ChemicalEntity <derivesFrom> ChemicalEntity (PUBCHEM.COMPOUND:6140 - L-phenylalanine)

[sstemann]

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)

[finnagin]

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.

[MarkDWilliams]

Expected result

Subject	Predicate	Object
PUBCHEM.COMPOUND:6057	biolink:derives_from	PUBCHEM.COMPOUND:6140

[webyrd]

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 — Reply to this email directly, view it on GitHub <#169 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAI5HBGTFJFDSAXXD3QXVKLUX3JJ7ANCNFSM5MWQW6LQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you were assigned.Message ID: ***@***.***>

[colleenXu]

To update: we have the data from SEMMEDDB. However, there are issues retrieving it.

There seems to be a semantic + ID-mapping mismatch between:

• this query: Phenylalanine + Tyrosine as chemicals
• the data in semmeddb: Phenylalanine UMLS:C0031453 is aapp, which the biolink-model maps to Polypeptide. Tyrosine UMLS:C0041485 is gngm, which biolink-model maps to GenomicEntity.
• the semantic types reported by SRI ID resolver. It reports both of the UMLS IDs as Protein (phenylalanine, tyrosine)

[cbizon]

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.

[vdancik]

@cbizon , @sierra-moxon , is there any appetite to bring Polypeptide back to chemical hierarchy?