fix: add x-translator.infores-curie, replace source strings with info…

…res curies also note: 3 apis don't have the hard-coded source field now: - text mining co-occurrence api - text mining targeted association api - drug response kp api also note: one api fits situation C of https://github.com/biothings/BioThings_Explorer_TRAPI/issues/208\#issuecomment-866620512: tcga mutational freq api
NCATS-Tangerine · Aug 3, 2021 · efff122 · efff122
1 parent 3fffcd5
commit efff122
Show file tree

Hide file tree

Showing 28 changed files with 948 additions and 876 deletions.
diff --git a/DISEASES/smartapi.yaml b/DISEASES/smartapi.yaml
@@ -11,6 +11,7 @@ info:
   title: DISEASES API
   version: '1.0'
   x-translator:
+    infores-curie: "infores:biothings-diseases"
     component: KP
     team:
       - Service Provider
@@ -212,8 +213,6 @@ paths:
               schema:
                 "$ref": "#/components/schemas/QueryPOSTResult"
           description: Query response objects with the "hits" property
-          x-bte-response-mapping:
-            "$ref": "#/components/x-bte-response-mapping/query-post"
         '400':
           content:
             application/json:
@@ -389,7 +388,7 @@ components:
       parameters:
         fields: DISEASES.associatedWith
       predicate: related_to
-      source: DISEASES
+      source: "infores:diseases"
       requestBody:
         body:
           q: "{inputs[0]}"
@@ -407,7 +406,7 @@ components:
       - id: SYMBOL
         semantic: Gene
       predicate: related_to
-      source: DISEASES
+      source: "infores:diseases"
       parameters:
         fields: DISEASES.doid
         size: '250'

diff --git a/EBIgene2phenotype/smartapi.yaml b/EBIgene2phenotype/smartapi.yaml
@@ -11,6 +11,7 @@ info:
   title: EBIgene2phenotype API
   version: '1.0'
   x-translator:
+    infores-curie: "infores:biothings-ebi-gene2phenotype"
     component: KP
     team:
       - Service Provider
@@ -385,7 +386,7 @@ components:
       - id: HP
         semantic: PhenotypicFeature
       predicate: related_to
-      source: EBI
+      source: "infores:ebi-gene2phenotype"
       parameters:
         fields: gene2phenotype
       requestBody:
@@ -405,7 +406,7 @@ components:
       - id: HP
         semantic: PhenotypicFeature
       predicate: related_to
-      source: EBI
+      source: "infores:ebi-gene2phenotype"
       parameters:
         fields: _id
         size: '350'

diff --git a/LINCS/smartapi.yml b/LINCS/smartapi.yml
@@ -12,6 +12,7 @@ info:
     email: [email protected]
     x-id: 'http://lincsportal.ccs.miami.edu/'
   x-translator:
+    infores-curie: "infores:lincs"
     component: KP
     team:
     - Service Provider
@@ -367,7 +368,7 @@ components:
       predicate: treats
       response_mapping:
         $ref: '#/components/x-bte-response-mapping/drug-indication'
-      source: LINCS
+      source: "infores:lincs"  ## ...so weird duplicate source info happens here
       supportBatch: false
   x-bte-response-mapping:
     drug-indication:

