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Recording an effect of a given drug/procedure on a patient condition?

Vocabulary Users
#1

Hello All,

I am complete novice to OMOP so please forgive me if my question is a bit naive.
How can I record an effect of a given drug on the patient condition?

In particular, the questionnaire contains the following question:

“Does the patient notice a tremor diminishment with alcohol intake?”
and possible answers are {Yes, No} or {1, 0}.

I assumed that the result could be stored as a record in the Observation Table using value_as_number property set to 1 or 0.

I checked in Athena which concepts can be related to this question and I found (I filtered Standard and Valid only):
35621943 Patient Global Impression of Improvement Staging / Scales Measurement SNOMED
35621963 Patient Global Impression of Improvement score Observable Entity Observation SNOMED
4052351 Alcohol intake Observable Entity Observation SNOMED
432456 Alcohol intake - finding Clinical Finding Observation SNOMED
43531003 Essential tremor Clinical Finding Condition SNOMED

However, I do not know how to use them to define the given observation (or even if the observation is a good guess here), since there is only one field: observation_concept_id, but there are a few concepts. Shall I extend vocabulary or just somehow encode it with use of disencouraged field: observation_source_concept_id? I was also thinking about FACT_RELATIONSHIP table to record indication relationship (between drug exposures and associated conditions), however I simply have no experience with it.

I realize that Survey Vocabularies are not a simple thing to deal with in OMOP according to the previous topics as Survey vocabularies in OMOP or Survey data mapping - Question and Response pairs and many others.

I will appreciate for any help.
Thanks
Andrzej Marciniak

#2

@Andrzej_Marciniak:

Looks like you want to capture a survey in OMOP. The way to do it is to create concepts for all the questions and all the answers. Questions go into the observation_concept_id or measurement_concept_id of the OBSERVATION or MEASUREMENT tables. You don’t have to convert Yes to 1 and No to 2, you can put the Yesses and Nos, or any other answers, as concepts into the value_as_concept_id field.

If this survey is a public instrument we could consider adding it to the Standardized Vocabularies. If not, use your own concept ID space above 2 billion.

1 Like
#3

Thank You @Christian_Reich for very quick and useful response. You gave me very useful hints and actually a confirmation that I am going in the right direction.
As for the Answers, I suspected that I could use both concept and numbers, but you just made me sure about it - thanks.
As for extensions to Standardized Vocabularies - that would be great if we could add some instruments to it. I work in SPINE project (SPINE Platform | Center for Neurological Imaging) where we deal with a lot of instruments defined as questionnaires in CDISC (QRS | CDISC). A great amount of questions (or rather concepts) is already defined in SNOMED or LOINC but not all of them.
Maybe I could do some research and we could continue this topic in September (Today I am starting my holidays;-)
Thank you again
Best
Andrzej

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