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 8:21 AM, Luke Kenneth Casson Leighton wrote:

> in hierarchical terms this can be turned into the following:
> 
> ORC - 03000032-PATHC-0
>    |
>   +- OBX X10011 Pathologist Comments
>         |
>         +- Result 1
>         +- Result 2
>         +- Result 3
> 
> so in this example, i've had to represent that 2nd level of hierarchy
> by overloading the test_unit table to create test units with a
> different name (by appending OBX sub-id as a string in brackets to the
> test_unit nme field) but keeping the LOINC code the same of course.
> 
> ... it would be good to not have to do this, by having a
> clin.test_result.unit_sub_id field.

It maybe raises the question of whether upstream implementation decisions need 
to be mirrored (or need not be mirrored) in the receiving database, for example 
whether it may make clinical sense to depart from the upstream schema and, in 
the GNUmed result, concatenate the subid content into a single 
"pooled_other_data" column... if we would consider a urine culture (test for 
infection) which turned out within it to have 2 kinds of infection, where for 
each of these infections the lab was able to return whether the germs were 
sensitive or insensitive to certain antibiotics. In the example below ******, 
the message would not have blank lines, I only introduced them for clarity. We 
see:

1) identified as a Urine site specimen (LOINC 19803-6) which has a null subid 
i.e. || before "Urine"

2) a 6463-4^Culture the result of which is "Light growth of: Klebsiella sp." 
with subid 1
3) multiple antibiotics tested-against, each with distinct LOINC, with subid 1

4) 6463-4^Culture the result of which is "Light growth of: Staphylococcus 
aureus" with subid 2
5) multiple antibiotics tested-against, each with distinct LOINC, with subid 2

So, clinically, is the desire to store all of this as a single test i.e. in a 
single test result row with all of this subid stuff pooled into a single cell, 
or would it make more sense to have 3 rows, or maybe just two rows:

Urine site specimen row, including within it (coalesced) the data from all rows 
containing subid 1
Urine site specimen row, including within it (coalesced) the data from all rows 
containing subid 2


********************************
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