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SPARQLing data stars
       in the biology cloud

     Jerven Bolleman
       Developer
       Swiss-Prot Group
       Swiss Institute of Bioinformatics




Monday, September 3, 2012
Biohackathon
  A nursery galaxy for sparql endpoints
Monday, 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
                                                                  3
Monday, September 3, 2012
Data integration
        RDF/SPARQL

                                                            Own Lab Data
                            Developer&maintenance
                                  time saved


Chembl.rdf                                                         Triple Store
                                                                    SPARQL
                                                                   Federation

                                                    Triple Store
                                                     SPARQL
                                                      Queries        SPARQL
                                                                      Driving
UniProt.rdf                                                          Services



     © 2011 SIB


Monday, September 3, 2012
© 2012 SIB Swiss Instiute of Bioinformatics
                                                   5
Monday, 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
                                                   6
Monday, September 3, 2012
© 2012 SIB Swiss Instiute of Bioinformatics
                                                   7
Monday, 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
                                                    8
Monday, September 3, 2012
© 2012 SIB Swiss Instiute of Bioinformatics
                                                   9
Monday, 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
                                                   10
Monday, 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
                                                   11
Monday, September 3, 2012
Questions?




     © 2012 SIB Swiss Instiute of Bioinformatics
                                                   12
Monday, September 3, 2012

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Uni protsparqlcloud

  • 1. SPARQLing data stars in the biology cloud Jerven Bolleman Developer Swiss-Prot Group Swiss Institute of Bioinformatics Monday, September 3, 2012
  • 2. Biohackathon A nursery galaxy for sparql endpoints Monday, September 3, 2012
  • 3. 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 3 Monday, September 3, 2012
  • 4. Data integration RDF/SPARQL Own Lab Data Developer&maintenance time saved Chembl.rdf Triple Store SPARQL Federation Triple Store SPARQL Queries SPARQL Driving UniProt.rdf Services © 2011 SIB Monday, September 3, 2012
  • 5. © 2012 SIB Swiss Instiute of Bioinformatics 5 Monday, September 3, 2012
  • 6. 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 6 Monday, September 3, 2012
  • 7. © 2012 SIB Swiss Instiute of Bioinformatics 7 Monday, September 3, 2012
  • 8. 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 8 Monday, September 3, 2012
  • 9. © 2012 SIB Swiss Instiute of Bioinformatics 9 Monday, September 3, 2012
  • 10. 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 10 Monday, September 3, 2012
  • 11. 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 11 Monday, September 3, 2012
  • 12. Questions? © 2012 SIB Swiss Instiute of Bioinformatics 12 Monday, September 3, 2012