diff --git a/dgidb/openapi.yml b/dgidb/openapi.yml index 5bc87a48..b770e4c1 100644 --- a/dgidb/openapi.yml +++ b/dgidb/openapi.yml @@ -15,6 +15,8 @@ info: team: - Service Provider biolink-version: "2.2.13" +## during updates, update the paths' examples!!! association get and query get/post +## I'm having trouble setting a request body example for query-post... servers: - description: Encrypted Production server url: https://biothings.ncats.io/dgidb @@ -32,51 +34,12 @@ tags: - name: biothings - name: biothings_graph paths: - /association: - post: - parameters: - - $ref: '#/components/parameters/dotfield' - name: dotfield - - $ref: '#/components/parameters/fields' - name: fields - - $ref: '#/components/parameters/email' - name: email - - $ref: '#/components/parameters/format' - name: format - requestBody: - content: - application/x-www-form-urlencoded: - schema: - properties: - ids: - description: 'multiple association IDs separated by comma. Note that currently we only take the input ids up to 1000 maximum, the rest will be omitted. Type: string (list). Max: 1000.' - type: string - required: - - ids - responses: - '200': - content: - application/json: - schema: - items: - $ref: '#/components/schemas/Association' - type: array - description: A list of matching association objects - '400': - content: - application/json: - schema: - $ref: '#/components/schemas/ErrorResult' - description: A response indicating an improperly formatted query - summary: For a list of association IDs, return the matching disease object - tags: - - association /association/{associationid}: get: parameters: - description: Retrieve association objects based on Association ID Supports JSONP and CORS as well. - example: "275bfadd2b4c60c3" + example: '1fb7c7f0ef333cd2' in: path name: associationid required: true @@ -195,6 +158,14 @@ paths: requestBody: content: application/x-www-form-urlencoded: + ## commenting out the example since it's not working + ## using a simpler format because of the schema. + ## In reality, this schema would need to be expanded to support the multiple ways of querying this API + # examples: + # query_post: ## example's name + # value: ## this is where the example actually goes + # q: 'CHEMBL266510' + # scopes: 'subject.CHEMBL_COMPOUND' schema: properties: q: @@ -223,6 +194,7 @@ paths: summary: Make batch disease queries and return matching disease hits tags: - query + ## 12 sets (24 operations) x-bte-kgs-operations: - $ref: '#/components/x-bte-kgs-operations/activator' - $ref: '#/components/x-bte-kgs-operations/activator-rev' @@ -234,32 +206,38 @@ paths: - $ref: '#/components/x-bte-kgs-operations/antagonist-rev' - $ref: '#/components/x-bte-kgs-operations/antibody' - $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' +## commenting out because there's only 4 records for this set of operations + # - $ref: '#/components/x-bte-kgs-operations/antisense_oligonucleotide' + # - $ref: '#/components/x-bte-kgs-operations/antisense_oligonucleotide-rev' - $ref: '#/components/x-bte-kgs-operations/blocker' - $ref: '#/components/x-bte-kgs-operations/blocker-rev' - - $ref: '#/components/x-bte-kgs-operations/inducer' - - $ref: '#/components/x-bte-kgs-operations/inducer-rev' +## commenting out because there's only 1 record for this set of operations + # - $ref: '#/components/x-bte-kgs-operations/inducer' + # - $ref: '#/components/x-bte-kgs-operations/inducer-rev' - $ref: '#/components/x-bte-kgs-operations/inhibitor' - $ref: '#/components/x-bte-kgs-operations/inhibitor-rev' - - $ref: '#/components/x-bte-kgs-operations/inhibitory_allosteric_modulator' - - $ref: '#/components/x-bte-kgs-operations/inhibitory_allosteric_modulator-rev' +## commenting out because there's only 1 record for this set of operations + # - $ref: '#/components/x-bte-kgs-operations/inhibitory_allosteric_modulator' + # - $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/modulator' - $ref: '#/components/x-bte-kgs-operations/modulator-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' +## commenting out because there's only 5 records for this set of operations + # - $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/partial_agonist' - $ref: '#/components/x-bte-kgs-operations/partial_agonist-rev' - $ref: '#/components/x-bte-kgs-operations/positive_modulator' - $ref: '#/components/x-bte-kgs-operations/positive_modulator-rev' - - $ref: '#/components/x-bte-kgs-operations/suppressor' - - $ref: '#/components/x-bte-kgs-operations/suppressor-rev' - - $ref: '#/components/x-bte-kgs-operations/vaccine' - - $ref: '#/components/x-bte-kgs-operations/vaccine-rev' +## commenting out because there's only 1 record for this set of operations + # - $ref: '#/components/x-bte-kgs-operations/suppressor' + # - $ref: '#/components/x-bte-kgs-operations/suppressor-rev' +## commenting out because there's only 8 records for this set of operations + # - $ref: '#/components/x-bte-kgs-operations/vaccine' + # - $ref: '#/components/x-bte-kgs-operations/vaccine-rev' components: parameters: callback: @@ -412,18 +390,20 @@ components: type: array - type: string x-bte-kgs-operations: + ## - future: we could ingest subject.drug_name and object.SYMBOL fields ## - 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 + ## - only 154 records don't have this field: https://pending.biothings.io/dgidb/query?q=NOT%20_exists_:subject.CHEMBL_COMPOUND + ## those drugs may have had a name or wikidata ID that couldn't be mapped to chembl in MyChem. ## - 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 + ## - for interaction_claim_source info, see https://dgidb.org/sources + ## - for interaction_types