<i>microntology</i> : a lightweight, data-driven controlled vocabulary to describe Earth’s microbial habitats

MOTIVATION: Data-enabled studies of microbial ecology and evolution depend on high-quality descriptions of microbial habitats, based on curated and consolidated vocabularies. RESULTS: We introduce microntology v1.0, a pragmatic controlled vocabulary of 148 terms to describe microbial habitats and lifestyles, and provide manually curated microntology annotations for >300k metagenomic samples from public repositories. AVAILABILITY: microntology controlled vocabulary terms and term hierarchies (doi: 10.5281/zenodo.19730167), and curated annotations for 305,626 metagenomic samples (doi: 10.5281/zenodo.18164252) are available via Zenodo and spire.embl.de/downloads. Underlying code is available via github.com/grp-schmidt/microntology and Zenodo (doi: 10.5281/zenodo.20323497). User feedback, suggestions and bug reports are welcome at github.com/grp-schmidt/microntology/issues. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

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Publication Details

Journal
Bioinformatics
Published
2026-05-27
DOI
https://doi.org/10.1093/bioinformatics/btag343
Primary Topic
Microbial Community Ecology and Physiology
Type
article
Field-Weighted Citation Impact
0.00
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article

microntology : a lightweight, data-driven controlled vocabulary to describe Earth’s microbial habitats

P BORK, Michael Kuhn, Vishnu Prasoodanan PK, Anthony Fullam et al.
Bioinformatics
Microbial Community Ecology and Physiology
article

microntology : a lightweight, data-driven controlled vocabulary to describe Earth’s microbial habitats

P BORK, Michael Kuhn, Vishnu Prasoodanan PK, Anthony Fullam, Thomas S B Schmidt
article en

Abstract

MOTIVATION: Data-enabled studies of microbial ecology and evolution depend on high-quality descriptions of microbial habitats, based on curated and consolidated vocabularies. RESULTS: We introduce microntology v1.0, a pragmatic controlled vocabulary of 148 terms to describe microbial habitats and lifestyles, and provide manually curated microntology annotations for >300k metagenomic samples from public repositories. AVAILABILITY: microntology controlled vocabulary terms and term hierarchies (doi: 10.5281/zenodo.19730167), and curated annotations for 305,626 metagenomic samples (doi: 10.5281/zenodo.18164252) are available via Zenodo and spire.embl.de/downloads. Underlying code is available via github.com/grp-schmidt/microntology and Zenodo (doi: 10.5281/zenodo.20323497). User feedback, suggestions and bug reports are welcome at github.com/grp-schmidt/microntology/issues. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Bioinformatics
European Molecular Biology Laboratory (DE), APC Microbiome Institute (IE)
Openalex Percentile: Top 6%
Microbial Community Ecology and Physiology
DOIOpen Access PDFOpenAlex
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<i>microntology</i> : a lightweight, data-driven controlled vocabulary to describe Earth’s microbial habitats — P BORK, Michael Kuhn, et al. · Bioinformatics (2026) | TGRS Research Map | TGRS