TITLE: Guidance for populating GenomeTrakr metadata templates (BioSample and SRA)
AUTHORS: Ruth Timme, Maria  Balkey, William Wolfgang, Errol Strain

[DESCRIPTION]
PURPOSE: Guidance on how to populate NCBI's metadata packages, maximizing interoperability for foodborne pathogen surveillance. 

SCOPE: This protocol provides detailed instructions for populating the following two templates:

1. BioSample metadata: guidelines to populate the GenomeTrakr-extended pathogen package.

2. SRA metadata: NCBI's generic sequence metadata template for SRA submissions.

Versions:
v6: Added the One Health Enteric package presented at IAFP 2021 meeting.
v7: Updated the picklists in the GenomeTrakr-extended pathogen package, "GT-pathogen package-OHE v0.2.2.xlsx" and added an incremental update file for the DRAFT One Health Enteric Package that includes extensive edits compared to v6.
v8: Updated the picklists in the GenomeTrakr-extended pathogen package, "GT-pathogen package-OHE v0.2.2.xlsx".  Also provided a direct link to the newly published One Health Enteric package.
v9: Bug fix


[BEFORE_START]
Before collecting sequence data for your isolates, ensure that you can provide the minimum metadata recommended by your coordinating surveilliance body. The INSDC, in collaboration with the Global Microbial Identifer (GMI) (https://www.globalmicrobialidentifier.org), recommends using the Pathogen metadata template for pathogen surveilliance submissions: (NCBI: https://www.ncbi.nlm.nih.gov/pathogens/submit-data/and EMBL-EBI: https://www.ebi.ac.uk/ena/submit/pathogen-data). 


[STEPS]
SECTION: Overview
1. Guidance for organizing and populating the metadata templates required for direct submission to NCBI.  This guidance is applicable for most enterics and/or microbial pathogens. 

****If your laboratory uses the BioNumerics platform for submission, please follow this protocol.****

Two metadata templates are required:
1. BioSample metadata (metadata describing the sample source and submitter)
2. SRA metadata (metadata describing the sequence data collection)

  

SECTION: BioSample metadata template
2. Template for BioSample submission:

Download the Pathogen package (GenomeTrakr-extended) and follow the guidance included in this template:

  

SECTION: BioSample metadata template
2.1. New (optional) template: One Health Enteric Package (custom version):  https://github.com/CFSAN-Biostatistics/One_Health_Enteric_Package



SECTION: SRA sequence metadata template
3. Template for SRA metadata submission:


Download the "Metadata spreadsheet with sample names" file from the NCBI Submission Templates page:
https://submit.ncbi.nlm.nih.gov/templates/

And follow the guidance in the following table:

PRO TIPS:
If you have sequences to submit that belong to more than one BioProject, create a separate submission + metadata table for each of your BioProjects. 
Entering fastq filenames in the spreadsheet: On a Mac, you can directly copy the file names from the folder into a spreadsheet. This is not possible on a PC using copy and paste but can be done with some command-line operation. 
Finally, it is important to develop a QA/QC step to make sure the files are associated with the correct sample name. For example, use a left function in excel to strip of the appended text in the file name and then use the exact match to make sure the name matches the sample name.
SECTION: SRA sequence metadata template
3.1. 
 


Save the second sheet (SRA_data) as a TSV (tab-delimited file) for upload in the “SRA metadata” tab within the submission portal.


*NCBI should also accept the original excel formatted file.