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NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases.
https://www.ncbi.nlm.nih.gov/datasets
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"/note" feature retrieving through command lines #389

Open GabrielFalque opened 1 month ago

GabrielFalque commented 1 month ago

I am working on measle disease and want to retrieve metadata from sequenced genomes via the following command : datasets summary virus genome taxon 11234 --as-json-lines | dataformat tsv virus-genome --fields accession,geo-location,geo-region,virus-infraspecific-strain,virus-name,virus-tax-id,completeness,length,isolate-collection-date,release-date >> mease_metadata.tsv

And one information I need the most is the strain type. But in some numerous cases this information is stored in the following feature (example from MK393364.1 accession number) :

/note="genotype: [B3]"

But I can see that for the moment it is impossible to retrieve this feature, am I wrong ? Or is there another way ?

If not, is it possible for you to add this possibility ?

Thank you in advance.

Gabriel

olearyna commented 1 month ago

Hi GabrielFalque,

Thank you for opening this issue. We're working with the NCBI Virus Team to include this information in the virus data report. I'll keep this issue open until its implemented.

Nuala

GabrielFalque commented 1 month ago

Hi @olearyna ,

Thank you for this. Have a good day.

Gabriel

GabrielFalque commented 1 week ago

Hi @olearyna ,

I just wanted to know if it will be implemented soon. Have a good day.

Gabriel