Add "disease or disorder" to COB

[matentzn]

Addresses #19

Ludi Incipiant.

[wdduncan]

Oh boy ... let the games begin :)
@matentzn What would the definition be for disease or disorder?

[matentzn]

:) I added it to the PR! https://github.com/OBOFoundry/COB/pull/226/files#r1088050803

[lschriml]

Question: Is the plan to add a term in COB as: 'disease or disorder' ??

I would request to have disease added as a it's own COB term.

And the term disorder, if other want it, as it's own distinct term.

Thank you, Lynn

[wdduncan]

@matentzn I think the definition you reference is the source of contention:

A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.

This is a definition for disease and begs questions about what is a disorder.

A more fruitful approach may be to follow @cmungall suggestion to adopt Schultz' pathological structure.

I think it is also reasonable to stipulate that COB uses the term 'disease' in the dispositional sense of the word, and create other terms for other senses of the 'disease' (e.g., disorder).

In any case, I fear this conversation will never end.

[addiehl]

+1 to Bill's comment. Adding a single class labeled 'disease or disorder' seems to be straight out favoritism of the MONDO approach and ignores the distinctions between disease and disorder used by OGMS and related ontologies like the Infectious Disease Ontology and DO. Might be better to keep 'disease', 'disorder', and 'disease or disorder' out of COB rather than alienate folks using alternative approaches, particularly if COB becomes a requirement for OBO Foundry membership.

[hoganwr]

+1 to Bill and Alex

On Thu, Jan 26, 2023 at 10:45 AM Alexander Diehl @.***> wrote:

+1 to Bill's comment. Adding a single class labeled 'disease or disorder' seems to be straight out favoritism of the MONDO approach and ignores the distinctions between disease and disorder used by OGMS and related ontologies like the Infectious Disease Ontology and even DO. Might be better to keep 'disease', 'disorder', and 'disease or disorder' out of COB rather than alienate folks using alternative approaches, particularly if COB becomes a requirement for OBO Foundry membership.

— Reply to this email directly, view it on GitHub https://github.com/OBOFoundry/COB/pull/226#issuecomment-1405292978, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAJR55TADHX72OBY65LSIY3WUKS3PANCNFSM6AAAAAAUHU7UZQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>

[lschriml]

I think we need both terms; 'disease' and 'disorder' in COB.

OGMS disorder: A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease.

Disease is used too widely utilized not to enable it's inclusion in the OBO Foundry membership.

On Thu, Jan 26, 2023 at 11:45 AM Alexander Diehl @.***> wrote:

+1 to Bill's comment. Adding a single class labeled 'disease or disorder' seems to be straight out favoritism of the MONDO approach and ignores the distinctions between disease and disorder used by OGMS and related ontologies like the Infectious Disease Ontology and even DO. Might be better to keep 'disease', 'disorder', and 'disease or disorder' out of COB rather than alienate folks using alternative approaches, particularly if COB becomes a requirement for OBO Foundry membership.

— Reply to this email directly, view it on GitHub https://github.com/OBOFoundry/COB/pull/226#issuecomment-1405292978, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABBB4DMWLEO4G6WL53TZQN3WUKS3NANCNFSM6AAAAAAUHU7UZQ . You are receiving this because your review was requested.Message ID: @.***>

-- Lynn M. Schriml, Ph.D. Associate Professor

Institute for Genome Sciences University of Maryland School of Medicine Department of Epidemiology and Public Health 670 W. Baltimore St., HSFIII, Room 3061 Baltimore, MD 21201 P: 410-706-6776 | F: 410-706-6756 @.***

[lschriml]

the label disease is used in the following ontologies: Disease Ontology (DOID), EFO, OMIT, SIO, OGMS, ADO, AGRO, APOLLO_SV, CCO, CIDO, CTO, GENEPIO, GeXO, HTN, IDO, IDO-COVID-19, MFNO, MFOMD, OAE, OBI, OBIB, OHD, OHPI, OMIABIS, ONE, ONS, OPMI, PLANP, RO, ReTO, ReXO, VIDO, VO, Orphanet, GSSO, MI, BAO, ExO

Disease or Disorder is used by: NCIT, MONDO

On Thu, Jan 26, 2023 at 11:58 AM Lynn Schriml @.***> wrote:

I think we need both terms; 'disease' and 'disorder' in COB.

