Request for new ontology [Exercise Medicine Ontology]

[DarkKnight0-0]

Title

Exercise Medicine Ontology

Short Description

A core reference ontology built upon BFO about exercise medicine and it contains the related terms for healthy people, people with chronic conditions and people living with diability to exercise.

Description

The concept of "exercise is medicine" is gaining traction globally, highlighting the importance of personalized exercise prescriptions for better efficacy than standardized approaches. However, current guidelines often need more support for individualized prescriptions, posing a significant challenge. To bridge this gap, we gathered data from established guidelines, databases, and articles to develop the Exercise Medicine Ontology (EXMO), intending to offer comprehensive support for personalized exercise prescriptions. EXMO encompasses physical activity terms, health status terms, exercise prescription terms, and other related concepts. It has successfully undergone expert evaluation and consistency validation using the ELK and JFact reasoners. EXMO has the potential to provide a much-needed standard for individualized exercise prescription. Beyond prescription standardization, EXMO can also be an excellent tool for supporting databases and recommendation systems. In the future, it could serve as a valuable reference for the development of sub-ontologies and could facilitate the formation of an ontology network.

Identifier Space

EXMO

License

CC-BY 4.0

Domain

health

Source Code Repository

https://github.com/DarkKnight0-0/exmo

Homepage

https://github.com/DarkKnight0-0/exmo

Issue Tracker

https://github.com/DarkKnight0-0/exmo/issues

Contribution Guidelines

https://github.com/DarkKnight0-0/exmo/blob/master/CONTRIBUTING.md

Ontology Download Link

https://github.com/DarkKnight0-0/exmo/blob/master/exmo.owl

Contact Name

Xingyun Liu

Contact Email

xyz19940216@163.com

Contact GitHub Username

DarkKnight0-0

Contact ORCID Identifier

0000-0002-9295-2767

Formats

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

Dependencies

• bfo
• ro
• doid
• hsapdv

Related

No response

Usages

No response

Intended Use Cases and/or Related Projects

No response

Data Sources

No response

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.

[ddooley]

@DarkKnight0-0
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.
• 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!

[anitacaron]

Hi @DarkKnight0-0 You can check the OBO NOR Dashboard results here

[anitacaron]

@DarkKnight0-0 Please note that there's another step that runs a lexical matching tool to check for lexical overlap with existing OBO ontologies. The results will be available soon after 22 July.

[DarkKnight0-0]

• OBO NOR Dashboard.

Thank you for the review. We have fixed the license problem.

[pfabry]

@DarkKnight0-0
The lexical matching hasn't find any duplicate in your ontology.

[shawntanzk]

Hi, just noticed that you used ODK (from this readme and the look of your repo), however, you do declare a lot of terms from other ontologies directly in your edit file rather than as an import. This is not directly a problem, however, according to principal 16 on maintenance, I would like to know how you plan to keep these terms up to date with the ontologies as they update.

PS I would also recommend using the ODK inbuilt dynamic import system which automatically does this. Hope that helps :)

[pfabry]

@jsstevenson has been assigned to review this ontology.

[DarkKnight0-0]

Hi, just noticed that you used ODK (from this readme and the look of your repo), however, you do declare a lot of terms from other ontologies directly in your edit file rather than as an import. This is not directly a problem, however, according to principal 16 on maintenance, I would like to know how you plan to keep these terms up to date with the ontologies as they update.

PS I would also recommend using the ODK inbuilt dynamic import system which automatically does this. Hope that helps :)

Thanks for the advice. We will use the dynamic import system to update the next version.

[jsstevenson]

Hi @DarkKnight0-0 -- thanks again for your submission. Below is my initial review. You may use this issue thread to ask for clarification and/or to update us on progress. Please feel free to voice any other questions or concerns as well.

Criteria

1. Ontology scope

• Was the ontology developed for a very specific purpose or community?: Yes. As noted in the request PR, exercise medicine is a specific field with a corresponding academic community.

• Do the terms fall within the ontology’s stated target domain of knowledge?: As discussed below, there are many terms that are out of scope, and should be imported from higher-level and domain-specific ontologies -- but there is a core set of terms that are reasonable to define here.

2. Terms with the new ontology prefix

• Do the terms follow the OBO identifier scheme?: No, URIs do not consistently conform to the OBO Foundry Identifier Policy -- I'm seeing a few different URI schemas:

  • http://purl.obolibrary.org/obo/emo.owl/EXM_0000001
  • http://purl.obolibrary.org/obo/exmo.owl#patient
  • http://purl.obolibrary.org/obo/exmo.owl/EXM_0000214

These must all be in the format of e.g. http://purl.obolibrary.org/obo/EXMO_0000001.

• Are there terms with the same meaning available in another OBO Foundry ontology?: I did not perform an exhaustive check, but upon skimming the ontology I found a number of classes that are defined elsewhere in OBO domain ontologies:

  • http://purl.obolibrary.org/obo/exmo.owl/EXM_0000039 "skeletal muscle": http://purl.obolibrary.org/obo/UBERON_0001134
  • http://purl.obolibrary.org/obo/exmo.owl/EXM_0000043 "basal metabolic rate": http://purl.obolibrary.org/obo/CMO_0003955
  • http://purl.obolibrary.org/obo/exmo.owl/EXM_0000056 "total lung capacity": http://purl.obolibrary.org/obo/CMO_0000380
  • http://purl.obolibrary.org/obo/exmo.owl/EXM_0000074 "core body temperature": http://purl.obolibrary.org/obo/CMO_0001036
  • ... many other possible terms of overlap with CMO classes -- pulse, blood pressure, heart rate, cholesterol level, etc
  • http://purl.obolibrary.org/obo/exmo.owl/EXM_0000097 "questionnaire": http://purl.obolibrary.org/obo/OBI_0001000
  • http://purl.obolibrary.org/obo/exmo.owl/EXM_0000368 "electromyography": http://purl.obolibrary.org/obo/MAXO_0035091
  • http://purl.obolibrary.org/obo/exmo.owl#patient "patient": several possible candidates
  • http://purl.obolibrary.org/obo/exmo.owl/EXM_0000214 "person": several possible candidates

I suspect there are several other cases as well. New OBO ontologies are required to only define new terms unique to their intended scope, and import terms from existing ontologies when available. If a term from another ontology is within its scope but its definition is somehow lacking, we would strongly prefer that you work with maintainers of that ontology to improve their definition, rather than creating a new, redundant term.

