TITLE: Populating NCBI template for submissions using  BioNumerics v7.6
AUTHORS: Ruth  Timme, Maria   Balkey, Julie  Haendiges

[DESCRIPTION]
PURPOSE: to define the standard operating procedure for collecting isolate metadata using BioNumerics for submission of food/environmental isolates to NCBI.

SCOPE: to provide a standardized procedure to collect isolate metadata using BioNumerics for submission of food/environmental isolates to NCBI.

RESPONSIBILITIES- SOP Responsible Officials: Ruth Timme, Maria Balkey

The GenomeTrakr Network Management will be responsible to monitor GenomeTrakr submissions processed through Bionumerics and ensure that all GT labs are familiar with the mandatory metadata fields required for submission of GenomeTrakr sequencing records to NCBI. 

V3:  Dropdown menus from controlled vocabulary added to the ncbi_update submission sheet

[STEPS]
1. 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. 



   


2. 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.   
 
2.1.  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 ' denotes that the template value e.g. BioProject accession is mapping to the field in BioNumerics e.g. NCBI_bioproject.  



   
   Name of Field in BioNumerics TemplateDescription  ExampleBioProject accessionIdentifier for NCBI data collection that contatins data associated to GenomeTrakr.  Specific for organism and lab submitterPRJNA514285Organization nameSurveillance Program (example is the default value for GenomeTrakr submissions)GenomeTrakrSPUID namespaceSurveillance Program (example is the default value for GenomeTrakr submissions)GenomeTrakrTypeorganization type (example is the default value for GenomeTrakr submissions)consortiumRolelaboratory responsibility (example is the default value for GenomeTrakr submissions)ownerContact first nameFirst name for Lab POC for NCBI submissions.  Lab might choose to create alias name for WGS teamFirst NameContact last nameLast name Lab POC for NCBI submissions. Lab might choose to create alias name for WGS teamLast NameContact e-mailemail for Lab POC for NCBI submissions. Lab might choose to create alias name for WGS teamfirst.last@lab.govFTP upload directoryName of directory at NCBI FTP site (example is the default value for GenomeTrakr submissions)submit/Production
  



2.2. 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 https://www.ncbi.nlm.nih.gov/bioproject/593772

Make sure to submit to your lab bioproject.  Please don't submit to umbrella bioprojects. 
2.3. BioSample:  Metadata associate to the isolate might require the creation of new fields in BioNumerics. The term '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. 


   

 
    Name of Field in BioNumerics TemplateDescription  Name of Field in BioNumerics DataBaseExampleSubmitter Provided Unique ID Local lab strain ID  Key (field content)     21B00181-5BioSample accession (output)NCBI accession will get populated upon submission to NCBINCBI_ACCESSION (field content)     SAMN17385051 Organism nameGenus – species for organism  Listeria monocytogenes     Listeria monocytogenes     TitlePathogen: environmental/food/other sample from Listeria monocytogenesPathogen: environmental/food/other sample from Listeria monocytogenesPathogen: environmental/food/other sample from Listeria monocytogenesAttribute packageSample category  Pathogen: environmental/food/other sample from Listeria monocytogenesPathogen: environmental/food/otherStrain namePNUSA identifier (automatically populates at the time of registration)WGS_id (field content)PNUSAL008933Serovar (optional)Serotyping information for Escherichia coli and Salmonella enterica<Missing>missingIsolate (optional)Field is not required for GenomeTrakr<Missing>missingIsolate namea aliasOptional identifier for collaboration projects<Missing>missing
 

2.4. 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.

   

  
          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. Populate using ISO 8601 standard: “YYYY-mm-dd”, “YYYY-mm” or   “YYYY” (e.g., 1990–10–30, 1990–10, or 1990).        Including the month or month/day of collection is extremely valuble for   accessing seasonality in the database.  IsolateDate (field content)       2020    Geographical location  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>  missing    Isolation source  Detailed description for sample   product or environmental source   SourceSite (field content)       cheese    Host  Only provided for human   isolates     <Missing>  missing    Host disease  Only provided for human   isolates    <Missing>  missing  
 

2.5. NCBI submission settings – SRA Experiment and Run

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

 
   




3. NCBI submission settings – Submission Template

Save submission template according to PulseNet Instructions as -GenomeTrakr-Template-.
4. Import data
4.1. Import the GenomeTrakr Metadata form for BioNumerics (GT_BioNumerics_spreadsheet_v2.csv) according to PulseNet Instructions. 
4.2. When importing rules, the field source should match destination fields. 
4.3. In the importing links section, choose the -key- for linking records to database entries. 
4.4. Proceed with sequencing data import according to PulseNet Instructions. 
4.5. 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. 
4.6. 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. 
5. 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    spreadsheet and submit the update for these fields to NCBI by contacting biosamplehelp@ncbi.nlm.nih.gov.