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

Authors
Terlouw, Barbara R.Blin, KaiNavarro-Munoz, Jorge C.Avalon, Nicole E.Chevrette, Marc G.Egbert, SusanLee, SanghoonMeijer, DavidRecchia, Michael J. J.Reitz, Zachary L.van Santen, Jeffrey A.Selem-Mojica, NellyTorring, ThomasZaroubi, LianaAlanjary, MohammadAleti, GajenderAguilar, CesarAl-Salihi, Suhad A. A.Augustijn, Hannah E.Avelar-Rivas, J. AbrahamAvitia-Dominguez, Luis A.Barona-Gomez, FranciscoBernaldo-Aguero, JordanBielinski, Vincent A.Biermann, FriederikeBooth, Thomas J.Bravo, Victor J. CarrionCastelo-Branco, RaquelChagas, Fernanda O.Cruz-Morales, PabloChao DuKatherine R. DuncanGavriilidou, AthinaGayrard, DamienGutierrez-Garcia, KarinaHaslinger, KristinaHelfrich, Eric J. N.van der Hooft, Justin J. J.Jati, Afif P.Kalkreuter, EdwardKalyvas, NikolaosKang, Kyo B.Kautsar, SatriaKim, WonyongKunjapur, Aditya M.Li, Yong-XinLin, Geng-MinLoureiro, CatarinaLouwen, Joris J. R.Louwen, Nico L. L.Lund, GeorgeParra, JonathanPhilmus, BenjaminPourmohsenin, BitaPronk, Lotte J. U.Rego, AdrianaRex, Devasahayam Arokia BalayaRobinson, SerinaRosas-Becerra, L. RodrigoRoxborough, Eve T.Schorn, Michelle A.Scobie, Darren J.Singh, Kumar SaurabhSokolova, NikaTang, XiaoyuUdwary, DanielVigneshwari, ArunaVind, KristiinaVromans, Sophie P. J. M.Waschulin, ValentinWilliams, Sam E.Winter, Jaclyn M.Witte, Thomas E.Xie, HualiYang, DongYu, JingweiZdouc, MitjaZhong, ZhengCollemare, JeromeLinington, Roger G.Weber, TilmannMedema, Marnix H.
Issue Date
Jan-2023
Publisher
OXFORD UNIV PRESS
Citation
NUCLEIC ACIDS RESEARCH, v.51, no.D1, pp D603 - D610
Journal Title
NUCLEIC ACIDS RESEARCH
Volume
51
Number
D1
Start Page
D603
End Page
D610
URI
https://scholarworks.sookmyung.ac.kr/handle/2020.sw.sookmyung/152152
DOI
10.1093/nar/gkac1049
ISSN
0305-1048
1362-4962
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 upto-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/. [GRAPHICS] .
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