Snomed / archetype binding rules (was Re: procedure or finding?)
Eric Browne wrote (but it did not get to the list for some reason) I consider this issue of term/terminology binding and SNOMED particularly important and so worth clarifying the concepts and also articulating some principles. I've drafted some preliminary notes - now on the openEHR wiki (thanks Sam) at: http://www.openehr.org/wiki/display/healthmod/Terminology+binding eric
Snomed / archetype binding rules (was Re: procedure or finding?)
AThomas Beale wrote: they are working on the syntax, although it seems relatively solid at the moment. We are also working collectively within the NHS-sponsored Technical Advisory Group (TAG) on this. David Markwell is currently authoring an in-depth report on how to bind such exprssions to archetypes, and we are looking at what changes are needed to ADL etc to allow it to happen. There is a relatively simple change that would allow an expression rather than a single code on the right-hand side of any binding expresion that you currently find in an archetype - most likely that at least will happen, so you would get lines like the following in the ontology section: term_bindings = [Snomed_ct] = [at0012] = [417597005 116680003=250412004,363714003=282288009,418775008=271348005,363714003=1522] -- Urine dipstick test finding (finding) is a = Dipstick test finding (finding), Interprets (attribute) Microbiology interpretation(observable entity), Finding method (attribute)=Urine dipstick for pH (procedure), Interprets (attribute)=Laboratory test (procedure) *Andrew, I intended to finish by saying that if you need to implement something now, the above is a good guide to what is likely to happen in ADL, and the logical equivalent in XML (code_string= the whole thing). When the work on bindings is more complete, of course we will ensure it is made available as soon as possible. - thomas *
procedure or finding?
Hi, I think I thoroughly agree with Sam on most things, but would like to add another example: Urine? Acebutolol; arbitrary concentration(IOC Screen; 0 1) M = 336,43 g/mol Authority: IOC; IFCC/C-LDA; INN NPU01001 U?Acebutolol;arb.c.(IOC Screen; 0 1) = ? Here is a ordinal scale concentration (either it's there or it's not) of a substance on the IOC doping list. IOC has a specific procedure (or rather method) for performing the measurement to guarantee legal security. This is the level of detail presumably needed by laboratories, and in this case, athletes. Regards, Daniel On Thu, 2008-04-17 at 05:29 +1000, Sam Heard wrote: Hi Daniel I would suggest that SNOMED should try and keep the abstract concept of something that can be measured at the heart of its ontology. The fact that this can be used to define a finding, a target or goal, a procedure to measure it, the act of measuring it etc is probably better dealt with in the information model ie through post coordination. Within an archetype for urinalysis the idea of urine bilirubin is a non-ambiguous statement from the point of view of context - but capturing it in SNOMED is highly problematic as there are lots of sorts of dipsticks with different ranges or ordinals etc. I know Stan Huff (LOINC), who do use the same code for an order and the result (except when they are different - TFTs - TSH, FT4 etc) feels that the general alignment of the concept in the order and the result is very important from a safety point of view. Aligning general concepts such as Hb is relatively easy, but aligning a code for ordering a Hb measurement, the taking of the measurement and the result adds enormous overheads. We know that IHTSDO are beginning to see alignment with a logical EHR as important to simplify this space. Cheers, Sam Daniel Karlsson wrote: Dear Everyone, as said before Snomed (mostly) models lab properties as procedures and most other properties as observables. There might however be a change and a lab observable hierarchy (whatever a lab observable is?) is under discussion. Again however, the issue is a bit more tricky as some, although few, properties in lab medicine for comparability reasons needs to be defined up to the exact procedure used when measuring (or observing). Regards, Daniel Daniel Karlsson, IHTSDO QA Committee IFCC/IUPAC C-NPU On Wed, 2008-04-16 at 12:46 +1000, Andrew Patterson wrote: I am making some Snomed bindings for some sample archetypes but am having some meta-level problems. An example will probably help - Say I want to snomed code the urinalysis archetype. It lists a large set of potential measurements from a urine dipstick test - blood, glucose, ketones etc. Snomed has comprehensive coverage of all of these categories as 'procedures' 252384001 Urine dipstick for bilirubin (procedure) 270894005 Urine dipstick for blood (procedure) 269879003 Urine dipstick for glucose (procedure) 275714003 Urine dipstick for hemoglobin (procedure) 271347000 Urine dipstick for ketones (procedure) etc However, part of my brain says that the nodes within the archetype should really be a finding, as the actual procedure would perhaps be recorded in a different archetype and this observation is recording what was 'found'. However, my initial searching has found less comprehensive coverage of urianalysis findings in Snomed - though this may be just that I haven't searched hard enough. Would it be fundamentally wrong to have a procedure code in an observation archetype? Are there any hard and fast rules around this or is it case by case? Thanks Andrew ___ openEHR-clinical mailing list openEHR-clinical at openehr.org http://lists.chime.ucl.ac.uk/mailman/listinfo/openehr-clinical ___ openEHR-clinical mailing list openEHR-clinical at openehr.org http://lists.chime.ucl.ac.uk/mailman/listinfo/openehr-clinical -- Dr Sam Heard Chief Executive Officer Ocean Informatics Director, openEHR Foundation Senior Visiting Research Fellow, University College London Aus: +61 4 1783 8808 UK: +44 77 9871 0980 ___ openEHR-clinical mailing list openEHR-clinical at openehr.org http://lists.chime.ucl.ac.uk/mailman/listinfo/openehr-clinical
procedure or finding?
