Abstract
Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/.
| Original language | English |
|---|---|
| Pages (from-to) | D678-D690 |
| Journal | Nucleic Acids Research |
| Volume | 53 |
| Issue number | D1 |
| DOIs | |
| Publication status | Published - 6 Jan 2025 |
Bibliographical note
Publisher Copyright:© The Author(s) 2024.
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In: Nucleic Acids Research, Vol. 53, No. D1, 06.01.2025, p. D678-D690.
Research output: Contribution to journal › Article › Academic › peer-review
TY - JOUR
T1 - MIBiG 4.0
T2 - advancing biosynthetic gene cluster curation through global collaboration
AU - Zdouc, Mitja M.
AU - Blin, Kai
AU - Louwen, Nico L.L.
AU - Navarro, Jorge
AU - Loureiro, Catarina
AU - Bader, Chantal D.
AU - Bailey, Constance B.
AU - Barra, Lena
AU - Booth, Thomas J.
AU - Bozhüyük, Kenan A.J.
AU - Cediel-Becerra, José D.D.
AU - Charlop-Powers, Zachary
AU - Chevrette, Marc G.
AU - Chooi, Yit Heng
AU - D’Agostino, Paul M.
AU - de Rond, Tristan
AU - Pup, Elena Del
AU - Duncan, Katherine R.
AU - Gu, Wenjia
AU - Hanif, Novriyandi
AU - Helfrich, Eric J.N.
AU - Jenner, Matthew
AU - Katsuyama, Yohei
AU - Korenskaia, Aleksandra
AU - Krug, Daniel
AU - Libis, Vincent
AU - Lund, George A.
AU - Mantri, Shrikant
AU - Morgan, Kalindi D.
AU - Owen, Charlotte
AU - Phan, Chin Soon
AU - Philmus, Benjamin
AU - Reitz, Zachary L.
AU - Robinson, Serina L.
AU - Singh, Kumar Saurabh
AU - Teufel, Robin
AU - Tong, Yaojun
AU - Tugizimana, Fidele
AU - Ulanova, Dana
AU - Winter, Jaclyn M.
AU - Aguilar, César
AU - Akiyama, Daniel Y.
AU - Al-Salihi, Suhad A.A.
AU - Alanjary, Mohammad
AU - Alberti, Fabrizio
AU - Aleti, Gajender
AU - Alharthi, Shumukh A.
AU - Arias Rojo, Mariela Y.
AU - Arishi, Amr A.
AU - Augustijn, Hannah E.
AU - Avalon, Nicole E.
AU - Avelar-Rivas, J. Abraham
AU - Axt, Kyle K.
AU - Barbieri, Hellen B.
AU - Barbosa, Julio Cesar J.
AU - Segato, Lucas Gabriel Barboza
AU - Barrett, Susanna E.
AU - Baunach, Martin
AU - Beemelmanns, Christine
AU - Beqaj, Dardan
AU - Berger, Tim
AU - Bernaldo-Agüero, Jordan
AU - Bettenbühl, Sandra M.
AU - Bielinski, Vincent A.
AU - Biermann, Friederike
AU - Borges, Ricardo M.
AU - Borriss, Rainer
AU - Breitenbach, Milena
AU - Bretscher, Kevin M.
AU - Brigham, Michael W.
AU - Buedenbender, Larissa
AU - Bulcock, Brodie W.
AU - Cano-Prieto, Carolina
AU - Capela, João
AU - Carrion, Victor J.
AU - Carter, Riley S.
AU - Castelo-Branco, Raquel
AU - Castro-Falcón, Gabriel
AU - Chagas, Fernanda O.
AU - Charria-Girón, Esteban
AU - Chaudhri, Ayesha Ahmed
AU - Chaudhry, Vasvi
AU - Choi, Hyukjae
AU - Choi, Yukyung
AU - Choupannejad, Roya
AU - Chromy, Jakub
AU - Chue Donahey, Melinda S.
