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ICD9 concepts that do not map to a standard Condition concept

Vocabulary Users
#1

In updating our vocabulary to the March OHDSI CDM vocabulary, version v5.0 11-MAR-16, we found 3131 ICD9 concepts that do not have a mapping to a standard concept with the ‘Condition’ domain_id. The breakdown is:

  • 2541 have the ‘Observation’ domain_id, all standard concepts
  • 330 have the ‘Procedure’ domain_id, all standard concepts
  • 201 have the ‘Measurement’ domain_id, all standard concepts
  • 55 have the ‘Condition’ domain_id, but are not standard concepts

The issue with the ICD9 concepts that map to Observations and Measurements is that a record of an ICD9 code does not have the fields required to be valid entries in the observation or measurement tables. For example, records of ICD9 codes that have been mapped to a Measurement would be missing entries for value, unit, range etc.

The issue with the non-standard ‘Conditions’ is that they are being dropped from our data altogether if we follow the OHDSI CDM v5 guidelines.

Here is a spreadsheet with the number of patients (>= 50) with at least one record for any of these concepts, to indicate the effect of this issue at our site: https://www.dropbox.com/s/kjgz48n6r2b5s9i/ohdsi_cdmv5_concepts_counts.xlsx?dl=0

What would you recommend as a solution for keeping records with these concepts in our dataset?

Thanks,
Alison

#2

@acallahan:

That is quite correct. All you know is that that the measurement took place, but not the result. Unless there is a second CONCEPT_RELATIONSHIP record with the relationship_id='Maps to value", which will give you a concept for the value_as_concept_id.

Yeah, that needs to be fixed.

Thanks a lot for the list, that’s very helpful. If you have the capacity and want to map those, we will incorporate them immediately. If not, you will have to wait a few weeks till we get to them. In the mean time, just write records with the ICD9CM concepts in the source_concept_id field, and 0 in the concept_id field.

t