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Purpose of specimen_source_id?

CDM Builders
#1

What is the purpose of specimen_source_id and how does it differ from specimen_source_value?

http://www.ohdsi.org/web/wiki/doku.php?id=documentation:cdm:specimen

#2

After thinking some more, here’s an example of how I assume its supposed to work:

A specimen_source_value could be code “ABC123”, referring to “Soft tissue sample”
A specimen_source_id could be “001” for the first sample they had taken and “002” for the second sample. Both coming from the same person.

If someone could clarify it would be greatly appreciated! Thanks

#3

And this one from here as well:

I can see this is confusing:

  • specimen_id: Just the running number in this table, carries no meaning.
  • specimen_concept_id: The Concept representing what specimen, or sample piece of a body, this is in OMOP Vocab terms. Example is 4124271 “Abscess swab”.
  • specimen_source_value: This is what the source would call it. They might have a record like “Swap from abscess” or something.
  • specimen_source_id: This is a unique identifier in the lab management system of the source. They keep samples in gigantic freezers, often with fully automated sample management systems, and this would be the unique identifier. From an OMOP CDM perspective, this is an entirely meaningless number.
  • specimen_source_concept_id: This doesn’t exist, because there is no standard coding scheme for specimen, like there is ICD-10 for Conditions. There are a few lonely Read, CIEL and deprecated SNOMEDs, but they don’t count as dedicated source vocabularies.

Makes sense?

1 Like
OMOP v5 Specimen feedback
#4

Yes, that’s what I was expecting for specimen_source_id. Thanks Christian!

#5

What is the distinction between specimen.specimen_concept_id and specimen.anatomic_site_concept_id?

#6

Yes, thank you!

In this case should it be stored in cdm to trace back to the source data if necessary?

#7

The anatomical site contains where exactly the specimen was taken from.

Yes.

#8

Thank for above explanation about specimen table. What is specimen_type_concept_id? specimen type could be tissue or blood ? so this field requires standardized vocabulary term for specimen type?

#9

@Wamin:

“Blood” and the kind of tissue goes into the specimen_concept_id. Specimen_type_concept_id is for indicating where the information was obtained from. Right now we only have one type: Concept 581378 “EHR Detail”. If you need others let us know.

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