From 2a6029ffb008b3709c01b85b89e7a452f133a7ed Mon Sep 17 00:00:00 2001 From: Colleen Xu Date: Wed, 2 Nov 2022 12:23:36 -0700 Subject: [PATCH 1/6] update: smartapi yaml and name of one api in config --- docs/smartapi.yaml | 2 +- src/config/apis.js | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/smartapi.yaml b/docs/smartapi.yaml index cc45f91b..a6befaf9 100644 --- a/docs/smartapi.yaml +++ b/docs/smartapi.yaml @@ -23,7 +23,7 @@ info: ## test_data_location not included for now x-translator: infores: "infores:biothings-explorer" - biolink-version: 2.4.8 + biolink-version: "3.0.3" component: ARA team: - Exploring Agent diff --git a/src/config/apis.js b/src/config/apis.js index 07281d9b..be440048 100644 --- a/src/config/apis.js +++ b/src/config/apis.js @@ -79,7 +79,7 @@ exports.API_LIST = { }, { id: '34bad236d77bea0a0ee6c6cba5be54a6', - name: 'Gene Ontology Molecular Activity API' + name: 'Gene Ontology Molecular Function API' }, { id: 'a5b0ec6bfde5008984d4b6cde402d61f', From a75610b53b42ffe254cb0f701b50136f11fbb7a4 Mon Sep 17 00:00:00 2001 From: tokebe <43009413+tokebe@users.noreply.github.com> Date: Thu, 8 Dec 2022 14:37:31 -0500 Subject: [PATCH 2/6] test: fix tests --- __test__/integration/TRAPIv1.1.test.js | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/__test__/integration/TRAPIv1.1.test.js b/__test__/integration/TRAPIv1.1.test.js index 5ab11148..4687888f 100644 --- a/__test__/integration/TRAPIv1.1.test.js +++ b/__test__/integration/TRAPIv1.1.test.js @@ -73,8 +73,8 @@ describe("Testing v1.1 endpoints", () => { expect.arrayContaining([ expect.objectContaining({ "subject": "biolink:SmallMolecule", - "predicate": "biolink:entity_positively_regulates_entity", - "object": "biolink:Gene", + "predicate": "biolink:treats", + "object": "biolink:Disease", }) ]) ); @@ -106,8 +106,8 @@ describe("Testing v1.1 endpoints", () => { expect.arrayContaining([ expect.objectContaining({ "subject": "biolink:SmallMolecule", - "predicate": "biolink:entity_positively_regulates_entity", - "object": "biolink:Gene" + "predicate": "biolink:treats", + "object": "biolink:Disease" }) ]) ); From 5d1e7aac8a01302199d8d8345ee5fd4e91bfb008 Mon Sep 17 00:00:00 2001 From: Colleen Xu Date: Thu, 8 Dec 2022 21:06:26 -0800 Subject: [PATCH 3/6] API_LIST: adjust name for GO molecular activity api --- src/config/apis.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/config/apis.js b/src/config/apis.js index 48b9967f..ea9f7eff 100644 --- a/src/config/apis.js +++ b/src/config/apis.js @@ -79,7 +79,7 @@ exports.API_LIST = { }, { id: '34bad236d77bea0a0ee6c6cba5be54a6', - name: 'Gene Ontology Molecular Function API' + name: 'Gene Ontology Molecular Activity API' }, { id: 'a5b0ec6bfde5008984d4b6cde402d61f', From 8abd089a55ca5a6444d721b0aa4460039d307fe6 Mon Sep 17 00:00:00 2001 From: tokebe <43009413+tokebe@users.noreply.github.com> Date: Fri, 9 Dec 2022 13:48:48 -0500 Subject: [PATCH 4/6] fix: update recent specs --- 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 8e1b07ed..59873601 100644 --- a/data/predicates.json +++ b/data/predicates.json @@ -1 +1 @@ -[{"association":{"api_name":"ICEES PCD Instance API - development","smartapi":{"id":"229d89b6896b5c272e22d735eebe7e24","meta":{"date_created":"2022-02-24T16:00:19.971705+00:00","last_updated":"2022-08-18T07:01:01.769203+00:00","url":"https://icees-pcd-dev.apps.renci.org/openapi.json","username":"maximusunc"}},"x-translator":{"component":"KP","team":["Exposures Provider"]}},"tags":["translator","trapi"],"query_operation":{"path":"/query","server":"https://icees-pcd-dev.apps.renci.org","method":"post"},"predicates_path":"/meta_knowledge_graph","predicates":{"biolink:SmallMolecule":{"biolink:SmallMolecule":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:Drug":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:SequenceVariant":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:DiseaseOrPhenotypicFeature":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:ChemicalEntity":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:PhenotypicFeature":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:ClinicalIntervention":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:NamedThing":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:EnvironmentalExposure":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:Disease":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:ComplexMolecularMixture":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:ComplexChemicalMixture":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:ChemicalExposure":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"]},"biolink:Drug":{"biolink:SmallMolecule":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:Drug":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:SequenceVariant":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:DiseaseOrPhenotypicFeature":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:ChemicalEntity":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:PhenotypicFeature":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:ClinicalIntervention":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:NamedThing":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:EnvironmentalExposure":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:Disease":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:ComplexMolecularMixture":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:ComplexChemicalMixture":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:ChemicalExposure":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"]},"biolink:SequenceVariant":{"biolink:SmallMolecule":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:Drug":