Submit sequences with (structured) GISAID crossref accessions

[corneliusroemer]

Might be good to ask if GISAID can be added as an allowed db_xrefs db: https://www.ncbi.nlm.nih.gov/genbank/collab/db_xref/

Inquiries about the addition of other database types should be made to one of the collaborating databases.

Did a quick search (for "GISAID" across all of NCBI) on how others have crossreffed GISAID accessions:

• /note source qualifier: https://www.ncbi.nlm.nih.gov/nuccore/PV920727.1 and in biosample as GISAID accession and GISAID virus name https://www.ncbi.nlm.nih.gov/nuccore/PV920727.1

• Note in biosample: https://www.ncbi.nlm.nih.gov/biosample/48248324

• Description in biosample: https://www.ncbi.nlm.nih.gov/biosample/37081917

• /note source qualifier: https://www.ncbi.nlm.nih.gov/nuccore/PV424916.1

[anna-parker]

Adding in the notes field might be nice (we would have to check it goes through) because all revisions to fields in the manifest (i.e. the description field) cannot be made automatically and have to be revised via request - in theory changes to the embl flat file should be automated (in practice this also hasn't worked too well so might not make a difference)

[corneliusroemer]

For clarity, the description in the manifest maps to Genbank's "Comment"?

Do we know if it's actually easier to revise source qualifiers? Date/location updates have also not gone smoothly - maybe still better than manifest fields though.

[anna-parker]

For clarity, the description in the manifest maps to Genbank's "Comment"?

Yes, sorry we investigated this in the meeting today by checking our assembly submissions, for all our submissions the description field in the manifest has been mapped to the comments field in the genbank files

[anna-parker]

Do we know if it's actually easier to revise source qualifiers? Date/location updates have also not gone smoothly

We don't know - updating the authors for example (a field from the manifest) took almost 3 months in one case and now updating the geolocation has also been stuck for 3 weeks and it was a bit unclear how automatic this is (one was correctly updated the rest were not)

[anna-parker]

Update: We registered PPX with xref last year 9th October, 2024: https://loculus.slack.com/archives/C06JCAZLG14/p1724254720805059 and have not yet heard back... who should we best follow up with on this?

I filled out and sent this google form: https://docs.google.com/forms/d/1UHGQRHXoIbEL1nNaTt1dYzVGwY1v6BIlcPWQ03S5j9U/viewform?edit_requested=true

[corneliusroemer]

@anna-parker can you be more precise, who did we email/contact? I'm not aware of there being a single xref authority.

[anna-parker]

@anna-parker can you be more precise, who did we email/contact? I'm not aware of there being a single xref authority.

I filled out a google form, see link above

[corneliusroemer]

Hmm ok so to EBI, argh that they have a live form that's not replied to, I'll write a help desk ticket