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BioBrowsing: Making the Most of the Data Available in Entrez

Sarah Cohen-Boulakia 1, 2, * Kevin Masini 1
* Corresponding author
2 AMIB - Algorithms and Models for Integrative Biology
LIX - Laboratoire d'informatique de l'École polytechnique [Palaiseau], LRI - Laboratoire de Recherche en Informatique, UP11 - Université Paris-Sud - Paris 11, Inria Saclay - Ile de France
Abstract : One of the most popular ways to access public biological data is using portals, like Entrez (NCBI) which allows users to navigate through the data of 34 major biological sources, following cross-references. In this process, data entries are inspected one after the other and cross-references are followed. This navigational process may be time-consuming and may not be easily reproduced from one entry to another. Most importantly, only a few sources are initially queried, biologists do not exploit all the richness of the data provided by Entrez, and in particular they may not explore alternative source paths that provide complementary information. In this paper, we introduce BioBrowsing, a tool providing scientists with access to the data obtained when all the combinations between NCBI sources have been followed. Querying is done on-the-fly (no warehousing). As new sources and links between sources appear in Entrez, BioBrowsing has a module able to update automatically the schema used by its query engine. Finally, BioBrowsing makes it possible for users to define profiles as a way of focusing the results on users specific interests.
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Contributor : Sarah Cohen-Boulakia Connect in order to contact the contributor
Submitted on : Thursday, December 2, 2010 - 1:31:16 PM
Last modification on : Thursday, July 8, 2021 - 3:48:47 AM


  • HAL Id : inria-00542344, version 1



Sarah Cohen-Boulakia, Kevin Masini. BioBrowsing: Making the Most of the Data Available in Entrez. 21st Int. Conf. in Scientific and Statistical Database Management (SSDBM), LNCS 5566, Springer, Jun 2009, New Orlean, United States. pp.283-291. ⟨inria-00542344⟩



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