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:SequenceVariant":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:DiseaseOrPhenotypicFeature":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:ChemicalEntity":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:PhenotypicFeature":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:ClinicalIntervention":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:NamedThing":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:EnvironmentalExposure":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:Disease":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:ComplexMolecularMixture":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:ComplexChemicalMixture":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:ChemicalExposure":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"]},"biolink:DiseaseOrPhenotypicFeature":{"biolink:SmallMolecule":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:Drug":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:SequenceVariant":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:DiseaseOrPhenotypicFeature":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:ChemicalEntity":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:PhenotypicFeature":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:ClinicalIntervention":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:NamedThing":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:EnvironmentalExposure":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:Disease":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:ComplexMolecularMixture":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:ComplexChemicalMixture":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:ChemicalExposure":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"]},"biolink:ChemicalEntity":{"biolink:SmallMolecule":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:Drug":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:SequenceVariant":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:DiseaseOrPhenotypicFeature":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:ChemicalEntity":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:PhenotypicFeature":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:ClinicalIntervention":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:NamedThing":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:EnvironmentalExposure":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:Disease":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:ComplexMolecularMixture":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:ComplexChemicalMixture":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:ChemicalExposure":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"]},"biolink:PhenotypicFeature":{"biolink:SmallMolecule":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:Drug":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:SequenceVariant":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:DiseaseOrPhenotypicFeature":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:ChemicalEntity":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:PhenotypicFeature":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:ClinicalIntervention":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:NamedThing":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:EnvironmentalExposure":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:Disease":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:ComplexMolecularMixture":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:ComplexChemicalMixture":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:ChemicalExposure":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"]},"biolink:ClinicalIntervention":{"biolink:SmallMolecule":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:Drug":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:SequenceVariant":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:DiseaseOrPhenotypicFeature":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:ChemicalEntity":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:PhenotypicFeature":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:ClinicalIntervention":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:NamedThing":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:EnvironmentalExposure":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:Disease":["biolink:correlated_with","biolink:has_real_world_evidence_of_association_with"],"biolink:ComplexMolecul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[ICEES Overview page](https://researchsoftwareinstitute.github.io/data-translator/apps/icees)\n
[documentation](https://github.com/NCATS-Tangerine/icees-api/tree/master/docs) \n
[source](https://github.com/NCATS-Tangerine/icees-api/tree/master/) \n
[ICEES API example queries](https://github.com/NCATS-Tangerine/icees-api/tree/master/#examples)\n
dictionary for versioning of tables\n
\n\n \n \n \n \n \n \n \n \n
