Anybody have expereince mapping pathology cases/pathology case reports from Cerner?

mgurley · November 18, 2018, 8:35pm

Does anybody have experience mapping pathology cases/pathology case reports from Cerner to the OMOP CDM? Cerner has a table that contains all the types of pathology cases. Our are as follows:

Autopsy
Body Fluid
Bone Marrow
CMH Cytogenetics
CMH FISH
Cytogenetics
Cytology
Fine Needle Aspirate
FISH
Flow Cytometry
Gyn Cytology
Hematopathology
Molecular Genetics
Outside Autopsy
Outside Cytology
Outside Hematopathology
Outside Surgical
Pathology Research
Surgical Pathology

Does anybody know of any native mappings within Cerner that normalize these types of pathology procedures to a standardized procedure vocabulary?

Christian_Reich · November 24, 2018, 12:28pm

I’d map them all to SNOMED. Should be straightforward.

Dymshyts · January 28, 2019, 3:10pm

@mgurley, how is it going with the mapping of those?

Would it be better for you if everything above belong to the same domain?
like you requested here:

github.com/OHDSI/Vocabulary-v5.0

Can the SNOMED code '59000001' be moved to the Procedure domain?

opened 10:22PM - 08 Jan 19 UTC

mgurley

SNOMED code '59000001' is 'Surgical pathology consultation and report on referre…d slides prepared elsewhere". This is the only concept I can find within OMOP that represents a pathology procedure performed on outside slides. This SNOMED code lives within the SNOMED Procedure axis and it has a 'Pocedure' concept class. Currently this concept (4244107) is placed in the 'Observation' domain. I believe it should be in the 'Procedure' domain. We at Northwestern have important use cases surrounding pathology procedures/reports. Being able to distinguish between In-house and outside surgical pathology procedures would help serve those use cases.