BioBuilder as a database development and functional annotation platform for proteins

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 , 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

BioBuilder as a database development and functional annotation platform for proteins

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.</p

BioBuilder as a database development and functional annotation platform for proteins-2

<p><b>Copyright information:</b></p><p>Taken from "BioBuilder as a database development and functional annotation platform for proteins"</p><p>BMC Bioinformatics 2004;5():43-43.</p><p>Published online 20 Apr 2004</p><p>PMCID:PMC406495.</p><p>Copyright © 2004 Navarro et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL.</p>te 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

BioBuilder as a database development and functional annotation platform for proteins-0

<p><b>Copyright information:</b></p><p>Taken from "BioBuilder as a database development and functional annotation platform for proteins"</p><p>BMC Bioinformatics 2004;5():43-43.</p><p>Published online 20 Apr 2004</p><p>PMCID:PMC406495.</p><p>Copyright © 2004 Navarro et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL.</p>est 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)

BioBuilder as a database development and functional annotation platform for proteins-3

<p><b>Copyright information:</b></p><p>Taken from "BioBuilder as a database development and functional annotation platform for proteins"</p><p>BMC Bioinformatics 2004;5():43-43.</p><p>Published online 20 Apr 2004</p><p>PMCID:PMC406495.</p><p>Copyright © 2004 Navarro et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL.</p>of shapes and colors as shown in the screenshot

BioBuilder as a database development and functional annotation platform for proteins-1

<p><b>Copyright information:</b></p><p>Taken from "BioBuilder as a database development and functional annotation platform for proteins"</p><p>BMC Bioinformatics 2004;5():43-43.</p><p>Published online 20 Apr 2004</p><p>PMCID:PMC406495.</p><p>Copyright © 2004 Navarro et al; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL.</p>n is complete, it is submitted for review. An external reviewer can then assess the quality by using the 'Edit Gene' option