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BioBuilder as a database development and functional annotation platform for proteins.

J Daniel Navarro1, Naveen Talreja, Suraj Peri

  • 1McKusick-Nathans Institute of Genetic Medicine and the Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA. dnavarro@jhmi.edu

BMC Bioinformatics
|April 22, 2004
PubMed
Summary
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BioBuilder is an open-source software tool that simplifies the creation and maintenance of protein databases for biologists. It enables intuitive data entry, custom annotation, and collaborative review, facilitating proteomic data management.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Proteomics

Background:

  • The rapid growth of biological data necessitates user-friendly database solutions for biologists.
  • Developing scalable and extensible biological databases typically requires significant technical expertise.

Purpose of the Study:

  • To introduce BioBuilder, a Zope-based software tool designed for the intuitive creation of protein databases.
  • To enable biologists to easily develop, maintain, and manipulate protein-centric databases.

Main Methods:

  • Utilizes web forms for intuitive data entry and annotation.
  • Supports customized annotation features for protein entries.
  • Incorporates a built-in review system for global scientific collaboration.

Related Experiment Videos

Main Results:

  • Successfully developed the Human Protein Reference Database (HPRD) using BioBuilder.
  • Facilitates data export in Extensible Markup Language (XML) format for data exchange.
  • Demonstrates ease of use for annotators and database development.

Conclusions:

  • BioBuilder is an invaluable platform for functional annotation and developing customizable protein databases as proteomic data grows.
  • The software is open-source and available under the GNU Lesser General Public License (LGPL).
  • Promotes efficient management and sharing of proteomic information.