There are three (general) concepts related to the extent of antimicrobial resistance MDR, XDR, and PDR. Based on the definitions of these concepts, it seems from a subtype/subset point of view they create a logical hierarchy. At present, they are positioned as discrete non-overlapping categories, which I believe is how microbiologists view them. I'd like your input. There is one question on the slide (in the document) and a sort of follow-up question:
Which hierarchy diagram position
The existing content treats the relationship between resistance and the factors responsible for resistance in two different ways. The file associated with this discussion is a PDF of the notes pages for slides 5, 6 and 7 of the presentation given during the May 2019 OIDM PG meeting. During the meeting, we learned from Farzaneh Ashrafi that existing editorial policy indicates that production of a resistance principle by a bacteria DOES NOT EQUATE with clinical resistance among bacteria.
The introduction to this discussion lists a number of questions related to preferences for term styles and hierarchy content. The file associated with this discussion is the notes view of slide #4 from a presentation given during the May 2019 OIDM meeting. There are three major questions I've associated with this slide and I'd like your help determining the answers.
Should the drug names in these terms conform to names in the substance hierarchy?
Should the "main" term, some combinati
I'm trying to scope out some work relating to virus and wanting to confirm what the preferred reference source is.
I was looking at O http://www.ontobee.org/search?ontology=NCIT&keywords=Nairoviridae&submit=Search+termsntoBee/OBO work (specifically http://www.ontobee.org/ontology/NCIT?iri=http://purl.obolibrary.org/obo/NCIT_C14283 http://www.ontobee.org/ontology/NCIT?iri=http://purl.obolibrary.org/obo/NCIT_C14283)
The ICTV work (https://talk.ictvonline.org/taxonomy/ https://talk.ictvonli
I just want to ask about concept like 702938004 |Klebsiella pneumoniae or Klebsiella oxytoca (finding)|
I notice that since 2014 these sort of things have been modeled as findings (I vaguely recall the discussions at the time).
However, this does complicate things for some microbial reports where a more specific identification isn't available/possible. And these sort of groupers are as clinically useful, and as specific as is required.
(To me at least) It seems on par with saying 127535004
Thanks Jeff.
I think my view was clouded by assuming it was "obviously" exclusive or that what intended (since an "organism" can't simultaneously be two species). But the description logic doesn't show that.
It seems like exclusive or might be applicable to primitive the "primitive hierarchies".. (organisms, body structures ...).
61685007|Limb structure (body structure)|
effectively means "arm structure or leg structure". However, Lower limb structure and Upper limb structure are disjoint. As a specific structure won't simultaneously be subtypes of both.**
Similarly, the Linnean classes are always disjoint.
inclusive or (and/or) makes sense for findings, where conjunction can exist. (mixed infections, multiple fractures etc).
Maybe the new DL profile will help?
** "Combined sites" might complicate things, I'm not sure what's happening there. The more I think about it, body structures might be a poor example :/
Even a cursory review of the antimicrobial resistant content in the organism hierarchy suggests that it could be used to facilitate flagging of antimicrobial resistant organism isolates for antimicrobials of specific, even dire, concern. Some editing is in order as described in documents posted for the November 2018 - OIDM Meeting. What is less clear is how this content might be logically (and automatically) associated with clinical laboratory reports of actual isolates. Without a use cas
For the NHSN use case, users (healthcare facilities) reporting healthcare-associated infections requested selected drug resistant organisms to be made available in the pathogens Value Set / pick list. For analysis and reporting purposes, the 3 drug resistant Klebsiella pneumoniae organisms displayed below are aggregated in the same bucket of data based on the root 'NHSN Code' without the *#.
NHSN Display Name
NHSN Code
SCTID
Klebsiella pneumoniae
KP
56415008
multidrug resistant Klebsiella pneumoniae
KP*2
714315002
carbapenem resistant Klebsiella pneumoniae
KP*3
446870005
Extended spectrum beta-lactamase producing Klebsiella pneumoniae
KP*4
409801009
If the premise that 41146007 | Bacterium (organism) duplicates the meaning of 409822003 | Superkingdom Bacteria (organism), then it should be retired. If this concept class is retired, its first generation descendants will be assigned by transitive closure to the next higher supertype, in this case 409822003 | Superkingdom Bacteria. The newly edited hierarchy can be divided into roughly into two classifications - one based on so-called "Linnaean" principles (e.g. Phylum Proteobacteria) like
I can respond to what I perceive to be a (well-deserved) criticism of the accuracy of SNOMED's this way: With adequate resources it can be made more accurate. I don't know what adequate resources might be (how many editors) and I think we're still left having to figure out appropriate sources of truth (references that change depending on where you are in the organism hierarchy). Check out NCBI's list of Taxonomic advisors: https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=advisors https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=advisors
I'm not sure what to make of the value of leaving out everything between Phylum and Family. I'd be interested in what others think. I'll guess it won't save as much effort as you an I might like to think it would...
