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OHDSI / Themis

Repository for OMOP CDM conventions as defined by THEMIS. These can be reference lists of concepts, pieces of standardized code for data generation or quality certification, and debates.
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Allergies: store it to OMOP CDM and link it with the allergic reactions #59

Open tbanokina opened 5 years ago

tbanokina commented 5 years ago

PROBLEM: Allergies. There are ambiguities on:

  1. How to store allergies to OMOP CDM;
  2. How to link allergic reactions and the associated drugs/allergens.

FORUM: https://forums.ohdsi.org/t/observation-event-id-to-link-allergic-reactions/7354

https://forums.ohdsi.org/t/put-allergy-in-omop/2737/9

https://forums.ohdsi.org/t/how-to-encode-allergy/2024/4

https://forums.ohdsi.org/t/new-fact-relationship-relationship-id/4937/7

CURRENT SOLUTIONS DISCUSSED:

  1. Drugs/allergens can be stored to OBSERVATION table to the column value_as_concept_id with one of the following observation_concept_id's = 439224 (Drug allergy) or 4169307 (Allergy to substance)
  2. To store allergic reactions, 2 cases possible: a) If the condition_start_date is given, then, it can be populated to CONDITION_OCCURRENCE table to condition_concept_id column; b) If instead of the start_date there is an input date, then, it can be populated to OBSERVATION table to value_as_concept_id with observation_concept_id 4166257 (Allergic reaction to drug) or 441488 (Adverse reaction to substance).
  3. To link allergic reactions and the associated drugs/allergens, 2 cases possible: a) Through observation_event_id column from OBSERVATION table. A record with an associated allergen from OBSERVATION table can be linked back to a record with an associated allergic reaction (to condition_occurrence_id or to observation_id); b) Through FACT_RELATIONSHIP table. Currently, there are no valid concepts to be used to link allergic reactions and the associated drugs/allergens.
cgreich commented 5 years ago

How about this:

  1. If an allergy against a drug is recorded generally (not the acute manifestation requiring attention or treatment) then put 4166257 "Allergic reaction to drug" into OBSERVATION_CONCEPT_ID and the Drug Ingredient Concept ID into VALUE_AS_CONCEPT_ID (not the other way around).
  2. If there is an acute manifestation with records in DRUG_EXPOSURE and/or CONDITION_OCCURRENCE use FACT_RELATIONSHIP to link them up. We probably need a new RELATIONSHIP_CONCEPT_ID for that.