Change concepts.concept_code to concepts.source_code

[jenniferduryea]

Originally in MarksJigsawIssues.xlsx

Concepts table uses “concept_code” instead of “source_value” which is used in all of our other tables — change that?

Tagging everyone for discussion.

[aguynamedryan]

If we're going to change the name, I'd argue code is preferable to source_code. To me,source_code signifies the raw, straight-from-the-data code in a dataset. The code column contains the properly formatted, canonical version of a concept's code.

[jenniferduryea]

Re-reading this ticket, I think we need to keep these two values the named differently. The column in the clinical_codes table (in gdm) called "clinical_code_source_value" is the actual "source_value" from the data. So for example, for ICD10CM codes, where Medicare does not include the period, we have the code "C714" under clinical_code_source_value. However, the clinical_code_concept_id assigned to this source_value is linked to the concept_id with concept_code of "C71.4". The concept_code refers to the correct or standard code (e.g. the ICD10CM notation with the period in there). So source_value is the data that comes directly from the raw data. concept_code is the standard/correct notation for the code.

Also, the "source_value" output from Jigsaw's Events table, is also the "source_value" saved in GDM. So the data output and terminology is consistent.

Pending closing this ticket.