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Deprecate CPT4 code

Vocabulary Users
#1

Hi All,
During the process of mapping CPT4 codes to standard procedure concepts we found some concepts that are deprecate, like code ‘0135T’ which map to ‘Ablation, renal tumor(s), unilateral, percutaneous, cryotherapy (Deprecated)](Athena)’.
This concept is a standard procedure concept but it deprecate and map only to itself.

What we can do in order to map it to valid standard concept?
Can we use text similarity script and in this case connect to ‘Ablation, renal tumor(s), unilateral, percutaneous, cryotherapy](Athena)’?

Thanks,
Guy

#2

Hi @guy_livne, this is the specificity of CPT4. In OMOP, there are 1892 Standard CPT4 codes marked as “Deprecated”. They have been removed by the source without providing replacement codes at some point in the past (see valid_end_date). However, such codes may occur in the source data to this date, that is why they alive and Standard in OMOP. Thus, according to the OMOP mapping rules, if a concept is Standard, you do not have to map it to another Standard concept. So, you can use “0135T” as is.

#3

Thanks @Polina_Talapova
The reason to change from deprecate to valid concept is that deprecate concepts has no hierarchy and no relations connect to it.

That why I’m looking for a replace concept.

Thanks,
Guy

#4

@guy_livne

It is still a “valid” and “standard” concept as seen in it’s attributes.

All standard concept_ids map to themselves.

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#5

@guy_livne to embed old CPT4 codes into the hierarchy I recommend you to do this locally using manual mapping or automated string matching that you mentioned earlier.

By the way, if you want to share your mappings with the community later, the vocabulary team can help you to validate and implement them officially :slight_smile:

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