Where and how to store Suspected Diagnosis in OMOP CDM

[jiawei-qian]

Where and how to store Suspected Diagnosis in OMOP CDM

CDM or THEMIS convention?

THEMIS

Table or Field level?

Table

Is this a general convention?

No

Summary of issues

1. Where and how to store Suspected Diagnosis in OMOP CDM

Summary of answer

1. Christian: suggested to put them in OBSERVATION table. Keep the CONDITION_OCCURRENCE table clean. (All agreed to add 'value_source_value' field in OBSERVATION table and store the verbatim result in this field)

2. Melanie: let’s find/create a concept for “suspected diagnosis”, give it a domain_id = Observation and put the suspected Condition in the Observation.value_as_concept_id field. We already do this to represent Medical History, Surgical History, Family History, etc. Let’s keep our representation of the data consistent. ( The direct representation of the suspected disease will remain intact in the Observation.value_as_concept_id (when the Condition maps to a concept_id) or Observation.value_as_string (when the Condition is string format) field. The Observation.concept_id = ‘suspected diagnosis’ or something.

Example: Observation.concept_id = ‘suspected diagnosis’ Observation.value_as_concept_id = 312327 Observation.value_as_string = Acute Myocardial Infarction )

3. Alexander Davydov: Can use 4219847 (Disease suspected) for OBSERVATION.observation_concept_id.

Related links

OHDSI Forum (Christian): https://forums.ohdsi.org/t/suspected-diagnosis-and-its-place-in-the-omop-cdm/11323/2 OHDSI Forum (Melanie): https://forums.ohdsi.org/t/suspected-diagnosis-and-its-place-in-the-omop-cdm/11323/15

Other comments/notes

I see 'value_source_value' field is added in v5.4 OBSERVATION table now. Thus, the OBSERVATION.value_as_string should be NULL and set OBSERVATION.value_source_value = 'Acute Myocardial Infarction' according to above example. Because this suspected diagnosis is mapped and store in OBSERVATION.value_as_concept_id field.

@MelaniePhilofsky, @clairblacketer, in one of my previous ETL project, I stored the (suspected) condition into CONDITION_OCCURRENCE.condition_concept_id field and set condition_status_concept_id= 32899 (Preliminary diagnosis). So, does it mean I need to use the above discussed convention (into OBSERVATION table) to store Suspected Diagnosis in the future?

[MelaniePhilofsky]

@jiawei-qian Preliminary diagnosis could be different than suspected diagnosis. I am moving this to the Needs More Work column since there is not a ratified convention. Themis needs to decided how to correctly represent these data in the OMOP CDM.

[cgreich]

@jiawei-qian: We have the condition status concepts Admission diagnosis, Preliminary diagnosis and Referral diagnosis. These are usually the situations when you are not sure, yet. Does one of them work for you?

To shove the suspected diagnosis into Observation would work, but essentially would bury them there. Nobody is ever going to look for it, I am afraid.