OGMS disorder: A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease.

Disease is used too widely utilized not to enable it's inclusion in the OBO Foundry membership.

On Thu, Jan 26, 2023 at 11:45 AM Alexander Diehl @.***> wrote:

+1 to Bill's comment. Adding a single class labeled 'disease or disorder' seems to be straight out favoritism of the MONDO approach and ignores the distinctions between disease and disorder used by OGMS and related ontologies like the Infectious Disease Ontology and even DO. Might be better to keep 'disease', 'disorder', and 'disease or disorder' out of COB rather than alienate folks using alternative approaches, particularly if COB becomes a requirement for OBO Foundry membership.

— Reply to this email directly, view it on GitHub https://github.com/OBOFoundry/COB/pull/226#issuecomment-1405292978, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABBB4DMWLEO4G6WL53TZQN3WUKS3NANCNFSM6AAAAAAUHU7UZQ . You are receiving this because your review was requested.Message ID: @.***>

-- Lynn M. Schriml, Ph.D. Associate Professor

Institute for Genome Sciences University of Maryland School of Medicine Department of Epidemiology and Public Health 670 W. Baltimore St., HSFIII, Room 3061 Baltimore, MD 21201 P: 410-706-6776 | F: 410-706-6756 @.***

-- Lynn M. Schriml, Ph.D. Associate Professor

Institute for Genome Sciences University of Maryland School of Medicine Department of Epidemiology and Public Health 670 W. Baltimore St., HSFIII, Room 3061 Baltimore, MD 21201 P: 410-706-6776 | F: 410-706-6756 @.***

[matentzn]

"Mondo favouritism" is a great accusation to start a discussion with if you want it to finish quickly!

In Mondo, it was decided to treat disease and disorder synonymous - which means Mondo classes will never be aligned with COB if we separate the two. COB is explicitly not supposed to be BFO. The point is to create categories that are useful for biology / biomedical domain. Schulz conflation won't solve the disease vs disorder debate.

The matter of fact is:

mondo, ncit, ogms, doid and all other interpretations of "disease" can go under "diease or disorder". Mondo and NCIT cant align with a dual "disease" ... "disorder" solution.

EDIT: I am NOT the right person to have this discussion. I only care about one thing: the success of OBO and the unification of OBO ontologies.

[lschriml]

I don't see how doid and all other interpretations of "disease" can go under "disease or disorder"

Looking at the mondo term, disease or disorder, it is defined as: A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. [ OGMS : 0000031 ]

-- so the label is 'disease or disorder', but the definition is of a 'disease'

-- OGMS:0000031 is 'disease'

so why then, couldn't mondo's 'disease or disorder' fit in a COB disease term ?

On Thu, Jan 26, 2023 at 12:14 PM Nico Matentzoglu @.***> wrote:

"Mondo favouritism" is a great accusation to start a ticket with if you want this ticket to finish quickly!

— Reply to this email directly, view it on GitHub https://github.com/OBOFoundry/COB/pull/226#issuecomment-1405332591, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABBB4DNZE3TBD3ICYBBAU3LWUKWFTANCNFSM6AAAAAAUHU7UZQ . You are receiving this because your review was requested.Message ID: @.***>

-- Lynn M. Schriml, Ph.D. Associate Professor

Institute for Genome Sciences University of Maryland School of Medicine Department of Epidemiology and Public Health 670 W. Baltimore St., HSFIII, Room 3061 Baltimore, MD 21201 P: 410-706-6776 | F: 410-706-6756 @.***

[alanruttenberg]

If "disorder" is used as a synonym for disease, then add "disorder" as an alternate term. I believe the objection is that it's important to keep a distinction between disease and disorder, whatever they are called. Offering the disjunctive class will encourage its use, and then uses of it will mean one can't make the distinction.

