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

Elife. 2021 Dec 3;10:e68292. doi: 10.7554/eLife.68292.

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.

Keywords: computational biology; crowdsource; curation tool; genetics; genomics; knowledge base; none; pathway analysis; science forum; systems biology.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Computational Biology / instrumentation
  • Computational Biology / methods*
  • Databases, Factual
  • Genomics / instrumentation
  • Genomics / methods*
  • Pilot Projects