E Shoop1, K A Silverstein, J E Johnson, E F Retzel. 1. Computational Biology Centers, Academic Health Center, University of Minnesota, Mayo Mail Code 43, 420 Delaware St SE, Minneapolis, MN 55455-0312, USA.
Abstract
MOTIVATION: Protein sequence and family data is accumulating at such a rapid rate that state-of-the-art databases and interface tools are required to aid curators with their classifications. We have designed such a system, MetaFam, to facilitate the comparison and integration of public protein sequence and family data. This paper presents the global schema, integration issues, and query capabilities of MetaFam. RESULTS: MetaFam is an integrated data warehouse of information about protein families and their sequences. This data has been collected into a consistent global schema, and stored in an Oracle relational database. The warehouse implementation allows for quick removal of outdated data sets. In addition to the relational implementation of the primary schema, we have developed several derived tables that enable efficient access from data visualization and exploration tools. Through a series of straightforward SQL queries, we demonstrate the usefulness of this data warehouse for comparing protein family classifications and for functional assignment of new sequences.
MOTIVATION: Protein sequence and family data is accumulating at such a rapid rate that state-of-the-art databases and interface tools are required to aid curators with their classifications. We have designed such a system, MetaFam, to facilitate the comparison and integration of public protein sequence and family data. This paper presents the global schema, integration issues, and query capabilities of MetaFam. RESULTS: MetaFam is an integrated data warehouse of information about protein families and their sequences. This data has been collected into a consistent global schema, and stored in an Oracle relational database. The warehouse implementation allows for quick removal of outdated data sets. In addition to the relational implementation of the primary schema, we have developed several derived tables that enable efficient access from data visualization and exploration tools. Through a series of straightforward SQL queries, we demonstrate the usefulness of this data warehouse for comparing protein family classifications and for functional assignment of new sequences.
Authors: K A Silverstein; E Shoop; J E Johnson; A Kilian; J L Freeman; T M Kunau; I A Awad; M Mayer; E F Retzel Journal: Nucleic Acids Res Date: 2001-01-01 Impact factor: 16.971
Authors: John Drakos; Marina Karakantza; Nicholas C Zoumbos; John Lakoumentas; George C Nikiforidis; George C Sakellaropoulos Journal: BMC Bioinformatics Date: 2008-02-14 Impact factor: 3.169
Authors: Lila O Vodkin; Anupama Khanna; Robin Shealy; Steven J Clough; Delkin Orlando Gonzalez; Reena Philip; Gracia Zabala; Françoise Thibaud-Nissen; Mark Sidarous; Martina V Strömvik; Elizabeth Shoop; Christina Schmidt; Ernest Retzel; John Erpelding; Randy C Shoemaker; Alicia M Rodriguez-Huete; Joseph C Polacco; Virginia Coryell; Paul Keim; George Gong; Lei Liu; Jose Pardinas; Peter Schweitzer Journal: BMC Genomics Date: 2004-09-29 Impact factor: 3.969