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biothings / mygene.info

MyGene.info: A BioThings API for gene annotations
http://mygene.info
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Transcript-specific matching with mygene.info? #123

Closed sigven closed 2 years ago

sigven commented 2 years ago

Hi,

I have tried your service in various ways, most frequently with the R client, and was curious if I could use the service to get transcript-specific annotations, which I have not yet succeded in doing.

Example: Let's say I am interested in a particular isoform of MITF. I want to get the corresponding RefSeq mRNA and UniProt accession for ENST00000352241.9. I seem to get the full set of transcript cross-references (RefSeq, UniProt) whatever transcript i use as a query, and this might be the intended function. But is there any way one can get transcript-specific annotations using mygene.info?

kind regards, Sigve

erikyao commented 2 years ago

Hi @sigven, thanks for reaching out!

I think it's possible to get transcript-specific ExAC annotations, as with https://mygene.info/v3/query?q=symbol:MITF%20AND%20exac.transcript:ENST00000352241&fields=exac

Note that the query string is actually q=symbol:MITF AND exac.transcript:ENST00000352241 with the white spaces encoded. You can change the tailing fields=exac to fields=all to explore, but I don't think we can manage to filter other sources of annotations by transcripts.

On the other hand, queries on ensembl transcripts, as with https://mygene.info/v3/query?q=symbol:MITF%20AND%20ensembl.transcript:ENST00000352241&fields=ensembl, are not transcript-specific, but you can filter out the information you need if possible.

sigven commented 2 years ago

Thanks for the feedback, @erikyao! Will look into the ExAC annotations to see what can be pulled out there.

regards, Sigve