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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) likely affected credibly by genomics and a second one based on phenotype expression identified by classic laboratory testing (e.g. "Gram negative rod") also likely affected credibly by genomics. Please see the document file "New first generation of bacteria" posted with the November 2018 - OIDM Meeting information.
I would like you to consider 3 questions:
- There are 56 concept classes that will be first generation descendants of Domain Bacteria in SCT. Roughly half of these concepts are bacterial phyla and half are expressions of class used by clinical medicine and epidemiology. It's a hard list to digest presented alphabetically. Does it matter how Domain Bacteria "looks" in a browser?
- The need for organism content at and distal to bacterial genus(es) is clearly supported by uses of SCT as values for laboratory reporting. Is the intermediate classical Linnaean (allegedly official) taxonomy of value in clinical or laboratory systems?
- Is the so-called "common name" hierarchy that comes from diagnostic microbiology and establishes a clinical disorder hierarchy (e.g. gram negative infection(s)) of value in clinical or laboratory systems?
2 Comments
Sheila Abner
In a recent conversation with colleagues, a suggestion was made that SNOMED should consider just listing all genera of bacteria and not worry about the taxonomic hierarchy between Phylum and Family. What would be the consequences of an approach like that? When I needed to identify all genera that are members of Family Enterobacteriaceae, I had to use resources other than SNOMED to get it right. Similarly, to identify all members of 'Enterobacter cloacae complex', a CDC subject matter expert advised me that SNOMED is not accurate.
For NHSN (healthcare-associated infection tracking system), we do have concepts such as 87172008 | Gram-negative bacillus (organism) in our Value Set because clinical labs sometimes report an isolate to that level of granularity.
Jeff Wilcke
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
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.