Yeast Knowledge Graphs Database for Exploring Saccharomyces Cerevisiae and Schizosaccharomyces Pombe: Yeast Knowledge Graphs for Saccharomyces and Pombe

Mani R. Kumar, Karthick Raja Arulprakasam, An Nikol Kutevska, Marek Mutwil*, Guillaume Thibault

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

Biomedical literature contains an extensive wealth of information on gene and protein function across various biological processes and diseases. However, navigating this vast and often restricted-access data can be challenging, making it difficult to extract specific insights efficiently. In this study, we introduce a high-throughput pipeline that leverages OpenAI's Generative Pre-Trained Transformer Model (GPT) to automate the extraction and analysis of gene function information. We applied this approach to 84,427 publications on Saccharomyces cerevisiae and 6,452 publications on Schizosaccharomyces pombe, identifying 3,432,749 relationships for budding yeast and 421,198 relationships for S. pombe. This resulted in a comprehensive, searchable online Knowledge Graph database, available at yeast.connectome.tools and spombe.connectome.tools, which offers users extensive access to various interactions and pathways. Our analysis underscores the power of integrating artificial intelligence with bioinformatics, as demonstrated through key insights into important nodes like Hsp104 and Atg8 proteins. This work not only facilitates efficient data extraction in yeast research but also presents a scalable model for similar studies in other biological systems.

Original languageEnglish
Article number169072
JournalJournal of Molecular Biology
Volume437
Issue number10
DOIs
Publication statusPublished - May 15 2025
Externally publishedYes

Bibliographical note

Publisher Copyright:
© 2025 The Author(s)

ASJC Scopus Subject Areas

  • Biophysics
  • Structural Biology
  • Molecular Biology

Keywords

  • bioinformatics
  • knowledge graph
  • Saccharomyces
  • Schizosaccharomyces
  • yeast

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