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Pathological examination specimen mapping question


(wjdans) #1

hi, everyone.

I’m trying to map the samples used for pathological examination.

Unlike a lab test specimen, it is difficult to find a suitable concept id if the domain is set only as a ‘specimen’.

I think Domain ‘Spec Anatomic Site’ seems to have a more detailed concept ids,
is it wrong to specify the domain as ‘Spec Anatomic Site’ when mapping specimen used for pathologic examination?

Thanks you for all your help!


(Vlad Korsik) #2

Hello @wjdans9507. If I understood you in the right way, you want to represent the most accurate location of a sample obtained for pathologist’s evaluation.
Maybe usage of SPECIMEN table fields according to specs will be a solution: primarily use specimen_concept_id to define the generic meaning and in order to preserve source_data granularity use anatomic_site_concept_id.
Eg, you have ‘Prostate septum sample’ as a source entity
you can represent as
specimen_concept_id 4001186 119386002 Specimen from prostate and
anatomic_site_concept_id = 4089447 279683002 Septum of prostate


(wjdans) #3

thanks for the reply :slight_smile:


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