• Is there another OBO Foundry ontology whose scope covers any of the new terms?: Noted above that there's a good deal of possible overlap with terms already defined in Uberon, CMO, the Cell Ontology, and others. There are definitely a decent number of terms in here that wouldn't be within scope anywhere else (e.g. exercise equipment).

• I found a handful of cases where term definitions were copied directly from other resources, without attribution. For example, the textual definition for EXM_0000378 ("glutamate") is from NCIt, the definition for EXM_0000373 ("endorphin") is from MeSH (at minimum this definition should probably be revised given the different context), and the definition for EXM_0000375 ("norepinephrine") is from PubChem. Each of these example terms should probably be imported from another OBO ontology anyway, but this does raise independent concerns about attribution (both in terms of good academic practice and FAIRness, and for potential data license issues). It is very important that direct textual content be properly annotated to reflect its original source.

• Around 80 of the 380 new classes lack definitions. I think that's within acceptable limits but it might be good to review and provide definitions for more ambiguous instances.

3. Correct use of imported terms

• If the ontology reuses terms from other OBO ontologies, are they used accurately?: There's reasonable use of DO, uberon, and human developmental stage classes. As noted by @shawntanzk, they're manually declared rather than imported via ODK -- so there could be some slippage in the future unless this is remedied.

• Are imported terms in appropriate hierarchies, and do they preserve the term’s upper-level alignment?:

• Are any additional axioms used for these terms correct in both a technical (e.g. passes reasoning) and substantive sense?: I'm concerned with how restrictions are added to some upper ontologic terms. For example, this restriction that BFO_0000019 ("quality") must be a quality of a EXM_0000214 ("person").

<owl:Class rdf:about="http://purl.obolibrary.org/obo/BFO_0000019">
    <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000020"/>
    <rdfs:subClassOf>
        <owl:Restriction>
            <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000080"/>
            <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/exmo.owl/EXM_0000214"/>
        </owl:Restriction>
    </rdfs:subClassOf>

Similar restrictions are added to BFO_0000034 and HsapDv_0000000. It's not clear why it would be preferable to further restrict the BFO "quality" concept rather than creating some kind of new class reflecting the particular type of quality that is associated with a person. Because this is a fairly significant case, I think it's reasonable to require that this is fixed, assuming there isn't a pressing justification.

4. Basic review of axiomatic patterns

• Are axioms generally stated simply or are they highly complex? (Highly complex axioms will require extra scrutiny.): Generally quite straightforward. No complaints.

• Are existential restrictions used correctly?: yes.

5. Appropriate use of object properties

• Are object properties used in a manner consistent with their definitions, domain, and range?:

  • There's one new object property defined, as far as I can tell -- EXM_0000006, "Abbreviation". I'm not sure if it would be desirable to instead import this from somewhere, given that this is obviously not the first place that you'd want to annotate a class with an abbreviation, but I'm not sure if there's a standard source to pull from.

  • a lot of the values for oboInOwl:hasDbXref are formatted in a nonstandard way, as <Name>: <LUI> (for example UMLS CUI: C0005938) rather than a more standard CURIE. These should be restructured to ensure they are more easily computable by removing the space and using prefixes as defined in a central entity like the Bioregistry or identifiers.org. So, for example, I would expect this value to be umls:C0005938.

6. Responsiveness to suggested changes

• Have the developers been willing to fix any identified issues during the review?: The developers have been responsive so far to individual comments. This is the first iteration of the formal review.

Other

• The EXMO repository is located under a GitHub user account -- we generally recommend that ontologies are housed within a GitHub organization to ensure sustainability.

Action items

• MUST: Fix URI format for all new terms to adhere to the OBO identifier standard
• MUST: import all out-of-scope classes from other OBO ontologies, and not define redundantly within EXMO. At a glance, I found a number of violations; I would recommend a term-by-term review.
• MUST: annotate all cases of textual definitions copied from external sources appropriately. I also found a number of instances of this, and would recommend a term-by-term review.
• CONSIDER: Review remaining terms lacking textual definitions and add where helpful
• SHOULD: Import terms from other ontologies via ODK rather than re-declaring manually
• MUST: remove axioms/restrictions placed on imported terms, and develop alternate constructions to perform the equivalent logical operations.
• MUST: format hasDbXref property values as proper identifiers and using standardized namespace prefixes
• CONSIDER: relocate the EXMO repository to a GitHub organization, rather than an individual user account's repo

[wdduncan]

Hello. We are checking in about the status of the requested update to your ontology. Please let us know if you have further questions.

[DarkKnight0-0]

Hello. We are checking in about the status of the requested update to your ontology. Please let us know if you have further questions.

Thanks for your comments, the criteria is very clear and easy to understand. We will revise the problems and release a new version.

[nicolevasilevsky]

@DarkKnight0-0 Hi - thanks for your comments, if you could kindly provide an update on the status of your release, we would appreciate it, thanks!