Re: [Gnumed-devel] HL7 OBX result messages that involve multiple lines esp Microbiology

[Karsten Hilbert]

> OBX contains a field
> 
>       004 Observation Sub ID
> 
> Which is used to enumerate multiple OBX records when they
> 
> 1) pertain to the same LOINC code, for example when there are  
> multiple pathologists' comments:

IMO those should be rolled into the relevant parent OBX note_test_org.

This is where the importer will actually have to have some intelligence
as to the *content* of the data.

Welcome to the idiosyncrasies of HL7 :-(

> 2) describe Microbiology results that describe sites, potentially  
> multiple organisms, and their antibiotic susceptibilities (see also  
> HL7 V2.3 Section 7.4.5):
> 
> Here is one format and example in which reported first are all the  
> Culture results; the Observation Sub-ID contains 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:
> 
> OBR|1||02-123456-URC-0^bcb|URC^URINE CULTURE^L||200011081429|
> 200011081429|||||||200011081429||TTTT2^TEST^BLAIR^^^^^L|||||| 
> 200011300944|MICRO|LAB_ORG
> |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
> 
> The above would carry little meaning as individual items in a GNUmed  
> test_result table...
I agree. However, if I were to write an importer I'd attempt to roll
the above into some tabular format to be put into val_alpha (note that
there can be multiline results in val_alpha).

Note: site == "Urin" ;-))

> They seem to need to be linked to the test panel  
> from which they originated (in this case, Urine culture) so maybe we  
> need a foreign key to the test_profile as a nullable column in  
> test_results...
I'd rather handle this particular case as a test_result of test_type ==
"Urine Culture" with a multiline val_alpha.

There's one argument against doing so in a simplistic way: computability.
The way it is structured in the original HL7 it, well sort of, lends
itself to clinical reuse -- GNUmed might check AB sensitivity against
currently prescribed antibiotics. One way to preserve that information
would be to use a well-defined structure for the multiline text, say,
XML or StructuredText (as in a wiki).

> Do we see some value or need (or none) to the OBX sequence counter  
> (above, OBX|1 through OBX|18) and similarly any need to store the  
> 'Observation SubID" which in this case associates the individual  
> species (Klebsiella sp versus Staphylococcus aureus) with their  
> specific antibiotic profile?
I absolutely see value in preserving the information it carries.
We'd need to analyze more instances of this to develop a suitable
relational structure if needed.

Karsten
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