This page has been taken forward as a formal work item for the group, and further editing should be performed here: Basic Formal Ontology Discussion
Apologies for any mis-attribution or duplication that may have occurred in the transition. I hope we can edit that document into a discussion that could be left for future generations, working with comments and annotations as required in order to enhance the discussion, rather than forming the main body of the text as it has below. These comments are also not visible to users without a confluence account.
2019-07-15 10:02
Here is a brief discussion. BFO wants terms to be about "things in the real world", not "thoughts"
BFO feels most terms should be fully defined.
https://bmcmedinformdecismak.biomedcentral.com/articles/10.1186/s12911-018-0651
Some of the objections are
1 SNOMED should be about things in the real world and not about "concepts"
2 SNOMED should have most of it's terms fully defined
2 SNOMED should be based on BFO and there should be Continuants and Occurents and they should be mutually exclusive
3 SNOMED should have single inheritance.
I address these with counter arguments.
-----------------------------------
Single inheritance is not an advantage to SNOMED.
Viral Pneumonia should be both an Infectous Disease and
a Respiratory Disease. For Logical retrieval this is
and advantage not a problem that needs fixing.
Viral Pneumonia is only a Respiratory Disease in ICD and
that is a big disadvantage for concept retrieval in ICD.
SNOMED can not be an ontology that is not about "concepts"
but is about "things in the real world".
Past, current,
and future medical science can never know "things in the
real world". All of the historical "diseases" that no longer exist
because of subsequent scientific studies prove that.
A good example today is the "concept" of "Systemic Lupus
Erythematosis". This term is quite useful and necessary
today. But is is only a concept. It is NOT something in
the real world.
Once lupus is understood
what exact combinations of genetics and environmental triggers
cause "lupus", it will be discovered that either lupus is
a term for many different diseases "in reality" or depending
on where we draw the line, we might in the future discover that
Sjogrens, and perhaps other diseases should in fact all be
given a new concept name and grouped together.
This also is related to the criticism that most terms in an ontology
should be fully defined. In the real world of clinical medicine,
many diseases cannot be fully defined.
Rheumatoid Arthritis is a good example.
We don't know what it is. We have somewhat arbitrary clinical
criteria that will certainly later be thrown away once we know
the exact genetic and environmental mechanisms. Then we may even
throw away the whole idea of Rheumatoid Arthritis. We may divide
it into many sub diseases, or we may group it with another disease
under a more broad heading. So the idea that SNOMED needs to fully
define more terms, and the other idea that SNOMED should not be
"concepts" but represent things in reality is already a contradiction.
Another problem in BFO is the disjointness between Continuants
and Occurents. BFO would have one term for Asthma that is
a Dependent Continuant for the propensity for Asthma Attacks.
Then Asthma attacks would be Occurants. But for a real patient
who has Asthma, they probably always also have some small component
of the Occurant going on. Sometimes it's bad enough to go to the
Emergency Room, or to take rescue inhalers, but there is no
particular arbitarary severity when all of a sudden the Occurent
is turned on and becomes present.
It is far more useful in clinical medicine to
Think of Chronic and Acute Asthma. And all clinicians understand
that the line for Acute Asthma is subjective and partly dependent
on the subjective experience of the patient. (Some go to the
Emergency room when others would not).
When reading criticism of SNOMED, it appears that many of the critics
dont understand what clinical medicine really is. It is not so much
about "things in the real world" where everything is either a Continuant
or and Occurent, but as discussed above, it is a temporary, always
changing world of ideas "concepts" that are very useful for deciding
treatments. It is understood that these concepts always are in a state
of flux. They come and go, and as they do the usefulness of the concepts
progress and become closer to the real world, and the concepts become
more useful in making treatment decisions, and in research.
----------------------------------
2019-07-15 10:03
Are we all in USA and EU? So we can usually meet around the same time as the MAG meeting today?
I don't know how to set up a doodle poll to pick meeting times. Do any of you have an admin assistant who can help coordinate times and dates for meetings?
2019-07-16 08:50
Here's the Doodle: https://doodle.com/poll/g3hgn3pn45qvw73e
I made 1-hour slots, but we could extend to 90 minutes if needed.
/Daniel
2019-07-16 08:53
Michael Lawley is down under, so 20.00-ish UTC is likely the sweet spot.
2019-07-16 08:49
Hi All,
About single inheritance, what I remember from discussions with Barry and Werner during the Semantic Mining project (2004-8) was that they had objections to having multiple stated parents (multiple genera) (see Buidling ontologies with BFO, page 79). 75570004 |Viral pneumonia (disorder)| fulfills this criteria, although sometimes by necessity multiple stated primitive parents are needed to account for multiple aspects of meaning not defined through attributes.
