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

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<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

Human protein reference database as a discovery resource for proteomics

The rapid pace at which genomic and proteomic data is being generated necessitates the development of tools and resources for managing data that allow integration of information from disparate sources. The Human Protein Reference Database (http://www.hprd.org) is a web-based resource based on open source technologies for protein information about several aspects of human proteins including protein–protein interactions, post-translational modifications, enzyme–substrate relationships and disease associations. This information was derived manually by a critical reading of the published literature by expert biologists and through bioinformatics analyses of the protein sequence. This database will assist in biomedical discoveries by serving as a resource of genomic and proteomic information and providing an integrated view of sequence, structure, function and protein networks in health and disease

Development of Human Protein Reference Database as an Initial Platform for Approaching Systems Biology in Humans

Human Protein Reference Database (HPRD) is an object database that integrates a wealth of information relevant to the function of human proteins in health and disease. Data pertaining to thousands of protein-protein interactions, posttranslational modifications, enzyme/substrate relationships, disease associations, tissue expression, and subcellular localization were extracted from the literature for a nonredundant set of 2750 human proteins. Almost all the information was obtained manually by biologists who read and interpreted >300,000 published articles during the annotation process. This database, which has an intuitive query interface allowing easy access to all the features of proteins, was built by using open source technologies and will be freely available at http://www.hprd.org to the academic community. This unified bioinformatics platform will be useful in cataloging and mining the large number of proteomic interactions and alterations that will be discovered in the postgenomic era