Request for new ontology [Ontology of Laboratory Animal Science]

[zhengj2007]

Title

Ontology of Laboratory Animal Science

Short Description

The OLAS is a community-based biomedical ontology for ontologically representing entities and their relationships in laboratory animal science.

Description

The Ontology for Laboratory Animal Science (OLAS) is a community-driven biomedical ontology that focuses on the field of laboratory animal science. Its purpose is to provide an ontological framework to represent the various entities and their relations involved in laboratory animal science such as lab animal models for studying human diseases and medical interventions (e.g. vaccines). This enables a standardized and structured approach to organizing and sharing information within this field.

Identifier Space

OLAS

License

CC-BY 4.0

Domain

investigations

Source Code Repository

https://github.com/OLAS-ontology/OLAS

Homepage

https://github.com/OLAS-ontology/OLAS

Issue Tracker

https://github.com/OLAS-ontology/OLAS/issues

Contribution Guidelines

https://github.com/OLAS-ontology/OLAS/blob/master/CONTRIBUTING.md

Ontology Download Link

https://raw.githubusercontent.com/OLAS-ontology/OLAS/refs/heads/master/olas.owl

Contact Name

Jie Zheng

Contact Email

zhengj2007@gmail.com

Contact GitHub Username

zhengj2007

Contact ORCID Identifier

0000-0002-2999-0103

Formats

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

Dependencies

• BFO
• OMO
• IAO
• RO
• NCBITaxon
• OBI
• OPMI
• VO

Related

No response

Usages

Intended Use Cases and/or Related Projects

VIOLIN, a vaccine knowledge base, contains over 1000 immune response studies using around 30 different lab animals. We are intend to use OLAS to standardize these studies.
We are also going to use OLAS to standardize various lab animal studies in University of Michigan, such as sepsis and vascular disease studies.

Data Sources

VIOLIN, datasets in Unit for Laboratory Animal Medicine (ULAM) in University of Michigan, and literature

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]

Dear @zhengj2007,

Thank you for your submission. The review will be executed as a two stage process:

First, you will have to pass OBO NOR Dashboard. Pass means that no check apart from Users and Versioning may be red. In addition, a new check is currently implemented: it consists in a lexical match of your original terms with those already existing in OBO Foundry published ontologies. The goal is to prevent the duplication of terms with similar meanings (cf. Review SOP). A list of terms that are potential duplicates will be provided soon.

After you have successfully passed the Dashboard you will be assigned an OBO Operations committee member to review the ontology. The assigned reviewer is to be considered the final arbiter of requirements; look to that reviewer's guidance regarding which suggestions made by other reviewers must be done, which suggestions are simply good to do but not required, and which should not be done.

Usually, the review will result in an opportunity for you to improve the ontology. When the reviewer believes the ontology is ready for presentation to the OBO Operations Committee, they will present your ontology during an OBO Operations Call. This gives other members of the committee the opportunity to assess your work.

When a decision is reached by the committee you will be informed here on the issue tracker. The process can take any number of weeks or months, depending on the case at hand.
Please let us know about any reasons you might have for increased urgency.

You will be informed once your ontology is loaded in the OBO NOR Dashboard.

Good luck!

[zhengj2007]

Thanks! @pfabry

[pfabry]

@zhengj2007
Your ontology has been added to the OBO NOR Dashboard and has passed the technical review.
Lexmatch results are available here: OLAS - lexmatch 20250228.txt

[zhengj2007]

@pfabry Glad to know that OLAS passed the technical review. We will review the lexmatch results and update the OLAS if the OLAS terms are the same as the existing ontology terms.

@zhengj2007 Your ontology has been added to the OBO NOR Dashboard and has passed the technical review. Lexmatch results are available here: OLAS - lexmatch 20250228.txt

[bpeters42]

A quick question: What terms in OLAS would not be in OBI scope? Would it not be more efficient to add to OBI directly?

[zhengj2007]

@bpeters42 I think OBI is designed for general biomedical investigations, with a current focus on assays. OLAS, on the other hand, concentrates on laboratory animal science, a specialized area of investigation. We intend to incorporate a wide range of laboratory animal models, genetic modification strains, and to address relevant animal welfare legislation. I view OLAS as an application ontology that will reuse numerous OBO Foundry ontologies, including OBI. We will submit requests to OBI for new terms that fall within their defined scope.

[bpeters42]

Every investigation is specialized. My own work in OBI was originally to facilitate capturing a lot of animal vaccination studies. Should I now create an 'animal immunology studies' ontology? Should I create a new 'pneumonia ontology' because this is the last grant that I got? Where does it end and who is maintaining all these splinter ontologies? Who is the 'community' that is asking for this, that is not being served current ontologies? Are there examples of requests made that were not granted?

