Project Information

The items with * are required.
The items with ** are conditionally required.

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.
RelevanceDescription
Agricultural
Medical
IndustrialCould include bio-remediation, bio-fuels and other areas of research where there are areas of mass production.
Environmental
Evolution
ModelOrganism
OtherUnspecified 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 typeDescription
Genome Sequencingwhole, or partial, genome sequencing project (with or without a genome assembly)
Clone Endsclone-end sequencing project
EpigenomicsDNA methylation, histone modification, chromatin accessibility datasets
Exomeexome resequencing project
Mapproject that results in non-sequence map data such as genetic map, radiation hybrid map, cytogenetic map, optical map, and etc.
Metagenomesequence analysis of environmental samples
Phenotype and Genotypeproject correlating phenotype and genotype
Proteomelarge scale proteomics experiment including mass spec. analysis
Random Surveysequence 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 Expressionlarge scale RNA sequencing or expression analysis. Includes cDNA, EST, RNA_seq, and microarray.
Variationproject with a primary goal of identifying large or small sequence variation across populations.
Othera 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 scopeDescription
MonoisolateA 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).
MultiisolateMultiple individuals, a population (representation of a species).
Multi-speciesSample represents multiple species.
EnvironmentSpecies content of the sample is not known.
SyntheticSample is synthetically created by a machine.
OtherSpecify 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.
MaterialDescription
GenomeA whole genome initiative. May be only the nuclear genome. Use for DNA of a metagenome sample.
Partial GenomeOne or more chromosomes or replicons were experimentally purified.
TranscriptomeTranscript data.
ReagentMaterial studied was obtained by chemical reaction, precipitation.
ProteomeProtein or peptide data.
PhenotypePhenotypic descriptive data.
OtherSpecify 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.
CaptureDescription
WholeThe project makes use of the whole sample material (most common case).
Clone EndsCapturing clone end data.
ExomeCapturing exon-specific data.
Targeted Locus/LociCapturing specific loci (gene, genomic region, barcode standard).
Random SurveyNot using whole sample, an incomplete survey of the sample.
OtherSpecify 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.
MethodologyDescription
SequencingSequencing using Sanger, 454, Illumina, etc wit
ArrayData/Sequence are generated by hybridization arrays.
Mass SpectroscopyData are generated by mass spectroscopy.
OtherPlease 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.
ObjectiveDescription
Raw Sequence ReadsSubmission of raw sequencing information as it comes out of machine.
SequenceSequence which is not raw - meaning processed (clipped, matepaired, oriented).
AnalysisHigher level interpretation of the data.
AssemblyExperiment will result in assemblies (genome or transcriptome).
AnnotationExperiment wil result in Annotation.
VariationSubmission of variations.
Epigenetic MarkersExperiment will result in Epigenetic markers.
ExpressionSubmission of gene expression.
MapsExperiment will result in cytogenetic, physical, Rh, etc...maps.
PhenotypeExperiment 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.

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.
ShapeDescription
Bacillirod-shaped
Coccispherical-shaped
Spirillaspiral-shaped
Coccobacillielongated coccal form
Filamentousfilament-shaped (bacilli thar occur in long threads)
Vibriosvibrio-shaped (short, slightly curved rods)
Fusobacteriafusiform 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.
<Publication id="15557739">
	<DbType>ePubmed</DbType>
</Publication>
<ProjectReleaseDate> ...
DOI
Provide a DOI if a PubMed ID is not available. Provide the additional reference information.
<Publication id="10.1093/nar/gku1120">
	<DbType>eDOI</DbType>
</Publication>
<ProjectReleaseDate> ...
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.