Enhancing access to pharmacogenomics knowledge with Semantic Web technologies: Supplementary Material

This page holds supplementary material (e.g. URIs, SPARQL queries) for the article "Enhancing access to pharmacogenomics knowledge with Semantic Web technologies".

Ontology

The ontology can be accessed at http://www.w3.org/2001/sw/hcls/ns/transmed/tmo

You can view the ontology by installing an ontology editor such as Protege 4. Alternatively, you can also view it with the web-based application OwlSight or ontology browser.

Datasets we created

Triples describing pharmacogenomic associations automatically extracted from PubMed

http://www.loria.fr/~coulet/material/phare.w.owl

PharmGKB in OWL

TODO

PHP script that converts PharmGKB data to an OWL file (created by Michel Dumontier)

dbSNP as a SPARQL endpoint

See documentation on using swobjects with dbsnp through the mysql port

dbSNP in OWL

TODO

Iker's SPARQL endpoint: http://85.48.202.13:8891/sparql

Aggregated OWL data from SNPedia

TODO

Relevant datasets from third parties

TODO

Example 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 WEB SERVER CURRENTLY DOWN

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>);

Other query collections

From the work of Baker et al.: http://unbsj.biordf.net/mutation-impact/AIMM2010-BMC-Bioinformatics-supplementary-materials.html