Remove clinical-trial-data/aeolus-indication operations

mychem.info/openapi_full.yml

@@ -321,8 +321,6 @@ paths:
       tags:
       - query
       x-bte-kgs-operations:
-      - "$ref": "#/components/x-bte-kgs-operations/aeolusTreats"
-      - "$ref": "#/components/x-bte-kgs-operations/aeolusTreats-rev"
       - "$ref": "#/components/x-bte-kgs-operations/chebiToReactome"
       - "$ref": "#/components/x-bte-kgs-operations/chebiToReactome-rev"
       - "$ref": "#/components/x-bte-kgs-operations/chebiToRhea"
@@ -331,8 +329,6 @@ paths:
       - "$ref": "#/components/x-bte-kgs-operations/drugMechChemblEnsembl-rev"
       - "$ref": "#/components/x-bte-kgs-operations/drugMechChemblUniprot"
       - "$ref": "#/components/x-bte-kgs-operations/drugMechChemblUniprot-rev"
-      - "$ref": "#/components/x-bte-kgs-operations/treatsChembl"
-      - "$ref": "#/components/x-bte-kgs-operations/treatsChembl-rev"
       - "$ref": "#/components/x-bte-kgs-operations/drugcentral-bioactivity-activator"
       - "$ref": "#/components/x-bte-kgs-operations/drugcentral-bioactivity-activator-rev"
       - "$ref": "#/components/x-bte-kgs-operations/drugcentral-bioactivity-agonist"
@@ -629,12 +625,6 @@ components:
   #       type: array
   #     - type: string
   x-bte-response-mapping:
-    aeolusIndication-meddra:
-      MEDDRA: aeolus.indications.meddra_code
-      "biolink:evidence_count": aeolus.indications.count
-    aeolusIndication-unii:
-      UNII: aeolus.unii
-      "biolink:evidence_count": aeolus.indications.count
     chebiXrefs-reactome:
       REACT: chebi.xrefs.reactome
     chebi:
@@ -676,20 +666,6 @@ components:
       ref_pmcid: chembl.drug_mechanisms.mechanism_refs.PMC                         ## no prefix (but IDs start with "PMC")
       ref_url: chembl.drug_mechanisms.mechanism_refs.url
       output_name: chembl.drug_mechanisms.target_name
-    chembl-treats:
-      MESH: chembl.drug_indications.mesh_id
-      ref_clinicaltrials: chembl.drug_indications.indication_refs.ClinicalTrials     ## no prefix
-      ## this url field will include expanded clinicaltrials (aka duplicates!)
-      ##   but is required for other references: ATC, DailyMed, FDA
-      ref_url: chembl.drug_indications.indication_refs.url
-      "biolink:max_research_phase": chembl.drug_indications.max_phase_for_ind
-      ## commenting out because data-processing / biolink-modeling issues
-      # year_first_approved: chembl.drug_indications.first_approval
-    chembl-treats-rev:
-      "CHEMBL.COMPOUND": chembl.molecule_chembl_id  ## no prefix
-      ref_clinicaltrials: chembl.drug_indications.indication_refs.ClinicalTrials     ## no prefix
-      ref_url: chembl.drug_indications.indication_refs.url
-      "biolink:max_research_phase": chembl.drug_indications.max_phase_for_ind
     drugcentral-bioactivity:
       UniProtKB: drugcentral.bioactivity.uniprot.uniprot_id  ## no prefix
       ## commenting out because data-processing / biolink-modeling issues
@@ -731,73 +707,15 @@ components:
     fdaOrphanDrug-pubchemCompound:
       "PUBCHEM.COMPOUND": fda_orphan_drug.pubchem_cid  ## no prefix
   x-bte-kgs-operations:
-  ## deciding not to annotate aeolus.outcomes since this list of side effects can be very long
+  ## AEOLUS:
+  ## - not annotating indications because Translator CQS/Matt Brush team asked us not to;
+  ##   asked us to use Multiomics Drug Approvals instead
+  ## - deciding not to annotate aeolus.outcomes since this list of side effects can be very long
   ##   this says mychem truncates it to 5000...https://docs.mychem.info/en/latest/doc/data_source.html
-  ## deciding not to annotate sider since it's not clear how the records are structured (is meddra ID for the side effect?)
+  ## SIDER: deciding not to annotate since it's not clear how the records are structured (is meddra ID for the side effect?)
   ##   it is also long...https://docs.mychem.info/en/latest/doc/data_source.html
-    aeolusTreats:
-    ## - chose to map to Disease semantic type since I saw SRI map some MEDDRA IDs to Disease...