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Block Groups are aggregates of an average of 39 Blocks each, each of which is delineated by visible and invisible geographic boundaries. Block groups, in turn, are aggregated into Census Tracts, which generally have a population size between 1,200 and 8,000 people, with an optimum size of 4,000 people. Census Tracts aggregate into counties and counties into states. Metropolitan and micropolitan areas are aggregates of counties. See https://www2.census.gov/geo/pdfs/reference/geodiagram.pdf for further detail. Census geography, even Block Groups, may cross municipal lines and may include both urbanized and rural areas. Because population is a large factor in determining Census geography, some Block Groups may cover an extensive rural or wilderness area while others are quite compact. Census Block, Block Group, and Tract boundaries may change somewhat with each decennial Census, but remain stable in between Censuses.\n\nThe US Census Bureau is mandated to preserve the confidentiality of individual-level data. Therefore, data are often summarized, coarsened into categories, or suppressed by complex secret algorithms (especially, but not limited to household income data). In addition, because the variables of interest may only apply to a small subset of Block Group missing data can occur. In some versions of the data, calculated values are suppressed in Block Groups with less than 50 residents.\n\nStandard errors for the socio-demographic variables are provided. Because each of the values in the ACS data files are summary statistics calculated from sample survey data for each Block Group, different samples yield somewhat different values. Therefore, the Census Bureau generates 80 replicate values for selected variables. These provide the basis for the estimated standard errors of the estimates.\n\nThe currently available variables are listed here:\n\n **(2007-2011 data)**\n- **YEARS** – the range of years for which this census data is valid\n- **GEOID** – a FIPS like code for identifying which census block group this data pertains to, see (https://www.census.gov/geo/reference/geoidentifiers.html)\n- **EstTotalPopulation** - estimated population count in block group\n- **MedianHouseholdIncome** - estimated median household income\n- **EstResidentialDensity** - block group population density\n- **EstPropNonHispWhite** – proportion of the block group population that is non-Hispanic white\n- **EstPropPersons5PlusNoEnglish** - proportion of the block group population aged 5 plus sometimes speaking a language other than English at home\n- **EstPropMaleLittleWork** - proportion of block group males aged 16-64 who worked less than 26 weeks in the previous year\n- **EstPropHouseholdsNoAuto** - proportion of the block group households with no automobile\n- **EstPropHouseholdSSI** - proportion of the block group households receiving Supplemental Security Income\n- **EstPropHouseholdPA** - proportion of the block group households receiving Public Assistance\n- **EstPropHighSchoolMaxEducation** - proportion of the block group population aged 25 and up with a HS diploma or less\n- **EstPropHighSchoolDropout** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates\n- **EstPropHighSchoolDropoutNoWork** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates and are without work\n- **EstPropFemaleHouseholdNoSpouse** - proportion of the block group family households headed by a female (no male partner present)\n- **EstPropFemaleHouseholdFamilyChild** - proportion of the block group family households headed by a female with related children aged 18 or under (no male partner present)\n- **EstPropFemaleHouseholdAnyChild** - proportion of the block group total households headed by a female with any children aged 18 or less (no male partner present)\n\n **(2012-2016 data)**\n- **YEARS** – the range of years for which this census data is valid\n- **GEOID** – a FIPS like code for identifying which census block group this data pertains to, see (https://www.census.gov/geo/reference/geoidentifiers.html)\n- **EstTotalPopulation** - estimated population count in block group\n- **EstTotalPopulation_SE** - standard error of total population in block group\n - **EstResidentialDensity** - block group population density\n- **EstResidentialDensity_SE** - standard error of residential population density in block group\n- **MedianHouseholdIncome** - estimated median household income\n- **MedianHouseholdIncome_SE** - standard error of median household income\n- **EstPropPersonsNoHealthIns** - proportion of the block group population with no health insurance - **EstPropPersonsNoHealthIns_SE** - standard error of proportion of the block group population with no health insurance\n- **EstPropNonHispWhite** – proportion of the block group population that is non-Hispanic white\n- **EstPropNonHispWhite_SE** - standard error of proportion of the block group population that is non-Hispanic white\n- **EstPropPersons5PlusNoEnglish** - proportion of the block group population aged 5 plus sometimes speaking a language other than English at home\n- **EstPropPersons5PlusNoEnglish_SE** - standard error of proportion of the block group population aged 5 plus sometimes speaking a language other than English at home\n- **EstPropMaleLittleWork** - proportion of block group males aged 16-64 who worked less than 26 weeks in the previous year\n- **EstPropHouseholdsNoAuto** - proportion of the block group households with no automobile\n- **EstPropHouseholdsNoAuto_SE** - standard error of proportion of the block group households with no automobile\n- **EstPropHouseholdSSI** - proportion of the block group households receiving Supplemental Security Income\n- **EstPropHouseholdSSI_SE** - standard error of proportion of the block group households receiving Supplemental Security Income\n- **EstPropHouseholdPA** - proportion of the block group households receiving Public Assistance\n- **EstPropHouseholdPA_SE** - standard error of proportion of the block group households receiving Public Assistance\n- **EstPropHighSchoolMaxEducation** - proportion of the block group population aged 25 and up with a HS diploma or less\n- **EstPropHighSchoolMaxEducation_SE** - standard error of proportion of the block group population aged 25 and up with a HS diploma or less\n- **EstPropHighSchoolDropout** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates\n- **EstPropHighSchoolDropoutNoWork** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates and are without work\n- **EstPropFemaleHouseholdNoSpouse** - proportion of the block group family households headed by a female (no male partner present)\n- **EstPropFemaleHouseholdNoSpouse_SE** - standard error of proportion of the block group family households headed by a female (no male partner present)\n- **EstPropFemaleHouseholdFamilyChild** - proportion of the block group family households headed by a female with related children aged 18 or under (no male partner present)\n- **EstPropFemaleHouseholdFamilyChild_SE** - standard error of proportion of the block group family households headed by a female with related children aged 18 or under (no male partner present)\n- **EstPropFemaleHouseholdAnyChild** - proportion of the block group total households headed by a female with any children aged 18 or less (no male partner present)\n- **EstPropFemaleHouseholdAnyChild_SE** - standard error of proportion of the block group total households headed by a female with any children aged 18 or less (no male partner present)\n\nLocations are expressed using WGS84 decimal format. WGS84 is the World Geodetic System for expressing latitude and longitude. For example, Raleigh, North Carolina is at latitude 35.7796 and longitude -78.6382.\n\nAdditional details on the data can be found in this documentation: (https://github.com/lstillwe/socio-economic-api/blob/master/docs/CensusData.md)\n","license":{"name":"MIT","url":"http://opensource.org/licenses/MIT"},"title":"Socio-Environmental Exposures API","version":"1.0.1","x-translator":{"component":"KP","team":["Exposures Provider"]}},"paths":{"/values":{"get":{"description":"By passing in a location specification (lat, lon) and a year range, you can retrieve the the ACS Values for that location and year range\n","operationId":"get_values","parameters":[{"description":"latitude in decimal degrees format, ie: 32.47","in":"query","name":"latitude","required":true,"schema":{"type":"string"}},{"description":"longitude in decimal degrees format, ie: -86.5","in":"query","name":"longitude","required":true,"schema":{"type":"string"}},{"description":"ACS data year range 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dictionary for versioning of tables\n
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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":"2.2.13","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":[{"$ref":"#/components/x-bte-kgs-operations/anatomy-gene"}]}},"/bioentity/disease/{id}/genes":{"get":{"parameters":[{"description":"CURIE identifier of disease, e.g. OMIM:605543, DOID:678. 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Equivalent IDs can be used with same results","example":"MONDO:0004747","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"$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":[{"$ref":"#/components/x-bte-kgs-operations/gene-anatomy"}]}},"/bioentity/gene/{id}/diseases":{"get":{"parameters":[{"description":"CURIE identifier of gene, e.g. NCBIGene:4750. 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Equivalent IDs can be used with same results","example":"HGNC:2950","in":"path","name":"id","required":true,"schema":{"type":"string"}},{"$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}/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"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns diseases associated with a 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phenotype","tags":["phenotype"],"x-bte-kgs-operations":[{"$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 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`drugs_fp_embed.txt` | model_id: `disease_hp_embed.txt` |\n| to check the drugs similar to a given drug | to check the diseases similar to a given disease |\n","operationId":"Get_similar_entities_similarity_get","parameters":[{"in":"query","name":"types","required":false,"schema":{"allOf":[{"$ref":"#/components/schemas/SimilarityTypes"}],"default":"Diseases"}},{"in":"query","name":"drug_id","required":false,"schema":{"title":"Drug Id","type":"string"}},{"in":"query","name":"disease_id","required":false,"schema":{"default":"OMIM:246300","title":"Disease Id","type":"string"}},{"in":"query","name":"model_id","required":false,"schema":{"default":"disease_hp_embed.txt","title":"Model Id","type":"string"}},{"in":"query","name":"min_score","required":false,"schema":{"title":"Min Score","type":"number"}},{"in":"query","name":"max_score","required":false,"schema":{"title":"Max Score","type":"number"}},{"in":"query","name":"n_results","required":false,"schema":{"title":"N 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Stillwell"},"description":"\nThis API returns data from the US Census Bureau American Community Survey (ACS) for a given spatial location of interest.\n\nThe API returns estimated values for socio-economic variables and related variables for small geographic areas that may act as indirect indicators of relevant health behaviors and outcomes. The data are collected by the US Census Bureau and are publicly available.\n\nThe variables are taken from the five-year summary data file of the US Census Bureau ACS, which is constructed from five annual waves of the bureau’s largest household survey. Approximately, two million households have completed the survey annually since calendar year 2005. (Five waves of the survey before 2005 sampled approximately 500,000 households each.) See https://www.census.gov/acs/www/methodology/sample-size-and-data-quality/sample-size/ for more detail. Microdata are available, but small-area data are only available in summary tabulations.\n\nValues are provided at the US Census Block Group level, representing the 2007-2011 and 2012-2016 calendar-year periods for locations within the continental USA. Block groups, the smallest geographic area for which sample survey data are released, generally contain 600 to 3,000 people (e.g., the size of a single city apartment building). Block Groups are aggregates of an average of 39 Blocks each, each of which is delineated by visible and invisible geographic boundaries. Block groups, in turn, are aggregated into Census Tracts, which generally have a population size between 1,200 and 8,000 people, with an optimum size of 4,000 people. Census Tracts aggregate into counties and counties into states. Metropolitan and micropolitan areas are aggregates of counties. See https://www2.census.gov/geo/pdfs/reference/geodiagram.pdf for further detail. Census geography, even Block Groups, may cross municipal lines and may include both urbanized and rural areas. Because population is a large factor in determining Census geography, some Block Groups may cover an extensive rural or wilderness area while others are quite compact. Census Block, Block Group, and Tract boundaries may change somewhat with each decennial Census, but remain stable in between Censuses.\n\nThe US Census Bureau is mandated to preserve the confidentiality of individual-level data. Therefore, data are often summarized, coarsened into categories, or suppressed by complex secret algorithms (especially, but not limited to household income data). In addition, because the variables of interest may only apply to a small subset of Block Group missing data can occur. In some versions of the data, calculated values are suppressed in Block Groups with less than 50 residents.\n\nStandard errors for the socio-demographic variables are provided. Because each of the values in the ACS data files are summary statistics calculated from sample survey data for each Block Group, different samples yield somewhat different values. Therefore, the Census Bureau generates 80 replicate values for selected variables. These provide the basis for the estimated standard errors of the estimates.\n\nThe currently available variables are listed here:\n\n **(2007-2011 data)**\n- **YEARS** – the range of years for which this census data is valid\n- **GEOID** – a FIPS like code for identifying which census block group this data pertains to, see (https://www.census.gov/geo/reference/geoidentifiers.html)\n- **EstTotalPopulation** - estimated population count in block group\n- **MedianHouseholdIncome** - estimated median household income\n- **EstResidentialDensity** - block group population density\n- **EstPropNonHispWhite** – proportion of the block group population that is non-Hispanic white\n- **EstPropPersons5PlusNoEnglish** - proportion of the block group population aged 5 plus sometimes speaking a language other than English at home\n- **EstPropMaleLittleWork** - proportion of block group males aged 16-64 who worked less than 26 weeks in the previous year\n- **EstPropHouseholdsNoAuto** - proportion of the block group households with no automobile\n- **EstPropHouseholdSSI** - proportion of the block group households receiving Supplemental Security Income\n- **EstPropHouseholdPA** - proportion of the block group households receiving Public Assistance\n- **EstPropHighSchoolMaxEducation** - proportion of the block group population aged 25 and up with a HS diploma or less\n- **EstPropHighSchoolDropout** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates\n- **EstPropHighSchoolDropoutNoWork** - proportion of the block group 16-19 year olds who are neither attending school nor HS graduates and are without work\n- **EstPropFemaleHouseholdNoSpouse** - proportion of the block group family households headed by a female (no male partner present)\n- **EstPropFemaleHouseholdFamilyChild** - proportion of the block group family households headed by a female with related children aged 18 or under (no male partner present)\n- **EstPropFemaleHouseholdAnyChild** - proportion of the block group total households headed by a female with any children aged 18 or less (no male partner present)\n\n **(2012-2016 data)**\n- **YEARS** – the range of years for which this census data is valid\n- **GEOID** – a FIPS like code for identifying which census block group this data pertains to, see (https://www.census.gov/geo/reference/geoidentifiers.html)\n- **EstTotalPopulation** - estimated population count in block group\n- **EstTotalPopulation_SE** - standard error of total population in block group\n - 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See https://www.fhwa.dot.gov/policyinformation/travel_monitoring/pubs/aadt/ for information on how AADT is computed.\n\nThe following roadway types are supported:\n* Off-Network\n* Rural Restricted Access\n* Rural Unrestricted Access\n* Urban Restricted Access\n* Urban Unrestricted Access\n\nIn some cases, roadway type, AADT, and speed are not available in the HPMS data set. In this case, data from the US Census Bureau TIGER (Topologically Integrated Geographic Encoding and Referencing) data set (available at census.gov) was used to obtain roadway type. Roadway segments without roadway type were dropped from the dataset; this amounted to approximately 5% of roadways, many of which had not yet been built. Missing AADT and speeds were populated using a variety of methods. First, a lookup table was built with county averages by roadway type and facility type and populated with values from segments that already had AADT and/or speed. 