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NCATSTranslator / Feedback

A repo for tracking gaps in Translator data and finding ways to fill them.
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Need some facets on MVP2 results #537

Open sstemann opened 11 months ago

sstemann commented 11 months ago

Genes don't have any facets - is there a list somewhere of what was discussed?

https://ui.ci.transltr.io/demo/results?l=Eletriptan&i=PUBCHEM.COMPOUND:77993&t=3&q=d1c6af0a-8f60-4f24-87fe-a5268c338cea

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Genomewide commented 11 months ago

Do you mean the chebi roles? Genes don't have them if so. The other facets like FDA don't apply here either.

sstemann commented 11 months ago

For MVP2 0 Find Genes regulated by a particular chemical, a starting point to investigate would be:

tissues or cells gene regulatory networks chromosome Genome Browser has categories

Not sure what's currently available in Annotator or mygene.info @newgene

Genomewide commented 10 months ago

Did a review of mygene.info and found GO and pathways. I don't think tissue is available here. @newgene Is that right? If not, who is the GTEX contact?

newgene commented 10 months ago

@Genomewide you are right, we don't have tissue info at mygene.info. We do have the genomic location, and this type_of_gene field might be useful too:

https://mygene.info/v3/query?species=human&facets=type_of_gene&facet_size=20

newgene commented 10 months ago

How about these GO categories?

https://mygene.info/v3/gene/5871?fields=go

Genomewide commented 10 months ago

yeah those go categories would work. We would probably have to create our own go slim or filter for high level terms