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. 2004 Apr 20:5:43.
doi: 10.1186/1471-2105-5-43.

BioBuilder as a database development and functional annotation platform for proteins

J Daniel Navarro  1 , Naveen Talreja, Suraj Peri, B M Vrushabendra, B P Rashmi, N Padma, Vineeth Surendranath, Chandra Kiran Jonnalagadda, P S Kousthub, Nandan Deshpande, K Shanker, Akhilesh Pandey
Affiliations

BioBuilder as a database development and functional annotation platform for proteins

J Daniel Navarro et al. BMC Bioinformatics. .

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.

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Figures

Figure 1
Figure 1
A schematic showing BioBuilder in the context of Zope environment. When a client or any other remote database calls Zope, the ZServer processes the request and sends it to ZPublisher. The ZPublisher acts as an object request broker, finding the requested object, and delivering the objects back to the ZServer in their requested form. BioBuilder was built on top of the Zope core application code. Part of the application code is stored in the file system and other parts are in object database (ZODB).
Figure 2
Figure 2
A screenshot showing a web form to enter the attributes for a 'protein' instance. The tabs facilitate entering of features of proteins. When the annotation of a protein is complete, it is submitted for review. An external reviewer can then assess the quality by using the 'Edit Gene' option.
Figure 3
Figure 3
A screenshot showing the 'Interactions' tab of BioBuilder. While reviewing the interactions for a given protein, one can intuitively add or delete interactions. Here protein 1 indicates the protein that is being annotated and protein 2 is the interacting protein. The 'Check' function assists if protein 2 already exists in the database. This feature avoids the redundancy that would arise from entering the same interactions from different proteins. An option to annotate non-protein types of interacting molecules such as drugs, DNA or carbohydrates is also available.
Figure 4
Figure 4
Review system for features in BioBuilder. The central approval system helps in choosing domain and motif shapes from a library of shapes and colors as shown in the screenshot.
See this image and copyright information in PMC

References

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    1. Human Protein Reference Database http://www.hprd.org
    1. Zope Homepage http://www.zope.org
    1. Python Home page http://www.python.org

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