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Bio2RDF to go, rdfizer for bioinformatic using Sesame is made available on sourceforge

From: François Belleau <francoisbelleau@yahoo.ca>
Date: Thu, 2 Nov 2006 06:42:37 -0800 (PST)
Message-ID: <20061102144238.78430.qmail@web56602.mail.re3.yahoo.com>
To: public-semweb-lifesci@w3.org

How to RDFize bioinformatics databases: the Bio2RDF’s recipe 

The integration of bioinformatics knowledge can be achieved through the inherent aggregate 
capabilities of the Semantic web technologies based on the use of RDF. We all know that.  One of the primary objectives of the BIORDF group is to explore the effectiveness of the currents tools for making data available as 
RDF. Bio2RDF project (http://bio2rdf.org in construction), a new knowledge atlas for human and mouse, has also the 
same goal. 

In order to make the bioinformatics Semantic web available to life science scientists, the first 
mandatory step is to convert bioinformatics databases to RDF. With hundreds of bioinformatics 
databases publicly available on the web, the effort to convert even part of it will be a long and hard 
task. What should be a fast and easy method to convert raw data from different databases ? We have 
found that using traditional tool like the JSP technology with JSTL taglib package is a fast way to 
produce RDF document from SQL databases, HTML pages, tabulated and formatted text file, and 
finally, XML or RDF documents. 

Once converted to RDF, documents are stored in a Sesame repository where the knowledge can be 
queried using SeRQL queries. Other tools of the Semantic web community such as Protege, Semantic 
bank and Welkin as well as the recent lsidBrowser can then be used to browse, transform, edit of draw 
a knowledge graph. 

This first version of Bio2RDF that can be installed locally under a Tomcat server.  It shows how we converted NCBI’s OMIM, GeneID, GENBANK and 
PubMed documents from XML to RDF. UniProt text format to RDF and PDB XML is also supported. 

The bio2rdf.war package and the source code of the JSP RDFizer with a functional Sesame server version 1.2.5 is made available at the following web site 


Install it, try it (the query builder is the fun part) and let us know what you think of this approach.

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Received on Thursday, 2 November 2006 19:09:39 UTC

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