AU - Collemare, Jérôme
AU - Connolly, Jack A.
AU - Creamer, Kaitlin E.
AU - Crüsemann, Max
AU - Cruz, Andres Arredondo
AU - Cumsille, Andres
AU - Dallery, Jean Felix
AU - Damas-Ramos, Luis Caleb
AU - Damiani, Tito
AU - de Kruijff, Martinus
AU - Martín, Belén Delgado
AU - Sala, Gerardo Della
AU - Dillen, Jelle
AU - Doering, Drew T.
AU - Dommaraju, Shravan R.
AU - Durusu, Suhan
AU - Egbert, Susan
AU - Ellerhorst, Mark
AU - Faussurier, Baptiste
AU - Fetter, Artem
AU - Feuermann, Marc
AU - Fewer, David P.
AU - Foldi, Jonathan
AU - Frediansyah, Andri
AU - Garza, Erin A.
AU - Gavriilidou, Athina
AU - Gentile, Andrea
AU - Gerke, Jennifer
AU - Gerstmans, Hans
AU - Gomez-Escribano, Juan Pablo
AU - González-Salazar, Luz A.
AU - Grayson, Natalie E.
AU - Greco, Claudio
AU - Gris Gomez, Juan E.
AU - Guerra, Sebastian
AU - Flores, Shaday Guerrero
AU - Gurevich, Alexey
AU - Gutiérrez-García, Karina
AU - Hart, Lauren
AU - Haslinger, Kristina
AU - He, Beibei
AU - Hebra, Teo
AU - Hemmann, Jethro L.
AU - Hindra, Hindra
AU - Höing, Lars
AU - Holland, Darren C.
AU - Holme, Jonathan E.
AU - Horch, Therese
AU - Hrab, Pavlo
AU - Hu, Jie
AU - Huynh, Thanh Hau
AU - Hwang, Ji Yeon
AU - Iacovelli, Riccardo
AU - Iftime, Dumitrita
AU - Iorio, Marianna
AU - Jayachandran, Sidharth
AU - Jeong, Eunah
AU - Jing, Jiayi
AU - Jung, Jung J.
AU - Kakumu, Yuya
AU - Kalkreuter, Edward
AU - Kang, Kyo Bin
AU - Kang, Sangwook
AU - Kim, Wonyong
AU - Kim, Geum Jin
AU - Kim, Hyunwoo
AU - Kim, Hyun Uk
AU - Klapper, Martin
AU - Koetsier, Robert A.
AU - Kollten, Cassandra
AU - Kovács, Ákos T.
AU - Kriukova, Yelyzaveta
AU - Kubach, Noel
AU - Kunjapur, Aditya M.
AU - Kushnareva, Aleksandra K.
AU - Kust, Andreja
AU - Lamber, Jessica
AU - Larralde, Martin
AU - Larsen, Niels J.
AU - Launay, Adrien P.
AU - Le, Ngoc Thao Hien
AU - Lebeer, Sarah
AU - Lee, Byung Tae
AU - Lee, Kyungha
AU - Lev, Katherine L.
AU - Li, Shu Ming
AU - Li, Yong Xin
AU - Licona-Cassani, Cuauhtémoc
AU - Lien, Annette
AU - Liu, Jing
AU - Lopez, Julius Adam V.
AU - Machushynets, Nataliia V.
AU - Macias, Marla I.
AU - Mahmud, Taifo
AU - Maleckis, Matiss
AU - Martinez-Martinez, Añadir Maharai
AU - Mast, Yvonne
AU - Maximo, Marina F.
AU - McBride, Christina M.
AU - McLellan, Rose M.
AU - Bhatt, Khyati Mehta
AU - Melkonian, Chrats
AU - Merrild, Aske
AU - Metsä-Ketelä, Mikko
AU - Mitchell, Douglas A.
AU - Müller, Alison V.
