Re: [Gnumed-devel] Incoming HL7 result microbiology report handling

[Jim Busser]

On 2011-07-06, at 4:31 PM, Jim Busser wrote:

> On 2011-07-06, at 2:27 PM, Jim Busser wrote:
> 
>>      where OBX 005 exhibits a change and is non-empty ('1')
>>      --> create a row and put result in val_alpha
> 
> The above happens to provide dually for
> 
>       OBX 005 to match the sensitivities with the organism in microbiology
> 
>       OBX 005 to allow for multiple uses of the same OBX3.1 loinc code

Above, 005 is wrong, it should be 004.

Appended is another example of a urine culture result. It gives more examples 
of the limitations of HL7 / LOINC and usage.

Based on the unwritten program logic (as currently drafted), which would take 
into account subIDs, 5 rows would be imported from this HL7 message:

row 1: Site: Urine

row 2: Special Requests: None

row 3: Report Status: Final 02Sep2010

row 4: Culture: 100 million CFU/L E. coli
                        + internally-concatenated sensitivity results

row 5: Culture: 80 million CFU/L Enterococcus faecalis
                        + internally-concatenated sensitivity results

The *problem* with the LOINC taxonomy or its implementation sees the lab 
treating each of

        Site: Urine
        Special Requests: None
        Report Status: Final 02Sep2010
        Culture: 100 million CFU/L E. coli
        Culture: 80 million CFU/L Enterococcus faecalis

as properties of the "order" when they would better be observations / 
measurements of a "part of a patient" (i.e. the urine). The "special request" 
information as well as the redundant "report status" information should really 
be subID within the urine. Each of the cultures should also be subID within 
that same urine. But that would make the subID inaccessible for preserving the 
organism-antibiotic relationship.

As a consequence, rows 2, 3, 4, 5 each sit as "contextually orphaned" atomic 
data. They lack a pointer to row 1 ("Urine").

Good news… there exists _already_ within GNUmed a possible solution in the 
fk_request which

(a) will be shared by all these OBX and
(b) will permit a select of

        clin.ordered_service (OBR:4 Universal Service ID)

which in this case would be

        URC^Urine Culture

so I suggest that the tooltip include – for non NULL fk_request – the 
clin.ordered_service.

Suggest it be incorporated just above or below the "Date" as currently seen in

        http://lists.gnu.org/archive/html/gnumed-devel/2011-07/msg00064.html

-- Jim

************************************************************************************
An HL7 urine culture result (MSH and PID removed) and reformatted for visual 
benefit…

*****
ORC:
*****

ORC|RE||M121288-13951597-URC-1|||||||||90909^MDCARE^BOB

*****
OBR:
*****

OBR|1||M121288-13951597-URC-1|URC^Urine 
Culture||20100830164800|20100830161500|||||||20100830164800||90909^MDCARE^BOB||||||20100902132501||MICRO3|F|||90909^MDCARE^BOB

*****
OBX – first 3 lines lack subIDs so would be imported one per row, followed by 
two clusters (one per organism) each cluster of which would be imported one per 
row:
*****

OBX|1|FT|19803-6^Site||Urine||||||F|||20100830164831

OBX|2|FT|X10095^Special Requests||None||||||F|||20100830164831

OBX|3|FT|X10114^Report Status||Final\.br\02Sep2010||||||F|||20100902132501

OBX|4|FT|6463-4^Culture|1|>100 million CFU/L E. coli||||||F|||20100902080251
OBX|5|FT|28-1^Ampicillin|1|S||||||F|||20100901090918
OBX|6|FT|20-8^Amoxicillin-Clavulanate|1|S||||||F|||20100901090918
OBX|7|FT|X10042^Cephalothin/Cephalexin|1|S||||||F|||20100901090918
OBX|8|FT|145-3^Cefuroxime Parenteral|1|S||||||F|||20100901090918
OBX|9|FT|412-7^Piperacillin-Tazobactam|1|S||||||F|||20100901090918
OBX|10|FT|279-0^Imipenem|1|S||||||F|||20100901090918
OBX|11|FT|516-5^Trimethoprim-Sulfa|1|S||||||F|||20100901090918
OBX|12|FT|185-9^Ciprofloxacin|1|S||||||F|||20100901090918
OBX|13|FT|267-5^Gentamicin|1|S||||||F|||20100901090918
OBX|14|FT|496-0^Tetracycline|1|S||||||F|||20100901090918
OBX|15|FT|363-2^Nitrofurantoin|1|S||||||F|||20100901090918

OBX|16|FT|6463-4^Culture|2|80 million CFU/L Enterococcus 
faecalis||||||F|||20100902080251
OBX|17|FT|28-1^Ampicillin|2|S||||||F|||20100902080251
OBX|18|FT|185-9^Ciprofloxacin|2|R||||||F|||20100902080251
OBX|19|FT|496-0^Tetracycline|2|R||||||F|||20100902080251
OBX|20|FT|363-2^Nitrofurantoin|2|S||||||F|||20100902080251


-- Jim