Merge branch 'master' of https://github.com/edmcouncil/idmp into IDMP…

…-592
edmcouncil · Sep 28, 2023 · 0593770 · 0593770
2 parents 303a7f6 + 8cbeeba
commit 0593770
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diff --git a/.github/workflows/unit_tests_run.yml b/.github/workflows/unit_tests_run.yml
@@ -93,10 +93,7 @@ jobs:
           done
       - name: Combine GSRS with IDMP
         run: |
-          sudo wget --no-verbose -m -nH -nd https://idmp-datasets.s3.eu-central-1.amazonaws.com/GSRS/gsrs-active-moiety.ttl
-          sudo wget --no-verbose -m -nH -nd https://idmp-datasets.s3.eu-central-1.amazonaws.com/GSRS/gsrs-dct-identifier.ttl
-          sudo wget --no-verbose -m -nH -nd https://idmp-datasets.s3.eu-central-1.amazonaws.com/GSRS/gsrs-skos-altLabel.ttl
-          source_files=(gsrs-transformed.ttl AboutIDMPDev-ReferenceIndividuals.ttl gsrs-active-moiety.ttl gsrs-dct-identifier.ttl gsrs-skos-altLabel.ttl)
+          source_files=(gsrs-transformed.ttl AboutIDMPDev-ReferenceIndividuals.ttl)
           output_file=gsrs-final.ttl
           # Loop through the source files and append their contents to the output file
           for file in "${source_files[@]}"; do

diff --git a/etc/transformation/GSRS/gsrs-public-data-substances.rqg b/etc/transformation/GSRS/gsrs-public-data-substances.rqg
@@ -35,29 +35,34 @@ GENERATE {
     # Molecular Structure
     ?MolecularStructure a idmp-sub:MolecularStructure ;
         idmp-sub:hasSMILESValue ?structureSmilesString ;
-        cmns-dsg:isDescribedBy ?MolfileURI;
+        cmns-dsg:isDescribedBy ?StructureMolfileURI;
     .
 
-    ?MolfileURI a idmp-sub:Molfile;
-        idmp-sub:hasStructuralRepresentationAttachment ?structureMolfile;
+    # Molecular Structure Molfile
+    ?StructureMolfileURI a idmp-sub:Molfile;
+        idmp-sub:hasStructuralRepresentationText ?structureMolfile;
     .
 
 
     GENERATE{
-        ?Substance idmp-sub:hasMoiety ?SubstanceMoiety;
+        ?Substance idmp-sub:hasMoiety ?Moiety;
         .
 
-        ?SubstanceMoiety a idmp-sub:Moiety; 
+        ?Moiety a idmp-sub:Moiety;
             rdfs:label ?moietyFormula;
-            idmp-sub:hasDefiningStructure ?MoietyMolecularStructure;
+            idmp-sub:hasDefiningStructure ?MoietyStructure;
             idmp-sub:hasDefiningMolecularWeight ?MoietyStructureMolecularWeight ;
             idmp-sub:hasDefiningMolecularFormula ?moietyFormula ;
             idmp-sub:hasDefiningStereochemistry ?MoietyStereochemistry ;
         .
 
-        ?MoietyMolecularStructure a idmp-sub:MolecularStructure ;
+        ?MoietyStructure a idmp-sub:MolecularStructure ;
             idmp-sub:hasSMILESValue ?MoietyStructureSmilesString ;
-            cmns-dsg:isDescribedBy ?MoietyStructureMolfile;
+            cmns-dsg:isDescribedBy ?MoietyStructureMolfileURI;
+        .
+
+        ?MoietyStructureMolfileURI a idmp-sub:Molfile;
+            idmp-sub:hasStructuralRepresentationText ?MoietyStructureMolfile;
         .
     }
     # Molecular Structure Moieties
@@ -81,10 +86,9 @@ GENERATE {
     ?MoietyStructureMolecularWeight
     ?moietyStructureID
 
-    BIND(str(StrUUID()) as ?MoietyUUID)
-    BIND(<https://gsrs.ncats.nih.gov/api/v1/substances/{ ?RelatedSubstanceApprovalID }/{ ?MoietyUUID }> AS ?SubstanceMoiety )
-
-    BIND(<https://data.pistoiaalliance.org/idmp/gsrs/structure/{ ?MoietyUUID }> AS ?MoietyMolecularStructure )
+    BIND(<https://gsrs.ncats.nih.gov/api/v1/substances/{ ?approvalID }/moieties({ ?moietyStructureID })> AS ?Moiety )
+    BIND(<https://gsrs.ncats.nih.gov/api/v1/substances/{ ?approvalID }/moieties({ ?moietyStructureID })/structure> AS ?MoietyStructure )
+    BIND(<https://gsrs.ncats.nih.gov/api/v1/substances/{ ?approvalID }/moieties({ ?moietyStructureID })/structure/molfile> AS ?MoietyStructureMolfileURI )
 
     BIND(IF(str(?MoietystructureStereochemistry) = "ABSOLUTE", idmp-sub:Stereochemistry-Absolute ,
     IF(str(?MoietystructureStereochemistry) = "ACHIRAL", idmp-sub:Stereochemistry-Achiral ,
@@ -113,17 +117,17 @@ GENERATE {
 
     GENERATE{
         # Relationships
-        ?Substance ?SubstancesRelationshipProperty ?RelatedSubstance; 
+        ?Substance ?SubstancesRelationshipProperty ?RelatedSubstance;
         .
         # Is Active Moiety Of
-        ?RelatedSubstance ?IsActiveMoietyOfProperty ?Substance; 
+        ?RelatedSubstance ?IsActiveMoietyOfProperty ?Substance;
         .
     }
-    ITERATOR iter:JSONSurfer(?relationships, 
+    ITERATOR iter:JSONSurfer(?relationships,
         "$[*]",
         "$.type",
         "$.relatedSubstance.approvalID"
-    ) AS 
+    ) AS
     ?Relationship
     ?RelationshipType
     ?RelatedSubstanceApprovalID
@@ -173,7 +177,8 @@ ITERATOR iter:JSONSurfer(<public_data.json>,
 ?relationships
 
 BIND(<https://gsrs.ncats.nih.gov/api/v1/substances/{ ?approvalID }> AS ?Substance )
-BIND(<https://data.pistoiaalliance.org/idmp/gsrs/structure/{ ?structureID }> AS ?MolecularStructure )
+BIND(<https://gsrs.ncats.nih.gov/api/v1/substances/{ ?approvalID }/structure> AS ?MolecularStructure )
+BIND(<https://gsrs.ncats.nih.gov/api/v1/substances/{ ?approvalID }/structure/molfile> AS ?StructureMolfileURI )
 
 BIND(IF(contains(str(?structureFormula), "."), idmp-sub:hasDefiningMolecularFormulaByMoiety , ?nothing ) AS ?hasMolecularFormulaByMoietyProperty)
 
@@ -210,6 +215,3 @@ BIND(IF(str(?structureStereochemistry) = "ABSOLUTE", idmp-sub:Stereochemistry-Ab
     IF(str(?structureStereochemistry) = "UNKNOWN", idmp-sub:Stereochemistry-Unknown ,
     ?structureStereochemistry )))))))))))))))))))))
     AS ?Stereochemistry)
-
- BIND(IF(?structureMolfile != "",<https://data.pistoiaalliance.org/idmp/gsrs/molfile/{ StrUUID() }>, ?unbound) as ?MolfileURI)
-