MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters

Date
0022-11-18
Authors
Terlouw, Barbara R.
Blin, Kai
Navarro-Muñoz, Jorge C.
Avalon, Nicole E.
Chevrette, Marc G.
Egbert, Susan
Lee, Sanghoon
Meijer, David
Recchia, Michael J. J.
Reitz, Zachary L.
Journal Title
Journal ISSN
Volume Title
Publisher
Nucleic Acids Research
Abstract
With an ever-increasing amount of (meta)genomic data being deposited in sequence databases, (meta)genome mining for natural product biosynthetic pathways occupies a critical role in the discovery of novel pharmaceutical drugs, crop protection agents and biomaterials. The genes that encode these pathways are often organised into biosynthetic gene clusters (BGCs). In 2015, we defined the Minimum Information about a Biosynthetic Gene cluster (MIBiG): a standardised data format that describes the minimally required information to uniquely characterise a BGC. We simultaneously constructed an accompanying online database of BGCs, which has since been widely used by the community as a reference dataset for BGCs and was expanded to 2021 entries in 2019 (MIBiG 2.0). Here, we describe MIBiG 3.0, a database update comprising large-scale validation and re-annotation of existing entries and 661 new entries. Particular attention was paid to the annotation of compound structures and biological activities, as well as protein domain selectivities. Together, these new features keep the database up-to-date, and will provide new opportunities for the scientific community to use its freely available data, e.g. for the training of new machine learning models to predict sequence-structure-function relationships for diverse natural products. MIBiG 3.0 is accessible online at https://mibig.secondarymetabolites.org/.
Description
This article was originally published in Nucleic Acids Research. The version of record is available at: https://doi.org/10.1093/nar/gkac1049
Keywords
Citation
Terlouw, Barbara R, Kai Blin, Jorge C Navarro-Muñoz, Nicole E Avalon, Marc G Chevrette, Susan Egbert, Sanghoon Lee, et al. “MIBiG 3.0: A Community-Driven Effort to Annotate Experimentally Validated Biosynthetic Gene Clusters.” Nucleic Acids Research 51, no. D1 (January 6, 2023): D603–10. https://doi.org/10.1093/nar/gkac1049.