Michael K Martin
Forum Replies Created
Looking at the veterinary codes, I would say the vast majority are the same concept as human bodily fluid except for species. That is, the milk is a body fluid specimen used to tell us something about the health of the mother animal (cow, goat, sheep, camel, water buffalo, etc.). There are a few cases such as “20965-0 Somatic cells [#/volume] in Milk” are both a measure of food safety and the mother’s health status. And then there are a bunch of purely food safety tests. Those still tell us something about the mother in most cases. In every case, the substance is the same thing but for the species it comes from and how much processing may have been done. So unmodified “Milk” seems right to me in most cases. Should we have a “Milk – Product” for cases that only apply to milk as a food product that has been through some manipulation on the way toward being a human food. (Of course human milk that has been stored for later use would fall in the same category, right?)
The Ser/Plas case makes sense. I shouldn’t have tacked my issue to that one. Sorry.
I wasn’t ready to submit a request for our “weird” veterinary use case. I really wanted to see if I could get some discussion about the alternatives. As stated on pg 26
We will likely argue for either adding a distinct code for the dominantly common specimen (e.g. Stool for ameba histolytica) or the specimen prescribed by the package insert, or for entertaining a new specimen code broader than those now available but narrower than XXX to accommodate a particular need, e.g. sterile body fluid, or Genital/anal/throat (for STD specimens). This will, of course, take time and discussion.
I’m torn between asking for a new System Type for “Meat Juice” (we aren’t even sure how to SNOMED code that one) and then test codes with “Ser/Oral Fluid/Meat Juice; asking for a new System Type something like “Serum Substitute” (yuck) and “Ser/Serum Substitute”; or just saying the test is based on serum and we allow the use of those substitutes. In any case, these tests can all be hidden behind “veterinary:true”.
At this point, I think the least “ugly” but also least “pure” approach would be the last one; we just use the Ser codes even with the weird substitutes.
We have a similar issue in veterinary medicine. We have a number of serologic tests that were designed to be run on serum. Because serum is often difficult or impossible to obtain, some of these have been validated for other specimens such as oral fluid or “meat juice” (fluid from a frozen and thawed muscle sample). Because we are trying to get away from XXX as a specimen type, we would really like a specimen type of “Serum or appropriate substitute.” This would be much more precise than simply saying “Body fluid” but wouldn’t make it seem wrong to use a “Serum” LOINC code with a substitute.2012-11-07 at 13:28 in reply to: how do I get a LOINC code for a new document type? #16647
I would like to gang up on this question. The documentation and the excellent in-person tutorials do a wonderful job of teaching how to submit most “normal” observation code requests. That leaves a number of areas around the edges that would make great material for an “advanced tutorial.” In addition to new document types, which I haven’t actually had to try, I would include new panels, tests with new methods (bacteria identification by MALDI-TOF?), etc.
A recent Nature article points to why we want to be able to order and result actual sequences for key parts of the influenza virus isolated from various species.
An example of the way these would end up can be seen in the way the GenBank data are queried using NCBI
The thing that makes our use case different from the past is that it is no longer just the NVSL national lab at Ames doing the sequencing but also the NAHLN labs they “contract out” to. So we need a way to order and result these “Please sequence that virus” or “Please sequence the HA gene of that virus” tests.
Let me throw one more complication into this discussion and hope we’ll get some more input.
What if instead of returning the sequence of bases, we instead return the GenBank key for the sequence? That is more clearly a NOM, but what would differentiate it from strain-typing by sequencing. 49532-5 (FLUAV HA cDNA Islt Amp/Seq) is I think intended for strain-typing but the LOINC parts are pretty much what I would have put for sequencing reported as a GenBank key.
I know the basic difference between NAR and NOM. But I can’t tell if there are any existing LOINC codes where the actual sequence “ACGTCGTAACTGGCTAC…..ACGT” is the “answer.” I confused things by pointing out that the vocabulary of this “narrative” is limited to four characters.
What I really need is how to request a code for
Influenza A Hemagglutinin cDNA genetic base sequence
Influenza A Hemagglutinin cDNA:PRID:Isolate:Pt:?:Amplification/Sequencing (I’m assuming Prid is right.)
with the result being a base sequence.
I’m not sure 49532-5 Influenza virus A hemagglutinin cDNA [Identifier] in Isolate by Amplification/Sequencing is what I’m looking for because I suspect the “answer” is a coded value for the strain.
How do I know for sure?