TITLE: Populating NCBI template for submissions using  BioNumerics  
AUTHORS: Ruth Timme, Maria Balkey, Julie Haendiges, Brian Sauders, Tina.Pfefer

[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:  Added dropdown menus from controlled vocabulary to sequenced by and project name to metadata template PulseNet_Bionumerics_Isolate_Metadata
V4:  Changes in metadata template PulseNet_Bionumerics_Isolate_Metadata. 
- Added dropdown menus from controlled vocabulary to collected_by ,  SourceCountryState
- Added fields: collected by, isolation source
- Added mapping table of attribute names.
- Remove requirement to send biosample update to NCBI to make changes on sequenced by and project name. 



[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 
  

Create the fields NCBI_bioproject, Attribute_package, Organism_name, NCBI_LabID, Collected by, SourceCountryState, Latitude_longitude, ProjectName, SequencedBy, Isolation source if they are not in the BioNumerics interface.

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

3. 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.   
 
3.1.  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.  


 
 

  



3.2. 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. 
3.3. 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. OrganismName.  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, Isolate name alias and Project name.   Isolate name alias is a mandatory field for GenomeTrakr submissions.  Provide serovar when available. 

 
  

 

 

3.4. 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, Isolate source, Sequenced by and Source name/type.   Isolate name alias is a mandatory field for GenomeTrakr submissions.  Provide Geographical coordinates when available.  For human, animal, and plant hosts, include the full taxonomic name of the host when available, "Homo sapiens" or "Bos Taurus". Animal livestock terms are also acceptable entries, e.g. porcine, bovine, equine, etc.


 

   
3.5. NCBI submission settings – SRA Experiment and Run

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

 
  
 


    




4. NCBI submission settings – Submission Template

Save submission template according to PulseNet Instructions as -GenomeTrakr-Template-.
5. Import data
5.1. Import the GenomeTrakr Metadata form for BioNumerics  according to PulseNet Instructions. 
5.2. When importing rules, the field source should match destination fields. 
5.3. In the importing links section, choose the -key- for linking records to database entries. 
5.4. Proceed with sequencing data import according to PulseNet Instructions. 
5.5. 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. 
5.6. 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. 
2. The metadata fields created in Bionumerics will map metadata fields at NCBI.  Table 1 describes each of the fields submitted to NCBI along mapping against name of the fields in Bionumerics templates.