DDBJ BioProject Handbook

BioProject

Overview

Purpose

New sequencing technologies have significantly increased the volume of data that can be generated. Coupled with this, research is increasingly collaborative and data resulting from collaboration can include distinct types of data which may be submitted by more than one research group to more than one archival database.

The BioProject resource organizes both the projects and the data from those projects which is deposited into several archival databases maintained by members of the INSDC. This allows searching by characteristics of these projects, using the project description and project content across the INSDC-associated databases.

Overview of BioSample and BioProject integration with other DDBJ databases
Overview of BioSample and BioProject integration with other DDBJ databases

Project

The definition of a set of related data, a 'project' is very flexible and supports the need to define a complex project and various distinct sub-projects using different parameters.

For example, BioProject records can be established for:

  • Genome sequencing and assembly
  • Metagenomes
  • Transcriptome sequencing and expression
  • Targeted locus sequencing
  • Genetic or RH Maps
  • Epigenetics
  • Phenotype or Genotype
  • Variation detection

BioProject represents a submission, initiative, or group of data that is logically related in some manner, or is of interest to retrieve as a distinct dataset. A project may be identified in terms of distinctions in the type of data produced.

Complex project

By selecting Project Data Types(for example, "Genome Sequencing" and "Transcriptome or Gene Expression"), multiple studies can be merged into single project.

In the project spanning multiple species, enter a taxonomic classification common to the species (e.g., genus name).

In the Sample scope, Materialand Capture, select "Other" if appropriate ones are not available.

A series of publications can be listed in the Publication.

Primary and Umbrella projects

There are two basic types of projects; primary and umbrella projects.

Primary project:

Submitted projects which are intended to represent and be linked to current or future data submissions. Primary projects can be kept private.

Umbrella project:

Administrative project that is created to group multiple projects that are related by a single effort from a single submitter or group of submitters. Umbrella projects may be created automatically using a rule-based logic or may be created by database staff upon request or upon identification of a needed grouping. Umbrella projects cannot be kept private.

Umbrella projects exist to provide an organizational structure to a large collaborative project and to group projects that are related via funding or submitting source or collaboration. Submitted primary projects are linked to data as it is submitted, and are linked to one or many umbrella projects. Submitted primary projects are not directly linked to other primary projects; they are linked indirectly by way of links to the umbrella project.

Nucleotide sequence data can not directly refer an umbrella project. Sequence data are linked to an umbrella via a primary project.

BioProject hierarchy

Definition of an umbrella project may be done in collaboration with a funding source. For example, there may be a top-most administrative project to represent the overarching initiative ("Genome Support Project"), with a secondary layer of primary projects defining core components of this initiative (reference genomes, rRNA sequencing, metagenomes, etc.).

Some large initiatives are represented by more than one layer of umbrella projects (see Figure B below); for instance, a top-most level may identify the largest definition of the collaboration; a second level of umbrella projects identify the primary categories of data production; and finally a third layer represents the projects that actually generate the data that is submitted. The Human Microbiome project is an example of this type of complex hierarchy where the top-most project, PRJNA43021, represents the most inclusive definition of the initiative, and a secondary level (such as PRJNA28331) identifies a major sub-project to sequence multiple reference genomes each of which has a distinct project accession.

Schematic diagram of BioProject hierarchies. (A)Two layers. (B)Three layers.
Schematic diagram of BioProject hierarchies. (A)Two layers. (B)Three layers.
Two layers (A)

Initiatives may be organized as a single Umbrella project with one or many submitted projects that are connected to data. Example: Neanderthal Metagenome.

Three layers (B)

Very large initiatives which have distinct sub-projects may have two levels of Umbrella project. For example, a top-level Umbrella project groups all components of the initiative; mid-level Umbrella projects reflect two distinct branches of the project (such as sequencing vs. epigenetics); and several primary projects denote distinct project data types (e.g., genome sequencing, transcriptome, epigenetics, etc.). Example: NIH Human Microbiome Project (HMP) Roadmap Project.

