TITLE: Populating metadata templates for NCBI submissions using  PulseNet 2.0
AUTHORS: Ruth Timme, Maria Balkey, Tina Lusk Pfefer, Candace Hope Bias

[DESCRIPTION]
PURPOSE: to define the standard operating procedure for collecting isolate metadata using PulseNet 2.0 for submission of food/environmental isolates to NCBI.

SCOPE: to provide a standardized procedure to collect isolate metadata using PulseNet 2.0 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 PulseNet 2.0 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. 
V5: Changes implemented to handle NCBI submissions for GenomeTrakr through the PulseNet 2.0 platform. 



[STEPS]
2. Metadata SampleSheet preparation 

Populate the metadata spreadsheet form before uploading your sequencing run or linking NCBI sequencing records within PulseNet 2.0. 

Please download the following metadata template, Guidance is included in the first tab. 

  

Once you have filled out the template, import metadata according PulseNet Instructions
 
    
4. NCBI Submissions

Submit data to NCBI according to PulseNet Instructions, if you have several submissions from different sample types, make sure to group records accordingly and select the appropriate custom NCBI GenomeTrakr-labeled Template. If NCBI accessions are not available at PulseNet 2.0 in 1 business day, please contact NCBI (pd-help@ncbi.nlm.nih.gov) 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. 
3. Creation of NCBI Submission Templates

Before submitting data to NCBI, set up sample specific submission templates in PulseNet 2.0 according to PulseNet Instructions, following GenomeTrakr mapping guidelines included in this protocol. 

Map each field name to the corresponding field value as described in steps 
 for Food isolates
 for Food Facility inspection isolates
 for Animal isolates
 for Farm or other environmental isolates.  

Make sure to add the the GenomeTrakr-required fields to each template depending on the source type designation, using the Add Field functionality in the Pipeline Template section.  

The creation of NCBI Submission Templates in PulseNet 2.0 will only be done once, then the saved templates can be used for all future submissions.  
3.1. NCBI Template for Food Isolates 
 
  
 Save submission template according to PulseNet Instructions as -GenomeTrakr-FoodGroup-.

 
3.2.  NCBI Template for Food Facility Environment Isolates
 
Save submission template according to PulseNet Instructions as 
-GenomeTrakr-FoodFacilityEnvironment-.
3.3. NCBI Template for Animal Isolates
 
 
 Save submission template according to PulseNet Instructions as -GenomeTrakr-AnimalHost-.
3.4.  NCBI Template for Farm Environment Isolates
 
 
 
 Save submission template according to PulseNet Instructions as -GenomeTrakr-FarmEnvironment-.
1. Data Ownership
Laboratory scientists that use PN2.0 to submit GenomeTrakr data to NCBI should be included in the PulseNet NCBI submission group. 

Please reach out to PulseNet to ensure your name is included in this group. 

Membership in the PulseNet submission group will grant you the correct privileges for viewing and managing your GenomeTrakr submissions within the NCBI submission portal.  If you login to NCBI and *don't* see your GenomeTrakr submissions, you likely not a member.