HCLSIG/Pharmacogenomics/Queries

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Competency Questions and Queries

For a drug D, are there known genetic variations in the drug target or enzymes responsible for pharmacokinetics (such as cytochrome proteins) that could be used as markers for patient stratification?

Execute on SPARQL endpoint at http://85.48.202.13:8891/sparql

For enzymes:

 PREFIX drugbank: <http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugbank/>
 PREFIX biomoby: <http://biomoby.org/RESOURCES/MOBY-S/Objects/>
 PREFIX dbsnp: <http://localhost:2020/vocab/resource/>
 SELECT DISTINCT ?variation ?validatedBy ?methods ?geneName ?chromosome ?ancestralAllele
 WHERE {
   <http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugs/DB00682> drugbank:enzyme ?enzyme .
   ?enzyme drugbank:geneName ?geneName.
   ?variation a biomoby:AnnotatedSNP.
   ?variation dbsnp:gene_symbol ?geneName.
   ?variation dbsnp:validation ?validatedBy.
   ?variation dbsnp:methods ?methods.
   ?variation dbsnp:unique_chr ?chromosome.
   ?variation dbsnp:ancestral_allele ?ancestralAllele.
 }


For drug targets:

 PREFIX drugbank: <http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugbank/>
 PREFIX biomoby: <http://biomoby.org/RESOURCES/MOBY-S/Objects/>
 PREFIX dbsnp: <http://localhost:2020/vocab/resource/>
 SELECT DISTINCT ?variation ?validatedBy ?methods ?geneName ?chromosome ?ancestralAllele
 WHERE {
   <http://www4.wiwiss.fu-berlin.de/drugbank/resource/drugs/DB00682> drugbank:target ?target .
   ?target drugbank:geneName ?geneName.
   ?variation a biomoby:AnnotatedSNP.
   ?variation dbsnp:gene_symbol ?geneName.
   ?variation dbsnp:validation ?validatedBy.
   ?variation dbsnp:methods ?methods.
   ?variation dbsnp:unique_chr ?chromosome.
   ?variation dbsnp:ancestral_allele ?ancestralAllele.
 }

Query triples extracted from Medline abstracts for variants associated with warfarin

Execute on SPARQL endpoint at http://sparql.bioontology.org/webui/

 select $y $z
 from <rmi:phare.owl#w>
 where $z <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.stanford.edu/~coulet/phare.owl#Variant>
 and <http://www.stanford.edu/~coulet/phare.owl#warfarin> $y $z;

Query triples extracted from Medline abstracts for relationships that involve warfarin, gene variants and their provenance

Execute on SPARQL endpoint at http://sparql.bioontology.org/webui/

 select $p $o $provenance
 from <rmi:phare.owl#w>
 where  $rel <http://www.w3.org/2000/01/rdf-schema#comment> $provenance
 and ($rel <owl:annotatedSource> <http://www.stanford.edu/~coulet/phare.owl#warfarin>
      and $rel <owl:annotatedProperty> $p
      and $rel <owl:annotatedTarget> $o
      and $o <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.stanford.edu/~coulet/phare.owl#Variant>);