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BioProject information
<!DOCTYPE html> <html lang="en"> <head> <meta charset="UTF-8" /> <meta property="og:title" content="BioProject information" /> <meta property="og:url" content="https://www.ddbj.nig.ac.jp/bioproject/project-info-e.html" /> <meta property="og:description" content="Required *Conditionally required *SubmitterSubmitterContact information of submi..." /> <meta property6="og:image" content="/images/thumbnail/logo_ddbj_fb.png" /> <meta name="viewport" content="width=device-width, initial-scale=1.0" /> <title>BioProject information</title> <script async src="https://www.google-analytics.com/analytics.js"></script> <script src="https://code.jquery.com/jquery-3.5.0.js" integrity="sha256-r/AaFHrszJtwpe+tHyNi/XCfMxYpbsRg2Uqn0x3s2zc=" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/jquery.hoverintent/1.10.1/jquery.hoverIntent.min.js" integrity="sha512-gx3WTM6qxahpOC/hBNUvkdZARQ2ObXSp/m+jmsEN8ZNJPymj8/Jamf8+/3kJQY1RZA2DR+KQfT+b3JEB0r9YRg==" crossorigin="anonymous"></script> <script src="https://cdnjs.cloudflare.com/ajax/libs/spin.js/4.1.0/spin.min.js" integrity="sha512-CbohqWjAgarTqRHcX1MbwkF2pujwbsCee1PABpnBWC+VqSldvlNEEI5+4OSsR/HbFQOFFpwY2YvZZNjBMxNnXg==" crossorigin="anonymous"></script> <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/jquery.colorbox/1.6.4/jquery.colorbox-min.js"></script> <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/jquery-deparam/0.5.3/jquery-deparam.min.js"></script> <script type="text/javascript" src="https://www.ddbj.nig.ac.jp/assets/js/jquery.trace.js"></script> <script type="text/javascript" src="https://www.ddbj.nig.ac.jp/assets/js/jquery.json_search.js"></script> <link rel="icon" href="https://www.ddbj.nig.ac.jp/assets/images/favicon_ddbj.ico"> <link rel="stylesheet" href="https://www.ddbj.nig.ac.jp/assets/css/colorbox.css" /> <link rel="stylesheet" href="https://www.ddbj.nig.ac.jp/assets/css/main.css" /> <link rel="alternate" type="application/rss+xml" title="My Site RSS" href="/feed.xml" /> <script src="https://www.ddbj.nig.ac.jp/assets/js/main.js"></script> </head> <body data-category="bioproject"> <script src="https://www.ddbj.nig.ac.jp/assets/js/ddbj_common_framework.js" id="DDBJ_common_framework" style="display: block; height: 40px;" data-bottom-menu="true" data-ddbj-home-page="true" data-search="true" ></script> <section class="top-news-view"> <div class="inner"> <ul> <li class="item"> <a href="https://www.ddbj.nig.ac.jp/news/en/2024-10-22-e">On Cyber Threats against DDBJ, a node of the International Nucleotide Sequence Database Collaboration</a> </li> <li class="item"> <a href="https://www.ddbj.nig.ac.jp/news/en/2024-11-22-e">(27th November 9:00-November 28th 12:00)Announcement of D-way/MSS suspension</a> </li> <li class="item"> <a href="https://www.ddbj.nig.ac.jp/news/en/">(12th December 8:00-20th December 12:00(JST)) Suspension of DDBJ services due to NIG supercomputer maintenance</a> </li> </ul> </div> </section> <div id="primary"> <header id="PageHeader"> <div class="inner"> <div class="page-title"> <p class="title -normal">BioProject</p> </div> <nav class="tab-menu-view"> <ul class="tabmenucontainer"> <li class=""> <a href="/bioproject/index-e.html">Home</a> </li> <li class=" -haschild -current"> <a href="/bioproject/submission-e.html">Submission</a> <ul> <li> <a href="/bioproject/overview-e.html">Overview</a> </li> <li> <a href="/bioproject/project-info-e.html">Project Information</a> </li> </ul> </li> <li class=""> <a href="/faq/en/index-e.html?tag=bioproject">FAQ</a> </li> <li class=" -haschild"> <a href="http://ddbj.nig.ac.jp/search/">Search</a> <ul> <li> <a href="https://ddbj.nig.ac.jp/public/ddbj_database/bioproject/">Downloads</a> </li> </ul> </li> <li class=""> <a href="/bioproject/about-bioproject-e.html">About BioProject</a> </li> </ul> </nav> </div> </header> <section id="NavigationAndMainView"> <div class="inner"> <div class="subview"> <nav id="TableOfContents" class="internal-link"> </nav> </div> <section id="MainContentView" class="mainview"> <header class="header"> <nav class="breadcrumb-view"> <ul> <li> <a href="https://www.ddbj.nig.ac.jp/index-e.html">Home</a> </li> <li> <a href="https://www.ddbj.nig.ac.jp/bioproject/index-e.html">bioproject</a> </li> <li><a>BioProject information</a></li> </ul> </nav> <h1 class="title">BioProject information</h1> </header> <main class="md-content"> <p>Required <span class="red">*</span><br /> Conditionally required <span class="conditionally_required">*</span></p> <h2 id="Submitter">Submitter</h2> <h3 id="Area_bioproject-submitter">Submitter</h3> <p>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.