Pathway information extracted from 25 years of pathway figures

Kristina Hanspers, Anders Riutta, Martina Summer-Kutmon, Alexander R. Pico*

*Corresponding author for this work

Research output: Contribution to journalArticleAcademicpeer-review

5 Citations (Web of Science)

Abstract

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.

Original languageEnglish
Article number273
Number of pages18
JournalGenome Biology
Volume21
Issue number1
DOIs
Publication statusPublished - 9 Nov 2020

Keywords

  • Pathways
  • Figures
  • Literature
  • OCR
  • Gene sets
  • CELL-PROLIFERATION
  • HIPPO PATHWAY
  • WIKIPATHWAYS
  • APOPTOSIS
  • ENCODES
  • PROTEIN
  • YAP
  • CONJUNCTION
  • DATABASES
  • HOMOLOG

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