Open DarkKnight0-0 opened 2 months ago
@DarkKnight0-0 Thank you for your submission. The review will be executed as a two stage process:
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Hi @DarkKnight0-0 You can check the OBO NOR Dashboard results here
@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.
Thank you for the review. We have fixed the license problem.
@DarkKnight0-0 The lexical matching hasn't find any duplicate in your ontology.
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 :)
@jsstevenson has been assigned to review this ontology.
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.
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.
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.
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
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 candidateshttp://purl.obolibrary.org/obo/exmo.owl/EXM_0000214
"person": several possible candidatesI 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.
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.
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.
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
.
hasDbXref
property values as proper identifiers and using standardized namespace prefixesHello. We are checking in about the status of the requested update to your ontology. Please let us know if you have further questions.
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.
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
Dependencies
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
dc:license
annotation, serialised in RDF/XML.