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Accesskeys

Guidance on submitting data relevant to Public Health

Data submission overview

To ensure sequences relevant to public health are findable, accessible, interoperable, and reusable (FAIR) and to provide a consistent and transparent data structure for downstream analyses, they should have a BioProject (BP), BioSample (BS), and SRA and/or GenBank accessions (Fig. 1 below, Timme et al. 2023). This document provides an overview of the submissions needed at NCBI to create this data structure. If you have sequencing data relevant to public health, such as those from public health surveillance efforts:

Figure 1. The record structure you'll create when submitting your data.
A BioProject is an organizational "container" that groups all related data from a research or surveillance project. A BioProject record is a single web page in the BioProject database accessible through a stable, accession-based link (URL). The record contains information about the research initiative, its objective and scope, and other metadata such as submitting organization, and grant information. Moreover, it provides a single location to access all linked data stored across NCBI databases, such as one or more BioSample records, Sequence Read Archive (SRA) data, and genome assemblies.
A BioSample record contains descriptions of biological source materials used in sequencing. Each BioSample is linked to Sequence Read archive (SRA) for unassembled sequence reads and/or GenBank for assembled sequences.
Stable accession numbers assigned to each type of record allow for persistent links between the data, supporting data organization, discovery, and retrieval.

  • BioProject

    PRJNA######

    BioProject
    • Objective and scope
    • Submitting organization
    • Grant information
    • Data links

  • BioSample

    SAMN######

    BioSample
    • Organism name
    • Sample attributes

  • SRA

    SRR######

    SRA
    • Unassembled sequence reads
    • Additional metadata

  • GenBank

    various accession formats

    GenBank
    • Assembled sequences
    • Feature annotation
    • Additional metadata

Before you submit

  • All submissions require you to be logged into your account.
  • We encourage all submissions to be part of a submission group. Using a submission group will allow you and your colleagues to manage the submission data during submission and after accession assignment.
    • Find out if your laboratory has a submission group. If so, check if you are a group member and work with your group admin to be added and set up proper permissions.
    • If you do not yet have a submission group, create one and add group members.
    • Once you start a submission, you can link it to a submission group.
    • For ease in data management, link related BP, BS, SRA, and GenBank submissions to the same group. This will allow members of the submission group to see, edit, and update the submission.
  • Review the Use cases tab to determine which submission workflows you will need to follow.

Use cases

Select the case that applies to your data and follow the instructions for that case.

NOTE: Throughout these instructions, "SP-" refers to a Submission Portal application, to distinguish it from the corresponding public database. For example, SP-SRA refers to the Submission Portal application for submitting to SRA, while SRA refers to the public SRA database.

Prokaryotic or Eukaryotic genomes

Use case 1: both unassembled and assembled sequences

  1. Read the guidance on feature annotation first. If you are submitting:
    1. With your own feature annotation: You must first submit in SP-BioProject to obtain a locus_tag prefix and use it in your annotation. If you already have a BioProject and a BioSample and do not have a locus_tag prefix, contact the help desk to obtain one.
    2. Without feature annotation or requesting PGAP annotation: Proceed to step 2.
  2. For the unassembled sequence reads, submit in SP-SRA
    • See the link above for guidance on how to upload sequence data.
    • If you do not already have a BioProject and/or BioSample(s), you will be prompted to create them within your SRA submission.
    • See more SP-SRA submission help and watch a 10 min video tutorial.
  3. For the assembled sequences, submit in SP-Genome
    • Within your genome submission, link your genome submission to the BioProject and BioSamples obtained in previous steps.
    • SRA accessions may be emailed to the help desk and we will link them to your genome submission.
    • See more SP-Genomes submission help for more detailed guidance.

Use case 2: unassembled sequence reads only

For the unassembled sequence reads, submit in SP-SRA

  • See the link above for guidance on how to upload sequence data.
  • If you do not already have a BioProject and/or BioSample(s), you will be prompted to create them within your SRA submission.
  • See more SP-SRA submission help and watch a 10 min video tutorial.

Use case 3: assembled sequences only

  1. Read the guidance on feature annotation first. If you are submitting:
    1. With your own feature annotation: You must first submit in SP-BioProject to obtain a locus_tag prefix and use it in your annotation. If you already have a BioProject and a BioSample and do not have a locus_tag prefix, contact the help desk to obtain one.
    2. Without feature annotation or requesting PGAP annotation: Proceed to step 2.
  2. Submit in SP-Genome
    • If you do not have a BioProject and/or BioSample(s), you will be prompted to create them within your genome submission.
    • See more SP-Genomes submission help for more detailed guidance.

Virus genomes

Use case 1: both unassembled and assembled sequences

Submit the unassembled sequence reads to SRA first. Then submit the assembled sequences to GenBank.

