":{"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/MetaKnowledgeGraph"}}},"description":"Returns meta knowledge graph representation of this TRAPI web service."}},"summary":"Meta knowledge graph representation of this TRAPI web service.","tags":["meta_knowledge_graph"]}},"/query":{"post":{"description":"","requestBody":{"content":{"application/json":{"example":"{\n  \"message\": {\n    \"query_graph\": {\n      \"nodes\": {\n        \"n00\": {\n          \"ids\": [\"DOID:1681\"],\n          \"categories\": [\"biolink:Disease\"]\n        },\n        \"n01\": {\n          \"categories\": [\"biolink:Gene\"]\n        }\n      },\n      \"edges\": {\n        \"e00\": {\n          \"subject\": \"n00\",\n          \"object\": \"n01\"\n        }\n      }\n    }\n  },\n}","schema":{"$ref":"#/components/schemas/Query"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Response"}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"413":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Payload too large. Indicates that batch size was over the limit specified in x-trapi."},"429":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Too many requests. Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"Initiate a query and wait to receive a Response","tags":["query"]}},"/asyncquery":{"post":{"description":"","requestBody":{"content":{"application/json":{"example":"{\n  \"message\": {\n    \"query_graph\": {\n      \"nodes\": {\n        \"n00\": {\n          \"ids\": [\"DOID:1681\"],\n          \"categories\": [\"biolink:Disease\"]\n        },\n        \"n01\": {\n          \"categories\": [\"biolink:Gene\"]\n        }\n      },\n      \"edges\": {\n        \"e00\": {\n          \"subject\": \"n00\",\n          \"object\": \"n01\"\n        }\n      }\n    }\n  },\n  \"callback\": \"https://example.com/notimplemented\"\n}","schema":{"$ref":"#/components/schemas/AsyncQuery"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AsyncQueryResponse"}}},"description":"The query is accepted for processing and the Response will be sent to the callback url when complete."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"413":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Payload too large. Indicates that batch size was over the limit specified in x-trapi."},"429":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Too many requests. 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Sites that implement /asyncquery MUST implement /asyncquery_status/{job_id}, but those that do not implement /asyncquery SHOULD NOT implement /asyncquery_status."}},"summary":"Retrieve the current status of a previously submitted asyncquery given its job_id","tags":["asyncquery_status"]}}},"servers":[{"description":"ITRB CI server","url":"https://spokekp.ci.transltr.io/api/v1.4/","x-maturity":"staging"},{"description":"dev","url":"https://spokekp.healthdatascience.cloud/api/v1.4/","x-maturity":"development"}],"tags":[{"description":"Retrieve the meta knowledge graph representation of this TRAPI web service. KPs MUST provide all subject category - predicate - object category triplets that are supported by the service, NOT including all implied ancestor relationships. ARAs SHOULD provide the union of all meta knowledge graphs of all the KPs that they can consult.","name":"meta_knowledge_graph"},{"description":"Initiate a query and wait to receive the response","name":"query"},{"description":"Initiate a query with a callback to receive the response","name":"asyncquery"},{"description":"Retrieve the current status of a previously submitted asyncquery given its job_id","name":"asyncquery_status"},{"description":"Required for SmartAPI validation of x-translator","name":"translator"},{"description":"Required for SmartAPI validation of x-trapi","name":"trapi"}]},{"_id":"671b45c0301c8624abbd26ae78449ca2","_ignored":["paths.pathitem.get.description.raw"],"_meta":{"date_created":"2021-02-10T05:26:25.703523+00:00","last_updated":"2023-05-22T07:06:13.463136+00:00","url":"https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/mydisease.info/smartapi.yaml","username":"newgene"},"components":{"x-bte-kgs-operations":{"chemical-disease":[{"inputs":[{"id":"MESH","semantic":"SmallMolecule"}],"outputs":[{"id":"MESH","semantic":"Disease"}],"parameters":{"fields":"ctd.mesh","size":1000},"predicate":"related_to","requestBody":{"body":{"q":"{{ queryInputs }}","scopes":"ctd.chemical_related_to_disease.mesh_chemical_id"}},"response_mapping":{"$ref":"#/components/x-bte-response-mapping/ctd-mesh-disease"},"source":"infores:ctd","supportBatch":true,"useTemplating":true}],"chemical-disease2":[{"inputs":[{"id":"MESH","semantic":"SmallMolecule"}],"outputs":[{"id":"OMIM","semantic":"Disease"}],"parameters":{"fields":"ctd.omim","size":1000},"predicate":"related_to","requestBody":{"body":{"q":"{{ queryInputs }}","scopes":"ctd.chemical_related_to_disease.mesh_chemical_id"}},"response_mapping":{"$ref":"#/components/x-bte-response-mapping/ctd-omim-disease"},"source":"infores:ctd","supportBatch":true,"useTemplating":true}],"disease-chemical":[{"inputs":[{"id":"MESH","semantic":"Disease"}],"outputs":[{"id":"MESH","semantic":"SmallMolecule"}],"parameters":{"fields":"ctd.chemical_related_to_disease.mesh_chemical_id, ctd.chemical_related_to_disease.direct_evidence, 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payload."}},"tags":["query"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/bpoc-LOCATION_OF-neop"},{"$ref":"#/components/x-bte-kgs-operations/bpoc-LOCATION_OF-neop-rev"},{"$ref":"#/components/x-bte-kgs-operations/bdsu-LOCATION_OF-aapp"},{"$ref":"#/components/x-bte-kgs-operations/bdsu-LOCATION_OF-aapp-rev"},{"$ref":"#/components/x-bte-kgs-operations/bpoc-LOCATION_OF-patf"},{"$ref":"#/components/x-bte-kgs-operations/bpoc-LOCATION_OF-patf-rev"},{"$ref":"#/components/x-bte-kgs-operations/topp-TREATS-dsyn"},{"$ref":"#/components/x-bte-kgs-operations/topp-TREATS-dsyn-rev"},{"$ref":"#/components/x-bte-kgs-operations/topp-TREATS-neop"},{"$ref":"#/components/x-bte-kgs-operations/bpoc-LOCATION_OF-dsyn"},{"$ref":"#/components/x-bte-kgs-operations/bpoc-LOCATION_OF-fndg"},{"$ref":"#/components/x-bte-kgs-operations/bpoc-LOCATION_OF-fndg-rev"},{"$ref":"#/components/x-bte-kgs-operations/cell-PART_OF-bpoc"},{"$ref":"#/components/x-bte-kgs-operations/cell-PART_OF-bpoc-rev"},{"$ref":"#/components/x-bte-kgs-operations/bpoc-LOCATION_OF-aapp"},{"$ref":"#/components/x-bte-kgs-operations/bpoc-LOCATION_OF-aapp-rev"},{"$ref":"#/components/x-bte-kgs-operations/phsu-TREATS-dsyn"},{"$ref":"#/components/x-bte-kgs-operations/phsu-TREATS-dsyn-rev"},{"$ref":"#/components/x-bte-kgs-operations/bpoc-PART_OF-bpoc"},{"$ref":"#/components/x-bte-kgs-operations/bpoc-PART_OF-bpoc-rev"},{"$ref":"#/components/x-bte-kgs-operations/cell-LOCATION_OF-aapp"},{"$ref":"#/components/x-bte-kgs-operations/cell-LOCATION_OF-aapp-rev"},{"$ref":"#/components/x-bte-kgs-operations/topp-USES-phsu"},{"$ref":"#/components/x-bte-kgs-operations/topp-USES-phsu-rev"},{"$ref":"#/components/x-bte-kgs-operations/bpoc-LOCATION_OF-diap"},{"$ref":"#/components/x-bte-kgs-operations/bpoc-LOCATION_OF-diap-rev"},{"$ref":"#/components/x-bte-kgs-operations/bpoc-LOCATION_OF-inpo"},{"$ref":"#/components/x-bte-kgs-operations/tisu-PART_OF-bpoc-rev"},{"$ref":"#/components/x-bte-kgs-operations/bdsu-LOCATION_OF-bacs"},{"$ref":"#/components/x-bte-kgs-operations/bdsu-LOCATION_OF-bacs-rev"},{"$ref":"#/components/x-bte-kgs-operations/cell-LOCATION_OF-celf"},{"$ref":"#/components/x-bte-kgs-operations/cell-LOCATION_OF-celf-rev"},{"$ref":"#/components/x-bte-kgs-operations/bacs-PART_OF-aapp"},{"$ref":"#/components/x-bte-kgs-operations/bacs-PART_OF-aapp-rev"},{"$ref":"#/components/x-bte-kgs-operations/topp-USES-medd"},{"$ref":"#/components/x-bte-kgs-operations/topp-USES-medd-rev"},{"$ref":"#/components/x-bte-kgs-operations/aapp-ASSOCIATED_WITH-dsyn"},{"$ref":"#/components/x-bte-kgs-operations/aapp-ASSOCIATED_WITH-dsyn-rev"},{"$ref":"#/components/x-bte-kgs-operations/topp-USES-aapp"},{"$ref":"#/components/x-bte-kgs-operations/topp-USES-aapp-rev"},{"$ref":"#/components/x-bte-kgs-operations/tisu-LOCATION_OF-aapp-rev"},{"$ref":"#/components/x-bte-kgs-operations/aapp-INTERACTS_WITH-aapp"},{"$ref":"#/components/x-bte-kgs-operations/aapp-INTERACTS_WITH-aapp-rev"},{"$ref":"#/components/x-bte-kgs-operations/dsyn-COEXISTS_WITH-dsyn"},{"$ref":"#/components/x-bte-kgs-operations/dsyn-COEXISTS_WITH-dsyn-rev"},{"$ref":"#/components/x-bte-kgs-operations/aapp-STIMULATES-gngm"},{"$ref":"#/components/x-bte-kgs-operations/aapp-STIMULATES-gngm-rev"},{"$ref":"#/components/x-bte-kgs-operations/celc-LOCATION_OF-aapp"},{"$ref":"#/components/x-bte-kgs-operations/celc-LOCATION_OF-aapp-rev"},{"$ref":"#/components/x-bte-kgs-operations/bdsu-LOCATION_OF-orch"},{"$ref":"#/components/x-bte-kgs-operations/aapp-PART_OF-celc"},{"$ref":"#/components/x-bte-kgs-operations/aapp-PART_OF-celc-rev"},{"$ref":"#/components/x-bte-kgs-operations/topp-PRECEDES-topp"},{"$ref":"#/components/x-bte-kgs-operations/topp-PRECEDES-topp-rev"},{"$ref":"#/components/x-bte-kgs-operations/blor-LOCATION_OF-neop"},{"$ref":"#/components/x-bte-kgs-operations/blor-LOCATION_OF-neop-rev"},{"$ref":"#/components/x-bte-kgs-operations/bdsu,umls-LOCATION_OF-aapp,ncbigene"},{"$ref":"#/components/x-bte-kgs-operations/bdsu,umls-LOCATION_OF-aapp,ncbigene-rev"},{"$ref":"#/components/x-bte-kgs-operations/diap-DIAGNOSES-dsyn"},{"$ref":"#/components/x-bte-kgs-operations/diap-DIAGNOSES-dsyn-rev"},{"$ref":"#/components/x-bte-kgs-operations/aapp-PART_OF-bpoc"},{"$ref":"#/components/x-bte-kgs-operations/aapp-PART_OF-bpoc-rev"},{"$ref":"#/components/x-bte-kgs-operations/aapp-ASSOCIATED_WITH-neop"},{"$ref":"#/components/x-bte-kgs-operations/bpoc-LOCATION_OF-orch"},{"$ref":"#/components/x-bte-kgs-operations/bpoc-LOCATION_OF-orch-rev"},{"$ref":"#/components/x-bte-kgs-operations/bpoc-LOCATION_OF-anab"},{"$ref":"#/components/x-bte-kgs-operations/blor-LOCATION_OF-dsyn"},{"$ref":"#/components/x-bte-kgs-operations/phsu-TREATS-neop"},{"$ref":"#/components/x-bte-kgs-operations/bpoc,umls-LOCATION_OF-aapp,ncbigene"},{"$ref":"#/components/x-bte-kgs-operations/bpoc,umls-LOCATION_OF-aapp,ncbigene-rev"},{"$ref":"#/components/x-bte-kgs-operations/cell,umls-LOCATION_OF-aapp,ncbigene"},{"$ref":"#/components/x-bte-kgs-operations/cell,umls-LOCATION_OF-aapp,ncbigene-rev"},{"$ref":"#/co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Note that Service Provider endpoints are also registered separately as a KP in the SmartAPI Registry","example":"Service Provider","in":"path","name":"team_name","required":true,"schema":{"enum":["Multiomics Provider","Text Mining Provider","Service Provider"],"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/MetaKnowledgeGraph"}}},"description":"Returns a TRAPI-compliant meta-knowledge-graph representation for one KP team's SmartAPI KP APIs (that have x-bte annotation)"}},"summary":"TRAPI-compliant meta-knowledge-graph representation for one KP team's SmartAPI KP APIs (that have x-bte annotation)","tags":["meta_knowledge_graph"]}},"/query":{"post":{"parameters":[{"description":"option to choose whether or not to enable caching","in":"query","name":"caching","required":false,"schema":{"type":"boolean"}},{"description":"dryrun a query (logs the queries BTE will make)","in":"query","name":"dryrun","required":false,"schema":{"type":"boolean"}}],"requestBody":{"content":{"application/json":{"example":{"message":{"query_graph":{"edges":{"e1":{"object":"n1","subject":"n0"}},"nodes":{"n0":{"categories":["biolink:SequenceVariant"],"ids":["DBSNP:rs121913521"]},"n1":{"categories":["biolink:Disease"]}}}}},"schema":{"$ref":"#/components/schemas/Query"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Response"}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"413":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Payload too large. Indicates that batch size was over the limit specified in x-trapi."},"429":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Too many requests. Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"Initiate a TRAPI-format query to BTE (operating as an ARA) and wait to receive a Response","tags":["query"]}},"/smartapi/{smartapi_id}/query":{"post":{"parameters":[{"description":"SmartAPI ID of an API with x-bte annotation. The easiest way to find these is to read the list of APIs BTE uses https://github.com/biothings/biothings_explorer/blob/main/src/config/apis.js","example":"09c8782d9f4027712e65b95424adba79","in":"path","name":"smartapi_id","required":true,"schema":{"type":"string"}},{"description":"option to choose whether or not to enable caching","in":"query","name":"caching","required":false,"schema":{"type":"boolean"}},{"description":"dryrun a query (logs the queries BTE will make)","in":"query","name":"dryrun","required":false,"schema":{"type":"boolean"}}],"requestBody":{"content":{"application/json":{"example":{"message":{"query_graph":{"edges":{"e1":{"object":"n1","subject":"n0"}},"nodes":{"n0":{"categories":["biolink:SequenceVariant"],"ids":["DBSNP:rs121913521"]},"n1":{"categories":["biolink:Disease"]}}}}},"schema":{"$ref":"#/components/schemas/Query"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Response"}}},"description":"OK. There may or may not be results. Note that some of the provided identifiers may not have been recognized."},"400":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Bad request. The request is invalid according to this OpenAPI schema OR a specific identifier is believed to be invalid somehow (not just unrecognized)."},"413":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Payload too large. Indicates that batch size was over the limit specified in x-trapi."},"429":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Too many requests. Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"Query individual SmartAPI KP API (that has x-bte annotation) as a TRAPI KP API","tags":["query"]}},"/team/{team_name}/query":{"post":{"parameters":[{"description":"Translator Team Name. Current options: Service Provider, Multiomics Provider, Text Mining Provider. The easiest way to find what KP APIs would be included under these teams is to read the list of APIs BTE uses https://github.com/biothings/biothings_explorer/blob/main/src/config/apis.js. Note that Service Provider endpoints are also registered separately as a KP in the SmartAPI Registry","example":"Service Provider","in":"path","name":"team_name","required":true,"schema":{"enum":["Multiomics Provider","Text Mining Provider","Service Provider"],"type":"string"}},{"description":"option to choose whether or not to enable caching","in":"query","name":"caching","required":false,"schema":{"type":"boolean"}},{"description":"dryrun a query (logs the queries BTE will make)","in":"query","name":"dryrun","required":false,"schema":{"type":"boolean"}}],"requestBody":{"content":{"application/json":{"example":{"message":{"query_graph":{"edges":{"e1":{"object":"n1","subject":"n0"}},"nodes":{"n0":{"categories":["biolink:SequenceVariant"],"ids":["DBSNP:rs121913521"]},"n1":{"categories":["biolink:Disease"]}}}}},"schema":{"$ref":"#/components/schemas/Query"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/Response"}}},"description":"OK. 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Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"Query an individual Translator team's SMARTAPI KP APIs (that have x-bte annotation) as an individual TRAPI service by specifying the team name","tags":["query"]}},"/asyncquery":{"post":{"parameters":[{"description":"option to choose whether or not to enable caching","in":"query","name":"caching","required":false,"schema":{"type":"boolean"}},{"description":"dryrun a query (logs the queries BTE will make)","in":"query","name":"dryrun","required":false,"schema":{"type":"boolean"}}],"requestBody":{"content":{"application/json":{"example":{"message":{"query_graph":{"edges":{"e1":{"object":"n1","subject":"n0"}},"nodes":{"n0":{"categories":["biolink:SequenceVariant"],"ids":["DBSNP:rs121913521"]},"n1":{"categories":["biolink:Disease"]}}}}},"schema":{"$ref":"#/components/schemas/AsyncQuery"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AsyncQueryResponse"}}},"description":"The query is accepted for processing. 