As for "gram-negative bacillus (organism)," my experience suggests that such a concept is excluded from every "taxonomy" I can find and yet medically, it's an important kind of organism. SNOMED's stuck with it, others not so much.
During our last OIDM Web conference, I failed to include an important group of concepts related to antimicrobial resistance. The present discussion is mostly about the fate of a few "odd" organisms but the conversation also has bearing on an eventual need to discuss a proper "fit" for organisms in laboratory results, disorders, etc. meant to convey information about resistance. I'd appreciate any time you could take to review the attached documents (see attachments on drop-down menu for this
You are correct. The last two (inactivations) worry me because they are associated with disorder definitions that MUST be handled. I don't have a very positive opinion about the affected disorder classes. Here they are:
431380001 | Infection caused by sulfonamide resistant organism (0 descendants)
372292006 | Infection caused by resistant organism (38 descendants, 32 are infection caused by bacteria (often specific bacteria) resistant to specific antimicrobials).
409798003 | Infection caused by antimicrobial resistant virus (0 descendants)
409797008 | Infection caused by antimicrobial resistant fungi (0 descendants)
444200003 | Infection caused by tetracycline resistant organism (0 descendants)
371064006 | Therapy failure due to antibiotic resistance (0 descendants)
371095004 | Infection resistant to penicillin (0 descendants)
3 and 4 can be removed from this list as their causative agent can/should be the more specific 'resistant fungus and resistant virus.' I do not believe and cannot prove that the remaining 5 were EVER intended to relate to "organism of ANY class resistant to X". I believe that in a clinical record, more specific concepts (likely all related to bacteria) would be preferred. I don't believe that there is great value in retrieving, aggregating and analyzing resistance across unrelated organisms (resistance in viruses and fungi related to resistance in bacteria??). So personally, I have no problem retiring these 5.
The fundamental problem we have with retiring 409792002 | Antimicrobial resistant organism is that (to me) it triggers the retirement of disorders 1,2,5,6 and 7.
I think we have to consider inter-related problems as well.
1) Staying current with WHO CC Salm (Kauffman-White scheme) is certainly a challenge. I am unaware of "annual updates" so clearly I'm not well enough connected. Even if we get WHO CC Salm updates in a timely fashion, there's a built-in time lag for editorial processes at WHO, then editorial processes and timed updates for SNOMED CT.
2) There really are "new" Salmonella serotypes discovered (even if infrequently) all the time. It is NOT POSSIBLE for any terminology to have a code waiting for an organism subtype that's never been seen before.
In the veterinary world, we created the veterinary extension so that appropriate concept classes and codes could be created DURING disease outbreaks (and distributed to labs in real time). This almost always means new specimen types, new diagnostic tests. We have never attempted to stay out in front of new organisms.
3) We don't actually have a strategy for maintaining/naming/defining serotypes in SNOMED CT. Consider one of the most common serotypes, 50136005 | S. Typhimurium. The antigenic formula listed (as a synonym) is Salmonella 1,4,[5],12:i:1,2 - the brackets indicate that O5 is optional. The antigenic formaula listed in KW is Salmonella 1,4,[5],12:i:1,2. Both O1 and O5 are optional. There are 4 actual ISOLATE (serotypes) 4,12,:i:1,2 | 1,4,12,:i:1,2 | 4,5,12,:i:1,2 | 1,4,5,12:i:1,2 (the antigenic formulas of actual Salmonella Typhimurium isolates). These formulas are NOT IN SNOMED CT. It is often not possible to look up an antigenic formula for an organism you've just isolated in the lab (no real isolate has an optional antigen - they have what they have).
The biggest problem related to our recent telecon discussion (as I see it) are reporting requirements by public health agencies that are actually IMPOSSIBLE to meet. That problem aside, we really do have an unmet editorial challenge with serotypes.
Matt Cordell