Author-sourced capture of pathway knowledge in computable form using Biofactoid

Jeffrey V. Wong, Max Franz, Metin Can Siper, Dylan Fong, Funda Durupinar, Christian Dallago, Augustin Luna, John Giorgi, Igor Rodchenkov, Ozgun Babur, John A. Bachman, Benjamin M. Gyori, Emek Demir, Gary D. Bader, Chris Sander

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish (US)
Article numbere68292
JournaleLife
Volume10
DOIs
StatePublished - Dec 2021
Externally publishedYes

ASJC Scopus subject areas

  • Neuroscience(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)

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