Bio2RDF
Should we do it ?

Bio2RDF Architecture
XML KGML CSV
RDF
Bio*2RDF
converter
Sourceforge side
Ready to use files available with CVS
User side

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 Protégé
Full text search

Go.rdf in Protégé
Hierarchical browsing

Go.rdf in Protégé
DAG 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