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Handling "Behavioral Prescriptions" and Epinephrine Questions

vocabularies

(Mark Wlodarski) #1

As a part of our project to code our Food Allergy Data Dictionary in OMOP. I am interested in knowing how behavioral prescriptions are handled in the OMOP vocabulary.

I find myself needing to store these concepts relating to avoiding known food allergy triggers:
“Strict avoidance of Food” - this needs the ability to also store the food in question
“Avoid Food at home” - again with the food in question

Also when it comes to a patient being prescribed an EPI Pen I would need to be able to record the following:

  • Carries Epinephrine Injector
  • Demonstrated Correct Epinephrine administration technique
  • Food Allergy Counseling Received

The Epinephrine concepts are requested by our panel of food allergy experts as they are interested in tracking not just if a person is prescribed Epinephrine, but also if they are carrying and able to use an epi pen.


(Qi Yang) #2

Strict avoidance of Food

36305943 Most important health event to avoid
Then put the actual food concept in the value_as_concept_id field

Avoid Food at home

36305943 Most important health event to avoid
Then put the 4331740 (Family food) in the value_as_concept_id field

Carries Epinephrine Injector

40479815 Carries epinephrine preloaded injection pen

Demonstrated Correct Epinephrine administration technique

40491319 Injection technique
Then put the 1343916 (epinephrine) in the value_as_concept_id field

Food Allergy Counseling Received

44799025 Dietary education for food allergy

You may want to search Athena for other concepts that are more appropriate. But this gives something to start with.


(Christian Reich) #3

@wlodarmt:

Are you planning on studying this in a network of data assets? If it is a local effort, and you want to use the OMOP CDM for cohort definitions, feel free to create custom concepts. The concept_id space above 2 Billion is all yours.


(Dmytry Dymshyts) #4

Should we think of some table to be a part of the usual vocabulary batch, that will serve as a storage of 2 billion concepts?
You can’t just keep them in basic tables (concept, concept_relationship etc), because you lose custom concepts, once you update the vocabulary (replace with the new batch from Athena).


(Christian Reich) #5

Not following. What are you proposing? An extra table with >2B concepts?


(Dmytry Dymshyts) #6

Yes.
Something like an extension of Source_to_concept_map with fields added:

source_concept_id,
source_standard_concept,
source_concept_class_id,
source_domain_id,
source_invalid_reason,
relationship_id

Or it can be done stage tables used in a OMOP vocabulary development.


(Alexander Davydov) #7

You need to move the content from this table to concept/concept_relationship and back. Why is it better than transferring custom concepts from one concept’s version to another?

Or you’re saying that all the scripts and tools should start using 2 different concept tables at once? :slight_smile:

Stage tables - even more complicated. We’d need to develop another generic script with 2 billl+ support.
Or people’ll build their custom tools what’s not a part of the entire model anyway.


(Dmytry Dymshyts) #8

How?


(Alexander Davydov) #9

SELECT *
FROM concept
WHERE concept_id >= 2000000000


(Mark Wlodarski) #10

Thank you! I figured there were concepts for the epi pen information but I was unable to find them. Thank you as well for the advice on the food avoidance.


(Mark Wlodarski) #11

This data commons is planned to include at least 20 institutions. So it wont be local. We would prefer to avoid custom concepts.


(Christian Reich) #12

Aren’t we working on the wide mapping table?


(Christian Reich) #13

Wow. Yes, we want to help them. Do you think @QI_omop’s list is sufficient?


(Mark Wlodarski) #14

The suggestion for strict avoidance of food seems sufficient, though ideally we would want a “Strict avoidance of Food” concept.
However

36305943 Most important health event to avoid
Then put the 4331740 (Family food) in the value_as_concept_id field

This does not seem to leave a way for indicating what food is used - would I link that to the other event via the FACT_RELATIONSHIP table?


(Alexander Davydov) #15

This LOINC concept isn’t performing anyway - it’s a kidney disease panel with predefined list of answers.
So no need to say that fact_relationship is inappropriate.

I’m for a new OMOP Extension concept where you even can store a food as a value_concept_id or value_as_string.
There’s a decision to store a food as a string since it’s not standardizable. Or will you have a clear list of possible allergens?


(Alexander Davydov) #16

Actually 2 new concepts:

Recommendation given to subject to strictly avoid the food

Subsumes

Recommendation given to subject to strictly avoid the food at home


(Mark Wlodarski) #17

We will have a clear list of “Most Common” allergens. But this list will not be exhaustive.


(Alexander Davydov) #18

So we can either precoordinate or use the value_concept_id field.


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