This document discusses the Bio2RDF project, which aims to convert life sciences data from various sources and formats like XML, KGML, and CSV into the RDF format. It notes that there are too many knowledge sources in different formats for scientists to easily integrate. The document proposes adopting RDF and converting popular knowledge sources into RDF as a community effort through the Bio2RDF project. It describes RDF and the Protege ontology editor, showing examples of loading ontologies and pathways converted to RDF into Protege for browsing and visualization. The Bio2RDF website is presented as a central repository for RDF conversion tools and files.

1. Bio2RDF
Should we do it ?

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

3. 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

4. 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)

5. 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)

6. GO definition in RDF

7. 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

8. 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

9. Go.rdf in Protege

10. Go.rdf in Protégé
Full text search

11. Go.rdf in Protégé
Hierarchical browsing

12. Go.rdf in Protégé
DAG graph

13. Citratecycle.kgml.rdf from Kegg
with TouchGraph visualisation

14. Knowledge integration :
Kegg+GO+Affymetrix+EntrezGene

15. 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

16. Bio2RDF.sourceforge.net
Who is in ?
FrancoisBelleau@yahoo.ca