@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!
@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!
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Hi All,
Iām looking forward to our meeting tomorrow morning (10am EST). Iāll 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:
https://gatech.webex.com/gatech/j.php?MTID=ma2ab814c9561bb4e1f965af2edf5f0ea
I really wanted to attend the meeting, but I couldnāt stay up yesterday.
Iām 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).
No worries, @SCYou! We all understand that a midnight meeting time is not exactly optimal. 
Thanks for reviewing the slides. Iām 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 āGold Standardā 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 itās 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 Iām taking back to the drawing board! Weāll need a way to incorporate user experiences so we can track what worked or didnāt work over time, as people try the phenotype out; this doesnāt necessarily have to be as formal as a validation set. Weāll also want a way to search and filter results according to phenotype performance and also the CDM elements used in its construction. Iāll also need to start filling in more of the data elements in greater detail. Iāll be in touch later on with updates!
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!
Also, I think we donāt need redundant phenotyping works in the community. Iām looking forward to what youāll update!
Good morning (or evening ) folks,
For our meeting this coming Tuesday, Iām looking forward to sharing a prototype Shiny app Iāve 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 didnāt have), how it should look, etc. The emphasis of work so far has been on the UI portion, so thereās plenty of room for adaptations at this stage. Thank you, and Iām looking forward to your feedback!
Great @apotvien
I cannot find the Shiny App in Phenotype github. Do you mean youāll make the Shiny App public at the next meeting?
Hi @SCYou, thatās correct that it isnāt there. I havenāt pushed anything out just yet, as itās not quite ready, but I should be able to do so soon after our meeting.
All, please find the link below to use for tomorrowās meeting (at 10am ET):
https://gatech.webex.com/gatech/j.php?MTID=m8fa406cec34ed30bc59c695f7caf20b7
Folks, thanks for the great discussion this past Tuesday! As a follow-up, Iām looking forward to teaming up to create the perfect templates for:
What are the key data elements that should be included? Which elements are mandatory vs. optional, and can the elements be kept general enough to be reasonably expected to be filled in each time yet specific enough to be meaningful?
To help with brainstorming, Iāve started a separate Google Doc for each one of these, starting with the template I used in the Shiny app demo. However, the template I used was largely intended to be illustrative, so now is a good time to dive deeper into the details. Please contribute your ideas to help build the perfect templates, and thank you in advance for your contributions!
From an implementation perspective, I think our templates can eventually exist as Markdown (or R Markdown) documents, which can be flexibly rendered inside a viewer program such as the Shiny app and directly on the phenotypeās GitHub page. However, for ease of editing, we should be able develop them as Google Docs for the time being.
Good morning,
Today at 10am ET, weāll be reviewing and working through developing the documents in the post above: The Authorship and Validation templates to identify the key data elements required of each entry.
Please find the link to todayās meeting below:
https://gatech.webex.com/gatech/j.php?MTID=mdd4af3e9b84212fc7df3eb0150703df5
Hello everyone,
Itās been a while since the phenotype viewer application was first introduced at one of our biweekly meetings. Since then, I have been pursuing a way to make this application and underlying source code more functional and available to everyone. After working through some nuances of locally hosting the app versus running it in a deployed setting, Iām happy to say that a version stable enough to share is finally available here:
http://data.ohdsi.org/PhenotypeLibraryViewer/
The repo for the code is here:
https://github.com/OHDSI/ShinyDeploy/tree/master/PhenotypeLibraryViewer
A special thank you goes out to @lee_evans and @schuemie for making the hosting of this app possible!
I invite you to play around with the application and to provide any feedback (Yes, really ā any feedbackā¦ I can take it! 
). Please keep in mind that this is far from a finished product since weāre still at a conceptual stage; a lot of features are not āhooked upā in the sense that they all refer to the same templates, and when data are used, it is randomly generated.
Nonetheless, I strongly believe itās helpful to have something concrete to look to at in order to help generate discussion and ideas. What do/donāt you like? What else should be included or tweaked? Thanks for your attention, and I hope this initial launch acts as a stepping stone on the path to an improved library!
Hello everyone,
For tomorrowās meeting, @juan_banda will be talking to us a bit about FAIR definitions and how they pertain to phenotyping.
As time permits, Iāll also walk through a status update and overview of upcoming objectives with respect to the architecture/implementation piece of the library.
The meeting link is the same one as before, here:
https://gatech.webex.com/gatech/j.php?MTID=mdd4af3e9b84212fc7df3eb0150703df5
Good morning folks,
For tomorrowās meeting, Iād like to talk about how the phenotype and validation data are being organized in the repository (link) and how that data can be assembled for use in the viewer application.
Iāll attempt to walk through a live example so we can see the process starting to take shape from entering a new phenotype with validation sets into the library to seeing that data reflected in the viewer application.
For reference, the meeting link is below (10-11am ET):
https://gatech.webex.com/gatech/j.php?MTID=mdd4af3e9b84212fc7df3eb0150703df5
If we have time Iād like to go through the data elements our group thinks should be included in the phenotype library.
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Hello all,
Please find the link to tomorrowās meeting below (10-11am ET):
https://gatech.webex.com/gatech/j.php?MTID=mdd4af3e9b84212fc7df3eb0150703df5
Iād like to reattempt the walkthrough I had planned for last time; I apologize for the technical difficulties preventing me from doing so two weeks ago. I anticipate this walkthrough will automatically generate further discussion about the data elements of the library and feedback about how they are currently stored and organized in the repository.
Hello everyone,
Thanks for the energizing discussion this morning. One item we wanted to reach out to this community about is regarding the aspects of the phenotype that are not currently captured by the phenotype JSON template (example attached populated with dummy data).
Specifically, the āPurpose and Intended Useā section might be better broken down into smaller components. These components could be themes that are commonly characteristic of phenotypes. For example, definitions often critically rely on a lookback period, can be intended to target incident or prevalent cases, or might be best suited for use in a comparative effectiveness study.
Do others have ideas for themes along these lines that we could draw from to better broadly characterize phenotypes in a standardized way?
Thanks,
Aaron
Children versus adults
Individual versus population, e.g., in reviewing diabetes phenotypes for a project, one from Mayo was overly sensitive in detecting potential diabetics prior to surgery versus one that might balance metrics to characterize a population.
Thanks for letting lurk on your call today.
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