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bioRxiv · 10.1101/2024.12.04.626523

Yeast Knowledge Graphs Database for Exploring Saccharomyces cerevisiae and Schizosaccharomyces pombe

Kumar, M. R.·Arulprakasam, K. R.·Kutevska, A.-N.·Mutwil, M.·Thibault, G.
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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 OpenAIs 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. HIGHLIGHTSO_LIGenerated Yeast Knowledge Graphs from full-text research articles. C_LIO_LIAnalyzed over 90,000 publications for Saccharomyces and Schizosaccharomyces species. C_LIO_LIExtracted millions of relationships using GPT-based natural language processing. C_LIO_LIYeast Knowledge Graphs accessible through interactive web platforms and APIs. C_LIO_LIAdvanced tool enabling insights into gene networks and functional interactions. C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=76 SRC="FIGDIR/small/626523v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@15afd5corg.highwire.dtl.DTLVardef@afa4bcorg.highwire.dtl.DTLVardef@16858f2org.highwire.dtl.DTLVardef@1a7a19f_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Kumar, M. R., Arulprakasam, K. R., Kutevska, A.-N., Mutwil, M., Thibault, G.. 2024-12-09. Yeast Knowledge Graphs Database for Exploring Saccharomyces cerevisiae and Schizosaccharomyces pombe. https://doi.org/10.1101/2024.12.04.626523

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