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Updated: Oct 11, 2025

A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
Author-sourced capture of pathway knowledge in computable form using Biofactoid
Jeffrey V Wong1, Max Franz1, Metin Can Siper2
1The Donnelly Centre, University of Toronto, Toronto, Canada.
Abstract:
Making the knowledge contained in scientific papers machine-readable and formally computable would allow researchers to take full advantage of this information by enabling integration with other knowledge sources to support data analysis and interpretation. Here we describe Biofactoid, a web-based platform that allows scientists to specify networks of interactions between genes, their products, and chemical compounds, and then translates this information into a representation suitable for computational analysis, search and discovery. We also report the results of a pilot study to encourage the wide adoption of Biofactoid by the scientific community.
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