Uni protsparqlcloud
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Uni protsparqlcloud

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This 15 minute presentation shows how we can use multiple SPARQL endpoints to integrate biological data. SPARQL we no longer need to start a data warehouse project to integrate multiple datasources we ...

This 15 minute presentation shows how we can use multiple SPARQL endpoints to integrate biological data. SPARQL we no longer need to start a data warehouse project to integrate multiple datasources we just use the SPARQL 1.1 service keyword.

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Uni protsparqlcloud Uni protsparqlcloud Presentation Transcript

  • SPARQLing data stars in the biology cloud Jerven Bolleman Developer Swiss-Prot Group Swiss Institute of BioinformaticsMonday, September 3, 2012
  • Biohackathon A nursery galaxy for sparql endpointsMonday, September 3, 2012
  • http://beta.sparql.uniprot.org • 5.2 Billion triples – All UniProt data • Taxonomy • Sequences • Enzymes • Pathways • etc... etc... • SPARQL 1.1 (January 05 2012 Working Draft) – SERVICE keyword • No blank nodes – SHA-512 series used to stabilize anonymous resources © 2012 SIB Swiss Instiute of Bioinformatics 3Monday, September 3, 2012
  • Data integration RDF/SPARQL Own Lab Data Developer&maintenance time savedChembl.rdf Triple Store SPARQL Federation Triple Store SPARQL Queries SPARQL DrivingUniProt.rdf Services © 2011 SIBMonday, September 3, 2012
  • © 2012 SIB Swiss Instiute of Bioinformatics 5Monday, September 3, 2012
  • SELECT ?name (COUNT(?protein) as ?size) WHERE {   {     ?protein :enzyme ?name.     ?name rdfs:subClassOf enzyme:1.-.-.-   } UNION { Text ?protein :enzyme ?name.     ?name rdfs:subClassOf enzyme:2.-.-.- } ... } GROUP BY ?name ORDER BY ?name © 2012 SIB Swiss Instiute of Bioinformatics 6Monday, September 3, 2012
  • © 2012 SIB Swiss Instiute of Bioinformatics 7Monday, September 3, 2012
  • SELECT ?japaneseTerm ?geneSymbol ?protein WHERE { SERVICE<http://data.allie.dbcls.jp/sparql>{ ?pc a allie:PairCluster; allie:hasShortFormRepresentationOf ?sfr ; allie:hasLongFormRepresentationOf ?lfr . ?sfr rdfs:label ?sf . ?lfr rdfs:label “β1アドレナリン受容体, β1アドレナリン レセプター”@ja, ?japaneseTerm. FILTER (lang(?sf) = "en" ) } BIND(str(?sf) as ?geneSymbol) . ?gene skos:prefLabel ?geneSymbol . ?protein uniprot:encodedBy ?gene . } © 2012 SIB Swiss Instiute of Bioinformatics 8Monday, September 3, 2012
  • © 2012 SIB Swiss Instiute of Bioinformatics 9Monday, September 3, 2012
  • SELECT ?target ?protein WHERE { SERVICE <http://rdf.farmbio.uu.se/chembl/sparql> { ?target a chembl:Target. ?target owl:sameAs ?bio2rdfUniprot . FILTER(contains(str(?bio2rdfUniprot), "uniprot:")) } BIND(iri(concat("http://purl.uniprot.org/ uniprot/",substr(str(?bio2rdfUniprot), 28))) as ?protein ) ?protein a up:Protein . FILTER (NOT EXISTS { ?protein up:annotation ?annotation . ?annotation a up:Disease_Annotation . }) } © 2012 SIB Swiss Instiute of Bioinformatics 10Monday, September 3, 2012
  • SELECT ?target ?protein WHERE { SERVICE <http://rdf.farmbio.uu.se/chembl/sparql> { ?target a chembl:Target. ?target owl:sameAs ?protein } ?protein a up:Protein . FILTER (NOT EXISTS { ?protein up:annotation ?annotation . ?annotation a up:Disease_Annotation . }) } © 2012 SIB Swiss Instiute of Bioinformatics 11Monday, September 3, 2012
  • Questions? © 2012 SIB Swiss Instiute of Bioinformatics 12Monday, September 3, 2012