[matentzn]

I don't see how doid and all other interpretations of "disease" can go under "disease or disorder

Can you elaborate @lschriml? the idea here is to create a conjunctive class that conflates the concepts of disease or disorder. Disease is a subclass of Disease or Disorder, so is "Disorder". This term can encapsulate all interpretations of disease/disorder, including "disease as a disposition" or "disease as a material entity". In any case, remember the point of COB: have a useful upper level - not a BFO conformant one. Now here is the crux I think: we may have different definitions of useful. For me it is: integrate all OBO ontologies into a reasonable knowledge graph that can be used, for example, to group genetic mechanisms for disease, or phenotypic profiles associated with them and provide background knowledge for AI systems of the future. This is a large scale, pretty dirty affair - unless you believe that everyone curating this kind of data (GWAS?) is thinking about the fine distinctions between disease and disorder. Or worse NLP: how will an NLP process ever understand whether a paper is talking about a disorder or a disease? Reality (biocuration, NLP) is dirty - if we insist cleaning it up BFO-style, we will never integrate our data, we will never build the grand OBO biomedical KG, and we will slowly fade into irrelevance, seeding ever more of our hard-earned knowledge into the abyss of neural networks with 1000 of layers and no way for us (as humanity) to even begin to grasp what's happening. It's our role as OBO to represent the Human side of the upcoming AI revolution, and hackling about fine-grained ontological distinctions will simply prevent us from being integrated into the AI stack that is being built right now.

[lschriml]

• 1 Alan's recommendation: add "disorder" as an alternate term to 'disease'

@Nico Matentzoglu @.***> -- It is not an OR situation, disorders, in disease nomenclature are a type of disease Naming of diseases: There is a long history here. Disorder has long been used synonymously (to disease) to name many types of diseases. e.g. mental health disorder -- Clinicians are and do think about the fine distinctions between disease and disorder.

• they consider the distinctions, as that drives the diagnosis and treatment, due to the cause (genetic mutation/environmental driver) and the timing of what went wrong (stage of development)

• physical disorders (e.g. orofacial cleft, spina bifida) are congenital diseases - that are present at birth - this is how 'disorder' is defined in the genetic/clinical world.

  -- how will an NLP process ever understand whether a paper is talking about a disorder or a disease?

  • NLP will be supported by utilizing the proper disease nomenclature - that is the proper disease names.
  • These are the names and language defined by the research disciplines. The names and their direct parents will be most useful for NLP. This will tell them the etiology of the disease.

Cheers, Lynn

On Fri, Jan 27, 2023 at 5:55 AM Nico Matentzoglu @.***> wrote:

I don't see how doid and all other interpretations of "disease" can go under "disease or disorder

Can you elaborate @lschriml https://github.com/lschriml? the idea here is to create a conjunctive class that conflates the concepts of disease or disorder. Disease is a subclass of Disease or Disorder, so is "Disorder". This term can encapsulate all interpretations of disease/disorder, including "disease as a disposition" or "disease as a material entity". In any case, remember the point of COB: have a useful upper level - not a BFO conformant one. Now here is the crux I think: we may have different definitions of useful. For me it is: integrate all OBO ontologies into a reasonable knowledge graph that can be used, for example, to group genetic mechanisms for disease, or phenotypic profiles associated with them and provide background knowledge for AI systems of the future. This is a large scale, pretty dirty affair - unless you believe that everyone curating this kind of data (GWAS?) is thinking about the fine distinctions between disease and disorder. Or worse NLP: how will an NLP process ever understand whether a paper is talking about a disorder or a disease? Reality (biocuration, NLP) is dirty - if we insist cleaning it up BFO-style, we will never integrate our data, we will never build the grand OBO biomedical KG, and we will slowly fade into irrelevance, seeding ever more of our hard-earned knowledge into the abyss of neural networks with 1000 of layers and no way for us (as humanity) to even begin to grasp what's happening. It's our role as OBO to represent the Human side of the upcoming AI revolution, and hackling about fine-grained ontological distinctions will simply prevent us from being integrated into the AI stack that is being built right now.

