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Oncology extension: about Base Diagnosis and Overarching Disease Episode

(Matteo Gabetta) #1

since I’m planning to use the Oncology Extension I’ve followed the OHDSI 2020 - Oncology Tutorial.

I have a couple of questions about Base Diagnosis (CONDITION_OCCURRENCE) and Overarching Disease Episode (EPISODE):

  • since both tables can be referenced by Diagnostic Modifiers (MEASUREMENT table), for example Tumor Dimension, should I double the “Tumor Dimension” measurement in order to link the fact to both tables? (it is not possible to link one modifier to two different facts)
  • more in general, if on the one hand it is clearly stated that Overarching Disease Episode is one and only one, I’m not sure on how many cancer Base Diagnosis could be associated to a patient.


(Christian Reich) #2


@rimma might answer you with more detail, but briefly:

Thanks for having interest in the Oncology Extension the Oncology WG is developing. We probably should stop calling it “Extension”, it will be part of the standard OMOP CDM.

The idea is this: The Episodes should have links from the Modifiers that support their instantiation. For example, the Metastatic Disease should be connected to from the metastasis Modifiers providing the evidence for it. Similarly, the metastasis Modifiers should also connect to the Condition it modifies. Clearly, we will need to get some experience with real data and make a decision what is the best choice. Right now I’d write both links if you have the information. If not, you leave the Modifiers free standing.

I would not duplicate records to make the links work. If you want to connect the Modifier to both the Condition and Episode, do so. However, we realize this is not fully specified yet. The Episode could be the Overarching or the individual Extent or Dynamic one. For the Condition there could be many potential records as well. Please let us know what you find in your data.

(shilpa) #3

@MatteoGabetta, In addition to Christian’s response, in response to your first questions about referencing CONDITION_OCCURRENCE and EPISODE from MEASUREMENT, here is a link with an example Patient Journey we put together that demonstrates how you can do that without doubling the Measurement entries.

Hopefully this helps answer your questions. We also have a bi-weekly Development Meeting and a weekly CDM/Vocabulary Meeting that you could attend and bring your questions to. Here are links to those meetings this week.