Data release

Triggering of data release between primary projects and data records.
Triggering of data release between primary projects and data records.

You can "immediately release" or "hold" the registered primary project.

The submitted primary project data can be kept private until the linked DDBJ, DRA, DTA and DOR records made be public. Hold date of the project data cannot be specified. Primary project data are automatically released when the linked DDBJ record(s) is published. On the other hand, publication of the primary project data do not cause automatic release of the linked DDBJ record(s). Thus, under a primary project, publication of a data record does not cause the indirect release of the other records. Publication of the DDBJ records is independent from the release of the linked project(s).

FAQ: How are linked BioProject/BioSample/sequence data released?

Visibility of relationships between public umbrella and primary projects.
Visibility of relationships between a public umbrella and primary projects.

An umbrella project cannot be kept private.An umbrella project can have public and private primary projects. Hierarchical relationship between the public umbrella project and the un-released primary project is invisible.

Released project data are exchanged with the other two INSDC partners NCBIand EBIBioProject databases.

Use an umbrella project

Please group related primary projects by using an umbrella project. An umbrella project can group and present outputs from research project.

NCBI visualizes data under an umbrella project with some statistics for easy navigation.

Project presentation examples:
Neanderthal Metagenome
Escherichia coli O104:H4

You can submit an umbrella project from DDBJ submission systemin the same way as primary project. To remind the DDBJ BioProject team, you need to enter "this is an umbrella project" in the Private comments to DDBJ staff. Registered umbrella project cannot be kept private, but some fields can be omitted.

To group primary projects under an umbrella, please follow the steps below.
First, submit and release an umbrella project. If necessary, please share the assigned PRJDB number with relevant researchers.
When submitting related primary projects, please provide the PRJDB number of parent umbrella in the Umbrella BioProject. Released primary projects are automatically linked to the specified umbrella project.

If you want to add already registered primary projects to the umbrella, please e-mailthe PRJDB numbers of umbrella and related primary projects to the DDBJ BioProject team.

Private primary projects are not released by linking to public umbrella project.

Metadata

Required *
Conditionally required *

Submitter

Submitter

Contact information of submitter(s). Questions and notifications about a submission are contacted to the e-mail address(es) listed here. Personal contact information is considered confidential and is collected to be used by DDBJ BioProject staff should questions arise; the general information about the research center is used for public display.

First name
Submitter's first name.
Last name*
Submitter's last name.
E-mail *
E-mail address. Enter an address from the organizations domain.

Organization

Organization to which a contact person belongs.

Submitting organization *
full name of organization.
Submitting organization URL
The URL of submitter's organization.

Data Release

Select "Hold" or "Release". You cannot specify hold date. Please see Release of projects for detailed release mechanism.

Hold
Released concurrently when the DDBJ, DRA, DTA and DOR record(s) citing this ID is released.
Release
Release project data immediately. Private DDBJ record(s) citing this ID is not released.

General info

Project Description

An informative paragraph that describes the project and provides informative context for the displayed project record.

Project title*
Very short descriptive name of the project for caption, labels, etc for public display. For example: Chromosome Y sequencing, Global studies of microbial diversity on human skin.
Description*
Description (a paragraph) of the project goals and purposes. Provide enough information (more than 100 characters) in the description for other users to interpret the data.
Private comments to DDBJ staff
Use this field if you have questions for database support staff. The content is not made public. If you intend to submit an umbrella project, please inform us that "this is umbrella project".
Relevance
Select the primary general relevance of the study.
Relevance Description
Agricultural
Medical
Industrial Could include bio-remediation, bio-fuels and other areas of research where there are areas of mass production.
Environmental
Evolution
ModelOrganism
Other Unspecified major impact categories to be defined in the "Relevance description".
Relevance description*
Describe the relevance when the Other is selected.

