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Requirements Development for the OHDSI Gold Standard Phenotype Library


(Luke Rasmussen) #61

@apotvien - I know OHDSI has a lot going on, and fortunately @psbrandt alerted me to this very interesting workgroup. I need to do some reading of the materials/discussions so far, but wanted to ask if you had discussed collaborating/aligning with the Phenotype KnowledgeBase (https://phekb.org/) that was developed as part of eMERGE? It would be great to see if there is an opportunity to at least share experiences across these projects. Thanks!


(Aaron Potvien) #62

@lrasmussen, thank you for your post. We would absolutely be interested in sharing experiences and learnings with the PheKB community. The substantial amount of development that PheKB has done is definitely relevant here. We would be very interested in hearing about the governance processes PheKB uses for phenotype design and evaluation. An information exchange at a future meeting would be great!


(Aaron Potvien) #63

Hi All,

I’m looking forward to our meeting tomorrow morning (10am EST). I’ll be presenting about one possible framework for the library architecture/implementation.

It is up to date on the Wiki and WG Meeting Document, but just in case, we have changed the link for our meeting space to be the following one:


(Seng Chan You) #64

I really wanted to attend the meeting, but I couldn’t stay up yesterday.
I’m sorry, @apotvien .

I saw the slides you posted. Though I might not understand the whole thing, it is really really fascinating!

I think I can participate as a secondary librarian and validator for a while (of course can be a user).
After setting up the environment, the algorithmic evaluation (eg Phevulator) can be automatically validate and produce a metadata for the validation results.
The json file for the phenotype should be comprehensive for the two phenotyping softwares, ATALS (rule-based) and APHRODITE (computable).


(Aaron Potvien) #65

No worries, @SCYou! We all understand that a midnight meeting time is not exactly optimal. :slight_smile:

Thanks for reviewing the slides. I’m still thinking about this a high level. I used PheValuator as an example, but the framework is flexible enough to encompass manual chart review too, and in principle, whatever “Gold Standard” design/evaluation practices this group ultimately adopts. Likewise, I also used JSON as an example export, but that may not be appropriate for exporting computable phenotypes. Nonetheless, if the implementation can be represented as a single file (even if it’s an archive of multiple files), it can still be hashed; then, all of the metadata that pertains to that phenotype (definition, validation, user experiences, etc.) can always be linked to that hash without any ambiguity about what definition was being referred to.

The group had some great suggestions yesterday that I’m taking back to the drawing board! We’ll need a way to incorporate user experiences so we can track what worked or didn’t work over time, as people try the phenotype out; this doesn’t necessarily have to be as formal as a validation set. We’ll also want a way to search and filter results according to phenotype performance and also the CDM elements used in its construction. I’ll also need to start filling in more of the data elements in greater detail. I’ll be in touch later on with updates!


(Seng Chan You) #66

I agree, @apotvien

The json you chose for the exporting format and the hashing module is the most fascinating part in your slide. It was really brilliant! :slight_smile:

Also, I think we don’t need redundant phenotyping works in the community. I’m looking forward to what you’ll update!


(Aaron Potvien) #67

Good morning (or evening :slight_smile: ) folks,

For our meeting this coming Tuesday, I’m looking forward to sharing a prototype Shiny app I’ve been developing. Moving in the direction of the Shiny/GitHub framework that was discussed last week, the app expectantly gets us closer to an interface which connects users to the library phenotype entries.

I hope that this will help to generate discussion about additional data elements we would like to see, how/where they should be displayed, features we wish it had (or perhaps didn’t have), how it should look, etc. The emphasis of work so far has been on the UI portion, so there’s plenty of room for adaptations at this stage. Thank you, and I’m looking forward to your feedback!


(Seng Chan You) #68

Great @apotvien
I cannot find the Shiny App in Phenotype github. Do you mean you’ll make the Shiny App public at the next meeting?


(Aaron Potvien) #69

Hi @SCYou, that’s correct that it isn’t there. I haven’t pushed anything out just yet, as it’s not quite ready, but I should be able to do so soon after our meeting.


(Seng Chan You) #70

@apotvien Ok, I’m looking forward to it!


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