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OHDSI / Vocabulary-v5.0

Build process for the OHDSI Standardized Vocabularies. Currently not available as independent release.
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Issues with coding for Food Allergy Data Commons #307

Open MarkWlodarski opened 4 years ago

MarkWlodarski commented 4 years ago

Hello, we are working to develop a food allergy data commons using the OMOP data model. As a part of this we have been working to code our data dictionary to standard ATHENA codes. During this process we have run into a couple issues with the way the existing codes handle food allergies.

In OMOP the ‘Allergic Reaction’ (40589905) concept is a condition as a result of its coding in SNOMED as a child of ‘Allergic Condition’. ‘Food Allergy’ (4188027) on the other hand appears to be classified as an Observation. To us this seems to be the inverse of what would be expected and we would be interested in why this was decided. It seems that Food Allergy is a clear condition / diagnosis and would fit better as a Condition, while Allergic reaction would fit better as an Observation.

There are a number of gaps in the Food Allergy diagnosis codes when it comes to specific food allergies. The areas of specific fish allergies, such as Tuna, Catfish, and Salmon. Also missing are codes for allergy to items such as Pecans, Pistachios, Squid and Octopus Ink, and allergies to cooked egg and milk. A more complete list of missing codes can be provided. On investigation, the Substance tree for food is fairly exhaustive, is it possible to use this existing tree to expand the allergy codes?

cgreich commented 4 years ago

@MarkWlodarski:

This seems the same issue as mentioned here. Any resolution on the issues?

MarkWlodarski commented 4 years ago

@cgreich This is more of an evolution of the issue we previously posted. This is addressing issues we have with some items missing from the SNOMED Diagnosis tree. On the OMOP side our big issue here is that we are interested in learning why Food Allergy was coded as an Observation instead of a condition, and why Allergic reaction was coded as a condition instead of an observation.

mik-ohdsi commented 4 years ago

relates to this issue

ekorchmar commented 3 years ago

Hello! There is a distinction, both in source SNOMED Vocabulary and OMOP Standards between allergic disposition as a state and active allergic reaction that happens when the organism is actually exposed to the allergen. Because of this, Allergic reaction to food is a Condition that represents event of ongoing reaction, and Allergy to food is an Observation. They have separate hierarchy.

Acute allergic reaction belongs to Condition domain, because it represents an occurrence that represents changes in patients organism. Allergy in general is a property of organism that does not have a clear start/end date, so we treat it as Observation.