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MIBiG 2.0: a repository for biosynthetic gene clusters of known function

Fueled by the explosion of (meta)genomic data, genome mining of specialized metabolites has become a major technology for drug discovery and studying microbiome ecology. In these efforts, computational tools like antiSMASH have played a central role through the analysis of Biosynthetic Gene Clusters...

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Autores principales: Kautsar, Satria A, Blin, Kai, Shaw, Simon, Navarro-Muñoz, Jorge C, Terlouw, Barbara R, van der Hooft, Justin J J, van Santen, Jeffrey A, Tracanna, Vittorio, Suarez Duran, Hernando G, Pascal Andreu, Victòria, Selem-Mojica, Nelly, Alanjary, Mohammad, Robinson, Serina L, Lund, George, Epstein, Samuel C, Sisto, Ashley C, Charkoudian, Louise K, Collemare, Jérôme, Linington, Roger G, Weber, Tilmann, Medema, Marnix H
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145714/
https://www.ncbi.nlm.nih.gov/pubmed/31612915
http://dx.doi.org/10.1093/nar/gkz882
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author Kautsar, Satria A
Blin, Kai
Shaw, Simon
Navarro-Muñoz, Jorge C
Terlouw, Barbara R
van der Hooft, Justin J J
van Santen, Jeffrey A
Tracanna, Vittorio
Suarez Duran, Hernando G
Pascal Andreu, Victòria
Selem-Mojica, Nelly
Alanjary, Mohammad
Robinson, Serina L
Lund, George
Epstein, Samuel C
Sisto, Ashley C
Charkoudian, Louise K
Collemare, Jérôme
Linington, Roger G
Weber, Tilmann
Medema, Marnix H
author_facet Kautsar, Satria A
Blin, Kai
Shaw, Simon
Navarro-Muñoz, Jorge C
Terlouw, Barbara R
van der Hooft, Justin J J
van Santen, Jeffrey A
Tracanna, Vittorio
Suarez Duran, Hernando G
Pascal Andreu, Victòria
Selem-Mojica, Nelly
Alanjary, Mohammad
Robinson, Serina L
Lund, George
Epstein, Samuel C
Sisto, Ashley C
Charkoudian, Louise K
Collemare, Jérôme
Linington, Roger G
Weber, Tilmann
Medema, Marnix H
author_sort Kautsar, Satria A
collection PubMed
description Fueled by the explosion of (meta)genomic data, genome mining of specialized metabolites has become a major technology for drug discovery and studying microbiome ecology. In these efforts, computational tools like antiSMASH have played a central role through the analysis of Biosynthetic Gene Clusters (BGCs). Thousands of candidate BGCs from microbial genomes have been identified and stored in public databases. Interpreting the function and novelty of these predicted BGCs requires comparison with a well-documented set of BGCs of known function. The MIBiG (Minimum Information about a Biosynthetic Gene Cluster) Data Standard and Repository was established in 2015 to enable curation and storage of known BGCs. Here, we present MIBiG 2.0, which encompasses major updates to the schema, the data, and the online repository itself. Over the past five years, 851 new BGCs have been added. Additionally, we performed extensive manual data curation of all entries to improve the annotation quality of our repository. We also redesigned the data schema to ensure the compliance of future annotations. Finally, we improved the user experience by adding new features such as query searches and a statistics page, and enabled direct link-outs to chemical structure databases. The repository is accessible online at https://mibig.secondarymetabolites.org/.
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spelling pubmed-71457142020-04-13 MIBiG 2.0: a repository for biosynthetic gene clusters of known function Kautsar, Satria A Blin, Kai Shaw, Simon Navarro-Muñoz, Jorge C Terlouw, Barbara R van der Hooft, Justin J J van Santen, Jeffrey A Tracanna, Vittorio Suarez Duran, Hernando G Pascal Andreu, Victòria Selem-Mojica, Nelly Alanjary, Mohammad Robinson, Serina L Lund, George Epstein, Samuel C Sisto, Ashley C Charkoudian, Louise K Collemare, Jérôme Linington, Roger G Weber, Tilmann Medema, Marnix H Nucleic Acids Res Database Issue Fueled by the explosion of (meta)genomic data, genome mining of specialized metabolites has become a major technology for drug discovery and studying microbiome ecology. In these efforts, computational tools like antiSMASH have played a central role through the analysis of Biosynthetic Gene Clusters (BGCs). Thousands of candidate BGCs from microbial genomes have been identified and stored in public databases. Interpreting the function and novelty of these predicted BGCs requires comparison with a well-documented set of BGCs of known function. The MIBiG (Minimum Information about a Biosynthetic Gene Cluster) Data Standard and Repository was established in 2015 to enable curation and storage of known BGCs. Here, we present MIBiG 2.0, which encompasses major updates to the schema, the data, and the online repository itself. Over the past five years, 851 new BGCs have been added. Additionally, we performed extensive manual data curation of all entries to improve the annotation quality of our repository. We also redesigned the data schema to ensure the compliance of future annotations. Finally, we improved the user experience by adding new features such as query searches and a statistics page, and enabled direct link-outs to chemical structure databases. The repository is accessible online at https://mibig.secondarymetabolites.org/. Oxford University Press 2020-01-08 2019-10-15 /pmc/articles/PMC7145714/ /pubmed/31612915 http://dx.doi.org/10.1093/nar/gkz882 Text en © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Database Issue
Kautsar, Satria A
Blin, Kai
Shaw, Simon
Navarro-Muñoz, Jorge C
Terlouw, Barbara R
van der Hooft, Justin J J
van Santen, Jeffrey A
Tracanna, Vittorio
Suarez Duran, Hernando G
Pascal Andreu, Victòria
Selem-Mojica, Nelly
Alanjary, Mohammad
Robinson, Serina L
Lund, George
Epstein, Samuel C
Sisto, Ashley C
Charkoudian, Louise K
Collemare, Jérôme
Linington, Roger G
Weber, Tilmann
Medema, Marnix H
MIBiG 2.0: a repository for biosynthetic gene clusters of known function
title MIBiG 2.0: a repository for biosynthetic gene clusters of known function
title_full MIBiG 2.0: a repository for biosynthetic gene clusters of known function
title_fullStr MIBiG 2.0: a repository for biosynthetic gene clusters of known function
title_full_unstemmed MIBiG 2.0: a repository for biosynthetic gene clusters of known function
title_short MIBiG 2.0: a repository for biosynthetic gene clusters of known function
title_sort mibig 2.0: a repository for biosynthetic gene clusters of known function
topic Database Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7145714/
https://www.ncbi.nlm.nih.gov/pubmed/31612915
http://dx.doi.org/10.1093/nar/gkz882
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