OBOFoundry
Add "disease or disorder" to COB
Oh boy ... let the games begin :)
@matentzn What would the definition be for disease or disorder?
:) I added it to the PR! https://github.com/OBOFoundry/COB/pull/226/files#r1088050803
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
@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.
+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.
+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.
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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.
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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.
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-- 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 @.***
"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.
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!
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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.
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.
- 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.
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+1 to Bill and Alex
I am OK with Alan's recommendation: add "disorder" as an alternate term to 'disease'
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.
@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.
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.
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.
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.
FWIW: NCIT also has a top-level Disease, Disorder, or Finding class. Do you wish to conflate findings too?
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.
Clinical abnormality as term name? I'll leave the definition to the experts.
@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.
No problem, we just need someone to do that then!
Sorry ... I'm not volunteering to do that :)
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.
+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.
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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.
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?
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.