Merge pull request #153 from NCATS-Tangerine/pfocr-source-urls

BioThings PFOCR: add source_record_url field

pfocr/smartapi.yaml

@@ -581,7 +581,7 @@ components:
   ## - Pathways don't have formal IDs that can be used
     gene-chem:
     ## https://biothings.ncats.io/pfocr/query?q=_exists_:associatedWith.mentions.chemicals%20AND%20_exists_:associatedWith.mentions.genes
-    ## 44081 documents. not clear how many gene-chem pairs there are. 
+    ## 34857 documents. not clear how many gene-chem pairs there are. 
       - supportBatch: true
         useTemplating: true ## flag to say templating is being used below
         inputs:
@@ -599,7 +599,7 @@ components:
         parameters:
           fields: >-
             associatedWith.mentions.chemicals.mesh,
-            associatedWith.figureUrl,associatedWith.pmc
+            associatedWith.figureUrl,associatedWith.pmc,associatedWith.pfocrUrl
           size: 1000
         predicate: occurs_together_in_literature_with
         source: "infores:pfocr"
@@ -609,7 +609,7 @@ components:
           "$ref": "#/components/x-bte-response-mapping/chem"
         testExamples:
           - qInput: "NCBIGene:3620"      ## IDO1
-            oneOutput: "MESH:D004958"    ## Estradiol
+            oneOutput: "MESH:D004958"    ## Estradiol / CHEBI:16469
         ## should have 2 figures: https://biothings.ncats.io/pfocr/query?q=associatedWith.mentions.chemicals.mesh:D004958%20AND%20associatedWith.mentions.genes.ncbigene:3620
     chem-gene:
       - supportBatch: true
@@ -629,7 +629,7 @@ components:
         parameters:
           fields: >-
             associatedWith.mentions.genes.ncbigene,
-            associatedWith.figureUrl,associatedWith.pmc
+            associatedWith.figureUrl,associatedWith.pmc,associatedWith.pfocrUrl
           size: 1000
         predicate: occurs_together_in_literature_with
         source: "infores:pfocr"
@@ -643,7 +643,7 @@ components:
         ## should have 9 figures: https://biothings.ncats.io/pfocr/query?q=associatedWith.mentions.chemicals.mesh:C000541%20AND%20associatedWith.mentions.genes.ncbigene:208
     disease-chem:
     ## https://biothings.ncats.io/pfocr/query?q=_exists_:associatedWith.mentions.diseases%20AND%20_exists_:associatedWith.mentions.chemicals
-    ## 9232 documents. not clear how many disease-chem pairs there are. 
+    ## 10180 documents. not clear how many disease-chem pairs there are. 
       - supportBatch: true
         useTemplating: true ## flag to say templating is being used below
         inputs:
@@ -661,7 +661,7 @@ components:
         parameters:
           fields: >-
             associatedWith.mentions.chemicals.mesh,
-            associatedWith.figureUrl,associatedWith.pmc
+            associatedWith.figureUrl,associatedWith.pmc,associatedWith.pfocrUrl
           size: 1000
         predicate: occurs_together_in_literature_with
         source: "infores:pfocr"
@@ -671,8 +671,8 @@ components:
           "$ref": "#/components/x-bte-response-mapping/chem"
         testExamples:
           - qInput: "MESH:D006623"       ## von Hippel-Lindau Disease
-            oneOutput: "MESH:C516667"    ## pazopanib
-        ## should have 9 figures: https://biothings.ncats.io/pfocr/query?q=associatedWith.mentions.chemicals.mesh:C516667%20AND%20associatedWith.mentions.diseases.mesh:D006623
+            oneOutput: "MESH:C516667"    ## pazopanib / CHEBI:71219
+        ## should have 2 figures: https://biothings.ncats.io/pfocr/query?q=associatedWith.mentions.chemicals.mesh:C516667%20AND%20associatedWith.mentions.diseases.mesh:D006623
     chem-disease:
       - supportBatch: true
         useTemplating: true ## flag to say templating is being used below
