Hello @Alexdavv
What concept_id should I use to identify the subject in Cohort_Definition.subject_concept_id field are persons? These are the standard concepts I found on Athena:
I’m looking at rows 1,2,5
My guess is that the subject_concept_id was designed to hold the Person domain concept, which is deprecated since September 2022:
To be consistent with recent CDM changes, we should have a field like subject_field_concept_id that then would refer to person.person_id or provider.provider_id. Or drop the column altogether because in 99% of the cases it will be person anyways.
Thank you for finding this, @MaximMoinat! I was only looking at standard concept_ids.
My question to the vocab team, why was this concept_id deprecated and not replaced?
It was implicitly replaced by 1147026 person.person_id. At least, such a field-level references should be used in fields like the meas_event_field_concept_id.
This can also be used for cohort_definition.subject_field_concept_id. Only the description/convention for this field on the CDM documentation should be updated.
Thanks again, @MaximMoinat!
I am going to create a GitHub issue on the CDM page to update the description for this field with a pointer on how to find the appropriate concept_id for the field. Are these the correct requirements for this field:
Domain = Metadata
Class = Field
Standard_concept = S
And once the correct concept_name is found, one must look at the relationship_id = “Table/field contained in OMOP CDM Version (OMOP)” to ensure the concept_id is part of their CDM version since it’s a 1:M relationship between concept_name with the above attributes and concept_ids. As seen in the screen shot below.
@MaximMoinat I think this last part could be worded better. Any suggestions?
This should at least be consistent with the meas_event_field_concept_id description (emphasis mine).
User guide: If the Measurement record is related to another record in the database, this field is the CONCEPT_ID that identifies which table the primary key of the linked record came from.
ETL Conventions: Put the CONCEPT_ID that identifies which table and field the MEASUREMENT_EVENT_ID came from.
Seems to be an inconsistency in here: the user guide mentions only about the table, the ETL Conventions about table and field. So actually not clear whether to refer to person_id field or person table. Table should be enough, as I can imagine you would only refer to the primary key of a table