OHDSI Home | Forums | Wiki | Github

Biopsy on prostate cancer

Hello everyone,
I’m relatively new to implementing OMOP, and I’m seeking guidance regarding the handling of biopsy data within the framework. Specifically, I have biopsy data comprising the type, side, and zone of the biopsy for each patient. After some research, I came across with a concept ID (37397012) in the ATHENA vocabulary that seems to describe both the zone and side of the biopsy.
However, I’m unsure if my approach aligns with best practices, especially since my data is divided into columns based on size, type, and zone. From what I understand, this data should be stored in the observation table. Could someone kindly confirm if I’m heading in the right direction?


Right now, procedures are fully defined pre-coordinated things. Adding attributes like surgical details is possible as you said through OBSERVATION and FACT_RELATIONSHIP, but that is not particularly satisfying: Nobody will be trying to follow such modelling gymnastics when doing analytics, and there is also no particular use case: Details for the biopsy are relevant for optimal treatment of individual patients, but not for research of cohorts. Not sure there is a “best” practice, but generally people are already happy if there is the sheer fact of a biopsy they can rely on.

Thank you Christian,
Your response was very helpful. I will try to adapt the biopsy info the observation table.