  1. For the unassembled sequence reads, submit in SP-SRA
    • See the link above for guidance on how to upload sequence data.
    • If you do not have a BioProject and/or BioSample(s), you will be prompted to create them within your SRA submission.
    • See more SP-SRA submission help and watch a 10 min video tutorial.
  2. For the assembled sequences, submit in SP-GenBank

Use case 2: unassembled sequence reads only

For the unassembled sequence reads, submit in SP-SRA

  • See the link above for guidance on how to upload sequence data.
  • If you do not have a BioProject and/or BioSample(s), you will be prompted to create them within your SRA submission.
  • See more SP-SRA submission help and watch a 10 min video tutorial.

Use case 3: assembled sequences only

Obtain BioProject and BioSample accessions before submitting your viral sequence data, if you do not already have them by doing the following:

  1. Submit your project scope and description in SP-BioProject and obtain a BioProject accession number
  2. Submit sample information in SP-BioSample and obtain a BioSample accession number
  3. Submit your viral sequence data in SP-GenBank

Non-genome scale sequence data (e.g. individual genes from any organism)

Non-genome scale sequence data may include individual genes (e.g. INSDC accession KM364031.1), multiple coding regions (e.g. INSDC Accession OR835046.1), or pathogenic islands (e.g. INSDC Accession JN181158.1). These types of sequences should be submitted in SP-GenBank.

While it is currently optional, we encourage non-genome scale public health sequence submissions to include the corresponding BioProject, BioSample, and SRA accessions.

Use case 1:

If you already have your BioProject, BioSample, and SRA accessions for your data, use them when submitting your sequence to GenBank.
  1. Submit in SP-GenBank
  2. Link your submission to your BioProject, BioSample, and SRA accessions on the Source Modifiers page within your SP-GenBank submission. See our knowledgebase article on how to link a BioProject in a SP-GenBank submission.

Use case 2:

If you do not already have BioProject, BioSample, and SRA accessions, obtain those accession numbers before submitting your non-genome scale assembled sequence data.
  1. If you have corresponding unassembled sequence reads, submit the unassembled sequence reads in SP-SRA. You will be prompted to create a BioProject and BioSample within your SP-SRA submission. Go to step 2 if you do not have SRA data.
  2. If you do not have unassembled sequence reads, then:
  3. Submit your assembled sequence data in SP-GenBank

Use case 3:

If you are researching microbial antibiotic resistance or Shiga toxins, see also the information on how to request:

Additional information

BioProject recommendations

Best practices for related data

A BioProject will serve as an organizational data container (see Fig 1 under the Overview tab), so ensure that you have all the related data under the same BioProject. Here are some do’s and don’ts on creating BioProjects:

  • Do use one BioProject for the entire research or surveillance project, even if data are submitted at different times:
    • You may register for a BioProject ahead of data submission. See the Use cases tab for more guidance.
    • You will be able to add more data to a BioProject through time.
  • Do not create a new BioProject for every submission or each individual assembly from the same isolate.
  • Do use the same BioProject for assemblies and SRA reads for related data.
  • Do not create a BioProject unless you or your colleagues also plan to submit BioSample, SRA, and/or assembly data that will be linked to it.

BioProject accession numbers and stable links

Each BioProject receives a single accession number with the “PRJNA” prefix. Remember to provide the BioProject accession (PRJNA) in your paper. Because BioProject sits at the very top of the linked data structure, the single accession number leads to all your data once public.

More questions? See our BioProject FAQs for more information.

Organizational Umbrella BioProjects

There are situations when establishing separate BioProjects makes sense because of differences in funding, sequencing goals, methodology, or organism scope. You may organize these separate BioProjects under a large initiative, known as an Umbrella BioProject.

An Umbrella BioProject is a higher-level BioProject that organizes multiple related BioProjects within a large research initiative or collaborative effort. Large initiatives can include multiple levels of Umbrella BioProjects, with top-level Umbrella projects linking to sub-Umbrella projects, which in turn link to the primary BioProjects that link to the submitted data.

To request an Umbrella BioProject, write to the Bioproject help desk with details about which BioProjects you want to group and why.

BioSample recommendations

A BioSample contains descriptive information about the biological materials from which sequence data was derived. There are various BioSample "packages" which have relevant attributes for a type of sample. These packages are intended to help standardize the descriptions of the biological sources. You will need to select the most appropriate BioSample package for your source material. You may Preview BioSample Packages in advance of submission. On the preview page, filter to find the appropriate packages for your use case by typing in the organism name. More guidance on filtering BioSample packages is presented on the Preview page.

Best practices for creating BioSamples

  • Do use the same BioSample for unassembled and assembled sequence data from the same source.
    • You may register BioSamples ahead of data submission. See the Use cases tab for more guidance.
    • You will be able to add more data to a BioSample through time.
  • Do follow the BioSample guidance for organism names.

More information