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BioBuilder as a database development and functional annotation platform for proteins

J Daniel Navarro12, Naveen Talreja4, Suraj Peri13, BM Vrushabendra4, BP Rashmi4, N Padma4, Vineeth Surendranath4, Chandra Kiran Jonnalagadda4, PS Kousthub4, Nandan Deshpande4, K Shanker4 and Akhilesh Pandey1*

  • * Corresponding author: Akhilesh Pandey

  • † Equal contributors

Author Affiliations

1 McKusick-Nathans Institute of Genetic Medicine and the Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, U.S.A

2 Departamento de Automática y Computación, Área de Ciencias de la Computación e Inteligencia Artificial, Universidad Pública de Navarra, 31006, Pamplona, Spain

3 Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark

4 Institute of Bioinformatics, Discoverer 7th Floor, International Technology Park Ltd., Bangalore 560 066, India

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BMC Bioinformatics 2004, 5:43  doi:10.1186/1471-2105-5-43

Published: 20 April 2004



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.


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 webcite, 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.


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.