Bio2RDF: Towards A Mashup To Build Bioinformatics Knowledge System

With the increasing popularity of the semantic web technology and the ever-growing number of databases in bioinformatics, there is a pressing need to develop mashup systems to integrate bioinformatics knowledge. Bio2RDF is such a system, built from an rdfizer written in JSP, the Sesame open source triplestore technology and an OWL ontology. With Bio2RDF, all documents from public bioinformatics databases, GeneID, OMIM, UniProt, Kegg, Ligand, OBO, PDB and MGI are now made available to the scientific community in RDF format. A total of 140 gigabytes of XML and text data have been converted into 46 million RDF documents in the Bio2RDF repository. Each one is accessible through a unique URL in the form of http://bio2rdf.org/namespace:id or by an LSID. In addition to this service myBio2RDF is an open source application that lets the user drag and drop knowledge from the bioinformatics semantic web into a local Sesame triplestore where it can be further analyzed with SeRQL queries. The Bio2RDF project has successfully applied the use of 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. The Bio2RDF repository of RDF documents can be queried at http://bio2rdf.org. The myBio2RDF application, which is a modified version of Sesame triplestore with rdfizers, can be downloaded at http://sourceforge.net/projects/bio2rdf/. The project's OWL ontology is located at http://bio2rdf.org/bio2rdf-2007-02.owl