GenFS Metadata Cleanup Challenge protocol V.7

• The primary focus is on submissions made between September 2024 and August 2025.
• Laboratories may include submissions outside this timeframe if doing so improves metadata completeness or consistency.

• source_type ​
• collected_by
• sequenced_by
• project_name ​
• purpose_of_sampling
• isolation_source
• host (human and animal isolates only) 
• food_origin (food isolates only) 

• Example:

• The downloaded file will be a comma-delimited txt file containing both BioSample and SRA metadata.

• Remove all metadata columns that are not relevant for this exercise.
• Move the BioSample accession column to be the first column.
• Save the file and proceed with metadata updates.

For guidance on which columns to retain, refer to the example template: Example_Template.xlsx150.8KB

• Submit one bulk update file per:
• laboratory, or
• laboratory + organism, or
• another logical aggregation agreed upon in advance.

• The first row must contain the column headers.
• Each subsequent row must represent exactly one BioSample and its associated updatable attributes.
• All rows must contain the same number of columns.

• Column headers must correspond to attribute names included in the One Health Enteric package (either full attribute names or harmonized names).
• The first column must contain the BioSample accession (e.g. SAMN123456789)

• The update file must be a tab-delimited text file with a .tsv or .txt file extension.
• If you use Microsoft Excel for editing, export the final file in tab-delimited format.
• Verify that date fields are correctly exported and retain the intended format.

• Blank field in update file (with existing value in NCBI) → existing value will be replaced with NULL.
• Field already correct in NCBI → populate the field with its current value to prevent changes.
• Field not currently present in NCBI → value will be added.
• Blank field for a non-existent attribute → attribute will not be added.

• collected_by
• geo_loc_name
• food_origin
• host
• project_name
• sequenced_by
• source_type
• isolation_source
• collection_date
• purpose_of_sampling
• env_local_scale
• env_medium
• animal_env
• env_broad_scale
• facility_type
• intended_consumer
• food_type_processed
• food_processing_method

• biosample_acc/BioSample – This is the primary key of the entire BioSample system - Keep this accession in the first column, but DO NOT EDIT OR UPDATE ENTRIES.
• bioproject_acc/BioProject - changes to linked bioProject, linked SRA, or linked Assembly.
• strain or isolate
• sample_name
• attribute package – This requires validation of all the fields together. 
• center name – This is a property of SRA and cannot be changed using the bulk update channel.
• organism - Change to the BioSample species (the identification of the isolate). 
• Salmonella serovar/serotype  - changes to organism species or sub-species names (ex Salmonella enterica => Salmonella enterica subsp. enterica serovar Infantis)
• Any kind of SRA to BioSample, BioSample to BioProject, or SRA to BioProject mapping. 
• Any of the computed fields in Pathogen Detection (epi_type, min_same, min_diff, computed_types, or amr/virulence analysis outputs). These attributes cannot be updated by the record owner.

• human
• animal
• food
• environmental
• other
• Not Applicable
• Not Collected
• Not Provided
• Missing
• Restricted Access

• GenomeTrakr
• GenomeTrakr; LFFM-FY1
• GenomeTrakr; LFFM-FY2
• GenomeTrakr; LFFM-FY3
• GenomeTrakr; LFFM-FY4
• GenomeTrakr; LFFM-FY5
• GenomeTrakr; LFFM-FY6
• NARMS
• NARMS Cecal
• NARMS Retail Meat
• PulseNet
• USDA-FSIS
• Vet-LIRN
• NAHLN

• If an isolate belongs to more than one project or network, include all applicable terms.
• Separate multiple values using a semicolon followed by a space, example: GenomeTrakr; USDA-ARS

Adding new project_name terms

• If your isolate is associated with a project or network not listed above, you may:
• Enter a new term directly into the update template, and
• Request that the term be added to the official picklist by emailing: [email protected]
• Newly requested terms will be reviewed and added in the next picklist update, as appropriate.

• Use only values from the One Health Enteric package picklist.
• Enter one value per record.
• Do not use free text, abbreviations, or alternate spellings.

Allowed values (controlled vocabulary)

• Use standardized laboratory names consistently across all records.
• For sequenced_by select the laboratory name exactly as listed in the current One Health Enteric package picklist.
• Do not use abbreviations, alternate spellings, or free-text variations.

Updating laboratory names

• Email the corrected or preferred laboratory name to: [email protected]
• The GenomeTrakr team will update the picklist to reflect the change in a future release.

• host: Required for isolates derived from human or animal samples.
• food_origin: Required for isolates derived from food products or other commercial products sampled for pathogens, including (but not limited to): foods, medical products, cosmetics, tatoo ink, etc.

1. Filter for human and animal records → populate host
2. Filter for food records → populate food_origin

• Filter for source_type = human or animal in Excel.
• Do not populate host for non–host-associated sample types.

How to determine the host value

• Use the isolation_source column to inform the appropriate host entry.
• Enter the scientific (binomial) name whenever possible, examples: Homo sapiens, Bos taurus

• If the scientific name is unknown, enter a common name recognized by the NCBI taxonomy database examples: porcine, bovine

Unknown host

• Not Applicable
• Not Collected
• Not Provided
• Missing
• Restricted Access

• Sort or filter the dataset using the source_type column.
• Select records where source_type = food.

• geo_loc_name – Location where the sample was physically collected (e.g., U.S. state, port of entry, retail location)
• food_origin – Geographic origin of the food or product sampled (e.g., country or state where the product was produced)

• Move that geographic value to food_origin
• Update geo_loc_name to reflect the actual collection location, if known

• Leave geo_loc_name unchanged
• Populate food_origin with the country or state of origin, if known

• animal_env picklist:

• intended_consumer picklist:

• food_processing_method picklist

• facility_type picklist:

• food_type_processed picklist:

• env_broad_scale picklist:

• env_local_scale picklist:

• env_medium picklist:

• Remove all the non-required columns that are not being updated.
• Ensure the following columns are retained: BioSample accession (must be Column 1) and strain (retain for tracking and reconciliation)

• Save the final file as a tab-delimited text file with a .tsv extension
• Confirm that formatting (especially date fields) is preserved correctly after export.

• Confirmation that the update file has been submitted
• The exact filename of the uploaded .tsv file

Optional: Metadata office hours support

• Bring your draft or finalized template to the February 11, 2026 GenomeTrakr Metadata Office Hours.
• GenomeTrakr staff will be available to assist with questions or required clarifications prior to submission.