Evidence map›Paper›PMID 41378881›Full record

ArticleBriefings in bioinformatics2025

Strategies for community-sourced biocuration in bioinformatics: a case study on MIBiG 4.0.

Kai Blin, Catarina Loureiro, Nico L L Louwen, Jorge C Navarro-Muñoz, Hans Gerstmans, Serina L Robinson, Adriano Rutz, Zachary L Reitz, Drew T Doering, Justin J J van der Hooft and 3 more

Abstract read
In one paragraph

Article in Briefings in bioinformatics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

13 authors.

Kai BlinThe Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, Kongens Lyngby 2800, Denmark.ORCID 0000-0003-3764-6051
Catarina LoureiroBioinformatics Group, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, the Netherlands.ORCID 0000-0002-6258-2080
Nico L L LouwenBioinformatics Group, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, the Netherlands.
Jorge C Navarro-MuñozBioinformatics Group, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, the Netherlands.ORCID 0000-0003-2992-1607
Hans GerstmansVIB-KU Leuven Center for Microbiology, Flanders Institute for Biotechnology, Kasteelpark Arenberg 31, Leuven 3001, Belgium.
Serina L RobinsonDepartment of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology, Ueberlandstrasse 133, Duebendorf 8600, Switzerland.
Adriano RutzInstitute for Molecular Systems Biology, ETH Zürich, Otto-Stern-Weg 3, Zürich 8093, Switzerland.ORCID 0000-0003-0443-9902
Zachary L ReitzDepartment of Ecology, Evolution and Marine Biology, University of California, 1169 Biological Sciences II, Santa Barbara, CA 93106, United States.
Drew T DoeringLawrence Berkeley National Laboratory, US Department of Energy Joint Genome Institute, 1 Cyclotron Road, Berkeley, CA 94720, United States.
Justin J J van der HooftBioinformatics Group, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, the Netherlands.ORCID 0000-0002-9340-5511
Tilmann WeberThe Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Søltofts Plads, Building 220, Kongens Lyngby 2800, Denmark.ORCID 0000-0002-8260-5120
Marnix H MedemaBioinformatics Group, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, the Netherlands.ORCID 0000-0002-2191-2821
Mitja M ZdoucBioinformatics Group, Wageningen University & Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, the Netherlands.ORCID 0000-0001-6534-6609

Funding

Danish National Research Foundation CeMiSt DNRF137Dutch Research Council KICH1.LWV04.21.013Novo Nordisk Foundation NNF20CC003558Research Foundation-Flanders 1229222 NSwiss National Science Foundation PZPGP2_209124
6 · The paper itself

Abstract

Biocuration is essential to transform molecular sequence data into standardized, machine-readable resources. Such curated datasets enable comparative analysis, predictive modeling, and data integration across bioinformatics platforms. While professional biocuration is resource-intensive and usually limited to institutional settings, community-driven approaches can mobilize large-scale annotation of specialized datasets and are more resilient to disruptions in scientific funding. Here, we present a model for community-powered curation applied to the Minimum Information about a Biosynthetic Gene Cluster (MIBiG) repository. Through a framework of workflows for metadata capture, annotation validation, and contributor coordination, the MIBiG 4.0 initiative recruited 267 scientists across 178 institutions from 33 countries, volunteering an estimated 4000 h of work. These efforts expanded the MIBiG repository by 22% and enhanced its usability in downstream molecular data analyses in comparative genomic analyses, natural product discovery, and machine learning applications. We provide strategies and actionable lessons for adopting this model, supporting the sustainability of curated bioinformatics resources central to nucleic acid research and related fields.

Indexed as

Computational BiologyDatabases, GeneticData CurationMultigene FamilyBiocurationGenomicsMachine Learningbiocurationdata standardsgenome miningopen sciencesecondary metabolites

Identifiers

PMID41378881
PMCPMC12696713

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.