AU - Nguyen, Giang Son
AU - Nguyen, Hera T.
AU - Niedermeyer, Timo H.J.
AU - O’Hare, Julia H.
AU - Ossowicki, Adam
AU - Ostash, Bohdan O.
AU - Otani, Hiroshi
AU - Padva, Leo
AU - Paliyal, Sunaina
AU - Pan, Xinya
AU - Panghal, Mohit
AU - Parade, Dana S.
AU - Park, Jiyoon
AU - Parra, Jonathan
AU - Rubio, Marcos Pedraza
AU - Pham, Huong T.
AU - Pidot, Sacha J.
AU - Piel, Jörn
AU - Pourmohsenin, Bita
AU - Rakhmanov, Malik
AU - Ramesh, Sangeetha
AU - Rasmussen, Michelle H.
AU - Rego, Adriana
AU - Reher, Raphael
AU - Rice, Andrew J.
AU - Rigolet, Augustin
AU - Romero-Otero, Adriana
AU - Rosas-Becerra, Luis Rodrigo
AU - Rosiles, Pablo Y.
AU - Rutz, Adriano
AU - Ryu, Byeol
AU - Sahadeo, Libby Ann
AU - Saldanha, Murrel
AU - Salvi, Luca
AU - Sánchez-Carvajal, Eduardo
AU - Santos-Medellin, Christian
AU - Sbaraini, Nicolau
AU - Schoellhorn, Sydney M.
AU - Schumm, Clemens
AU - Sehnal, Ludek
AU - Selem, Nelly
AU - Shah, Anjali D.
AU - Shishido, Tania K.
AU - Sieber, Simon
AU - Silviani, Velina
AU - Singh, Garima
AU - Singh, Hemant
AU - Sokolova, Nika
AU - Sonnenschein, Eva C.
AU - Sosio, Margherita
AU - Sowa, Sven T.
AU - Steffen, Karin
AU - Stegmann, Evi
AU - Streiff, Alena B.
AU - Strüder, Alena
AU - Surup, Frank
AU - Svenningsen, Tiziana
AU - Sweeney, Douglas
AU - Szenei, Judit
AU - Tagirdzhanov, Azat
AU - Tan, Bin
AU - Tarnowski, Matthew J.
AU - Terlouw, Barbara R.
AU - Rey, Thomas
AU - Thome, Nicola U.
AU - Ortega, Laura Rosina Torres
AU - Tørring, Thomas
AU - Trindade, Marla
AU - Truman, Andrew W.
AU - Tvilum, Marie
AU - Udwary, Daniel W.
AU - Ulbricht, Christoph
AU - Vader, Lisa
AU - van Wezel, Gilles P.
AU - Walmsley, Max
AU - Warnasinghe, Randika
AU - Weddeling, Heiner G.
AU - Weir, Angus N.M.
AU - Williams, Katherine
AU - Williams, Sam E.
AU - Witte, Thomas E.
AU - Wood Rocca, Steffaney M.
AU - Yamada, Keith
AU - Yang, Dong
AU - Yang, Dongsoo
AU - Yu, Jingwei
AU - Zhou, Zhenyi
AU - Ziemert, Nadine
AU - Zimmer, Lukas
AU - Zimmermann, Alina
AU - Zimmermann, Christian
AU - van der Hooft, Justin J.J.
AU - Linington, Roger G.
AU - Weber, Tilmann
AU - Medema, Marnix H.
N1 - Publisher Copyright: © The Author(s) 2024.
PY - 2025/1/6
Y1 - 2025/1/6
N2 - Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/.
AB - Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/.
UR - http://www.scopus.com/inward/record.url?scp=85214414411&partnerID=8YFLogxK
U2 - 10.1093/nar/gkae1115
DO - 10.1093/nar/gkae1115
M3 - Article
C2 - 39657789
AN - SCOPUS:85214414411
SN - 0305-1048
VL - 53
SP - D678-D690
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - D1
ER -