diff --git a/dgidb/openapi.yml b/dgidb/openapi.yml index b06b1cea..5bc87a48 100644 --- a/dgidb/openapi.yml +++ b/dgidb/openapi.yml @@ -8,16 +8,13 @@ info: description: Documentation of the BioThings DGIdb query web services. termsOfService: https://biothings.io/about title: BioThings DGIdb API - version: '1.0' + version: '4.2.0' x-translator: infores: "infores:biothings-dgidb" component: KP team: - Service Provider - biolink-version: "2.2.8" -## current parser issues: -## - some chem may have incorrectly imported IDs (have a wikidata ID and a non-matching CHEMBL ID in the object.id field...) -## - the relationships in DGIdb are drug -> gene, but the API is set up with subject as gene and object as chem + biolink-version: "2.2.13" servers: - description: Encrypted Production server url: https://biothings.ncats.io/dgidb @@ -140,7 +137,7 @@ paths: get: parameters: - description: Query string. - example: object.id:CHEMBL.COMPOUND\:CHEMBL26 + example: "subject.CHEMBL_COMPOUND:CHEMBL1017" in: query name: q required: true @@ -229,8 +226,6 @@ paths: x-bte-kgs-operations: - $ref: '#/components/x-bte-kgs-operations/activator' - $ref: '#/components/x-bte-kgs-operations/activator-rev' - - $ref: '#/components/x-bte-kgs-operations/adduct' - - $ref: '#/components/x-bte-kgs-operations/adduct-rev' - $ref: '#/components/x-bte-kgs-operations/agonist' - $ref: '#/components/x-bte-kgs-operations/agonist-rev' - $ref: '#/components/x-bte-kgs-operations/allosteric_modulator' @@ -241,16 +236,8 @@ paths: - $ref: '#/components/x-bte-kgs-operations/antibody-rev' - $ref: '#/components/x-bte-kgs-operations/antisense_oligonucleotide' - $ref: '#/components/x-bte-kgs-operations/antisense_oligonucleotide-rev' - - $ref: '#/components/x-bte-kgs-operations/binder' - - $ref: '#/components/x-bte-kgs-operations/binder-rev' - $ref: '#/components/x-bte-kgs-operations/blocker' - $ref: '#/components/x-bte-kgs-operations/blocker-rev' - - $ref: '#/components/x-bte-kgs-operations/chaperone' - - $ref: '#/components/x-bte-kgs-operations/chaperone-rev' - - $ref: '#/components/x-bte-kgs-operations/cleavage' - - $ref: '#/components/x-bte-kgs-operations/cleavage-rev' - - $ref: '#/components/x-bte-kgs-operations/cofactor' - - $ref: '#/components/x-bte-kgs-operations/cofactor-rev' - $ref: '#/components/x-bte-kgs-operations/inducer' - $ref: '#/components/x-bte-kgs-operations/inducer-rev' - $ref: '#/components/x-bte-kgs-operations/inhibitor' @@ -259,30 +246,16 @@ paths: - $ref: '#/components/x-bte-kgs-operations/inhibitory_allosteric_modulator-rev' - $ref: '#/components/x-bte-kgs-operations/inverse_agonist' - $ref: '#/components/x-bte-kgs-operations/inverse_agonist-rev' - - $ref: '#/components/x-bte-kgs-operations/ligand' - - $ref: '#/components/x-bte-kgs-operations/ligand-rev' - $ref: '#/components/x-bte-kgs-operations/modulator' - $ref: '#/components/x-bte-kgs-operations/modulator-rev' - - $ref: '#/components/x-bte-kgs-operations/multitarget' - - $ref: '#/components/x-bte-kgs-operations/multitarget-rev' - $ref: '#/components/x-bte-kgs-operations/negative_modulator' - $ref: '#/components/x-bte-kgs-operations/negative_modulator-rev' - - $ref: '#/components/x-bte-kgs-operations/no_dgidb_relationship' - - $ref: '#/components/x-bte-kgs-operations/no_dgidb_relationship-rev' + # - $ref: '#/components/x-bte-kgs-operations/no_dgidb_relationship' + # - $ref: '#/components/x-bte-kgs-operations/no_dgidb_relationship-rev' - $ref: '#/components/x-bte-kgs-operations/partial_agonist' - $ref: '#/components/x-bte-kgs-operations/partial_agonist-rev' - - $ref: '#/components/x-bte-kgs-operations/partial_antagonist' - - $ref: '#/components/x-bte-kgs-operations/partial_antagonist-rev' - $ref: '#/components/x-bte-kgs-operations/positive_modulator' - $ref: '#/components/x-bte-kgs-operations/positive_modulator-rev' - - $ref: '#/components/x-bte-kgs-operations/potentiator' - - $ref: '#/components/x-bte-kgs-operations/potentiator-rev' - - $ref: '#/components/x-bte-kgs-operations/product_of' - - $ref: '#/components/x-bte-kgs-operations/product_of-rev' - - $ref: '#/components/x-bte-kgs-operations/stimulator' - - $ref: '#/components/x-bte-kgs-operations/stimulator-rev' - - $ref: '#/components/x-bte-kgs-operations/substrate' - - $ref: '#/components/x-bte-kgs-operations/substrate-rev' - $ref: '#/components/x-bte-kgs-operations/suppressor' - $ref: '#/components/x-bte-kgs-operations/suppressor-rev' - $ref: '#/components/x-bte-kgs-operations/vaccine' @@ -439,20 +412,19 @@ components: type: array - type: string x-bte-kgs-operations: - ## CURRENT - ## - examples aren't currently formatted to the standard. See https://github.com/biothings/BioThings_Explorer_TRAPI/issues/357#issue-1054150561 - ## - the relationships in DGIdb are drug -> gene, but the API is set up with subject as gene and object as chem - ## - all records have subject.NCBIGene and object.CHEMBL_COMPOUND - ## - relationship meaning: https://dgidb.org/interaction_types - ## - BTE expects no prefixes for NCBIGene / CHEMBL.COMPOUND. - ## however, data's object.CHEMBL_COMPOUND has CHEMBL.COMPOUND prefix in its values... - ## in the future, could edit parser + queries to handle prefixes - ## - joinSafe is only needed if the delimiter isn't a comma - ## - only some records have pubmed. all records have interaction_group_score, provided_by + ## - we will only use records with subject.CHEMBL_COMPOUND + ## - the others currently only have their name https://pending.biothings.io/dgidb/query?q=NOT _exists_:subject.CHEMBL_COMPOUND + ## the original data might have had wikidata IDs https://github.com/biothings/pending.api/issues/40 + ## - all records have object.NCBIGene + ## - not all records have an original relation_name. + ## their meanings: https://dgidb.org/interaction_types ## - to understand interaction_group_score, look at "interaction score" here: https://dgidb.org/score + ## - only some records have pubmed. all records have interaction_group_score, provided_by + ## - in the future, could edit parser + queries to handle prefixes + ## - joinSafe is only needed if the delimiter isn't a comma activator: ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:activator - ## 311 records + ## 195 records - supportBatch: true useTemplating: true ## flag to say templating is being used below inputs: @@ -462,12 +434,12 @@ components: requestBody: body: >- { - "q": [ {{ queryInputs | wrap( '["CHEMBL.COMPOUND:' , '","activator"]') }} ], - "scopes": ["object.CHEMBL_COMPOUND", "association.relation_name"] + "q": [ {{ queryInputs | wrap( '["' , '","activator"]') }} ], + "scopes": ["subject.CHEMBL_COMPOUND", "association.relation_name"] } parameters: fields: >- - subject.NCBIGene,association.interaction_group_score, + object.NCBIGene,association.interaction_group_score, association.provided_by,association.pubmed,association.relation_name size: 1000 outputs: @@ -478,10 +450,10 @@ components: ## CX decided to use the entity-entity version of positively_regulates, after reading some triples' linked pubmed papers predicate: entity_positively_regulates_entity response_mapping: - "$ref": "#/components/x-bte-response-mapping/gene-subject" - ## Example: - ## paper: https://pubmed.ncbi.nlm.nih.gov/23828908/ - # - CHEMBL.COMPOUND:CHEMBL2252949 ((-)-CAMPHOR) -> NCBIGene:79054 (TRPM8) + "$ref": "#/components/x-bte-response-mapping/forward" + # testExamples: + # - qInput: "CHEMBL.COMPOUND:CHEMBL266510" ## FLINDOKALNER + # oneOutput: "NCBIGene:9132" ## KCNQ4 activator-rev: - supportBatch: true useTemplating: true ## flag to say templating is being used below @@ -493,11 +465,11 @@ components: body: >- { "q": [ {{ queryInputs | wrap( '["' , '","activator"]') }} ], - "scopes": ["subject.NCBIGene", "association.relation_name"] + "scopes": ["object.NCBIGene", "association.relation_name"] } parameters: fields: >- - object.CHEMBL_COMPOUND,association.interaction_group_score, + subject.CHEMBL_COMPOUND,association.interaction_group_score, association.provided_by,association.pubmed,association.relation_name size: 1000 outputs: @@ -508,68 +480,13 @@ components: ## CX decided to use the entity-entity version of positively_regulates, after reading some triples' linked pubmed papers predicate: entity_positively_regulated_by_entity response_mapping: - "$ref": "#/components/x-bte-response-mapping/chem-object" - ## Examples: - ## - NCBIGene:8856 (NR1I2) -> CHEMBL.COMPOUND:CHEMBL104 (CLOTRIMAZOLE) - adduct: - ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:adduct - ## 10 records - - supportBatch: true - useTemplating: true ## flag to say templating is being used below - inputs: - - id: "CHEMBL.COMPOUND" - semantic: SmallMolecule - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | wrap( '["CHEMBL.COMPOUND:' , '","adduct"]') }} ], - "scopes": ["object.CHEMBL_COMPOUND", "association.relation_name"] - } - parameters: - fields: >- - subject.NCBIGene,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name - size: 1000 - outputs: - - id: NCBIGene - semantic: Gene - ## biolink 2.2.8: using mapping to GAMMA:adduct - predicate: directly_interacts_with - response_mapping: - "$ref": "#/components/x-bte-response-mapping/gene-subject" - ## Examples: - ## - CHEMBL.COMPOUND:CHEMBL159 (VINBLASTINE) -> NCBIGene:7846 (TUBA1A) - adduct-rev: - - supportBatch: true - useTemplating: true ## flag to say templating is being used below - inputs: - - id: NCBIGene - semantic: Gene - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | wrap( '["' , '","adduct"]') }} ], - "scopes": ["subject.NCBIGene", "association.relation_name"] - } - parameters: - fields: >- - object.CHEMBL_COMPOUND,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name - size: 1000 - outputs: - - id: "CHEMBL.COMPOUND" - semantic: SmallMolecule - ## biolink 2.2.8: using mapping to GAMMA:adduct - predicate: directly_interacts_with - response_mapping: - "$ref": "#/components/x-bte-response-mapping/chem-object" - ## Examples: - ## - NCBIGene:7283 (TUBG1) -> CHEMBL.COMPOUND:CHEMBL159 (VINBLASTINE) + "$ref": "#/components/x-bte-response-mapping/reverse" + # testExamples: + # - qInput: "NCBIGene:2983" ## GUCY1B1 + # oneOutput: "CHEMBL.COMPOUND:CHEMBL730 ## NITROGLYCERIN agonist: ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:agonist - ## 3304 records + ## 2234 records - supportBatch: true useTemplating: true ## flag to say templating is being used below inputs: @@ -579,12 +496,12 @@ components: requestBody: body: >- { - "q": [ {{ queryInputs | wrap( '["CHEMBL.COMPOUND:' , '","agonist"]') }} ], - "scopes": ["object.CHEMBL_COMPOUND", "association.relation_name"] + "q": [ {{ queryInputs | wrap( '["' , '","agonist"]') }} ], + "scopes": ["subject.CHEMBL_COMPOUND", "association.relation_name"] } parameters: fields: >- - subject.NCBIGene,association.interaction_group_score, + object.NCBIGene,association.interaction_group_score, association.provided_by,association.pubmed,association.relation_name size: 1000 outputs: @@ -593,9 +510,10 @@ components: ## for biolink 2.2.8, DGIdb:agonist maps to this predicate predicate: increases_activity_of response_mapping: - "$ref": "#/components/x-bte-response-mapping/gene-subject" - ## Examples: - ## - CHEMBL.COMPOUND:CHEMBL1201670 (SARGRAMOSTIM) -> NCBIGene:6383 (SDC2) + "$ref": "#/components/x-bte-response-mapping/forward" + # testExamples: + # - qInput: "CHEMBL.COMPOUND:CHEMBL1200833" ## DIPIVEFRIN HYDROCHLORIDE + # oneOutput: "NCBIGene:155" ## ADRB3 agonist-rev: - supportBatch: true useTemplating: true ## flag to say templating is being used below @@ -607,11 +525,11 @@ components: body: >- { "q": [ {{ queryInputs | wrap( '["' , '","agonist"]') }} ], - "scopes": ["subject.NCBIGene", "association.relation_name"] + "scopes": ["object.NCBIGene", "association.relation_name"] } parameters: fields: >- - object.CHEMBL_COMPOUND,association.interaction_group_score, + subject.CHEMBL_COMPOUND,association.interaction_group_score, association.provided_by,association.pubmed,association.relation_name size: 1000 outputs: @@ -620,12 +538,13 @@ components: ## for biolink 2.2.8, DGIdb:agonist maps to the inverse of this predicate predicate: activity_increased_by response_mapping: - "$ref": "#/components/x-bte-response-mapping/chem-object" - ## Examples: - ## - NCBIGene:150 (ADRA2A) -> CHEMBL.COMPOUND:CHEMBL778 (DEXMEDETOMIDINE) + "$ref": "#/components/x-bte-response-mapping/reverse" + # testExamples: + # - qInput: "NCBIGene:1814" ## DRD3 + # oneOutput: "CHEMBL.COMPOUND:CHEMBL2146110 ## SARIZOTAN HYDROCHLORIDE allosteric_modulator: ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:allosteric_modulator - ## 178 records + ## 170 records - supportBatch: true useTemplating: true ## flag to say templating is being used below inputs: @@ -635,12 +554,12 @@ components: requestBody: body: >- { - "q": [ {{ queryInputs | wrap( '["CHEMBL.COMPOUND:' , '","allosteric_modulator"]') }} ], - "scopes": ["object.CHEMBL_COMPOUND", "association.relation_name"] + "q": [ {{ queryInputs | wrap( '["' , '","allosteric_modulator"]') }} ], + "scopes": ["subject.CHEMBL_COMPOUND", "association.relation_name"] } parameters: fields: >- - subject.NCBIGene,association.interaction_group_score, + object.NCBIGene,association.interaction_group_score, association.provided_by,association.pubmed,association.relation_name size: 1000 outputs: @@ -649,9 +568,10 @@ components: ## for biolink 2.2.8, DGIdb:allosteric_modulator maps to this predicate predicate: affects_activity_of response_mapping: - "$ref": "#/components/x-bte-response-mapping/gene-subject" - ## Examples: - ## - CHEMBL.COMPOUND:CHEMBL1200907 (TRILOSTANE) -> NCBIGene:2099 (ESR1) + "$ref": "#/components/x-bte-response-mapping/forward" + # testExamples: + # - qInput: "CHEMBL.COMPOUND:CHEMBL3305985" ## ALCURONIUM + # oneOutput: "NCBIGene:1132" ## CHRM4 allosteric_modulator-rev: - supportBatch: true useTemplating: true ## flag to say templating is being used below @@ -663,11 +583,11 @@ components: body: >- { "q": [ {{ queryInputs | wrap( '["' , '","allosteric_modulator"]') }} ], - "scopes": ["subject.NCBIGene", "association.relation_name"] + "scopes": ["object.NCBIGene", "association.relation_name"] } parameters: fields: >- - object.CHEMBL_COMPOUND,association.interaction_group_score, + subject.CHEMBL_COMPOUND,association.interaction_group_score, association.provided_by,association.pubmed,association.relation_name size: 1000 outputs: @@ -676,12 +596,13 @@ components: ## for biolink 2.2.8, DGIdb:allosteric_modulator maps to the inverse of this predicate predicate: activity_affected_by response_mapping: - "$ref": "#/components/x-bte-response-mapping/chem-object" - ## Examples: - ## - NCBIGene:5148 (PDE6G) -> CHEMBL.COMPOUND:CHEMBL1520 (VARDENAFIL) + "$ref": "#/components/x-bte-response-mapping/reverse" + # testExamples: + # - qInput: "NCBIGene:207" ## AKT1 + # oneOutput: "CHEMBL.COMPOUND:CHEMBL1079175 ## MK-2206 antagonist: ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:antagonist - ## 3936 records + ## 2330 records - supportBatch: true useTemplating: true ## flag to say templating is being used below inputs: @@ -691,12 +612,12 @@ components: requestBody: body: >- { - "q": [ {{ queryInputs | wrap( '["CHEMBL.COMPOUND:' , '","antagonist"]') }} ], - "scopes": ["object.CHEMBL_COMPOUND", "association.relation_name"] + "q": [ {{ queryInputs | wrap( '["' , '","antagonist"]') }} ], + "scopes": ["subject.CHEMBL_COMPOUND", "association.relation_name"] } parameters: fields: >- - subject.NCBIGene,association.interaction_group_score, + object.NCBIGene,association.interaction_group_score, association.provided_by,association.pubmed,association.relation_name size: 1000 outputs: @@ -712,9 +633,10 @@ components: ## Instead they block the agonist or signal / dampen the response to the agonist or signal... ## think of the drug that blocks a binding site so the body's signals can't bind as often, to reduce overactivity response_mapping: - "$ref": "#/components/x-bte-response-mapping/gene-subject" - ## Examples: - ## - CHEMBL.COMPOUND:CHEMBL651 (METHADONE) -> NCBIGene:3359 (HTR3A) + "$ref": "#/components/x-bte-response-mapping/forward" + # testExamples: + # - qInput: "CHEMBL.COMPOUND:CHEMBL3545038" ## S-237648 + # oneOutput: "NCBIGene:4889" ## NPY5R antagonist-rev: - supportBatch: true useTemplating: true ## flag to say templating is being used below @@ -726,11 +648,11 @@ components: body: >- { "q": [ {{ queryInputs | wrap( '["' , '","antagonist"]') }} ], - "scopes": ["subject.NCBIGene", "association.relation_name"] + "scopes": ["object.NCBIGene", "association.relation_name"] } parameters: fields: >- - object.CHEMBL_COMPOUND,association.interaction_group_score, + subject.CHEMBL_COMPOUND,association.interaction_group_score, association.provided_by,association.pubmed,association.relation_name size: 1000 outputs: @@ -739,12 +661,13 @@ components: ## for biolink 2.2.8, DGIdb:antagonist maps to the inverse of this predicate predicate: activity_decreased_by response_mapping: - "$ref": "#/components/x-bte-response-mapping/chem-object" - ## Examples: - ## - NCBIGene:4306 (NR3C2) -> CHEMBL.COMPOUND:CHEMBL1393 (SPIRONOLACTONE) + "$ref": "#/components/x-bte-response-mapping/reverse" + # testExamples: + # - qInput: "NCBIGene:185" ## AGTR1 + # oneOutput: "CHEMBL.COMPOUND:CHEMBL1017 ## TELMISARTAN antibody: ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:antibody - ## 266 records + ## 222 records - supportBatch: true useTemplating: true ## flag to say templating is being used below inputs: @@ -754,12 +677,12 @@ components: requestBody: body: >- { - "q": [ {{ queryInputs | wrap( '["CHEMBL.COMPOUND:' , '","antibody"]') }} ], - "scopes": ["object.CHEMBL_COMPOUND", "association.relation_name"] + "q": [ {{ queryInputs | wrap( '["' , '","antibody"]') }} ], + "scopes": ["subject.CHEMBL_COMPOUND", "association.relation_name"] } parameters: fields: >- - subject.NCBIGene,association.interaction_group_score, + object.NCBIGene,association.interaction_group_score, association.provided_by,association.pubmed,association.relation_name size: 1000 outputs: @@ -768,9 +691,10 @@ components: ## biolink 2.2.8: using the mapping for GAMMA:antibody, rather than mapping for the relation (molecularly_interacts_with) predicate: directly_interacts_with response_mapping: - "$ref": "#/components/x-bte-response-mapping/gene-subject" - ## Examples: - ## - CHEMBL.COMPOUND:CHEMBL1201587 (ALEMTUZUMAB) -> NCBIGene:1043 (CD52) + "$ref": "#/components/x-bte-response-mapping/forward" + # testExamples: + # - qInput: "CHEMBL.COMPOUND:CHEMBL4297570" ## AMP-224 + # oneOutput: "NCBIGene:80380" ## PDCD1LG2 antibody-rev: - supportBatch: true useTemplating: true ## flag to say templating is being used below @@ -782,11 +706,11 @@ components: body: >- { "q": [ {{ queryInputs | wrap( '["' , '","antibody"]') }} ], - "scopes": ["subject.NCBIGene", "association.relation_name"] + "scopes": ["object.NCBIGene", "association.relation_name"] } parameters: fields: >- - object.CHEMBL_COMPOUND,association.interaction_group_score, + subject.CHEMBL_COMPOUND,association.interaction_group_score, association.provided_by,association.pubmed,association.relation_name size: 1000 outputs: @@ -795,12 +719,13 @@ components: ## biolink 2.2.8: using the mapping for GAMMA:antibody, rather than mapping for the relation (molecularly_interacts_with) predicate: directly_interacts_with response_mapping: - "$ref": "#/components/x-bte-response-mapping/chem-object" - ## Examples: - ## - NCBIGene:3560 (IL2RB) -> CHEMBL.COMPOUND:CHEMBL1201439 (BASILIXIMAB) + "$ref": "#/components/x-bte-response-mapping/reverse" + # testExamples: + # - qInput: "NCBIGene:56963" ## RGMA + # oneOutput: "CHEMBL.COMPOUND:CHEMBL4297743 ## ELEZANUMAB antisense_oligonucleotide: ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:antisense_oligonucleotide - ## 5 records + ## 4 records - supportBatch: true useTemplating: true ## flag to say templating is being used below inputs: @@ -810,12 +735,12 @@ components: requestBody: body: >- { - "q": [ {{ queryInputs | wrap( '["CHEMBL.COMPOUND:' , '","antisense_oligonucleotide"]') }} ], - "scopes": ["object.CHEMBL_COMPOUND", "association.relation_name"] + "q": [ {{ queryInputs | wrap( '["' , '","antisense_oligonucleotide"]') }} ], + "scopes": ["subject.CHEMBL_COMPOUND", "association.relation_name"] } parameters: fields: >- - subject.NCBIGene,association.interaction_group_score, + object.NCBIGene,association.interaction_group_score, association.provided_by,association.pubmed,association.relation_name size: 1000 outputs: @@ -824,9 +749,10 @@ components: ## for biolink 2.2.8, DGIdb:antisense_oligonucleotide maps to this predicate predicate: decreases_expression_of response_mapping: - "$ref": "#/components/x-bte-response-mapping/gene-subject" - ## Examples: - ## - CHEMBL.COMPOUND:CHEMBL2108324 (OBLIMERSEN) -> NCBIGene:596 (BCL2) + "$ref": "#/components/x-bte-response-mapping/forward" + # testExamples: + # - qInput: "CHEMBL.COMPOUND:CHEMBL2108309" ## CUSTIRSEN + # oneOutput: "NCBIGene:1191" ## CLU antisense_oligonucleotide-rev: - supportBatch: true useTemplating: true ## flag to say templating is being used below @@ -838,11 +764,11 @@ components: body: >- { "q": [ {{ queryInputs | wrap( '["' , '","antisense_oligonucleotide"]') }} ], - "scopes": ["subject.NCBIGene", "association.relation_name"] + "scopes": ["object.NCBIGene", "association.relation_name"] } parameters: fields: >- - object.CHEMBL_COMPOUND,association.interaction_group_score, + subject.CHEMBL_COMPOUND,association.interaction_group_score, association.provided_by,association.pubmed,association.relation_name size: 1000 outputs: @@ -851,68 +777,13 @@ components: ## for biolink 2.2.8, DGIdb:antisense_oligonucleotide maps to the inverse of this predicate predicate: expression_decreased_by response_mapping: - "$ref": "#/components/x-bte-response-mapping/chem-object" - ## Examples: - ## - NCBIGene:1191 (CLU) -> CHEMBL.COMPOUND:CHEMBL2108309 (CUSTIRSEN) - binder: - ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:binder - ## 254 records - - supportBatch: true - useTemplating: true ## flag to say templating is being used below - inputs: - - id: "CHEMBL.COMPOUND" - semantic: SmallMolecule - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | wrap( '["CHEMBL.COMPOUND:' , '","binder"]') }} ], - "scopes": ["object.CHEMBL_COMPOUND", "association.relation_name"] - } - parameters: - fields: >- - subject.NCBIGene,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name - size: 1000 - outputs: - - id: NCBIGene - semantic: Gene - ## for biolink 2.2.8, DGIdb:binder maps to this predicate - predicate: directly_interacts_with - response_mapping: - "$ref": "#/components/x-bte-response-mapping/gene-subject" - ## Examples: - ## - CHEMBL.COMPOUND:CHEMBL770 (TOLAZOLINE) -> NCBIGene:152 (ADRA2C) - binder-rev: - - supportBatch: true - useTemplating: true ## flag to say templating is being used below - inputs: - - id: NCBIGene - semantic: Gene - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | wrap( '["' , '","binder"]') }} ], - "scopes": ["subject.NCBIGene", "association.relation_name"] - } - parameters: - fields: >- - object.CHEMBL_COMPOUND,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name - size: 1000 - outputs: - - id: "CHEMBL.COMPOUND" - semantic: SmallMolecule - ## for biolink 2.2.8, DGIdb:binder maps to this predicate - predicate: directly_interacts_with - response_mapping: - "$ref": "#/components/x-bte-response-mapping/chem-object" - ## Examples: - ## - NCBIGene:51305 (KCNK9) -> CHEMBL.COMPOUND:CHEMBL931 (HALOTHANE) + "$ref": "#/components/x-bte-response-mapping/reverse" + # testExamples: + # - qInput: "NCBIGene:332" ## BIRC5 + # oneOutput: "CHEMBL.COMPOUND:CHEMBL2219774 ## GATAPARSEN blocker: ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:blocker - ## 1167 records + ## 1134 records - supportBatch: true useTemplating: true ## flag to say templating is being used below inputs: @@ -922,12 +793,12 @@ components: requestBody: body: >- { - "q": [ {{ queryInputs | wrap( '["CHEMBL.COMPOUND:' , '","blocker"]') }} ], - "scopes": ["object.CHEMBL_COMPOUND", "association.relation_name"] + "q": [ {{ queryInputs | wrap( '["' , '","blocker"]') }} ], + "scopes": ["subject.CHEMBL_COMPOUND", "association.relation_name"] } parameters: fields: >- - subject.NCBIGene,association.interaction_group_score, + object.NCBIGene,association.interaction_group_score, association.provided_by,association.pubmed,association.relation_name size: 1000 outputs: @@ -938,9 +809,10 @@ components: ## for biolink 2.2.8, DGIdb:blocker maps to this predicate predicate: decreases_activity_of response_mapping: - "$ref": "#/components/x-bte-response-mapping/gene-subject" - ## Examples: - ## - CHEMBL.COMPOUND:CHEMBL629 (AMITRIPTYLINE) -> NCBIGene:3274 (HRH2) + "$ref": "#/components/x-bte-response-mapping/forward" + # testExamples: + # - qInput: "CHEMBL.COMPOUND:CHEMBL91" ## MICONAZOLE + # oneOutput: "NCBIGene:7226" ## TRPM2 blocker-rev: - supportBatch: true useTemplating: true ## flag to say templating is being used below @@ -952,11 +824,11 @@ components: body: >- { "q": [ {{ queryInputs | wrap( '["' , '","blocker"]') }} ], - "scopes": ["subject.NCBIGene", "association.relation_name"] + "scopes": ["object.NCBIGene", "association.relation_name"] } parameters: fields: >- - object.CHEMBL_COMPOUND,association.interaction_group_score, + subject.CHEMBL_COMPOUND,association.interaction_group_score, association.provided_by,association.pubmed,association.relation_name size: 1000 outputs: @@ -965,12 +837,13 @@ components: ## for biolink 2.2.8, DGIdb:blocker maps to the inverse of this predicate predicate: activity_decreased_by response_mapping: - "$ref": "#/components/x-bte-response-mapping/chem-object" - ## Examples: - ## - NCBIGene:6323 (SCN1A) -> CHEMBL.COMPOUND:CHEMBL1198 (PRAMOXINE) - chaperone: - ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:chaperone - ## 10 records + "$ref": "#/components/x-bte-response-mapping/reverse" + # testExamples: + # - qInput: "NCBIGene:775" ## CACNA1C + # oneOutput: "CHEMBL.COMPOUND:CHEMBL1648 ## ISRADIPINE + inducer: + ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:inducer + ## 1 record - supportBatch: true useTemplating: true ## flag to say templating is being used below inputs: @@ -980,24 +853,25 @@ components: requestBody: body: >- { - "q": [ {{ queryInputs | wrap( '["CHEMBL.COMPOUND:' , '","chaperone"]') }} ], - "scopes": ["object.CHEMBL_COMPOUND", "association.relation_name"] + "q": [ {{ queryInputs | wrap( '["' , '","inducer"]') }} ], + "scopes": ["subject.CHEMBL_COMPOUND", "association.relation_name"] } parameters: fields: >- - subject.NCBIGene,association.interaction_group_score, + object.NCBIGene,association.interaction_group_score, association.provided_by,association.pubmed,association.relation_name size: 1000 outputs: - id: NCBIGene semantic: Gene - ## not using the mapping GAMMA:chaperone (directly_interacts_with) - predicate: affects_folding_of + ## for biolink 2.2.8, DGIdb:inducer maps to this predicate + predicate: increases_activity_of response_mapping: - "$ref": "#/components/x-bte-response-mapping/gene-subject" - ## Examples: - ## - CHEMBL.COMPOUND:CHEMBL1200679 (ZINC CHLORIDE) -> NCBIGene:7161 (TP73) - chaperone-rev: + "$ref": "#/components/x-bte-response-mapping/forward" + # testExamples: + # - qInput: "CHEMBL.COMPOUND:CHEMBL71263" ## VADIMEZAN + # oneOutput: "NCBIGene:7124" ## TNF + inducer-rev: - supportBatch: true useTemplating: true ## flag to say templating is being used below inputs: @@ -1007,26 +881,27 @@ components: requestBody: body: >- { - "q": [ {{ queryInputs | wrap( '["' , '","chaperone"]') }} ], - "scopes": ["subject.NCBIGene", "association.relation_name"] + "q": [ {{ queryInputs | wrap( '["' , '","inducer"]') }} ], + "scopes": ["object.NCBIGene", "association.relation_name"] } parameters: fields: >- - object.CHEMBL_COMPOUND,association.interaction_group_score, + subject.CHEMBL_COMPOUND,association.interaction_group_score, association.provided_by,association.pubmed,association.relation_name size: 1000 outputs: - id: "CHEMBL.COMPOUND" semantic: SmallMolecule - ## not using the mapping GAMMA:chaperone (directly_interacts_with) - predicate: folding_affected_by + ## for biolink 2.2.8, DGIdb:inducer maps to the inverse of this predicate + predicate: activity_increased_by response_mapping: - "$ref": "#/components/x-bte-response-mapping/chem-object" - ## Examples: - ## - NCBIGene:3630 (INS) -> CHEMBL.COMPOUND:CHEMBL1200679 (ZINC CHLORIDE) - cleavage: - ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:cleavage - ## 5 records + "$ref": "#/components/x-bte-response-mapping/reverse" + # testExamples: + # - qInput: "NCBIGene:7124" ## TNF + # oneOutput: "CHEMBL.COMPOUND:CHEMBL71263" ## VADIMEZAN + inhibitor: + ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:inhibitor + ## 6928 records - supportBatch: true useTemplating: true ## flag to say templating is being used below inputs: @@ -1036,24 +911,25 @@ components: requestBody: body: >- { - "q": [ {{ queryInputs | wrap( '["CHEMBL.COMPOUND:' , '","cleavage"]') }} ], - "scopes": ["object.CHEMBL_COMPOUND", "association.relation_name"] + "q": [ {{ queryInputs | wrap( '["' , '","inhibitor"]') }} ], + "scopes": ["subject.CHEMBL_COMPOUND", "association.relation_name"] } parameters: fields: >- - subject.NCBIGene,association.interaction_group_score, + object.NCBIGene,association.interaction_group_score, association.provided_by,association.pubmed,association.relation_name size: 1000 outputs: - id: NCBIGene semantic: Gene - ## biolink 2.2.8: mapped to CTD:increases_cleavage (no mapping for relation) - predicate: increases_degradation_of + ## for biolink 2.2.8, DGIdb:inhibitor maps to this predicate + predicate: decreases_activity_of response_mapping: - "$ref": "#/components/x-bte-response-mapping/gene-subject" - ## Examples: - ## - CHEMBL.COMPOUND:CHEMBL4297953 (ANTI-INHIBITOR COAGULANT COMPLEX) -> NCBIGene:2243 (FGA) - cleavage-rev: + "$ref": "#/components/x-bte-response-mapping/forward" + # testExamples: + # - qInput: "CHEMBL.COMPOUND:CHEMBL1229517" ## VEMURAFENIB + # oneOutput: "NCBIGene:673" ## BRAF + inhibitor-rev: - supportBatch: true useTemplating: true ## flag to say templating is being used below inputs: @@ -1063,26 +939,27 @@ components: requestBody: body: >- { - "q": [ {{ queryInputs | wrap( '["' , '","cleavage"]') }} ], - "scopes": ["subject.NCBIGene", "association.relation_name"] + "q": [ {{ queryInputs | wrap( '["' , '","inhibitor"]') }} ], + "scopes": ["object.NCBIGene", "association.relation_name"] } parameters: fields: >- - object.CHEMBL_COMPOUND,association.interaction_group_score, + subject.CHEMBL_COMPOUND,association.interaction_group_score, association.provided_by,association.pubmed,association.relation_name size: 1000 outputs: - id: "CHEMBL.COMPOUND" semantic: SmallMolecule - ## biolink 2.2.8: inverse mapped to CTD:increases_cleavage (no mapping for relation) - predicate: degradation_increased_by + ## for biolink 2.2.8, DGIdb:inhibitor maps to the inverse of this predicate + predicate: activity_decreased_by response_mapping: - "$ref": "#/components/x-bte-response-mapping/chem-object" - ## Examples: - ## - NCBIGene:2335 (FN1) -> CHEMBL.COMPOUND:CHEMBL2095222 (OCRIPLASMIN) - cofactor: - ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:cofactor - ## 142 records + "$ref": "#/components/x-bte-response-mapping/reverse" + # testExamples: + # - qInput: "NCBIGene:3481" ## IGF2 + # oneOutput: "CHEMBL.COMPOUND:CHEMBL2109355" ## DUSIGITUMAB + inhibitory_allosteric_modulator: + ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:inhibitory_allosteric_modulator + ## 1 record - supportBatch: true useTemplating: true ## flag to say templating is being used below inputs: @@ -1092,24 +969,25 @@ components: requestBody: body: >- { - "q": [ {{ queryInputs | wrap( '["CHEMBL.COMPOUND:' , '","cofactor"]') }} ], - "scopes": ["object.CHEMBL_COMPOUND", "association.relation_name"] + "q": [ {{ queryInputs | wrap( '["' , '","inhibitory_allosteric_modulator"]') }} ], + "scopes": ["subject.CHEMBL_COMPOUND", "association.relation_name"] } parameters: fields: >- - subject.NCBIGene,association.interaction_group_score, + object.NCBIGene,association.interaction_group_score, association.provided_by,association.pubmed,association.relation_name size: 1000 outputs: - id: NCBIGene semantic: Gene - ## for biolink 2.2.8, DGIdb:cofactor maps to this predicate - predicate: directly_interacts_with + ## for biolink 2.2.8, DGIdb:inhibitory_allosteric_modulator maps to this predicate + predicate: decreases_activity_of response_mapping: - "$ref": "#/components/x-bte-response-mapping/gene-subject" - ## Examples: - ## - CHEMBL.COMPOUND:CHEMBL459 (METHYLDOPA) -> NCBIGene:443 (ASPA) - cofactor-rev: + "$ref": "#/components/x-bte-response-mapping/forward" + # testExamples: + # - qInput: "CHEMBL.COMPOUND:CHEMBL1079175" ## MK-2206 + # oneOutput: "NCBIGene:207" ## AKT1 + inhibitory_allosteric_modulator-rev: - supportBatch: true useTemplating: true ## flag to say templating is being used below inputs: @@ -1119,26 +997,27 @@ components: requestBody: body: >- { - "q": [ {{ queryInputs | wrap( '["' , '","cofactor"]') }} ], - "scopes": ["subject.NCBIGene", "association.relation_name"] + "q": [ {{ queryInputs | wrap( '["' , '","inhibitory_allosteric_modulator"]') }} ], + "scopes": ["object.NCBIGene", "association.relation_name"] } parameters: fields: >- - object.CHEMBL_COMPOUND,association.interaction_group_score, + subject.CHEMBL_COMPOUND,association.interaction_group_score, association.provided_by,association.pubmed,association.relation_name size: 1000 outputs: - id: "CHEMBL.COMPOUND" semantic: SmallMolecule - ## for biolink 2.2.8, DGIdb:cofactor maps to this predicate - predicate: directly_interacts_with + ## for biolink 2.2.8, DGIdb:inhibitory_allosteric_modulator maps to the inverse of this predicate + predicate: activity_decreased_by response_mapping: - "$ref": "#/components/x-bte-response-mapping/chem-object" - ## Examples: - ## - NCBIGene:1312 (COMT) -> CHEMBL.COMPOUND:CHEMBL1088977 (ADEMETIONINE) - inducer: - ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:inducer - ## 78 records + "$ref": "#/components/x-bte-response-mapping/reverse" + # testExamples: + # - qInput: "NCBIGene:207" ## AKT1 + # oneOutput: "CHEMBL.COMPOUND:CHEMBL1079175" ## MK-2206 + inverse_agonist: + ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:inverse_agonist + ## 24 records - supportBatch: true useTemplating: true ## flag to say templating is being used below inputs: @@ -1148,24 +1027,25 @@ components: requestBody: body: >- { - "q": [ {{ queryInputs | wrap( '["CHEMBL.COMPOUND:' , '","inducer"]') }} ], - "scopes": ["object.CHEMBL_COMPOUND", "association.relation_name"] + "q": [ {{ queryInputs | wrap( '["' , '","inverse_agonist"]') }} ], + "scopes": ["subject.CHEMBL_COMPOUND", "association.relation_name"] } parameters: fields: >- - subject.NCBIGene,association.interaction_group_score, + object.NCBIGene,association.interaction_group_score, association.provided_by,association.pubmed,association.relation_name size: 1000 outputs: - id: NCBIGene semantic: Gene - ## for biolink 2.2.8, DGIdb:inducer maps to this predicate - predicate: increases_activity_of + ## for biolink 2.2.8, DGIdb:inverse_agonist maps to this predicate + predicate: decreases_activity_of response_mapping: - "$ref": "#/components/x-bte-response-mapping/gene-subject" - ## Examples: - ## - CHEMBL.COMPOUND:CHEMBL59 (DOPAMINE) -> NCBIGene:6531 (SLC6A3) - inducer-rev: + "$ref": "#/components/x-bte-response-mapping/forward" + # testExamples: + # - qInput: "CHEMBL.COMPOUND:CHEMBL1200986" ## HALOPERIDOL DECANOATE + # oneOutput: "NCBIGene:1814" ## DRD3 + inverse_agonist-rev: - supportBatch: true useTemplating: true ## flag to say templating is being used below inputs: @@ -1175,26 +1055,27 @@ components: requestBody: body: >- { - "q": [ {{ queryInputs | wrap( '["' , '","inducer"]') }} ], - "scopes": ["subject.NCBIGene", "association.relation_name"] + "q": [ {{ queryInputs | wrap( '["' , '","inverse_agonist"]') }} ], + "scopes": ["object.NCBIGene", "association.relation_name"] } parameters: fields: >- - object.CHEMBL_COMPOUND,association.interaction_group_score, + subject.CHEMBL_COMPOUND,association.interaction_group_score, association.provided_by,association.pubmed,association.relation_name size: 1000 outputs: - id: "CHEMBL.COMPOUND" semantic: SmallMolecule - ## for biolink 2.2.8, DGIdb:inducer maps to the inverse of this predicate - predicate: activity_increased_by + ## for biolink 2.2.8, DGIdb:inverse_agonist maps to the inverse of this predicate + predicate: activity_decreased_by response_mapping: - "$ref": "#/components/x-bte-response-mapping/chem-object" - ## Examples: - ## - NCBIGene:3356 (HTR2A) -> CHEMBL.COMPOUND:CHEMBL502 (DONEPEZIL) - inhibitor: - ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:inhibitor - ## 9093 records + "$ref": "#/components/x-bte-response-mapping/reverse" + # testExamples: + # - qInput: "NCBIGene:3356" ## HTR2A + # oneOutput: "CHEMBL.COMPOUND:CHEMBL1084617" ## TEMANOGREL + modulator: + ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:modulator + ## 222 records - supportBatch: true useTemplating: true ## flag to say templating is being used below inputs: @@ -1204,24 +1085,26 @@ components: requestBody: body: >- { - "q": [ {{ queryInputs | wrap( '["CHEMBL.COMPOUND:' , '","inhibitor"]') }} ], - "scopes": ["object.CHEMBL_COMPOUND", "association.relation_name"] + "q": [ {{ queryInputs | wrap( '["' , '","modulator"]') }} ], + "scopes": ["subject.CHEMBL_COMPOUND", "association.relation_name"] } parameters: fields: >- - subject.NCBIGene,association.interaction_group_score, + object.NCBIGene,association.interaction_group_score, association.provided_by,association.pubmed,association.relation_name size: 1000 outputs: - id: NCBIGene semantic: Gene - ## for biolink 2.2.8, DGIdb:inhibitor maps to this predicate - predicate: decreases_activity_of + ## could also