Check on why GenBank record page does not always show links to Biosample/Bioproject/(SRA?).

[nbx0]

Is this related to a specific database? If so, which database?
NCBI

Describe your issue below:

Ask @donutbrew for possible examples...

[donutbrew]

In these, the Genbank submission files do not contain the BioSample IDs even though they are available in the biosample report.xml. This does not happen consistently, so it's hard to pinpoint the problem.

https://git.biotech.cdc.gov/sars2seq/gad-pyspark/-/issues/588

[peterwc-cdc]

These boil down to not enough "time" between the initial biosample submission, and makeing the genbank submission. Some sort of double check should be added, but other than that not much else at issue

[DOH-KEW4303]

I have been looking into this issue myself and NCBI has told me that for the db's to be linked, the Biosample accession needs to be added to the definition lines of the fasta file

Seq1 [BioProject=PRNJAXXXXXX] [BioSample=SAMNXXXXXX]
ATCG....

Seq2 [BioProject=PRNJAXXXXXX] [BioSample=SAMNXXXXXX]
ATCG...

[peterwc-cdc]

Well that will make them more complicated. I'll double check our recent submissions, but I think we had this somewhat solved with waiting until the databases returned the information.

[dthoward96]

@DOH-KEW4303 @peterwc-cdc I've went through NCBI's documentation for definition lines and they do not show BioProject/BioSample/SRA as an available field for definition lines.
https://www.ncbi.nlm.nih.gov/WebSub/html/help/genbank-source-table.html
https://www.ncbi.nlm.nih.gov/genbank/mods_fastadefline/

From what I've discussed with NCBI previously, they typically discourage adding a lot of data to the definition lines. It's not required to add them to the definition lines for them to link correctly. https://github.com/ncbi/submission-schema/blob/master/genbank/SARS-CoV-2/SARS-CoV-2-ProgrammaticHelp.pdf Definition line modifiers can be provided as a source modifiers table instead which is what SeqSender uses to provide the accessions from BioSample/SRA.

However, I have added the option for them to be added to the fasta files by modifying the config file to include the additional field "Add_Definition_Line_Accessions" and setting it to True. This is an optional field so it won't cause any issues for config files missing this field. However, I cannot guarantee this won't cause issues with submissions on NCBI's side since they don't label these as available fields to use for submission.

[DOH-KEW4303]

Well that will make them more complicated. I'll double check our recent submissions, but I think we had this somewhat solved with waiting until the databases returned the information.

I will give this a try with our next submission and see how it goes!

[DOH-KEW4303]

I have tried a couple of submissions where I wait to receive the Biosample accessions before running submission_status to push the pipeline along to Genbank but that has not worked for me (I haven't done a deep dive to see where in the workflow the SAMN # should be getting added to the the .src file but it doesn't seem to be happening). The only way I have been able to see the DBLINK in my records is when I have manually added the SAMN to my metadata file and then run seqsender submit
Any suggestions @dthoward96 ?

Thanks!