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A Web Tool for Generating High Quality Machine-readable Biological Pathways
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Published on: February 8, 2017

Building models using Reactome pathways as templates.

David Croft1

  • 1EMBL Outstation-European Bioinformatics Institute, Cambridge, UK.

Methods in Molecular Biology (Clifton, N.J.)
|May 30, 2013
PubMed
Summary
This summary is machine-generated.

Building biological pathway models is time-consuming. Reactome provides tools to accelerate this process by automatically constructing models from user-provided information, saving researchers significant effort.

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Area of Science:

  • Systems Biology
  • Bioinformatics

Background:

  • Constructing biological models is a complex and time-intensive process.
  • Researchers often consult numerous papers to gather reaction network information.

Purpose of the Study:

  • To introduce tools that expedite the creation of biological models.
  • To demonstrate how Reactome can automate model construction.

Main Methods:

  • Utilizing the Reactome database, which contains extensive pathway information for Homo sapiens and other species.
  • Employing Reactome's tools to extract relevant reactions and layout information.
  • Describing two use cases where Reactome automatically builds models based on essential input.

Main Results:

  • Reactome facilitates the rapid extraction of pathway reactions and associated layout data.
  • Automated model construction is demonstrated through specific use cases.
  • Generated models are output in the Systems Biology Markup Language (SBML-ML) format.

Conclusions:

  • Reactome significantly accelerates the initial stages of biological model development.
  • The database offers valuable tools for researchers building models from scratch.
  • Automated model generation streamlines the workflow for systems biology research.