HCLSIG/Pharmacogenomics/Queries
< HCLSIG | Pharmacogenomics
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>);