— Reply to this email directly, view it on GitHub https://github.com/OBOFoundry/COB/pull/226#issuecomment-1406335996, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABBB4DPNMBXCECHWUYG2R6TWUOSRRANCNFSM6AAAAAAUHU7UZQ . You are receiving this because you were mentioned.Message ID: @.***>

-- Lynn M. Schriml, Ph.D. Associate Professor

Institute for Genome Sciences University of Maryland School of Medicine Department of Epidemiology and Public Health 670 W. Baltimore St., HSFIII, Room 3061 Baltimore, MD 21201 P: 410-706-6776 | F: 410-706-6756 @.***

[zhengj2007]

+1 to Bill and Alex

I am OK with Alan's recommendation: add "disorder" as an alternate term to 'disease'

[matentzn]

Disorder is a type of disease? I guess if that is true, than we can solve this problem here by just renaming the class to disease and just getting common understanding that the disease class also subsumes all disorders? That could be doable.

[alanruttenberg]

@matentzn The suggestion isn't that disorder is a kind of disease. The definitions are primary. If someone wants to use the word disorder to mean what the disease definition says, that's ok, and that's what my proposal was about. There would still be a class disorder whose primary label will remain disorder. It would be a mistake to put a bona fide disorder as defined as a subclass of disease.

[matentzn]

While I disagree, can we make a suggestion that allows us to define a single term that encapsulates all ontologies including DO, Mondo and NCIT? Something sane we can use as a parent class.

[wdduncan]

I think it would really helpful if a definition can be provided for disease or disorder that permits the conflation you wish. At present, the definition doesn't allow this. We are only relying on our intuitions about what kinds of things would be encompassed by this conflation.

[wdduncan]

While I disagree, can we make a suggestion that allows us to define a single term that encapsulates all ontologies including DO, Mondo and NCIT? Something sane we can use as a parent class.

@matentzn This is what I am asking for. A definition for such a term has yet to be provided.

[wdduncan]

FWIW: NCIT also has a top-level Disease, Disorder, or Finding class. Do you wish to conflate findings too?

[matentzn]

You know me @wdduncan i have zero interest in defining things and a huge passion for integrating things that are defined in incompatible ways - I don't know what I want other than to start using COB and putting a domain on “disease has feature” relationship in RO (and all the other disease relations). I neither know what a disease is, not what a finding is; I just need a class to do my work of building the OBO knowledge graph.

[nataled]

Clinical abnormality as term name? I'll leave the definition to the experts.

[wdduncan]

@matentzn Unfortunately, I think in order of this proposal move forward (or gain consensus) a definition needs to be provided. As far as I know, giving such definitions has been a principle for the Foundry since its inception.

[matentzn]

No problem, we just need someone to do that then!

[wdduncan]

No problem, we just need someone to do that then!

Sorry ... I'm not volunteering to do that :)

[ddooley]

Stemming from @alanruttenberg comment, one test of disease and disorder placement is disability: it may be important for folks seeking to explain disabilities in terms of disorders rather than disease. "A disorder is a medical condition that may or may not give rise to disability depending on its severity. Disability is the functional disadvantage suffered by a person affected by that condition." https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6532374/ . Perhaps someone in the group can answer: A disability can sometimes stem from a disease, but it always ultimately stems from a disorder? If so, as supported by OGMS, disorder can't be a subclass of disease. +1 to making it an alternate term of disease tho.

[lschriml]

+1 for having both a disease and a disorder term.

potential 'disorder' definitions:

*disorder*: OGMS:0000045 OGMS disorder: A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease.

