additional metadata fields

ewels / sra-explorer

Web application to explore the Sequence Read Archive.

https://sra-explorer.info/

GNU General Public License v2.0

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additional metadata fields #11

Open igordot opened 5 years ago

igordot commented 5 years ago

Is it possible to include more metadata fields in the output?

More specifically:

It would be great to have MD5 checksums.
I came across a dataset where all the sample titles are the same, so the generated metadata table is not very helpful. In the ENA interface, the actual sample names show up in "Submitter's sample name".

ewels commented 5 years ago

In the ENA interface, the actual sample names show up in "Submitter's sample name".

Note that this tool doesn't search the ENA, only the SRA. It only contacts the ENA at the very end to get the FastQ download path for a given SRA accession. Are the sample names available on the SRA as well?

I agree that MD5s would be nice 👍

igordot commented 5 years ago

This was from an SRA submission, so there should not be any extra ENA information. In case you want to check, one of the experiments is SRX111071. There is "sample_type" under "Experiment attributes". The relevant sample info also show up if you check sample SAMN00013598 as "sample name". I am not sure if any of this would actually be possible to retrieve.

pxthxk commented 4 years ago

Adding Accession IDs for SRA Experiment, SRA Study, BioProject, BioSample and quite useful meta-info in the BioSample (Collection date, Geographic location, Isolation source etc.) would be very handy IMO.