Bio2RDF: Towards a mashup to build bioinformatics knowledge systems

  • Authors:

  • François Belleau;Marc-Alexandre Nolin;Nicole Tourigny;Philippe Rigault;Jean Morissette

  • Affiliations:

  • Centre de Recherche du CHUL, Université Laval, 2705 Boulevard Laurier, Que., Canada G1V 4G2;Centre de Recherche du CHUL, Université Laval, 2705 Boulevard Laurier, Que., Canada G1V 4G2 and Département d'informatique et de génie logiciel, Université Laval, Cité Uni ...;Département d'informatique et de génie logiciel, Université Laval, Cité Universitaire, Que., Canada G1K 7P4;Centre de Recherche du CHUL, Université Laval, 2705 Boulevard Laurier, Que., Canada G1V 4G2;Centre de Recherche du CHUL, Université Laval, 2705 Boulevard Laurier, Que., Canada G1V 4G2 and Département d'anatomie-physiologie, Université Laval, Cité Universitaire, Que., ...

  • Venue:
  • Journal of Biomedical Informatics
  • Year:
  • 2008

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Abstract

Presently, there are numerous bioinformatics databases available on different websites. Although RDF was proposed as a standard format for the web, these databases are still available in various formats. With the increasing popularity of the semantic web technologies and the ever growing number of databases in bioinformatics, there is a pressing need to develop mashup systems to help the process of bioinformatics knowledge integration. Bio2RDF is such a system, built from rdfizer programs written in JSP, the Sesame open source triplestore technology and an OWL ontology. With Bio2RDF, documents from public bioinformatics databases such as Kegg, PDB, MGI, HGNC and several of NCBI's databases can now be made available in RDF format through a unique URL in the form of http://bio2rdf.org/namespace:id. The Bio2RDF project has successfully applied the semantic web technology to publicly available databases by creating a knowledge space of RDF documents linked together with normalized URIs and sharing a common ontology. Bio2RDF is based on a three-step approach to build mashups of bioinformatics data. The present article details this new approach and illustrates the building of a mashup used to explore the implication of four transcription factor genes in Parkinson's disease. The Bio2RDF repository can be queried at http://bio2rdf.org.