PanKB: An interactive microbial pangenome knowledgebase for research, biotechnological innovation, and knowledge mining.
Journal:
Nucleic acids research
PMID:
39574409
Abstract
The exponential growth of microbial genome data presents unprecedented opportunities for unlocking 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 from 8 industrially relevant microbial families, comprising 8402 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 its knowledge. PanKB empowers researchers and bioengineers to harness the potential of microbial pangenomics and serves as a valuable resource bridging the gap between pangenomic data and practical applications.