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

Motivation: Protein sequence and family data is accumulating at such a rapi d rate that state-of-the-art databases and interface tools are required to aid curators with their classifications. We have designed such a system, Me taFam, to facilitate the comparison and integration of public protein seque nce and family data, This paper presents the global schema, integration iss ues, and query capabilities of MetaFam. Results: MetaFam is an integrated data warehouse of information about prote in families and their sequences. This data has been collected into a consis tent global schema, and stored in an Oracle relational database. The wareho use implementation allows for quick removal of outdated data sets, in addit ion to the relational implementation of the primary schema, we have develop ed several derived tables that enable efficient access from data visualizat ion 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 app let 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 t o obtain the data in Oracle 'export dump' format. Supplementary information: The complete relational schema, integration scri pts, and analysis queries are available from the authors.