Merge branch 'master' into v3-biolink-monarch

NCATS-Tangerine · Feb 28, 2024 · 81dc6dc · 81dc6dc
2 parents c28ecb4 + 419e74a
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diff --git a/AGR/agr.yaml b/AGR/agr.yaml
diff --git a/CTD/smartapi.yaml b/CTD/smartapi.yaml
diff --git a/DISEASES/smartapi.yaml b/DISEASES/smartapi.yaml
@@ -601,9 +601,9 @@ components:
       source: "infores:diseases"
       response_mapping:
         "$ref": "#/components/x-bte-response-mapping/disease-gene"
-      # testExamples:
-      #   - qInput: "DOID:0060041"     ## Autism spectrum disorder
-      #     oneOutput: "ENSEMBL:ENSP00000482335"    ## MAP7
+      testExamples:
+        - qInput: "DOID:0060041"     ## Autism spectrum disorder
+          oneOutput: "ENSEMBL:ENSP00000482335"    ## MAP7
       ## should be able to see results with all 3 methods/combos of edge attributes
     gene-disease:
     - supportBatch: true
@@ -627,9 +627,9 @@ components:
       source: "infores:diseases"
       response_mapping:
         "$ref": "#/components/x-bte-response-mapping/gene-disease"
-      # testExamples:
-      #   - qInput: "ENSEMBL:ENSP00000298910"    ## LRRK2
-      #     oneOutput: "DOID:1926"               ## Gaucher disease
+      testExamples:
+        - qInput: "ENSEMBL:ENSP00000298910"    ## LRRK2
+          oneOutput: "DOID:1926"               ## Gaucher disease
   x-bte-response-mapping:
     disease-gene:
       ENSEMBL: DISEASES.associatedWith.ensembl  ## no prefix

diff --git a/EBIgene2phenotype/smartapi.yaml b/EBIgene2phenotype/smartapi.yaml
@@ -619,9 +619,9 @@ components:
       source: "infores:ebi-gene2phenotype"
       response_mapping:
         "$ref": "#/components/x-bte-response-mapping/disease-object"
-      # testExamples:
-      #   - qInput: "HGNC:1020"         ## BCS1L
-      #     oneOutput: "OMIM:603358"    ## GRACILE SYNDROME
+      testExamples:
+        - qInput: "HGNC:1020"         ## BCS1L
+          oneOutput: "OMIM:603358"    ## GRACILE SYNDROME
     disease_to_gene:
     - supportBatch: true
       useTemplating: true
@@ -644,9 +644,9 @@ components:
       source: "infores:ebi-gene2phenotype"
       response_mapping:
         "$ref": "#/components/x-bte-response-mapping/gene-object"
-      # testExamples:
-      #   - qInput: "OMIM:615355"      ## NOONAN SYNDROME 8
-      #     oneOutput: "HGNC:10023"    ## RIT1
+      testExamples:
+        - qInput: "OMIM:615355"      ## NOONAN SYNDROME 8
+          oneOutput: "HGNC:10023"    ## RIT1
   x-bte-response-mapping:
   ## data:
   ## - allelic_requirement seems similar to "inheritance" but focused on the affected individual 

diff --git a/LINCS/smartapi.yml b/LINCS/smartapi.yml
@@ -409,9 +409,9 @@ components:
       response_mapping:
         $ref: '#/components/x-bte-response-mapping/drug-indication'
       supportBatch: false  ## no batch support (get operation)
-      # testExamples:
-      #   - qInput: "LINCS:LSM-1023"      ## Imatinib
-      #     oneOutput: "MESH:D046152"   ## GASTROINTESTINAL STROMAL TUMORS
+      testExamples:
+        - qInput: "LINCS:LSM-1023"      ## Imatinib
+          oneOutput: "MESH:D046152"   ## GASTROINTESTINAL STROMAL TUMORS
       ## example raw query: http://lincsportal.ccs.miami.edu/dcic/api/drugindication?id=LSM-1008
   x-bte-response-mapping:
     drug-indication:

diff --git a/MGIgene2phenotype/smartapi.yaml b/MGIgene2phenotype/smartapi.yaml
@@ -594,9 +594,9 @@ components:
       source: "infores:mgi"
       response_mapping:
         "$ref": "#/components/x-bte-response-mapping/gene_related_to_disease"
-      # testExamples:
-      #   - qInput: "MGI:104511"        ## Tnfsf4
-      #     oneOutput: "DOID:14557"     ## primary pulmonary hypertension
+      testExamples:
+        - qInput: "MGI:104511"        ## Tnfsf4
+          oneOutput: "DOID:14557"     ## primary pulmonary hypertension
     disease_related_to_gene:
     ## "reverse-type" operation
     - supportBatch: true
@@ -618,9 +618,9 @@ components:
       source: "infores:mgi"
       response_mapping:
         "$ref": "#/components/x-bte-response-mapping/mgi"
-      # testExamples:
-      #   - qInput: "DOID:0110731"      ## neuronal ceroid lipofuscinosis 3
-      #     oneOutput: "MGI:103555"     ## Clcn3
+      testExamples:
+        - qInput: "DOID:0110731"      ## neuronal ceroid lipofuscinosis 3
+          oneOutput: "MGI:103555"     ## Clcn3
     gene_related_to_phenotype:
     ## there are 1447 records with mgi.associated_with_phenotype field
     ##   1359 of these records also have mgi.has_homolog field (NCBIGene ID for mouse gene)
@@ -645,9 +645,9 @@ components:
       source: "infores:mgi"
       response_mapping:
         "$ref": "#/components/x-bte-response-mapping/gene_related_to_phenotype"
-      # testExamples:
-      #   - qInput: "MGI:102539"        ## Tbx6
-      #     oneOutput: "MP:0002151"     ## abnormal neural tube morphology
+      testExamples:
+        - qInput: "MGI:102539"        ## Tbx6
+          oneOutput: "MP:0002151"     ## abnormal neural tube morphology
     phenotype_related_to_gene:
     ## "reverse-type" operation
     - supportBatch: true
@@ -669,9 +669,9 @@ components:
       source: "infores:mgi"
       response_mapping:
         "$ref": "#/components/x-bte-response-mapping/mgi"
-      # testExamples: 
-      #   - qInput: "MP:0000623"         ## decreased salivation
-      #     oneOutput: "MGI:88398"       ## Chrm3
+      testExamples: 
+        - qInput: "MP:0000623"         ## decreased salivation
+          oneOutput: "MGI:88398"       ## Chrm3
   x-bte-response-mapping:
     gene_related_to_disease:
       DOID: mgi.associated_with_disease.doid  ## has prefix

diff --git a/bindingdb/smartapi.yaml b/bindingdb/smartapi.yaml
@@ -602,9 +602,9 @@ components:
         source: "infores:bindingdb"
         response_mapping:
           "$ref": "#/components/x-bte-response-mapping/pubchem-object"
-        # testExamples:
-        #   - qInput: "UniProtKB:Q08722"                               ## Leukocyte surface antigen CD47
-        #     oneOutput: "INCHIKEY:CLTVCCLZSPKLRB-NRGGWPRRSA-N"        ## CHEMBL4474790 / H-D-Lys-N(Me)Arg-Phe-Tyr-Val-Val-Nle-Trp-Lys-D-Lys-OH
+        testExamples:
+          - qInput: "UniProtKB:Q08722"                               ## Leukocyte surface antigen CD47
+            oneOutput: "INCHIKEY:CLTVCCLZSPKLRB-NRGGWPRRSA-N"        ## CHEMBL4474790 / H-D-Lys-N(Me)Arg-Phe-Tyr-Val-Val-Nle-Trp-Lys-D-Lys-OH
     ligand-protein:
       - supportBatch: true
         useTemplating: true
@@ -632,9 +632,9 @@ components:
         source: "infores:bindingdb"
         response_mapping:
           "$ref": "#/components/x-bte-response-mapping/uniprot-subject"
-        # testExamples:
-        #   - qInput: "INCHIKEY:NZLXOECMDRNZDN-GUYCJALGSA-N"     ## US10736883, Example 387.0
-        #     oneOutput: "UniProtKB:P35414"                      ## Apelin receptor / APLNR
+        testExamples:
+          - qInput: "INCHIKEY:NZLXOECMDRNZDN-GUYCJALGSA-N"     ## US10736883, Example 387.0
+            oneOutput: "UniProtKB:P35414"                      ## Apelin receptor / APLNR
   x-bte-response-mapping:
   ## note on references:
   ##   sometimes the doi + pmid will refer to the same publication (so..."duplicate" references)

