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More adequate standard concepts for "Carpal tunnel release" procedure

Vocabulary Users
#1

Hi everyone,

I’m looking for the best standard concept to represent the “carpal tunnel release” procedure (from the procedure domain) - I only found this which is a non-standard one:

Release of carpal tunnel

I’m looking for a standard concept that is not too specific and is not too generic as well.
carpal tunnel release can be bileteral or unilateral and also open or endoscopic.

There are only few specific concepts and I’m not quite satisfied with their specificity:

I couldn’t find any adequate standard concepts to use.
Are there any more concepts that I’m missing or do we need to add them?

Thank you.

#2

Hi, @gil.frenkel :slight_smile:

The concept you found has ‘Maps to’ relationship (which connects Non-standard concepts to standard) with Decompression of median nerve. Even more important, Snomed concept Decompression of median nerve at wrist, you may be interested in, became invalid and was remapped to decompression of median nerve. So go with it :slight_smile:

Consider this concept unilateral, unless otherwise stated (you’ve already found the right concept for bilateral procedure)

If you need to combine attributes (bilateral, endoscopic, open, etc.) you can populate modifier_concept_id or use 1-to-many mapping, where one source code from your data mapped to >1 standard concept (eg. bilateral endoscopic carpal tunnel release → bilateral carpal tunnel release + endoscopic carpal tunnel release, etc.).

You definitely don’t need any new concepts.

1 Like
#3

Thank you very much @zhuk for all your help!

#4

You are welcome!

Feel free to ask your questions in one of your themes, no need to create new for each question

1 Like
#5

Hi @zhuk

I’m trying to map microbiology lab tests from a govermental hospital to OMOP.

I’ve encountered a lab test performed on a specific culture (known specimen and culture) which called gram stain.
The problem is, All gram stains in Measurement domain only contains very specific ones such as:

But in my source_code I don’t have this kind of specifications, the only thing I have is “Gram Stain”, the type of culture or specimen are a seperate source_codes.

Should I go for Microscopic observation [Identifier] in Unspecified specimen by Gram stain?

Although I know what kind of specimen was used for the gram stain?

I can see there is a more general concept:
Gram stain microscopy

But this is a procedure and not measurement. Why? This means this lab test is populated in the PROCEDURE_OCCURRENDCE table?

I thought procedure_occurrence is only for procedures that have been conducted on the patient himself.

I would love some help with this matter!

#6

@gil.frenkel

So, you have the information or not? If so, can you pre-coordinate with the gram stain?

#7

Hi @gil.frenkel,

If you have cultures or specimens as separate source codes, I recommend you concatenate your lab tests with cultures or specimens to get new entities that can be easily mapped to detailed LOINC terms.

For example, if there is one table (PostgreSQL):
select distinct concat(lab_test_code, ’ | ', specimen_code), concat(lab_test_name, ’ | ', specimen_name) from your_table;

If there are separate tables you need to have a foreign key to join them.

#8

Hi @Christian_Reich and @Polina_Talapova!

First of all thank you fo your help, much appreciated.

I do have the information, but as two seperate source_codes (“urine culture” + “gram stain”), so I understand I can pre-cooridnate by concatenateing both source codes to one source_code and map it to the specific gram stain measurement Microscopic observation [Identifier] in Urine by Gram stain

Thanks!

#9

Exactly. Would that work?

1 Like
#10

Yes, indeed.

Thanks!

#11

Hi @zhuk,

I’m trying to find a concept for “rectus sheath block” only.
As far as I know, rectus sheath block is not the same as TAP block - I couldn’t find it in Athena - should I be happy with the concept 46257606, which aggregates both procedures (TAP and rectus sheath) together?

Maybe I’m missing a synonym?
I’m just trying to avoid customizing source concepts as much as possible.

Thanks!!

#12

Seems like I can’t find them too.

Are you interested in these particular concepts in your study?

I would recommend 44808433 for TAP block. And maybe choose some more general concept or the custom one for ‘rectus sheath block’.

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