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Bioinformatics. 2005 Apr 15;21(8):1685-92. Epub 2004 Nov 25.

Constructing ontology-driven protein family databases.

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  • 1School of Biological Sciences, Michael Smith Building, University of Manchester, Oxford Road, Manchester, M13 9PT, UK.



Protein family databases provide a central focus for scientific communities as well as providing useful resources to aide research. However, such resources require constant curation and often become outdated and discontinued. We have developed an ontology-driven system for capturing and managing protein family data that addresses the problems of maintenance and sustainability.


Using protein phosphatases and ABC transporters as model protein families, we constructed two protein family database resources around a central DAML+OIL ontology. Each resource contains specialist information about each protein family, providing specialized domain-specific resources based on the same template structure. The formal structure, combined with the extraction of biological data using GO terms, allows for automated update strategies. Despite the functional differences between the two protein families, the ontology model was equally applicable to both, demonstrating the generic nature of the system.


The protein phosphatase resource, PhosphaBase, is freely available on the internet ( The DAML+OIL ontology for the protein phosphatases and the ABC transporters is available on request from the authors.


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