Metadata SampleSheet preparation

Before uploading your sequencing run or linking NCBI sequencing records at the BioNumerics platform make sure to fill out the metadata spreadsheet form.

Please download the template and guidelines included in the file 'GT_BioNumerics_spreadsheet_v2.xlsx'.

Create the fields NCBI_bioproject, Attribute_package, Organism_name, NCBI_LabID, SourceCountryState, Latitude_longitude, Reference_material, Culture_collection or Description if they are not in the BioNumerics interface and are needed to process the metadata for your isolates.

Once you have filled out the template information, save the template sheet as .csv and import the metadata to BioNumerics.

GT_BioNumerics_spreadsheet_v2.xlsx

NCBI Submission Settings (Manage submission template)

Create the NCBI metadata template in BioNumerics following PulseNet instructions making sure fields are populated according to GT requirements which are described in the following steps.

BioProject and Organization: GenomeTrakr labs by submitting independently become owners of their data and are responsible for managing individual bioprojects for each sequenced organism. The term 'field content ' field content ' denotes that the template value e.g. BioProject accession is mapping to the field in BioNumerics e.g. NCBI_bioproject.

A	B	C
Name of Field in BioNumerics Template	Description	Example
BioProject accession	Identifier for NCBI data collection that contatins data associated to GenomeTrakr.  Specific for organism and lab submitter	PRJNA514285
Organization name	Surveillance Program (example is the default value for GenomeTrakr submissions)	GenomeTrakr
SPUID namespace	Surveillance Program (example is the default value for GenomeTrakr submissions)	GenomeTrakr
Type	organization type (example is the default value for GenomeTrakr submissions)	consortium
Role	laboratory responsibility (example is the default value for GenomeTrakr submissions)	owner
Contact first name	First name for Lab POC for NCBI submissions.  Lab might choose to create alias name for WGS team	First Name
Contact last name	Last name Lab POC for NCBI submissions. Lab might choose to create alias name for WGS team	Last Name
Contact e-mail	email for Lab POC for NCBI submissions. Lab might choose to create alias name for WGS team	first.last@lab.gov
FTP upload directory	Name of directory at NCBI FTP site (example is the default value for GenomeTrakr submissions)	submit/Production

Table 1. Guidelines for Bioproject and Organization metadata

Laboratories will be submitting to specific bioprojects for lab/organisms. Find the organism/lab specific bioproject under each of the GenomeTrakr umbrella bioprojects included at http://www.ncbi.nlm.nih.gov/bioproject/593772

Make sure to submit to your lab bioproject. Please don't submit to umbrella bioprojects.

BioSample: Metadata associate to the isolate might require the creation of new fields in BioNumerics. The term 'field content ' field content ' denotes that the template value e.g. Organism name is mapping to the field in BioNumerics e.g. Organism_name. The template values might map to default values e.g. Pathogen: environmental/food/other; version 1.0. Make sure to include the metadata associated to the isolates in the mandatory fields such as: Submitter Provided Unique ID, BioSample accession (output), Organism name, Title, Attribute package, Strain name and Isolate name alias. Isolate name alias is a mandatory field for GenomeTrakr submissions . Provide serovar when available.

A	B	C	D
Name of Field in BioNumerics Template	Description	Name of Field in BioNumerics DataBase	Example of metadata value
Submitter Provided Unique ID	Local lab strain ID	Entry Key	21B00181-5
BioSample accession (output)	NCBI accession will get populated upon submission to NCBI	NCBI_ACCESSION (field content)	SAMN17385051
Organism name	Genus – species for organism	Organism_name (field content)	Listeria monocytogenes
Title	Organism name	Organism_name (field content)	Listeria monocytogenes
Attribute package	Sample category	Pathogen: environmental/food/other; version 1.0	Pathogen: environmental/food/other; version 1.0
Strain name	PNUSA identifier (automatically populates at the time of registration)	WGS_id (field content)	PNUSAL008933
Serovar (optional)	Serotyping information for Escherichia coli and Salmonella enterica	Serovar (field content)	missing
Isolate (optional)	Field is not required for GenomeTrakr		missing
Isolate namea alias (optional)	Optional identifier for collaboration projects	Isolate_name_alias (field content)	21B00181-5; RS_21290

Table 2. Guidelines for BioSample metadata

BioSample: Make sure to include the metadata associated to the isolates in the mandatory fields such as: Collected by, Collection / Isolate date, Collection / Isolate date format, Title, Geographical origin and Isolate source. Isolate name alias is a mandatory field for GenomeTrakr submissions. Provide Geographical coordinates when available. Host or host disease are provided only for isolates obtained from human, indicate "missing" for isolates from food or environmental sources.

A	B	C	D
Name of Field in BioNumerics Template	Description	Name of Field in BioNumerics DataBase	Example of metadata value
Collected by	Full name of laboratory that collected the sample or has taken over curation of the isolate.	NCBI_LabID (field content)	NY Department of Agriculture and Markets
Collection date	Date on which the sample was collected.	IsolateDate (field content)	2020
Geographical	Country and State for sample collection	SourceCountryState (field  content)	USA:NY
Geographical coordinates	latitude and longitude for site of collection.  Missing if it is not provided		missing
Isolation source	Detailed description for sample product or environmental source	SourceSite (field content)	cheese
Host	Only provided for human isolates		missing
Host disease	Only provided for human isolates		missing

Table 3. Guidelines for BioSample metadata (2)

NCBI submission settings – SRA Experiment and Run

Populate fields for SRA Experiment and Run according to PulseNet instructions.

NCBI submission settings – Submission Template

Save submission template according to PulseNet Instructions as - GenomeTrakr-Template -.

Import data

Import the GenomeTrakr Metadata form for BioNumerics ( GT_BioNumerics_spreadsheet_v2 .csv ) according to PulseNet Instructions.

When importing rules, the field source should match destination fields.

In the importing links section, choose the -key- for linking records to database entries.

Proceed with sequencing data import according to PulseNet Instructions.

Submit data to NCBI according to PulseNet Instructions. If NCBI accessions are not available at BioNumerics in 1 business day, please contact NCBI and PulseNet to troubleshoot issues with submissions.

Contact GenomeTrakr by email genometrakr@fda.hhs.gov if issues with submissions are delayed for more than 3 days. GenomeTrakr can support urgent submissions if needed.

NCBI submission for fields not included in the BioNumerics Template.

Laboratories need to include the name of the laboratory sequencing the isolates and the surveillance effort name in the sequenced_by and project_name fields, respectively. After receiving biosample accessions, fill out the BioNumerics_update.xlsx spreadsheet and submit the update for these fields to NCBI by contacting biosamplehelp@ncbi.nlm.nih.gov.