Merge pull request #508 from udel-cbcb/revert-b303ead

Revert b303ead

Author: mahir256

docs/registry/queries/prokn/lincs_kinase_perturbations.rq

@@ -8,42 +8,42 @@ PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
 PREFIX bao: <http://www.bioassayontology.org/bao#BAO_>
 PREFIX ncit: <http://purl.obolibrary.org/obo/NCIT_>
 PREFIX upcore: <http://purl.uniprot.org/core/>
-PREFIX ro: <http://purl.obolibrary.org/obo/RO_>
+PREFIX blv: <https://w3id.org/biolink/vocab/>
 PREFIX sio: <http://semanticscience.org/resource/SIO_>
 PREFIX dc: <http://purl.org/dc/terms/>
 PREFIX obo: <http://purl.obolibrary.org/obo/>
 PREFIX edam: <http://edamontology.org/>
-
+ 
 SELECT DISTINCT ?compoundLabel ?pubchemURI
 WHERE {
   # Perturbagen
   ?pert rdf:type bao:0003059 ;
             dc:source "LINCS_P100" ;
             obo:has_dbxref ?pubchemURI.
-
+ 
   # Compound
   ?comp rdf:type ncit:C43366 ;
             dc:source "DDKG_LINCS" ;
             rdfs:label ?compoundLabel.
    optional {
-  		?comp rdfs:seeAlso ?pubchemURI .
+  		?comp blv:exact_match ?pubchemURI .
   }
-
+ 
   # Relationship: Compound -> Gene
-  { ?comp ro:0002213 ?kgene. } # POSITIVELY_REGULATES
+  { ?comp blv:process_positively_regulates_process ?kgene. }
   UNION
-  { ?comp ro:0002212 ?kgene. } # NEGATIVELY_REGULATES
-
+  { ?comp blv:entity_negatively_regulates_entity ?kgene. }
+ 
   # Gene
   ?kgene rdf:type upcore:Gene.
-
+ 
   # Relationship: Gene -> Protein(IS_PROTEIN)
   ?kgene sio:010078 ?pr.
-
+ 
   # Protein
   ?pr rdf:type upcore:Protein ;
     edam:data_1011 ?ecNumber.
-
+ 
   FILTER regex(?ecNumber, "(^|;)2\\.7[^;]*")
 }
 ORDER BY ?compoundLabel ?pubchemURI

docs/registry/queries/prokn/protein_opioid_abuse.rq

@@ -23,7 +23,7 @@ SELECT * {
       {
         SELECT DISTINCT ?phenotype ?resource
         WHERE {
-          SERVICE <https://frink.apps.renci.org/biohealth/sparql> {
+          SERVICE <https://apps.okn.us/biohealth/sparql> {
             BIND (<https://biohealthkg.proto-okn.net/kg/node/C0029095> AS ?opioid)
             BIND (w3id:coexists_with AS ?coexists_with)
 

docs/registry/queries/prokn/protein_variant_sdoh.rq

@@ -16,7 +16,7 @@ PREFIX schema: <http://schema.org/>
 SELECT 
 DISTINCT ?sdoh_label ?disease_label ?disease_rel1 ?variant_desc ?variant_label ?other_diseases_label
 WHERE {
-SERVICE <https://frink.apps.renci.org/spoke-okn/sparql> {
+SERVICE <https://apps.okn.us/spoke-okn/sparql> {
     # Diseases associated with SDoH class
     ?sdoh rdf:type spcore:SDoH ;
         rdfs:label ?sdoh_label ;