About real world vs. thoughts (i.e. mind-dependent entities such as ideas, plans, suggestions, ...), first, thoughts are also part of the real world and not accepting that is being relativistic about ontology (Barry, the relativist!), second, mind-dependent entities are clearly relevant in the health care domain, so at least a health care ontology should comprise both mind-dependent and mind-independent entities. Does SNOMED always clearly separate the two? Probably not, but that requires an analysis beyond the analysis of the definition of disease (...and "a disease is a concept" seems to have been removed from the editorial guide) in SNOMED. Further, the second-order (instances-to-types) relationship between mind-dependent and -independent makes a faithful representation in OWL (and EL in particular) a challenge to say the least (see Schulz et al An Ontological Analysis of Reference in Health Record Statements). In e.g. the Observables model this issue has been discussed but deemed not worth the effort and complexity (e.g. does the alcohol concentration of non-alcoholic beer exist? and then what are the implications for use of existential restrictions?)
Regarding the definition status of some pre-theoretical classes of disease I think Flier and de Vries-Robbé has a good paper here: https://www.ncbi.nlm.nih.gov/pubmed/10765492
/Daniel
2019-07-16 04:54
A further email with Barry.
From Barry
---------------------
I agree with this.
So can we give necessary but not sufficient conditions for someone's having (what we are pleased to call) SLE?
Werner and I wrote a paper on precisely this problem as it arises for Bruxism (see attached) -- it arises for very many putative diseases. The paper shows what confusions arise if people think that something can be both a dependent continuant and an occurrent.
The solution, of course, is to distinguish Asthma (the disposition) from Asthma attack (the realization of this disposition).
Computers need handholding. People are much clever and can cope without.
I agree with SNOMED's use of disorder (which we replicate here -- this paper became http://www.ontobee.org/ontology/OGMS )
I also sympathize with the use of 'finding' as articulated here:
The problem with the latter reading is when SNOMED states that :\?The Clinical finding hierarchy contains the sub-hierarchy of Disorder"
Cancer is not an observation.
------------------------------------------
My most practical objection is clinicians "need handholding" too. You will never get EHR users or vendors to have two separate terms for diseases like Asthma.
One meaning propensity (Continuant) and the other meaning Asthma Attach (Occurent). Then you'd have to use separate terms for Problem List and Reason For Visit.
Kaiser would never go for that. Even though it would be more ontologically correct, it would never happen in the real world because it would complicate EHR implementations considerably, and in fact, clinicians would use them wrong all the time.
2019-07-16 05:33
And very useful research is done all the time with SNOMED. It's very useful to find all the patients who have "SNOMED" Asthma who received drug X. People do research with ICD too, and they conflate the Occurrent and Continuant. It would not help this kind of cohort comparing research at all, and in fact would lead to coding errors (hardly anyone would understand the difference and code correctly) And no way will the existing EHR systems all over the world retrofit to have different lists for Problem List (Continuant) and reason for visit (either maintenance check of Continuant or accute episode of Occurent). It may work for biological processes, but not for clinical medicine.
2019-07-17 06:46
This is Barry Smith's response.
OGMS distinguishes the disease course from the disorder
The disease course includes things like asthma attacks
SCT has 'asthma attack' as a synonym of 'Acute exacerbation of asthma (disorder)'
I am proposing a new semantic tag, 'occurrent', with subtypes 'event' and 'procedure'
I would then propose that certain terms currently treated as synonyms of disorder terms would be positioned as children of 'event', for instance 'asthma attack', 'myocardial infarction', and probably nearly all 'acute terms'
2019-07-18 11:36
According to the Doodle all of us available today (Stefan hasn't responded though) whereas no other day has full availability. Could we have the meeting today (Thursday July 18)?
2019-07-19 08:24
The following is the comments from Stefan's email:
--------
Here are some comments to Peter and Daniel:
Peter:
SNOMED can not be an ontology that is not about "concepts"
but is about "things in the real world". Past, current,
and future medical science can never know "things in the
real world".
Stefan:
"knowing" is epistemology, "being" is ontology. Things in the real world exist, even if we classify them differently. Or if a clinician makes a wrong diagnosis. I do not see a contradiction with BFO here.
Peter:
"Systemic Lupus Erythematosis". This term is quite useful and necessary
today. But is is only a concept. It is NOT something in the real world. Once lupus is understood what exact combinations of genetics and environmental triggers cause "lupus", it will be discovered that either lupus is a term for many different diseases "in reality" or depending
on where we draw the line, we might in the future discover that Sjogrens, and perhaps other diseases should in fact all be given a new concept name and grouped together.
