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BMC Bioinformatics. 2004 Apr 20;5:43.

BioBuilder as a database development and functional annotation platform for proteins.

Author information

1
McKusick-Nathans Institute of Genetic Medicine and the Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA. dnavarro@jhmi.edu

Abstract

BACKGROUND:

The explosion in biological information creates the need for databases that are easy to develop, easy to maintain and can be easily manipulated by annotators who are most likely to be biologists. However, deployment of scalable and extensible databases is not an easy task and generally requires substantial expertise in database development.

RESULTS:

BioBuilder is a Zope-based software tool that was developed to facilitate intuitive creation of protein databases. Protein data can be entered and annotated through web forms along with the flexibility to add customized annotation features to protein entries. A built-in review system permits a global team of scientists to coordinate their annotation efforts. We have already used BioBuilder to develop Human Protein Reference Database http://www.hprd.org, a comprehensive annotated repository of the human proteome. The data can be exported in the extensible markup language (XML) format, which is rapidly becoming as the standard format for data exchange.

CONCLUSIONS:

As the proteomic data for several organisms begins to accumulate, BioBuilder will prove to be an invaluable platform for functional annotation and development of customizable protein centric databases. BioBuilder is open source and is available under the terms of LGPL.

PMID:
15099404
PMCID:
PMC406495
DOI:
10.1186/1471-2105-5-43
[Indexed for MEDLINE]
Free PMC Article

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