Your browser has javascript turned off or blocked. This will lead to some parts of our website to not work properly or at all. Turn on javascript for best performance.

The browser you are using is not supported by this website. All versions of Internet Explorer are no longer supported, either by us or Microsoft (read more here: https://www.microsoft.com/en-us/microsoft-365/windows/end-of-ie-support).

Please use a modern browser to fully experience our website, such as the newest versions of Edge, Chrome, Firefox or Safari etc.

Rashmi Prasad

Rashmi Prasad

Assistant researcher

Rashmi Prasad

BioBuilder as a database development and functional annotation platform for proteins

Author

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

Summary, in English

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.

Publishing year

2004-04-20

Language

English

Publication/Series

BMC Bioinformatics

Volume

5

Document type

Journal article

Publisher

BioMed Central (BMC)

Keywords

  • Computational Biology
  • Database Management Systems
  • Databases, Protein
  • Humans
  • Internet
  • Proteins
  • Software
  • Software Design
  • Journal Article
  • Research Support, Non-U.S. Gov't

Status

Published

ISBN/ISSN/Other

  • ISSN: 1471-2105