Our Danish pathology register uses SNOMED topography codes (T-codes) to record the anatomical localisation of the recieved tissue. Do any of you know how to translate these T-codes to the OMOP SNOMED concept id’s? Fx T-28000 refers to Lung, NOS. The same question applyes to the M-codes which are morphology.
Hi @TineKopp:
Aren’t these already like old SNOMED codes? All you need is to look them up in the concept_code field of the CONCEPT table. But I don’t remember.
The problem you also have is to combine the T and M together to a cancer diagnosis, without which you won’t be able to find the patients.
Can you ask Agnes Moesgård Eschen (@AgnesEschen) from Rijgshospitalet? Want me to bring you together?
Hi @Christian_Reich
Sorry for the late reply (I thought I would get a notification, but didnt). The Danish SNOMED codes for topography are different from the SNOMED CT ID’s as far as I can see. For instance, T28000 is lung in the Danish edition, but in SNOMED CT, its 4213162 (lung structure). I know I need to combine T and M for a diagnosis, but right now, I just need to translate anatomical localisation for the tissue sample. I would appreciate to be connected to @AgnesEschen. Thank you.
Many thanks,
Tine
Hi @TineKopp
DICOM has a content mapping resource “DICOM PS3.16 2025c - Content Mapping Resource’”
It contains a section on “SNOMED Concept ID to SNOMED ID Mapping” that may be helpful. It appears to have about 1500 T codes and 400 M codes with mappings to current SNOMED concept codes.
Lars is right, this indeed seems to be a problem of you using old SNOMED RT codes. And Dicom has a mapping table, but it is only a subset. The real RT has 28k T- codes and 5k M-codes. I’ll attach the zip file of SNOMED RT to CT (in OMOP ID notation), so you don’t have to do any more gymnastics.
SNOMED RT to OMOP.txt (557.9 KB)