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

E. Shoop, K. A.T. Silverstein, J. E. Johnson, E. F. Retzel

Research output: Contribution to journalArticle

9 Scopus citations

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 The warehouse implementation allows for quick removal of outdated data sets.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

Original languageEnglish (US)
Pages (from-to)262-271
Number of pages10
JournalBioinformatics
Volume17
Issue number3
DOIs
StatePublished - Jan 1 2001

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