Umbrella BioProject

If you are registering a project that is part of an initiative which is already registered in the BioProject database, then please tell us the existing BioProject accession number and provide a general description of the larger initiative. This information is needed for project linking.

Initiative description*
Description of an initiative.
Umbrella BioProject accession*
A BioProject accession number of an initiative which is already registered in the BioProject database.

An URL may be provided, with a label for the resource, to reference a resource that is directly relevant to the submitted project.

Link description
Display name of web site that is related to this study.
URL
URL of web site that is related to this study.

Grants

Funding information for a project.

Agency
Name of funding agency. For example: Japan Society for the Promotion of Science.
Agency abbreviation
Abbreviation of funding agency. For example: JSPS.
Grant ID
Grant number is collected to support searches (e.g., publications often cite Grant numbers). For example: JSPS KAKENHI Grant Number 12345678.
Grant title
Grant title may also support searches.

Consortium

Consortium name
If study is carried out as part of a consortium, provide the consortium name.
Consortium URL
If the consortium maintains a web site, provide the URL.

Project type

Project data type

Project data type*

A general label indicating the primary study goal. Select appropriate types. News: A BioProject record can have multiple project data types

NCBI individually assigns the Project data type based on the experimental data linked to the project. This type is not used by EBI.

Project Data type Description
Genome Sequencing whole, or partial, genome sequencing project (with or without a genome assembly)
Clone Ends clone-end sequencing project
Epigenomics DNA methylation, histone modification, chromatin accessibility datasets
Exome exome resequencing project
Map project that results in non-sequence map data such as genetic map, radiation hybrid map, cytogenetic map, optical map, and etc.
Metagenome sequence analysis of environmental samples
Phenotype and Genotype project correlating phenotype and genotype
Proteome large scale proteomics experiment including mass spec. analysis
Random Survey sequence generated from a random sampling of the collected sample; not intended to be comprehensive sampling of the material.
Targeted Locus (Loci) project to sequence specific loci, such as a 16S rRNA sequencing
Transcriptome or Gene Expression large scale RNA sequencing or expression analysis. Includes cDNA, EST, RNA_seq, and microarray.
Variation project with a primary goal of identifying large or small sequence variation across populations.
Other a free text description is provided to indicate Other data type
Project data type description*
Describe the project data type when the Other is selected.

Sample scope/Material/Capture/Methodology

Sample scope*
The scope and purity of the biological sample used for the study.
Sample scope Description
Monoisolate A single animal, cultured cell-line, inbred population (or possibly a heterogeneous population when a single genome assembly is generated from the pooled sample; not preferred).
Multiisolate Multiple individuals, a population (representation of a species).
Multi-species Sample represents multiple species.
Environment Species content of the sample is not known.
Synthetic Sample is synthetically created by a machine.
Other Specify the sample scope that was used in the "Target description".
Material*
The type of material that is isolated from the sample for use in the experimental study.
Material Description
Genome A whole genome initiative. May be only the nuclear genome. Use for DNA of a metagenome sample.
Partial Genome One or more chromosomes or replicons were experimentally purified.
Transcriptome Transcript data.
Reagent Material studied was obtained by chemical reaction, precipitation.
Proteome Protein or peptide data.
Phenotype Phenotypic descriptive data.
Other Specify the material that was used in the "Target description".
Capture*
The scale, or type, of information that the study is designed to generate from the sample material.
Capture Description
Whole The project makes use of the whole sample material (most common case).
Clone Ends Capturing clone end data.
Exome Capturing exon-specific data.
Targeted Locus/Loci Capturing specific loci (gene, genomic region, barcode standard).
Random Survey Not using whole sample, an incomplete survey of the sample.
Other Specify the scale or type of the captured material in the "Target description".
Target description*
Describe the Sample scope/Material/Capture when the Other(s) is selected.
Methodology*
The core experimental approach used to obtain the data that is submitted to archival databases.
Methodology Description
Sequencing Sequencing using Sanger, 454, Illumina, etc wit
Array Data/Sequence are generated by hybridization arrays.
Mass Spectroscopy Data are generated by mass spectroscopy.
Other Please provide data description in the "Methodogy description".
Methodology description*
Describe the methodology type when the Other is selected.

