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Bioinformatics Vol. 18 no. 12 2002
Pages 1666-1672
© 2002 Oxford University Press

PFDB: a generic protein family database integrating the CATH domain structure database with sequence based protein family resources

Adrian J. Shepherd 1,2,*, Nigel J. Martin 2, Roger G. Johnson 2, Paul Kellam 3 and Christine A. Orengo 1

1 Department of Biochemistry and Molecular Biology, University College, London, Gower Street, London WC1E 6BT
2 School of Computer Science and Information Systems, Birkbeck College, Malet Street, London WC1E 7HX
3 Wohl Virion Centre, Department of Immunology and Molecular Pathology, Windeyer Institute of Medical Sciences, 46 Cleveland Street, London W1P 6DB, UK

Received on December 21, 2001 ; revised on May 8, 2002 ; accepted on May 16, 2002

Motivation: The PFDB (Protein Family Database) is a new database designed to integrate protein family-related data with relevant functional and genomic data. It currently manages biological data for three projects—the CATH protein domain database (Orengo et al., 1997; Pearl et al., 2001), the VIDA virus domains database (Albà et al., 2001) and the Gene3D database (Buchan et al., 2001). The PFDB has been designed to accommodate protein families identified by a variety of sequence based or structure based protocols and provides a generic resource for biological research by enabling mapping between different protein families and diverse biochemical and genetic data, including complete genomes.

Results: A characteristic feature of the PFDB is that it has a number of meta-level entities (for example aggregation, collection and inclusion) represented as base tables in the final design. The explicit representation of relationships at the meta-level has a number of advantages, including flexibility—both in terms of the range of queries that can be formulated and the ability to integrate new biological entities within the existing design. A potential drawback with this approach—poor performance caused by the number of joins across meta-level tables—is avoided by implementing the PFDB with materialized views using the mature relational database technology of Oracle 8i. The resultant database is both fast and flexible.

This paper presents the principles on which the database has been designed and implemented, and describes the current status of the database and query facilities supported.

Availability: http://bsmsn01.biochem.ucl.ac.uk/

* To whom correspondence should be addressed.


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