Bio2RDF linked data about Human and Mouse genome

François Belleau (Bio2RDF project)Kingsley Idehen (OpenLink Software)

Bioinformatics creepy world of data

from Carole Goble presentation at ISWC2005Using the Semantic Web for e-Science: inspiration, incubation, irritationhttp://iswc2005.semanticweb.org/keynoteabstracts.html

http://bio2rdf.org● Bio2RDF project goal is to make as much

boinformatics data available to the scientific community in semantic web RDF format.

● The main service of Bio2RDF server is to give access to millions of well formed RDF document, extracted from public databases, with normalized URI identified by a derefencable URL.

● Our vision is to use the semantic web paradigm to realize data integration in bioinformatics.

HTML document about Paget disease

HTML to RDF conversion : the art of rdfizing

http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=602080

http://bio2rdf.org/omim:602080

Paget page seen with Tabulator

Bio2RDF URI syntax● http://bio2rdf.org/public_namespace:private_id● For example :

– http://bio2rdf.org/omim:602080– http://bio2rdf.org/go:0032283– http://bio2rdf.org/geneid:15275

● #1 : URI are normalized and dereferencable● #2 : Authoritative public namespace are used● #3 : Mandatory predicates are used● #4 : Resource predicate are prefixed with an "x"● #5 : Blank nodes are forbidden● #6 : RDFizer program are made available

according to the GNU licence for open source● #7 : Deferenceable ontologies

Banff Manifesto rules of thumb used to design RDF document from existing web page

So what, just another look.

Not really, with Virtuoso if you can browse RDF from derefencable URI,

you can query the web with SPARQL !

A first query

Bio2RDF semantic mashup of 65 millions triples was build from 30 differents sources, each node is

a bioinformatic public database

Let's ask this 65 millions nodes graph a real question :

Which caracteristics of protein were assigned to genes involved in Paget disease ?

● Three databases are needed to answer this question :● http://www.ncbi.nlm.nih.gov/sites/entrez?db=omim● http://www.pir.uniprot.org/● http://www.geneontology.org/

The SPARQL query submitted to Virtuoso

SELECT ?lab1, ?sub, ?lab3WHERE {<http://bio2rdf.org/omim:602080>

<http://bio2rdf.org/bio2rdf#xGeneticDisorder> ?omim .?omim <http://www.w3.org/2002/07/owl#sameAs> ?mim .?omim <http://www.w3.org/2000/01/rdf-schema#label> ?lab1 .?sub ?p ?mim .?sub <http://www.w3.org/2000/01/rdf-schema#label> ?lab2 .?sub <http://bio2rdf.org/uniprot:classifiedWith> ?clas .?clas <http://www.w3.org/2000/01/rdf-schema#label> ?lab3 .}

This knowledge map represents links that could have been visited by the last query.

Results are almost instantaneous.

Try it ...● We invite you to discover the potential of

bioinformatics linked data queried with SPARQL using Virtuoso.

● Install your own copy of Virtuoso server and download our Bio2RDF data about human and mouse genome.

Thank you● Virtuoso Open-Source Edition

– http://virtuoso.openlinksw.com/wiki/main/● Bio2RDF web site

– http://www.bio2rdf.org/● Bio2RDF download page

– http://www.bio2rdf.org/download– http://sourceforge.net/projects/bio2rdf/