Shepherd, Adrian J. and Martin, Nigel and Johnson, Roger and Kellam, P. and Orengo, C.A. (2002) PFDB: a generic protein family database integrating the CATH domain structure database with sequence based protein family resources. Bioinformatics 18 (12), pp. 1666-1672. ISSN 1367-4803.
Abstract
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.
Metadata
| Item Type: | Article |
|---|---|
| School: | Birkbeck Faculties and Schools > Faculty of Science > School of Natural Sciences Birkbeck Faculties and Schools > Faculty of Science > School of Computing and Mathematical Sciences |
| Research Centres and Institutes: | Bioinformatics, Bloomsbury Centre for (Closed), Structural Molecular Biology, Institute of (ISMB), Birkbeck Knowledge Lab |
| Depositing User: | Administrator |
| Date Deposited: | 15 Aug 2013 10:37 |
| Last Modified: | 09 Aug 2023 12:34 |
| URI: | https://eprints.bbk.ac.uk/id/eprint/8012 |
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