[2022 US Symposium] #69 - Allergies to Substances

ericaVoss · October 7, 2022, 1:20am

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Allergies: store it to OMOP CDM and link it with the allergic reactions

opened 04:29PM - 15 Jul 19 UTC

**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.

DaveraG · September 17, 2024, 6:19pm

Hello Hello! I see in the links there’s an Themis GitHub record for this issue, but it looks to me as if its still a “stub.” Is this not true (there is a convention) and I’m not looking in the right place?

Allergies are in scope for the Joint FHIR to OMOP IG build underway. Currently we have input from two projects providing FHIR source to OMOP maps for allergies (Georgia Tech & CareEvolution). It would be important for our project to have an established convention for the appropriate OMOP target for our FHIR resources to map to. If its not yet established, maybe we can use our need and project timeframe (urgency) to encourage development of this?

How can we help?

Cheers,
Davera
davera.gabriel@evidentli.com

MPhilofsky · September 18, 2024, 4:47pm

Hello @DaveraG,

The issue needs a sponsor to move it through the Themis process. Should I assign it to you or someone else from your work group?

DaveraG · September 20, 2024, 12:51pm

That seems quite reasonable, but I want to discuss with our group and establish who might take the lead on this. We got just up to this topic in our discussion this week, but didn’t cover this item. Its in the queue next for our upcoming agenda(s) and I’ll be sure to confer with the group about taking on responsibility for this. So: please standby & I will reply again soon.

PS: these meetings are open to all - we meet weekly on Wednesdays at 4pm EASTERN. Inviting anyone interested to come join us!

[Launch Meeting - Zoom]

DaveraG · September 25, 2024, 9:08pm

@MPhilofsky we discussed it in our WG meeting today and the group present agreed that we will accept responsibility for this THEMIS issue. Our take on this will go into the first draft HL7 ballot and we will use the balloting process / feedback as input to resolving / proposing solution to this THEMIS issue.

I know there are templates to be filled out. Beyond that please let us know what we need to do to be responsive to the OHDSI processes, and we will respond (as a group).

Alexdavv · September 26, 2024, 1:41pm

Hi @DaveraG I’m glad to hear it! I added a couple of points to the GitHub issue since there might be vocabulary implications along the road.

MPhilofsky · September 26, 2024, 2:30pm

Team work makes the dream work! And this will be a valuable contribution to the community.

The Themis process is located here. Let me know if you have any questions along the way!