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Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"Initiate a query that will be handled in an asynchronous manner (there is a queue and queries will be executed in the order that they enter the queue). For BTE, it is optional to have a callback property in the request-body. If the callback property is not included, BTE will handle the query in a polling manner: it will provide a job-id that can be used to check the status or retrieve the Response.","tags":["asyncquery"]}},"/smartapi/{smartapi_id}/asyncquery":{"post":{"parameters":[{"description":"SmartAPI ID of an API with x-bte annotation. The easiest way to find these is to read the list of APIs BTE uses https://github.com/biothings/biothings_explorer/blob/main/src/config/apis.js","example":"09c8782d9f4027712e65b95424adba79","in":"path","name":"smartapi_id","required":true,"schema":{"type":"string"}},{"description":"option to choose whether or not to enable caching","in":"query","name":"caching","required":false,"schema":{"type":"boolean"}},{"description":"dryrun a query (logs the queries BTE will make)","in":"query","name":"dryrun","required":false,"schema":{"type":"boolean"}}],"requestBody":{"content":{"application/json":{"example":{"message":{"query_graph":{"edges":{"e1":{"object":"n1","subject":"n0"}},"nodes":{"n0":{"categories":["biolink:SequenceVariant"],"ids":["DBSNP:rs121913521"]},"n1":{"categories":["biolink:Disease"]}}}}},"schema":{"$ref":"#/components/schemas/AsyncQuery"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AsyncQueryResponse"}}},"description":"The query is accepted for processing. 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Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"This endpoint is for asynchronously querying an individual SmartAPI KP API (that has x-bte annotation)  as a TRAPI KP API.\nInitiate a query that will be handled in an asynchronous manner (there is a queue and queries will be executed in the order that they enter the queue). For BTE, it is optional to have a callback property in the request-body. If the callback property is not included, BTE will handle the query in a polling manner: it will provide a job-id that can be used to check the status or retrieve the Response.","tags":["asyncquery"]}},"/team/{team_name}/asyncquery":{"post":{"parameters":[{"description":"Translator Team Name. Current options: Service Provider, Multiomics Provider, Text Mining Provider. The easiest way to find what KP APIs would be included under these teams is to read the list of APIs BTE uses https://github.com/biothings/biothings_explorer/blob/main/src/config/apis.js. Note that Service Provider endpoints are also registered separately as a KP in the SmartAPI Registry","example":"Service Provider","in":"path","name":"team_name","required":true,"schema":{"enum":["Multiomics Provider","Text Mining Provider","Service Provider"],"type":"string"}},{"description":"option to choose whether or not to enable caching","in":"query","name":"caching","required":false,"schema":{"type":"boolean"}},{"description":"dryrun a query (logs the queries BTE will make)","in":"query","name":"dryrun","required":false,"schema":{"type":"boolean"}}],"requestBody":{"content":{"application/json":{"example":{"message":{"query_graph":{"edges":{"e1":{"object":"n1","subject":"n0"}},"nodes":{"n0":{"categories":["biolink:SequenceVariant"],"ids":["DBSNP:rs121913521"]},"n1":{"categories":["biolink:Disease"]}}}}},"schema":{"$ref":"#/components/schemas/AsyncQuery"}}},"description":"Query information to be submitted","required":true},"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AsyncQueryResponse"}}},"description":"The query is accepted for processing. 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Indicates that the client issued requests that exceed the rate limit specified in x-trapi."},"500":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Internal server error."},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Not implemented."}},"summary":"This endpoint is for asynchronously querying an individual Translator team's SMARTAPI KP APIs (that have x-bte annotation)  as an individual TRAPI service by specifying the team name.