Bio2RDF should we do it

Bio2RDF

Should we do it ?

Bio2RDF Architecture

Bio*2RDFconverter

KGMLXML CSV

User side

Sourceforge side

RDF

User sideReady to use files available with CVS

The problem

● Too many knowledge sources available for life science scientists

● Too many formats (text, XML, HTML)● New source each day with specialized tool or

web interface● Integration problem recognised by global

community

One early solution

● Semantic web browser (BioDash) are in development - so what can we do in the mean time ?

– Adopt the semantic web format (RDF)– BioPax, Swissprot already offer RDF documents– Select a strong knowledge tool to work with

(Protege)– Convert popular knowledge source to RDF in a

community effort (Bio2RDF)

What is RDF

● Simple XML format from the semantic web initiative of the W3C made of triples

● RDF is the predecessor of OWL● Many tools from the computer science

community already read RDF (Protege)● Inference tools are available (RACER, FACT)

GO definition in RDF

What is Protege

● Mature software to work with knowledge bases and ontologies

● Open source Java application used by 30,000 users community

● Ontology editor with GUI interface● It support RDF, natively● Many specialized plugins

– Visualisation– Import/Export to specialized file format

● Gives the experience of semantic browsing

Protege+RDF demo

● GO ontology in Protege ● BioPAX from the Reactome glycolysis

pathway converted into RDF for visualisation with the TouchGraph plugin

● GO + MGI – An example of merging knowledge

Go.rdf in Protege

Go.rdf in ProtégéFull text search

Go.rdf in ProtégéHierarchical browsing

Go.rdf in ProtégéDAG graph

Citratecycle.kgml.rdf from Kegg with TouchGraph visualisation

Knowledge integration :Kegg+GO+Affymetrix+EntrezGene

Bio2RDF.sourceforge.net

● A central repository for tools to convert bioinformatics data and knowledge bases to RDF format

● A repository of ready to use RDF files for loading in Protege or other semantic tools

● A place for the semantic web life science community to develope and grow

Bio2RDF.sourceforge.net

Who is in ?

FrancoisBelleau@yahoo.ca