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

TitleMIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters
Authors
Issue Date18-Nov-2022
PublisherOxford University Press
Citation
Nucleic Acids Research, 2022, v. 51, n. D1, p. 603-610 How to Cite?
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/.


Persistent Identifierhttp://hdl.handle.net/10722/331313
ISSN
2023 Impact Factor: 16.6
2023 SCImago Journal Rankings: 7.048
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorTerlouw, BR-
dc.contributor.authorBlin, K-
dc.contributor.authorNavarro-Munoz, JC-
dc.contributor.authorAvalon, NE-
dc.contributor.authorChevrette, MG-
dc.contributor.authorEgbert, S-
dc.contributor.authorLee, S-
dc.contributor.authorMeijer, D-
dc.contributor.authorRecchia, MJJ-
dc.contributor.authorReitz, ZL-
dc.contributor.authorvan Santen, JA-
dc.contributor.authorSelem-Mojica, N-
dc.contributor.authorTorring, T-
dc.contributor.authorZaroubi, L-
dc.contributor.authorAlanjary, M-
dc.contributor.authorAleti, G-
dc.contributor.authorAguilar, C-
dc.contributor.authorAl-Salihi, SAA-
dc.contributor.authorAugustijn, HE-
dc.contributor.authorAvelar-Rivas, JA-
dc.contributor.authorAvitia-Dominguez, LA-
dc.contributor.authorBarona-Gomez, F-
dc.contributor.authorBernaldo-Aguero, J-
dc.contributor.authorBielinski, VA-
dc.contributor.authorBiermann, F-
dc.contributor.authorBooth, TJ-
dc.contributor.authorBravo, VJC-
dc.contributor.authorCastelo-Branco, R-
dc.contributor.authorChagas, FO-
dc.contributor.authorCruz-Morales, P-
dc.contributor.authorDu, C-
dc.contributor.authorDuncan, KR-
dc.contributor.authorGavriilidou, A-
dc.contributor.authorGayrard, D-
dc.contributor.authorGutierrez-Garcia, K-
dc.contributor.authorHaslinger, K-
dc.contributor.authorHelfrich, EJN-
dc.contributor.authorvan der Hooft, JJJ-
dc.contributor.authorJati, AP-
dc.contributor.authorKalkreuter, E-
dc.contributor.authorKalyvas, N-
dc.contributor.authorKang, KB-
dc.contributor.authorKautsar, S-
dc.contributor.authorKim, W-
dc.contributor.authorKunjapur, AM-
dc.contributor.authorLi, YX-
dc.contributor.authorLin, GM-
dc.contributor.authorLoureiro, C-
dc.contributor.authorLouwen, JJR-
dc.contributor.authorLouwen, NLL-
dc.contributor.authorLund, G-
dc.contributor.authorParra, J-
dc.contributor.authorPhilmus, B-
dc.contributor.authorPourmohsenin, B-
dc.contributor.authorPronk, LJU-
dc.contributor.authorRego, A-
dc.contributor.authorRex, DAB-
dc.contributor.authorRobinson, S-
dc.contributor.authorRosas-Becerra, LR-
dc.contributor.authorRoxborough, ET-
dc.contributor.authorSchorn, MA-
dc.contributor.authorScobie, DJ-
dc.contributor.authorSingh, KS-
dc.contributor.authorSokolova, N-
dc.contributor.authorTang, XY-
dc.contributor.authorUdwary, D-
dc.contributor.authorVigneshwari, A-
dc.contributor.authorVind, K-
dc.contributor.authorVromans, SPJM-
dc.contributor.authorWaschulin, V-
dc.contributor.authorWilliams, SE-
dc.contributor.authorWinter, JM-
dc.contributor.authorWitte, TE-
dc.contributor.authorXie, HL-
dc.contributor.authorYang, D-
dc.contributor.authorYu, JW-
dc.contributor.authorZdouc, M-
dc.contributor.authorZhong, Z-
dc.contributor.authorCollemare, J-
dc.contributor.authorLinington, RG-
dc.contributor.authorWeber, T-
dc.contributor.authorMedema, MH-
dc.date.accessioned2023-09-21T06:54:37Z-
dc.date.available2023-09-21T06:54:37Z-
dc.date.issued2022-11-18-
dc.identifier.citationNucleic Acids Research, 2022, v. 51, n. D1, p. 603-610-
dc.identifier.issn0305-1048-
dc.identifier.urihttp://hdl.handle.net/10722/331313-
dc.description.abstract<p>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 <a href="https://mibig.secondarymetabolites.org/">https://mibig.secondarymetabolites.org/</a>.</p>-
dc.languageeng-
dc.publisherOxford University Press-
dc.relation.ispartofNucleic Acids Research-
dc.rightsThis work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.-
dc.titleMIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters-
dc.typeArticle-
dc.identifier.doi10.1093/nar/gkac1049-
dc.identifier.scopuseid_2-s2.0-85146851279-
dc.identifier.volume51-
dc.identifier.issueD1-
dc.identifier.spage603-
dc.identifier.epage610-
dc.identifier.eissn1362-4962-
dc.identifier.isiWOS:000898752800001-
dc.identifier.issnl0305-1048-

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