-    ##   https://nodenormalization-sri.renci.org/1.2/get_normalized_nodes?curie=MEDDRA%3A10021639&conflate=true
-    ##   But some seem like PhenotypicFeatures...
-    - supportBatch: true
-      useTemplating: true
-      inputs:
-      - id: UNII
-        semantic: SmallMolecule
-      requestBody:
-        body:
-          q: "{{ queryInputs }}"  ## no prefix
-          scopes: aeolus.unii
-          ## all 1551 records have unii and rxcui (another option), only 1016 have inchikey 
-      outputs:
-      - id: MEDDRA
-        semantic: Disease
-      parameters:
-        filter: _exists_:aeolus.indications   ## need the field to exist for jmespath to work
-        fields: aeolus.indications     ## need the whole thing for jmespath to work
-        jmespath: aeolus.indications|[?count>`20`]
-        ## don't need always_list because aeolus.indications can be a single-element array
-        size: 1000  ## note size limit; added just in case
-      ## seem to come from the drug adverse event self-reporting
-      predicate: applied_to_treat
-      source: "infores:aeolus"
-      knowledge_level: observation
-      agent_type: manual_agent
-      response_mapping:
-        "$ref": "#/components/x-bte-response-mapping/aeolusIndication-meddra"
-      testExamples:
-        - qInput: "UNII:90347YTW5F"     ## alfuzosin aka PUBCHEM.COMPOUND:2092
-          oneOutput: "MEDDRA:10004446"  ## Benign prostatic hyperplasia aka MONDO:0010811
-    aeolusTreats-rev:
-    - supportBatch: false
-      useTemplating: true
-      inputs:
-      - id: MEDDRA
-        semantic: Disease
-      requestBody:
-        body:
-          q: "{{ queryInputs }}"  ## no prefix
-          scopes: aeolus.indications.meddra_code
-      outputs:
-      - id: UNII
-        semantic: SmallMolecule
-      parameters:
-        filter: _exists_:aeolus.indications   ## need the field to exist for jmespath to work
-      ## need the whole thing for jmespath to work
-        fields: aeolus.unii,aeolus.indications  ## no prefix
-        size: 1000  ## note size limit
-        jmespath: "aeolus.indications|[?count>`20` && meddra_code=='{{ queryInputs }}']"
-        jmespath_exclude_empty: true
-      predicate: treatment_applications_from
-      source: "infores:aeolus"
-      knowledge_level: observation
-      agent_type: manual_agent
-      response_mapping:
-        "$ref": "#/components/x-bte-response-mapping/aeolusIndication-unii"
-      testExamples:
-        - qInput: "MEDDRA:10012378"        ## Depression aka MONDO:0002050
-          oneOutput: "UNII:82VFR53I78"     ## Aripiprazole aka PUBCHEM.COMPOUND:60795
-  ## chebi xrefs actually include relationships to other bioentities...
+  ## CHEBI:
+  ## - chebi xrefs actually include relationships to other bioentities...
   ## - note that truncation was done by MyChem for rhea...
   ##   see https://docs.mychem.info/en/latest/doc/data_source.html
   ## - not including chebi.xrefs.uniprot because:
@@ -915,6 +833,7 @@ components:
           oneOutput: "CHEBI:16885"  ## 1-kestose / 1(F)-beta-D-fructosylsucrose aka PUBCHEM.COMPOUND:440080
     ## chembl
     ## knowledge_level / agent_type: assuming manual curation. 
+    ## - not including drug_indications. Translator wants us to use Multiomics Clinical Trials KP (CTKP) instead
     ## - drug_mechanisms: 
     ##   - Gene field: always ensembl_id or uniprot, never both. Not sure if any entity-merging was ever done
     ##   - can filter for human vs non-human targets and by target-type
@@ -1064,73 +983,6 @@ components:
       testExamples:
         - qInput: "UniProtKB:Q16539"                   ## MAP kinase p38 alpha
           oneOutput: "CHEMBL.COMPOUND:CHEMBL585902"    ## AMG-548 aka PUBCHEM.COMPOUND:11167112
-    treatsChembl:
-    ## all drug_indication records have a mesh ID for the indication...
