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A repo for tracking gaps in Translator data and finding ways to fill them.
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Many Edges with Fairly Similar Predicates and Evidence #834

Open sstemann opened 2 months ago

sstemann commented 2 months ago

https://ui.test.transltr.io/main/results?l=Bivalirudin&i=CHEBI:59173&t=4&r=0&q=0e10870d-261b-4a35-af01-4df4815038f9

Lookup Edge:

  1. "Mpo Has Decreased Activity Caused By Bivalirudin" EPC: Bivalirudin Decreases No Bioavailability By Vascular Immobilization Of Myeloperoxidase. > Drugbank

Inferred Edge:

  1. "Mpo Has Decreased Activity Or Abundance Affected By Bivalirudin", EPC: ARAGORN
  2. Inferred Subpath1: "Mpo Has Decreased Expression Caused By Bivalirudin" EPC: Bivalirudin Decreases No Bioavailability By Vascular Immobilization Of Myeloperoxidase. > CTD
  3. Inferred Subpath2: "Mpo Has Decreased Activity Caused By Bivalirudin" EPC: Bivalirudin Decreases No Bioavailability By Vascular Immobilization Of Myeloperoxidase. > DrugBank

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I dont really understand why we are calling the same edge/EPC LOOKUP and INFERRED, both within the same ARAGORN result (see the ARAX GUI) https://arax.ncats.io/?r=0e10870d-261b-4a35-af01-4df4815038f9 > ARAGORN > Search MPO

It looks like ARAX does the same reasoning but doesn't call it Inferred.

sstemann commented 2 months ago

i'm posting this one also which may be more complicated to troubleshoot but i just dont understand why we have so many paths that are ultimately one hops

https://ui.test.transltr.io/main/results?l=Ruxolitinib&i=CHEBI:66919&t=4&r=0&q=ce9b3de1-aaf5-4326-be44-492d04cb6cff

image

cbizon commented 2 months ago

I'll check this to be sure, but it looks to me like we might be including some redundant rules in ARAGORN, i.e. some reasoning rules that replicate the expected sub-predicate reasoning that should be done by default anyway.

sstemann commented 1 month ago

https://ui.test.transltr.io/main/results?l=Ruxolitinib&i=CHEBI:66919&t=4&r=0&q=ccf53e03-fbb3-48e2-a3ed-0a6c2990a883

seems related to #743 which we said at TAQA was a next phase issue so I'm not sure what's being done here for Guppy