BioProject
BioProject information
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/GEA/MetaboBank data citing this ID are released.
- Release
- Release project data immediately. Private DDBJ/DRA/GEA/MetaboBank data citing this ID are 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” (e.g., Please register this project as an umbrella project).
To submit data corresponding to personal identification code, write the approved NBDC data submission application ID (for example, J-DS000001-001).
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.
External Links
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.
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 |
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.
If the project targets multiple organisms, enter a common lineage e.g. “Mammalia” (taxonomy id: 40674) for the project targeting “Homo sapiens” and “Mus musculus”.
If an organism name is not found in the NCBI Taxonomy, enter a lineage or a species name with sp. e.g. “Escherichia sp.” (tax id: 1884818) for a novel species “Escherichia sp. ABCDEF”.
Apply a novel organism name in BioSample.
- 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.
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.
<Publication id="10.1093/nar/gku1120">
<DbType>eDOI</DbType>
</Publication>
<ProjectReleaseDate>