BFO and SNOMED

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.
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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.

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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