Releases: CFSAN-Biostatistics/One_Health_Enteric_Package
OHE Template v1.9
The following custom version of NCBI's One Health Enteric package for US genomic surveillance of foodborne pathogens includes several key modifications from NCBI's generic template:
Detailed Guidance: An "Instructions" tab provides detailed guidance for populating out each attribute. This guidance is tailored to support the missions of GenomeTrakr, PulseNet, NARMS, and Vet-LIRN laboratory networks, but is also general enough for broad adoption across the global enteric surveillance community. This tab also includes versioning information.
Custom Picklists for Attributes: The "UserEntry" template features custom picklists for nearly all attributes, facilitating more accurate and standardized data entry.
Full Package and Sub-Packages Downloads:
Users can download the complete package or sub-packages for each major sample type, including food products, food facilities, human/animal hosts, and environment/farm samples.
The v1.9 update of this package includes several picklist term updates, including:
- Requested updates to the entries in the collected_by and sequenced_by fields
- Improved legibility of collected_by and sequenced_by entries featuring a pipe ( | ).
- Addition of "sediment" and updated ENVO codes the picklist for env_medium.
- Addition and removal of some food_processing_method entries to improve coverage of methods and decrease confusion.
Full Package:
OneHealthEntericMetadata_v1.9.xlsx
Sub-packages:
OneHealthEntericMetadataHumanAnimalHost_v1.9.xlsx
OneHealthEntericMetadataFarmEnvironment_v1.9.xlsx
OneHealthEntericMetadataFoodFacility_v1.9.xlsx
OneHealthEntericMetadataFoodGroup_v1.9.xlsx
Validation: After populating one of the following templates, please validate your entries here, gmvs.fda.gov, before submitting them to NCBI BioSample.
OHE release v1.8
The following custom version of NCBI's One Health Enteric package for US genomic surveillance of foodborne pathogens includes several key modifications from NCBI's generic template:
Detailed Guidance: An "Instructions" tab provides detailed guidance for populating out each attribute. This guidance is tailored to support the missions of GenomeTrakr, PulseNet, NARMS, and Vet-LIRN laboratory networks, but is also general enough for broad adoption across the global enteric surveillance community. This tab also includes versioning information.
Custom Picklists for Attributes: The "UserEntry" template features custom picklists for nearly all attributes, facilitating more accurate and standardized data entry.
Full Package and Sub-Packages Downloads:
Users can download the complete package or sub-packages for each major sample type, including food products, food facilities, human/animal hosts, and environment/farm samples.
The v1.8 update of this package includes several picklist term updates.
Full Package:
OneHealthEntericMetadata-v1.8.xlsx
Sub-packages:
OneHealthEntericMetadataHumanAnimalHost-v1.8.xlsx
OneHealthEntericMetadataFarmEnvironment-v1.8.xlsx
OneHealthEntericMetadataFoodFacility-v1.8.xlsx
OneHealthEntericMetadataFoodGroup-v1.8.xlsx
Validation: After populating one of the following templates, please validate your entries here, gmvs.fda.gov, before submitting them to NCBI BioSample.
OHE package v1.7
The following custom version of NCBI's One Health Enteric package for US genomic surveillance of foodborne pathogens includes several key modifications from NCBI's generic template:
Detailed Guidance: An "Instructions" tab provides detailed guidance for populating out each attribute. This guidance is tailored to support the missions of GenomeTrakr, PulseNet, NARMS, and Vet-LIRN laboratory networks, but is also general enough for broad adoption across the global enteric surveillance community. This tab also includes versioning information.
Custom Picklists for Attributes: The "UserEntry" template features custom picklists for nearly all attributes, facilitating more accurate and standardized data entry.
Full Package and Sub-Packages Downloads:
Users can download the complete package or sub-packages for each major sample type, including food products, food facilities, human/animal hosts, and environment/farm samples.
The v1.7 update of this package includes
- Darker shaded color for mandatory / conditional mandatory fields
Full Package:
OneHealthEntericMetadataFull_v1.7.xlsx
Sub-packages:
OneHealthEntericMetadataFood_v1.7.xlsx
OneHealthEntericMetadataFoodFacility_v1.7.xlsx
OneHealthEntericMetadataHumanAnimalHost_v1.7.xlsx
OneHealthEntericMetadataFarmEnvironment_v1.7.xlsx
Validation: After populating one of the following templates, please validate your entries here, gmvs.fda.gov, before submitting them to NCBI BioSample.
OHE package v1.5
The following custom version of NCBI's One Health Enteric package for US genomic surveillance of foodborne pathogens includes several key modifications from NCBI's generic template:
-
Detailed Guidance: An "Instructions" tab provides detailed guidance for populating out each attribute. This guidance is tailored to support the missions of GenomeTrakr, PulseNet, NARMS, and Vet-LIRN laboratory networks, but is also general enough for broad adoption across the global enteric surveillance community. This tab also includes versioning information.
-
Custom Picklists for Attributes: The "UserEntry" template features custom picklists for nearly all attributes, facilitating more accurate and standardized data entry.
-
Full Package and Sub-Packages Downloads: Users can download the complete package or sub-packages for each major sample type, including food products, food facilities, human/animal hosts, and environment/farm samples.