info, see https://dgidb.org/interaction_types + ## Most records did not have a value for that column. We put the value to "not_applicable" in those cases... + ## - for interaction_group_score info, see https://dgidb.org/score + ## - only some records have PMIDs. all records have interaction_group_score, interaction_claim_source ## - 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 + ## https://biothings.ncats.io/dgidb/query?q=association.interaction_types:activator ## 195 records - supportBatch: true useTemplating: true ## flag to say templating is being used below @@ -435,12 +415,12 @@ components: body: >- { "q": [ {{ queryInputs | wrap( '["' , '","activator"]') }} ], - "scopes": ["subject.CHEMBL_COMPOUND", "association.relation_name"] + "scopes": ["subject.CHEMBL_COMPOUND", "association.interaction_types"] } parameters: fields: >- object.NCBIGene,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name + association.interaction_claim_source,association.pmids,association.interaction_types size: 1000 outputs: - id: NCBIGene @@ -465,12 +445,12 @@ components: body: >- { "q": [ {{ queryInputs | wrap( '["' , '","activator"]') }} ], - "scopes": ["object.NCBIGene", "association.relation_name"] + "scopes": ["object.NCBIGene", "association.interaction_types"] } parameters: fields: >- subject.CHEMBL_COMPOUND,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name + association.interaction_claim_source,association.pmids,association.interaction_types size: 1000 outputs: - id: "CHEMBL.COMPOUND" @@ -485,7 +465,7 @@ components: # - qInput: "NCBIGene:2983" ## GUCY1B1 # oneOutput: "CHEMBL.COMPOUND:CHEMBL730 ## NITROGLYCERIN agonist: - ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:agonist + ## https://biothings.ncats.io/dgidb/query?q=association.interaction_types:agonist ## 2234 records - supportBatch: true useTemplating: true ## flag to say templating is being used below @@ -497,12 +477,12 @@ components: body: >- { "q": [ {{ queryInputs | wrap( '["' , '","agonist"]') }} ], - "scopes": ["subject.CHEMBL_COMPOUND", "association.relation_name"] + "scopes": ["subject.CHEMBL_COMPOUND", "association.interaction_types"] } parameters: fields: >- object.NCBIGene,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name + association.interaction_claim_source,association.pmids,association.interaction_types size: 1000 outputs: - id: NCBIGene @@ -514,6 +494,9 @@ components: # testExamples: # - qInput: "CHEMBL.COMPOUND:CHEMBL1200833" ## DIPIVEFRIN HYDROCHLORIDE # oneOutput: "NCBIGene:155" ## ADRB3 + ## some records have multiple interaction_types + ## 1 record, agonist + allosteric_modulator: https://pending.biothings.io/dgidb/query?q=association.interaction_types:agonist%20AND%20association.interaction_types:allosteric_modulator + ## 17 records, agonist + antagonist: https://pending.biothings.io/dgidb/query?q=association.interaction_types:agonist%20AND%20association.interaction_types:antagonist agonist-rev: - supportBatch: true useTemplating: true ## flag to say templating is being used below @@ -525,12 +508,12 @@ components: body: >- { "q": [ {{ queryInputs | wrap( '["' , '","agonist"]') }} ], - "scopes": ["object.NCBIGene", "association.relation_name"] + "scopes": ["object.NCBIGene", "association.interaction_types"] } parameters: fields: >- subject.CHEMBL_COMPOUND,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name + association.interaction_claim_source,association.pmids,association.interaction_types size: 1000 outputs: - id: "CHEMBL.COMPOUND" @@ -543,7 +526,7 @@ components: # - qInput: "NCBIGene:1814" ## DRD3 # oneOutput: "CHEMBL.COMPOUND:CHEMBL2146110 ## SARIZOTAN HYDROCHLORIDE allosteric_modulator: - ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:allosteric_modulator + ## https://biothings.ncats.io/dgidb/query?q=association.interaction_types:allosteric_modulator ## 170 records - supportBatch: true useTemplating: true ## flag to say templating is being used below @@ -555,12 +538,12 @@ components: body: >- { "q": [ {{ queryInputs | wrap( '["' , '","allosteric_modulator"]') }} ], - "scopes": ["subject.CHEMBL_COMPOUND", "association.relation_name"] + "scopes": ["subject.CHEMBL_COMPOUND", "association.interaction_types"] } parameters: fields: >- object.NCBIGene,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name + association.interaction_claim_source,association.pmids,association.interaction_types size: 1000 outputs: - id: NCBIGene @@ -583,12 +566,12 @@ components: body: >- { "q": [ {{ queryInputs | wrap( '["' , '","allosteric_modulator"]') }} ], - "scopes": ["object.NCBIGene", "association.relation_name"] + "scopes": ["object.NCBIGene", "association.interaction_types"] } parameters: fields: >- subject.CHEMBL_COMPOUND,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name + association.interaction_claim_source,association.pmids,association.interaction_types size: 1000 outputs: - id: "CHEMBL.COMPOUND" @@ -601,7 +584,7 @@ components: # - qInput: "NCBIGene:207" ## AKT1 # oneOutput: "CHEMBL.COMPOUND:CHEMBL1079175 ## MK-2206 antagonist: - ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:antagonist + ## https://biothings.ncats.io/dgidb/query?q=association.interaction_types:antagonist ## 2330 records - supportBatch: true useTemplating: true ## flag to say templating is being used below @@ -613,12 +596,12 @@ components: body: >- { "q": [ {{ queryInputs | wrap( '["' , '","antagonist"]') }} ], - "scopes": ["subject.CHEMBL_COMPOUND", "association.relation_name"] + "scopes": ["subject.CHEMBL_COMPOUND", "association.interaction_types"] } parameters: fields: >- object.NCBIGene,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name + association.interaction_claim_source,association.pmids,association.interaction_types size: 1000 outputs: - id: NCBIGene @@ -637,6 +620,8 @@ components: # testExamples: # - qInput: "CHEMBL.COMPOUND:CHEMBL3545038" ## S-237648 # oneOutput: "NCBIGene:4889" ## NPY5R + ## some records have multiple interaction_types + ## 1 record, antagonist + allosteric_modulator: https://pending.biothings.io/dgidb/query?q=association.interaction_types:allosteric_modulator%20AND%20association.interaction_types:antagonist antagonist-rev: - supportBatch: true useTemplating: true ## flag to say templating is being used below @@ -648,12 +633,12 @@ components: body: >- { "q": [ {{ queryInputs | wrap( '["' , '","antagonist"]') }} ], - "scopes": ["object.NCBIGene", "association.relation_name"] + "scopes": ["object.NCBIGene", "association.interaction_types"] } parameters: fields: >- subject.CHEMBL_COMPOUND,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name + association.interaction_claim_source,association.pmids,association.interaction_types size: 1000 outputs: - id: "CHEMBL.COMPOUND" @@ -666,7 +651,7 @@ components: # - qInput: "NCBIGene:185" ## AGTR1 # oneOutput: "CHEMBL.COMPOUND:CHEMBL1017 ## TELMISARTAN antibody: - ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:antibody + ## https://biothings.ncats.io/dgidb/query?q=association.interaction_types:antibody ## 222 records - supportBatch: true useTemplating: true ## flag to say templating is being used below @@ -678,12 +663,12 @@ components: body: >- { "q": [ {{ queryInputs | wrap( '["' , '","antibody"]') }} ], - "scopes": ["subject.CHEMBL_COMPOUND", "association.relation_name"] + "scopes": ["subject.CHEMBL_COMPOUND", "association.interaction_types"] } parameters: fields: >- object.NCBIGene,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name + association.interaction_claim_source,association.pmids,association.interaction_types size: 1000 outputs: - id: NCBIGene @@ -706,12 +691,12 @@ components: body: >- { "q": [ {{ queryInputs | wrap( '["' , '","antibody"]') }} ], - "scopes": ["object.NCBIGene", "association.relation_name"] + "scopes": ["object.NCBIGene", "association.interaction_types"] } parameters: fields: >- subject.CHEMBL_COMPOUND,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name + association.interaction_claim_source,association.pmids,association.interaction_types size: 1000 outputs: - id: "CHEMBL.COMPOUND" @@ -723,66 +708,67 @@ components: # testExamples: # - qInput: "NCBIGene:56963" ## RGMA # oneOutput: "CHEMBL.COMPOUND:CHEMBL4297743 ## ELEZANUMAB - antisense_oligonucleotide: - ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:antisense_oligonucleotide - ## 4 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( '["' , '","antisense_oligonucleotide"]') }} ], - "scopes": ["subject.CHEMBL_COMPOUND", "association.relation_name"] - } - parameters: - fields: >- - 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:antisense_oligonucleotide maps to this predicate - predicate: decreases_expression_of - response_mapping: - "$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 - inputs: - - id: NCBIGene - semantic: Gene - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | wrap( '["' , '","antisense_oligonucleotide"]') }} ], - "scopes": ["object.NCBIGene", "association.relation_name"] - } - 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 - ## for biolink 2.2.8, DGIdb:antisense_oligonucleotide maps to the inverse of this predicate - predicate: expression_decreased_by - response_mapping: - "$ref": "#/components/x-bte-response-mapping/reverse" - # testExamples: - # - qInput: "NCBIGene:332" ## BIRC5 - # oneOutput: "CHEMBL.COMPOUND:CHEMBL2219774 ## GATAPARSEN +## commenting out because there's only 4 records for this set of operations + # antisense_oligonucleotide: + # ## https://biothings.ncats.io/dgidb/query?q=association.interaction_types:antisense_oligonucleotide + # ## 4 records + # - supportBatch: true + # useTemplating: true ## flag to say templating is being used below + # inputs: + # - id: "CHEMBL.COMPOUND" + # semantic: SmallMolecule + # requestBodyType: object + # requestBody: + # body: >- + # { + # "q": [ {{ queryInputs | wrap( '["' , '","antisense_oligonucleotide"]') }} ], + # "scopes": ["subject.CHEMBL_COMPOUND", "association.interaction_types"] + # } + # parameters: + # fields: >- + # object.NCBIGene,association.interaction_group_score, + # association.interaction_claim_source,association.pmids,association.interaction_types + # size: 1000 + # outputs: + # - id: NCBIGene + # semantic: Gene + # ## for biolink 2.2.8, DGIdb:antisense_oligonucleotide maps to this predicate + # predicate: decreases_expression_of + # response_mapping: + # "$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 + # inputs: + # - id: NCBIGene + # semantic: Gene + # requestBodyType: object + # requestBody: + # body: >- + # { + # "q": [ {{ queryInputs | wrap( '["' , '","antisense_oligonucleotide"]') }} ], + # "scopes": ["object.NCBIGene", "association.interaction_types"] + # } + # parameters: + # fields: >- + # subject.CHEMBL_COMPOUND,association.interaction_group_score, + # association.interaction_claim_source,association.pmids,association.interaction_types + # size: 1000 + # outputs: + # - id: "CHEMBL.COMPOUND" + # semantic: SmallMolecule + # ## 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/reverse" + # # testExamples: + # # - qInput: "NCBIGene:332" ## BIRC5 + # # oneOutput: "CHEMBL.COMPOUND:CHEMBL2219774 ## GATAPARSEN blocker: - ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:blocker + ## https://biothings.ncats.io/dgidb/query?q=association.interaction_types:blocker ## 1134 records - supportBatch: true useTemplating: true ## flag to say templating is being used below @@ -794,12 +780,12 @@ components: body: >- { "q": [ {{ queryInputs | wrap( '["' , '","blocker"]') }} ], - "scopes": ["subject.CHEMBL_COMPOUND", "association.relation_name"] + "scopes": ["subject.CHEMBL_COMPOUND", "association.interaction_types"] } parameters: fields: >- object.NCBIGene,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name + association.interaction_claim_source,association.pmids,association.interaction_types size: 1000 outputs: - id: NCBIGene @@ -813,6 +799,9 @@ components: # testExamples: # - qInput: "CHEMBL.COMPOUND:CHEMBL91" ## MICONAZOLE # oneOutput: "NCBIGene:7226" ## TRPM2 + ## some records have multiple interaction_types + ## 2 records, blocker + activator: https://pending.biothings.io/dgidb/query?q=association.interaction_types:blocker%20AND%20association.interaction_types:activator + ## 1 record, blocker + inhibitor: https://pending.biothings.io/dgidb/query?q=association.interaction_types:blocker%20AND%20association.interaction_types:inhibitor blocker-rev: - supportBatch: true useTemplating: true ## flag to say templating is being used below @@ -824,12 +813,12 @@ components: body: >- { "q": [ {{ queryInputs | wrap( '["' , '","blocker"]') }} ], - "scopes": ["object.NCBIGene", "association.relation_name"] + "scopes": ["object.NCBIGene", "association.interaction_types"] } parameters: fields: >- subject.CHEMBL_COMPOUND,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name + association.interaction_claim_source,association.pmids,association.interaction_types size: 1000 outputs: - id: "CHEMBL.COMPOUND" @@ -841,66 +830,67 @@ components: # 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: - - id: "CHEMBL.COMPOUND" - semantic: SmallMolecule - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | wrap( '["' , '","inducer"]') }} ], - "scopes": ["subject.CHEMBL_COMPOUND", "association.relation_name"] - } - parameters: - fields: >- - 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 - response_mapping: - "$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: - - id: NCBIGene - semantic: Gene - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | wrap( '["' , '","inducer"]') }} ], - "scopes": ["object.NCBIGene", "association.relation_name"] - } - 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 - ## for biolink 2.2.8, DGIdb:inducer maps to the inverse of this predicate - predicate: activity_increased_by - response_mapping: - "$ref": "#/components/x-bte-response-mapping/reverse" - # testExamples: - # - qInput: "NCBIGene:7124" ## TNF - # oneOutput: "CHEMBL.COMPOUND:CHEMBL71263" ## VADIMEZAN +## commenting out because there's only 1 record for this set of operations + # inducer: + # ## https://biothings.ncats.io/dgidb/query?q=association.interaction_types:inducer + # ## 1 record + # - supportBatch: true + # useTemplating: true ## flag to say templating is being used below + # inputs: + # - id: "CHEMBL.COMPOUND" + # semantic: SmallMolecule + # requestBodyType: object + # requestBody: + # body: >- + # { + # "q": [ {{ queryInputs | wrap( '["' , '","inducer"]') }} ], + # "scopes": ["subject.CHEMBL_COMPOUND", "association.interaction_types"] + # } + # parameters: + # fields: >- + # object.NCBIGene,association.interaction_group_score, + # association.interaction_claim_source,association.pmids,association.interaction_types + # size: 1000 + # outputs: + # - id: NCBIGene + # semantic: Gene + # ## for biolink 2.2.8, DGIdb:inducer maps to this predicate + # predicate: increases_activity_of + # response_mapping: + # "$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: + # - id: NCBIGene + # semantic: Gene + # requestBodyType: object + # requestBody: + # body: >- + # { + # "q": [ {{ queryInputs | wrap( '["' , '","inducer"]') }} ], + # "scopes": ["object.NCBIGene", "association.interaction_types"] + # } + # parameters: + # fields: >- + # subject.CHEMBL_COMPOUND,association.interaction_group_score, + # association.interaction_claim_source,association.pmids,association.interaction_types + # 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 + # response_mapping: + # "$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 + ## https://biothings.ncats.io/dgidb/query?q=association.interaction_types:inhibitor ## 6928 records - supportBatch: true useTemplating: true ## flag to say templating is being used below @@ -912,12 +902,12 @@ components: body: >- { "q": [ {{ queryInputs | wrap( '["' , '","inhibitor"]') }} ], - "scopes": ["subject.CHEMBL_COMPOUND", "association.relation_name"] + "scopes": ["subject.CHEMBL_COMPOUND", "association.interaction_types"] } parameters: fields: >- object.NCBIGene,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name + association.interaction_claim_source,association.pmids,association.interaction_types size: 1000 outputs: - id: NCBIGene @@ -940,12 +930,12 @@ components: body: >- { "q": [ {{ queryInputs | wrap( '["' , '","inhibitor"]') }} ], - "scopes": ["object.NCBIGene", "association.relation_name"] + "scopes": ["object.NCBIGene", "association.interaction_types"] } parameters: fields: >- subject.CHEMBL_COMPOUND,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name + association.interaction_claim_source,association.pmids,association.interaction_types size: 1000 outputs: - id: "CHEMBL.COMPOUND" @@ -957,66 +947,67 @@ components: # 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: - - id: "CHEMBL.COMPOUND" - semantic: SmallMolecule - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | wrap( '["' , '","inhibitory_allosteric_modulator"]') }} ], - "scopes": ["subject.CHEMBL_COMPOUND", "association.relation_name"] - } - parameters: - fields: >- - 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 - predicate: decreases_activity_of - response_mapping: - "$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: - - id: NCBIGene - semantic: Gene - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | wrap( '["' , '","inhibitory_allosteric_modulator"]') }} ], - "scopes": ["object.NCBIGene", "association.relation_name"] - } - 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 - ## for biolink 2.2.8, DGIdb:inhibitory_allosteric_modulator maps to the inverse of this predicate - predicate: activity_decreased_by - response_mapping: - "$ref": "#/components/x-bte-response-mapping/reverse" - # testExamples: - # - qInput: "NCBIGene:207" ## AKT1 - # oneOutput: "CHEMBL.COMPOUND:CHEMBL1079175" ## MK-2206 +## commenting out because there's only 1 record for this set of operations + # inhibitory_allosteric_modulator: + # ## https://biothings.ncats.io/dgidb/query?q=association.interaction_types:inhibitory_allosteric_modulator + # ## 1 record + # - supportBatch: true + # useTemplating: true ## flag to say templating is being used below + # inputs: + # - id: "CHEMBL.COMPOUND" + # semantic: SmallMolecule + # requestBodyType: object + # requestBody: + # body: >- + # { + # "q": [ {{ queryInputs | wrap( '["' , '","inhibitory_allosteric_modulator"]') }} ], + # "scopes": ["subject.CHEMBL_COMPOUND", "association.interaction_types"] + # } + # parameters: + # fields: >- + # object.NCBIGene,association.interaction_group_score, + # association.interaction_claim_source,association.pmids,association.interaction_types + # size: 1000 + # outputs: + # - id: NCBIGene + # semantic: Gene + # ## for biolink 2.2.8, DGIdb:inhibitory_allosteric_modulator maps to this predicate + # predicate: decreases_activity_of + # response_mapping: + # "$ref": "#/components/x-bte-response-mapping/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: + # - id: NCBIGene + # semantic: Gene + # requestBodyType: object + # requestBody: + # body: >- + # { + # "q": [ {{ queryInputs | wrap( '["' , '","inhibitory_allosteric_modulator"]') }} ], + # "scopes": ["object.NCBIGene", "association.interaction_types"] + # } + # parameters: + # fields: >- + # subject.CHEMBL_COMPOUND,association.interaction_group_score, + # association.interaction_claim_source,association.pmids,association.interaction_types + # size: 1000 + # outputs: + # - id: "CHEMBL.COMPOUND" + # semantic: SmallMolecule + # ## 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/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 + ## https://biothings.ncats.io/dgidb/query?q=association.interaction_types:inverse_agonist ## 24 records - supportBatch: true useTemplating: true ## flag to say templating is being used below @@ -1028,12 +1019,12 @@ components: body: >- { "q": [ {{ queryInputs | wrap( '["' , '","inverse_agonist"]') }} ], - "scopes": ["subject.CHEMBL_COMPOUND", "association.relation_name"] + "scopes": ["subject.CHEMBL_COMPOUND", "association.interaction_types"] } parameters: fields: >- object.NCBIGene,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name + association.interaction_claim_source,association.pmids,association.interaction_types size: 1000 outputs: - id: NCBIGene @@ -1056,12 +1047,12 @@ components: body: >- { "q": [ {{ queryInputs | wrap( '["' , '","inverse_agonist"]') }} ], - "scopes": ["object.NCBIGene", "association.relation_name"] + "scopes": ["object.NCBIGene", "association.interaction_types"] } parameters: fields: >- subject.CHEMBL_COMPOUND,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name + association.interaction_claim_source,association.pmids,association.interaction_types size: 1000 outputs: - id: "CHEMBL.COMPOUND" @@ -1074,7 +1065,7 @@ components: # - qInput: "NCBIGene:3356" ## HTR2A # oneOutput: "CHEMBL.COMPOUND:CHEMBL1084617" ## TEMANOGREL modulator: - ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:modulator + ## https://biothings.ncats.io/dgidb/query?q=association.interaction_types:modulator ## 222 records - supportBatch: true useTemplating: true ## flag to say templating is being used below @@ -1086,12 +1077,12 @@ components: body: >- { "q": [ {{ queryInputs | wrap( '["' , '","modulator"]') }} ], - "scopes": ["subject.CHEMBL_COMPOUND", "association.relation_name"] + "scopes": ["subject.CHEMBL_COMPOUND", "association.interaction_types"] } parameters: fields: >- object.NCBIGene,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name + association.interaction_claim_source,association.pmids,association.interaction_types size: 1000 outputs: - id: NCBIGene @@ -1115,12 +1106,12 @@ components: body: >- { "q": [ {{ queryInputs | wrap( '["' , '","modulator"]') }} ], - "scopes": ["object.NCBIGene", "association.relation_name"] + "scopes": ["object.NCBIGene", "association.interaction_types"] } parameters: fields: >- subject.CHEMBL_COMPOUND,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name + association.interaction_claim_source,association.pmids,association.interaction_types size: 1000 outputs: - id: "CHEMBL.COMPOUND" @@ -1132,70 +1123,10 @@ components: # 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 - inputs: - - id: "CHEMBL.COMPOUND" - semantic: SmallMolecule - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | wrap( '["' , '","negative_modulator"]') }} ], - "scopes": ["subject.CHEMBL_COMPOUND", "association.relation_name"] - } - parameters: - fields: >- - 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:negative_modulator maps to this predicate - predicate: decreases_activity_of - response_mapping: - "$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: - - id: NCBIGene - semantic: Gene - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | wrap( '["' , '","negative_modulator"]') }} ], - "scopes": ["object.NCBIGene", "association.relation_name"] - } - 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 - ## for biolink 2.2.8, DGIdb:negative_modulator maps to the inverse of this predicate - predicate: activity_decreased_by - response_mapping: - "$ref": "#/components/x-bte-response-mapping/reverse" - # testExamples: - # - qInput: "NCBIGene:920" ## CD4 - # oneOutput: "CHEMBL.COMPOUND:CHEMBL2108475" ## PRILIXIMAB - ## currently not accessible because no field values correspond to this set - ## 44557 records - # no_dgidb_relationship: - # ## would need to review the parser to figure out what this corresponds to in dgidb - # ## likely corresponds to "n/a" and "other/unknown" interaction types https://dgidb.org/interaction_types - # ## https://pending.biothings.io/dgidb/query?q=NOT _exists_:association.relation_name +## commenting out because there's only 5 records for this set of operations + # negative_modulator: + # ## https://biothings.ncats.io/dgidb/query?q=association.interaction_types:negative_modulator + # ## 5 records # - supportBatch: true # useTemplating: true ## flag to say templating is being used below # inputs: @@ -1205,24 +1136,25 @@ components: # requestBody: # body: >- # { - # "q": [ {{ queryInputs | wrap( '["' , '","physically_interacts_with"]') }} ], - # "scopes": ["subject.CHEMBL_COMPOUND", "association.edge_label"] + # "q": [ {{ queryInputs | wrap( '["' , '","negative_modulator"]') }} ], + # "scopes": ["subject.CHEMBL_COMPOUND", "association.interaction_types"] # } # parameters: # fields: >- # object.NCBIGene,association.interaction_group_score, - # association.provided_by,association.pubmed,association.relation_name + # association.interaction_claim_source,association.pmids,association.interaction_types # size: 1000 # outputs: # - id: NCBIGene # semantic: Gene - # ## DGIdb drug-gene interactions - # predicate: interacts_with + # ## for biolink 2.2.8, DGIdb:negative_modulator maps to this predicate + # predicate: decreases_activity_of # response_mapping: # "$ref": "#/components/x-bte-response-mapping/forward" - # ## Examples: - # ## - CHEMBL.COMPOUND:CHEMBL454 (BUTALBITAL) -> NCBIGene:2556 (GABRA3) - # no_dgidb_relationship-rev: + # # 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: @@ -1232,26 +1164,28 @@ components: # requestBody: # body: >- # { - # "q": [ {{ queryInputs | wrap( '["' , '","physically_interacts_with"]') }} ], - # "scopes": ["object.NCBIGene", "association.edge_label"] + # "q": [ {{ queryInputs | wrap( '["' , '","negative_modulator"]') }} ], + # "scopes": ["object.NCBIGene", "association.interaction_types"] # } # parameters: # fields: >- # subject.CHEMBL_COMPOUND,association.interaction_group_score, - # association.provided_by,association.pubmed,association.relation_name + # association.interaction_claim_source,association.pmids,association.interaction_types # size: 1000 # outputs: # - id: "CHEMBL.COMPOUND" # semantic: SmallMolecule - # ## DGIdb drug-gene interactions - # predicate: interacts_with + # ## for biolink 2.2.8, DGIdb:negative_modulator maps to the inverse of this predicate + # predicate: activity_decreased_by # response_mapping: # "$ref": "#/components/x-bte-response-mapping/reverse" - # ## Examples: - # ## - NCBIGene:6555 (SLC10A2) -> CHEMBL.COMPOUND:CHEMBL2387408 (LINERIXIBAT) - partial_agonist: - ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:partial_agonist - ## 74 records + # # testExamples: + # # - qInput: "NCBIGene:920" ## CD4 + # # oneOutput: "CHEMBL.COMPOUND:CHEMBL2108475" ## PRILIXIMAB + no_dgidb_relationship: + ## 44557 records + ## Most records did not have a value for that column. We put the value to "not_applicable" in those cases... + ## https://pending.biothings.io/dgidb/query?q=association.interaction_types:not_applicable - supportBatch: true useTemplating: true ## flag to say templating is being used below inputs: @@ -1261,25 +1195,25 @@ components: requestBody: body: >- { - "q": [ {{ queryInputs | wrap( '["' , '","partial_agonist"]') }} ], - "scopes": ["subject.CHEMBL_COMPOUND", "association.relation_name"] + "q": [ {{ queryInputs | wrap( '["' , '","not_applicable"]') }} ], + "scopes": ["subject.CHEMBL_COMPOUND", "association.interaction_types"] } parameters: fields: >- object.NCBIGene,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name + association.interaction_claim_source,association.pmids,association.interaction_types size: 1000 outputs: - id: NCBIGene semantic: Gene - ## for biolink 2.2.8, DGIdb:partial_agonist maps to this predicate - predicate: increases_activity_of + ## DGIdb drug-gene interactions + predicate: interacts_with response_mapping: "$ref": "#/components/x-bte-response-mapping/forward" # testExamples: - # - qInput: "CHEMBL.COMPOUND:CHEMBL3544917" ## RAPASTINEL - # oneOutput: "NCBIGene:2903" ## GRIN2A - partial_agonist-rev: + # - qInput: "CHEMBL.COMPOUND:CHEMBL3989914" ## GLESATINIB + # oneOutput: "NCBIGene:7010" ## TEK + no_dgidb_relationship-rev: - supportBatch: true useTemplating: true ## flag to say templating is being used below inputs: @@ -1289,27 +1223,27 @@ components: requestBody: body: >- { - "q": [ {{ queryInputs | wrap( '["' , '","partial_agonist"]') }} ], - "scopes": ["object.NCBIGene", "association.relation_name"] + "q": [ {{ queryInputs | wrap( '["' , '","not_applicable"]') }} ], + "scopes": ["object.NCBIGene", "association.interaction_types"] } parameters: fields: >- subject.CHEMBL_COMPOUND,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name + association.interaction_claim_source,association.pmids,association.interaction_types 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 + ## DGIdb drug-gene interactions + predicate: interacts_with response_mapping: "$ref": "#/components/x-bte-response-mapping/reverse" # testExamples: - # - qInput: "NCBIGene:1137" ## CHRNA4 - # oneOutput: "CHEMBL.COMPOUND:CHEMBL3707250" ## CP-601927 - positive_modulator: - ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:positive_modulator - ## 602 records + # - qInput: "NCBIGene:4985" ## OPRD1 + # oneOutput: "CHEMBL.COMPOUND:CHEMBL2159122" ## ELUXADOLINE + partial_agonist: + ## https://biothings.ncats.io/dgidb/query?q=association.interaction_types:partial_agonist + ## 74 records - supportBatch: true useTemplating: true ## flag to say templating is being used below inputs: @@ -1319,25 +1253,25 @@ components: requestBody: body: >- { - "q": [ {{ queryInputs | wrap( '["' , '","positive_modulator"]') }} ], - "scopes": ["subject.CHEMBL_COMPOUND", "association.relation_name"] + "q": [ {{ queryInputs | wrap( '["' , '","partial_agonist"]') }} ], + "scopes": ["subject.CHEMBL_COMPOUND", "association.interaction_types"] } parameters: fields: >- object.NCBIGene,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name + association.interaction_claim_source,association.pmids,association.interaction_types size: 1000 outputs: - id: NCBIGene semantic: Gene - ## biolink 2.2.8: using mapping to GAMMA / CHEMBL.MECHANISM positive_modulator term + ## for biolink 2.2.8, DGIdb:partial_agonist maps to this predicate predicate: increases_activity_of response_mapping: "$ref": "#/components/x-bte-response-mapping/forward" # testExamples: - # - qInput: "CHEMBL.COMPOUND:CHEMBL30219" ## METHOHEXITAL SODIUM - # oneOutput: "NCBIGene:2565" ## GABRG1 - positive_modulator-rev: + # - 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: @@ -1347,85 +1281,27 @@ components: requestBody: body: >- { - "q": [ {{ queryInputs | wrap( '["' , '","positive_modulator"]') }} ], - "scopes": ["object.NCBIGene", "association.relation_name"] + "q": [ {{ queryInputs | wrap( '["' , '","partial_agonist"]') }} ], + "scopes": ["object.NCBIGene", "association.interaction_types"] } parameters: fields: >- subject.CHEMBL_COMPOUND,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name + association.interaction_claim_source,association.pmids,association.interaction_types size: 1000 outputs: - id: "CHEMBL.COMPOUND" semantic: SmallMolecule - ## biolink 2.2.8: using inverse of mapping to GAMMA / CHEMBL.MECHANISM positive_modulator term + ## for biolink 2.2.8, DGIdb:partial_agonist maps to the inverse of this predicate predicate: activity_increased_by response_mapping: "$ref": "#/components/x-bte-response-mapping/reverse" # testExamples: - # - qInput: "NCBIGene:2557" ## GABRA4 - # oneOutput: "CHEMBL.COMPOUND:CHEMBL969" ## PRAZEPAM - suppressor: - ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:suppressor - ## 1 record - - supportBatch: true - useTemplating: true ## flag to say templating is being used below - inputs: - - id: "CHEMBL.COMPOUND" - semantic: SmallMolecule - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | wrap( '["' , '","suppressor"]') }} ], - "scopes": ["subject.CHEMBL_COMPOUND", "association.relation_name"] - } - parameters: - fields: >- - object.NCBIGene,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name - size: 1000 - outputs: - - id: NCBIGene - semantic: Gene - ## biolink 2.2.8: using mapping for GAMMA:suppressor - predicate: decreases_activity_of - response_mapping: - "$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: - - id: NCBIGene - semantic: Gene - requestBodyType: object - requestBody: - body: >- - { - "q": [ {{ queryInputs | wrap( '["' , '","suppressor"]') }} ], - "scopes": ["object.NCBIGene", "association.relation_name"] - } - 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 - ## biolink 2.2.8: using inverse of mapping for GAMMA:suppressor - predicate: activity_decreased_by - response_mapping: - "$ref": "#/components/x-bte-response-mapping/reverse" - # testExamples: - # - qInput: "NCBIGene:2247" ## FGF2 - # oneOutput: "CHEMBL.COMPOUND:CHEMBL4297755" ## FP-1039 - vaccine: - ## https://biothings.ncats.io/dgidb/query?q=association.relation_name:vaccine - ## 8 records + # - qInput: "NCBIGene:1137" ## CHRNA4 + # oneOutput: "CHEMBL.COMPOUND:CHEMBL3707250" ## CP-601927 + positive_modulator: + ## https://biothings.ncats.io/dgidb/query?q=association.interaction_types:positive_modulator + ## 602 records - supportBatch: true useTemplating: true ## flag to say templating is being used below inputs: @@ -1435,26 +1311,25 @@ components: requestBody: body: >- { - "q": [ {{ queryInputs | wrap( '["' , '","vaccine"]') }} ], - "scopes": ["subject.CHEMBL_COMPOUND", "association.relation_name"] + "q": [ {{ queryInputs | wrap( '["' , '","positive_modulator"]') }} ], + "scopes": ["subject.CHEMBL_COMPOUND", "association.interaction_types"] } parameters: fields: >- object.NCBIGene,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name + association.interaction_claim_source,association.pmids,association.interaction_types size: 1000 outputs: - id: NCBIGene semantic: Gene - ## using a different predicate than the biolink 2.2.8 mapping (decreases_activity_of) - ## reasoning: thought its def https://dgidb.org/interaction_types was similar to https://github.com/biolink/biolink-model/blob/c73899cd33753c5d2ff937213b6c5911c579b001/biolink-model.yaml#L2918 - predicate: affects_response_to + ## biolink 2.2.8: using mapping to GAMMA / CHEMBL.MECHANISM