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What is the most appropriate way to incorporate ICD10 codes not from Condition domain into OMOP CDM?


(Alexander Sivura) #1

Hi there,

We are working on ETL for EHR data for outpatient encounters. What is the right way to convert billing ICD10 codes to OMOP CDM? We convert them to standard concepts and put them into a condition_occurance table. But we noticed that some of ICD 10 codes are mapped to concepts not from the “Condition” domain.

There are some examples:

  1. Z01.82 - Encounter for allergy testing
  2. V26.33 - Genetic counseling

Some ICD10 codes also have “map to value” relationships:

  1. R71.8 - Other abnormality of red blood cells
  2. R76.8 - Other specified abnormal immunological findings in serum

What is the right way to incorporate this information into OMOP CDM?


(Christian Reich) #2

Gotta read the Book, @alexander. Secion 5.3.1 Mapping Relationships explains it. Bottom line: The domain_id in combination with the ‘Maps to’ and ‘Maps to value’ tells you where to put things.


(Alexander Sivura) #3

Thanks, @Christian_Reich. I just want to get a confirmation on it. Folks from our medical team were going to incorporate information about ICD encounters (like Z01.82) into the visit details table somehow. My proposal was just to put it into the Observation table. What about measurement ICD codes with values, should we put them into Observation table or Measurement table or both? In the book, it says “AND”…


(Christian Reich) #4

@alexander:

You are stressing too much. :slight_smile: Make it easy for you:

  1. Take the code
  2. Look it up and find the concept
  3. Map it to a standard using “Maps to” (if it already was a standard it will map to itself, no harm)
  4. Look at the domain_id
  5. Write the record into the table that corresponds to it. E.g. if you get Domain “Procedure” you write it into the PROCEDURE_OCCURRENCE table.
  6. Place the code into the <domain_name>_source_value field
  7. Place the looked up concept into the <domain_name>_source_concept_id field
  8. Place the standard concept into the <domain_name>_concept_id field.
  9. Check if there is a “Maps to value”
  10. If so, write the concept into value_as_concept_id field of that record.

Couple of lines of SQL. No medical experts needed. The Vocabulary does it all for you.


(Alexander Sivura) #5

Thanks again. It resolves our internal disagreements.


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