Feb 03, 2022

Public workspaceNCBI data curation protocol - SOP for editing GenomeTrakr submissions V.2

DOI
dx.doi.org/10.17504/protocols.io.bx4tpqwn
  • 1US Food and Drug Administration;
  • 2Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, USA;
  • 3Bacteriology Laboratory, Wadsworth Center, New York State Department of Health, Albany, New York, USA;
  • 4Center for Veterinary Medicine, U.S. Food and Drug Administration, College Park, Maryland, USA;
  • 5Wadsworth Center NYSDOH
  • GenomeTrakr
  • Springer Nature Books
Ruth Timme
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DOI: dx.doi.org/10.17504/protocols.io.bx4tpqwn
Protocol Citation: Ruth Timme, Candace Hope Bias, Sai Laxmi Gubbala Venkata, Robyn Randolph, William Wolfgang, Errol Strain, Maria Balkey 2022. NCBI data curation protocol - SOP for editing GenomeTrakr submissions. protocols.io https://dx.doi.org/10.17504/protocols.io.bx4tpqwnVersion created by Maria Balkey
Manuscript citation:
Timme, R.E., Wolfgang, W.J., Balkey, M. et al. Optimizing open data to support one health: best practices to ensure interoperability of genomic data from bacterial pathogens. One Health Outlook 2, 20 (2020). https://doi.org/10.1186/s42522-020-00026-3. Timme R.E., Sanchez Leon M., Allard M.W. (2019) Utilizing the Public GenomeTrakr Database for Foodborne Pathogen Traceback. In: Bridier A. (eds) Foodborne Bacterial Pathogens. Methods in Molecular Biology, vol 1918. Humana, New York, NY. https://doi.org/10.1007/978-1-4939-9000-9_17
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it’s working
Created: September 09, 2021
Last Modified: February 03, 2022
Protocol Integer ID: 53107
Keywords: NCBI submission, GenomeTrakr, curation, genomic pathogen surveillance
Abstract
PURPOSE: After data are submitted to NCBI submitters often encounter the need to update, retract, or replace these records. This is called data curation. This protocol provides instructions for keeping these records up-to-date for each relevant database at NCBI.

SCOPE: This protocol covers curation for the following NCBI databases:

  • BioProject
  • BioSample
  • Sequence Read Archive

V2. Edit submissions using the NCBI portal (Manage data). Moved "how to find my data" content to a new protocol.
Before start
Most updates to existing NCBI submissions are performed through email requests to each respective NCBI database (e.g. BioSample, BioProject, Sequence Read Archive, and Pathogen Detection). NCBI curators within each respective database expect these emails to update and retract data. It is their job to help the data stay current, so do not hesitate to correct errors when they are spotted.
BioProject Curation
BioProject Curation
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
BioSample curation
BioSample curation
How to edit BioSamples.
All edits or updates to BioSample records are submitted via email to the BioSample database: 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:
Download FDA_biosample_update_20220203_fb.txtFDA_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:
BioSamplecollection_dateisolation_source
SAMN129873352019-10-12cilantro
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.

Thanks,
Ruth
SRA curation
SRA curation
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:
Download FDA_SRA_update_20210203_ct.txtFDA_SRA_update_20210203_ct.txt (adding custom wastewater attributes)
Download FDA_SRA_update_20210203_fb.txtFDA_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:
ABCDE
Runenrichment_kitamplicon _PCR_primer_schemelibrary_preparation_kitdehosting_method
SRR17540870NEBNext ARTIC SARS-CoV-2 RT-PCR ModuleNEB VarSkip ShortIllumina DNA prepSRA 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