NCATSTranslator / Feedback

A repo for tracking gaps in Translator data and finding ways to fill them.
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Pathfinder Support Graph Display #940

Open sstemann opened 2 weeks ago

sstemann commented 2 weeks ago

I ran Pathfinder for Cystic Fibrosis and Joubert Syndrome

https://ui.ci.transltr.io/pathfinder/results?lone=Cystic%20Fibrosis&ltwo=Joubert%20Syndrome&ione=MONDO:0009061&itwo=MONDO:0018772&t=p&r=0&q=114f0fad-0b21-4248-94f0-fa0daa8dbd37

If you expand the first result - direct path, it looks like the support graphs (with genes) are displayed (i was expecting only direct paths)

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If you expand the second result - with gene intermediary, all of the paths EPC are "BTE" only

image image

It seems like the actual EPC is in the direct path.

dnsmith124 commented 2 weeks ago

After reviewing this with Gus the data that's coming back from BTE appears to be correct--they seem to be intending to return predicted edges as in the first result. So the first result is actually being displayed as BTE intended.

Both of the edges in each path in the second result are also marked as predictions in the data, but presently the UI does not support displaying more than 1 support graph per path, so they are appearing like direct edges. This will require a change to the UI backend to fix

sstemann commented 2 weeks ago

this is an example of a direct path with 8000+ paths

https://ui.ci.transltr.io/pathfinder/results?lone=GNRHR&ltwo=KISS1R&ione=NCBIGene:2798&itwo=NCBIGene:84634&t=p&r=0&q=da53c98c-569d-4827-82f7-618d5db16905

my chrome wont expand it

Genomewide commented 2 weeks ago

Another example: https://ui.ci.transltr.io/pathfinder/results?lone=MAPK8IP3&ltwo=Amantadine&ione=NCBIGene:23162&itwo=CHEBI:2618&t=p&r=0&q=58abd604-0797-42ca-83b5-1b1ee6f8804b

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ARAX graph:

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In ARAX bottom edge

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Left edge:

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Right edge:

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Inferred 'related' does not make sense to me for this?