Hi, Just to add some historical context - SNOMED evolved from a terminology designed to be a Reference Terminology (as opposed to Interface/Clinical Terminology) at a time where ontologies were non existent or very primitive (<90s). Hence the poor formal ontological commitment as of today - in the past 10-15 years they have transformed the content to serve a different purpose - to act as Interface/Clinical terminology and most flaws are related to this baggage. That said they are actively working to align with current ontology good practices; e.g. I learned there's work underway to restructure anatomical sites as per FMA which is a good step forward. I heard they are also looking at other content areas to align with OBO etc.
Cheers, -koray From: openEHR-technical [mailto:openehr-technical-boun...@lists.openehr.org] On Behalf Of Thomas Beale Sent: Saturday, 30 April 2016 2:43 a.m. To: openehr-technical@lists.openehr.org Subject: Re: SNOMED Hi Bert Erik and Ian partly answered this, but it is always worth remembering that SNOMED CT, if based on proper ontological principles, contains assertions that represent entities in the real world. This means taxonomy (IS-A) and properties, qualities, possible relationships and so on (see BFO2 <https://www.google.co.uk/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&ved=0ahUKEwjkjrG8hrTMAhWEWxQKHc_dDsIQFggcMAA&url=https%3A%2F%2Fbfo.googlecode.com%2Fsvn%2Ftrunk%2Fdocs%2Fbfo2-reference%2FBFO2-Reference.docx&usg=AFQjCNFaciudhkU555FkqpQscrO0rRJUmQ&sig2=wWITHga_L6Vp1RTU4lvEEw&bvm=bv.120853415,d.d24> for a modern top-level ontology providing these ideas). These are properties, qualities and relationships of real things in the real world, i.e. actual hearts, cardiac arrests, disease types and so on. The openEHR RM and derivative archetypes are built to represent information 'about' these real things. The relationship is often written as 'is-about'. There are important differences to be aware of: * what information is written 'about' many things can sometimes resemble a description of the thing itself, e.g. parts of a colonoscopy report tend to follow anatomical structure of colon and things found in it; * sometimes it relates to a surrogate phenomenon, e.g. an archetype for heart rate that actually records pulse; a great deal of clinical observation is of surrogates e.g. state of skin, palpation, heart sounds, asking about pain, blood glucose etc, but they are actually about something else; * what gets recorded can be what is cheap and painless to record; consider that we don't do an echocardiogram every time you want simple BP or heart rate. * what gets recorded about X can be culturally determined; different in other ways from 'how X really is' in nature. * most important: most clinical data recordings don't replicate 'textbook' relationships found in an ontology, e.g. the fact that there are 5 heart Korotkoff sounds at different phases of the cardiac cycle will never be written down by a physician, neither will the fact that systolic BP is-a pressure of blood in a vessel is-a pressure of fluid in a vessel etc. So if we were to generate an information structure from part of an ontology representing the heart / CV system, it would generate numerous useless data points and relationships on the information side. How well or how much SNOMED CT follows underlying ontologies like BFO2 or Biotoplite or whatever is another question. I am not up to date on the progress, but I am fairly sure that most of SNOMED has not been validated against these kinds of ontologies. The waters are muddied further by the attempts to represent informational, timing and context-related entities in SNOMED CT. Thus, my view is that: in principle, generating information structures straight from an ontology (even a perfectly built one) will simply never work, for the reasons in the list above; in practice, what you would get from SNOMED CT, given its imperfect adherence to ontology would be even harder to understand or use. - thomas On 29/04/2016 07:50, Bert Verhees wrote: Hi, I got an idea when reading the nice story from Heather on LinkedIn. In fact it is hers idea, but in a opposing way. https://www.linkedin.com/pulse/journey-interoperability-part-i-heather-leslie https://www.linkedin.com/pulse/journey-interoperability-part-ii-heather-leslie I wonder in how far it is feasible and useful to create archetypes from SNOMED concepts, it would be possible to generate them, with attributes and so on. In a few hours time, one would have a complete forest with archetypes, including ontology in more languages. Maybe some smart handling, filtering, combining can create a better collection, also looking at the paths, so that there are similar paths for similar situations, to keep the number of different datapoints low, which can help creating a faster key-value storage. I don't know how it is about copyright, with members, and licensing, that should be looked at. The argument that SNOMED is fragmented should not count, I think (however without having an expertise on this), because, when working with handwritten archetypes will always be incomplete and fragmented. Bert _______________________________________________ openEHR-technical mailing list openEHR-technical@lists.openehr.org<mailto:openEHR-technical@lists.openehr.org> http://lists.openehr.org/mailman/listinfo/openehr-technical_lists.openehr.org
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