diff --git a/bioplanet/bioplanet-pathway-disease.yaml b/bioplanet/bioplanet-pathway-disease.yaml
@@ -606,9 +606,9 @@ components:
         source: "infores:bioplanet"
         response_mapping:
           "$ref": "#/components/x-bte-response-mapping/disease"
-        # testExamples:
-        #   - qInput: "ncats.bioplanet:bioplanet_276"     ## Alpha-hemoglobin stabilizing enzyme (AHSP) pathway
-        #     oneOutput: "OMIM:300751"                    ## Anemia, sideroblastic, X-linked, 300751 (3)
+        testExamples:
+          - qInput: "ncats.bioplanet:bioplanet_276"     ## Alpha-hemoglobin stabilizing enzyme (AHSP) pathway
+            oneOutput: "OMIM:300751"                    ## Anemia, sideroblastic, X-linked, 300751 (3)
     disease-pathway:
       - supportBatch: true
         useTemplating: true ## flag to say templating is being used below
@@ -641,9 +641,9 @@ components:
         source: "infores:bioplanet"
         response_mapping:
           "$ref": "#/components/x-bte-response-mapping/pathway"
-        # testExamples:
-        #   - qInput: "OMIM:603909"                        ## Autoimmune lymphoproliferative syndrome, type II, 603909 (3) 
-        #     oneOutput: "ncats.bioplanet:bioplanet_26"    ## D4-GDI signaling pathway
+        testExamples:
+          - qInput: "OMIM:603909"                        ## Autoimmune lymphoproliferative syndrome, type II, 603909 (3) 
+            oneOutput: "ncats.bioplanet:bioplanet_26"    ## D4-GDI signaling pathway
   x-bte-response-mapping:
     disease:
       OMIM: subject.PHENO_TYPE                         ## no prefix

diff --git a/bioplanet/bioplanet-pathway-gene.yaml b/bioplanet/bioplanet-pathway-gene.yaml
@@ -595,9 +595,9 @@ components:
         source: "infores:bioplanet"
         response_mapping:
           "$ref": "#/components/x-bte-response-mapping/gene"
-        # testExamples:
-        #   - qInput: "ncats.bioplanet:bioplanet_869"     ## Chondroitin sulfate/dermatan sulfate metabolism
-        #     oneOutput: "NCBIGene:9672"                  ## SDC3
+        testExamples:
+          - qInput: "ncats.bioplanet:bioplanet_869"     ## Chondroitin sulfate/dermatan sulfate metabolism
+            oneOutput: "NCBIGene:9672"                  ## SDC3
     gene-pathway:
       - supportBatch: true
         useTemplating: true ## flag to say templating is being used below
@@ -622,9 +622,9 @@ components:
         source: "infores:bioplanet"
         response_mapping:
           "$ref": "#/components/x-bte-response-mapping/pathway"
-        # testExamples:
-        #   - qInput: "NCBIGene:1463"                         ## NCAN 
-        #     oneOutput: "ncats.bioplanet:bioplanet_789"      ## Dermatan sulfate biosynthesis
+        testExamples:
+          - qInput: "NCBIGene:1463"                         ## NCAN 
+            oneOutput: "ncats.bioplanet:bioplanet_789"      ## Dermatan sulfate biosynthesis
   x-bte-response-mapping:
     gene:
       NCBIGene: subject.GENE_ID           ## no prefix

