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BioBuilder as a database development and functional annotation platform for proteins

Navarro, J Daniel; Talreja, Naveen; Peri, Suraj; Vrushabendra, B M; Rashmi, BP LU ; Padma, N; Surendranath, Vineeth; Jonnalagadda, Chandra Kiran; Kousthub, P S and Deshpande, Nandan, et al. (2004) In BMC Bioinformatics 5.
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... (More)

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.

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type
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publication status
published
keywords
Computational Biology, Database Management Systems, Databases, Protein, Humans, Internet, Proteins, Software, Software Design, Journal Article, Research Support, Non-U.S. Gov't
in
BMC Bioinformatics
volume
5
publisher
BioMed Central
external identifiers
  • scopus:2942576052
ISSN
1471-2105
DOI
10.1186/1471-2105-5-43
language
English
LU publication?
no
id
7399b085-fdbb-462c-9499-f96c56241989
date added to LUP
2017-06-16 09:47:44
date last changed
2017-06-18 05:07:05
@article{7399b085-fdbb-462c-9499-f96c56241989,
  abstract     = {<p>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.</p><p>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.</p><p>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.</p>},
  articleno    = {43},
  author       = {Navarro, J Daniel and Talreja, Naveen and Peri, Suraj and Vrushabendra, B M and Rashmi, BP and Padma, N and Surendranath, Vineeth and Jonnalagadda, Chandra Kiran and Kousthub, P S and Deshpande, Nandan and Shanker, K and Pandey, Akhilesh},
  issn         = {1471-2105},
  keyword      = {Computational Biology,Database Management Systems,Databases, Protein,Humans,Internet,Proteins,Software,Software Design,Journal Article,Research Support, Non-U.S. Gov't},
  language     = {eng},
  month        = {04},
  publisher    = {BioMed Central},
  series       = {BMC Bioinformatics},
  title        = {BioBuilder as a database development and functional annotation platform for proteins},
  url          = {http://dx.doi.org/10.1186/1471-2105-5-43},
  volume       = {5},
  year         = {2004},
}