I am very new to the OHDSI community … I hope I have posted the question to the right place.
We have a source system that organizes pathology data in Question-Answer format. For example, the data can be like:
‘Q’ - Skin Invasion (with a CAPECC code)
‘A’ - Invasive carcinoma does not invade into the dermis or epidermis (with another CAPECC code)
In this example, I can find the mapping of the CAPECC code to the Standard code through the concept_relationship table. With the mapping, the Standard codes look like:
‘Q’ - Skin observable (concept id: 4265704, under domain: “Observation”)
‘A’ - Intact skin (concept id: 40481164, under domain “Condition”)
Since the ‘Q’ and ‘A’ are under 2 different domains, I expect they will end up being stored in 2 different tables - The ‘Q’ will go to the “Observation” table, and the ‘A’ will go to the “Condition_occurrence” table.
Following the documentation:
I am thinking to use the “observation_event_id” and “obs_event_field_concept_id”, of the “Observation” table, to link the ‘Q’ and ‘A’ data together.
So in the “Observation” table, the “value_as_concept_id” field will become null (because the ‘A’ will be stored in the “Condition_occurrence” table). Instead, the “observation_event_id” field will store the ‘condition_occurrence_id’ value of ‘A’ (from the “Condition_occurrence” table), and the “obs_event_field_concept_id” will store the concept id 1147333 (to indicate it comes from the “condition_occurrence” table).
Is my understanding correct?
I am asking this because I initially thought that both the ‘Q’ and ‘A’ would always be stored in the same table, but this does not seem like the case here. Also, looking at another post:
it seems these 2 fields - “observation_event_id” and “obs_event_field_concept_id” - might have been created for other purpose before. So I want to check with other people whether I am on the right track.
Any feedback is welcome. Thank you!!