Request for new ontology The Pain Ontology

[wdduncan]

Title

The Pain Ontology

Short Description

The Pain Ontology contains terms for representing pain aligned with the International Association For the Study of Pain (IASP)

Description

The Pain Ontology contains terms for representing pain as defined by the International Association For the Study of Pain (IASP), meaning that pain is both an unpleasant physical sensation and unpleasant emotional experience. It includes terms and axioms to represent the multidimensional aspect of pain, such as temporality (e.g., acute, chronic), qualitative (e.g., sharp, throbbing), extent (e.g., local, widespread), biological mechanism (e.g., nociceptive, neuropathic), and specific anatomical locations (e.g., back, knee).

Identifier Space

PAIN

License

CC0

Domain

health

Source Code Repository

https://github.com/uflcod/pain-ontology/

Homepage

https://bioportal.bioontology.org/ontologies/PAIN

Issue Tracker

https://github.com/uflcod/pain-ontology/issues

Contribution Guidelines

https://github.com/uflcod/pain-ontology/blob/main/CONTRIBUTING.md

Ontology Download Link

https://raw.githubusercontent.com/uflcod/pain-ontology/refs/heads/main/pain.owl

Contact Name

Bill Duncan

Contact Email

wdduncan@gmail.com

Contact GitHub Username

wdduncan

Contact ORCID Identifier

0000-0001-9625-1899

Formats

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

Dependencies

• GO
• UBERON
• RO
• OMO
• BFO
• COB
• CL
• EMRO (if it is approved by the OBO Foundry)

Related

HP, NCIT, OMIT, SCDO, OGMS, MFOEM, PATO

Usages

Intended Use Cases and/or Related Projects

This ontology is being created in support of the NIH project Collaborative for REsearch to AdvanceTMD Evidence (CREATE).

Because of this, we have placed a version on bioportal: https://bioportal.bioontology.org/ontologies/PAIN

We were told using bioportal purls was fine when the ontology was being reviewed. We will change to using OBO purls if the PAIN ontology is accepted into the Foundry.

We recognize that there a number of ontologies that also have pain terms. We have provided a background review of these ontologies here: https://github.com/uflcod/pain-ontology/tree/main/background/ontologies

The title of the ontology is "The Pain Ontology" b/c there is already a Pain Ontology on bioportal and we had to have a different title.

Data Sources

We have a team of pain experts as part of the effort.

Additional comments or remarks

Just a few points to reemphasis:

• We are using bioportal purls, but we will change to using OBO purls if the PAIN ontology is accepted into the Foundry.
• We provide a background review of other pain terms: https://github.com/uflcod/pain-ontology/tree/main/background/ontologies
• We are presently using bioportal purls so that the ontology can be publicly viewed, but we will change to OBO obo purls if accepted to the Foundry.

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 @wdduncan

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!

[ddooley]

OBO Operations call May 26th - I Damion volunteer to review this if need be. Awaiting @pfabry call on this.

[pfabry]

Dear @wdduncan

Your ontology is available on the OBO NOR dashboard.
In addition, lexical matching did not identify any duplicate labels with respect to OBO Foundry ontologies.

A few minor issues should be addressed, although they do not need to delay the review process:

The IRI format does not follow OBO principles, notably the use of "/" instead of "_" between the IDSPACE and the LOCALID (as is also the case in EMRO).
There is a discrepancy between the license specified in the GitHub repository (CC0) and the license declared in the ontology (CC BY 4.0).
For the object property PAIN/0000062 ("experienced in"), the definition has been incorrectly annotated using rdfs:label.

As a side note, there are a lot of asserted taxonomy axioms that are redundant. For example, "neuron" and all equivalent axioms are duplicated by asserted subclass axioms.

@ddooley has been assigned to the review.

[wdduncan]

Thanks @pfabry. I will fix the IRI and label issue.

Re: there are a lot of asserted taxonomy axioms that are redundant. For example, "neuron" and all equivalent axioms are duplicated by asserted subclass axioms.

Yes. The reasoner outputs the subclass axioms from the equivalence axioms. This is redundant but not wrong. Having the subclass axiom helps with certain queries. AFIK, this is not an OBO violation. Please let me know if it is.

[wdduncan]

OBO principles, notably the use of "/" instead of "_" between the IDSPACE and the LOCALID

I thought this had been discussed. If the ontology is accepted into the Foundry, I will change the IRIs to match the Foundry's specifications. Currently, the IRIs are formatted to work on Bioportal. Did the Foundry change their minds about this?

[addiehl]

Hi Paul, we agreed at the OBO Foundry meeting on 4-28-2026 that non-standard IRIs are acceptable during the review process: "We agreed that nonstandard IRIs are acceptable during the review process, but need to be updated upon acceptance. James O. posted a comment on the ticket." Note that you were absent from this meeting.

Best regards, Alex

[wdduncan]

With the exception of IRIs, the pain ontology has been updated to address the problems noted.

[nlharris]

Thanks, Bill. @ddooley can you please take a look at this when you have a moment?