</p> <dl> <dt><a href="#BioProject_First_name">First name</a><a name="BioProject_First_name"></a></dt> <dd>Submitter’s first name.</dd> <dt><a href="#BioProject_Last_name">Last name</a><span class="red">*</span><a name="BioProject_Last_name"></a></dt> <dd>Submitter’s last name.</dd> <dt><a href="#BioProject_E-mail">E-mail</a> <span class="red">*</span><a name="BioProject_E-mail"></a></dt> <dd>E-mail address. Enter an address from the organizations domain.</dd> </dl> <h3 id="Area_organization">Organization</h3> <p>Organization to which a contact person belongs.</p> <dl> <dt><a href="#BioProject_Submitting_organization">Submitting organization</a><span class="red">*</span><a name="BioProject_Submitting_organization"></a></dt> <dd>full name of organization.</dd> <dt><a href="#BioProject_Submitting_organization_URL">Submitting organization URL</a><a name="BioProject_Submitting_organization_URL"></a></dt> <dd>The URL of submitter’s organization.</dd> </dl> <h3 id="Area_data-release">Data Release</h3> <p>Select “Hold” or “Release”. You cannot specify hold date. Please see <a href="#Release_of_projects">Release of projects</a> for detailed release mechanism.</p> <dl> <dt><a href="#BioProject_Hold">Hold</a><a name="BioProject_Hold"></a></dt> <dd>Released concurrently when the DDBJ/DRA/GEA/MetaboBank data citing this ID are released.</dd> <dt><a href="#BioProject_Release">Release</a><a name="BioProject_Release"></a></dt> <dd>Release project data immediately. Private DDBJ/DRA/GEA/MetaboBank data citing this ID are not released.</dd> </dl> <h2 id="General-info">General info</h2> <h3 id="Area_project-description">Project Description</h3> <p>An informative paragraph that describes the project and provides informative context for the displayed project record.</p> <dl> <dt><a href="#Project_title">Project title</a><span class="red">*</span><a name="Project_title"></a></dt> <dd>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.</dd> <dt><a href="#Public_description">Description</a><span class="red">*</span><a name="Public_description"></a></dt> <dd>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.</dd> <dt><a href="#Private_comments">Private comments to DDBJ staff</a><a name="Private_comments"></a></dt> <dd>Use this field if you have questions for database support staff. The content is not made public. If you intend to <a href="/bioproject/submission-e.html#submit-umbrella-project">submit an umbrella project</a>, please inform us that “this is umbrella project” (e.g., Please register this project as an umbrella project).<br /> To submit data corresponding to personal identification code, write the approved data submission application ID (for example, J-DS000001-001).</dd> </dl> <h3 id="Area_linked-project">Umbrella BioProject</h3> <p>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 <a href="/bioproject/submission-e.html#link-primary-project-umbrella">project linking</a>.</p> <dl> <dt><a href="#Initiative_description">Initiative description</a><span class="conditionally_required">*</span><a name="Initiative_description"></a></dt> <dd>Description of an initiative.</dd> <dt><a href="#BioProject_BioProject_ID">Umbrella BioProject accession</a><span class="conditionally_required">*</span><a name="BioProject_BioProject_ID"></a></dt> <dd>A BioProject accession number of an initiative which is already registered in the BioProject database.</dd> </dl> <h3 id="Area_external-links">External Links</h3> <p>An URL may be provided, with a label for the resource, to reference a resource that is directly relevant to the submitted project.</p> <dl> <dt><a href="#URL_link_description">Link description</a><a name="URL_link_description"></a></dt> <dd>Display name of web site that is related to this study.</dd> <dt><a href="#BioProject_URL">URL</a><a name="BioProject_URL"></a></dt> <dd>URL of web site that is related to this study.