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Phenotype Phebruary 2023 - Announcements

General
#23

@Gowtham_Rao @Patrick_Ryan @Azza_Shoaibi is there a Phenotype Phebruary meeting today (Fri Feb 10, 2023)? What time EST/CST? I see a Teams link above, but its not on my calendar so have to check my availability.

#24

Yes, we’re meeting today at 9 am EST (very soon). I am afraid I don’t know how to obtain the link… @Gowtham_Rao should know how.

#25

@allanwu Today we have the standing meeting of the OHDSI Phenotype Development and Evaluation Workgroup

Meeting invite

To access meeting information - please use the OHDSI MS teams as shown in screenshot

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Proposed agenda

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#26

Sorry I have a conflict at that time; I will see if I can join at the end. I see the Phea discussion coming up near the end; I’ll reply to @fabkury logic of the Phea SQL addition to tiered consensus in that thread to contribute.

1 Like
#27

Hi, are there instructions anywhere for how to do this? I have executed CohortDiagnostics and got results but I do not know how to make them available on data.ohdsi.org. Thanks!

#28

Great question.

If the data object is <100mb and you want to make a shiny app on data.ohdsi.org, then the steps are:

  1. Go to the Shiny repo: https://github.com/OHDSI/ShinyDeploy
  2. Log in to your github account
  3. Create a fork:
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  4. Select your user account name as the place to create the fork
  5. Clone your fork

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  1. Create a folder in your clone for your shiny, e.g. “SLECohortDiagnostics”
  2. [Important] Download the latest version of CohortDiagnostics as zip from https://github.com/OHDSI/CohortDiagnostics/ .
    1.Unzip and find the folder CohortDiagnostics\inst\shiny\DiagnosticsExplorer folder
  3. Copy all files, as is, from the folder above to the folder you created in Step 6
  4. Create a new folder in your folder (created in step 6) – rename it as “data”
  5. Add your .sqlite file to the ‘data’ folder
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  6. Test your app: Click on the below file object in your folder to open Rstudio and run app locally by clicking on RunApp after opening server.R file.
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  7. Commit your work to github
  8. Create a Pull Request
    a. Click
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    b. Click
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  9. Enter the information for your pull request and save
  10. Notify a repo administrator (erica, Gowtham Patrick, Jenna, Martijn) of your pull request
  11. Will be available at https://data.ohdsi.org/SLECohortDiagnostics
#29

If your .sqlite file > 100mb, then you cannot host it on github because of file size limitation - you will have to load to a postgres server exposed to the internet and data.ohdsi.org shiny server should know how to talk to it. Thats more complicated.

#30

Thank you, really appreciate this. Will work on these steps.

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