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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 1 year ago

sstemann commented 1 year 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 1 year 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 1 year 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 1 year 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 1 year 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 1 year ago

How about these GO categories?

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

Genomewide commented 1 year ago

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