Pathway information extracted from 25 years of pathway figures

2020/11/09 by Kristina Hanspers, Anders Riutta, Martina Kutmon +1 · 1 voice
Biochemistry, Genetics and Molecular Biology · #Hippo pathway signaling and YAP/TAZ #Biomedical Text Mining and Ontologies #Cancer-related gene regulation

paper · pdf · doi:10.1186/s13059-020-02181-2

openalex publication_date 2020/11/09 · openalex created_date 2025/10/10 · openalex updated_date 2026/08/01

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.

Citations

• Inactivation of YAP oncoprotein by the Hippo pathway is involved in cell contact inhibition and tissue growth control
• The FAIR Guiding Principles for scientific data management and stewardship
• The advantages of the Matthews correlation coefficient (MCC) over F1 score and accuracy in binary classification evaluation

Discussions

• HOW did I miss this article???❤️ ...Oh It was published in 2020 lol doi.org/10.1186/s130... [bsky, 0 points, 0 comments]