-    - supportBatch: true
-      useTemplating: true
-      inputs:
-      - id: CHEMBL.COMPOUND
-        semantic: SmallMolecule
-      requestBody:
-        body:
-          q: "{{ queryInputs }}"  ## no prefix
-          scopes: chembl.molecule_chembl_id
-      outputs:
-      - id: MESH
-        semantic: Disease
-      parameters:
-      ## not including: mesh_heading (name)
-      ## including: first_approval is only in some records (not indexed right now)
-      ## commenting out because data-processing / biolink-modeling issues
-        # fields: >-
-        #   chembl.drug_indications.mesh_id,
-        #   chembl.drug_indications.max_phase_for_ind,
-        #   chembl.drug_indications.indication_refs.url,
-        #   chembl.drug_indications.first_approval
-        fields: >-
-          chembl.drug_indications.mesh_id,
-          chembl.drug_indications.indication_refs.ClinicalTrials,
-          chembl.drug_indications.indication_refs.url,
-          chembl.drug_indications.max_phase_for_ind
-        size: 1000  ## note size limit; added just in case
-      predicate: in_clinical_trials_for
-      source: "infores:chembl"
-      knowledge_level: knowledge_assertion
-      agent_type: manual_agent
-      response_mapping:
-        "$ref": "#/components/x-bte-response-mapping/chembl-treats"
-      testExamples:
-        - qInput: "CHEMBL.COMPOUND:CHEMBL471737"   ## IVABRADINE aka PUBCHEM.COMPOUND:132999
-          oneOutput: "MESH:D000072658"             ## Non-ST Elevated Myocardial Infarction aka UMLS:C4255010
-    treatsChembl-rev:
-    - supportBatch: false
-      useTemplating: true
-      inputs:
-      - id: MESH
-        semantic: Disease
-      requestBody:
-        body:
-          q: "{{ queryInputs }}"  ## no prefix
-          scopes: chembl.drug_indications.mesh_id
-      outputs:
-      - id: CHEMBL.COMPOUND
-        semantic: SmallMolecule
-      parameters:
-        filter: _exists_:chembl.drug_indications   ## need the field to exist for jmespath to work
-      ## need the whole thing for jmespath to work
-        fields: chembl.molecule_chembl_id,chembl.drug_indications  ## no prefix
-        size: 1000  ## note size limit
-        jmespath: "chembl.drug_indications|[?mesh_id=='{{ queryInputs }}']"
-        ## don't need always_list because chembl.drug_indications can be a single-element array
-      predicate: tested_by_clinical_trials_of
-      source: "infores:chembl"
-      knowledge_level: knowledge_assertion
-      agent_type: manual_agent
-      response_mapping:
-        "$ref": "#/components/x-bte-response-mapping/chembl-treats-rev"
-      testExamples:
-        - qInput: "MESH:D014376"                    ## Tuberculosis aka MONDO:0018076
-          oneOutput: "CHEMBL.COMPOUND:CHEMBL1441"   ## ETHIONAMIDE aka PUBCHEM.COMPOUND:2761171
   ## DrugCentral source
   ## Not annotating: 
   ## - drugcentral.approval (node properties?)

repodb/smartapi.yaml

@@ -313,12 +313,10 @@ paths:
       # summary: Make batch gene queries and return matching gene hits
       tags:
       - query
-      ## 4 operations (2 sets)
+      ## 2 operations (1 set)
       x-bte-kgs-operations:
       - $ref: '#/components/x-bte-kgs-operations/drug-disease-approved'
       - $ref: '#/components/x-bte-kgs-operations/disease-drug-approved'
-      - $ref: '#/components/x-bte-kgs-operations/drug-disease-not-approved'
-      - $ref: '#/components/x-bte-kgs-operations/disease-drug-not-approved'
 components:
   parameters:
     callback:
@@ -580,9 +578,10 @@ components:
   #     - type: string
   x-bte-kgs-operations:
   ## NOTES
+  ## - not annotating non-approved drug info: this is from parsing/cleaning clinicaltrials.gov data.
