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The initial Bio2RDF project description shown at Semantic Web bird of a feather during ISMB2005. Thank to Chistopher Baker, Kei Cheung, Johanne Luciano and Eric Neumann for initial inspiration.
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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
