Uni protsparqlcloud

SPARQLing data stars in the biology cloud

Jerven BollemanDeveloperSwiss-Prot GroupSwiss Institute of Bioinformatics

Monday, September 3, 2012

Biohackathon A nursery galaxy for sparql endpoints Monday, September 3, 2012

© 2012 SIB Swiss Instiute of Bioinformatics

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

3Monday, September 3, 2012



© 2011 SIB

Data integration RDF/SPARQL

Chembl.rdf

UniProt.rdf

Own Lab Data

Developer&maintenance time saved

Triple StoreSPARQLQueries

Triple StoreSPARQL

Federation

SPARQLDriving

Services


© 2012 SIB Swiss Instiute of Bioinformatics5



Text

SELECT ?name (COUNT(?protein) as ?size)WHERE{ { ?protein :enzyme ?name. ?name rdfs:subClassOf enzyme:1.-.-.- } UNION { ?protein :enzyme ?name. ?name rdfs:subClassOf enzyme:2.-.-.- } ...}GROUP BY ?name ORDER BY ?name


http://beta.sparql.uniprot.org/sparql?query=PREFIX%20:%3Chttp://purl.uniprot.org/core/%3E%20PREFIX%20rdfs:%3Chttp://www.w3.org/2000/01/rdf-schema%23%3E%20%20SELECT%20?name%20(COUNT(?protein)%20as%20?size)%20%20WHERE%20%7B%20%7B%20?protein%20%3Chttp://purl.uniprot.org/core/enzyme%3E%20?name.%20?name%20rdfs:subClassOf%20%3Chttp://purl.uniprot.org/enzyme/1.-.-.-%3E%20%7D%20%20UNION%20%7B%20?protein%20%3Chttp://purl.uniprot.org/core/enzyme%3E%20?name.%20?name%20rdfs:subClassOf%20%3Chttp://purl.uniprot.org/enzyme/2.-.-.-%3E%20%7D%20%20UNION%20%7B%20?protein%20%3Chttp://purl.uniprot.org/core/enzyme%3E%20?name.%20?name%20rdfs:subClassOf%20%3Chttp://purl.uniprot.org/enzyme/3.-.-.-%3E%20%7D%20%20%20UNION%20%7B%20?protein%20%3Chttp://purl.uniprot.org/core/enzyme%3E%20?name.%20?name%20rdfs:subClassOf%20%3Chttp://purl.uniprot.org/enzyme/4.-.-.-%3E%20%7D%20%20UNION%20%7B%20?protein%20%3Chttp://purl.uniprot.org/core/enzyme%3E%20?name.%20?name%20rdfs:subClassOf%20%3Chttp://purl.uniprot.org/enzyme/5.-.-.-%3E%20%7D%20%20UNION%20%7B%20?protein%20%3Chttp://purl.uniprot.org/core/enzyme%3E%20?name.%20?name%20rdfs:subClassOf%20%3Chttp://purl.uniprot.org/enzyme/6.-.-.-%3E%20%7D%20%20%7D%20GROUP%20BY%20?name%20order%20by%20?name



























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 .}


http://data.allie.dbcls.jp/sparql

http://data.allie.dbcls.jp/sparql




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 . })}


http://rdf.farmbio.uu.se/chembl/sparql


http://purl.uniprot.org/uniprot/





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

Questions?

12Monday, September 3, 2012

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Uni protsparqlcloud