Re: [Gnumed-devel] Matching was Re: Mirth (2 of 3): HL7 import for the GNUmed project - test source message

[Jim Busser]

On 2010-08-17, at 9:06 AM, Luke Kenneth Casson Leighton wrote:

> i'm trying to make it clear - perhaps this helps: any HL7-formatted
> "observational report" which contains OBXs that do not have a
> preceding OBR is rejected at the HL7 parsing (syntax) level.

I erred in providing only a part of the message (lest I be required to include 
all the way up to the MSH) however the example from which I cut and pasted 
*did* have an OBR, and all OBX (the one with no subid, and the ones that 
contained subid1 and those that contained subid 2) all related back to the same 
OBR (see below *****)

These were provided as a single block.

The subids provide a solution for two scenarios. For each is provided a 
scenario and my (maybe flawed) thoughts as to some options:

1) when a lab supplies multiple (and therefore non-unique) OBX having the same 
LOINC inside a single message... the subid here preserves granularity among 
these:

ORC|RE||03000032-PATHC-0|||||||||22333^MEDIC^IAN^TEST
OBR|5||03000032-PATHC-0|PATHC^Pathologist 
Comments|R|20030827091101|20030827091101|||||||20030827091101||22333^MEDIC^IAN^TEST||||||20030901105929|||F||^^^^^R|87878^TEST^JANE~22333^MEDIC^IAN^TEST
OBX|1|TX|X10011^Pathologist Comments|1|Result 1||||||F|||20030901105401
OBX|2|TX|X10011^Pathologist Comments|2|Result 2||||||F|||20030901105401
OBX|3|TX|X10011^Pathologist Comments|3|Result 3||||||F|||20030901105401

... the above is kind of understandable as to not need to be (clinically) 
separated into separate rows if GNUmed would choose instead to coalesce them 
into a single row,  because these are all comments about a single OBR specimen 
(such as a biopsy... a single piece of tissue)

2) microbiology results -- the method provides a way for an initial OBX (which 
does not have a subid) to keep associated with it the data contained inside the 
remaining OBX which both follow and which *do* contain a subid, so GNUmed could 
choose to coalesce all of these into one row (for the urine result) despite 
that this urine result contains -- if you like -- two subresults.

this second scenario especially seems to make the case for logical, 
computational, and clinical legitimacy to keep OBR and OBX meaningfully 
associated?

 

******************************
Since the Microbiology results for the testing of susceptibility to antibiotics 
is different from typical results, the following format is used for 
transmission (see also HL7 V2.3 Section 7.4.5):

Reported first are all the Culture results, with the Observation Sub-ID 
containing the id of the culture (i.e. 1, 2, 3 etc); after this, the Organism 
is reported, followed by all the antibiotics, in the order of the culture 
result.
  
See the following sample:

OBR|1||02-123456-URC-0^bcb|URC^URINE CULTURE^L||200011081429|< style=' 
margin:0in; margin-bottom:.0001pt;} >  
200011081429|||||||200011081429||TTTT2^TEST^BLAIR^^^^^L||||||200011300944|MICRO|BCBIO|F||^^^200011081429|||||||204
OBX|1|FT|19803-6^SITE^L||Urine|||N|||F|||200011081430|EDM|204
OBX|2|FT|6463-4^Culture^L|1|Light growth of: Klebsiella 
sp.|||N|||F|||200011081434
OBX|3|FT|28-1^Ampicillin^L|1|R|||N|||F|||200011081434
OBX|4|FT|149-5^Cephalexin^L|1|R|||N|||F|||200011081434
OBX|5|FT|267-5^Gentamicin^L|1|S|||N|||F|||200011081434
OBX|6|FT|7057-3^TMP/SMX^L|1|S|||N|||F|||200011081434
OBX|7|FT|363-2^Nitrofurantoin^L|1|S|||N|||F|||200011081434
OBX|8|FT|6463-4^Culture^L|2|Light growth of: Staphylococcus 
aureus|||N|||F|||200011081434
OBX|9|FT|6932-8^Penicillin^L|2|R|||N|||F|||200011081434
OBX|10|FT|197-4^Cloxacillin^L|2|R|||N|||F|||200011081434
OBX|11|FT|233-7^Erythromycin^L|2|S|||N|||F|||200011081434
OBX|12|FT|7057-3^TMP/SMX^L|2|S|||N|||F|||200011081434
OBX|13|FT|193-3^Clindamycin^L|2|R|||N|||F|||200011081434
OBX|14|FT|524-9^Vancomycin^L|2|R|||N|||F|||200011081434
OBX|15|FT|Ms.OX2^Cloxacillin^L|2|R|||N|||F|||200011081434
OBX|16|FT|28-1^Ampicillin^L|2|S|||N|||F|||200011081434
OBX|17|FT|149-5^Cephalexin^L|2|S|||N|||F|||200011081434
OBX|18|FT|20-8^Amoxicillin/clavulanate^L|2|S|||N|||F|||200011081434
-- Jim