diff --git a/biothings_foodb/smartapi.yaml b/biothings_foodb/smartapi.yaml
@@ -597,9 +597,9 @@ components:
         source: "infores:fooddb"
         response_mapping:
           "$ref": "#/components/x-bte-response-mapping/compound"
-        # testExamples:
-        #   - qInput: "foodb.food:FOOD00914"                       ## Soybean oil
-        #     oneOutput: "INCHIKEY:KZJWDPNRJALLNS-VJSFXXLFSA-N"    ## beta-Sitosterol
+        testExamples:
+          - qInput: "foodb.food:FOOD00914"                       ## Soybean oil
+            oneOutput: "INCHIKEY:KZJWDPNRJALLNS-VJSFXXLFSA-N"    ## beta-Sitosterol
     food-compound-rev:
     ## not including compound name because getting this nested info from reverse queries is tricky
       - supportBatch: true
@@ -622,9 +622,9 @@ components:
         source: "infores:fooddb"
         response_mapping:
           "$ref": "#/components/x-bte-response-mapping/food"
-        # testExamples:
-        #   - qInput: "INCHIKEY:QZAYGJVTTNCVMB-UHFFFAOYSA-N"      ## Serotonin
-        #     oneOutput: "foodb.food:FOOD00022"                   ## Oat
+        testExamples:
+          - qInput: "INCHIKEY:QZAYGJVTTNCVMB-UHFFFAOYSA-N"      ## Serotonin
+            oneOutput: "foodb.food:FOOD00022"                   ## Oat
   x-bte-response-mapping:
     compound:
       INCHIKEY: compounds.moldb_inchikey

diff --git a/complexportal/smartapi.yaml b/complexportal/smartapi.yaml
@@ -88,9 +88,9 @@ components:
       predicate: part_of
       response_mapping:
         "$ref": "#/components/x-bte-response-mapping/complex-output"
-      # testExamples:
-      #   - qInput: "UniProtKB:P69905"             ## Hemoglobin subunit alpha
-      #     oneOutput: "ComplexPortal:CPX-2158"    ## Hemoglobin HbA complex
+      testExamples:
+        - qInput: "UniProtKB:P69905"             ## Hemoglobin subunit alpha
+          oneOutput: "ComplexPortal:CPX-2158"    ## Hemoglobin HbA complex
     chemical2complex:
     - supportBatch: false 
       useTemplating: true
@@ -105,14 +105,14 @@ components:
       predicate: part_of
       response_mapping:
         "$ref": "#/components/x-bte-response-mapping/complex-output"
-      # testExamples:
-      #   - qInput: "CHEBI:30413"                  ## heme
-      #     oneOutput: "ComplexPortal:CPX-2158"    ## Hemoglobin HbA complex
+      testExamples:
+        - qInput: "CHEBI:30413"                  ## heme
+          oneOutput: "ComplexPortal:CPX-2158"    ## Hemoglobin HbA complex
     disease2complex:
     - supportBatch: false
       useTemplating: true
       inputs:
-      - id: ORPHANET
+      - id: orphanet
         semantic: Disease
       outputs:
       - id: ComplexPortal
@@ -124,9 +124,9 @@ components:
       ##   https://www.ebi.ac.uk/complexportal/documentation
       response_mapping:
         "$ref": "#/components/x-bte-response-mapping/complex-output"
-      # testExamples:
-      #   - qInput: "ORPHANET:848"                 ## Beta-thalassemia
-      #     oneOutput: "ComplexPortal:CPX-2158"    ## Hemoglobin HbA complex
+      testExamples:
+        - qInput: "orphanet:848"                 ## Beta-thalassemia
+          oneOutput: "ComplexPortal:CPX-2158"    ## Hemoglobin HbA complex
     bp2complex:
     - supportBatch: false
       useTemplating: true
@@ -143,9 +143,9 @@ components:
       ## not sure if a different predicate should be used...
       response_mapping:
         "$ref": "#/components/x-bte-response-mapping/complex-output"
-      # testExamples:
-      #   - qInput: "GO:0015670"                   ## carbon dioxide transport
-      #     oneOutput: "ComplexPortal:CPX-2936"    ## Hemoglobin HbH complex
+      testExamples:
+        - qInput: "GO:0015670"                   ## carbon dioxide transport
+          oneOutput: "ComplexPortal:CPX-2936"    ## Hemoglobin HbH complex
     mf2complex:
     - supportBatch: false
       useTemplating: true
@@ -162,9 +162,9 @@ components:
       ## not sure if a different predicate should be used...
       response_mapping:
         "$ref": "#/components/x-bte-response-mapping/complex-output"
-      # testExamples:
-      #   - qInput: "GO:0070026"                  ## nitric oxide binding
-      #     oneOutput: "ComplexPortal:CPX-52"     ## iNOS-S100A8/A9 complex
+      testExamples:
+        - qInput: "GO:0070026"                  ## nitric oxide binding
+          oneOutput: "ComplexPortal:CPX-52"     ## iNOS-S100A8/A9 complex
     ## Commenting out for now
     ## Complex -> entity x-bte operations use JQ post-processing
     ## MISSING: Complex -> BP, Complex -> MF operations. Will need different custom JQ post-processing
@@ -185,9 +185,9 @@ components:
     #       .participants |= map(if (.identifier | contains(":") | not) then . else empty end)
     #   response_mapping:
     #     "$ref": "#/components/x-bte-response-mapping/complex2protein"
-    #   # testExamples:
-    #   #   - qInput: "ComplexPortal:CPX-2158"    ## Hemoglobin HbA complex
-    #   #     oneOutput: "UniProtKB:P69905"       ## Hemoglobin subunit alpha
+    #   testExamples:
+    #     - qInput: "ComplexPortal:CPX-2158"    ## Hemoglobin HbA complex
+    #       oneOutput: "UniProtKB:P69905"       ## Hemoglobin subunit alpha
     # complex2chemical:
     # - supportBatch: false
     #   useTemplating: true
@@ -205,17 +205,17 @@ components:
     #       .participants |= map(if (.identifier | contains(":")) then .identifier = (.identifier | split(":") | last) else empty end)
     #   response_mapping:
     #     "$ref": "#/components/x-bte-response-mapping/complex2chemical"
-    #   # testExamples:
-    #   #   - qInput: "ComplexPortal:CPX-2158"        ## Hemoglobin HbA complex
-    #   #     oneOutput: "CHEBI:30413"                ## heme
+    #   testExamples:
+    #     - qInput: "ComplexPortal:CPX-2158"        ## Hemoglobin HbA complex
+    #       oneOutput: "CHEBI:30413"                ## heme
     # complex2disease:
     # - supportBatch: false
     #   useTemplating: true
     #   inputs:
     #   - id: ComplexPortal
     #     semantic: MacromolecularComplex
     #   outputs:
-    #   - id: ORPHANET
+    #   - id: orphanet
     #     semantic: Disease
     #   parameters:
     #     id: "{{ queryInputs }}" ## no prefix
@@ -230,7 +230,7 @@ components:
     #     "$ref": "#/components/x-bte-response-mapping/complex2disease"
     #   # testExamples:
     #   #   - qInput: "ComplexPortal:CPX-2158"      ## Hemoglobin HbA complex
-    #   #     oneOutput: "ORPHANET:848"             ## Beta-thalassemia
+    #   #     oneOutput: "orphanet:848"             ## Beta-thalassemia
   x-bte-response-mapping:
     complex-output:
       ComplexPortal: elements.complexAC
@@ -246,5 +246,5 @@ components:
       CHEBI: participants.identifier
     complex2disease:
       ## this is a field made with JQ-post-processing
-      ORPHANET: disease_ids
+      orphanet: disease_ids
 
