Student 2 Verification: Crohn's disease (Conditions)

[callahantiff]

Student (GitHub Username): @kandrews11 Verification Number: 2

Verification Assignments: Crohns_Disease_Conditions

• Phenotype Definition
• Spreadsheet

[kandrews11]

@callahantiff @jwyrwa https://docs.google.com/spreadsheets/d/1UjLqoHIcJxsKiSwVkHSJBLPEd5XlgKY2CwyuFnGY4ZQ/edit?ts=5ceb22a5#gid=1867034949&range=628:628-wasn't sure how to categorize this one since there is an association of increased risk of developing RA if you have been diagnosed with MG

[kandrews11]

@jwyrwa kind of the same scenario here-https://docs.google.com/spreadsheets/d/1UjLqoHIcJxsKiSwVkHSJBLPEd5XlgKY2CwyuFnGY4ZQ/edit?ts=5ceb22a5#gid=1867034949&range=627:627

[callahantiff]

@kandrews11 - For these examples, the strings are specifically related to conditions for excluding control patients. Did you see the post I made Thursday evening? It's directly related to both of your questions above (shown below for reference).

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.

Perhaps it will be easiest if we have a quick chat on the phone or via Skype? I want to make sure I go over with you how to use the phenotype definitions with these codes so you can easily recognize when a code is in reference to a control group and thus a situation when you . should use these new categories versus when it is in reference to a case.

[callahantiff]

@kandrews11 - Per advice from @jwyrwa there are 500 additional rows that have been added to the bottom of your spreadsheet, just wanted to let you know 🙏 😄

[kandrews11]

@callahantiff sounds good I'll take a look this afternoon after clinic! Question for the selecting a category for control-if a source name matches a string clinically but doesn't include the exact string name (ie. the string is "degenerative joint disease" but the source name is "osteoarthritis" is that considered a match or not? thanks!

[callahantiff]

@callahantiff sounds good I'll take a look this afternoon after clinic! Question for the selecting a category for control-if a source name matches a string clinically but doesn't include the exact string name (ie. the string is "degenerative joint disease" but the source name is "osteoarthritis" is that considered a match or not? thanks!

@kandrews11 - you're awesome 👍, thank you so much for being flexible.

Great question regarding the control criteria. In the example you raise, I would categorize the mapping between the source_string "degenerative joint disease" and the source_name "osteoarthritis" as Control Group Criteria - Exactly Matches Definition String. The reason being that these terms are synonyms. If the connection between the two terms is a bit more complicated than synonyms (e.g. the anti-smith antibodies lab and lupus connection), then I would have chosen Control Group Criteria - Partially (and Appropriately) Matches Definition String.

Does that help?

[kandrews11]

@callahantiff yep that's great! thank you!

[kandrews11]

@callahantiff hey Tiffany-just wanted to keep you updated that I am still working through this particular verification-there is a section in the middle that seems to be time consuming with SLE and different sleep disorders where I am finding evidence linking the two conditions but it has involved wading through some papers/data. just wanted to let you know I am working on it, and I'm sorry it's all of a sudden become slow going! but that i'm hoping to have this particular spreadsheet done by the end of this weekend

[callahantiff]

@callahantiff hey Tiffany-just wanted to keep you updated that I am still working through this particular verification-there is a section in the middle that seems to be time consuming with SLE and different sleep disorders where I am finding evidence linking the two conditions but it has involved wading through some papers/data. just wanted to let you know I am working on it, and I'm sorry it's all of a sudden become slow going! but that i'm hoping to have this particular spreadsheet done by the end of this weekend

@kandrews11 - thank you so much for the update! I really appreciate it and am glad to hear things are going well. It's really interesting to hear about these connections. Would you mind providing an example (once you are ready)? I'd love to be able to present it as evidence at my next update meeting and having your expertise behind the example will help it to be taken seriously :D!

[kandrews11]

@callahantiff I believe this one is complete, please let me know if there are any issues/things you would like me to adjust going forward!