Andrew, Finding codes in this case are what should be used - procedure codes are also used in openEHR archetypes - but in orders (i..e INSTRUCTIONs). We need to be extremely careful not to mix them up, in case users/application software does queries based only on Snomed codes and ignores instances of e.g. Urine dipstick for bilirubin (procedure) (which should be ignored in most cases), and fails to find any results. This is a classic case of 'status of a clinical statement' and needs to be handled properly to avoid potentially serious errors when querying solely using Snomed or similar terminologies. - thomas beale Andrew Patterson wrote: I am making some Snomed bindings for some sample archetypes but am having some meta-level problems. An example will probably help - Say I want to snomed code the urinalysis archetype. It lists a large set of potential measurements from a urine dipstick test - blood, glucose, ketones etc. Snomed has comprehensive coverage of all of these categories as 'procedures' 252384001 Urine dipstick for bilirubin (procedure) 270894005 Urine dipstick for blood (procedure) 269879003 Urine dipstick for glucose (procedure) 275714003 Urine dipstick for hemoglobin (procedure) 271347000 Urine dipstick for ketones (procedure) etc However, part of my brain says that the nodes within the archetype should really be a finding, as the actual procedure would perhaps be recorded in a different archetype and this observation is recording what was 'found'. However, my initial searching has found less comprehensive coverage of urianalysis findings in Snomed - though this may be just that I haven't searched hard enough. Would it be fundamentally wrong to have a procedure code in an observation archetype? Are there any hard and fast rules around this or is it case by case? Thanks Andrew ___ openEHR-clinical mailing list openEHR-clinical at openehr.org http://lists.chime.ucl.ac.uk/mailman/listinfo/openehr-clinical -- *Thomas Beale Chief Technology Officer, Ocean Informatics http://www.oceaninformatics.com/* Chair Architectural Review Board, /open/EHR Foundation http://www.openehr.org/ Honorary Research Fellow, University College London http://www.chime.ucl.ac.uk/ * *
procedure or finding?
On Wed, Apr 16, 2008 at 02:17:09PM +0200, Thilo Schuler wrote: This is a bit problematic as there is one subconcept Urine dipstick test finding (finding) - 417597005 mentions urine explicitly while the others don't. Clinically, to my knowledge, in 99,99% urine will be tested with a dipstick. Thus when using the other concepts that don't mention urine it can be assumed to it is a urine dipstick test Or rather *not* as if it was then the *urine* dipstick code really ought to have been used. Karsten -- GPG key ID E4071346 @ wwwkeys.pgp.net E167 67FD A291 2BEA 73BD 4537 78B9 A9F9 E407 1346
procedure or finding?
Dear Everyone, as said before Snomed (mostly) models lab properties as procedures and most other properties as observables. There might however be a change and a lab observable hierarchy (whatever a lab observable is?) is under discussion. Again however, the issue is a bit more tricky as some, although few, properties in lab medicine for comparability reasons needs to be defined up to the exact procedure used when measuring (or observing). Regards, Daniel Daniel Karlsson, IHTSDO QA Committee IFCC/IUPAC C-NPU On Wed, 2008-04-16 at 12:46 +1000, Andrew Patterson wrote: I am making some Snomed bindings for some sample archetypes but am having some meta-level problems. An example will probably help - Say I want to snomed code the urinalysis archetype. It lists a large set of potential measurements from a urine dipstick test - blood, glucose, ketones etc. Snomed has comprehensive coverage of all of these categories as 'procedures' 252384001 Urine dipstick for bilirubin (procedure) 270894005 Urine dipstick for blood (procedure) 269879003 Urine dipstick for glucose (procedure) 275714003 Urine dipstick for hemoglobin (procedure) 271347000 Urine dipstick for ketones (procedure) etc However, part of my brain says that the nodes within the archetype should really be a finding, as the actual procedure would perhaps be recorded in a different archetype and this observation is recording what was 'found'. However, my initial searching has found less comprehensive coverage of urianalysis findings in Snomed - though this may be just that I haven't searched hard enough. Would it be fundamentally wrong to have a procedure code in an observation archetype? Are there any hard and fast rules around this or is it case by case? Thanks Andrew ___ openEHR-clinical mailing list openEHR-clinical at openehr.org http://lists.chime.ucl.ac.uk/mailman/listinfo/openehr-clinical
