OHDSI Home | Forums | Wiki | Github

PheValuator yet run for Cancer Phenotypes?

(Daniel Smith) #1

Hi everyone,

Per the topic. Specific call out to @rimma, @mgurley, @Christian_Reich, and @Shilpa_Ratwani (or @shilparatwani?).

We’re defining our cohort for inclusion at Emory Winship Cancer Institute from the broader data warehouse, and we have a local phenotype definition that had been used for some time. There’s also always the NCI Casefinding list that overlaps with our phenotype somewhat, but we don’t include all of the supplemental codes (https://seer.cancer.gov/tools/casefinding/).

I’d like to take what I’ve learned at OHDSI 2020 about the Phenotype Library however, and apply it locally for Winship Data by using the “Cancer” phenotype (phenotype ID 443392000). I’m currently unsure as to how the definition holds up with PheValuator. As we’re not bringing in all of our datawarehouse data in at this time, and only focusing on cancer patients, we won’t be able to run PheValuator locally, unfortunately and our data import depends upon the phenotype we end up using.

As an aside, it was wonderful to see everyone virtually at OHDSI 2020! Was a great conference and a lot was learned.

(Erica Voss) #2

Also tagging @jswerdel

(Christian Reich) #3

Yeah. That’s a catch-22, then. You can only double guess your inclusion criteria using PheValuator if you give it a chance to learn how to distinguish cancer from non-cancer. If all your patients are cancer patients there is not much to do.

Why are you not bringing in the entire warehouse? The additional burden is small, but the value is much larger.