Open sstemann opened 2 years ago
Hey @MarkDWilliams , just as an fyi I made a workflowatized version of this query you could try looking at. It basically takes the query from above but overlays normalized google distance as well as fisher exact test values over the edges. It then scores and ranks the results using those values.
Unfortunately, it cannot currently be run through the workflow runner since @kennethmorton is still hard at work getting its fanning and merging functionality implemented. However, you can still run it through ARAX for the time being.
Expected result
Subject | Predicate | Object |
---|---|---|
PUBCHEM.COMPOUND:6057 | biolink:derives_from | PUBCHEM.COMPOUND:6140 |
Thanks, Sarah and Mark!
Sorry I missed the call today. I'll look into why Unsecret didn't return any answers.
Cheers,
--Will
On Tue, Jan 25, 2022 at 12:00 PM MarkDWilliams @.***> wrote:
Expected result Subject Predicate Object PUBCHEM.COMPOUND:6057 biolink:derives_from PUBCHEM.COMPOUND:6140
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To update: we have the data from SEMMEDDB. However, there are issues retrieving it.
There seems to be a semantic + ID-mapping mismatch between:
UMLS:C0031453
is aapp, which the biolink-model maps to Polypeptide
. Tyrosine UMLS:C0041485
is gngm, which biolink-model maps to GenomicEntity
.Hi @colleenXu can you make an issue for the semantic types here: https://github.com/TranslatorSRI/NodeNormalization/issues
FWIW, if the NN matched the biolink model mappings (which we will revisit), that won't allow there will still be a mismatch to the query. There's a mixin, I think, that would allow chemicals + proteins.
@cbizon , @sierra-moxon , is there any appetite to bring Polypeptide back to chemical hierarchy?
Query: derivesFrom.json PK: 15f5935e-4479-405c-9e4b-f0cda7194df7 Control: Looking for what metabolite (chemicalEntity ) derives from L-phenylalanine. The control should be L-tyrosine (Tyrosine also fine)