• OR*

Orphanet: Orphanet:557493 A clinical entity characterised by a set of homogeneous phenotypic abnormalities and evolution allowing a definitive clinical diagnosis.

• OR*

A disturbance of function, structure, or both of any part, organ, or system of the body resulting from a genetic or embryonic failure in development.

disease: A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.

On Fri, Jan 27, 2023 at 1:09 PM Damion Dooley @.***> wrote:

Stemming from @alanruttenberg https://github.com/alanruttenberg comment, one test of disease and disorder placement is disability: it may be important for folks seeking to explain disabilities in terms of disorders rather than disease. "A disorder is a medical condition that may or may not give rise to disability depending on its severity. Disability is the functional disadvantage suffered by a person affected by that condition." https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6532374/ . Perhaps someone in the group can answer: A disability can sometimes stem from a disease, but it always ultimately stems from a disorder? If so, as supported by OGMS, disorder can't be a subclass of disease. +1 to making it an alternate term of disease tho.

— Reply to this email directly, view it on GitHub https://github.com/OBOFoundry/COB/pull/226#issuecomment-1406901221, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABBB4DPCLVAH6BII53NZLCDWUQFMNANCNFSM6AAAAAAUHU7UZQ . You are receiving this because you were mentioned.Message ID: @.***>

-- Lynn M. Schriml, Ph.D. Associate Professor

Institute for Genome Sciences University of Maryland School of Medicine Department of Epidemiology and Public Health 670 W. Baltimore St., HSFIII, Room 3061 Baltimore, MD 21201 P: 410-706-6776 | F: 410-706-6756 @.***

[addiehl]

COB becomes much less interesting to me if 'disease or disorder' is the only allowed class. I could live with three classes, 'disease' and 'disorder' per the OGMS definitions and placements, and 'disease or disorder' under the root for MONDO's use.

[matentzn]

Ok. While many people in my world would probably oppose this, I guess a compromise would be to add a disease class and a disorder class for those ontologies that care about the separation and a union class “disease or disorder” which is logically defined as “disease” or “disorder”. This would give me what I need to continue my quest. I only care that there is one class, whatever its name or definition, that captures all Mondo, DO, OGMS etc ids. I also think that if we are able to supply a logical definition we do not need to supply a human readable one - it's an ontology after all. We can instead supply a comment and clarify that this class is a grouping class?

[alanruttenberg]

I don't think the disjunctive class should be added to COB. It's an invitation to ignore the distinction. Let it remain part of Mondo.

[matentzn]

Alright. So I am trying to find a solution for all of OBO (including OGmS DO and Mondo), and your proposal just covers what you think is right? So Alex and you do not want to use COb if there is a disease or disorder grouping class in there, and mondo, which closes more tickets in a year an than all of the rest of OBO combined, is just “wrong”, therefore should not be subsumed under COb? I don't get it y’all.. standardisation is not about asserting your position repeatedly, it is about trying to understand all sides of the debate, and finding out a solution that works for all of us. can you see a solution with Mondo being cob compliant or are you essentially saying that mondo (with all its doing for OBO) should be pushed out of the OBO library? Because COB compliance will be made mandatory for OBO ontologies in the mid term.. anyways I know this is a heated subject. Sorry if this all hits close to home but yes, it's simply wrong to say that just because there is a conceptual difference between disease and disorder, conflating them in a single term is always wrong. It is sometimes good sometimes bad. Some people like it others don't. Depending on the use case.

[addiehl]

Nico, just to be clear, I proposed the compromise position of having three classes, 'disease', 'disorder', and 'disease or disorder'. Alan Ruttenberg states he is opposed to having 'disease or disorder'.

I said that if 'disease or disorder' is the only allowed class in COB, I would lose interest in COB because the disease ontologies I work with and build care about the distinction between 'disease' and 'disorder'. And if use of a COB that discounts the distinction between 'disease' and 'disorder' becomes obligatory for the OBO Foundry, then I would think that that the OBO Foundry is imposing poor ontological practice on those who wish to participate in it.

