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Disease Status

(Denys Kaduk) #1

HI All! We doing ETL on oncology data and facing with table which contain specimens information. It has field called tumor_type. We thought to put those as disease_status_ in CDM.SPECIMEN table, but this opinion is wrong. We started to think, what’s from data we can define as disease_status_ . Through the field disease_status_concept_id SPECIMEN must be connected with CONDITION_OCCURRENCE, but I can’t find any information what we should to keep there. @Christian_Reich @MPhilofsky @Maria_ya can you help to clarify about it?

(Christian Reich) #2


Wait wait. There is a whole Oncology WG dealing with that. Don’t think, ask (which you did).

What is in that field? Can you provide a list of values?

(Dmytry Dymshyts) #3

in short:
what is the purpose of SPECIMEN.disease_status_concept_id ?

and where should we report that? in ONCO WG github issue? it is not an issue but a question.

(Denys Kaduk) #4

Sure, example of values:

lung adenocarcinoma
lung large cell carcinoma
unknown primary squamous cell carcinoma (scc)

But source table describe specimen and these values describe tumor.

(Qi Yang) #5


These values are diagnosis and should be loaded into CONDITION_OCCURRENCE table. The concept id for the listed values are:

4112738 lung adenocarcinoma
4110589 lung large cell carcinoma
36402371 unknown primary squamous cell carcinoma (scc)

@Dymshyts The purpose of SPECIMEN.disease_status_concept_id is to record whether the specimen is from normal tissue or abnormal tissue. That is my guess. A relevant post is here

(Dmytry Dymshyts) #6

Thanks @QI_omop

Let’s see what they answer