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Specimen table lacking source_concept_id

(Melanie Philofsky) #1

@clairblacketer @Christian_Reich,

I am using the SPECIMEN table for the first time. There is a field named “specimen_source_id” the description reads “The Specimen identifier as it appears in the source data”. What is an example of a “specimen identifier”?

Also, there is specimen_concept_id and anatomic_site_concept_id, but not source_concept_ids for either. Why are these fields excluded?

(Roger Carlson) #2

Interestingly, I’m also looking into the Specimen table. My question is similar. Are we just looking for specimens taken during surgery? (like 46274042::Paraffin embedded slide) Or are all Lab Draws specimens also? If so, should we relate the specimen to the lab result in the Fact Relationship?

(Melanie Philofsky) #3

This specific post references source data coming from lab draws & results/lab cultures/microbiology specimens. So, I would also look at the domain_id for your lab draw codes. The source has one row of data which will ETL to 3 rows in the OMOP CDM. Two belong to the Measurement domain and one belongs to the Specimen. All will be related via the Fact Relationship table. There is some discussion about the appropriate relationship_concept_ids for these relations. See this relevant post.