Step-by-Step Guide

Step 1: Select a Sample Checklist

BioSamples uses Sample Checklists to ensure that each sample is registered with at least a minimum amount of metadata. For more information, see the BioSamples Metadata Model page.

Note

Please note that registering a BioSample with an ENA checklist is a requirement for submitting data referencing this sample in ENA.

Select either the BioSamples Minimal Checklist (tsv) (json), or select a Sample Checklist from the collection of ENA GSC-based Sample Checklists and make a note of the mandatory, recommended, and optional fields.

Step 2: Download a Template Spreadsheet

BioSamples provides a number of template spreadsheets corresponding to the most commonly used Sample Checklists. Please find the tsv template spreadsheets here. If your selected Sample Checklist from Step 1 is not present, you will have to create your own template for your checklist.

Step 3: Complete the Template Spreadsheet

The file format for uploading sample metadata to BioSamples is ISA-Tab, a tab delimited file format (TSV). Although ISA-Tab is specifically for Investigation, Study and Assay data, we have tried to use the sample table format specified in the ISA-Tab specification.

1. ISA-TAB requires columns to be in a specific order to be successfully validated and processed.

2. Every Characteristics you select as a column header in the TSV file must have Term Source Ref and Term Accession Number column headers following it. While filling up the data (rows) in the file, you may choose to provide blank values if you don’t have the information for it. In the below example, you can always opt to not provide the Term Source Ref and Term Accession Number but the column headers must be present as in the example below.

3. Be aware that if you are not specifying any values for Term Source Ref or Term Accession Number, the tab delimiter must still be provided. This allows for proper parsing of the files.

4. We expect all sample names to be unique in the file.

Example Characteristic

Characteristics[Organism]	Term Source REF	Term Accession Number	unit
Marine metagenome	NCBITAXON	http://purl.obolibrary.org/obo/NCBITaxon_408172

Table 1. TSV file columns (BioSamples drag’n’drop uploader)

Column	Description	Mandatory? (Column)	Mandatory? (Value)
Source Name	Name/ID of investigation, study, assay, project, donor, or sample. Required by ISA-Tab; BioSamples ignores its value.	Mandatory	Optional
Sample Name	Unique name of the sample within the uploaded TSV.	Mandatory	Mandatory
Release Date	The public release date of the sample.	Mandatory	Mandatory
Characteristics[<name>]	Sample attributes. You may include multiple characteristics. Each Characteristics column must be followed by matching Term Source REF and Term Accession Number columns. Characteristics[Organism] is mandatory, and its value must be valid.	Optional (repeating); Characteristics[Organism] is Mandatory and its value must be valid against NCBI Taxonomy	Optional; for Characteristics[Organism] the value is Mandatory
Term Source REF	Controlled vocabulary/ontology providing the term (e.g. NCBITAXON, BTO). Must follow each Characteristics column.	Mandatory	Optional
Term Accession Number	Accession/ID from the Term Source (e.g. NCBITaxon_9606 for Homo sapiens).	Mandatory	Optional
Comment[bsd_relationship:<relationship_type>]	Sample Relationships in BioSamples between samples (by sample name if within the same file, or by accession if already in BioSamples).	Optional	Optional
Comment[external DB REF]	Reference to this sample in another database.	Optional	Optional
Comment[submission_contact:name]	Submitter’s name(s).	Optional	Optional
Comment[submission_contact:email]	Submitter’s email address.	Optional	Optional* (if providing contact info, the email is required)
Comment[submission_contact:affiliation]	Submitter’s affiliation.	Optional	Optional
Comment[submission_contact:role]	Submitter’s role.	Optional	Optional
Comment[submission_contact:url]	Submitter’s URL.	Optional	Optional
Comment[publication:doi]	Publication DOI.	Optional	Optional
Comment[publication:pubmed_id]	PubMed ID.	Optional	Optional
Comment[submission_organization:email]	Email address of the submitting organization.	Optional	Optional* (if providing organization info, the organization name is required)
Comment[submission_organization:name]	Name of the submitting organization.	Optional	Optional
Comment[submission_organization:address]	Address of the submitting organization.	Optional	Optional
Comment[submission_organization:role]	Role of the submitting organization.	Optional	Optional
Comment[submission_organization:url]	URL of the submitting organization.	Optional	Optional
Sample Identifier	Sample ID/accession. Optional for new submissions; mandatory when updating existing samples.	Optional (new) / Mandatory (updates)	Optional (new) / Mandatory (updates)

Table 2. Example File

Source Name	Sample Name	Release Date	Characteristics[Organism]	Term Source REF	Term Accession Number	Comment[bsd_relationship:same_as]	Comment[external DB REF]	Comment[submission_contact:email]
source_name	name_1	2021-01-01	Homo sapiens	NCBITAXON	http://purl.obolibrary.org/obo/NCBITaxon_9606	name_2	https://www.ebi.ac.uk/ena/browser/view/SAMEA100000	dgupta@ebi.ac.uk
source_name	name_2	2021-01-01	Homo sapiens	NCBITAXON	http://purl.obolibrary.org/obo/NCBITaxon_9606	name_1	https://www.ebi.ac.uk/ena/browser/view/SAMEA100001	dgupta@ebi.ac.uk

After upload is successful, the uploader will send back a file with the sample metadata uploaded and the accessions. The accessions are defined by the Sample Identifier field in the TSV post upload.

Table 3. Example Output File

Source Name	Sample Name	Release Date	Characteristics[Organism]	Term Source REF	Term Accession Number	Comment[bsd_relationship:same_as]	Comment[external DB REF]	Comment[submission_contact:email]	Sample Identifier
source_name	name_1	2021-01-01	Homo sapiens	NCBITAXON	http://purl.obolibrary.org/obo/NCBITaxon_9606	name_2	https://www.ebi.ac.uk/ena/browser/view/SAMEA100000	dgupta@ebi.ac.uk	SAMEA100033
source_name	name_2	2021-01-01	Homo sapiens	NCBITAXON	http://purl.obolibrary.org/obo/NCBITaxon_9606	name_1	https://www.ebi.ac.uk/ena/browser/view/SAMEA100001	dgupta@ebi.ac.uk	SAMEA100034

Step 4: Submit the Completed Spreadsheet

1. After completing the template spreadsheet with the appropriate metadata, login to BioSamples at the drag’n’drop interface with your Webin credentials. See Registering a WEBIN Submission Account for more details.

2. Select the appropriate checklist for validation from the dropdown list, and then upload your completed spreadsheet.

3. The uploader sends back a file for download with the submission result. In the case of same time uploads where the file size is less than 20 KB and the file has less than 200 samples, the result file will have the sample metadata and the accessions. In case of queued uploads where the file size is greater than 20 KB or the file has more than 200 samples, this will take longer and the result file will have a unique submission ID for the upload. The unique submission ID can be used to get the result of the upload using the View Submissions tab.

4. If you are looking to update existing samples that have been uploaded, you can use the file returned to you after your submission. Please remember to remove the receipt section.