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Bioinformatics Vol. 17 no. 3 2001
Pages 262-271
© 2001 Oxford University Press

Original Paper

MetaFam: a unified classification of protein families. II. Schema and query capabilities

Elizabeth Shoop *, Kevin A. T. Silverstein , James E. Johnson and Ernest F. Retzel *

Computational Biology Centers, Academic Health Center, University of Minnesota, Mayo Mail Code 43, 420 Delaware St SE, Minneapolis, MN 55455-0312, USA

Received on May 31, 2000 ; revised on September 22, 2000 ; accepted on November 23, 2000

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 The warehouse implementation allows for quick removal of outdated data sets.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.

Availability: Access to the MetaFam database is provided through a Java applet called MetaFamView, which can be run from the MetaFam web site at http://www.metafam.ahc.umn.edu/. Access to the relational data via named Oracle accounts can be arranged with the authors. Arrangements can also be made to obtain the data in Oracle ‘export dump’ format.

Contact: metafam{at}ahc.umn.edu

Supplementary information: The complete relational schema, integration scripts, and analysis queries are available from the authors.

* To whom correspondence should be addressed.


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