diff --git a/ddinter/ddinter.yaml b/ddinter/ddinter.yaml
@@ -601,9 +601,9 @@ components:
         response_mapping:
           "$ref": "#/components/x-bte-response-mapping/drugB"
         ## compare to http://ddinter.scbdd.com/ddinter/interact/977140/
-        # testExamples:
-        #   - qInput: "DRUGBANK:DB00244"      ## Mesalazine 
-        #     oneOutput: "DRUGBANK:DB00414"   ## Acetohexamide
+        testExamples:
+          - qInput: "DRUGBANK:DB00244"      ## Mesalazine 
+            oneOutput: "DRUGBANK:DB00414"   ## Acetohexamide
     drugB-to-drugA:
       - supportBatch: true
         useTemplating: true
@@ -627,9 +627,9 @@ components:
         response_mapping:
           "$ref": "#/components/x-bte-response-mapping/drugA"
         ## compare to http://ddinter.scbdd.com/ddinter/interact/1047482/
-        # testExamples:
-        #   - qInput: "DRUGBANK:DB00540"      ## Nortriptyline 
-        #     oneOutput: "DRUGBANK:DB00451"   ## Levothyroxine
+        testExamples:
+          - qInput: "DRUGBANK:DB00540"      ## Nortriptyline 
+            oneOutput: "DRUGBANK:DB00451"   ## Levothyroxine
   x-bte-response-mapping:
     drugB:
       DRUGBANK: drug_b.drugbank