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Equivalent IDs can be used with same results","in":"path","required":true,"example":"MONDO:0011562","schema":{"type":"string"}},{"name":"association_type","description":"Additional filters: causal, non_causal, both","in":"query","required":false,"example":"causal","schema":{"type":"string","enum":["causal","non_causal","both"],"default":"both"}},{"$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"},{"$ref":"#/components/x-bte-kgs-operations/disease-gene-2"}]}},"/bioentity/disease/{id}/pathways":{"get":{"parameters":[{"name":"id","description":"CURIE identifier of disease, e.g. DOID:4450. Equivalent IDs can be used with same results","in":"path","required":true,"example":"MONDO:0010524","schema":{"type":"string"}},{"$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":[{"name":"id","description":"CURIE identifier of disease, e.g. OMIM:605543, Orphanet:1934, DOID:678. Equivalent IDs can be used with same results","in":"path","required":true,"example":"MONDO:0008974","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":[{"$ref":"#/components/x-bte-kgs-operations/disease-phenotype"}]}},"/bioentity/disease/{id}/variants":{"get":{"parameters":[{"name":"id","description":"CURIE identifier of disease, e.g. OMIM:605543, DOID:678. Equivalent IDs can be used with same results","in":"path","required":true,"example":"MONDO:0004747","schema":{"type":"string"}},{"$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":[{"name":"id","description":"CURIE identifier of gene, e.g. NCBIGene:13434","in":"path","required":true,"example":"HGNC:8548","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":[{"$ref":"#/components/x-bte-kgs-operations/gene-anatomy"}]}},"/bioentity/gene/{id}/diseases":{"get":{"parameters":[{"name":"id","description":"CURIE identifier of gene, e.g. NCBIGene:4750. Equivalent IDs can be used with same results","in":"path","required":true,"example":"HGNC:11138","schema":{"type":"string"}},{"name":"association_type","description":"Additional filters: causal, non_causal, both","in":"query","required":false,"example":"causal","schema":{"type":"string","enum":["causal","non_causal","both"],"default":"both"}},{"$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"},{"$ref":"#/components/x-bte-kgs-operations/gene-disease-2"}]}},"/bioentity/gene/{id}/interactions":{"get":{"parameters":[{"name":"id","description":"id, e.g. NCBIGene:3630. Equivalent IDs can be used with same results","in":"path","required":true,"example":"HGNC:2950","schema":{"type":"string"}},{"$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}/phenotypes":{"get":{"parameters":[{"name":"id","description":"CURIE identifier of gene, e.g. NCBIGene:4750. Equivalent IDs can be used with same results","in":"path","required":true,"example":"HGNC:2950","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":[{"$ref":"#/components/x-bte-kgs-operations/gene-phenotype"}]}},"/bioentity/gene/{id}/variants":{"get":{"parameters":[{"name":"id","description":"CURIE identifier of gene, e.g. HGNC:10896","in":"path","required":true,"example":"HGNC:2950","schema":{"type":"string"}},{"$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":[{"name":"id","description":"CURIE any pathway element. E.g. REACT:R-HSA-5387390","in":"path","required":true,"example":"REACT:R-HSA-2644606","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":[{"$ref":"#/components/x-bte-kgs-operations/pathway-disease"}]}},"/bioentity/phenotype/{id}/diseases":{"get":{"parameters":[{"name":"id","description":"CURIE identifier of phenotype, e.g. HP:0007359. Equivalent IDs can be used with same results","in":"path","required":true,"example":"HP:0000272","schema":{"type":"string"}},{"$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":[{"name":"id","description":"Pheno class CURIE identifier, e.g WBPhenotype:0000180 (axon morphology variant), MP:0001569 (abnormal circulating bilirubin level)","in":"path","required":true,"example":"HP:0000183","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":[{"$ref":"#/components/x-bte-kgs-operations/phenotype-gene"}]}},"/bioentity/phenotype/{id}/variants":{"get":{"parameters":[{"name":"id","description":"Pheno class CURIE identifier, e.g WBPhenotype:0000180 (axon morphology variant), MP:0001569 (abnormal circulating bilirubin level)","in":"path","required":true,"example":"HP:0002944","schema":{"type":"string"}},{"$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":[{"name":"id","description":"CURIE identifier of variant, e.g. ClinVarVariant:14925","in":"path","required":true,"example":"dbSNP:rs227731","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 variant","tags":["variant"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/variant-disease"}]}},"/bioentity/variant/{id}/genes":{"get":{"parameters":[{"name":"id","description":"CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, ClinVarVariant:39783","in":"path","required":true,"example":"dbSNP:rs11879191","schema":{"type":"string"}},{"$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"},{"$ref":"#/components/parameters/q"}],"responses":{"200":{"description":"Success"}},"summary":"Returns genes associated with a variant","tags":["variant"],"x-bte-kgs-operations":[{"$ref":"#/components/x-bte-kgs-operations/variant-gene"}]}},"/bioentity/variant/{id}/phenotypes":{"get":{"parameters":[{"name":"id","description":"CURIE identifier of variant, e.g. ZFIN:ZDB-ALT-010427-8, 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queryInputs }}","rows":-1,"direct":true,"unselect_evidence":true,"taxon":"NCBITaxon:9606"},"outputs":[{"id":"HGNC","semantic":"Gene"}],"predicate":"expresses","source":"infores:monarchinitiative","response_mapping":{"$ref":"#/components/x-bte-response-mapping/gene-hgnc"}}],"disease-gene-1":[{"supportBatch":false,"useTemplating":true,"inputs":[{"id":"MONDO","semantic":"Disease"}],"parameters":{"id":"{{ queryInputs }}","rows":-1,"direct":true,"unselect_evidence":true,"taxon":"NCBITaxon:9606","association_type":"causal"},"outputs":[{"id":"HGNC","semantic":"Gene"}],"predicate":"caused_by","source":"infores:monarchinitiative","response_mapping":{"$ref":"#/components/x-bte-response-mapping/gene-hgnc"}}],"disease-gene-2":[{"supportBatch":false,"useTemplating":true,"inputs":[{"id":"MONDO","semantic":"Disease"}],"parameters":{"id":"{{ queryInputs 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[source](https://github.com/NCATS-Tangerine/icees-api/tree/master/) \n
