Bio2RDF Should we do it ?
Bio2RDF should we do it
Jun 30, 2015
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.
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
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