Back

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

Fullam, A.; Prasoodanan P K, V.; Kuhn, M.; Bork, P.; Schmidt, T. S.

2026-01-12 bioinformatics
10.64898/2026.01.12.698811 bioRxiv
Show abstract

SummaryWe 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. Data Availabilitymicrontology controlled vocabulary terms and term hierarchies 1, and curated annotations for 305,626 metagenomic samples 2 are available via Zenodo and as supplemental tables S1 and S2. User feedback, suggestions and bug reports are welcome under https://github.com/grp-schmidt/microntology/issues.

Published in Bioinformatics (predicted rank #10) · training set

Matching journals

The top 2 journals account for 50% of the predicted probability mass.

1
Scientific Data
○ 209 papers in training set
Top 0.1%
33.3%
Similar papers in this journal
2
Nature Communications
○ 5641 papers in training set
Top 8%
18.6%
Similar papers in this journal
50% of probability mass above
3
Microbiome
○ 154 papers in training set
Top 0.3%
9.8%
Similar papers in this journal
4
Nature Biotechnology
○ 172 papers in training set
Top 0.5%
6.3%
Similar papers in this journal
5
iMeta
○ 10 papers in training set
Top 0.1%
3.2%
Similar papers in this journal
6
Genome Biology
○ 637 papers in training set
Top 4%
2.7%
7
Scientific Reports
○ 3612 papers in training set
Top 45%
2.1%
8
Nature Methods
○ 385 papers in training set
Top 4%
2.0%
9
Environmental Microbiome
○ 29 papers in training set
Top 0.3%
1.9%
Bioinformatics · published here
◐ 1204 papers in training set
Top 7%
1.7%
11
Nature Microbiology
○ 155 papers in training set
Top 2%
1.7%
12
mSystems
● 394 papers in training set
Top 5%
1.1%
13
GigaScience
◐ 212 papers in training set
Top 3%
1.1%
14
Environmental Science & Technology Letters
● 21 papers in training set
Top 0.2%
1.1%
15
ISME Communications
◐ 120 papers in training set
Top 2%
1.0%
16
Nucleic Acids Research
◐ 1281 papers in training set
Top 12%
1.0%
17
Briefings in Bioinformatics
◐ 354 papers in training set
Top 7%
0.8%
18
iScience
○ 1154 papers in training set
Top 40%
0.6%

"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.