positive_modulator term + predicate: increases_activity_of response_mapping: "$ref": "#/components/x-bte-response-mapping/forward" # testExamples: - # - qInput: "CHEMBL.COMPOUND:CHEMBL75094" ## PRINOMASTAT - # oneOutput: "NCBIGene:4323" ## MMP14 - vaccine-rev: + # - 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: @@ -1464,35 +1339,154 @@ components: requestBody: body: >- { - "q": [ {{ queryInputs | wrap( '["' , '","vaccine"]') }} ], - "scopes": ["object.NCBIGene", "association.relation_name"] + "q": [ {{ queryInputs | wrap( '["' , '","positive_modulator"]') }} ], + "scopes": ["object.NCBIGene", "association.interaction_types"] } parameters: fields: >- subject.CHEMBL_COMPOUND,association.interaction_group_score, - association.provided_by,association.pubmed,association.relation_name + association.interaction_claim_source,association.pmids,association.interaction_types 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 + ## biolink 2.2.8: using inverse of mapping to GAMMA / CHEMBL.MECHANISM positive_modulator term + predicate: activity_increased_by response_mapping: "$ref": "#/components/x-bte-response-mapping/reverse" # testExamples: - # - qInput: "NCBIGene:4313" ## MMP2 - # oneOutput: "CHEMBL.COMPOUND:CHEMBL297792" ## S-3304 + # - qInput: "NCBIGene:2557" ## GABRA4 + # oneOutput: "CHEMBL.COMPOUND:CHEMBL969" ## PRAZEPAM +## commenting out because there's only 1 record for this set of operations + # suppressor: + # ## https://biothings.ncats.io/dgidb/query?q=association.interaction_types:suppressor + # ## 1 record + # - supportBatch: true + # useTemplating: true ## flag to say templating is being used below + # inputs: + # - id: "CHEMBL.COMPOUND" + # semantic: SmallMolecule + # requestBodyType: object + # requestBody: + # body: >- + # { + # "q": [ {{ queryInputs | wrap( '["' , '","suppressor"]') }} ], + # "scopes": ["subject.CHEMBL_COMPOUND", "association.interaction_types"] + # } + # parameters: + # fields: >- + # object.NCBIGene,association.interaction_group_score, + # association.interaction_claim_source,association.pmids,association.interaction_types + # size: 1000 + # outputs: + # - id: NCBIGene + # semantic: Gene + # ## biolink 2.2.8: using mapping for GAMMA:suppressor + # predicate: decreases_activity_of + # response_mapping: + # "$ref": "#/components/x-bte-response-mapping/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: + # - id: NCBIGene + # semantic: Gene + # requestBodyType: object + # requestBody: + # body: >- + # { + # "q": [ {{ queryInputs | wrap( '["' , '","suppressor"]') }} ], + # "scopes": ["object.NCBIGene", "association.interaction_types"] + # } + # parameters: + # fields: >- + # subject.CHEMBL_COMPOUND,association.interaction_group_score, + # association.interaction_claim_source,association.pmids,association.interaction_types + # 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: + # "$ref": "#/components/x-bte-response-mapping/reverse" + # # testExamples: + # # - qInput: "NCBIGene:2247" ## FGF2 + # # oneOutput: "CHEMBL.COMPOUND:CHEMBL4297755" ## FP-1039 +## commenting out because there's only 8 records for this set of operations + # vaccine: + # ## https://biothings.ncats.io/dgidb/query?q=association.interaction_types:vaccine + # ## 8 records + # - supportBatch: true + # useTemplating: true ## flag to say templating is being used below + # inputs: + # - id: "CHEMBL.COMPOUND" + # semantic: SmallMolecule + # requestBodyType: object + # requestBody: + # body: >- + # { + # "q": [ {{ queryInputs | wrap( '["' , '","vaccine"]') }} ], + # "scopes": ["subject.CHEMBL_COMPOUND", "association.interaction_types"] + # } + # parameters: + # fields: >- + # object.NCBIGene,association.interaction_group_score, + # association.interaction_claim_source,association.pmids,association.interaction_types + # size: 1000 + # outputs: + # - id: NCBIGene + # semantic: Gene + # ## using a different predicate than the biolink 2.2.8 mapping (decreases_activity_of) + # ## reasoning: thought its def https://dgidb.org/interaction_types was similar to https://github.com/biolink/biolink-model/blob/c73899cd33753c5d2ff937213b6c5911c579b001/biolink-model.yaml#L2918 + # predicate: affects_response_to + # response_mapping: + # "$ref": "#/components/x-bte-response-mapping/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: + # - id: NCBIGene + # semantic: Gene + # requestBodyType: object + # requestBody: + # body: >- + # { + # "q": [ {{ queryInputs | wrap( '["' , '","vaccine"]') }} ], + # "scopes": ["object.NCBIGene", "association.interaction_types"] + # } + # parameters: + # fields: >- + # subject.CHEMBL_COMPOUND,association.interaction_group_score, + # association.interaction_claim_source,association.pmids,association.interaction_types + # 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/reverse" + # # testExamples: + # # - qInput: "NCBIGene:4313" ## MMP2 + # # oneOutput: "CHEMBL.COMPOUND:CHEMBL297792" ## S-3304 x-bte-response-mapping: forward: NCBIGene: object.NCBIGene - pubmed: association.pubmed - dgidb_interaction_claim_source: association.provided_by - "biolink:original_predicate": association.relation_name ## or dgidb interaction types + pubmed: association.pmids + dgidb_interaction_claim_source: association.interaction_claim_source + "biolink:original_predicate": association.interaction_types ## 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 + pubmed: association.pmids + dgidb_interaction_claim_source: association.interaction_claim_source + "biolink:original_predicate": association.interaction_types ## or dgidb interaction types dgidb_interaction_group_score: association.interaction_group_score