Pediatric Obesity Tracking Ontology (OTO)

[duygucelikertugrul]

Title

Obesity Tracking Ontology

Short Description

OTO

Description

OTO Knowledgebase. Protégé ontology editor was used to develop the OTO. OTO encompasses a representation, formal naming and definition of the categories, properties and relations between the concepts, data and entities in pediatric obesity management and treatment.
The main root class of OTO is “Thing” class that is divided into various sub-concepts such as “Development_Feedback”, “Gender”, “Patient”, “Risk_Factor”, “Suggestions”, “Intake_Suggestions”, and “Z-Score”, etc. In addition, based on these sub-concepts, several Object Type Properties (OTP) are generated using “owl: top Object Property” element such as “has_Development_Feedback”, “has_Gender”, “has_Risk”, “has_Suggestion”, etc. Besides, various Data Type Properties (DTP) are created using “owl: top Data Property” such as “has_Age”, “has_BMI”, “has_BMI Percentile”, “has_BMI”, “has_Z-Score”, “has_Decimal_Age”, “has_Weight”, “has_Height”, “has_Health_Risk”, “has_Height_Percentile”, “has_Height_Z-Score”, “has_L_value_BMI”, “has_M_value_BMI”, “has_S_value_BMI”, etc. Lastly, semantically structured relation belonging to the OWL classes is “OWL individual” elements.
STotally, 118 different SWRL rules were created on the OTO. The rules were considered in two categories: (1) “56 rules for computation through mathematical expressions” and (2) “62 rules for inferring personalized supportive treatment suggestions”. WRL Rules on OTO.

Identifier Space

OTO

License

CC0

Domain

diet, metabolomics, and nutrition

Source Code Repository

https://github.com/duygucelikertugrul/OTO/blob/main/OTO.owl

Homepage

https://github.com/duygucelikertugrul/OTO

Issue Tracker

https://github.com/duygucelikertugrul/OTO

Contribution Guidelines

https://github.com/duygucelikertugrul/OTO

Ontology Download Link

https://github.com/duygucelikertugrul/OTO

Contact Name

Prof.Dr.Duygu Çelik Ertuğrul

Contact Email

[email protected]

Contact GitHub Username

duygucelikertugrul

Contact ORCID Identifier

https://orcid.org/0000-0003-1380-705X

Formats

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

Dependencies

No response

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.

[pfabry]

Dear @duygucelikertugrul,

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!

[bpeters42]

While this is not the official review, we wanted to point out that there seem to be significant issues with how the ontology is designed. Please check the pre-registration checklist carefully, and make sure that you have understood and implemented these.

[matentzn]

@duygucelikertugrul

In my opinion OTO is not an ontology - It is technically in OWL format, but it comprises mostly a huge ABox:

There is a tiny bit of RBox modelling, but zero TBox, most axiomatisation is in the form of SWRL rules, which is not compatible with any OBO ontology.

You also check all your checkboxes above, but a few are totally wrong, like

No identifier in OTO is designed according to OBO standards.

No small attempt was made to reuse RO relations.

I think this ontology is too far out of scope. @duygucelikertugrul please feel free to argue against me, I am happy to be wrong!

[nataled]

To add to the above, there appear to be no definitions (violation of Principle 6), and the term names violate OBO standards against capitalization (for example, Parent), camel case (for example, MomSuggestions), and use of underscores (for example, Risk_Factor), all of which violate Principle 12.

[pfabry]

@duygucelikertugrul
Your ontology is available on the dashboard.
As indicated by the dashboard and previous comments, several issues must be addressed before this ontology can be considered a candidate for the OBO Foundry.

[matentzn]

@duygucelikertugrul please feel free to respond to our comments - we will close this request on the 10th of December, but you should always feel free to reopen the request or submit a new one! Thank you for your submission.