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We came across this issue with ICD9 code V85.54 (concept_id: 44826272) when moving hospital data to OMOP. The ICD code maps to both a condition (40481140) and measurement (4014603). Since the concept code is mapping from an ICD code, there is no value to put in the measurement table.
I’m wondering if 44826272 should only be map to the SNOMED code under the condition domain (40481140).
A measurement record does not have to have a value in order to be valid.
In this case, i would map to both places.
But from a practical point of view, you can’t really do much with the data. Just not sure if it makes sense to have the mapping. We will probably ignore it for the ETL.
In this case, the measurement concept contains the value (greater than 95
percentile). If a researcher uses that standard concept, theyd expect it
to be in measurement table, since that is the only allowable place for that
concept.
Why is that so? The fact that a Measurement was performed is already of value. Even if you didn’t know the result.
It makes sense now. It depends on your source. I can see how it is useful to have the code for the measurement domain when you’re using claims data. If your data source is the EHR, using the mapping from ICD to the measurement domain is redundant because the BMI would already be recorded within the EHR. Instead we would take that value and put it into the measurement table.
@khartik:
Correct.
I wouldn’t “overthink” this too much. Take the codes, find the concepts, map them and drop them where the domain_id tells you. If that results in some duplication - don’t worry. Don’t second-guess during the ETL.
This question arose from my naive understanding of OMOP mappings. It appears that thousands of codes in ICD map to multiple codes in multiple domains - most frequently a condition and either an observation or measurement. For example, many specific conditions also map to “Aftercare” in observation. In general, do both codes go into the OMOP db? I’m not sure I understand this semantically. Can someone explain or point me to an explanation of how this is used?
Also, many ICD codes map to a different domain than I would anticipate… some ICD-9 diagnosis codes map to the procedure domain and some ICD-9 procedure codes map to the diagnosis domain. Why is that? How were the domains determined?
Thanks!
Domains are a construct in OMOP to organize vocabularies to standard concepts. The OMOP Vocabulary group determines the mappings. If there are issues that the community finds with the mappings, people either post them in the forums or in the GitHub repo. You can find out a little more about domains here.
As for concepts mapping to multiple domains, the general rule is to create a row for each mapping in the appropriate domain table. Not all ICD codes, as you’ve seen, are in the condition domain. @Patrick_Ryan discusses it a little here.