BioBuilder as a database development and functional annotation platform for proteins

J. Daniel Navarro, Naveen Talreja, Suraj Peri, B. M. Vrushabendra, B. P. Rashmi, N. Padma, Vineeth Surendranath, Chandra Kiran Jonnalagadda, P. S. Kousthub, Nandan Deshpande, Kalyan Shanker, Akhilesh Pandey

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
Article number43
JournalBMC Bioinformatics
Volume5
DOIs
StatePublished - Apr 20 2004

ASJC Scopus subject areas

  • Medicine(all)
  • Structural Biology
  • Applied Mathematics

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    Navarro, J. D., Talreja, N., Peri, S., Vrushabendra, B. M., Rashmi, B. P., Padma, N., Surendranath, V., Jonnalagadda, C. K., Kousthub, P. S., Deshpande, N., Shanker, K., & Pandey, A. (2004). BioBuilder as a database development and functional annotation platform for proteins. BMC Bioinformatics, 5, [43]. https://doi.org/10.1186/1471-2105-5-43