use "entity regulates entity"? see def: https://dgidb.org/interaction_types + ## for biolink 2.2.8, DGIdb:modulator maps to this predicate + predicate: affects_activity_of response_mapping: - "$ref": "#/components/x-bte-response-mapping/gene-subject" - ## Examples: - ## - CHEMBL.COMPOUND:CHEMBL622 (ETODOLAC) -> NCBIGene:5742 (PTGS1) - inhibitor-rev: + "$ref": "#/components/x-bte-response-mapping/forward" + # testExamples: + # - qInput: "CHEMBL.COMPOUND:CHEMBL3301626" ## BASIMGLURANT + # oneOutput: "NCBIGene:2915" ## GRM5 + modulator-rev: - supportBatch: true useTemplating: true ## flag to say templating is being used below inputs: @@ -1231,25 +1114,26 @@ components: requestBody: body: >- { - "q": [ {{ queryInputs | wrap( '["' , '","inhibitor"]') }} ], - "scopes": ["subject.NCBIGene", "association.relation_name"] + "q": [ {{ queryInputs | wrap( '["' , '","modulator"]') }} ], + "scopes": ["object.NCBIGene", "association.relation_name"] } parameters: fields: >- - object.CHEMBL_COMPOUND,association.interaction_group_score, + subject.CHEMBL_COMPOUND,association.interaction_group_score, association.provided_by,association.pubmed,association.relation_name size: 1000 outputs: - id: "CHEMBL.COMPOUND" semantic: SmallMolecule - ## for biolink 2.2.8, DGIdb:inhibitor maps to the inverse of this predicate - predicate: activity_decreased_by + ## for biolink 2.2.8, DGIdb:modulator maps to the inverse of this predicate + predicate: activity_affected_by response_mapping: - "$ref": "#/components/x-bte-response-mapping/chem-object" - ## Examples: - ## - NCBIGene:8972 (MGAM) -> CHEMBL.COMPOUND:CHEMBL476960 (VOGLIBOSE) - inhibitory_allosteric_modulator: - ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:inhibitory_allosteric_modulator + "$ref": "#/components/x-bte-response-mapping/reverse" + # testExamples: + # - qInput: "NCBIGene:5241" ## PGR + # oneOutput: "CHEMBL.COMPOUND:CHEMBL2105694" ## TELAPRISTONE ACETATE + negative_modulator: + ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:negative_modulator ## 5 records - supportBatch: true useTemplating: true ## flag to say templating is being used below @@ -1260,24 +1144,25 @@ components: requestBody: body: >- { - "q": [ {{ queryInputs | wrap( '["CHEMBL.COMPOUND:' , '","inhibitory_allosteric_modulator"]') }} ], - "scopes": ["object.CHEMBL_COMPOUND", "association.relation_name"] + "q": [ {{ queryInputs | wrap( '["' , '","negative_modulator"]') }} ], + "scopes": ["subject.CHEMBL_COMPOUND", "association.relation_name"] } parameters: fields: >- - subject.NCBIGene,association.interaction_group_score, + object.NCBIGene,association.interaction_group_score, association.provided_by,association.pubmed,association.relation_name size: 1000 outputs: - id: NCBIGene semantic: Gene - ## for biolink 2.2.8, DGIdb:inhibitory_allosteric_modulator maps to this predicate + ## for biolink 2.2.8, DGIdb:negative_modulator maps to this predicate predicate: decreases_activity_of response_mapping: - "$ref": "#/components/x-bte-response-mapping/gene-subject" - ## Examples: - ## - CHEMBL.COMPOUND:CHEMBL1496 (ROSUVASTATIN) -> NCBIGene:3683 (ITGAL) - inhibitory_allosteric_modulator-rev: + "$ref": "#/components/x-bte-response-mapping/forward" + # testExamples: + # - qInput: "CHEMBL.COMPOUND:CHEMBL2109095" ## ERLIZUMAB + # oneOutput: "NCBIGene:3689" ## ITGB2 + negative_modulator-rev: - supportBatch: true useTemplating: true ## flag to say templating is being used below inputs: @@ -1287,26 +1172,86 @@ components: requestBody: body: >- { - "q": [ {{ queryInputs | wrap( '["' , '","inhibitory_allosteric_modulator"]') }} ], - "scopes": ["subject.NCBIGene", "association.relation_name"] + "q": [ {{ queryInputs | wrap( '["' , '","negative_modulator"]') }} ], + "scopes": ["object.NCBIGene", "association.relation_name"] } parameters: fields: >- - object.CHEMBL_COMPOUND,association.interaction_group_score, + subject.CHEMBL_COMPOUND,association.interaction_group_score, association.provided_by,association.pubmed,association.relation_name size: 1000 outputs: - id: "CHEMBL.COMPOUND" semantic: SmallMolecule - ## for biolink 2.2.8, DGIdb:inhibitory_allosteric_modulator maps to the inverse of this predicate + ## for biolink 2.2.8, DGIdb:negative_modulator maps to the inverse of this predicate predicate: activity_decreased_by response_mapping: - "$ref": "#/components/x-bte-response-mapping/chem-object" - ## Examples: - ## - NCBIGene:207 (AKT1) -> CHEMBL.COMPOUND:CHEMBL1079175 (MK-2206) - inverse_agonist: - ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:inverse_agonist - ## 49 records + "$ref": "#/components/x-bte-response-mapping/reverse" + # testExamples: + # - qInput: "NCBIGene:920" ## CD4 + # oneOutput: "CHEMBL.COMPOUND:CHEMBL2108475" ## PRILIXIMAB + ## currently not accessible because no field values correspond to this set + ## 44557 records + # no_dgidb_relationship: + # ## would need to review the parser to figure out what this corresponds to in dgidb + # ## likely corresponds to "n/a" and "other/unknown" interaction types https://dgidb.org/interaction_types + # ## https://pending.biothings.io/dgidb/query?q=NOT _exists_:association.relation_name + # - supportBatch: true + # useTemplating: true ## flag to say templating is being used below + # inputs: + # - id: "CHEMBL.COMPOUND" + # semantic: SmallMolecule + # requestBodyType: object + # requestBody: + # body: >- + # { + # "q": [ {{ queryInputs | wrap( '["' , '","physically_interacts_with"]') }} ], + # "scopes": ["subject.CHEMBL_COMPOUND", "association.edge_label"] + # } + # parameters: + # fields: >- + # object.NCBIGene,association.interaction_group_score, + # association.provided_by,association.pubmed,association.relation_name + # size: 1000 + # outputs: + # - id: NCBIGene + # semantic: Gene + # ## DGIdb drug-gene interactions + # predicate: interacts_with + # response_mapping: + # "$ref": "#/components/x-bte-response-mapping/forward" + # ## Examples: + # ## - CHEMBL.COMPOUND:CHEMBL454 (BUTALBITAL) -> NCBIGene:2556 (GABRA3) + # no_dgidb_relationship-rev: + # - supportBatch: true + # useTemplating: true ## flag to say templating is being used below + # inputs: + # - id: NCBIGene + # semantic: Gene + # requestBodyType: object + # requestBody: + # body: >- + # { + # "q": [ {{ queryInputs | wrap( '["' , '","physically_interacts_with"]') }} ], + # "scopes": ["object.NCBIGene", "association.edge_label"] + # } + # parameters: + # fields: >- + # subject.CHEMBL_COMPOUND,association.interaction_group_score, + # association.provided_by,association.pubmed,association.relation_name + # size: 1000 + # outputs: + # - id: "CHEMBL.COMPOUND" + # semantic: SmallMolecule + # ## DGIdb drug-gene interactions + # predicate: interacts_with + # response_mapping: + # "$ref": "#/components/x-bte-response-mapping/reverse" + # ## Examples: + # ## - NCBIGene:6555 (SLC10A2) -> CHEMBL.COMPOUND:CHEMBL2387408 (LINERIXIBAT) + partial_agonist: + ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:partial_agonist + ## 74 records - supportBatch: true useTemplating: true ## flag to say templating is being used below inputs: @@ -1316,24 +1261,25 @@ components: requestBody: body: >- { - "q": [ {{ queryInputs | wrap( '["CHEMBL.COMPOUND:' , '","inverse_agonist"]') }} ], - "scopes": ["object.CHEMBL_COMPOUND", "association.relation_name"] + "q": [ {{ queryInputs | wrap( '["' , '","partial_agonist"]') }} ], + "scopes": ["subject.CHEMBL_COMPOUND", "association.relation_name"] } parameters: fields: >- - subject.NCBIGene,association.interaction_group_score, + object.NCBIGene,association.interaction_group_score, association.provided_by,association.pubmed,association.relation_name size: 1000 outputs: - id: NCBIGene semantic: Gene - ## for biolink 2.2.8, DGIdb:inverse_agonist maps to this predicate - predicate: decreases_activity_of + ## for biolink 2.2.8, DGIdb:partial_agonist maps to this predicate + predicate: increases_activity_of response_mapping: - "$ref": "#/components/x-bte-response-mapping/gene-subject" - ## Examples: - ## - CHEMBL.COMPOUND:CHEMBL462605 (PITOLISANT) -> NCBIGene:11255 (HRH3) - inverse_agonist-rev: + "$ref": "#/components/x-bte-response-mapping/forward" + # testExamples: + # - qInput: "CHEMBL.COMPOUND:CHEMBL3544917" ## RAPASTINEL + # oneOutput: "NCBIGene:2903" ## GRIN2A + partial_agonist-rev: - supportBatch: true useTemplating: true ## flag to say templating is being used below inputs: @@ -1343,26 +1289,27 @@ components: requestBody: body: >- { - "q": [ {{ queryInputs | wrap( '["' , '","inverse_agonist"]') }} ], - "scopes": ["subject.NCBIGene", "association.relation_name"] + "q": [ {{ queryInputs | wrap( '["' , '","partial_agonist"]') }} ], + "scopes": ["object.NCBIGene", "association.relation_name"] } parameters: fields: >- - object.CHEMBL_COMPOUND,association.interaction_group_score, + subject.CHEMBL_COMPOUND,association.interaction_group_score, association.provided_by,association.pubmed,association.relation_name size: 1000 outputs: - id: "CHEMBL.COMPOUND" semantic: SmallMolecule - ## for biolink 2.2.8, DGIdb:inverse_agonist maps to the inverse of this predicate - predicate: activity_decreased_by + ## for biolink 2.2.8, DGIdb:partial_agonist maps to the inverse of this predicate + predicate: activity_increased_by response_mapping: - "$ref": "#/components/x-bte-response-mapping/chem-object" - ## Examples: - ## - NCBIGene:3357 (HTR2B) -> CHEMBL.COMPOUND:CHEMBL1112 (ARIPIPRAZOLE) - ligand: - ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:ligand - ## 286 