Request for new ontology [MICRONT]

[defleury]

Title

microntology

Short Description

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

Description

microntology encompasses (in v1.0) a controlled vocabulary of 148 crosslinked terms that fall into five broad habitat categories (terrestrial, aquatic, aerial, host-associated and anthropogenic environments) and additional categories that describe broad physicochemical properties, morphology, human host properties, animal host captivity status, and miscellaneous informative features such as (chemical) contamination or ancient (paleontological) sample provenance. MICRONT is designed as a pragmatic lightweight complement to existing detailed ontologies like ENVO, UBERON or GOLD; MICRONT terms are crosslinked to these where appropriate. Its purpose is a fast, automatable annotation of (meta)genomic microbial samples with browsable informative tags.

MICRONT follows five core design principles: it is (i) data-driven, encompassing terms to describe frequent sample types in existing data; (ii) pragmatic and query-oriented, defining terms at intermediate resolutions to facilitate user access and browsing; (iii) shallow, with only few hierarchical levels of classes; (iv) cross-linked between related terms from different hierarchical paths (e.g., a lake [MICRONT:02010100] would also be considered a lentic water body [MICRONT:02060100]); and (v) designed for parsimonious multi-tagging where individual samples are described by multiple independent terms, rather than a ‘best match’ highly detailed single term.

More details are available in a preprint at https://www.biorxiv.org/content/10.64898/2026.01.12.698811v1.full

Identifier Space

MICRONT

License

CC-BY 4.0

Domain

microbiology

Source Code Repository

https://github.com/grp-schmidt/microntology

Homepage

https://github.com/grp-schmidt/microntology

Issue Tracker

https://github.com/grp-schmidt/microntology/issues

Contribution Guidelines

https://github.com/grp-schmidt/microntology/blob/main/CONTRIBUTING.md

Ontology Download Link

https://github.com/grp-schmidt/microntology/blob/main/micront.owl

Contact Name

Sebastian Schmidt

Contact Email

sebastian.schmidt@ucc.ie

Contact GitHub Username

defleury

Contact ORCID Identifier

0000-0001-8587-4177

Formats

• OWL RDF/XML (.owl)
• OBO (.obo)
• OBO Graph JSON (.json)

Dependencies

• envo
• uberon
• chebi

Related

• envo
• uberon

Usages

- user: spire.embl.de
  description: SPIRE uses MICRONT annotations to ease browsing of publicly available metagenomic data
  examples:
    - url: https://spire.embl.de/environment?microntology=&add=aquatic&page=1
      description: "Query for all aquatic samples available in SPIRE"
- user: vire.embl.de
  description: VIRE uses MICRONT annotations to ease browsing of reconstructed viral genomes
  examples:
    - url: https://spire.embl.de/vire/environment/human_gut
      description: "Query for all human gut samples available in VIRE"

Intended Use Cases and/or Related Projects

microntology annotations are used by SPIRE (spire.embl.de) and associated databases, such as VIRE (vire.embl.de). It will continue to be developed in coordination with and as a lightweight complement to manually curated sample metadata in Metalog (metalog.embl.de).

MICRONT has been used in several previous projects, including (but not limited to):

• the Global Microbial SmORFs Catalogue (https://pubmed.ncbi.nlm.nih.gov/39214983/)
• to benchmark global-scale microbial habitat unsupervised taxonomic clusterings and modeling (https://www.biorxiv.org/content/10.1101/2025.07.18.664989.abstract)
• to categorize the main reservoirs of discoverable microbial diversity in existing data (https://www.biorxiv.org/content/10.1101/2025.06.26.661807v2.full)

We have moreover used MICRONT to semi-automatically annotate >300k publicly available metagenomes, available via Zenodo (https://zenodo.org/records/18164252).

Data Sources

Metalog (metalog.embl.de), publicly available sample contextual data on the European Nucleotide Archive, and manual curation.