diff --git a/MGIgene2phenotype/smartapi.yaml b/MGIgene2phenotype/smartapi.yaml
@@ -11,6 +11,7 @@ info:
   title: MGIgene2phenotype API
   version: '1.0'
   x-translator:
+    infores-curie: "infores:biothings-mgi-g2p"
     component: KP
     team:
       - Service Provider
@@ -351,10 +352,11 @@ components:
       type: array
     QueryResult:
       properties:
-        hits:
-          items:
-            "$ref": "#/components/schemas/Chem"
-          type: array
+      ## to remove semantic error of missing reference
+        # hits:
+        #   items:
+        #     "$ref": "#/components/schemas/Chem"
+        #   type: array
         max_score:
           format: float
           type: number
@@ -389,7 +391,7 @@ components:
       parameters:
         fields: mgi.associated_with_disease
       predicate: related_to
-      source: mgi_gene2phenotype
+      source: "infores:mgi"
       requestBody:
         body:
           q: "{inputs[0]}"
@@ -407,7 +409,7 @@ components:
       - id: MP
         semantic: PhenotypicFeature
       predicate: related_to
-      source: mgi_gene2phenotype
+      source: "infores:mgi"
       parameters:
         fields: mgi.associated_with_phenotype
       requestBody:
@@ -430,7 +432,7 @@ components:
         fields: _id
         size: '300'
       predicate: related_to
-      source: mgi_gene2phenotype
+      source: "infores:mgi"
       requestBody:
         body:
           q: "{inputs[0]}"
@@ -448,7 +450,7 @@ components:
       - id: MP
         semantic: PhenotypicFeature
       predicate: related_to
-      source: mgi_gene2phenotype
+      source: "infores:mgi"
       parameters:
         fields: _id
         size: '300'

diff --git a/biolink/openapi.yml b/biolink/openapi.yml
@@ -10,6 +10,7 @@ info:
   title: BioLink API
   version: 1.0.1
   x-translator:
+    infores-curie: "infores:biolink-api"
     component: KP
     team:
     ## check what teams are involved
@@ -492,7 +493,7 @@ components:
       - id: HGNC
         semantic: Gene
       predicate: expresses
-      source: "Monarch Initiative"
+      source: "infores:monarchinitiative"
       supportBatch: false
       response_mapping:
         "$ref": "#/components/x-bte-response-mapping/anatomy-gene-hgnc"
@@ -509,7 +510,7 @@ components:
       - id: HGNC
         semantic: Gene
       predicate: condition_associated_with_gene
-      source: "Monarch Initiative"
+      source: "infores:monarchinitiative"
       supportBatch: false
       response_mapping:
         "$ref": "#/components/x-bte-response-mapping/disease-gene-hgnc"
@@ -526,7 +527,7 @@ components:
       - id: REACT
         semantic: Pathway
       predicate: related_to
-      source: "Monarch Initiative"
+      source: "infores:monarchinitiative"
       supportBatch: false
       response_mapping:
         "$ref": "#/components/x-bte-response-mapping/disease-pathway"
@@ -543,7 +544,7 @@ components:
       - id: HP
         semantic: PhenotypicFeature
       predicate: has_phenotype
-      source: "Monarch Initiative"
+      source: "infores:monarchinitiative"
       supportBatch: false
       response_mapping:
         "$ref": "#/components/x-bte-response-mapping/disease-phenotype"
@@ -560,7 +561,7 @@ components:
       - id: UBERON
         semantic: AnatomicalEntity
       predicate: expressed_in
-      source: "Monarch Initiative"
+      source: "infores:monarchinitiative"
       supportBatch: false
       response_mapping:
         "$ref": "#/components/x-bte-response-mapping/gene-anatomy"
@@ -577,7 +578,7 @@ components:
       - id: MONDO
         semantic: Disease
       predicate: gene_associated_with_condition
-      source: "Monarch Initiative"
+      source: "infores:monarchinitiative"
       supportBatch: false
       response_mapping:
         "$ref": "#/components/x-bte-response-mapping/gene-disease"
@@ -594,7 +595,7 @@ components:
       - id: HP
         semantic: PhenotypicFeature
       predicate: has_phenotype
-      source: "Monarch Initiative"
+      source: "infores:monarchinitiative"
       supportBatch: false
       response_mapping:
         "$ref": "#/components/x-bte-response-mapping/gene-phenotype"
@@ -611,7 +612,7 @@ components:
       - id: HGNC
         semantic: Gene
       predicate: interacts_with
-      source: "Monarch Initiative"
+      source: "infores:monarchinitiative"
       supportBatch: false
       response_mapping:
         "$ref": "#/components/x-bte-response-mapping/gene-interaction-hgnc"
@@ -628,7 +629,7 @@ components:
       - id: MONDO
         semantic: Disease
       predicate: related_to
-      source: "Monarch Initiative"
+      source: "infores:monarchinitiative"
       supportBatch: false
       response_mapping:
         "$ref": "#/components/x-bte-response-mapping/pathway-disease"
@@ -645,7 +646,7 @@ components:
       - id: HP
         semantic: PhenotypicFeature
       predicate: related_to
-      source: "Monarch Initiative"
+      source: "infores:monarchinitiative"
       supportBatch: false
       response_mapping:
         "$ref": "#/components/x-bte-response-mapping/pathway-phenotype"
@@ -662,7 +663,7 @@ components:
       - id: MONDO
         semantic: Disease
       predicate: phenotype_of
-      source: "Monarch Initiative"
+      source: "infores:monarchinitiative"
       supportBatch: false
       response_mapping:
         "$ref": "#/components/x-bte-response-mapping/phenotype-disease"
@@ -679,7 +680,7 @@ components:
       - id: HGNC
         semantic: Gene
       predicate: condition_associated_with_gene
-      source: "Monarch Initiative"
+      source: "infores:monarchinitiative"
       supportBatch: false
       response_mapping:
         "$ref": "#/components/x-bte-response-mapping/phenotype-gene-hgnc"
@@ -696,7 +697,7 @@ components:
       - id: REACT
         semantic: Pathway
       predicate: related_to
-      source: "Monarch Initiative"
+      source: "infores:monarchinitiative"
       supportBatch: false
       response_mapping:
         "$ref": "#/components/x-bte-response-mapping/phenotype-pathway"
@@ -713,7 +714,7 @@ components:
       - id: DBSNP
         semantic: SequenceVariant
       predicate: phenotype_of
-      source: "Monarch Initiative"
+      source: "infores:monarchinitiative"
       supportBatch: false
       response_mapping:
         "$ref": "#/components/x-bte-response-mapping/phenotype-variant"
diff --git a/dgidb/openapi.yml b/dgidb/openapi.yml
@@ -10,6 +10,7 @@ info:
   title: BioThings DGIdb API
   version: '1.0'
   x-translator:
+    infores-curie: "infores:biothings-dgidb"
     component: KP
     team:
       - Service Provider
@@ -431,7 +432,7 @@ components:
       predicate: physically_interacts_with
       response_mapping:
         $ref: '#/components/x-bte-response-mapping/chemical-gene'
-      source: DGIdb
+      source: "infores:dgidb"
       supportBatch: false
       inputSeparator: ","
     gene-chemical:
@@ -452,7 +453,7 @@ components:
         header: application/x-www-form-urlencoded
       response_mapping:
         $ref: '#/components/x-bte-response-mapping/gene-chemical'
-      source: DGIdb
+      source: "infores:dgidb"
       supportBatch: true
       inputSeparator: ","
   x-bte-response-mapping:

diff --git a/drug_response_kp/smartapi.yaml b/drug_response_kp/smartapi.yaml
@@ -10,6 +10,7 @@ info:
   title: Drug Response KP API
   version: '1.0'
   x-translator:
+    infores-curie: "infores:biothings-multiomics-drug-response"
     component: KP
     team:
       - Multiomics Provider
@@ -392,7 +393,8 @@ components:
       predicate: response_affected_by 
       response_mapping:
         $ref: '#/components/x-bte-response-mapping/chemical-gene'
-      source: Multiomics Provider
+      ## note: source should be the source of data used
+      # source: Multiomics Provider
       supportBatch: false
     gene-chemical:
     - inputs:
@@ -410,7 +412,8 @@ components:
       predicate: affects_response_to 
       response_mapping:
         $ref: '#/components/x-bte-response-mapping/gene-chemical'
-      source: Multiomics Provider
+      ## note: source should be the source of data used
+      # source: Multiomics Provider
       supportBatch: false
   x-bte-response-mapping:
     chemical-gene: