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Observation_event_id to link allergic reactions?

CDM Builders
#1

Dear CDM builders,

I would like to ask you about a new field observation_event_id in Observation table.

I have the following use case: there is an information about allergic reactions on drugs. I was thinking to store allergic reactions to Observation table to the field value_as_concept_id with observation_concept_id = 4166257 (Allergic reaction to drug) and to store drugs to Observation table to the field value_as_concept_id with observation_concept_id = 439224 (Drug allergy).

The question is: could I use observation_event_id column to link allergic reaction and an associated drug? I was also thinking to link it with Fact_relationship table, but I didnt find the corresponding concept.

Many thanks in advance for your help,

Tatiana

#2

@TBanokina:

This is a THEMIS question. We need to establish how to do this properly. But I think you are right. We should put into Observation and link it both to the drug and to the Condition.

Can you?

#3

@TBanokina - THEMIS has a Github repo where we track new issues to discuss during the THEMIS meetings.

Please add your issue here. https://github.com/OHDSI/Themis/issues

Also, our meeting are every other week Tuesday, at 10 AM EST with the last one this week cancelled. (https://www.ohdsi.org/web/wiki/doku.php?id=projects:workgroups:themis). Please let me know if you can attend one of these meetings to discuss your issue.

#4

@TBanokina,

Another idea is to use either observation_concept_id = 4166257 or 439224 to distinguish this record as a drug allergy record. And then use the OBSERVATION.value_as_concept_id = the drug the person has an allergy.

@Christian_Reich I don’t think we should add the allergic reaction / condition suffered from taking the drug to the Condition table. Unless the Person sought treatment at a Care Site or the reaction happened during a Visit, the date isn’t very reliable or the date may be the date of the Visit in which the Person reported the allergy to their Provider with the actual reaction happening in the past. Also, the Condition only happens when exposed to the allergen. Unless someone is creating a cohort for a Condition due to / associated with a Drug, adding a Person to a cohort because they had Condition X most likely isn’t what a researcher is looking at. It’s similar to adding Gestational Diabetes to a Diabetes cohort, probably not what the researcher is seeking.

Things to take under consideration as conventions are created…

#5

Hello @mvanzandt .

Thank you for your advise. I just added an issue to GitHub repo. I also decided to include a question on how to store allergies to OMOP CDM as I have seen different approaches proposed on the forum.

Sure, I will try to join weekly meeting.

#6

Hello @Christian_Reich,

Thank you for your reply.

By this

do you mean to link it to drugs/allergens from drug_exposure and to conditions from condition_occurrence table? I was thinking that both drugs/allergens and allergic reactions will be stored in Observation table as I don’t have an actual start_date.

#7

Hello @MPhilofsky,

It is exactly what I was planning to do. I have summarized discussions on allergies from forum and have created an issue on GitHub. Please feel free to share your thoughts and experience :slight_smile:

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#8

Right. Why this is an Observation. But if there is an acute Drug or Condition you should link it.

So: Allergy should be an Observation, with the drug as VALUE_AS_CONCEPT_ID. If there is an acute allergic reaction with the Drug and the Condition actually happening - link it. I’ll respond to your proposal.

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t