Biological data integration using Semantic Web technologies.

@article{citeulike:2610461, abstract = {Current research in biology heavily depends on the availability and efficient use of information. In order to build new knowledge, various sources of biological data must often be combined. Semantic Web technologies, which provide a common framework allowing data to be shared and reused between applications, can be applied to the management of disseminated biological data. However, due to some specificities of biological data, the application of these technologies to life science constitutes a real challenge. Through a use case of biological data integration, we show in this paper that current Semantic Web technologies start to become mature and can be applied for the development of large applications. However, in order to get the best from these technologies, improvements are needed both at the level of tool performance and knowledge modeling.}, address = {Institute of Developmental Biology and Cancer, CNRS – UMR 6543, University of Nice Sophia-Antipolis, Parc Valrose, 06108 NICE Cedex 2, France.}, author = {Pasquier, C }, citeulike-article-id = {2610461}, comment = {The best tested system, DLDB-OWL, loads the largest dataset in more than 12 h and takes between few milliseconds to more than 5 min to respond to the queries. These results, while encouraging, appear to be quite insufficient to be applied to real biological datasets. RDF serialization of the UniProt database, for example, represents more than 25 GB of data. And this database is only one, amongst numerous other data sources that are used on a daily basis by researchers in biology.}, doi = {http://dx.doi.org/10.1016/j.biochi.2008.02.007}, issn = {0300-9084}, journal = {Biochimie}, keywords = {semantic-web}, month = {February}, posted-at = {2008-07-03 16:39:10}, priority = {2}, title = {Biological data integration using Semantic Web technologies.}, url = {http://dx.doi.org/10.1016/j.biochi.2008.02.007}, year = {2008} }

TY - JOUR ID - citeulike:2610461 L3 - citeulike-article-id:2610461 TI - Biological data integration using Semantic Web technologies. JF - Biochimie AD - Institute of Developmental Biology and Cancer, CNRS – UMR 6543, University of Nice Sophia-Antipolis, Parc Valrose, 06108 NICE Cedex 2, France. SN - 0300-9084 N2 - Current research in biology heavily depends on the availability and efficient use of information. In order to build new knowledge, various sources of biological data must often be combined. Semantic Web technologies, which provide a common framework allowing data to be shared and reused between applications, can be applied to the management of disseminated biological data. However, due to some specificities of biological data, the application of these technologies to life science constitutes a real challenge. Through a use case of biological data integration, we show in this paper that current Semantic Web technologies start to become mature and can be applied for the development of large applications. However, in order to get the best from these technologies, improvements are needed both at the level of tool performance and knowledge modeling. KW - semantic-web N1 - The best tested system, DLDB-OWL, loads the largest dataset in more than 12 h and takes between few milliseconds to more than 5 min to respond to the queries. These results, while encouraging, appear to be quite insufficient to be applied to real biological datasets. RDF serialization of the UniProt database, for example, represents more than 25 GB of data. And this database is only one, amongst numerous other data sources that are used on a daily basis by researchers in biology. AU - Pasquier, C PY - 2008/02/21/ UR - http://dx.doi.org/10.1016/j.biochi.2008.02.007 ER -