Objective

Project goals with respect to the type of data that will be generated and submitted to an INSDC-associated database. Select all relevant menu options.

Objective*
Project goals with respect to the type of data that will be generated and submitted to an INSDC-associated database. Select all relevant menu options.
Objective Description
Raw Sequence Reads Submission of raw sequencing information as it comes out of machine.
Sequence Sequence which is not raw - meaning processed (clipped, matepaired, oriented).
Analysis Higher level interpretation of the data.
Assembly Experiment will result in assemblies (genome or transcriptome).
Annotation Experiment wil result in Annotation.
Variation Submission of variations.
Epigenetic Markers Experiment will result in Epigenetic markers.
Expression Submission of gene expression.
Maps Experiment will result in cytogenetic, physical, Rh, etc...maps.
Phenotype Experiment will deliver phenotypes.
Other

Locus tag prefix

Locus tag prefix*
Locus tag prefix generation box will appear when [Project data type="Genome Sequencing" or "Metagenome"] AND [Capture="Whole"] AND [Objective="Sequence" or "Annotation" or "Assembly"].

Registration of a unique locus tag prefix is required for studies that result in genome assemblies. Please leave the prefix box empty, when a prefix is not necessary for WGS only submission.

Locus tag prefix guideline.

Locus tag prefix format
The locus_tag prefix can contain only alpha-numeric characters and it must be 3-12 characters long. It should start with a letter, but numerals can be in the 2nd position or later in the string. (ex. A1C). There should be no symbols, such as -_* in the prefix. The locus_tag prefix is to be separated from the tag value by an underscore ‘_’, eg A1C_00001.

DDBJ BioProject limits the maximum tag length to 12 characters. In the BioProject submission system, the locus tag is displayed in capital letters. However, the tag is reserved in case-insensitive manner.

Target

Organism information

Taxonomy and description of target organism.

Organism name*

Organism name in the Taxonomy database. Unclassified sequences including metagenome and environmental samples may be found at here.

In the project spanning multiple species, enter a taxonomic classification common to the species (e.g., genus name).

If you intend to submit un-registered novel organism, please provide us the detailed organism information in the Description of novel organism and proposed organism name in the Organism Name.

Taxonomy ID
NCBI Taxonomy ID
Strain, breed, cultivar
Microbial strain name, or eukaryotic breed or cultivar name. Please provide this or "Isolate name or label"
Isolate name or label
A label for an isolated sample, or name of an individual animal (e.g., Clint). Please provide this or "Strain, breed, cultivar".
Description
A brief description, to elaborate upon the brief label.
Description of novel organism
Enter necessary information to register an organism to the taxonomy database.

Environmental sample information

This section appears instead of the Organism information when the Sample scope="Environment" in the Target.

Environmental sample name*
Unclassified sequences including metagenome and environmental samples may be found at here. If an appropriate name was not found, describe a novel name you propose and details of sample information in the Environmental sample description.
Environmental sample description
Describe details of sample information.

General Properties

General properties of target organism.

Cellularity
Select a cellularity.
Cellularity
Unicellular
Multicellular
Colonial
Reproduction
Select a Reproduction.
Reproduction
Sexual
Asexual
Haploid genome size
Haploid genome size in Kb, Mb or cM.
Ploidy
Select a Ploidy.
Ploidy
Haploid
Diploid
Polyploid
Allopolyploid

Organism Replicons

Describe how many replicons this organism has, how they are named (e.g., 1, 2, 3 vs. I, II, III), the replicon type (chromosome etc.), and the subcellular structure that the replicon is located in.

