Add "disease or disorder" to COB

[matentzn]

Addresses #19

Ludi Incipiant.

[wdduncan]

For what it is worth, I wish we would explore the so-called Schultz approach (mentioned multiple times) a bit more instead of going back and forth endlessly about disease/disorder. Or, we should use different labels so that we don't continue arguing about which senses of 'disease' or 'disorder' are correct, and whether it is best to conflate the two.

But since those options have not garnered a lot of interest, I think the best option is to logically define disease or disorder as the union of disease or disorder, where disease is subtype of disposition and disorder is a subtype of material entity. This allows MONDO to use this class as well other ontologies that need the disposition / material entity distinction.

I realize there are drawbacks to this:

1. It may encourage annotators to gloss over relevant/important distinctions between the dispositional and material senses of 'disease'
2. To quote from above: "There is nothing to stop anyone to align with a huge disjunction of all class in COB."

As for (1), there are (based on @matentzn comments) are a fair number of professionals who are not bothered by the conflation. We should respect that. I would, however, be concerned if more of the conflated subclasses from MONDO wanted to be entered into COB. This could impose the conflation between disease and disorder on those of us who need to clearly disambiguate between diseases (as dispositions) and disorders (as material entities). I have worked with researchers in the domains of cancer and dentistry that were quite concerned with being clear about these distinctions.

As for (2), I'm not seeing why this is an alarming concern. Sure ... it is possible, but whether it actually happens is a different matter. There is nothing to stop other OBO ontologies from doing this within their own domains, but we don't find them.

[nataled]

The label aspect is one I thought might be the problem, hence why I suggested a different one.

[bpeters42]

For what it is worth: I am with Chris Stoeckert spelled out comment on how to re-label and align these 'pathological classes' based on the Schultz approach (It is SCHULTZ, not SHULTZ - we are talking real Germans here). That approach also allows people like myself that want to try to fit specific terms into the lowe level buckets as much as possible. But gives room to integrate MONDO.

[wdduncan]

@bpeters42

It is SCHULTZ, not SHULTZ - we are talking real Germans here

Yes. Thanks for pointing that out ... I corrected my misspellings.

I noted the Schultz approach (here) as an avenue to explore (not necessarily to commit to) for finding a middle ground between OGMS/DO and MONDO positions. While I am happy to see that @cstoeckert and @bpeters42 support this, I fear that the proposal to map COB to Biotop classes will (yet) create more arguments. This is something that needs to be considered as well.

To be honest, I don't see a perfect solution here. Each side has advocates that are unwilling to budge.
I endorsed the logical disjunction of disease or disorder in hopes that each side would see that are getting enough of what it wants to tolerate the other view points. A kind of ontological détente (I suppose).

Unfortunately, I fear my efforts have failed. I am planning to attend to disease/disorder call. Until each side starts seriously thinking about solutions that don't require jettisoning the other, I have strong doubts that anything will result from the call. In other words, if the call only amounts to each side saying why they are right and the other side is wrong, this debate will just continue.

[alanruttenberg]

I think the real problem here is the overlap of MONDO and DO and lack of a unified plan for how the Foundry will deal with pathology. Objection to the change stems from the feeling that we would be cementing in the current dysfunction with no path towards resolving the elephant in the room. I don't think anyone thinks that the Schulz/OGMS distinctions, sans disjunction, are bad distinctions or difficult to distinguish. I think that I would not have objections to the addition of the disjunctive term if there was a commitment to a) resolve the redundancy between DO and MONDO and b) commit to, in the longer term, refining terms to be in the more specific class. If there's some way to shift the conversation in that direction, we should attempt it. If you agree this is a plausible way forward, perhaps we could craft a message together to shift the conversation.

Absent that, I don't think I would support going forward with the change, and would instead modify the dictum that every ontology had terms directly below a COB term to be instead that every ontology be under a term fully defined in terms of the COB terms. That would allow for disease or disorder to still be conformant, but stay in MONDO. In speaking with Barry it was his suggestion that regardless of this issue, there should be the ability root under defined classes based on the COB terms.