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\"object.novelty\"]}"},"parameters":{"fields":"subject.umls,pmid,subject.name,predicate,object.umls,object.name","size":1000},"outputs":[{"id":"UMLS","semantic":"SmallMolecule"}],"predicate":"has_part","source":"infores:semmeddb","response_mapping":{"$ref":"#/components/x-bte-response-mapping/umls-subj"}}],"nsba-PREDISPOSES-sosy-rev":[{"supportBatch":true,"useTemplating":true,"inputs":[{"id":"UMLS","semantic":"PhenotypicFeature"}],"requestBodyType":"object","requestBody":{"body":"{\"q\": [ {{ queryInputs | wrap( '[\"', '\",\"PREDISPOSES\",\"nsba\",1,1]' )}}], \"scopes\": [\"object.umls\", \"predicate\", \"subject.semantic_type_abbreviation\", \"subject.novelty\", \"object.novelty\"]}"},"parameters":{"fields":"subject.umls,pmid,subject.name,predicate,object.umls,object.name","size":1000},"outputs":[{"id":"UMLS","semantic":"SmallMolecule"}],"predicate":"has_predisposing_factor","source":"infores:semmeddb","response_mapping":{"$ref":"#/components/x-bte-response-mapping/umls-subj"}}],"sosy-ASSOCIATED_WITH-mobd":[{"supportBatch":true,"useTemplating":true,"inputs":[{"id":"UMLS","semantic":"PhenotypicFeature"}],"requestBodyType":"object","requestBody":{"body":"{\"q\": [ {{ queryInputs | wrap( '[\"', '\",\"ASSOCIATED_WITH\",\"mobd\",1,1]' ) }} ], \"scopes\": [\"subject.umls\", \"predicate\", \"object.semantic_type_abbreviation\", \"subject.novelty\", \"object.novelty\"]}"},"parameters":{"fields":"object.umls,pmid,subject.umls,subject.name,predicate,object.name","size":1000},"outputs":[{"id":"UMLS","semantic":"Disease"}],"predicate":"related_to","source":"infores:semmeddb","response_mapping":{"$ref":"#/components/x-bte-response-mapping/umls-obj"}}],"eico-INTERACTS_WITH-imft-rev":[{"supportBatch":true,"useTemplating":true,"inputs":[{"id":"UMLS","semantic":"ChemicalEntity"}],"requestBodyType":"object","requestBody":{"body":"{\"q\": [ {{ queryInputs | wrap( '[\"', '\",\"INTERACTS_WITH\",\"eico\",1,1]' )}}], \"scopes\": [\"object.umls\", \"predicate\", \"subject.semantic_type_abbreviation\", \"subject.novelty\", \"object.novelty\"]}"},"parameters":{"fields":"subject.umls,pmid,subject.name,predicate,object.umls,object.name","size":1000},"outputs":[{"id":"UMLS","semantic":"SmallMolecule"}],"predicate":"interacts_with","source":"infores:semmeddb","response_mapping":{"$ref":"#/components/x-bte-response-mapping/umls-subj"}}],"food-CAUSES-anab":[{"supportBatch":true,"useTemplating":true,"inputs":[{"id":"UMLS","semantic":"Food"}],"requestBodyType":"object","requestBody":{"body":"{\"q\": [ {{ queryInputs | wrap( '[\"', '\",\"CAUSES\",\"anab\",1,1]' ) }} ], \"scopes\": [\"subject.umls\", \"predicate\", \"object.semantic_type_abbreviation\", \"subject.novelty\", \"object.novelty\"]}"},"parameters":{"fields":"object.umls,pmid,subject.umls,subject.name,predicate,object.name","size":1000},"outputs":[{"id":"UMLS","semantic":"Disease"}],"predicate":"causes","source":"infores:semmeddb","response_mapping":{"$ref":"#/components/x-bte-response-mapping/umls-obj"}}],"imft-PREDISPOSES-sosy":[{"supportBatch":true,"useTemplating":true,"inputs":[{"id":"UMLS","semantic":"ChemicalEntity"}],"requestBodyType":"object","requestBody":{"body":"{\"q\": [ {{ queryInputs | wrap( '[\"', '\",\"PREDISPOSES\",\"sosy\",1,1]' ) }} ], \"scopes\": [\"subject.umls\", \"predicate\", \"object.semantic_type_abbreviation\", \"subject.novelty\", 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\"object.novelty\"]}"},"parameters":{"fields":"object.umls,pmid,subject.umls,subject.name,predicate,object.name","size":1000},"outputs":[{"id":"UMLS","semantic":"Disease"}],"predicate":"treats","source":"infores:semmeddb","response_mapping":{"$ref":"#/components/x-bte-response-mapping/umls-obj"}}],"imft-PREDISPOSES-inpo":[{"supportBatch":true,"useTemplating":true,"inputs":[{"id":"UMLS","semantic":"ChemicalEntity"}],"requestBodyType":"object","requestBody":{"body":"{\"q\": [ {{ queryInputs | wrap( '[\"', '\",\"PREDISPOSES\",\"inpo\",1,1]' ) }} ], \"scopes\": [\"subject.umls\", \"predicate\", \"object.semantic_type_abbreviation\", \"subject.novelty\", \"object.novelty\"]}"},"parameters":{"fields":"object.umls,pmid,subject.umls,subject.name,predicate,object.name","size":1000},"outputs":[{"id":"UMLS","semantic":"PathologicalProcess"}],"predicate":"predisposes","source":"infores:semmeddb","response_mapping":{"$ref":"#/components/x-bte-response-mapping/umls-obj"}}],"antb-INHIBITS-imft-rev":[{"supportBatch":true,"useTemplating":true,"inputs":[{"id":"UMLS","semantic":"ChemicalEntity"}],"requestBodyType":"object","requestBody":{"body":"{\"q\": [ {{ queryInputs | wrap( '[\"', '\",\"INHIBITS\",\"antb\",1,1]' )}}], \"scopes\": [\"object.umls\", \"predicate\", \"subject.semantic_type_abbreviation\", \"subject.novelty\", 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Su","url":"https://github.com/andrewsu"},"description":"A TRAPI/Reasoner Standard API for BioThings