The v1.5 update of this package includes excel formatting improvements, dynamic filtering for the FDA product code entries, allowance for manual entry of multiple terms, updates to the attribute descriptions, and a new "example" column to be populated in the next release.
Full Package:
OneHealthEntericMetadata_v1.5.xlsx
Sub-packages:
OneHealthEntericMetadataFoodGroup_v1.5.xlsx
OneHealthEntericMetadataFoodFacility_v1.5.xlsx
OneHealthEntericMetadataHumanAnimalHost_v1.5.xlsx
OneHealthEntericMetadataFarmEnvironment_v1.5.xlsx
Validation: After populating one of the following templates, please validate your entries here, gmvs.fda.gov, before submitting them to NCBI BioSample.
OHE package v1.4
The following custom version of NCBI's One Health Enteric package for US genomic surveillance of foodborne pathogens includes several key modifications from NCBI's generic template:
1. Detailed Guidance: An "Instructions" tab provides detailed guidance for populating out each attribute. This guidance is tailored to support the missions of GenomeTrakr, PulseNet, NARMS, and Vet-LIRN laboratory networks, but is also general enough for broad adoption across the global enteric surveillance community. This tab also includes versioning information.
2. Custom Picklists for Attributes: The "UserEntry" template features custom picklists for nearly all attributes, facilitating more accurate and standardized data entry.
3. Full Package and Sub-Packages Downloads: Users can download the complete package or sub-packages for each major sample type, including food products, food facilities, human/animal hosts, and environment/farm samples.
The v1.4 update of this package includes minor updates to picklists and attribute descriptions, enhancing the usability and accuracy of the template for data entry and reporting.
Full Package:
OneHealthEntericMetadata_v1.4.xlsx
Sub-packages:
OneHealthEntericMetadataHumanAnimalHost_1.4.xlsx
OneHealthEntericMetadataFarmEnvironment_v1.4.xlsx
OneHealthEntericMetadataFoodFacility_v1.4.xlsx
OneHealthEntericMetadataFoodGroup_v1.4.xlsx
Validation: After populating one of the following templates, please validate your entries here, gmvs.fda.gov, before submitting them to NCBI BioSample.
OHE package v1.3
The following custom version of NCBI's One Health Enteric package for US genomic surveillance of foodborne pathogens includes several key modifications from NCBI's generic template:
-
Detailed Guidance: An "Instructions" tab provides detailed guidance for populating out each attribute. This guidance is tailored to support the missions of GenomeTrakr, PulseNet, NARMS, and Vet-LIRN laboratory networks, but is also general enough for broad adoption across the global enteric surveillance community. This tab also includes versioning information.
-
Custom Picklists for Attributes: The "UserEntry" template features custom picklists for nearly all attributes, facilitating more accurate and standardized data entry.
-
Full Package and Sub-Packages Downloads: Users can download the complete package or sub-packages for each major sample type, including food products, food facilities, human/animal hosts, and environment/farm samples.
The v1.3 update of this package includes performance updates and minor modifications to picklists and attribute descriptions, enhancing the usability and accuracy of the template for data entry and reporting.
Full Package:
OneHealthEntericMetadata_v1.3.xlsx
Sub-packages:
- OneHealthEntericMetadataFoodGroup_v1.3.xlsx
- OneHealthEntericMetadataFoodFacility_v1.3.xlsx
- OneHealthEntericMetadataFarmEnvironment_v1.3.xlsx
- OneHealthEntericMetadataHumanAnimalHost_v1.3.xlsx
Validation: After populating one of the following templates, please validate your entries here, gmvs.fda.gov, before submitting them to NCBI BioSample.
OHE package v1.1
This is a custom version of NCBI's One Health Enteric package for US surveillance of foodborne pathogens.
The templates available here include the following modifications from NCBI's generic template:
- A tab with detailed guidance for populating each attribute, targeting GenomeTrakr, PulseNet, NARMS, and Vet-LIRN laboratories, but general enough for broad adoption across the global enteric surveillance community.
- Custom picklists included for nearly all attributes
- Full package and sub-packages for each major sample type available for download (food products, food facilities, human/animal, and environment/farm).
v1.1 update includes minor modifications to picklists and attribute descriptions:
Full Package:
OneHealthEntericMetadata_v1.1.xlsx
Sub-packages:
OneHealthEntericMetadataHumanAnimalHost_v1.1.xlsx
OneHealthEntericMetadataFoodProducts_v1.1.xlsx
OneHealthEntericMetadataFoodFacility_v1.1.xlsx
OneHealthEntericMetadataFarmEnvironment_v1.1.xlsx
OHE package v1.0.0
This is the first custom "implementation release" of NCBI's One Health Enteric package for US surveillance of foodborne pathogens. The templates included here include the following modifications from NCBI's generic template:
- A tab with detailed guidance for populating each attribute, targeting GenomeTrakr, PulseNet, NARMS, and Vet-LIRN laboratories, but general enough for broad adoption across the enteric surveillance community.
- Picklists included for nearly all attributes
- Full package and sub-packages for each major sample type available for download (food, food facilities, human/animal, and environment/farm).
v1.0.0 templates
After populating one of the above templates, please validate your entries here, gmvs.fda.gov, before submitting them to NCBI BioSample.
metadata package v0.9
Version 0.9 of the One Health Enteric-compatible genomic metadata package including a detailed reference guide, an empty template and real use cases