records + "$ref": "#/components/x-bte-response-mapping/reverse" + # testExamples: + # - qInput: "NCBIGene:1137" ## CHRNA4 + # oneOutput: "CHEMBL.COMPOUND:CHEMBL3707250" ## CP-601927 + positive_modulator: + ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:positive_modulator + ## 602 records - supportBatch: true useTemplating: true ## flag to say templating is being used below inputs: @@ -1372,24 +1319,25 @@ components: requestBody: body: >- { - "q": [ {{ queryInputs | wrap( '["CHEMBL.COMPOUND:' , '","ligand"]') }} ], - "scopes": ["object.CHEMBL_COMPOUND", "association.relation_name"] + "q": [ {{ queryInputs | wrap( '["' , '","positive_modulator"]') }} ], + "scopes": ["subject.CHEMBL_COMPOUND", "association.relation_name"] } parameters: fields: >- - subject.NCBIGene,association.interaction_group_score, + object.NCBIGene,association.interaction_group_score, association.provided_by,association.pubmed,association.relation_name size: 1000 outputs: - id: NCBIGene semantic: Gene - ## biolink 2.2.8: using mapping to GAMMA:ligand - predicate: directly_interacts_with + ## biolink 2.2.8: using mapping to GAMMA / CHEMBL.MECHANISM positive_modulator term + predicate: increases_activity_of response_mapping: - "$ref": "#/components/x-bte-response-mapping/gene-subject" - ## Examples: - ## - CHEMBL.COMPOUND:CHEMBL1457 (HYDROCODONE) -> NCBIGene:10280 (SIGMAR1) - ligand-rev: + "$ref": "#/components/x-bte-response-mapping/forward" + # testExamples: + # - qInput: "CHEMBL.COMPOUND:CHEMBL30219" ## METHOHEXITAL SODIUM + # oneOutput: "NCBIGene:2565" ## GABRG1 + positive_modulator-rev: - supportBatch: true useTemplating: true ## flag to say templating is being used below inputs: @@ -1399,26 +1347,27 @@ components: requestBody: body: >- { - "q": [ {{ queryInputs | wrap( '["' , '","ligand"]') }} ], - "scopes": ["subject.NCBIGene", "association.relation_name"] + "q": [ {{ queryInputs | wrap( '["' , '","positive_modulator"]') }} ], + "scopes": ["object.NCBIGene", "association.relation_name"] } parameters: fields: >- - object.CHEMBL_COMPOUND,association.interaction_group_score, + subject.CHEMBL_COMPOUND,association.interaction_group_score, association.provided_by,association.pubmed,association.relation_name size: 1000 outputs: - id: "CHEMBL.COMPOUND" semantic: SmallMolecule - ## biolink 2.2.8: using mapping to GAMMA:ligand - predicate: directly_interacts_with + ## biolink 2.2.8: using inverse of mapping to GAMMA / CHEMBL.MECHANISM positive_modulator term + predicate: activity_increased_by response_mapping: - "$ref": "#/components/x-bte-response-mapping/chem-object" - ## Examples: - ## - NCBIGene:3352 (HTR1D) -> CHEMBL.COMPOUND:CHEMBL716 (QUETIAPINE) - modulator: - ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:modulator - ## 288 records + "$ref": "#/components/x-bte-response-mapping/reverse" + # testExamples: + # - qInput: "NCBIGene:2557" ## GABRA4 + # oneOutput: "CHEMBL.COMPOUND:CHEMBL969" ## PRAZEPAM + suppressor: + ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:suppressor + ## 1 record - supportBatch: true useTemplating: true ## flag to say templating is being used below inputs: @@ -1428,25 +1377,25 @@ components: requestBody: body: >- { - "q": [ {{ queryInputs | wrap( '["CHEMBL.COMPOUND:' , '","modulator"]') }} ], - "scopes": ["object.CHEMBL_COMPOUND", "association.relation_name"] + "q": [ {{ queryInputs | wrap( '["' , '","suppressor"]') }} ], + "scopes": ["subject.CHEMBL_COMPOUND", "association.relation_name"] } parameters: fields: >- - subject.NCBIGene,association.interaction_group_score, + object.NCBIGene,association.interaction_group_score, association.provided_by,association.pubmed,association.relation_name size: 1000 outputs: - id: NCBIGene semantic: Gene - ## could also use "entity regulates entity"? see def: https://dgidb.org/interaction_types - ## for biolink 2.2.8, DGIdb:modulator maps to this predicate - predicate: affects_activity_of + ## biolink 2.2.8: using mapping for GAMMA:suppressor + predicate: decreases_activity_of response_mapping: - "$ref": "#/components/x-bte-response-mapping/gene-subject" - ## Examples: - ## - CHEMBL.COMPOUND:CHEMBL1788403 (BIOALLETHRIN) -> NCBIGene:6323 (SCN1A) - modulator-rev: + "$ref": "#/components/x-bte-response-mapping/forward" + # testExamples: + # - qInput: "CHEMBL.COMPOUND:CHEMBL4297755" ## FP-1039 + # oneOutput: "NCBIGene:2247" ## FGF2 + suppressor-rev: - supportBatch: true useTemplating: true ## flag to say templating is being used below inputs: @@ -1456,26 +1405,27 @@ components: requestBody: body: >- { - "q": [ {{ queryInputs | wrap( '["' , '","modulator"]') }} ], - "scopes": ["subject.NCBIGene", "association.relation_name"] + "q": [ {{ queryInputs | wrap( '["' , '","suppressor"]') }} ], + "scopes": ["object.NCBIGene", "association.relation_name"] } parameters: fields: >- - object.CHEMBL_COMPOUND,association.interaction_group_score, + subject.CHEMBL_COMPOUND,association.interaction_group_score, association.provided_by,association.pubmed,association.relation_name size: 1000 outputs: - id: "CHEMBL.COMPOUND" semantic: SmallMolecule - ## for biolink 2.2.8, DGIdb:modulator maps to the inverse of this predicate - predicate: activity_affected_by + ## biolink 2.2.8: using inverse of mapping for GAMMA:suppressor + predicate: activity_decreased_by response_mapping: - "$ref": "#/components/x-bte-response-mapping/chem-object" - ## Examples: - ## - NCBIGene:9900 (SV2A) -> CHEMBL.COMPOUND:CHEMBL3918017 (SELETRACETAM) - multitarget: - ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:multitarget - ## 10 records + "$ref": "#/components/x-bte-response-mapping/reverse" + # testExamples: + # - qInput: "NCBIGene:2247" ## FGF2 + # oneOutput: "CHEMBL.COMPOUND:CHEMBL4297755" ## FP-1039 + vaccine: + ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:vaccine + ## 8 records - supportBatch: true useTemplating: true ## flag to say templating is being used below inputs: @@ -1485,24 +1435,26 @@ components: requestBody: body: >- { - "q": [ {{ queryInputs | wrap( '["CHEMBL.COMPOUND:' , '","multitarget"]') }} ], - "scopes": ["object.CHEMBL_COMPOUND", "association.relation_name"] + "q": [ {{ queryInputs | wrap( '["' , '","vaccine"]') }} ], + "scopes": ["subject.CHEMBL_COMPOUND", "association.relation_name"] } parameters: fields: >- - subject.NCBIGene,association.interaction_group_score, + object.NCBIGene,association.interaction_group_score, association.provided_by,association.pubmed,association.relation_name size: 1000 outputs: - id: NCBIGene semantic: Gene - ## biolink 2.2.8: using mapping to GAMMA:multitarget - predicate: directly_interacts_with + ## using a different predicate than the biolink 2.2.8 mapping (decreases_activity_of) + ## reasoning: thought its def https://dgidb.org/interaction_types was similar to https://github.com/biolink/biolink-model/blob/c73899cd33753c5d2ff937213b6c5911c579b001/biolink-model.yaml#L2918 + predicate: affects_response_to response_mapping: - "$ref": "#/components/x-bte-response-mapping/gene-subject" - ## Examples: - ## - CHEMBL.COMPOUND:CHEMBL1218 (RAMELTEON) -> NCBIGene:4544 (MTNR1B) - multitarget-rev: + "$ref": "#/components/x-bte-response-mapping/forward" + # testExamples: + # - qInput: "CHEMBL.COMPOUND:CHEMBL75094" ## PRINOMASTAT + # oneOutput: "NCBIGene:4323" ## MMP14 + vaccine-rev: - supportBatch: true useTemplating: true ## flag to say templating is being used below inputs: @@ -1512,653 +1464,35 @@ components: requestBody: body: >- { - "q": [ {{ queryInputs | wrap( '["' , '","multitarget"]') }} ], - "scopes": ["subject.NCBIGene", "association.relation_name"] + "q": [ {{ queryInputs | wrap( '["' , '","vaccine"]') }} ], + "scopes": ["object.NCBIGene", "association.relation_name"] } parameters: fields: >- - object.CHEMBL_COMPOUND,association.interaction_group_score, + subject.CHEMBL_COMPOUND,association.interaction_group_score, association.provided_by,association.pubmed,association.relation_name size: 1000 outputs: - id: "CHEMBL.COMPOUND" semantic: SmallMolecule - ## biolink 2.2.8: using mapping to GAMMA:multitarget - predicate: directly_interacts_with - response_mapping: - "$ref": "#/components/x-bte-response-mapping/chem-object" - ## Examples: - ## - NCBIGene:25 (ABL1) -> CHEMBL.COMPOUND:CHEMBL1421 (DASATINIB) - negative_modulator: - ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:negative_modulator - ## 41 records - - supportBatch: true - useTemplating: true ## flag to say templating is being used below - inputs: - - id: "CHEMBL.COMPOUND" - semantic: SmallMolecule - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | wrap( '["CHEMBL.COMPOUND:' , '","negative_modulator"]') }} ], - "scopes": ["object.CHEMBL_COMPOUND", "association.relation_name"] - } - parameters: - fields: >- - subject.NCBIGene,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name - size: 1000 - outputs: - - id: NCBIGene - semantic: Gene - ## for biolink 2.2.8, DGIdb:negative_modulator maps to this predicate - predicate: decreases_activity_of + ## using a different predicate than the biolink 2.2.8 mapping (decreases_activity_of) + ## reasoning: thought its def https://dgidb.org/interaction_types was similar to https://github.com/biolink/biolink-model/blob/c73899cd33753c5d2ff937213b6c5911c579b001/biolink-model.yaml#L2918 + predicate: response_affected_by response_mapping: - "$ref": "#/components/x-bte-response-mapping/gene-subject" - ## Examples: - ## - CHEMBL.COMPOUND:CHEMBL1434 (MINOCYCLINE) -> NCBIGene:836 (CASP3) - negative_modulator-rev: - - supportBatch: true - useTemplating: true ## flag to say templating is being used below - inputs: - - id: NCBIGene - semantic: Gene - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | wrap( '["' , '","negative_modulator"]') }} ], - "scopes": ["subject.NCBIGene", "association.relation_name"] - } - parameters: - fields: >- - object.CHEMBL_COMPOUND,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name - size: 1000 - outputs: - - id: "CHEMBL.COMPOUND" - semantic: SmallMolecule - ## for biolink 2.2.8, DGIdb:negative_modulator maps to the inverse of this predicate - predicate: activity_decreased_by - response_mapping: - "$ref": "#/components/x-bte-response-mapping/chem-object" - ## Examples: - ## - NCBIGene:6530 (SLC6A2) -> CHEMBL.COMPOUND:CHEMBL43048 (MIDOMAFETAMINE) - no_dgidb_relationship: - ## would need to review the parser to figure out what this corresponds to in dgidb - ## likely corresponds to "n/a" and "other/unknown" interaction types https://dgidb.org/interaction_types - ## https://pending.biothings.io/dgidb/query?q=NOT _exists_:association.relation_name - ## 49899 records - - supportBatch: true - useTemplating: true ## flag to say templating is being used below - inputs: - - id: "CHEMBL.COMPOUND" - semantic: SmallMolecule - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | wrap( '["CHEMBL.COMPOUND:' , '","physically_interacts_with"]') }} ], - "scopes": ["object.CHEMBL_COMPOUND", "association.edge_label"] - } - parameters: - fields: >- - subject.NCBIGene,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name - size: 1000 - outputs: - - id: NCBIGene - semantic: Gene - ## DGIdb drug-gene interactions - predicate: interacts_with - response_mapping: - "$ref": "#/components/x-bte-response-mapping/gene-subject" - ## Examples: - ## - CHEMBL.COMPOUND:CHEMBL454 (BUTALBITAL) -> NCBIGene:2556 (GABRA3) - no_dgidb_relationship-rev: - - supportBatch: true - useTemplating: true ## flag to say templating is being used below - inputs: - - id: NCBIGene - semantic: Gene - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | wrap( '["' , '","physically_interacts_with"]') }} ], - "scopes": ["subject.NCBIGene", "association.edge_label"] - } - parameters: - fields: >- - object.CHEMBL_COMPOUND,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name - size: 1000 - outputs: - - id: "CHEMBL.COMPOUND" - semantic: SmallMolecule - ## DGIdb drug-gene interactions - predicate: interacts_with - response_mapping: - "$ref": "#/components/x-bte-response-mapping/chem-object" - ## Examples: - ## - NCBIGene:6555 (SLC10A2) -> CHEMBL.COMPOUND:CHEMBL2387408 (LINERIXIBAT) - partial_agonist: - ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:partial_agonist - ## 158 records - - supportBatch: true - useTemplating: true ## flag to say templating is being used below - inputs: - - id: "CHEMBL.COMPOUND" - semantic: SmallMolecule - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | wrap( '["CHEMBL.COMPOUND:' , '","partial_agonist"]') }} ], - "scopes": ["object.CHEMBL_COMPOUND", "association.relation_name"] - } - parameters: - fields: >- - subject.NCBIGene,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name - size: 1000 - outputs: - - id: NCBIGene - semantic: Gene - ## for biolink 2.2.8, DGIdb:partial_agonist maps to this predicate - predicate: increases_activity_of - response_mapping: - "$ref": "#/components/x-bte-response-mapping/gene-subject" - ## Examples: - ## - CHEMBL.COMPOUND:CHEMBL2218896 (NABILONE) -> NCBIGene:1269 (CNR2) - partial_agonist-rev: - - supportBatch: true - useTemplating: true ## flag to say templating is being used below - inputs: - - id: NCBIGene - semantic: Gene - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | wrap( '["' , '","partial_agonist"]') }} ], - "scopes": ["subject.NCBIGene", "association.relation_name"] - } - parameters: - fields: >- - object.CHEMBL_COMPOUND,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name - size: 1000 - outputs: - - id: "CHEMBL.COMPOUND" - semantic: SmallMolecule - ## for biolink 2.2.8, DGIdb:partial_agonist maps to the inverse of this predicate - predicate: activity_increased_by - response_mapping: - "$ref": "#/components/x-bte-response-mapping/chem-object" - ## Examples: - ## - NCBIGene:3350 (HTR1A) -> CHEMBL.COMPOUND:CHEMBL15245 (YOHIMBINE) - partial_antagonist: - ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:partial_antagonist - ## 2 records - - supportBatch: true - useTemplating: true ## flag to say templating is being used below - inputs: - - id: "CHEMBL.COMPOUND" - semantic: SmallMolecule - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | wrap( '["CHEMBL.COMPOUND:' , '","partial_antagonist"]') }} ], - "scopes": ["object.CHEMBL_COMPOUND", "association.relation_name"] - } - parameters: - fields: >- - subject.NCBIGene,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name - size: 1000 - outputs: - - id: NCBIGene - semantic: Gene - ## biolink 2.2.8: using mapping for GAMMA:partial_antagonist - predicate: decreases_activity_of - response_mapping: - "$ref": "#/components/x-bte-response-mapping/gene-subject" - ## Examples: - ## - CHEMBL.COMPOUND:CHEMBL1615438 (LEVOCABASTINE) -> NCBIGene:23620 (NTSR2) - partial_antagonist-rev: - - supportBatch: true - useTemplating: true ## flag to say templating is being used below - inputs: - - id: NCBIGene - semantic: Gene - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | wrap( '["' , '","partial_antagonist"]') }} ], - "scopes": ["subject.NCBIGene", "association.relation_name"] - } - parameters: - fields: >- - object.CHEMBL_COMPOUND,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name - size: 1000 - outputs: - - id: "CHEMBL.COMPOUND" - semantic: SmallMolecule - ## biolink 2.2.8: using mapping for GAMMA:partial_antagonist - predicate: activity_decreased_by - response_mapping: - "$ref": "#/components/x-bte-response-mapping/chem-object" - ## Examples: - ## - NCBIGene:4988 (OPRM1) -> CHEMBL.COMPOUND:CHEMBL33986 (BUTORPHANOL) - positive_modulator: - ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:positive_modulator - ## 667 records - - supportBatch: true - useTemplating: true ## flag to say templating is being used below - inputs: - - id: "CHEMBL.COMPOUND" - semantic: SmallMolecule - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | wrap( '["CHEMBL.COMPOUND:' , '","positive_modulator"]') }} ], - "scopes": ["object.CHEMBL_COMPOUND", "association.relation_name"] - } - parameters: - fields: >- - subject.NCBIGene,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name - size: 1000 - outputs: - - id: NCBIGene - semantic: Gene - ## biolink 2.2.8: using mapping to GAMMA / CHEMBL.MECHANISM positive_modulator term - predicate: increases_activity_of - response_mapping: - "$ref": "#/components/x-bte-response-mapping/gene-subject" - ## Examples: - ## - CHEMBL.COMPOUND:CHEMBL655 (MIDAZOLAM) -> NCBIGene:2554 (GABRA1) - positive_modulator-rev: - - supportBatch: true - useTemplating: true ## flag to say templating is being used below - inputs: - - id: NCBIGene - semantic: Gene - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | wrap( '["' , '","positive_modulator"]') }} ], - "scopes": ["subject.NCBIGene", "association.relation_name"] - } - parameters: - fields: >- - object.CHEMBL_COMPOUND,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name - size: 1000 - outputs: - - id: "CHEMBL.COMPOUND" - semantic: SmallMolecule - ## biolink 2.2.8: using inverse of mapping to GAMMA / CHEMBL.MECHANISM positive_modulator term - predicate: activity_increased_by - response_mapping: - "$ref": "#/components/x-bte-response-mapping/chem-object" - ## Examples: - ## - NCBIGene:2554 (GABRA1) -> CHEMBL.COMPOUND:CHEMBL22097 (LORMETAZEPAM) - potentiator: - ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:potentiator - ## 136 records - - supportBatch: true - useTemplating: true ## flag to say templating is being used below - inputs: - - id: "CHEMBL.COMPOUND" - semantic: SmallMolecule - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | wrap( '["CHEMBL.COMPOUND:' , '","potentiator"]') }} ], - "scopes": ["object.CHEMBL_COMPOUND", "association.relation_name"] - } - parameters: - fields: >- - subject.NCBIGene,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name - size: 1000 - outputs: - - id: NCBIGene - semantic: Gene - ## biolink 2.2.8: using mapping to GAMMA:potentiator - predicate: increases_activity_of - response_mapping: - "$ref": "#/components/x-bte-response-mapping/gene-subject" - ## Examples: - ## - CHEMBL.COMPOUND:CHEMBL468837 (HEPTABARBITAL) -> NCBIGene:2557 (GABRA4) - potentiator-rev: - - supportBatch: true - useTemplating: true ## flag to say templating is being used below - inputs: - - id: NCBIGene - semantic: Gene - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | wrap( '["' , '","potentiator"]') }} ], - "scopes": ["subject.NCBIGene", "association.relation_name"] - } - parameters: - fields: >- - object.CHEMBL_COMPOUND,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name - size: 1000 - outputs: - - id: "CHEMBL.COMPOUND" - semantic: SmallMolecule - ## biolink 2.2.8: using inverse of mapping to GAMMA:potentiator - predicate: activity_increased_by - response_mapping: - "$ref": "#/components/x-bte-response-mapping/chem-object" - ## Examples: - ## - NCBIGene:2555 (GABRA2) -> CHEMBL.COMPOUND:CHEMBL1200802 (TALBUTAL) - product_of: - ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:product_of - ## 41 records - - supportBatch: true - useTemplating: true ## flag to say templating is being used below - inputs: - - id: "CHEMBL.COMPOUND" - semantic: SmallMolecule - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | wrap( '["CHEMBL.COMPOUND:' , '","product_of"]') }} ], - "scopes": ["object.CHEMBL_COMPOUND", "association.relation_name"] - } - parameters: - fields: >- - subject.NCBIGene,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name - size: 1000 - outputs: - - id: NCBIGene - semantic: Gene - ## https://dgidb.org/interaction_types: "target gene produces the endogenous drug" - predicate: produced_by - response_mapping: - "$ref": "#/components/x-bte-response-mapping/gene-subject" - ## Examples: - ## - CHEMBL.COMPOUND:CHEMBL42336 (METHIONINE) -> NCBIGene:4548 (MTR) - product_of-rev: - - supportBatch: true - useTemplating: true ## flag to say templating is being used below - inputs: - - id: NCBIGene - semantic: Gene - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | wrap( '["' , '","product_of"]') }} ], - "scopes": ["subject.NCBIGene", "association.relation_name"] - } - parameters: - fields: >- - object.CHEMBL_COMPOUND,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name - size: 1000 - outputs: - - id: "CHEMBL.COMPOUND" - semantic: SmallMolecule - ## https://dgidb.org/interaction_types: "target gene produces the endogenous drug" - predicate: produces - response_mapping: - "$ref": "#/components/x-bte-response-mapping/chem-object" - ## Examples: - ## - NCBIGene:5337 (PLD1) -> CHEMBL.COMPOUND:CHEMBL920 (CHOLINE) - stimulator: - ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:stimulator - ## 22 records - - supportBatch: true - useTemplating: true ## flag to say templating is being used below - inputs: - - id: "CHEMBL.COMPOUND" - semantic: SmallMolecule - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | wrap( '["CHEMBL.COMPOUND:' , '","stimulator"]') }} ], - "scopes": ["object.CHEMBL_COMPOUND", "association.relation_name"] - } - parameters: - fields: >- - subject.NCBIGene,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name - size: 1000 - outputs: - - id: NCBIGene - semantic: Gene - ## for biolink 2.2.8, DGIdb:stimulator maps to this predicate - predicate: increases_activity_of - response_mapping: - "$ref": "#/components/x-bte-response-mapping/gene-subject" - ## Examples: - ## - CHEMBL.COMPOUND:CHEMBL405 (AMPHETAMINE) -> NCBIGene:6530 (SLC6A2) - stimulator-rev: - - supportBatch: true - useTemplating: true ## flag to say templating is being used below - inputs: - - id: NCBIGene - semantic: Gene - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | wrap( '["' , '","stimulator"]') }} ], - "scopes": ["subject.NCBIGene", "association.relation_name"] - } - parameters: - fields: >- - object.CHEMBL_COMPOUND,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name - size: 1000 - outputs: - - id: "CHEMBL.COMPOUND" - semantic: SmallMolecule - ## for biolink 2.2.8, DGIdb:stimulator maps to the inverse of this predicate - predicate: activity_increased_by - response_mapping: - "$ref": "#/components/x-bte-response-mapping/chem-object" - ## Examples: - ## - NCBIGene:2876 (GPX1) -> CHEMBL.COMPOUND:CHEMBL190461 (CANNABIDIOL) - substrate: - ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:substrate - ## 62 records - - supportBatch: true - useTemplating: true ## flag to say templating is being used below - inputs: - - id: "CHEMBL.COMPOUND" - semantic: SmallMolecule - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | wrap( '["CHEMBL.COMPOUND:' , '","substrate"]') }} ], - "scopes": ["object.CHEMBL_COMPOUND", "association.relation_name"] - } - parameters: - fields: >- - subject.NCBIGene,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name - size: 1000 - outputs: - - id: NCBIGene - semantic: Gene - ## biolink 2.2.8: no mapping for the relation - predicate: is_substrate_of - response_mapping: - "$ref": "#/components/x-bte-response-mapping/gene-subject" - ## Examples: - ## - CHEMBL.COMPOUND:CHEMBL773 (GLYCINE) -> NCBIGene:2841 (GPR18) - substrate-rev: - - supportBatch: true - useTemplating: true ## flag to say templating is being used below - inputs: - - id: NCBIGene - semantic: Gene - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | wrap( '["' , '","substrate"]') }} ], - "scopes": ["subject.NCBIGene", "association.relation_name"] - } - parameters: - fields: >- - object.CHEMBL_COMPOUND,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name - size: 1000 - outputs: - - id: "CHEMBL.COMPOUND" - semantic: SmallMolecule - predicate: has_substrate - response_mapping: - "$ref": "#/components/x-bte-response-mapping/chem-object" - ## Examples: - ## - NCBIGene:27010 (TPK1) -> CHEMBL.COMPOUND:CHEMBL1547 (THIAMINE) - suppressor: - ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:suppressor - ## 6 records - - supportBatch: true - useTemplating: true ## flag to say templating is being used below - inputs: - - id: "CHEMBL.COMPOUND" - semantic: SmallMolecule - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | wrap( '["CHEMBL.COMPOUND:' , '","suppressor"]') }} ], - "scopes": ["object.CHEMBL_COMPOUND", "association.relation_name"] - } - parameters: - fields: >- - subject.NCBIGene,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name - size: 1000 - outputs: - - id: NCBIGene - semantic: Gene - ## biolink 2.2.8: using mapping for GAMMA:suppressor - predicate: decreases_activity_of - response_mapping: - "$ref": "#/components/x-bte-response-mapping/gene-subject" - ## Examples: - ## - CHEMBL.COMPOUND:CHEMBL1201827 (PANITUMUMAB) -> NCBIGene:1956 (EGFR) - suppressor-rev: - - supportBatch: true - useTemplating: true ## flag to say templating is being used below - inputs: - - id: NCBIGene - semantic: Gene - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | wrap( '["' , '","suppressor"]') }} ], - "scopes": ["subject.NCBIGene", "association.relation_name"] - } - parameters: - fields: >- - object.CHEMBL_COMPOUND,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name - size: 1000 - outputs: - - id: "CHEMBL.COMPOUND" - semantic: SmallMolecule - ## biolink 2.2.8: using inverse of mapping for GAMMA:suppressor - predicate: activity_decreased_by - response_mapping: - "$ref": "#/components/x-bte-response-mapping/chem-object" - ## Examples: - ## - NCBIGene:8856 (NR1I2) -> CHEMBL.COMPOUND:CHEMBL522892 (DOVITINIB) - vaccine: - ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:vaccine - ## 8 records - - supportBatch: true - useTemplating: true ## flag to say templating is being used below - inputs: - - id: "CHEMBL.COMPOUND" - semantic: SmallMolecule - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | wrap( '["CHEMBL.COMPOUND:' , '","vaccine"]') }} ], - "scopes": ["object.CHEMBL_COMPOUND", "association.relation_name"] - } - parameters: - fields: >- - subject.NCBIGene,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name - size: 1000 - outputs: - - id: NCBIGene - semantic: Gene - ## using a different predicate than the biolink 2.2.8 mapping (decreases_activity_of) - ## reasoning: thought its def https://dgidb.org/interaction_types was similar to https://github.com/biolink/biolink-model/blob/c73899cd33753c5d2ff937213b6c5911c579b001/biolink-model.yaml#L2918 - predicate: affects_response_to - response_mapping: - "$ref": "#/components/x-bte-response-mapping/gene-subject" - ## Examples: - ## - CHEMBL.COMPOUND:CHEMBL75094 (PRINOMASTAT) -> NCBIGene:4314 (MMP3) - vaccine-rev: - - supportBatch: true - useTemplating: true ## flag to say templating is being used below - inputs: - - id: NCBIGene - semantic: Gene - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | wrap( '["' , '","vaccine"]') }} ], - "scopes": ["subject.NCBIGene", "association.relation_name"] - } - parameters: - fields: >- - object.CHEMBL_COMPOUND,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name - size: 1000 - outputs: - - id: "CHEMBL.COMPOUND" - semantic: SmallMolecule - ## using a different predicate than the biolink 2.2.8 mapping (decreases_activity_of) - ## reasoning: thought its def https://dgidb.org/interaction_types was similar to https://github.com/biolink/biolink-model/blob/c73899cd33753c5d2ff937213b6c5911c579b001/biolink-model.yaml#L2918 - predicate: response_affected_by - response_mapping: - "$ref": "#/components/x-bte-response-mapping/chem-object" - ## Examples: - ## - NCBIGene:4323 (MMP14) -> CHEMBL.COMPOUND:CHEMBL75094 (PRINOMASTAT) + "$ref": "#/components/x-bte-response-mapping/reverse" + # testExamples: + # - qInput: "NCBIGene:4313" ## MMP2 + # oneOutput: "CHEMBL.COMPOUND:CHEMBL297792" ## S-3304 x-bte-response-mapping: - chem-object: - "CHEMBL.COMPOUND": object.CHEMBL_COMPOUND - pubmed: association.pubmed - source: association.provided_by - relation: association.relation_name - ## need to look up what this score means... - dgidb_interaction_group_score: association.interaction_group_score - gene-subject: - NCBIGene: subject.NCBIGene + forward: + NCBIGene: object.NCBIGene pubmed: association.pubmed - source: association.provided_by - relation: association.relation_name + dgidb_interaction_claim_source: association.provided_by + "biolink:original_predicate": association.relation_name ## or dgidb interaction types dgidb_interaction_group_score: association.interaction_group_score + reverse: + "CHEMBL.COMPOUND": subject.CHEMBL_COMPOUND + pubmed: association.pubmed + dgidb_interaction_claim_source: association.provided_by + "biolink:original_predicate": association.relation_name ## or dgidb interaction types + dgidb_interaction_group_score: association.interaction_group_score