Additional comments or remarks

No response

OBO Foundry Pre-registration Checklist

• I have read and understood the registration process instructions and the registration checklist.
• There is no other ontology in the OBO Foundry which would be an appropriate place for my terms. If there were, I have contacted the editors, and we decided in mutual agreement that a separate ontology is more appropriate.
• My ontology has a specific release file with a version IRI and a dc:license annotation, serialised in RDF/XML.
• My identifiers (classes and properties IRIs) are formatted according to the OBO Foundry Identifier Policy
• My term labels are in English and conform to the OBO Foundry Naming Conventions
• I understand that term definitions are key to understanding the intentions of a term, especially when the ontology is used in curation. I made sure that a reasonable majority of terms in my ontology--and all top level terms--have definitions, in English, using the IAO:0000115 property.
• For every term in my ontology, I checked whether another OBO Foundry ontology has one with the same meaning. If so, I re-used that term directly (not by cross-reference, by directly using the IRI).
• For all relationship properties (Object and Data Property), I checked whether the Relation Ontology (RO) includes an appropriate one. I understand that aligning with RO is an essential part of the overall alignment between OBO ontologies!
• For the selection of appropriate annotation properties, I looked at OMO first. I understand that aligning ontology metadata and term-level metadata is essential for cross-integration of OBO ontologies.
• If I was not sure about the meaning of any of the checkboxes above, I have consulted with a member of the OBO Foundry for advice, e.g., through the obo-discuss Google Group.
• The requested ID space does not conflict with another ID space found in other registries such as the Bioregistry and BioPortal, see here for a complete list.

[pfabry]

Hi @defleury,

Thank you for submitting your ontology for consideration. I noticed that some items in the pre-registration checklist have not yet been completed. Could you please clarify whether you plan to address these items, and if so, how and on what timeline?

[cmungall]

Hi @defleury

I'm not part of the review process any more so apologies for hijacking the thread. I think what you have all done with micront is great, having consistent annotation across such a wide range of metagenomics data is fantastic. I think there are a few things to do that are non-obvious to people not deep in the OBO world that you could do that would make your ontology more broadly useful, and more likely to have a successful ride through the OBO process.

Would you like to join the OBO slack workspace and chat about this in the #environments channel? There are a few of us there interested in similar things (making subsets of larger ontologies for practical purposes like this), we'd love to chat about this. just go to obofoundry.org for the slack invite. Or you can reach out to me directly.

Some quick tips in the interim (the OBO team are working hard to make some of this more obvious)

You did check the box here:

[x] There is no other ontology in the OBO Foundry which would be an appropriate place for my terms. If there were, I have contacted the editors, and we decided in mutual agreement that a separate ontology is more appropriate.

There is a lot of obvious overlap with ENVO, I don't see anything in the tracker: https://github.com/EnvironmentOntology/envo/issues?q=micront

That's OK, now is a good time to start the conversation!

You also checked this:

[x] I understand that term definitions are key to understanding the intentions of a term, especially when the ontology is used in curation. I made sure that a reasonable majority of terms in my ontology--and all top level terms--have definitions, in English, using the IAO:0000115 property.

I'm not sure this is the case!

curl -L -s https://raw.githubusercontent.com/grp-schmidt/microntology/refs/heads/main/micront.owl | grep -c IAO_0000115
0

I can help with this one:

[ ] For every term in my ontology, I checked whether another OBO Foundry ontology has one with the same meaning. If so, I re-used that term directly (not by cross-reference, by directly using the IRI).

Here you minted new terms rather than reusing. But I totally get why you did that!

If you do this, then I think it's much better if you use standard ways of mapping to other ontologies. You can see plenty of examples of this in ontologies like ENVO.

To give an example:

rdfs:label "lake"
rdfs:comment "see also: http://purl.obolibrary.org/obo/ ENVO_00000020"
rdfs:comment "see also: http://purl.obolibrary.org/obo/ENVO_01000252"

here the IRI is embedded in a string so it's harder to use computationally, and harder to check for typos (e.g the space in the IRI above)

I'll be honest, I think there is a big misalignment between micront as it stands and OBO, but what you have done is really practical and useful. I'd go ahead and register on bioportal for now and let's chat about ways to align this work with ongoing work in making ENVO subsets etc.

[defleury]

Dear @pfabry , thank you for your message, and apologies for not replying sooner. I will go through all points in the checklist and ping here once I think the points are addressed. We (the developers behind microntology) are all new to the OBO world, so thanks in advance for your patience with us!

@cmungall thank you so much for your message, this is really helpful and I appreciate your taking the time to engage! I will go through these points with my colleagues, revise and come back with answers/updates. Most importantly we'll look to improve/clarify the mapping to existing ontologies. I will also more than gladly take you by your word to follow up on some of these points.