SynPuf conversion using icd10 codes about etl-cms HOT 5 CLOSED

Opme:

Why do you want ICD9 to ICD10? We are mapping to the Standard Concepts, and they are in SNOMED for Conditions. Anything I am missing?

from etl-cms.

I am not an expert in this area but at least the CONDITION_SOURCE_VALUE (condition_occurrence) and PROCEDURE_SOURCE_VALUE (procedure_occurrence) codes are still in icd9 after the SynPuf ETL is run.

I think it will cause issues for application developers when there are mixed icd codes for a multi-year study? At least for the use case I am developing to calculate surgeon complication rates the code only works when the data is not using mixed codes. To make it easier to analyze this data, all codes would need to be converted to a common code.

Mike

from etl-cms.

Yes, the source_value contains these values, but they should be the one actually in the source. Not some mapped alternative.

The mapping happens in the condition_concept_id and procedure_concept_id. Conditions are mapped to SNOMED, whether they are ICD-9-CM or ICD-10-CM. What you are trying to do is part of the OMOP standard. Use those.

from etl-cms.

I see. That is good news. I will close this and test with some icd10 codes to make sure it is working.

from etl-cms.

The ETL code is designed to transform the Synpuf data as it is. That is- the source data uses specific vocabularies, including ICD9. Stuffing ICD10 codes into ICD9 data columns and expecting it to convert makes no sense. The Synpuf data is 2008-2010, before adoption of ICD10 in the US.

from etl-cms.