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OMOP v5 Specimen feedback

Implementers
#1

All,

I’m working on mapping > 160,000 specimens into OMOP v5 for a client.

Missing fields
Client data contains fields to specify specimen quality (clotted, hemolyzed, necrotic, compromized…) and availability (available, unavailable, reserved) that have been judged to be necessary. I’m enhancing the v5 CDM model to hold these fields for the client.

Quality could potentially be a conceptual column that stores SNOMED coded concept ids, however these entities are mapped to the Condition domain rather than Specimen. Specimen appears to be a better location if specimen quality is added to the model.

4104931,Sample broken,Condition,SNOMED,Clinical Finding,S,281262008,19700101,20991231,
4104932,Sample leaked,Condition,SNOMED,Clinical Finding,S,281263003,19700101,20991231,
4104937,Sample clotted,Condition,SNOMED,Clinical Finding,S,281279002,19700101,20991231,
4104938,Sample turbid,Condition,SNOMED,Clinical Finding,S,281280004,19700101,20991231,

I cannot find any existing conceptual entity to support a specimen availability concept mapping.

Concept Mapping
I’m running into issues with conceptual mapping for specimen types. There do not appear to be any concepts mapped to the “Spec Type” domain. For this implementation the values appear to be high level types like whole blood, packed cells, urine, synovial fluid, plasma…

Bill

#2

Reviving an old feed…

I am having the same issue in my implementation. I have not found any concepts that would relate to a SPECIMEN_TYPE.

Does anyone have insights on where I could find these concepts?

#3

@Jerrod.George :

We have Concepts. But it’s not the stuff Bill needed a couple years ago. Whether they are the right ones you need to check for yourself:

select * from concept where domain_id like ‘Specimen’;

Let us know.

#4

All,

I am working on a Registry Study in which data have been captured for CRP and ESR lab parameters whereas there is nothing captured how the sample was taken in raw data sets.

Kindly guide me How do i populate specimen table.

Thank you.

Regards,
Nitish Jha

#5

Same as here.

#6

I have run into the same problem. I cannot find a suitable concept to fill in specimen_type_concept_id.
Usually we have special vocabulary_id for each particular domain.
For example, for Note we have vocabulary_id Note Type,
for Condition - Condition Type,
for Procedure - Procedure Type,
for Measurement - Meas Type
for Drug - Drug Type
etc

But we have nothing for Specimen. Have you got any ideas how to find it?

#7

@nzvyagina:

Because nobody ever requested one. What kind of specimen do you need?

#8

The data set I am working on contains just usual specimens like blood sample, urine sample, different kinds of swabs etc. Some specimens are just EHR records, some of them are related to measurements. But there are no concept_ids to reflect this in specimen_concept_id.

One more thing related to Specimen table. By the way, maybe it would be reasonable to have a foreign key (measurement_id) in Specimen table to Measurement table, what do you think?

#9

@nzvyagina:

I see. And those blood samples, are they identified individually or do you just know that the patient gave a “blood sample”? If the former, this is the right place, and you should provide the full list of those things, and we can identify the concepts. If not, it’s probably not relevant, because the Measurement knows where the sample came from. So, Glucose in Serum/Plasma as a lab test “knows” that it is measured in serum or plasma.

Absolutely it is “reasonable”. The question is: is it necessary. A change in the data model is expensive, and we are only spending the effort if there is a use case which needs it. Do you have such a use case?

#10

“are they identified individually”?, Yes, they are, in other words there are records with codes that map to the concepts with domain ‘Specimen’. Also there are records which have 2 different codes: one maps to a Measurement and another one to a Specimen (for example, one code means Blood test and another one Blood sample).

Purpose of specimen_source_id?
#11

@Christian_Reich,
I have a question about field specimen_source_id (The Specimen identifier as it appears in the source data). It seems like it should be specimen_source_concept_id, since specimen_source_concept_id is not presented in SPECIMEN table and this differ from other cdm event tables. Could you please check this matter?

Thank you,
Irina

Purpose of specimen_source_id?
#12

Answered here.

t