NCBI data curation protocol - SOP for editing GenomeTrakr submissions

How to edit a BioProject

1. Click on the "Manage Data" tab within the submission portal, or navigate directly to "Manage Data": https://dataview.ncbi.nlm.nih.gov to edit Title, Organism, Description, URL, or publications for your BioProject.

2. In the menu, select BioProject, a complete list of your NCBI group bioprojects will be displayed.

3. Click on the BioProject that you need to edit.

4. Fields available for editing will be displayed after selecting a BioProject.

5. Click in any of the edit/add fields and proceed to add the corresponding BioProject information. Once the information is changed or added, click next and submit.

6. A confirmation prompt will indicate that your updates are in progress.

Email for BioProject: bioprojecthelp@ncbi.nlm.nih.gov

Use this email for the following tasks, include the BioProject accession in the email subject:

• Questions about errors or processing of a BioProject submission

• Convert a Data BioProject to an Umbrella BioProject

• Re-assign a BioProject from one Umbrella BioProject to another

How to edit BioSamples.

All edits or updates to BioSample records are submitted via email to the BioSample database: biosamplehelp@ncbi.nlm.nih.gov biosamplehelp@ncbi.nlm.nih.gov

Use this email for the following tasks. Include your lab and the request date in your subject line for easy tracking, eg “FDA BioSample update, Dec 10, 2019”.

• Questions about validation errors or processing of a BioSample submission.

• Update, correct, or add fields to a BioSample(s)

• Retraction

• Add a linkage or re-assign linkage to a BioProject

You will receive a confirmation email that the updates were performed. These types of transactions are common for this database, so do not hesitate to submit multiple requests in one day.

How to retract one or multiple BioSamples

Email: biosamplehelp@ncbi.nlm.nih.gov

     _Dear BioSampleHelp,_ 





     _Please retract the following BioSamples due to sample mix-ups (or other reason):_ 





     _SAMN\#\#\#\#\#\#\#\#_ 



     _SAMN\#\#\#\#\#\#\#\#_ 



     _SAMN\#\#\#\#\#\#\#\#_ 



     _SAMN\#\#\#\#\#\#\#\#_ 

Thank you,

Ruth

How to update content in metadata fields or add new fields/attributes to a BioSample record(s)

Email: biosamplehelp@ncbi.nlm.nih.gov

Dear BioSampleHelp,

Please update the attached BioSample records.

Thanks,

Ruth

Attach a tab-delimited text file with the BioSample accessions in the first column and fields to update the right. You can attach a table to update one or multiple records at a time.

   **Example:** 

FDA_biosample_update_20220203_fb.txt (adding "sequenced_by" and "project_name" to a biosample)

• The following table will correct the collection date and isolation source on one BioSample record:

A	B	C
BioSample	collection_date	isolation_source
SAMN12987335	2019-10-12	cilantro

Tab-delimited table for updating a BioSample record.

Re-assign a BioSample from one BioProject to another

Submit an update request with the new BioProject accession(s) specified in a column.

     _Dear BioSampleHelp,_ 

Please process the attached BioSample updates and remove all previous BioProject links. remove all previous BioProject links.

Thanks,

Ruth

SRA updates and retractions

The following types of updates can be made within the submission portal under the “Manage data” tab:

• Sequence metadata, such as library ID, library strategy, sequencing platform or instrument.
• Associated BioSample or BioProject accession numbers
• Release date

1. Click on the "Manage Data" tab within the submission portal, or navigate directly to "Manage Data": https://dataview.ncbi.nlm.nih.gov

2. Query for SRR accession you'd like to update:

3. Click on the resulting "BioProject" link.

4. Click on the BioProject accession link:

5. All the SRA records submitted to this BioProject can now be edited! Search for the one(s) you want and click the box to edit.

6. You can now edit the metadata directly for this record. If you need to correct a sample-swap you can enter the correct BioSample accession here and the sequence will get re-parented.

Editing/updating custom SRA metadata attributes

Email: sra@ncbi.nlm.nih.gov

Dear SRA,

Please update the attached SRA records.

Thanks,

Ruth

Attach a tab-delimited text file with the SRR accessions in the first column and attributes to update included as additional columns (*** only include columns you want to update*** ).

Examples:

FDA_SRA_update_20210203_ct.txt (adding custom wastewater attributes)

FDA_SRA_update_20210203_fb.txt (updating core SRA metadata attributes)

The following table will update or add the custom attributes used for the covid wastewater project:

A	B	C	D	E
Run	enrichment_kit	amplicon _PCR_primer_scheme	library_preparation_kit	dehosting_method
SRR17540870	NEBNext ARTIC SARS-CoV-2 RT-PCR Module	NEB VarSkip Short	Illumina DNA prep	SRA human read removal tool

Tab-delimited table for updating an SRA record.

Email contact for SRA database: sra@ncbi.nlm.nih.gov

Use this email for the following tasks. Include your lab and the request date in your subject line for easy tracking, e.g. “FDA SRA retractions, Dec 10, 2019”.

• Questions about validation errors or processing of an SRA submission.

• Retractions

SRA retraction

An SRA record should only be retracted for the following reasons:

1. Discovery of poor quality data. Lab intends to re-generate data (starting at appropriate wet-lab step, re-isolation, DNA extraction, library prep, or sequencing) and re-submit the data.
2. Sample mix-ups that cannot be resolved by re-parenting or correcting the BioSamples. Lab intends to re-generate (starting at appropriate wet-lab step, re-isolation, DNA extraction, library prep, or sequencing) and re-submit the data.
3. Discovery of multiple runs per isolate. Laboratory would like to have only one run per isolate in the system. No re-sequencing planned.

DO NOT retract an SRA submission, then attempt to re-submit the same files. This will get flagged as a duplicate within NCBI's validation check and and will be rejected.

Emails should include a list of SRR accessions to retract and reason for retraction (i.e. sample mix-up, quality of data, etc.).

*Although the data submissions appear visibly linked at NCBI (you can navigate between databases with links on each record) the data may not be linked in a way that works with retractions. Therefore, if you need to retract a bad SRA run, you should also request that all other data (such as GenBank assemblies or Pathogen Detection analyses) also be retracted, even if you didn’t submit them yourself.

Email template:

     _Dear SRA,_ 





     _Please retract the following SRR accessions and any linked assemblies or PD analyses due to XXX issue._ 



     _We will re-sequence these isolates and re-submit new data._ 





     _SRRXXXXXX1_ 



     _SRRXXXXXX2_ 



     _SRRXXXXXX3_ 





     _Thanks,_ 



     _Ruth_