Name
The preferred standard for the replicon name.
Type
Select a replicon type.
Replicon type
Chromosome
Plasmid
Linkage Group
Segment
Other
Location
The replicon subcellular location. For instance, the nucleus, or a differentiated organella. Please select "Nuclear or Prokaryote" for the chromosomes of eularyotes, bacteria or archaea.
Location
Nuclear or Prokaryote
Macronuclear
Nucleomorph
Mitochondrion
Kinetoplast
Chloroplast
Chromoplast
Plastid
Virion or Phage
Proviral or Prophage
Viroid
Extrachrom
Cyanelle
Apicoplast
Leucoplast
Proplastid
Hydrogenosome
Chromatophore
Other
Size
The size and unit of measurement for the estimated genome size.
Description
A description of any unusual features of the replicon.

Phenotype

Phenotype of target organism.

Disease
Enter a disease name.
Biotic Relationship
Select a BioticRelationship.
BioticRelationship
FreeLiving
Commensal
Symbiont
Episymbiont
Intracellular
Parasite
Host
Endosymbiont
Trophic Level
Select a TrophicLevel.
TrophicLevel
Autotroph
Heterotroph
Mixotroph

Prokaryote Morphology

When the target organism is prokaryote, please describe the general morphology if known.

Shape
Select all relevant menu options.
Shape Description
Bacilli rod-shaped
Cocci spherical-shaped
Spirilla spiral-shaped
Coccobacilli elongated coccal form
Filamentous filament-shaped (bacilli thar occur in long threads)
Vibrios vibrio-shaped (short, slightly curved rods)
Fusobacteria fusiform or spindle-shaped (rods with tapered ends)
SquareShaped
CurvedShaped
Tailed
Gram
Choose gram positive or negative.
Gram
Positive
Negative
Motility
Choose a Motility.
Motility
Yes
No
Enveloped
Choose enveloped or not.
Enveloped
Yes
No
Endospores
Choose target bacteria forms endospores or not.
Endospores
Yes
No

Ecological Environment

The general habitat for any organism. Please indicate additional extremophile parameters if known.

Habitat
Choose a Habitat.
Habitat
HostAssociated
Aquatic
Terrestrial
Specialized
Multiple
Unknown
Salinity
Choose a Salinity.
Salinity
NonHalophilic
Mesophilic
ModerateHalophilic
ExtremeHalophilic
Unknown
Oxygen requirement
Choose an Oxygen requirement.
OxygenReq
Aerobic
Microaerophilic
Facultative
Anaerobic
Unknown
Temperature range
Choose a temperature range.
TemperatureRange
Cryophilic
Psychrophilic
Mesophilic
Thermophilic
Hyperthermophilic
Unknown
Optimum Temperature
Optimum temperature in Celsius.

Publication

PubMed ID
The PubMed ID(s) will be used to populate the publication information.
DOI
Provide a DOI if a PubMed ID is not available. Provide the additional reference information.
Reference title*
A title of reference.
Journal title*
A title of journal.
Year*
Publication year.
Volume*
Journal volume.
Issue*
Journal issue.
Pages from*
Reference start page.
Pages to*
Reference end page.
First name*
First name of author.
MI
Middle initial.
Last name*
Last name of author.
Suffix
Suffix for author.
This publication has multiple authors
If this is checked, then "et al" is added to the author name provided above.

XML schema

BioProject XML schema

Submission to BioProject

Submission of research data from human subjects
For submitting data from human subjects (human data) to the databases of DDBJ center, it is submitter's responsibility to ensure that the dignity and right of human subject are protected in accordance with all applicable laws, ordinances, guidelines and policies of submitter's institution. In principle, make sure to remove any direct personal identifiers of human subjects from your data to be submitted. Before submitting human data, read the "Submission of research data from human subjects".

Submission to BioProject

Cases requiring project registration

Registration for a BioProject accession is required in the following cases.

  • submit sequencing data to DRA
  • submit genome sequences to DDBJ

Registration for a BioProject accession is encouraged in the following cases.