Stefan:
Whether concepts, universals, etc. are in the real world or not is a matter of philosophical debate, which is mostly not relevant here. What's out there:
- there are objects in the real world we want to categorise
- this includes associations of objects (e.g. of medical conditions: syndromes)
- there are names we give to categories (concepts, classes …)
- there are definitions that help us classify things correctly into these categories (concepts, classes …)
- science advances, therefore we
- - create new categories
- - reclassify things
Re "Systemic Lupus Erythematosus" (SLE): according to the current diagnostic criteria, there are things (disease processes) that are members of this class (concept). Therefore I disagree that SLE is "only" a concept (like, e.g. unicorn).
Assuming there is a new definition of SLE, sanctioned by some international authority, a possible way to deal with it would be to rename the "old" SLE to, e.g., SLE_2019 and the new one SLE_2020. If both are formally defined then you may (ideally) even classify new clinical cases into the old SLE concept and old ones into the new one, which could be good for epidemiological analyses.
Assuming that in 2022 SLE is subdivided into SLE_A, SLE_B, and SLE_C, all of which are subclasses of SLE. An SLE_A patient would still a SLE patient, but this wouldn't make SLE "only a concept".
Peter:
Rheumatoid Arthritis is a good example.
We don't know what it is. We have somewhat arbitrary clinical
criteria that will certainly later be thrown away once we know
the exact genetic and environmental mechanisms. Then we may even
throw away the whole idea of Rheumatoid Arthritis. We may divide
it into many sub diseases, or we may group it with another disease
under a more broad heading.
Stefan:
I fully agree, this is in line with what I wrote before. But these arbitrary criteria can actually be expressed as full definitions. They only approximate the "real" disease (which probably represents a continuum from normal over subclinical to clinical and can only be diagnosed post mortem). But they are operational disease classes that do have members.
Peter:
So the idea that SNOMED needs to fully
define more terms, and the other idea that SNOMED should not be
"concepts" but represent things in reality is already a contradiction.
Stefan:
I don't see a contradiction here. There are – often temporary – disease concepts, which are created along very pragmatic criteria, but they do represent things in reality, otherwise they were useless.
Peter:
Another problem in BFO is the disjointness between Continuants
and Occurents. BFO would have one term for Asthma that is
a Dependent Continuant for the propensity for Asthma Attacks.
Then Asthma attacks would be Occurants. But for a real patient
who has Asthma, they probably always also have some small component
of the Occurant going on. Sometimes it's bad enough to go to the
Emergency Room, or to take rescue inhalers, but there is no
particular arbitarary severity when all of a sudden the Occurent
is turned on and becomes present.
Stefan:
According to what I wrote before, it's just both. Not as a logical conjunction (class overlap), which would violate the disjointness principle, but just two entities: There is both an instance of asthma propensity and an instance of asthma attack.
If you need to interpret just the term "Asthma" without any further information then you could just instantiate a class Asthma you define as equivalent to AsthmaPropensity OR AsthmaAttack.
SNOMED CT does not have the operator OR, but you could still do the following:
AsthmaAttack subclassOf Asthma
AsthmaPropensity subclassOf Asthma
Peter:
When reading criticism of SNOMED, it appears that many of the critics
dont understand what clinical medicine really is. It is not so much
about "things in the real world" where everything is either a Continuant
or and Occurent, but as discussed above, it is a temporary, always
changing world of ideas "concepts" that are very useful for deciding
treatments. It is understood that these concepts always are in a state
of flux. They come and go, and as they do the usefulness of the concepts
progress and become closer to the real world, and the concepts become
more useful in making treatment decisions, and in research.
Stefan:
Trying to reconcile ideas with the real world:
- There are observations of real phenomena in real patients
- There are results of biomedical research on real tissues, cells, populations etc.
- There are scientific hypotheses, which are information objects, i.e. in BFO
generically dependent continuants
- Medical communities decide whether to consolidate such hypotheses or "ideas" into disease definitions and names.
- These are often fully defined, not in terms of pathology and aetiology, but in terms of diagnostic criteria
- The underlying pathological mechanism is often unclear, which entails that re-definitions occur
- Confusingly, the name is kept but the underlying definition is changed
- A standard like SNOMED CT should elucidate the relation between name (at a certain time, according to a certain community) and the related class definitions.
Daniel:
About single inheritance, what I remember from discussions with Barry and Werner during the Semantic Mining project (2004-8) was that they had objections to having multiple stated parents (multiple genera) (see Buidling ontologies with BFO, page 79). 75570004 |Viral pneumonia (disorder)| fulfills this criteria, although sometimes by necessity multiple stated primitive parents are needed to account for multiple aspects of meaning not defined through attributes.
Stefan:
This is also what I remember. There is also often a confusion between an ontology and an OWL model. According to Barry and Werner, these are two separate things. An ontology must not have a class "unicorn" (because unicorns don't exist), but OWL models could, using classes like horn and horse, together with logical constructors.