[nataled]

My recollection is that early discussions touched on the issue of 'this or that' (defined class) terms, and that it was decided they would NOT be in COB. This of course would not work for those ontologies that make use of such terms at the very top levels but, again, this was previously viewed as okay.

[ddooley]

Where can I catch up on the result of the special meeting on "disease or disorder"?

[bpeters42]

I wish I could point you to the new consensus that emerged. That didn't happen, and wasn't the point of the meeting. We did succeed in pointing out much more clearly what different people are meaning and intending when they use the terms, and there was a general much more positive spirit.

If I were to summarize here what I think we agreed upon, I will likely not capture everything accurately. So apologies in advance.

• disease is a term that everyone uses and wants. It should be a characteristic of an individual organism, and it should be tied to a disease course (process in which the disease manifests or not).
• 'disorder' as a term needs to be avoided at all costs, as people have very different understandings what it means (a subclass of diseases or a physical property or a general abnormality). A very large part of the discussion focusessed again on different understandings of the term. So we really need to drop it.
• 'physical abnormality' would be a potential term that can capture the underlying material properties that can be causative for diseases - like infections, genetic mutations, injuries, oversensitized immune system. That would be OGMS:disorder - but avoiding 'disorder' as a label.

I should have summarized this right after the call, and I am likely forgetting things. And not everyone was extremely happy. But it seemed like the above would be a way to move forward in the spirit of COB to nail down better what we even mean, and expose differences in our understanding.

• Bjoern

On Thu, Mar 23, 2023 at 2:13 PM Damion Dooley @.***> wrote:

Where can I catch up on the result of the special meeting on "disease or disorder"?

— Reply to this email directly, view it on GitHub https://github.com/OBOFoundry/COB/pull/226#issuecomment-1481919149, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADJX2IRBQXGTJMORLYCJ4R3W5S4H7ANCNFSM6AAAAAAUHU7UZQ . You are receiving this because you were mentioned.Message ID: @.***>

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[matentzn]

I am afraid someone will need to dedicate some serious time to shepherd this issue forward. One option is to recruit a volunteer to OBO Ops whose sole responsibility is to mediate a solution, summarise the current situation from time to time and make a strategy?

[bpeters42]

Would you have a volunteer in mind? If so, I would love that solution.

[matentzn]

There are a few people I could imagine doing this (Role: COB mediator - a person whose role is the mediation of modelling disputes on the COB issue tracker). The problem is that the most suitable people are the ones that already have a very full plate. For me the key ingredients of a mediator are:

• reasonableness and not too strong personal opinions (excludes everyone that has already commented on this thread)
• ability for organising information (in this case, collecting and presenting arguments)
• sociability in the sense that they can work with people without riling them up
• a thick skin and proactivity to drive difficult discussions forward.
• Enough understanding of ontologies to understand the "building a formal ontology BFO style vs creating a semantically uncommitted upper structure for data integration" dichotomy that we have

A few people I think of that would fit the bill above:

• Allen Baron (DO team, of course I don't want to throw him to the wolves, but he is just very reasonable through and through)
• Sierra Moxon (Monarch/NCATS translator)
• Tiago Lubiana (Postdoc, Wikidata, Cell Ontology)
• Jim Balhoff (RENCI)

We could reach out to them 1 by 1, or we could propose the role on OBO level and see if people volunteer that I have not thought of yet.

[alanruttenberg]

What does it mean for an ontology to be "semantically uncommitted"?

[matentzn]

All root classes are subclasses of BFO:entity seems quite uncommitted wrt TLO, compared to using very specific BFO distinctions. The same logic would apply to COB.

[bpeters42]

I just wanted to add to the comment from Nico regarding semantic commitment: Most high-level COB classes are BFO classes or children thereof. We have some problem cases (like here: disease/disorder) where there is disagreement on the placement. But we are working towards trying to resolve that. In the meantime, we accept these uncommitted classes in order to make OBO ontologies interoperable as best we can - which is the primary goal for COB.

[allenbaron]

I appreciate the desire to add disease and disorder to COB. I didn't attend the last meeting on this (April?) but I was under the impression that it had been decided in that meeting that these two terms would be added (using the OGMS definitions? not sure about specifics).

What else, if anything, needs to be done?

I apologize for the long delay between this and previous responses.