Aug 08, 2022

Public workspaceGuidance for populating GenomeTrakr metadata templates (BioSample and SRA)

 Forked from Guidance for populating GenomeTrakr metadata templates (BioSample and SRA)
DOI
dx.doi.org/10.17504/protocols.io.dm6gpb71dlzp/v1
Guidance for populating GenomeTrakr metadata templates (BioSample and SRA)
  • Ruth Timme1,
  • Maria Balkey1,
  • William Wolfgang2,
  • Errol Strain1
  • 1US Food and Drug Administration;
  • 2Wadsworth Center NYSDOH
Maria Balkey
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DOI: https://dx.doi.org/10.17504/protocols.io.dm6gpb71dlzp/v1
Protocol Citation: Ruth Timme, Maria Balkey, William Wolfgang, Errol Strain 2022. Guidance for populating GenomeTrakr metadata templates (BioSample and SRA). protocols.io https://dx.doi.org/10.17504/protocols.io.dm6gpb71dlzp/v1
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
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: August 08, 2022
Last Modified: August 08, 2022
Protocol Integer ID: 68385
Keywords: GenomeTrakr, metadata, Pathogen package, NCBI Pathogen Detection, INSDC, genometrakr metadata template, populating genometrakr metadata template, extended pathogen package, biosample metadata, generic sequence metadata template for sra submission, pathogen package, added genometrakr, draft one health enteric package, picklists in the genometrakr, generic sequence metadata template, genometrakr, health enteric package, interoperability for foodborne pathogen surveillance, sra metadata, metadata package, foodborne pathogen surveillance, biosample, incremental update file for the draft, sra submission, guideline
Disclaimer
Please note that this protocol is public domain, which supersedes the CC-BY license default used by protocols.io.
Abstract
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: Added GenomeTrakr; LFFM-FY3 to drop-down menu.
Materials
Gather the following contextual information for each pure culture isolate:

  1. organism name
  2. lab name that collected the sample
  3. collection date
  4. collection source
  5. Geographic location of sample collection

Troubleshooting
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).

Overview
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)



BioSample metadata template
Template for BioSample submission:

Download the GenomeTrakr-extended pathogen package and follow the guidance included in this template. Download GT-pathogen package-OHE v0.2.3.xlsxGT-pathogen package-OHE v0.2.3.xlsx

DRAFT One Health Enteric Package, announced at IAFP 2021 (and the fall GenomeTrakr meeting) is ready for review and comment. Please download the file, review the attributes, and provide feedback here or email directly to ruth.timme@fda.hhs.gov.
Download One Health Enteric Package-DRAFT_v0.5.1-Nov1.xlsxOne Health Enteric Package-DRAFT_v0.5.1-Nov1.xlsx
Safety information
NOTE: DO NOT USE THIS VERSION FOR NCBI SUBMISSION. We expect the v1.0 release to be ready for use in Fall 2021.



SRA sequence metadata template
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:
  1. If you have sequences to submit that belong to more than one BioProject, create a separate submission + metadata table for each of your BioProjects.
  2. 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.
  3. 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.

ABC
FieldDescriptionExample
sample_nameInclude the same ID here as you entered for "sample_name" in the BioSample submission template. Populate this field using the values in the PHA4GE specification for "specimen collector sample ID".UT-12345
library_IDThe library name should be a unique ID relevant to your workflow. It can be an autogenerated ID from your LIMS system or a modification of your sample_name. Populate this field using the values in the PHA4GE specification for "library_id".UT-12345.6
TitleShort, free text description that identifies the data on public pages. For Example: {methodology} of {organism}: {sample_name}WGS of Salmonella enterica: UT-12345
library_strategyOverall sequencing strategy or approach. Choose from NCBI pick listSee NCBI SRA pick list. (e.g. WGS)
library_sourcemolecule type used to make the librarySee NCBI SRA pick list. (e.g. Genomic)
library_selectionLibrary capture methodSee NCBI SRA pick list. (e.g. random, PCR)
Library_layoutChoose from NCBI pick listSee NCBI SRA pick list, choose "paired"
platformSequencing platformSee NCBI SRA pick list. (e.g., Illumina).
instrument_modelName of the sequencing instrument.See NCBI SRA pick list. (e.g. Illumina MiSeq, iSeq 100)
Design_descriptionoptional field for free text description of methods
FiletypeFile format name for the raw sequence data Choose from NCBI pick listSee NCBI SRA pick list. (e.g. Fastq)
Filenameinclude ALL of the files resulting from this library. **Add additional fields if there are more than two files (e.g. Filename3). Populate this field using the values in the PHA4GE specification for "r1 fastq filename".genome_r1.fastq (*must be exact)
Filename2genome_r2.fastq (*must be exact) Populate this field using the values in the PHA4GE specification for "r2 fastq filename".genome_r2.fastq (*must be exact)
Filename3-8list other fastq file names (e.g. for NextSeq data)


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.