I think the pragmatic reasons that MONDO has chosen to conflate 'disease' and 'disorder' are a separate issue, but MONDO should not get to impose a standard for COB and the OBO Foundry. My compromise solution is a "live and let live" solution where nobody needs to feel excluded.

[matentzn]

Thanks @addiehl and everyone else, hopefully the new suggestion captures your suggestions.

I tried to capture the comments here as much as I could (which I don't even know if Mondo folks will even agree with). Let me know what you think! I am open to any changes, but the equivalent class axiom is the one thing I cannot sacrifice.

[wdduncan]

The classes disease and disorder should be placed as subclasses of disposition and material entity (respectively) so that they align with their definitions.

[wdduncan]

@matentzn If the lexical definition says "X is a Y" and X is not defined formally as a subclass of Y in the hierarchy, then this creates confusion about what kind of thing X is. An important purpose of definitions is to disambiguate different senses of a term. If you want to include the processual sense of 'disease' (which is also common) as part of the meaning of disease or disorder, then the disjunction could include disease course as well.

Re definition source: I was actually on a call (was there more than one?) many years ago in which (from what I recall) DO agreed to adopt the OGMS definition of disease. Based on this, I think it is more appropriate for the definition source to reference OGMS:disease. However, can we include both DO and OGMS as sources?

[alanruttenberg]

@wdduncan let's not damage things futher by adding disease course to the disjunction. I'm still not clear on why a special class should be added just for Mondo. They can easiliy define the disjunction by themselves to no ill effect I can discern. OTOH adding the disjunction to COM encourages others to also erase the distinction, hence my objection.

So, @matentzn, what exactly is gained by having this in COB vs leaving it in Mondo?

[wdduncan]

@alanruttenberg I wasn't necessarily endorsing adding disease course into the disjunction ... just pointing what should be done if the processual sense of 'disease' were to be included too :)

[zhengj2007]

As we agree that we need the distinction between disease and disorder. So, adding 'disease or disorder' does not make sense to me. Besides, the COB is intend to make OBO ontology interoperable. Add 'disease or disorder' for including Mondo does not achieve the goal. It brings in the ambiguous entity.

[matentzn]

I think we may not agree on what COB is.. for you it is a BFO for Biology. For me, it is a sane upper-level ontology that makes some rough distinctions between concepts in the biomedical domain which are left ambiguous if they are ambiguous. To say "disease is BFO:disposition" is just not how Mondo sees the world! Mondo and its curators do _not believe the distinction is necessary for most practical purposes. Are you trying to say that only your worldview is valid? Mondo and DO/OGMS do obviously not agree. What do you expect then that Mondo simply says, "well we don't agree with you, and we cant be under COB, no problem! Lets do how you say"? Mondo and DO will interoperate through mappings, not through logical alignment, this much is clear anyways. The same is true for many of the anatomy ontologies and Uberon.

Just answer this question for me and we can wrap this up. Given these two assumptions:

1. Any ontology in OBO will soon be required to be under COB.
2. Mondo is an OBO ontology (and, secondarily, a driving force behind much of our infrastructure development, paying for many of the active TWG members and by far the most active OBO ontology.)

Which of the two do you prefer:

1. Find a way to accommodate Mondo's valid world view in COB
2. Insist on your worldview and have Mondo be excluded from OBO

[alanruttenberg]

This isn't a question of world view, and the dichotomy you present is not accurate. MONDO has a term whose definition is the definition of disease in OGMS. It does not define "disease or disorder" as disease or disorder, it simply uses an alternative label for OGMS disease. That it has minted a new IRI for the same term is not something that should be done in the first place. However, given the current state the correct placement of the MONDO term would be as an equivalentClass to disease, as defined by OGMS, or to simply use the IRI that COB does for disease.

The proposal is that COB include both OGMS disease and OGMS disorder. Therefore, there is no problem placing MONDO within COB.

