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Laying the foundation for a Genomic Rosetta Stone: creating information hubs through the use of consensus identifiers

By Bart Van Brabant, Tanya Gray, Bert Verslyppe, Nikos Kyrpides, Karin Dietrich, Frank Oliver Glockner, James Cole, Ryan Farris, Lynn M. Schriml, Paul De Vos, Bernard De Baets, Dawn Field and Peter Dawyndt

Abstract

Given the growing wealth of downstream information, the integration of molecular and non-molecular data on a given organism has become a major challenge. For micro-organisms, this information now includes a growing collection of sequenced genes and complete genomes, and for communities of organisms it includes metagenomes. Integration of the data is facilitated by the existence of authoritative, community-recognized, consensus identifiers that may form the heart of so-called information knuckles. The Genomic Standards Consortium (GSC) is building a mapping of identifiers across a group of federated databases with the aim to improve navigation across these resources and to enable the integration of their information in the near future. In particular, this is possible because of the existence of INSDC Genome Project Identifiers (GPIDs) and accession numbers, and the ability of the community to define new consensus identifiers such as the culture identifiers used in the StrainInfo.net bioportal. Here we outline (1) the general design of the Genomic Rosetta Stone project, (2) introduce example linkages between key databases (that cover information about genomes, 16S rRNA gene sequences, and microbial biological resource centers), and (3) make an open call for participation in this project providing a vision for its future use.\ud \u

Topics: Biology and Microbiology, Data and Information
Year: 2008
DOI identifier: 10.1089/omi.2008.0020
OAI identifier: oai:nora.nerc.ac.uk:5539
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