Tabulator and Bio2RDF sparql point a new integrated way to surf genomic knowledge

Try the Tabulator generic data browser to surf the 2 billions triples from Bio2RDF sparql points network. Install the FireFox plugin and strart from here :

http://bio2rdf.org/demo

Semantic Web Challenge 2008 participation

The Bio2RDF team is presenting a demo at the Semantic Web Challenge 2008.

http://challenge.semanticweb.org/

Good luck to Marc-Alexandre, Michel and Peter and all the others team member.

The paper is available here.

Bio2RDF Network Of Linked Data

Bio2RDF OWL ontology finaly available

This is the new OWL ontology file description of Bio2RDF project. It is a rough description of most types and predicates in the new Bio2RDF network of sparql graph.

http://bio2rdf.org/bio2rdf-2008.owl

A nice way to discover it is by using Protege tool and the Ontoviz plugin.

Here is what 2 billions triples from 40 datasources looks like :

2,3 Billions triples made available by Bio2RDF 27 SPARQL endpoints

27 public SPARQL endpoints build with a Virtuoso server are made available to the scientific community. Enjoy.

The list of databases is available here :

http://www.freebase.com/view/user/bio2rdf/public/sparql

For example the followings SPARQL endpoints offer a complete copy of the corresponding databases :

http://biocyc.bio2rdf.org/sparql
http://kegg.bio2rdf.org/sparql
http://geneid.bio2rdf.org/sparql
http://go.bio2rdf.org/sparql
http://iproclass.bio2rdf.org/sparql
http://mesh.bio2rdf.org/sparql
http://obo.bio2rdf.org/sparql
http://reactome.bio2rdf.org/sparql
http://uniprot.bio2rdf.org/sparql

Bio2RDF project's litterature review

Those links brings you to the actual Bio2RDF publications available.

The presentation are on SlideShare.

Bio2RDF: Towards a mashup to build bioinformatics knowledge systems published in Journal of Biomedical Informatics. Its pubmed entry pubmed:18472304.

The initial version presented at WWW2007 HCLS Workshop.

Bio2RDF : A Semantic Web Atlas of Post Genomic Knowledge about Human and Mouse part of Data Integration in the Life Sciences 5th International Workshop, DILS 2008, Evry, France, June 25-27, 2008.

And a look in Google Scholar for citations.

The latest knowledge map of the 70 millions triples Atlas of Human and Mouse knowledge

Thanks to Cytoscape software and Marc-Alexandre.

Bio2RDF/Virtuoso demonstration of its SPARQL point will be held at ISMB2008

Technology Track: TT18

How to use Bio2RDF with a Virtuoso Server

Monday, July 21 - 2:45 p.m. - 3:10 p.m.

Room: 701B

Presented by: François Belleau, Centre de Recherche du CHUL (CHUQ), CA

Abstract:
Our vision apply semantic web technology to realize data integration in bioinformatics. In this demo we show how to use Virtuoso server to store Bio2RDF linked data. We also demonstrate how millions of triples from 30 different data providers, can be queried with SPARQL to answer question.

Bio2RDF-ISMB2008

view presentation (tags: bioinfomatics virtuoso ismb bio2rdf)

Presentation invitation: http://www.iscb.org/uploaded/css/25/4095.pdf

http://www.iscb.org/ismb2008/programwebconf.php