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A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

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Published on: February 8, 2017

PathBuilder--open source software for annotating and developing pathway resources.

Kumaran Kandasamy1, Shivakumar Keerthikumar, Rajesh Raju

  • 1Institute of Bioinformatics, International Tech Park, Bangalore 560066, India.

Bioinformatics (Oxford, England)
|July 25, 2009
PubMed
Summary
This summary is machine-generated.

PathBuilder is a new open-source web application for annotating biological signaling pathways and creating pathway resources. It facilitates manual and automated data import, visualization, and data exchange for pathway datasets.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Systems Biology

Background:

  • Developing robust tools for biological pathway annotation is crucial for understanding cellular mechanisms.
  • Existing resources often lack comprehensive annotation capabilities or user-friendly interfaces.

Purpose of the Study:

  • To introduce PathBuilder, an open-source web application for annotating biological signaling pathways.
  • To enable the creation of dynamic, web-based pathway resources.

Main Methods:

  • Developed PathBuilder as a platform-independent, open-source web application.
  • Implemented features for manual and automated annotation of molecular events (e.g., protein-protein interactions, enzyme-substrate relationships).
  • Integrated modules for data validation, pathway visualization, and data import/export in standard formats.

Main Results:

  • PathBuilder allows for detailed annotation of molecular events within signaling pathways.
  • The application supports automated data import from external databases and other pathway resources.
  • Features include data validation, pathway visualization, and an API for data retrieval.

Conclusions:

  • PathBuilder provides a flexible and comprehensive solution for biological pathway annotation and resource creation.
  • Its open-source nature and diverse features promote collaborative research and data sharing in systems biology.