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NCATSTranslator / Feedback

A repo for tracking gaps in Translator data and finding ways to fill them.
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Wrong path in What drugs may treat conditions related to: Seasonal Allergic Rhinitis #841

Open khanspers opened 1 month ago

khanspers commented 1 month ago

What drugs may treat conditions related to: Seasonal Allergic Rhinitis

https://ui.test.transltr.io/main/results?l=Seasonal%20Allergic%20Rhinitis&i=MONDO:0005324&t=0&r=0&q=6fff0b27-c22a-4b6b-982d-d8b03eb29421

Caseins is returned (page 2), but the path is wrong:

Caseins - Causes Increased Activity of -> IGHE - Causes -> Seasonal Allergies

image

Coming from Unsecret:

Screen Shot 2024-07-05 at 9 40 55 AM
sstemann commented 1 month ago

@kaiwenho it looks like caseins increase the activity of the genes that cause this disease, and therefore may not be a good path. can you take a look?

sstemann commented 2 weeks ago

@kaiwenho could you take a look at this report? i'm still seeing this in Test, not sure if its part of Unsecret reasoning we should expect going forward or if you do not expect these results?

If you search for IGHE you can see the recurrence

https://ui.test.transltr.io/main/results?l=Seasonal%20Allergic%20Rhinitis&i=MONDO:0005324&t=0&r=0&q=d3ac11bf-1456-442c-87e6-b62bf3aeade0

kaiwenho commented 2 weeks ago

@sstemann Thank you for highlighting the confusion. The result is not unexpected. When we refer to the edge (gene-causes-disease), it does not specify how the gene contributes to the disease—whether it's due to the gene's presence, its lack of expression, or other mechanisms. For this example/answer, it's possible that the disease is caused by a lack of IGHE activity, so increasing the gene's activity could be a logical approach. mediKanren takes a cautious approach to inference when information is insufficient - the system generates potential answers (chemicals) that might treat a disease based on algorithm and rules, then screens these answers and filters out any chemicals that are known to cause the disease. We want to ensure that we don't overlook these possibilities, especially in the context of rare diseases.