Requirements Development for the OHDSI Gold Standard Phenotype Library

SCYou · January 4, 2019, 3:37pm

I didn’t know that ATLAS has a validation module. Still, the primary purpose of this shiny app is querying and visualizing the discharge note of the event.

As long as I remeber, 4 among 200 cases with code of ischemic stroke was actually hemorrhagic stroke. And about 5% of ischemic stroke had hemorrhagic transformation.
I focused on the etiology of the stroke, which usually of interest .But I didn’t see the situation you mentioned, the case with both ischemic and hemorrhagic stroke together. Ther first cohort I tried to validate is ‘ischemic stroke’. The second would be ‘hemorrhagic stroke’. And the third can be ‘ischemic or hemorrhagic stroke.’

Thank you for invaluable comment again and Happy New Year, @Christian_Reich

jon_duke · January 7, 2019, 3:07am

@Christian_Reich @SCYou Here are @TreySchneider’s designs for his Atlas-integrated annotation widget (WebAPI and Atlas) and the code ready for testing by community (Atlas branch).

We will be discussing on the call Weds January 16th (WG link)

SCYou · January 7, 2019, 3:33am

Thank you for telling this to us, @jon_duke . It is a really awesome widget for ATLAS.

apotvien · January 9, 2019, 3:29pm

Hello everyone,

Happy New Year! Throughout last year, we had great support for the OHDSI Gold Standard Phenotype Library, including this forum, a use case document, a mock-up on the wiki including a submission form template, and great ideas, among others. As a new year’s resolution, let’s make a goal to have a functional library to debut at the symposium this year (likely in September)!

Some common phenotype subthemes arose during our bi-weekly meetings:

Design: Rule-Based (Heuristic) Phenotypes
Design: Computable (Probabilistic) Phenotypes
Evaluation: Manual Chart Review / Annotations
Evaluation: Automated / Algorithmic
Library Architecture and Implementation

Call for volunteers!
For each of the items listed above, we’re looking to have a community member act as a point person to help develop and formalize OHDSI best practices. The goal is to develop robust documentation that we can put to use, which may in some cases overlap with the documentation of accompanying packages (e.g. Aphrodite for #2). This work is particularly timely, since once they are sufficiently developed, it may make the most sense to house our best practices in the upcoming Book of OHDSI.

Folks, this is a call to arms! Are there any volunteers who would be willing to participate in and/or lead these subgroups?

SCYou · January 8, 2019, 4:56am

Thank you @apotvien for leading this work group.

I’m working on developing best practice for manual chart evaluation as I posted earlier. I’m happy to continue this effort.

Happy New Year

sseager · January 9, 2019, 12:25pm

I’d be keen to volunteer. I am however very new to the OHDSI world and so my learning curve is fairly vertical at present, but that being said I’d love to help where I can.

krfeeney · January 9, 2019, 2:59pm

@apotvien, perhaps @sseager and I could tag team. I’m always eager to help collaborators get off the ground and make an impact.

Plus, I’d personally really like to get better plugged into this WG. The need for this resource is enormously important – I’ve seen multiple studies where this could have expedited some of our decision making and helped us get closer to generating and disseminating high quality evidence. Count me in! Let’s chat on the 16th… (and maybe @MauraBeaton can add this to the 2019 OHDSI WG google doc. )

mattspotnitz · January 9, 2019, 4:56pm

I have been designing phenotypes and cohorts at Columbia, and am happy to help with this effort. Thanks!

Juan_Banda · January 9, 2019, 7:07pm

Hello Aaron, I would like to volunteer for #2 I am definitely doing some work on documenting and should overlap nicely.

apotvien · January 9, 2019, 7:54pm

Thank you all very much for volunteering and for your enthusiasm! We’re off to a great start!

I’ve just updated the wiki and have included all of you as members, with @Juan_Banda in charge of the computable phenotype design and @SCYou in charge of the manual chart evaluation.

We’ll certainly chat more about this on the 16th. The meeting time has been added to the wiki as well, but we may change the time for 2019 to best accomodate as many people as possible. I’d also like to point out that the Gold Standard Phenotype Library will be a subject of the community call on the 15th (12-1 ET), in case anyone wants to tune in then as well to hear more about this initiative.

Thanks again!

jswerdel · January 9, 2019, 8:05pm

Hi Aaron,
I’d like to be a part of the #4. It would be a good test for PheValuator.

apotvien · January 9, 2019, 8:10pm

That’s great to hear, @jswerdel! I’ve put you down as the lead for Task #4 on the Wiki. Thanks for joining in!

Andrew · January 10, 2019, 1:38am

Way to go @apotvien!
I’ll happily be Juan and/or Joel’s minion.

apotvien · January 10, 2019, 5:29pm

Glad to have you on board, @Andrew!

apotvien · January 10, 2019, 5:31pm

@SCYou, @Juan_Banda, and @jswerdel, would you like to share a bit about what you’ve been working on regarding your respective items for our meeting on the 16th? It appears 10am ET is midnight KST, so it would be unreasonable to expect @SCYou to join the call, and I believe @Juan_Banda is unavailable at this time, but even just a couple of slides or list of highlights would be welcomed so the WG can become introduced to what you’ve been thinking about and the direction you think we should be headed.

jswerdel · January 10, 2019, 6:47pm

Sounds good. I will have a few slides about the progress with PheValuator and what I see as future directions.

SCYou · January 11, 2019, 12:08am

@apotvien I’ll try to attend the meeting.
And I will prepare to show what I’m doing for phenotype library.

Vojtech_Huser · January 11, 2019, 2:38pm

I missed the formal group formation. But this is very relevant to what I am currently doing in the context of RWD/RWE. I would like to join the WG and will attend the future meetings. (and will volunteer for some tasks to do)

apotvien · January 11, 2019, 5:48pm

@jswerdel and @SCYou, thanks a bunch, and we’re looking forward to hearing your perspectives next week!

@Vojtech_Huser, welcome! This is a great time to join, as this WG group is still very much in a formation stage. Indeed, RWD/RWE needs RWP (real-world phenotypes)! I hope we can chat about how this ties in with your work at our upcoming meeting.

SCYou · January 15, 2019, 8:04am

I uploaded the manual chart review system for hemorrhagic stroke to the git hub, too.
It seems that the positive predictive value in hemorrhagic stroke is much better than in ischemic stroke. I’ll upload the result soon.