Hi,
- In OMOP what are the difference between the following 2 tables?
CONDITION_OCCURRENCE table
OBSERVATION table - If I want to ETL Allergy data, which table should I use?
Thanks!
We are working on an ETL that has allergy data. We found that we could map
over 80% of the allergy values to OMOP concepts. The domain id of the
majority of these is Condition. Example: concept id 4302207 (allergy to
grass pollen) has the domain id Condition. For the allergies we can map we
are using the domain id to determine the target table. Those that cannot
be mapped we are putting into the Observation table, but we feel that the
decision is arbitrary and you can make an argument for putting unmapped
values in the condition table.
Just to be clear - for those concepts you can map - you would enter it into the condition_occurrence table where condition_concept_id = 4302207. What would you enter into the condition_start_date if the information is not provided? The date of service/encounter?
Thanks
The start date column is NOT NULL, so you do need a date. And the only alternative is the service/encounter date.
If the allergy information is from patient history or patient reported the answer of where to put the data is more nuanced because patient history information can go into either Observation or Condition table. You have to think about how analysis will be done using the database. For example, the OMOP Condition Occurrence table is often used to answer questions like, person took drug X and had reaction Y. Or the other way around person has condition X and is treated with medication Y. To do these analysis requires that the condition and drug exposure start dates reflect the state of the person at the time recorded.
If your allergy data is historical or patient reported you can put it in the Observation table, which is where things get put when you donât want to loose the information, but are not sure what to do with it, or you can still put it in the Condition Occurrence table, but make sure to set the Condition Type concept to âEHR problem list entryâ or âPatient Self-Reported Conditionâ. These Condition Type values should be enough to alert researchers to the fact that the condition start date may not indicate when the Allergy diagnosis was made.
I suggest waiting to see if there are some other opinions. Part of answering these questions is to have your answer corrected.
Perfect! Thanks.
Thanks!
Friends:
Nice posting. We should clean this up. Here it is:
Allergies are always historical facts. Something the patient learned after the fact. An ongoing allergy is a Condition, but you wouldnât record the source, even if you knew it. You would record the local response (eczema, allergic rhinitis) or the systemic reaction (laryngeal edema, anaphylactic shock).
The typical allergy report should be an Observation, with the allergen, if known, recorded in value_as_concept_id. But thatâs not how it is mapped right now. Instead, the allergic âconditionsâ are now mapped to SNOMED Condition concepts or to 43530807 âAllergic dispositionâ if the allergen is not listed. We need to bring this up with the CDM WG. @Dymshyts has also looked into this before.
How would you suggest handling a substance allergy?
If the allergen is recorded in the observation.value_as_concept_id - for example oxycontin (19076182) then the fact it is a drug concept it is assumed to be an allergy? Or would you add additional information in the observation_type_concept_id and qualifier_concept_id to make it clear the observation entry?
Thanks
You also need to record in the observation_concept_id 4166257 (âAllergic reaction to drugâ). Only flaw in this picture: This is a Condition concept, not an observation concept. And in the Condition table you cannot have value_as_concept_id. We need to find a good solution for this problem. But thatâs what I would do in your situation right now.
The observation_type_concept_id depicts the origin of the information. It doesnât qualify the meaning. The qualifier_concept_id is for qualifiers like right or left, so it is not the right field either.
@Christian_Reich
just to be clear
43530807 âAllergic dispositionâ and 4166257 (âAllergic reaction to drugâ) are two different things.
and then you want to map for example
Pindolol allergy - Maps to - âAllergic dispositionâ;
- Maps to value - âpindololâ
and if itâs reaction you map in the same way. concept_id = 4166257 (âAllergic reaction to drugâ)
and value_as_concept_id = âDrug itselfâ
Is it right?
Correct. And yes about the difference between disposition and actual reaction. But here lies the problem: If it is a reaction we need to treat it as a Condition, and then we donât have a value_as_concept_id field.
Got it,
why?
âDermatitisâ, âAngioedemaâ or something like that should be treated as a condition,
but âAllergic reaction to drugâ is an observation.
Running into this same issue. We have distinct events of patients experiencing adverse reactions to drugs.
Just to be clear, was the resolution to ignore the (condition) domain of âAllergic reaction to drugâ (4166257) and use it as the observation_concept_id in the observation table?
There are similar concepts within the observation domain regarded as events but they are not standard and end up getting mapped to the aforementioned condition.
concept_id concept_name domain_id vocabulary_id concept_class_id
40421705 Adverse reaction to other drugs and medicines Observation SNOMED Event
Alternatively, drug interactions are regarded as clinical observations. This seems the most logical to me.
concept_id concept_name domain_id vocabulary_id concept_class_id
40488461 Adverse drug interaction Observation SNOMED Clinical FindingHm,
so whatâs the actual problem to use â441207 Adverse reaction to drugâ (domain_id = âConditionâ) and put it in Condition_occurrence table?
âAdverse reaction to drugâ is a kind of medical condition eventually - âBlood pressure decreaseâ, âKidney failureâ, âAngioedemaâ, etc.
@Dymshyts
If we use the condition table instead of the observation table we would lose the ability to use value_as_concept_id to specify the drug which caused the reaction.
There are conditions in the vocabularies that specify the drug (e.g 433658,Penicillin adverse reaction) though its not clear how inclusive they are or how you could map to these concepts without needing to do it manually.
As @rtmill says, and we already discussed.
Both âAdverse reaction to drugâ and âAllergic dispositionâ are Observations. And âAdverse reaction to drugâ is a current event, but not a Condition, because it denotes a relationship of some reaction (not given) to a drug. Hence an Observation. Makes sense?
Can you make them both Observations, and we are good?
Ok. Got it. Will change in the next release.
By the way, here is another issue,
@rtmill, have you had a use cases when you need to put there something like âAdverse reaction to antibioticsâ, i.e. you need to represent the group of drugs?
@Christian_Reich, if we want to make this possible, we need to make ATC standard. What do you think?
No, we havenât had any of those use cases. The reactions are qualified with an NDC code and description. That said, there are also instances of adverse reactions to foods without code identifiers.
I believe if there were an âAdverse reaction to substanceâ concept in the Observation domain it would resolve my issues, though having both âAdverse reaction to drugâ and âAdverse reaction to foodâ would be helpful.
Itâs odd to me that SNOMED would classify both the event of an allergic reaction (âAdverse Drug Reactionâ) and the allergy itself (âDrug Allergyâ) as disorders
Yep, thatâs strange,
especially taking into account that children of (âAdverse Drug Reactionâ) and (âDrug Allergyâ) are the allergies caused by different drugs (looks like events), not a different types of Allergy (anaphylactic shock, urticaria, etc. - that might be classified as a disease normally).
So weâll change it on our side making them Observations