- From: François Belleau <francoisbelleau@yahoo.ca>
- Date: Thu, 2 Nov 2006 06:42:37 -0800 (PST)
- 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 http://sourceforge.net/projects/bio2rdf Install it, try it (the query builder is the fun part) and let us know what you think of this approach. __________________________________________________ Do You Yahoo!? En finir avec le spam? Yahoo! Courriel vous offre la meilleure protection possible contre les messages non nollicités http://mail.yahoo.ca Yahoo! Courriel
Received on Thursday, 2 November 2006 19:09:39 UTC