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BioData Science Initiative

BioSample

Last updated 2026/06/29Edit

BioSample is DDBJ's central database for descriptive metadata of biological source materials used to generate experimental data, shared across the INSDC.

What is BioSample

BioSample is a central database that captures descriptive information about the biological source materials (samples) used to generate experimental data registered in DDBJ's primary databases. Records are bidirectionally mirrored across the three INSDC sites (DDBJ / EBI / NCBI); submitting at one site makes the record available at the others.

It sits alongside BioProject as a parallel metadata layer that the underlying experimental data (DRA / GEA / MetaboBank / DDBJ Sequence) reference.

NOTE

If you are not sure which service fits your study, narrow it down with the flowchart-style Submit Navigator.

Data accepted

What you submit is the descriptive information (attribute metadata) of the sample itself. Sequence data and experimental files are not registered in BioSample; they go to DRA / GEA / MetaboBank / DDBJ Sequence.

Sample typeExample
Individual organismindividual organism
Tissueprimary tissue biopsy
Cultured cellscell line
Environmental sampleenvironmental isolate

The organism name must be an NCBI Taxonomy scientific name at species rank or below. If the organism is not yet registered, enter the proposed name and DDBJ staff will mediate its registration.

INSDC rules make collection location (geo_loc_name, at minimum country or ocean) and collection date (collection_date, at minimum year) mandatory. If you cannot provide a value, you must follow the INSDC missing value reporting standard and record an appropriate reporting-level term (e.g. not collected, restricted access: human-identifiable). Blank values are not accepted.

Accession numbers

TypePrefixExampleDescription
Submission ID (temporary)SSUBSSUB000001Auto-assigned when a new submission is created. Do not cite in publications
Sample accessionSAMDSAMD00000001One per sample. Issued automatically after validation passes

When a submission contains an unregistered organism name or a locus_tag_prefix, SAMD is issued after curator review. Within the INSDC, DDBJ uses the SAMD prefix, NCBI uses SAMN, and EBI uses SAMEA.

WARNING

SSUB is an internal temporary ID. Always cite the SAMD accession in publications and public materials.

Packages and attributes

In BioSample you choose one package that matches your sample type, and that choice fixes the set of attributes you need to fill in. Samples that belong to different packages cannot be mixed within a single submission.

CategoryMain packages
StandardSARS-CoV-2 (clinical / wastewater) / Microbe / Model organism or animal / Metagenome or environmental / Invertebrate / Human / Plant / Virus / Beta-lactamase / Omics
Pathogenclinical or host-associated / environmental, food or other
MIxS compliantMIGS.ba / MIGS.eu / MIGS.vi / MIMS.me / MIMAG / MISAG / MIMARKS.specimen / MIMARKS.survey / MIUVIG
Environmental (MIxS env)soil / water / sediment / air / built / wastewater / host-associated / human-gut / plant-associated / hydrocarbon resources and others

The attribute file is a tab-separated text file: row 1 holds attribute names, and each subsequent row describes one sample. The required-field flags mean:

FlagMeaning
*Required attribute
**nAt least one attribute in group n is required

Download the attribute file template from the package definition and fill it in. You cannot submit until all validation errors are resolved.

Submission flow

  1. Obtain an account — Issue a D-way submission account.
  2. Create a new submission — In D-way, choose BioSample and click [New submission] to obtain an SSUB.
  3. Enter Submitter / General info — Enter submitter, affiliated organization, name, and an organization-domain email address in English.
  4. Select a package — Pick one that matches the sample type (no mixing).
  5. Build and upload the attribute file — Download the template, fill it in as tab-separated text, and upload it.
  6. Validate — You cannot submit until every error is resolved.
  7. Review & Submit — Review on the OVERVIEW tab and submit.
  8. Curation (when needed) — Submissions containing unregistered organisms or a locus_tag_prefix go through staff review.
  9. SAMD issued — You are notified by email.
  10. Release / Hold — Public release is coupled to the release of the underlying data (see below).

IMPORTANT

A single submission can contain at most 1,000 samples. Split your submissions if you have more.

Prerequisites

  • A DDBJ submission account (D-way submission account)
  • An organization-domain email address (free webmail addresses are not accepted)
  • Submitter first / last name and full organization name (in English)
  • One package chosen for the sample type (no mixing)
  • The attribute tab-separated text file (built from the package template)
  • Required attributes: organism (NCBI Taxonomy scientific name) / collection_date / geo_loc_name, plus any others required by the chosen package
  • If you plan to register a genome sequence to DDBJ Sequence, include the desired locus_tag_prefix (staff will reserve it with NCBI)

INSDC sharing and the release chain

BioSample is INSDC-mirrored metadata that is intended to become public. Samples that need controlled access at the human-individual level are handled by JGA and must not be registered to BioSample.

The release trigger behaves the same way as BioProject:

  • Releasing a BioProject or BioSample on its own does not release any underlying data.
  • Releasing a record in DDBJ Sequence / DRA / GEA / MetaboBank automatically releases the linked BioProject and BioSample.
  • When a BioSample is released, any upstream BioSample referenced via the derived_from attribute is released along with it.

WARNING

BioSample is a public-by-design database. If your samples need controlled access at the human-individual level, use JGA instead.

Post-submission updates

Attribute updates and withdrawals of existing records are handled on a request basis with the BioSample team. Reply to the email that delivered your SAMD accession to send the update request.