Nov 20, 2024
Version 3
Populating metadata templates for NCBI submissions using PulseNet 2.0 V.3
- Ruth Timme1,
- Maria Balkey1,
- Tina Pfefer1,
- Candace Hope Bias2
- 1US Food and Drug Administration;
- 2US FDA-CFSAN
- GenomeTrakrTech. support email: genomeTrakr@fda.hhs.gov
Protocol Citation: Ruth Timme, Maria Balkey, Tina Pfefer, Candace Hope Bias 2024. Populating metadata templates for NCBI submissions using PulseNet 2.0. protocols.io https://dx.doi.org/10.17504/protocols.io.3byl4qn4ovo5/v3Version created by Maria Balkey
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: February 09, 2024
Last Modified: November 20, 2024
Protocol Integer ID: 109475
Keywords: NCBI submission, biosample, SRA, metadata, bioproject, PulseNet, PulseNet 2.0
Abstract
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.
V6: New version of spreadsheet with updated dropdown menu. Add values to NCBI Templates
Safety warnings
We will be updating this protocol with each new PulseNet 2.0 upgrade that impacts NCBI submissions
Data Ownership
Laboratory scientists that use PN2.0 to submit GenomeTrakr data to NCBI shall 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.
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.
OneHealthEntericMetadataPN.xlsx153KB Once you have filled out the template, import metadata according PulseNet Instructions
Note
In order to access PulseNet Instructions, make sure you have successfully logged in at the SAMS Partner Portal.
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
go to step #3.1 for Food isolates
go to step #3.2 for Food Facility inspection isolates
go to step #3.3 for Animal isolates
go to step #3.4 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.
NCBI Template for Food Isolates
If the Strain name is mapped to the WGS_id, ensure the Submitter Provided Unique ID is mapped to the key.
If the Strain name is mapped to the key, ensure the Submitter Provided Unique ID is mapped to the WGS_id.
| A | B | C | |
| Field Name | Field Type | Field Value | |
| Strain name | Mapping | WGS_id OR Key | |
| Sample name | Mapping | Key | |
| Submitter Provided Unique ID | Mapping | WGS_id OR Key | |
| SPUID namespace | Value | GenomeTrakr | |
| BioProject accession | Mapping | BioProject | |
| Author | Mapping | Sequenced_by | |
| Serovar | Mapping | Serotype_wgs | |
| SourceType | Mapping | SourceType | |
| Isolate Name Alias if SourceType equals Human | Value | missing | |
| Isolate Name Alias if SourceType does not equal Human | Mapping | Key | |
| Isolation source if SourceType does not equal Human | Mapping | SourceSite, TypeDetails | |
| Isolation source if SourceType equals Human | Value | missing | |
| Geographical origin if SourceType equals Human | Value | missing | |
| Geographical origin if SourceType does not equal Human | Mapping | Geo_loc_name | |
| Organism name | Mapping | Genus, Species | |
| Collection / isolation date if SourceType equals Human | Value | missing | |
| Collection / isolation date if SourceType does not equal Human | Mapping | IsolatDate YYYY-mm-DD | |
| Collected by if SourceType equals Human | Value | missing | |
| Collected by if SourceType does not equal Human | Mapping | Collected_By | |
| Instrument model | Mapping | Instrument_Model | |
| Library strategy | Value | WGS | |
| Library source | Value | GENOMIC | |
| Library selection | Value | RANDOM | |
| Library layout | Value | PAIRED | |
| Library name | Mapping | Library | |
| Project name | Mapping | Project | |
| Sequenced by if SourceType equals Human | Value | missing | |
| Sequenced by if SourceType does not equal Human | Mapping | Sequenced_by | |
| ADD FIELD… | |||
| intended consumer | Mapping | Intended_consumer | |
| food product origin geographic location | Mapping | Food_origin | |
| food processing method | Mapping | Food_processing_method | |
| purpose of sampling | Mapping | Purpose_of_sampling |
NCBI Template for Food Facility Environment Isolates
If the Strain name is mapped to the WGS_id, ensure the Submitter Provided Unique ID is mapped to the key.
If the Strain name is mapped to the key, ensure the Submitter Provided Unique ID is mapped to the WGS_id.
| A | B | C | |
| Field Name | Field Type | Field Value | |
| Strain name | Mapping | WGS_id OR Key | |
| Sample name | Mapping | Key | |
| Submitter Provided Unique ID | Mapping | WGS_id OR Key | |
| SPUID namespace | Value | GenomeTrakr | |
| BioProject accession | Mapping | BioProject | |
| Author | Mapping | Sequenced_by | |
| Serovar | Mapping | Serotype_wgs | |
| SourceType | Mapping | SourceType | |
| Isolate Name Alias if SourceType equals Human | Value | missing | |
| Isolate Name Alias if SourceType does not equal Human | Mapping | Key | |
| Isolation source if SourceType does not equal Human | Mapping | SourceSite, TypeDetails | |
| Isolation source if SourceType equals Human | Value | missing | |
| Geographical origin if SourceType equals Human | Value | missing | |
| Geographical origin if SourceType does not equal Human | Mapping | Geo_loc_name | |
| Organism name | Mapping | Genus, Species | |
| Collection / isolation date if SourceType equals Human | Value | missing | |
| Collection / isolation date if SourceType does not equal Human | Mapping | IsolatDate YYYY-mm-DD | |
| Collected by if SourceType equals Human | Value | missing | |
| Collected by if SourceType does not equal Human | Mapping | Collected_By | |
| Instrument model | Mapping | Instrument_Model | |
| Library strategy | Value | WGS | |
| Library source | Value | GENOMIC | |
| Library selection | Value | RANDOM | |
| Library layout | Value | PAIRED | |
| Library name | Mapping | Library | |
| Project name | Mapping | Project | |
| Sequenced by if SourceType equals Human | Value | missing | |
| Sequenced by if SourceType does not equal Human | Mapping | Sequenced_by | |
| ADD FIELD… | |||
| facility type | Mapping | Facility_type | |
| food type processed in facility | Mapping | Food_type_processed | |
| purpose of sampling | Mapping | Purpose_of_sampling |
-GenomeTrakr-FoodFacilityEnvironment-.
