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Related Experiment Video

Updated: Jul 18, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

BioNetBuilder: automatic integration of biological networks.

Iliana Avila-Campillo¹, Kevin Drew, John Lin

¹Department of Biology, New York University, New York, NY, USA. iliana_avila-campillo@merck.com

Bioinformatics (Oxford, England)

|December 2, 2006

Summary

BioNetBuilder is an open-source Cytoscape plugin for creating biological networks from multiple databases. It supports 1500 organisms and integrates data from sources like KEGG and GO for broad research applications.

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Area of Science:

Bioinformatics
Computational Biology
Systems Biology

Background:

Biological network construction is crucial for understanding complex biological systems.
Integrating data from diverse public databases presents a significant challenge.

Purpose of the Study:

To develop an open-source Cytoscape plugin, BioNetBuilder, for user-friendly biological network creation.
To facilitate the integration of data from multiple public biological databases.

Main Methods:

Developed a client-server Cytoscape plugin named BioNetBuilder.
Implemented a user-friendly interface for network construction.
Integrated data from databases including DIP, BIND, Prolinks, KEGG, HPRD, The BioGrid, and GO.
Provided a Java Webstart client for platform-independent access.

Main Results:

BioNetBuilder enables the creation of biological networks for approximately 1500 organisms.
The plugin integrates data from a comprehensive list of major biological databases.
Offers a unified and accessible interface to disparate biological data sources.

Conclusions:

BioNetBuilder simplifies and enhances the process of biological network construction.
The tool supports a wide range of organisms and integrates key biological databases.
Provides a valuable resource for researchers in bioinformatics and systems biology.