@@ -691,7 +691,7 @@ components:
         parameters:
           fields: >-
             associatedWith.mentions.diseases.mesh,
-            associatedWith.figureUrl,associatedWith.pmc
+            associatedWith.figureUrl,associatedWith.pmc,associatedWith.pfocrUrl
           size: 1000
         predicate: occurs_together_in_literature_with
         source: "infores:pfocr"
@@ -701,11 +701,11 @@ components:
           "$ref": "#/components/x-bte-response-mapping/disease"
         testExamples:
           - qInput: "MESH:D002945"       ## Cisplatin 
-            oneOutput: "MESH:D009369"    ## Neoplasms
-        ## should have 18 figures: https://biothings.ncats.io/pfocr/query?q=associatedWith.mentions.chemicals.mesh:D002945%20AND%20associatedWith.mentions.diseases.mesh:D009369
+            oneOutput: "MESH:D009369"    ## Neoplasms / MONDO:0005070
+        ## should have 22 figures: https://biothings.ncats.io/pfocr/query?q=associatedWith.mentions.chemicals.mesh:D002945%20AND%20associatedWith.mentions.diseases.mesh:D009369
     disease-gene:
     ## https://biothings.ncats.io/pfocr/query?q=_exists_:associatedWith.mentions.diseases%20AND%20_exists_:associatedWith.mentions.genes
-    ## 13354 documents. not clear how many disease-gene pairs there are. 
+    ## 11338 documents. not clear how many disease-gene pairs there are. 
       - supportBatch: true
         useTemplating: true ## flag to say templating is being used below
         inputs:
@@ -723,7 +723,7 @@ components:
         parameters:
           fields: >-
             associatedWith.mentions.genes.ncbigene,
-            associatedWith.figureUrl,associatedWith.pmc
+            associatedWith.figureUrl,associatedWith.pmc,associatedWith.pfocrUrl
           size: 1000
         predicate: occurs_together_in_literature_with
         source: "infores:pfocr"
@@ -753,7 +753,7 @@ components:
         parameters:
           fields: >-
             associatedWith.mentions.diseases.mesh,
-            associatedWith.figureUrl,associatedWith.pmc
+            associatedWith.figureUrl,associatedWith.pmc,associatedWith.pfocrUrl
           size: 1000
         predicate: occurs_together_in_literature_with
         source: "infores:pfocr"
@@ -763,20 +763,23 @@ components:
           "$ref": "#/components/x-bte-response-mapping/disease"
         testExamples:
           - qInput: "NCBIGene:3791"      ## KDR 
-            oneOutput: "MESH:D002318"    ## Cardiovascular Diseases
-        ## should have 1 figure: https://biothings.ncats.io/pfocr/query?q=associatedWith.mentions.genes.ncbigene:3791%20AND%20associatedWith.mentions.diseases.mesh:D002318
+            oneOutput: "MESH:D002289"    ## non-small cell lung carcinoma / MONDO:0005233
+        ## should have 3 figures: https://biothings.ncats.io/pfocr/query?q=associatedWith.mentions.genes.ncbigene:3791%20AND%20associatedWith.mentions.diseases.mesh:D002289
   x-bte-response-mapping:
     ## not including because because data-processing / biolink-modeling issues
     ## - associatedWith.title (title of figure)
     chem:
       MESH: associatedWith.mentions.chemicals.mesh   ## no prefix
       ref_url: associatedWith.figureUrl
       ref_pmcid: associatedWith.pmc                  ## no prefix (but IDs start with "PMC")
+      source_url: associatedWith.pfocrUrl
     gene:
       NCBIGene: associatedWith.mentions.genes.ncbigene   ## no prefix
       ref_url: associatedWith.figureUrl
       ref_pmcid: associatedWith.pmc
+      source_url: associatedWith.pfocrUrl
     disease:
       MESH: associatedWith.mentions.diseases.mesh   ## no prefix
       ref_url: associatedWith.figureUrl
       ref_pmcid: associatedWith.pmc
+      source_url: associatedWith.pfocrUrl