NCBI Template for Animal Isolates
If the Strain name is mapped to the WGS_id, ensure the Submitter Provided Unique ID is mapped to the key.
If the Strain name is mapped to the key, ensure the Submitter Provided Unique ID is mapped to the WGS_id.
| A | B | C | |
| Field Name | Field Type | Field Value | |
| Strain name | Mapping | WGS_id OR Key | |
| Sample name | Mapping | Key | |
| Submitter Provided Unique ID | Mapping | WGS_id OR Key | |
| SPUID namespace | Value | GenomeTrakr | |
| BioProject accession | Mapping | BioProject | |
| Author | Mapping | Sequenced_by | |
| Serovar | Mapping | Serotype_wgs | |
| SourceType | Mapping | SourceType | |
| Isolate Name Alias if SourceType equals Human | Value | missing | |
| Isolate Name Alias if SourceType does not equal Human | Mapping | Key | |
| Isolation source if SourceType does not equal Human | Mapping | SourceSite, TypeDetails | |
| Isolation source if SourceType equals Human | Value | missing | |
| Geographical origin if SourceType equals Human | Value | missing | |
| Geographical origin if SourceType does not equal Human | Mapping | Geo_loc_name | |
| Organism name | Mapping | Genus, Species | |
| Collection / isolation date if SourceType equals Human | Value | missing | |
| Collection / isolation date if SourceType does not equal Human | Mapping | IsolatDate YYYY-mm-DD | |
| Collected by if SourceType equals Human | Value | missing | |
| Collected by if SourceType does not equal Human | Mapping | Collected_By | |
| Instrument model | Mapping | Instrument_Model | |
| Library strategy | Value | WGS | |
| Library source | Value | GENOMIC | |
| Library selection | Value | RANDOM | |
| Library layout | Value | PAIRED | |
| Library name | Mapping | Library | |
| Project name | Mapping | Project | |
| Sequenced by if SourceType equals Human | Value | missing | |
| Sequenced by if SourceType does not equal Human | Mapping | Sequenced_by | |
| ADD FIELD… | |||
| host | Mapping | Host | |
| animal environment | Mapping | Animal_env | |
| purpose of sampling | Mapping | Purpose_of_sampling |
NCBI Template for Farm Environment Isolates
If the Strain name is mapped to the WGS_id, ensure the Submitter Provided Unique ID is mapped to the key.
If the Strain name is mapped to the key, ensure the Submitter Provided Unique ID is mapped to the WGS_id.
| A | B | C | |
| Field Name | Field Type | Field Value | |
| Strain name | Mapping | WGS_id OR Key | |
| Sample name | Mapping | Key | |
| Submitter Provided Unique ID | Mapping | WGS_id OR Key | |
| SPUID namespace | Value | GenomeTrakr | |
| BioProject accession | Mapping | BioProject | |
| Author | Mapping | Sequenced_by | |
| Serovar | Mapping | Serotype_wgs | |
| SourceType | Mapping | SourceType | |
| Isolate Name Alias if SourceType equals Human | Value | missing | |
| Isolate Name Alias if SourceType does not equal Human | Mapping | Key | |
| Isolation source if SourceType does not equal Human | Mapping | SourceSite, TypeDetails | |
| Isolation source if SourceType equals Human | Value | missing | |
| Geographical origin if SourceType equals Human | Value | missing | |
| Geographical origin if SourceType does not equal Human | Mapping | Geo_loc_name | |
| Organism name | Mapping | Genus, Species | |
| Collection / isolation date if SourceType equals Human | Value | missing | |
| Collection / isolation date if SourceType does not equal Human | Mapping | IsolatDate YYYY-mm-DD | |
| Collected by if SourceType equals Human | Value | missing | |
| Collected by if SourceType does not equal Human | Mapping | Collected_By | |
| Instrument model | Mapping | Instrument_Model | |
| Library strategy | Value | WGS | |
| Library source | Value | GENOMIC | |
| Library selection | Value | RANDOM | |
| Library layout | Value | PAIRED | |
| Library name | Mapping | Library | |
| Project name | Mapping | Project | |
| Sequenced by if SourceType equals Human | Value | missing | |
| Sequenced by if SourceType does not equal Human | Mapping | Sequenced_by | |
| ADD FIELD… | |||
| local-scale environmental context | Mapping | Env_local_scale | |
| environmental medium | Mapping | Env_medium | |
| purpose of sampling | Mapping | Purpose_of_sampling |
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.