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

Ethnomedical survey of plants used by the Orang Asli in Kampung Bawong, Perak, West Malaysia

<p>Abstract</p> <p>Background</p> <p>A qualitative ethnomedical survey was carried out among a local Orang Asli tribe to gather information on the use of medicinal plants in the region of Kampung Bawong, Perak of West Malaysia in order to evaluate the potential medicinal uses of local plants used in curing different diseases and illnesses.</p> <p>Methods</p> <p>Sixteen informants ranging in age from 35 to 65 years were interviewed. A total of 62 species of plants used by Orang Asli are described in this study based on field surveys and direct face to face communication. These plants belonged to 36 families and are used to treat a wide range of discomforts and diseases.</p> <p>Results</p> <p>The results of this study showed that majority of the Orang Asli, of Kampung Bawong are still dependent on local plants as their primary source of medication. As the first ethnomedical study in this area, publishing this work is expected to open up more studies to identify and assess the pharmacological and toxicological action of the plants from this region.</p> <p>Conclusions</p> <p>Preservation and recording of ethnobotanical and ethnomedical uses of traditional medicinal plants is an indispensable obligation for sustaining the medicinal and cultural resource of mankind. Extensive research on such traditional plants is of prime importance to scientifically validate their ethnomedical claims.</p

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