\nInitiate a query that will be handled in an asynchronous manner (there is a queue and queries will be executed in the order that they enter the queue). For BTE, it is optional to have a callback property in the request-body. If the callback property is not included, BTE will handle the query in a polling manner: it will provide a job-id that can be used to check the status or retrieve the Response.","tags":["asyncquery"]}},"/asyncquery_status/{job_id}":{"get":{"operationId":"asyncquery_status","parameters":[{"description":"Identifier of the job for status request","in":"path","name":"job_id","required":true,"schema":{"type":"string"}}],"responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/AsyncQueryStatusResponse"}}},"description":"Returns the status and current logs of a previously submitted asyncquery."},"404":{"description":"job_id not found"},"501":{"content":{"application/json":{"schema":{"type":"string"}}},"description":"Return code 501 indicates that this endpoint has not been implemented at this site. Sites that implement /asyncquery MUST implement /asyncquery_status/{job_id}, but those that do not implement /asyncquery SHOULD NOT implement /asyncquery_status."}},"summary":"Retrieve the current status of a previously submitted asyncquery given its job_id","tags":["asyncquery_status"]}}},"servers":[{"description":"ITRB Production server","url":"https://bte.transltr.io/v1","x-maturity":"production"},{"description":"ITRB Test server","url":"https://bte.test.transltr.io/v1","x-maturity":"testing"},{"description":"ITRB CI server","url":"https://bte.ci.transltr.io/v1","x-maturity":"staging"},{"description":"Non-ITRB dev (internal use)","url":"https://api.bte.ncats.io/v1","x-maturity":"development"}],"tags":[{"name":"1.4.0"},{"name":"meta_knowledge_graph"},{"name":"query"},{"name":"asyncquery"},{"name":"asyncquery_status"},{"name":"translator"},{"name":"trapi"},{"name":"biothings"}]},{"_id":"a7f784626a426d054885a5f33f17d3f8","_ignored":["paths.pathitem.get.description.raw"],"_meta":{"date_created":"2020-12-07T23:02:08.115894+00:00","last_updated":"2023-12-11T08:03:40.604836+00:00","url":"https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/master/DISEASES/smartapi.yaml","username":"newgene"},"components":{"x-bte-kgs-operations":{"disease-gene":[{"inputs":[{"id":"DOID","semantic":"Disease"}],"outputs":[{"id":"ENSEMBL","semantic":"Gene"}],"parameters":{"fields":"DISEASES.associatedWith.ensembl","size":1000},"predicate":"condition_associated_with_gene","requestBody":{"body":{"q":"{{ queryInputs }}","scopes":"DISEASES.doid"}},"response_mapping":{"$ref":"#/components/x-bte-response-mapping/disease-gene"},"source":"infores:diseases","supportBatch":true,"useTemplating":true}],"gene-disease":[{"inputs":[{"id":"ENSEMBL","semantic":"Gene"}],"outputs":[{"id":"DOID","semantic":"Disease"}],"parameters":{"fields":"DISEASES.doid","size":1000},"predicate":"gene_associated_with_condition","requestBody":{"body":{"q":"{{ queryInputs }}","scopes":"DISEASES.associatedWith.ensembl"}},"response_mapping":{"$ref":"#/components/x-bte-response-mapping/gene-disease"},"source":"infores:diseases","supportBatch":true,"useTemplating":true}]},"x-bte-response-mapping":{"disease-gene":{"ENSEMBL":"DISEASES.associatedWith.ensembl"},"gene-disease":{"DOID":"DISEASES.doid"}}},"info":{"contact":{"email":"help@biothings.io","name":"BioThings Team","x-id":"https://github.com/biothings","x-role":"responsible developers"},"description":"Documentation of the BioThings API for [DISEASES](https://diseases.jensenlab.org/About)  data.","termsOfService":"https://biothings.io/about","title":"BioThings DISEASES API","version":"1.0","x-translator":{"biolink-version":"3.5.0","component":"KP","infores":"infores:biothings-diseases","team":["Service Provider"]}},"paths":{"/disease/{id}":{"get":{"description":"By default, this will return the complete disease record in JSON format. If the input is not valid, 404 (NOT FOUND) will be returned.