+  ##   Translator wants us to use Multiomics Clinical Trials KP (CTKP) instead
   ## - knowledge_level / agent_type: based on paper https://www.nature.com/articles/sdata201729
   ##   - approved drug info from downloading drugcentral / drugbank
-  ##   - non-approved drug info from data parsing/cleaning clinicaltrials.gov data 
   ## - possible edge-attributes:
   ##   - 2185 / 10602 records have detailed status (free-text): https://biothings.ncats.io/repodb/query?q=_exists_:trials.detailed_status
   ##   - status: all records have this, but the values need to be mapped to biolink-model ClinicalApprovalStatusEnum
@@ -648,103 +647,12 @@ components:
         testExamples:
           - qInput: "UMLS:C0032797"          ## Postpartum Hemorrhage / HP:0011891 Post-partum hemorrhage
             oneOutput: "DRUGBANK:DB00107"    ## Oxytocin / PUBCHEM.COMPOUND:439302
-    drug-disease-not-approved:
-    ## 2583 records (going off of existence of trials.phase which doesn't seem to exist in approved entries)
-    ## biothings.ncats.io/repodb/query?q=_exists_:trials.phase
-    ## phase values are either Phase 1, Phase 2, Phase 3 (so all went through clinical trials)
-    ## status values are either terminated, withdrawn, suspended
-      - supportBatch: true
-        useTemplating: true ## flag to say templating is being used below
-        inputs:
-          - id: DRUGBANK
-            semantic: SmallMolecule
-        requestBody:
-          body: 
-            q: "{{ queryInputs | rmPrefix() }}"
-            scopes: drug.drugbank
-        outputs:
-          - id: UMLS
-            semantic: Disease
-        parameters:
-        ## include clinical trial field since some will have it
-          fields: >-
-            indication.umls,
-            drug.name,
-            indication.name,
-            trials.id,
-            trials.status
-          size: 1000
-          filter: _exists_:trials.phase
-        predicate: in_clinical_trials_for
-        source: "infores:repodb"
-        knowledge_level: observation
-        agent_type: automated_agent
-        response_mapping:
-          "$ref": "#/components/x-bte-response-mapping/disease-clinicaltrial"
-        testExamples:
-        ## for Terminated
-          - qInput: "DRUGBANK:DB00043"    ## Omalizumab / UNII:2P471X1Z11
-            oneOutput: "UMLS:C0004096"    ## Asthma / MONDO:0004979
-        ## for Withdrawn
-          - qInput: "DRUGBANK:DB14482"    ## Sodium ascorbate / PUBCHEM.COMPOUND:23667548
-            oneOutput: "UMLS:C0004238"    ## Atrial Fibrillation / MONDO:0004981
-        ## for Suspended
-          - qInput: "DRUGBANK:DB00104"    ## Octreotide / PUBCHEM.COMPOUND:448601
-            oneOutput: "UMLS:C0001206"    ## Acromegaly / MONDO:0019933
-    disease-drug-not-approved:
-      - supportBatch: true
-        useTemplating: true
-        inputs:
-          - id: UMLS
-            semantic: Disease
-        requestBody:
-          body: 
-            q: "{{ queryInputs | rmPrefix() }}"
-            scopes: indication.umls
-        outputs:
-          - id: DRUGBANK
-            semantic: SmallMolecule
-        parameters:
-          fields: >-
-            drug.drugbank,
-            drug.name,
-            indication.name,
-            trials.id,
-            trials.status
-          size: 1000
-          filter: _exists_:trials.phase
-        predicate: tested_by_clinical_trials_of
-        source: "infores:repodb"
-        knowledge_level: observation
-        agent_type: automated_agent
-        response_mapping:
-          "$ref": "#/components/x-bte-response-mapping/drug-clinicaltrial"
-        testExamples:
-        ## for Terminated
-          - qInput: "UMLS:C0184567"          ## Acute onset pain / NCIT:C27003
-            oneOutput: "DRUGBANK:DB14123"    ## Menthol / PUBCHEM.COMPOUND:1254
-        ## for Withdrawn
-          - qInput: "UMLS:C0022104"          ## Irritable Bowel Syndrome / MONDO:0005052
-            oneOutput: "DRUGBANK:DB14005"    ## Dimethicone 410 / PUBCHEM.COMPOUND:131740050 Bis(tert-butylsilyloxy)-dimethylsilane
-        ## for Suspended
-          - qInput: "UMLS:C0406317"          ## Chronic small plaque psoriasis
-            oneOutput: "DRUGBANK:DB14006"    ## Choline salicylate / PUBCHEM.COMPOUND:54686350
   x-bte-response-mapping:
     disease-only:
       UMLS: indication.umls
       input_name: drug.name
       output_name: indication.name
-    disease-clinicaltrial:
-      UMLS: indication.umls
-      input_name: drug.name
-      output_name: indication.name
-      ref_clinicaltrials: trials.id  ## no prefix
     drug-only:
       DRUGBANK: drug.drugbank
       input_name: indication.name
       output_name: drug.name
-    drug-clinicaltrial:
-      DRUGBANK: drug.drugbank
-      input_name: indication.name
-      output_name: drug.name
-      ref_clinicaltrials: trials.id  ## no prefix