Project Meeting -- 08/07/2019 @ 16:15 MT

[callahantiff]

Meeting Date: August 7, 2019
Topic: Medication Code Set Verification Training
Attendees: @WhitleyMcCall

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Zoom Info:

• Meeting ID: 357 665 9200
• URL: https://ucdenver.zoom.us/j/3576659200
• Phone: 1 669 900 6833 US (San Jose) or 1 646 876 9923 US (New York)

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Proposed Agenda for Today's Training:

• Brief overview of the PheKnowVec project
• Review Verification Task Description
  • Go over assigned phenotype sheets to map - Medication Source Code Verification: Student 2 #42
• Go over how to use Abra-Collaboratory functionality within the verification task

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Discuss edits to original mapping plan:

Just an update. I have added 3 new categories to the selection choices. These choices are meant to be used when you are verifying the mappings for control patients. You can tell which codes may be used for control patients here. Please note that it is possible that the same exclusionary criteria be used for both cases and controls, thus these new categories should only be used when the criteria applies only to control patients .

• Control Group Criteria - Exactly Matches Definition String
• Control Group Criteria - Partially (and Appropriately) Matches Definition String
• Control Group Criteria - Does NOT Match Definition

These new options were added because the prior categories did not easily account for control patients in the sense that we can't possible know all the criteria that are used when selecting control patients, like we can with cases. Thus, there are scenarios where it would be very difficult to judge the clinical relevancy of a mapping.

[callahantiff]

@trinklek - just adding you here to keep you in the loop! 😄

[callahantiff]

@WhitleyMcCall - Great meeting today! 🎉

In case this helps, here is the general ordering I would utilize when performing a verification:

STEP 1: Start from the parent dashboard to identify which phenotypes you have to complete. The completed phenotypes should match what is indicated in your verification table in this DropBox Paper guide as well.

STEP 2: Select on the #number of phenotypes that are not checked as complete. That will lead you to that phenotype's specific issue. Within this issue you will see two hyperlinks:

• Phenotype Definition - which will link you to the GitHub Wiki page for that phenotype page. This page contains the information on the phenotype definition logic and has specific links to the code sets that are used in the original phenotype definitions.
• Spreadsheet - Will link you to the tab within your verification spreadsheet.

Step 3: If you have questions about a mapping, indicate it within that phenotype's specific issue and use @Trinklek to mention and link Katy into the issue so she can help.

STEP 4: Once you are finished with a phenotype, please do the following:

• Write a brief comment in that specific issue and then close it by clicking Close and comment.
• Navigate back to the parent dashboard and check the box for that phenotype.
• Go to your verification table in the DropBox Paper guide DropBox Paper guide and write the date and if a comment (if necessary).

OK, that's the general workflow. Let me know if you have any questions!

[callahantiff]

Closing this issue, please re-open if need be! 👍