Bio2RDF: Towards a mashup to build bioinformatics knowledge systems.

@article{citeulike:2794985, 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.}, address = {Centre de Recherche du CHUL, Universit\'{e} Laval, 2705 Boulevard Laurier, Que., Canada G1V 4G2.}, author = {Belleau, François and Nolin, Marc-Alexandre A. and Tourigny, Nicole and Rigault, Philippe and Morissette, Jean }, citeulike-article-id = {2794985}, doi = {10.1016/j.jbi.2008.03.004}, issn = {1532-0480}, journal = {Journal of biomedical informatics}, keywords = {mashup}, month = {March}, posted-at = {2008-05-16 04:10:57}, priority = {2}, title = {Bio2RDF: Towards a mashup to build bioinformatics knowledge systems.}, url = {http://dx.doi.org/10.1016/j.jbi.2008.03.004}, year = {2008} }

TY - JOUR ID - citeulike:2794985 L3 - citeulike-article-id:2794985 TI - Bio2RDF: Towards a mashup to build bioinformatics knowledge systems. JF - Journal of biomedical informatics AD - Centre de Recherche du CHUL, Université Laval, 2705 Boulevard Laurier, Que., Canada G1V 4G2. SN - 1532-0480 N2 - 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. KW - mashup AU - Belleau, François AU - Nolin, Marc-Alexandre AU - Tourigny, Nicole AU - Rigault, Philippe AU - Morissette, Jean PY - 2008/03/21/ UR - http://dx.doi.org/10.1016/j.jbi.2008.03.004 ER -