Bio2RDF should we do it

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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.

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)

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

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

Thanksgiving Day was first celebrated in the American Plymouth colony in 1621, when Governor William Bradford proclaimed a day of thanksgiving and prayer. Before that, a Native American named Squanto taught the pilgrims how to plant corn and how to survive in the new land. When the harvest came, it was celebrated by all the colonists and neighboring Native Americans who had helped them. Gradually it became a common annual custom to celebrate thanksgiving after the harvest. While turkeys were known to the colonists and Indians, we don't have any proof they were served at the first thanksgiving. But they were added later as part of the celebration that continues until today. Long before that, the Isrealites has a similar feast day to Thank God for what he had done for them. It was called the Feast of Tabernacles and can be found in Leviticus 23:33-44; Numbers 29:12-39; Deuteronomy 16:13. The games in this lesson use feathers, not only because they are associated with Thanksgiving, but also because there are places in the Bible where God is compared to a protective bird who covers us with his wings.

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