I am sorry to put you on the spot, but we have a real problem with the proliferation of ontologies in OBO that are making it harder for users to grasp what terms to use. And to be clear, if the need is to have 'ownership' of the development work - it would be delightful if Oliver and you would be first and last author on a paper describing the terms placed in OBI...

• Bjoern

[addiehl]

My group's work on MRIO is a model for collaborative development with OBI:
https://pubmed.ncbi.nlm.nih.gov/38763990/

Basically we moved all our general classes related to biomedical imaging and MRI to OBI for use by others, and use our ontology for highly specific application classes for specific use cases in MRI. We are continuing to extend our work with additional classes going into OBI in the near future. While we have not submitted MRIO to the OBO Foundry, by enhancing OBI directly, we have shared our most useful classes with the community without the need for another OBO Foundry ontology.

[yongqunh]

Thanks for the wonderful comments!

First, I would like to say that we have a strong 'community' behind OLAS. The community is lab animal medicine community. Indeed, my primary position in the University of Michigan is ULAM - Unit for Lab Animal Medicine, and my B.S. is veterinary medical science, so this is indeed my primary domain of research and service. The community also has its national association: The American Association for Laboratory Animal Science (AALAS) - https://archive.aalas.org/about-aalas . I have attended the annual AALAS meetings several times. Indeed, I attended last year's AALAS National Meeting 2024 in the Music City Center - Nashville, TN, and I presented a talk there in a panel focused on lab animal science and AI. I have many colleagues in ULAM and other universities who are also interested in this topic.

Why we need a separate ontology for lab animal science? In addition to its independent community as described above, it is also because of the envisioned broad term coverage of the OLAS ontology. Among many use cases, one representative use case is to classify various lab animal models for vaccine studies as well as infectious disease studies. Our first version of modeling has identified hundreds of OLAS terms, which have been added to the current OLAS already. A related paper is this one from us: https://pmc.ncbi.nlm.nih.gov/articles/PMC4825961/ . For example, we found many lab animal models for tuberculosis and tuberculosis vaccine research such as mice, cattle, macaques. Another typical example is the variety of flu lab animal models (mice, ferrets, guinea pigs, swine, non-human primates, etc.) ( https://pmc.ncbi.nlm.nih.gov/articles/PMC8228315 ). Each of these models have their pros and cons. For researchers who do research in these areas, such knowledge is critical for their research success and productivity. To deeply understand and study them, we propose to use ontological modeling and ontology-focused knowledge representation.

Another planned task for OLAS modeling is the taxonomical representation of the large number of lab animal models. These lab animal models and mutant strains are not covered by NCBITaxon. I remember over ten years ago we tried to ontologize Jax mouse models (such as the commonly Balb/c and C57 mice). Initially, Jackson Lab expressed some interest, but in the end it did not work out well. With the OLAS, we plan to ontologize various mouse models from Jax lab and other labs, and ontologize other animal models (e.g. rabbits) from other companies as well, and use ontology to represent their representative characteristics. This is a huge work but meanwhile we think it will benefit everyone who produce and use animal models.

Other planned use cases are many, including ontological modeling and analysis various lab animal models and the associated conditions and outcomes when they are used for biomedical studies such as sepsis and cardiovascular disease studies as well as pathology core data annotation and integration. We also have many collaborators in these use case studies, which will be conducted primarily in our University of Michigan. Meanwhile, we also welcome collaborations and joint development and usage from everyone who is interested.

Having all the above envisioned terms to be included in OBI would likely make OBI overcrowded and biased to the specific domain of lab animal science. I think that this is not what OBI would like to see either.
Nevertheless, we would like to use OBI as much as we can in the high level of biomedical investigation representation. In addition, we would be happy to contribute broadly applicable terms from the lab animal science community to OBI, and get back to OLAS for its integrative representation and usage. We can discuss more on this later.

[bpeters42]

I don't want to be the only one weighing in, as I have an obvious bias towards not wanting another duplicate ontology for OBI. This has been a persistent problem, with ontologies coming and going and covering overlapping parts, which makes it hard for an outsider to know what terms they should chose. And to be clear: Much of the scope defined here is completely duplicative, and laboratory animal model studies have been at the center of OBI development from the very start, and we routinely have representatives of those community on our calls.

The parts that I see here that could well live in a separate ontology are lab animal strains, and potentially cataloging specific animal models - as long as the experimental techniques come from OBI.

The one thing that quite upsets me is you saying: "I think that this is not what OBI would like to see either." - How about asking???