How To needed - genbank packager

[dustymc]

This apparently didn't get an Issue, but there's now a GenBank submission tool in Arctos.

Reports/DataServices/PackageGenBankData

• create a batch (probably corresponds to a publication, but whatever)
• add some people
• add sequences
• click the links at the bottom
• tell me what's missing/broken
• email the .sqn file to GenBank once everything is as it should be

[campmlc]

Schuyler and I looked at this - looks good so far. We didn't actually submit yet to know what other problems might arise, but we like the ability to put in a barcode and have the part type and catalog number auto-link. Looks much simpler and easier to use than the BankIt submission portal to NCBI. Also really like the ability to link to sequences directly to a Bioproject at NCBI.

Suggestion: Carry over the Reference Title and people between sequence additions for a multi-sequence submission.

On Tue, Aug 28, 2018 at 10:43 AM, dustymc notifications@github.com wrote:

This apparently didn't get an Issue, but there's now a GenBank submission tool in Arctos.

Reports/DataServices/PackageGenBankData

• create a batch (probably corresponds to a publication, but whatever)
• add some people
• add sequences
• click the links at the bottom
• tell me what's missing/broken
• email the .sqn file to GenBank once everything is as it should be

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[dustymc]

Thanks.

didn't actually submit yet

Can you let them know what's going on and include me in that when you do? Seems likely that there's room for improvement - I don't really speak genetics, GenBank's documentation is a bit cryptic, etc.

auto-link

Yup, I think that's the real power here - from the tool, it shouldn't really be possible to submit something that doesn't link to at least a specimen, and most things should link to parts. Barcodes do a lot more than finding specimens in the collection! (As anyone who uses barcodes very much knows.)

Carry over the Reference Title and people

It does; a "batch" is just the basic metadata including people associated with any number of sequences. (Or if not I need details - maybe this is an instance of me not quite being fluent in GenBank.)

I did this:

it saved back to this:

Scroll down and click a few times and...

it creates a submission for each sequence which includes author-stuff.

[Jegelewicz]

If this is functional and worthwhile, it needs a How To. Assigning those who have tested it.