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Retrieve all metadata from edirect that is accessible from SRArunTable #60

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kray02 opened this issue Sep 27, 2022 · 0 comments
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@kray02
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kray02 commented Sep 27, 2022

When retrieving runinfo from edirect as follows:

PRJN=PRJNA784998
~/edirect/esearch -db sra -query $PRJN | ~/edirect/efetch -format runinfo

there are different metadata fields than when accessing from the SRA Run Selector, and downloading metadata

This is the bioproject here:
https://www.ncbi.nlm.nih.gov/Traces/study/?page=2&query_key=3&WebEnv=MCID_633332599c0211437bc6a566&o=acc_s%3Aa

Of note: BIOMATERIAL_PROVIDER is not part of the efetch runinfo format. Is there a way to get all metadata through efetch? I have tried accessing that field specifically, but can't find it.

Are those two methods of accessing metadata considered equivalent? Or is efetch --format runinfo accessing different metadata?

Thanks,
Karina

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