\n\nOptionally, you can pass a \"fields\" parameter to return only the annotation you want  (by filtering returned object fields). \"fields\" accepts any attributes (a.k.a fields) available  from the association. Multiple attributes should be separated by commas. If an attribute is not  available for a specific disease, it will be ignored. Note that the attribute names are  case-sensitive.\n\nJust like the query service, you can also pass a \"callback\" parameter to make a JSONP call.","parameters":[{"example":"DOID:2987","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"$ref":"#/components/parameters/fields"},{"$ref":"#/components/parameters/callback"},{"$ref":"#/components/parameters/email"},{"$ref":"#/components/parameters/size"}],"responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["disease"]}},"/disease":{"post":{"description":"Although making simple GET requests above to our service is sufficient in most use cases,  there are some times you might find it easier to batch query (e.g., retrieving multiple diseases).  Fortunately, you can also make batch queries via POST requests when you need to.","parameters":[{"description":"Accepts multiple disease ids separated by commas. Note that currently we only take ids up to  1000 maximum, the rest will be omitted.\n\nThe request body can also be used to provide these ids.","in":"query","name":"ids","required":false,"schema":{"type":"string"}},{"$ref":"#/components/parameters/fields"},{"$ref":"#/components/parameters/email"},{"$ref":"#/components/parameters/size"}],"requestBody":{"content":{"application/json":{"example":{"ids":["DOID:2987","DOID:4645"]},"schema":{"properties":{"ids":{"description":"Accepts multiple disease ids. Note that currently we only take the input ids  up to 1000 maximum, the rest will be omitted.","items":{"type":"string"},"type":"array"}},"type":"object"}}}},"responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["disease"]}},"/metadata":{"get":{"description":"Get metadata about the data available from the API","responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["metadata"]}},"/metadata/fields":{"get":{"description":"Get metadata about the data fields available from the API","responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["metadata"]}},"/query":{"get":{"description":"Query service. In the output, \"total\" in the output gives the total number  of matching hits, while the actual hits are returned under \"hits\" field.","parameters":[{"description":"Required, passing user query. The detailed query syntax for parameter is explained  [here for a core BioThings  API](https://docs.mychem.info/en/latest/doc/chem_query_service.html#query-syntax).","example":"DISEASES.doid:\"DOID:2987\"","in":"query","name":"q","required":true,"schema":{"type":"string"}},{"$ref":"#/components/parameters/fields"},{"$ref":"#/components/parameters/size"},{"$ref":"#/components/parameters/from"},{"$ref":"#/components/parameters/fetch_all"},{"$ref":"#/components/parameters/scroll_id"},{"$ref":"#/components/parameters/sort"},{"$ref":"#/components/parameters/facets"},{"$ref":"#/components/parameters/facet_size"},{"$ref":"#/components/parameters/callback"},{"$ref":"#/components/parameters/dotfield"},{"$ref":"#/components/parameters/email"}],"responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["query"]},"post":{"description":"Although making simple GET requests above to our query service is sufficient for most use cases,  there are times you might find it more efficient to make batch queries (e.g., retrieving data  for multiple inputs). Fortunately, you can also make batch queries via POST requests when you need to.\n\nThe \"query” field in the returned object indicates the matching query term. If a query term has no match,  it will return with a “notfound” field with the value “true”.","parameters":[{"description":"Accepts multiple values separated by commas. Note that currently we only take the input values up to 1000  maximum, the rest will be omitted.\n\nThe request body can also be used to provide these ids.","in":"query","name":"q","required":false,"schema":{"items":{"type":"string"},"type":"array"}},{"description":"Optional, specify one or more fields (separated by commas) to search. 