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Put Allergy in OMOP

(Bryan Thurston) #22

Say I have a severe allergic reaction to penicillin and it results in hives, how do I store all of these data points? I have taken a shot below:

Drug Allergy ==> observation_source_value
Penicillin ==> value_as_a_string
Hives ==> condition_source_value
Severe Reaction ==> value_source_value (in Measurement Table)

And I associate these with a specific visit occurrence to relate them?

(Dmytry Dymshyts) #23

Here is my proposal how to put this. Still not sure where to put “Severe Reaction” though.

CONDITION_OCCURRENCE.condition_source_value =‘Hives’
CONDITION_OCCURRENCE.condition_concept_id = 4082588 (Standard concept_id for Hives)

OBSERVATION.observation_source_value = ‘Drug Allergy Penicillin’
OBSERVATION.observation_concept_id = 439224 (Standard concept_id for Drug allergy)
OBSERVATION.value_as_concept_id = 19126544 (Standard concept_id for Penicillin)
OBSERVATION.observation_source_value = ‘Drug Allergy Penicillin’
OBSERVATION.observation_concept_id = 4240903 Allergy to penicillin
the latest option is more in line with OMOP rules, but I think you can choose the one that is easier to obtain for you.

then connect them via FACT_RELATIONSHIP.
FACT_RELATIONSHIP.domain_concept_id_1 = 19 (Condition domain)
FACT_RELATIONSHIP.fact_id_1 = CONDITION_OCCURRENCE.condition_occurrence_id (corresponding to Hives entry)
FACT_RELATIONSHIP.domain_concept_id_2 = 27 (Observation domain)
FACT_RELATIONSHIP.fact_id_2 = OBSERVATION.observation_id (corresponding to Drug allergy entry)
FACT_RELATIONSHIP.relationship_concept_id = 46233685 (Condition relevant to)