Explorer (BTE)","termsOfService":"https://biothings.io/about","title":"BioThings Explorer (BTE) TRAPI","version":"2.8.1","x-translator":{"biolink-version":"2.4.8","component":"ARA","infores":"infores:biothings-explorer","team":["Exploring Agent"]},"x-trapi":{"asyncquery":true,"operations":["lookup"],"rate_limit":15,"test_data_location":{"default":{"url":"https://raw.githubusercontent.com/NCATS-Tangerine/translator-api-registry/5b19e854524c48a39125d545bec13f637661a09f/biothings_explorer/sri-test-bte-ara.json"}},"version":"1.3.0"}},"paths":{"/meta_knowledge_graph":{"get":{"responses":{"200":{"content":{"application/json":{"schema":{"$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"]}},"/smartapi/{smartapi_id}/meta_knowledge_graph":{"get":{"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_TRAPI/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. 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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. 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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_TRAPI/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_TRAPI/blob/main/src/config/apis.js. 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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"]}},"/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. 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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. 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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 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_TRAPI/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_TRAPI/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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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"}}},"servers":[{"description":"Default server","url":"https://cam-kp-api.renci.org/1.3.0","x-location":"RENCI","x-maturity":"development"}],"tags":[{"name":"maturity"},{"name":"translator"},{"name":"trapi"}]}]} \ No newline at end of file From f7da0695248508c8f5de99cecf53b962b36c4f04 Mon Sep 17 00:00:00 2001 From: tokebe <43009413+tokebe@users.noreply.github.com> Date: Fri, 9 Dec 2022 17:45:51 -0500 Subject: [PATCH 5/6] fix: update biolink-version --- docs/smartapi.yaml | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/docs/smartapi.yaml b/docs/smartapi.yaml index a6befaf9..7c1c1266 100644 --- a/docs/smartapi.yaml +++ b/docs/smartapi.yaml @@ -23,7 +23,7 @@ info: ## test_data_location not included for now x-translator: infores: "infores:biothings-explorer" - biolink-version: "3.0.3" + biolink-version: "3.1.1" component: ARA team: - Exploring Agent @@ -107,8 +107,8 @@ paths: 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_TRAPI/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 + Note that Service Provider endpoints are also advertised separately as a KP + http://smart-api.info/registry?q=36f82f05705c317bac17ddae3a0ea2f0 in: path name: team_name required: true @@ -331,8 +331,8 @@ paths: 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_TRAPI/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 + Note that Service Provider endpoints are also advertised separately as a KP + http://smart-api.info/registry?q=36f82f05705c317bac17ddae3a0ea2f0 in: path name: team_name required: true @@ -454,7 +454,7 @@ paths: schema: type: string description: >- - Logging level. The order of priority is ERROR, WARNING, INFO, DEBUG. BTE will return all logs at the + 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 @@ -596,7 +596,7 @@ paths: tags: - asyncquery summary: >- - This endpoint is for asynchronously querying an individual SmartAPI KP API (that has x-bte annotation) + This endpoint is for asynchronously querying an individual SmartAPI KP API (that has x-bte annotation) as a TRAPI KP API. Initiate a query that will be handled in an asynchronous manner (there is a @@ -709,7 +709,7 @@ paths: tags: - asyncquery summary: >- - This endpoint is for asynchronously querying an individual Translator team's SMARTAPI KP APIs (that have x-bte annotation) + 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. Initiate a query that will be handled in an asynchronous manner (there is a @@ -723,8 +723,8 @@ paths: 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_TRAPI/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 + Note that Service Provider endpoints are also advertised separately as a KP + http://smart-api.info/registry?q=36f82f05705c317bac17ddae3a0ea2f0 in: path name: team_name required: true @@ -830,7 +830,7 @@ components: ## - AsyncQuery: callback property not required (commented it out of the 'required' field), ## comment out workflow.allOf section ## - Response: comment out workflow.allOf section - ## - Attribute: comment out properties.attributes.items since the self-$ref breaks execution of + ## - Attribute: comment out properties.attributes.items since the self-$ref breaks execution of ## BTE's api-schema-builder/openapi-validator-middleware schemas: Query: From 88ef978b8be9975f50f21f2b8babc9079026a222 Mon Sep 17 00:00:00 2001 From: Colleen Xu Date: Tue, 13 Dec 2022 17:15:39 -0800 Subject: [PATCH 6/6] minor edit to API_LIST: change GO MF API name going to leave it as GO MF --- src/config/apis.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/config/apis.js b/src/config/apis.js index ea9f7eff..48b9967f 100644 --- a/src/config/apis.js +++ b/src/config/apis.js @@ -79,7 +79,7 @@ exports.API_LIST = { }, { id: '34bad236d77bea0a0ee6c6cba5be54a6', - name: 'Gene Ontology Molecular Activity API' + name: 'Gene Ontology Molecular Function API' }, { id: 'a5b0ec6bfde5008984d4b6cde402d61f',