hello every one
from an old post here, if we have a > 50 character result, then we should put the data in the Note table and link it to the measurement_id via the Fact Relationship table.
the question is how record the data in Note table and how to link it to the measurement_id via the Fact Relationship table.
hello every one
@alruod: You need to map it to a Measurement concept. What is it?
we already map it to Measurement concept (4107893 - Blood culture).
Well, you need a Measurement concept. 4107893 is a procedure concept. It shouldn’t even be standard, because blood culture is not a procedure by OMOP definition (it’s a lab procedure not performed on the patient).
So, what kind of information do you have?
And why do you want to put it into the NOTE table?
in athena its a standard and belong to Measurement domain
4107893 30088009 Blood culture Procedure Standard Valid Measurement SNOMED
The table to put data is determined by the domain_id of the standard concept_id representing the source code. In general, labs belong in the Measurement table. If the result of the lab is a Float data type, it belongs in the value_as_number field, results that map to a concept_id go in the value_as_concept_id field, a string text value of 50 characters or less goes to the value_source_value field, and if you have a > 50 character result, then put the data in the Note table and link it to the measurement_id via the Fact Relationship table.
this quote from link above and I follow it to record “> 50 character result” cause value_source_value field limited to 50 character .
Ha! You are correct. I retract what I said.
What are the values that have >50 characters? You should map them to concept if possible. Nobody will analyze those source values.
"MRN: JD000-003-906-609 02-BC-17-17650_x000D_
PROCEDURE: Blood Culture_x000D_
SOURCE: Blood COLLECTED: 19/11/17 18:42 AST_x000D_
BODY SITE: RECEIVED: 19/11/17 19:57 AST_x000D_
FREE TEXT SOURCE: STARTED: 19/11/17 19:57 AST_x000D_
*** FINAL REPORT ***x000D
Verified:26/11/17 22:16 AST_x000D_
No growth After 7 Days Incubation_x000D_
this what we have in some lab results.
how to deal with this
Easy. “No growth” is what you need to put into value_as_concept_id. Use Not detected.
ok, but what in value_source_value or no need to record something like this
value_source_value here is “No growth After 7 Days Incubation”.
If you can not reliably extract only this part, or absolutely have a use-case for preserving the entire mass of text, you can create a supplementary table without length restriction, and populate the field with URIs/references to this new table.
On a side note,
_x000D_ looks like a newline artifact. Somewhere in your pipeline, you need to specify CRLF as a newline char.