Request for new ontology Radiation Therapy Ontology

[jonathanbona]

Title

Radiation Therapy Ontology

Short Description

An ontology describing the domain of radiation therapy concerned primarily with the processes and equipment used to deliver therapeutic radiation in a clinical setting.

Description

An ontology describing the domain of radiation therapy concerned primarily with the processes and equipment used to deliver therapeutic radiation in a clinical setting. RTO aims to be useful in bridging institutional and clinical practice differences. It is also intended to useful in investigations in oncology which includes medical, surgical and genetic oncological domains. In modeling this domain, RTO uses terms from many existing OBO ontologies, including the Chemical entities of Biological Interest; Ontology for General Medical Science; Ontology for Biomedical Investigations; and more.

Identifier Space

RTO

License

CC-BY 4.0

Domain

health

Source Code Repository

https://github.com/aapm-bdsc-ontology-tg/rto

Homepage

https://github.com/aapm-bdsc-ontology-tg/rto

Issue Tracker

https://github.com/aapm-bdsc-ontology-tg/rto/issues

Contribution Guidelines

https://github.com/aapm-bdsc-ontology-tg/rto/blob/main/CONTRIBUTING.md

Ontology Download Link

https://github.com/aapm-bdsc-ontology-tg/rto/blob/main/rto.owl

Contact Name

Jonathan Bona

Contact Email

jonathanbona@gmail.com

Contact GitHub Username

jonathanbona

Contact ORCID Identifier

https://orcid.org/0000-0003-1402-9616

Formats

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

Dependencies

• bfo
• cob
• chebi
• doid
• iao
• obi
• ogms
• pato
• rbo
• ro

Related

No response

Usages

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.

[cmungall]

Links don't resolve - perhaps you accidentally made the repos private?

[jonathanbona]

Links don't resolve - perhaps you accidentally made the repos private?

Fixed, thanks!

[pfabry]

Dear @jonathanbona ,

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!

[pfabry]

Dear @jonathanbona
Your ontology has been added to the OBO NOR Dashboard.
The lexmatch results are available here: RTO lexmatch 20250228.txt
All terms IRI must follow the OBO Foundry format (cf. Principle 3).

[jonathanbona]

Thank you @pfabry. We haven't included OBO Foundry style IRIs yet because we did not want to presume that we would receive the requested namespace. Is this something we could change after a namespace is granted?

[pfabry]

Dear @jonathanbona,

Following Principle #3, a namespace should be in place at the time of submission, even if the IRI does not resolve. However, this can be adjusted during the review process. Since this was the only technical issue, a reviewer will be assigned soon.