We have a survey data which has to be transformed into OMOP CDM format. I have given an example below, so that it would be easy for you to understand.
Survey Question - How often do you drink alcohol? (**Concept_Id = “40771103” with class = “Survey” and domain = “observation” **)
User Response - 3 days a week (not found in Athena)
Survey Question - What is your annual income? (not found in Athena. PS - I am not looking for family income but indvidual’s annual income)
User Response - Annual Income: less 10k (Concept_Id = 1585376 with class = “Answer” and Domain = “Observation”)
As you can see from above examples, what should I do when I don’t find the right concepts for Question/Responses in Athena? Can we add the missing questions and responses as concepts in our Concept table with concept_id > 2B? I should just make an entry (using Insert Into query) in my Concept table. Is my understanding right? Is there anything that I should do with Source_to_Concept map table? Can you please guide us on mapping these survey items to CDM format?
In @ericaVoss @Patrick_Ryan @margaret 's work on survey data based on NHANES dataset (http://www.ohdsi.org/web/wiki/lib/exe/fetch.php?media=resources:using_the_omop_cdm_with_survey_and_registry_data_v6.0.pdf), I see that the response “Nearly every day” to Concept_id = 45882010 under “Answer” class and “Meas_value” domain. Can you please help me understand why not Concept_id = 763699 under “Qualifier Value” class and “observation” domain? Because the latter seems to indicate the frequency. I might totally be wrong here as well. I have started to learn OMOP and all medical terms only recently. Kindly request you to correct my understanding.
a) Is there any specific class and domain should I be looking into for survey questions?
b) Is there any specific class and domain should I be looking into for survey responses?
Am I right to think that “observation” table will be the large(in terms of size) table when compared to other cdm tables as it has 40 records per person, considering each patient has to answer 20 survey questions (20 records with different columns for questions (observation_concept_id) and responses (value_as_concept_id).
Is there anything else that I should be aware of when converting survey data to CDM data?
Adding missing concepts isn’t time consuming? I mean surveys can vary a lot between regions/groups. The only way is to add the concepts?
Once we learn how to do for one table, I believe it will be easy for us to do for the rest without any issues. Require your support