BioBrowsing: Making the Most of the Data Available in Entrez

  • Authors:

  • Sarah Cohen-Boulakia;Kevin Masini

  • Affiliations:

  • Laboratoire de Recherche en Informatique (LRI), Université Paris-Sud XI, Cedex Orsay, France 91405;Laboratoire de Recherche en Informatique (LRI), Université Paris-Sud XI, Cedex Orsay, France 91405

  • Venue:
  • SSDBM 2009 Proceedings of the 21st International Conference on Scientific and Statistical Database Management
  • Year:
  • 2009

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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 to additional data available in other sources may be 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. Availability: http://bioguide-project.net/biobrowsing