Microntology: a lightweight, data-driven controlled vocabulary to describe earth’s microbial habitats

Anthony Fullam; P. K.Vishnu Prasoodanan; Michael Kuhn; Peer Bork; Thomas S.B. Schmidt

doi:10.1093/bioinformatics/btag343

Microntology: a lightweight, data-driven controlled vocabulary to describe earth’s microbial habitats

Anthony Fullam
, P. K.Vishnu Prasoodanan
, Michael Kuhn
, Peer Bork
, Thomas S.B. Schmidt

European Molecular Biology Laboratory

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Article number	btag343
Pages (from-to)	1-5
Number of pages	5
Journal	Bioinformatics
Volume	42
Issue number	6
DOIs	https://doi.org/10.1093/bioinformatics/btag343
Publication status	Published - 27 May 2026

Keywords

Data-enabled studies
microbial ecology and evolution
Microbial habitats and lifestyles
[Microbiology]
[APCMicrobiome]

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10.1093/bioinformatics/btag343

btag343Final published version, 1.93 MBLicence: CC BY

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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. ",

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AU - Bork, Peer

AU - Schmidt, Thomas S.B.

N1 - © 2026, the Author(s). Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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AB - 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.

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Microntology: a lightweight, data-driven controlled vocabulary to describe earth’s microbial habitats

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Keywords

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