Even if they defined their term as disease or disorder, COB including disease and disorder terms would give it the technical means to define that term.

I hope we at least agree that we work off definitions in OBO.

There's more that might be said about "worldview", but I think we should take that up privately, if you would like to discuss that further, as it is not germane to the issue at hand.

[cstoeckert]

I'd like us to consider the approach raised by @cmungall described in Schulz et al. Journal of Biomedical Semantics 2011. @matentzn indicated above that the “Schulz conflation’ won’t work but it's not clear to me why it wouldn't. If that approach works it has the.benefit of the work done to relate to SNOMED (described in the paper) and potentially offer an approach for addressing phenotypic abnormality and perhaps phenotypes in general. Drawing from the Results section of the paper and starting with COB classes we could have: COB:pathological entity mapped to bt:pathological entity COB:pathological entity equivalent to COB:pathological structure or COB:pathological disposition or COB:pathological process COB:pathological structure mapped to bt:pathological structure COB:pathological structure mapped to OGMS:disorder COB:pathological disposition mapped to bt:pathological disposition COB:pathological disposition mapped to DOID:disease COB:pathological disposition mapped to MONDO:disease or disorder COB:pathological process mapped to bt:pathological process We can discuss whether any of the mappings are equivalent.

[lschriml]

In order to make progress on COB, could we all agree to add the two terms (1) disease and (2) disorder to COB. And to continue the other discussions, points raised in this issue, for a later date/time.

[zhengj2007]

In order to make progress on COB, could we all agree to add the two terms (1) disease and (2) disorder to COB. And to continue the other discussions, points raised in this issue, for a later date/time.

It sounds good to me.

[matentzn]

I am against doing this, sorry. It means creating a solution that does not work for Mondo and make it impossible to negotiate a solution later on that does. Sorry!

[alanruttenberg]

I'm very confused. As I pointed out, MONDO only /calls/ the term 'disease or disorder'. The definition is that of disease as given in OGMS. Adding 'disease or disorder', defined as 'disease' or 'disorder' doesn't help MONDO AFAICT.

[matentzn]

The definition does not reflect practice and I asked the Mondo team to remove or revise it. it does not reflect the current interpretation. Mondo does not distinguish between disease or disorder, the two concepts are conflated in the Mondo view of the world! They even met this week with a few medical experts to discuss this issue and the decision remains: while a small difference between disease and disorder seems to have been acknowledged conceptually, for pragmatic reason they are treated as synymous/conflated.

[alanruttenberg]

In that, case, once the definition is revised, which should be preliminary, the presence of disease and disorder in COB will allow then to completely define disease or disorder in MONDO. There is no need to have the disjunction in COB. It's a defined class.

[matentzn]

I had 5 people sending me emails and messages to recommend to change a bit how I communicate here, but right now, I need time to retreat and formulate a new way to argue this case. I will have to look also at @cstoeckert and @addiehl proposals a bit more. Also, it seems like my position is not understood at all (what you are suggesting does not solve my problem - I need 1 named class to be able to query all diseases and disorders at once), so I probably need to make some pictures and organise an in-person meeting to solve this issue! I cannot agree to adding the strict disease/disorder distinctions proposed here.

[alanruttenberg]

Ok. Regroup. I'm game when you've organized your thoughts.

[matentzn]

Argument for a named class that captures Mondo and DO definitions.

Note: This is not an argument for or against any particular definition, just establishing the need for a named class that captures the Mondo and DO viewpoints. We still need to think about how best to achieve a minimal model that makes everyone happy.

Just because I am at the airport, let's start with my motivation, not the modelling now.

Use case 1: querying

How would you write this query without a sane grouping?

Use case 2: Sane domains and ranges

I am assuming here we don't want all our relations to have a disjunctive expression as a domain, because this will cause problems for lower expressivity ontologies, and create a big overhead maintaining properties.

Use case 3: COB alignment as a strategic goal of the OBO Foundry

Using disjunctive expressions for alignment purposes will simply make the purpose of this effort nil.