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Default: _id","items":{"type":"string"},"type":"array"}},"type":"object"}}}},"responses":{"200":{"description":"A 200 status code indicates a successful query, and is accompanied by the query response payload."}},"tags":["query"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/disease-gene"},{"$ref":"#/components/x-bte-kgs-operations/gene-disease"}]}}},"servers":[{"description":"Encrypted Production server","url":"https://biothings.ncats.io/DISEASES","x-maturity":"production"},{"description":"Production server","url":"http://biothings.ncats.io/DISEASES","x-maturity":"production"}],"tags":[{"name":"gene"},{"name":"disease"},{"name":"annotation"},{"name":"query"},{"name":"translator"},{"name":"biothings"}]},{"_id":"3aed5c94696b352db3e12a24038cd1e9","_meta":{"date_created":"2023-05-10T17:07:00.277477+00:00","last_updated":"2023-12-11T08:03:12.139381+00:00","url":"https://trapi-openapi.apps.renci.org/trapi/infores:automat-string-db/1.4.0","username":"YaphetKG"},"info":{"contact":{"email":"kebedey@renci.org","name":"Yaphet Kebede","x-id":"https://github.com/yaphetkg","x-role":"contributor"},"description":"STRING is a database of known and predicted protein-protein interactions. The interactions include direct (physical) and indirect (functional) associations.","termsOfService":"http://robokop.renci.org:7055/tos?service_long=Automat STRING-DB&provider_long=RENCI","title":"Automat-string-db(Trapi v1.4.0)","version":"v1.4.0-2","x-translator":{"biolink-version":"3.2.1","component":"KP","infores":"infores:automat-string-db","team":["Ranking Agent"]},"x-trapi":{"operations":["lookup","overlay_connect_knodes","annotate_nodes"],"test_data_location":{"staging":{"url":"https://automat.ci.transltr.io/string-db/1.4/sri_testing_data"}},"version":"1.4.0"}},"paths":{"/meta_knowledge_graph":{"get":{"description":"Returns meta knowledge graph representation of this TRAPI web service.","operationId":"get_meta_knowledge_graph_meta_knowledge_graph_get","responses":{"200":{"content":{"application/json":{"schema":{"$ref":"#/components/schemas/MetaKnowledgeGraph"}}},"description":"Successful Response"}},"summary":"Meta knowledge graph representation of this TRAPI web 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\ No newline at end of file

From b26ac7123a367895d1c24940ebc0c39a736606ce Mon Sep 17 00:00:00 2001
From: tokebe <43009413+tokebe@users.noreply.github.com>
Date: Mon, 11 Dec 2023 13:49:20 -0500
Subject: [PATCH 2/2] feat: clear edge cache every midnight

---
 src/controllers/cron/clear_edge_cache.js | 18 ++++++++++++++++++
 src/controllers/cron/index.js            |  2 ++
 2 files changed, 20 insertions(+)
 create mode 100644 src/controllers/cron/clear_edge_cache.js

diff --git a/src/controllers/cron/clear_edge_cache.js b/src/controllers/cron/clear_edge_cache.js
new file mode 100644
index 00000000..274b466c
--- /dev/null
+++ b/src/controllers/cron/clear_edge_cache.js
@@ -0,0 +1,18 @@
+const { redisClient } = require("@biothings-explorer/query_graph_handler");
+const Debug = require("debug");
+const cron = require("node-cron");
+const debug = Debug("bte:biothings-explorer-trapi:cron");
+
+module.exports = () => {
+  cron.schedule("0 0 * * *", async () => {
+    debug("Checking status for edge cache clearing.");
+    if (!redisClient.clientEnabled) {
+      debug("Cache not enabled, skipping edge cache clearing");
+      return;
+    }
+    debug("Redis client enabled, proceeding with cache clearing.");
+    await redisClient.client.usingLock(["redisLock:EdgeCaching"], 600000, () => {
+      redisClient.client.clearEdgeCache();
+    });
+  });
+};
diff --git a/src/controllers/cron/index.js b/src/controllers/cron/index.js
index c958f6a1..060e5cbd 100644
--- a/src/controllers/cron/index.js
+++ b/src/controllers/cron/index.js
@@ -1,5 +1,7 @@
 const smartapiCron = require("./update_local_smartapi");
+const cacheClearCron = require("./clear_edge_cache");
 
 module.exports = () => {
   smartapiCron();
+  cacheClearCron();
 };