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.

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
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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
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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
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7. © 2012 SIB Swiss Instiute of Bioinformatics
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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
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9. © 2012 SIB Swiss Instiute of Bioinformatics
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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
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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
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Monday, September 3, 2012

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