Merge pull request #72 from NCATS-Tangerine/adverse-event-operations

Adverse event operations

mychem.info/openapi_full.yml

@@ -237,6 +237,8 @@ paths:
       - "$ref": "#/components/x-bte-kgs-operations/targetedBy"
       - "$ref": "#/components/x-bte-kgs-operations/treatedBy"
       - "$ref": "#/components/x-bte-kgs-operations/contraindicatedBy"
+      - "$ref": "#/components/x-bte-kgs-operations/causesAdverseEvent"
+      - "$ref": "#/components/x-bte-kgs-operations/adverseEventCausedBy"
 components:
   parameters:
     callback:
@@ -423,6 +425,9 @@ components:
       MESH: chembl.drug_indications.mesh_id
       max_phase: chembl.drug_indications.max_phase_for_ind
       first_approval: chembl.drug_indications.first_approval
+    adverseEvent:
+      name: drugcentral.fda_adverse_event.meddra_term
+      MEDDRA: drugcentral.fda_adverse_event.meddra_code
   x-bte-kgs-operations:
     metabolizedBy:
     - supportBatch: true
@@ -709,4 +714,56 @@ components:
       predicate: treated_by
       source: "infores:chembl"
       response_mapping:
-        "$ref": "#/components/x-bte-response-mapping/chembl"
+        "$ref": "#/components/x-bte-response-mapping/chembl"
+    causesAdverseEvent:
+    ## - chose to map to Disease semantic type due to more support for ID mapping there, will support queries
+    ##   link: https://github.com/biothings/BioThings_Explorer_TRAPI/issues/217#issuecomment-880204237
+    ## - example: https://mychem.info/v1/query?q=drugbank.name:nitisinone&fields=drugcentral.fda_adverse_event
+    ## - there are also counts for...having drug + adverse event (ae) (drug_ae), having drug but no adverse event (drug_no_ae)
+    ##     no drug but had adverse event (no_drug_ae), no drug and no adverse event (no_drug_no_ar)
+    ##     not sure what the llr, llr_threshold, level means
+    - supportBatch: true
+      inputSeparator: ","
+      parameters:
+        fields: drugcentral.fda_adverse_event
+      requestBody:
+        body:
+          q: "{inputs[0]}"
+          ## there are 2016 records with drugcentral.fda_adverse_event fields
+          ##   most of them (1994) also have the drugcentral.xrefs.chembl_id field
+          scopes: drugcentral.xrefs.chembl_id
+        header: application/x-www-form-urlencoded
+      inputs:
+      - id: CHEMBL.COMPOUND
+        semantic: ChemicalSubstance
+      outputs:
+      - id: MEDDRA
+        semantic: Disease
+      predicate: causes_adverse_event  ## current biolink predicate
+      ## through drugcentral, FDA Adverse Event Reporting System (FAERS) information
+      source: "infores:drugcentral"
+      response_mapping:
+        "$ref": "#/components/x-bte-response-mapping/adverseEvent"
+    adverseEventCausedBy:
+    - supportBatch: true
+      inputSeparator: ","
+      parameters:
+        ## there are 2016 records with drugcentral.fda_adverse_event fields
+        ##   most of them (1994) also have the drugcentral.xrefs.chembl_id field
+        fields: drugcentral.xrefs.chembl_id
+        size: '1000'
+      requestBody:
+        body:
+          q: "{inputs[0]}"
+          scopes: drugcentral.fda_adverse_event.meddra_code
+        header: application/x-www-form-urlencoded
+      outputs:
+      - id: CHEMBL.COMPOUND
+        semantic: ChemicalSubstance
+      inputs:
+      - id: MEDDRA
+        semantic: Disease
+      predicate: adverse_event_caused_by  ## current biolink predicate
+      source: "infores:drugcentral"
+      response_mapping:
+        "$ref": "#/components/x-bte-response-mapping/drugcentral-chembl"