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bioRxiv · 10.1101/2024.08.16.608241

PanKB: An interactive microbial pangenome knowledgebase for research, biotechnological innovation, and knowledge mining

Sun, B.·Pashkova, L.·Pieters, P. A.·Harke, A. S.·Palsson, B. O.·Phaneuf, P. V.
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Abstract

The exponential growth of microbial genome data presents unprecedented opportunities for mining the potential of microorganisms. The burgeoning field of pangenomics offers a framework for extracting insights from this big biological data. Recent advances in microbial pangenomic research have generated substantial data and literature, yielding valuable knowledge across diverse microbial species. PanKB (pankb.org), a knowledgebase designed for microbial pangenomics research and biotechnological applications, was built to capitalize on this wealth of information. PanKB currently includes 51 pangenomes on 8 industrially relevant microbial families, comprising 8, 402 genomes, over 500, 000 genes, and over 7M mutations. To describe this data, PanKB implements four main components: 1) Interactive pangenomic analytics to facilitate exploration, intuition, and potential discoveries; 2) Alleleomic analytics, a pangenomic- scale analysis of variants, providing insights into intra-species sequence variation and potential mutations for applications; 3) A global search function enabling broad and deep investigations across pangenomes to power research and bioengineering workflows; 4) A bibliome of 833 open- access pangenomic papers and an interface with an LLM that can answer in-depth questions using their knowledge. PanKB empowers researchers and bioengineers to harness the full potential of microbial pangenomics and serves as a valuable resource bridging the gap between pangenomic data and practical applications. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC="FIGDIR/small/608241v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@4d3daaorg.highwire.dtl.DTLVardef@10b6d49org.highwire.dtl.DTLVardef@133da4forg.highwire.dtl.DTLVardef@141ae7e_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Sun, B., Pashkova, L., Pieters, P. A., Harke, A. S., Palsson, B. O., Phaneuf, P. V.. 2024-08-19. PanKB: An interactive microbial pangenome knowledgebase for research, biotechnological innovation, and knowledge mining. https://doi.org/10.1101/2024.08.16.608241

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