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SNOMED Procedures and Domain of Measurement

CDM Builders
#1

This for CDM v5, Vocab V5.

Recently had an Achilles Heel error that mentioned:
ERROR: 600-Number of persons with at least one procedure occurrence, by procedure concept_id; 11 concepts in data are not in the correct vocabulary.

From what we can see, everything in our PROCEDURE_OCCURRENCE table is a SNOMED-procedure code, but some of them have the domain of MEASUREMENT or OBSERVATION. We are thinking this is what throws this Achilles Heel error.

For example, we have a record in our PROCEDURE_OCCURRENCE table that is mapped to 4246053-BLOOD TEST, but the DOMAIN is MEASUREMENT. What is the correct action here? In the source, this is just a record indicating the test was performed, the results have not come across yet. Do we consider the observation of a “Blood Test” without values something that should be a measurement? There is also an Achilles Heel check that complains when measurements have no value. We do not know how to think about this.

I appreciate any feedback.

#2

ACHILLES HEEL warnings were programmed for CDMv4. We need to revise the
vocabulary warnings for CDMv5 to simply check if the concept is 1)
standard, and 2) in the appropriate domain. So long as your data meets
that criteria, you’re fine with the CDMv5 conventions.

#3

Any source code that maps to a concept with the domain of MEASUREMENT
should be placed in the MEASUREMENT table. So, in the future, that would
be a valid ACHILLES HEEL warning if you have a record in the
PROCEDURE_OCCURRENCE table with a CONCEPT of domain MEASUREMENT, because it
would be located in the improper location.

#4

We are still trying to think about this . . .

#5

To follow the CDMv5 convention, your record should be placed int the table
corresponding to its DOMAIN. So, if the source code maps to a standard
concept whose domain is MEASUREMENT, then the record should be written to
the MEASUREMENT table. A MEASUREMENT record does not require a value, so
that would be an error to be reported on the ACHILLES git.

#6

Erica et al.:

As Patrick said. Measurements are no longer Procedures, and nor are they Observations. So, if they have the domain Measurement you have to move them over.

Measurements don’t have to have a value, so, Achilles Heel needs to be fixed here. Of course, in reality they do, but we may not have that fact available. So, you can end up with “Blood Test” and no result. (“Blood Test” is probably pretty useless anyway, but the mechanism is the same for real Measurements, like 4149519 “Glucose measurement”).

BTW: There is a whole group of Measurement concepts like 438557 “Abnormal glucose level”, which essentially combine both the test and the result in one concept. In future, we will split them up into their components 4149519 “Glucose measurement” and 4216167 “Outside reference range”. It’s in progress.

t