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

Bio2RDF at DILS2008 on June 27th in Evry (Paris)

The presentation about the lat Bio2RDF paper is planned at DILS2008.

DILS2008 Program

We hope to have the occasion to meet Bio2RDF futur users. See you there.

Here is the presentation :

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http://www.ncbi.nlm.nih.gov/pubmed/18472304 owl:sameAs http://bio2rdf.org/pubmed:18472304

Bo2RDF project is know self-conscious of itself.

http://www.ncbi.nlm.nih.gov/pubmed/18472304

also known as

urn:bm:pubmed:18472304

My deep thanks to my master project supervisor Jean Morissette and Nicole Tourigny, without whom this student project would not have get that far. I would also thank Marc-Alexandre Nolin for his precious collaboration and Philippe Rigault who make his lab essential resources available to the project.

Bio2RDF do SPARQL for the WWW2008 occasion

This is the unofficial presentation of Bio2RDF at the Linked Data on the Web (LDOW2008), thanks to Kingsley Idehen of Open Link software for is support.

You should read is paper Linked Data Spaces & Data Portability.

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65 million triples about Human and Mouse available for download

Bio2RDF project will be presented at the DILS2008 conference in Paris. The selected paper describes the 65 million triples mashup about Human and Mouse post genomic knowledge. 30 datasources have been merged together to build this semantic warehouse. The whole graph can be downloaded in N3 format from this adresse http://bio2rdf.org/download. The full list of datasources is available at the Banff Manifesto site on Freebase.

Bio2RDF first version of its knowledge map

We are using Many Eyes visualization service from IBM to let you explore interactively the knowledge map of Bio2RDF Atlas about Human and Mouse.

Banff Manifesto public namespace list is now available on Freebase

With the activity volume needed to load Banff Manifesto public namespace list on Freebase we are on the hall of fame front page of contributors for the first time.

Freebase editable version

RDF browsable version