Fact Relationship Table

[survitup]

The fact relationship table contains Domain Concept ID as an INTEGER but the Domain Concept ID has been changed to a VARCHAR(20). The fact relationship documentation and code needs to be updated to reflect the change to VARCHAR(20).

[gowthamrao]

@cgreich why is this a varchar and not an integer. Integer is more efficient to use. @cukarthik you had a similar concern?

[cgreich]

@gowthamrao, @anthonyjsl

We already pushed it out? We don't have the concepts ready yet for tables and fields. Dammit.

[cgreich]

@clairblacketer:

@anthonyjsl made a point that's wrong, but another point related to it is there: We changed the references to tables to Concepts? I thought that's a V6 thing?

[survitup]

@clairblacketer @cgreich

Yes the issue I opened was about me confusing the Domain ID with the Domain Concept ID. I closed it after I realized that that it was the domain concept id. So in V6 the change will be to concepts rather than domains correct?

[gowthamrao]

@cgreich @clairblacketer @vojtechhuser

yes - we need to have concept_id for each omop table - cdm, derived, metadata. we need it for a lot of reasons

[survitup]

@gowthamrao

Shall I change the details of the issue to reflect the change of Domain to Concept ID?

[cgreich]

@clairblacketer: Can you make a list of all tables and fields, in all versions you have? So we can make Concepts?

[cgreich]

@anthonyjsl: I realized what you were doing, but I reopened it, because you drew the attention on the other issue. Yes, that's the idea. But Clair pushed it already out. So, we either scramble to make the Concepts, or we pull it and wait till V6.

[gowthamrao]

So is it varchar or Integer (please say integer)

[clairblacketer]

@cgreich

I didn't make any changes to the fact_relationship table for v5.3.0, it has always used DOMAIN_CONCEPT_ID. The vocabulary_id 'Domain' contains concepts that represent each domain in the vocabulary. For example, 19 represents 'Condition' and 17 represents 'Device'. I don't think there is an error here, I think there is just some confusing naming conventions because DOMAIN_ID is a varchar and DOMAIN_CONCEPT_ID is an integer.

[clairblacketer]

@gowthamrao it is an integer :)

[clairblacketer]

@cgreich

I will make a list of all recently added tables so we can get them in the 'Domain' vocabulary

[gowthamrao]

@clairblacketer if it helps, here are all the tables that need concept_id https://docs.google.com/spreadsheets/d/1wFbq6Y7JbL5UjhUBKLE4hniDEdMnyDGGlyeew38u3NM/edit?usp=drivesdk

[gowthamrao]

@cgreich

Assign every table a concept_id and map that to parent domain_concept_id.