  • projects that result in a very large volume of data submissions
  • submissions from multiple members of a collaboration
  • submissions to multiple archival databases

Registration for a BioProject accession is not required in the following cases. Register an accession if necessary.

  • small datasets for which the results are found in one (or a small number) of accession numbers such as a single plasmid, viral or organelle genome sequencing study

A BioProject accession is required for submission to Sequence Read Archive, and microbial and eukaryotic genomes submissions to the DDBJ. If you obtain a BioProject accession from DDBJ, please submit your related biological data to the DDBJ, Sequence Read Archiveand Trace Archive.

The INSDC stopped to assigning strain-level taxonomy ID to microbes whose genomes have been submitted to the INSDC.

Submit a new BioProject submission

According to the Account Handbook, obtain a submission account.

Submit a new project by clicking the [New submission].

If there is no reply from submitters after three months of initial contact, submissions will be cancelled.

Submit a new BioProject

To submit a BioProject, enter content from left to right tabs. Submitter information is copied with account information.

For BioProject metadata, please see here.

Enter project content

To submit genome assemblies to DDBJ, a unique Locus tag prefixis necessary.

Locus tag prefix generation box will appear when [Project data type="Genome Sequencing" or "Metagenome"] AND [Capture="Whole"] AND [Objective="Sequence" or "Annotation" or "Assembly"]. Registration of a unique locus tag prefix is required for studies that result in genome assemblies.

The locus_tag prefix can contain only alpha-numeric characters and it must be at least 3 characters long. It should start with a letter, but numerals can be in the 2nd position or later in the string. (ex. A1C). There should be no symbols, such as -_* in the prefix. The locus_tag prefix is to be separated from the tag value by an underscore ‘_’, eg A1C_00001.

Please leave the prefix box empty, when a prefix is not necessary for WGSonly submission.

Prefix is managed by NCBI. When a project is submitted, our system tries to reserve prefix to NCBI. When the prefix has already been reserved, an error message will be displayed. Please enter a different prefix and submit again.

When multiple prefixes are necessary, please contact us.

Reserve a locus tag prefix

Check the content in "OVERVIEW" and submit a project by clicking the [Submit].

Submit BioProject

The "OVERVIEW" tab continue to display submitted content. Updates will not be reflected in the "OVERVIEW" tab.

Accession number

Temporary numbers with prefix PSUB are automatically assigned to submitted projects. Projects can be referred by the PSUB numbers until official accession numbers will be assigned. DDBJ BioProject staff review submissions and issue accession numbers with prefix PRJD to completed projects. Submitters can view accession numbers and submission status in your submission account.

  • Do NOT cite numbers with prefix PSUB in publication.
  • Do not double submit the projects which have been registered to EBI and NCBI.

Submit an umbrella project

Umbrella project can be submitted as primary project in submission account. Be sure to tell the DDBJ BioProject staff that submitting project is umbrella by writing so in the Private comments to DDBJ staff. Umbrell project cannot be kept private.

Tell DDBJ staff that submitting project is umbrella

When submitting project, in the Umbrella BioProject, enter abstract and accession number of an umbrella to be linked. The DDBJ BioProject staff link the submitted primary project to the umbrella based on this information.

Link to umbrella

Release of projects

Registered projects can be released in the following two ways:

  • Release immediately after registration.
  • Release when records citing the BioProject accession are made public.

The projects can be kept private. If DDBJ records citing the BioProject accession are made public, cited projects are automatically released. Private DDBJ records citing this BioProject accession are not made public.

Hold date cannot be set for BioProject.

Public projects are exchanged among NCBIand EBIBioProject databases.

Update

Registered projects can be updated. Please contact the BioProject staffto update the projects.

For the SRA submission, select the BioProject accession that you registered in advance in the Study.

For genome and TSA submissions to the DDBJ, enter the BioProject accession in the DBLINK.