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

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">PURPOSE: </span><span>Guidance on how to populate NCBI's metadata packages, maximizing interoperability for foodborne pathogen surveillance. </span></div><br/><div class = "text-block"><span style = "font-weight:bold;">SCOPE</span><span>: This protocol provides detailed instructions for populating the following two templates:</span></div><br/><div class = "text-block"><span>1.  </span><span style = "font-weight:bold;">BioSample metadata</span><span>: guidelines to populate the GenomeTrakr-extended pathogen package.</span></div><br/><div class = "text-block"><span>2. </span><span style = "font-weight:bold;">SRA metadata: </span><span>NCBI's generic sequence metadata template for SRA submissions.</span></div></div>

[STEPS]
?. [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.
?. [BioSample metadata template]
NOTE: DO NOT USE THIS VERSION FOR NCBI SUBMISSION. We expect the v1.0 release to be ready for use in Fall 2021.
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 template here and follow the guidance in the following table:ftp://ftp-trace.ncbi.nlm.nih.gov/sra/metadata_table/SRA_metadata.xlsxPRO 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.
?. [SRA sequence metadata template]
ABC1FieldDescriptionExample2sample_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-123453library_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-12345.64TitleShort, free text description that identifies the data on public pages.

For Example:
{methodology} of {organism}: {sample_name}WGS of Salmonella enterica: UT-123455library_strategyOverall sequencing strategy or approach. 
Choose from NCBI pick listSee NCBI SRA pick list. (e.g. WGS)6library_sourcemolecule type used to make the librarySee NCBI SRA pick list. (e.g. Genomic)7library_selectionLibrary capture methodSee NCBI SRA pick list. (e.g. random, PCR)8Library_layoutChoose from NCBI pick listSee NCBI SRA pick list, choose "paired"9platformSequencing platformSee NCBI SRA pick list. (e.g., Illumina).10instrument_modelName of the sequencing instrument.See NCBI SRA pick list. (e.g. Illumina MiSeq, iSeq 100)11Design_descriptionoptional field for free text description of methods12FiletypeFile format name for the raw sequence data
Choose from NCBI pick listSee NCBI SRA pick list. (e.g. Fastq)13Filenameinclude 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)14Filename2genome_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)15Filename3-8list 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.
ABC1FieldDescriptionExample2sample_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-123453library_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-12345.64TitleShort, free text description that identifies the data on public pages.

For Example:
{methodology} of {organism}: {sample_name}WGS of Salmonella enterica: UT-123455library_strategyOverall sequencing strategy or approach. 
Choose from NCBI pick listSee NCBI SRA pick list. (e.g. WGS)6library_sourcemolecule type used to make the librarySee NCBI SRA pick list. (e.g. Genomic)7library_selectionLibrary capture methodSee NCBI SRA pick list. (e.g. random, PCR)8Library_layoutChoose from NCBI pick listSee NCBI SRA pick list, choose "paired"9platformSequencing platformSee NCBI SRA pick list. (e.g., Illumina).10instrument_modelName of the sequencing instrument.See NCBI SRA pick list. (e.g. Illumina MiSeq, iSeq 100)11Design_descriptionoptional field for free text description of methods12FiletypeFile format name for the raw sequence data
Choose from NCBI pick listSee NCBI SRA pick list. (e.g. Fastq)13Filenameinclude 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)14Filename2genome_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)15Filename3-8list other fastq file names (e.g. for NextSeq data)