Pathway information extracted from 25 years of pathway figures

Genome Biol. 2020 Nov 9;21(1):273. doi: 10.1186/s13059-020-02181-2.


Thousands of pathway diagrams are published each year as static figures inaccessible to computational queries and analyses. Using a combination of machine learning, optical character recognition, and manual curation, we identified 64,643 pathway figures published between 1995 and 2019 and extracted 1,112,551 instances of human genes, comprising 13,464 unique NCBI genes, participating in a wide variety of biological processes. This collection represents an order of magnitude more genes than found in the text of the same papers, and thousands of genes missing from other pathway databases, thus presenting new opportunities for discovery and research.

Keywords: Figures; Gene sets; Literature; OCR; Pathways.

Publication types

  • Research Support, N.I.H., Extramural