Daniel:
About real world vs. thoughts (i.e. mind-dependent entities such as ideas, plans, suggestions, ...), first, thoughts are also part of the real world and not accepting that is being relativistic about ontology (Barry, the relativist!),
Stefan:
Those things are compatible with BFO (see Werner Ceuster's Mental Functioning Ontology)
but it seems they think (and misinterpret, partly due to unclear documentation and communication) that disorders are mind-dependent entities, which they are not: disorders themselves exist without anybody naming or classifying them, but the classification criteria, names and definitions for them are mind-dependent. But these are two completely different things.
Daniel:
second, mind-dependent entities are clearly relevant in the health care domain, so at least a health care ontology should comprise both mind-dependent and mind-independent entities. Does SNOMED always clearly separate the two? Probably not, but that requires an analysis beyond the analysis of the definition of disease (...and "a disease is a concept" seems to have been removed from the editorial guide) in SNOMED.
Stefan:
There is a tendency to ignore the difference between classes and meta-classes:
1. My headache is an instance of the SNOMED-concept Headache
2. The SNOMED-concept Headache is an instance of SNOMED-concept
From which we canNOT infer that my headache is an instance of SNOMED-concept
Daniel:
Further, the second-order (instances-to-types) relationship between mind-dependent and -independent makes a faithful representation in OWL (and EL in particular) a challenge to say the least (see Schulz et al An Ontological Analysis of Reference in Health Record Statements).
-----------
2019-07-23 11:53
In general I think that research helping the community to find and address issues in SNOMED CT is a good thing. Smith, Ceusters, Rector (and Schulz, Bodenreider, Cornet, ...) etc. often have relevant criticism which we should address or at least discuss and relate to in our work. However, not all such research is of high quality, and there seem to be a category of research which reference those relevant papers, and then over- and mis-interpret the findings with misleading conclusions as outcome. One recent (counter-)example being El-Sappagh et al. BMC Medical Informatics and Decision Making (2018) 18:76. Apart from misusing references, the main idea of the paper, mapping SNOMED CT and OGMS, is a gross over-simplification avoiding the difficult problems SNOMED has to address.
https://www.ncbi.nlm.nih.gov/pubmed/30170591
2019-08-06 04:33
Sounds like Jim Case and Kelly Kuru had a good experience in Buffalo. There is an informal verbal agreement about working together but Jim did stress the arguments against having two forms of each disease which would be a major turn off for clinicians. I'll let him tell what happened, but the result seems to be that Barry Smith, Peter Elkin and the BFO crew are now on friendlier terms with SNOMED. I think having Kelly there was a great thing too. Hopefully Jim will comment on this page.
2019-08-12 06:33
Here are my comments on Stephans most recent write up.
-------------------------------------------------------------------
Comments on sections.
What may contribute to misconceptions about SNOMED CT is its top class 138875005. Its FSN "SNOMED CT Concept (SNOMED RT+CTV3)" is a misnomer, because simple logics infers that, e.g., Queen Elizabeth is a SNOMED CT Concept, just as the aspirin tablet she took yesterday. For the use of SNOMED CT in practice, this may be hairsplitting, but not when communicating with philosophers or logicians.
Not really, because “SNOMED CT Concept” is just the same as “OWL Thing” or “Top”. How does it contribute to misconceptions. It doesn’t imply at all that Queen Elizabeth and Aspirin are the same, it only says they are both “things in the world”.
This is an unrealistic desideratum. It has not ever been met by any OBO ontology. Regarding SNOMED CT, this desideratum is unrealistic, because large parts of SNOMED cover areas where
(i) a simple logic is not sufficient to completely define most classes, such as in chemistry
(ii) full definitions are outside of the scope of SNOMED Intl's standardization, e.g. organisms, human anatomy, physical objects, occupations, religions, lifestyles, geographic entities, or certain qualities.
Another reason is diseases like Lupus and Rheumatoid Arthritis. Medical science does not know if these clinically useful terms are “in the real world” at all. It may be found that they are each a group of more than one entity that looksimilar from the outside but are quite different. Alternatively they might both be different manifestations of one disease. The reality is probably a bit of both. They probably share some common mechanisms and differ in others, just as within each term there may be many differences that will later be sub divided. The reality is not black and white, and it does not lend itself to being fully defined.
3 SNOMED should be based on BFO and there should be Continuants and Occurrents and they should be mutually exclusive
Somewhere in this section we must indicate that clinicians, who already complain that SNOMED is too complex will never agree to separate Asthma the continuant from Asthma the occurrent. They would just look for an alternative terminology that did not force them to make this distinction. And in most cases of most diseases, both the occurrent and the continuant are always both present in the same subject to some degree. For example, in Asthma the continuant, if you were to do pulmonary function tests, you would find some small degree of the occurrent present. Distinguishing them is not only a burden, but would have practically no use for most clinicians in the way they use the terms.