- There are a number of concept classes present in the first few generations of the organism hierarchy that Jeff Wilcke believes are of little practical value. These include:
- 115630000 | Renotrophic organism - (and its 2 descendants)
- 284666000 | Trophic life form - (and its 422 descendants, 407 of which are also properly classified as Trematodes, 15 have no descendants that are extant organisms)
- Antimicrobial resistant organism - (all its organism descendants are bacteria)
- Antimicrobial susceptible organism (its 2 organism descendants are bacteria)
1 & 2 would seem to have little clinical or epidemiologic value.
Certain subtypes of 3 & 4 would seem to have clinical or epidemiologic value. Can 3 & 4 be related to actual laboratory results (through SNOMED logical models or other)?
2 Comments
Xavier GANSEL
Jeff,
for item (2)
Farzaneh Ashrafi and Suzanne Santamaria might give us some guidance.
Any though on that ?
Best
Xavier
PS - By the way I have hard-time obtaining an OWL version of the last release. I only have a non-official OWL file for tech preview 3
Jeff Wilcke
Xavier,
Modifications that will appear in the July release are almost entirely related to what can presently be seen as "the life-cycle form" hierarchy". I don't think that it has a great deal of bearing on the upper levels of the organism hierarchy though it has solved one existing problem.
The difficulty I perceive for a "clean up" of the organism hierarchy (and the source of my questions), is that organism content such as "microorganism" and "antimicrobial resistant organism" was added (I think inappropriately) to facilitate creation of either findings or procedures. When added, there was little regard for logical difficulties and even inaccuracies created in the organism hierarchy. I'm not certain how this affects the "observables" work.
To move forward with existing resources, I must avoid distrupting existing content though I see it is important to maintain at least some awareness of other work (LOINC-SNOMED agreement/mapping, observables).
Let me attempt an example:
264395009 | Microorganism (organism) is used to define a (relatively) short list of concepts including: Source specific culture (procedure), Microbial culture of sputum (procedure), Urine culture (procedure), etc. Removing "microorganism" from the organism hierarchy will "break" definitions of these procedures. Is there harm in simply changing the value of the "component" role to "organism." I'm fairly certain that would not cause re-classification of the procedures.
As an aside, some procedures on the list (e.g. Quantitative urine culture (procedure)) would seem to apply to more specific concepts (are there non-bacterial cultures of urine that are quantitative?)...
So if you're asking me whether we should put our resources into dialogue with the "observables" or "LOINC-SNOMED" projects, I would understand the value and importance. But I have to respond with my tired old "inadequate resources for organism work." I can concentrate on the detailed analysis of the hierarchy itself (and cascade effects on existing content) OR I can concentrate on activities I look at as "the future" but I really can't handle both. On the other hand, this Project Group should be aware of and even involved in related projects. Your ideas about how we might proceed are welcome.
-Jeff