</dd> </dl> <h3 id="Area_grants">Grants</h3> <p>Funding information for a project.</p> <dl> <dt><a href="#Agency">Agency</a><a name="Agency"></a></dt> <dd>Name of funding agency. For example: Japan Society for the Promotion of Science.</dd> <dt><a href="#Agency_abbreviation">Agency abbreviation</a><a name="Agency_abbreviation"></a></dt> <dd>Abbreviation of funding agency. For example: JSPS.</dd> <dt><a href="#Grant_ID">Grant ID</a><a name="Grant_ID"></a></dt> <dd>Grant number is collected to support searches (e.g., publications often cite Grant numbers). For example: JSPS KAKENHI Grant Number 12345678.</dd> <dt><a href="#Grant_title">Grant title</a><a name="Grant_title"></a></dt> <dd>Grant title may also support searches.</dd> </dl> <h2 id="Project-type">Project type</h2> <h3 id="Project_data_type">Project data type</h3> <dl> <dt><a href="#Project_data_type">Project data type</a><span class="red">*</span><a name="Project_data_type"></a></dt> <dd>A general label indicating the primary study goal. Select appropriate types. <a href="/news/en/2014-11-12-e.html">News: A BioProject record can have multiple project data types</a></dd> </dl> <p>NCBI individually assigns the <a href="https://www.ncbi.nlm.nih.gov/books/NBK54364/def-item/project-data-type/">Project data type</a> based on the experimental data linked to the project. This type is not used by <a href="https://www.ebi.ac.uk/ena/submit/project-format">EBI</a>.</p> <table> <thead> <tr> <th>Project Data type</th> <th>Description</th> </tr> </thead> <tbody> <tr> <td>Genome Sequencing</td> <td>whole, or partial, genome sequencing project (with or without a genome assembly)</td> </tr> <tr> <td>Clone Ends</td> <td>clone-end sequencing project</td> </tr> <tr> <td>Epigenomics</td> <td>DNA methylation, histone modification, chromatin accessibility datasets</td> </tr> <tr> <td>Exome</td> <td>exome resequencing project</td> </tr> <tr> <td>Map</td> <td>project that results in non-sequence map data such as genetic map, radiation hybrid map, cytogenetic map, optical map, and etc.</td> </tr> <tr> <td>Metagenome</td> <td>sequence analysis of environmental samples</td> </tr> <tr> <td>Phenotype and Genotype</td> <td>project correlating phenotype and genotype</td> </tr> <tr> <td>Proteome</td> <td>large scale proteomics experiment including mass spec. analysis</td> </tr> <tr> <td>Random Survey</td> <td>sequence generated from a random sampling of the collected sample; not intended to be comprehensive sampling of the material.</td> </tr> <tr> <td>Targeted Locus (Loci)</td> <td>project to sequence specific loci, such as a 16S rRNA sequencing</td> </tr> <tr> <td>Transcriptome or Gene Expression</td> <td>large scale RNA sequencing or expression analysis. Includes cDNA, EST, RNA_seq, and microarray.</td> </tr> <tr> <td>Variation</td> <td>project with a primary goal of identifying large or small sequence variation across populations.</td> </tr> <tr> <td>Other</td> <td>a free text description is provided to indicate Other data type</td> </tr> </tbody> </table> <dl> <dt><a href="#Project_data_type_description">Project data type description</a><span class="conditionally_required">*</span><a name="Project_data_type_description"></a></dt> <dd>Describe the project data type when the Other is selected.</dd> </dl> <h3 id="Area_sample-scopematerialcapturemethodology">Sample scope/Material/Capture/Methodology</h3> <dl> <dt><a href="#BioProject_Sample_scope">Sample scope</a><span class="red">*</span><a name="BioProject_Sample_scope"></a></dt> <dd>The scope and purity of the biological sample used for the study.</dd> </dl> <table> <thead> <tr> <th>Sample scope</th> <th>Description</th> </tr> </thead> <tbody> <tr> <td>Monoisolate</td> <td>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).</td> </tr> <tr> <td>Multiisolate</td> <td>Multiple individuals, a population (representation of a species).</td> </tr> <tr> <td>Multi-species</td> <td>Sample represents multiple species.</td> </tr> <tr> <td>Environment</td> <td>Species content of the sample is not known.</td> </tr> <tr> <td>Synthetic</td> <td>Sample is synthetically created by a machine.</td> </tr> <tr> <td>Other</td> <td>Specify the sample scope that was used in the “Target description”.</td> </tr> </tbody> </table> <dl> <dt><a href="#Material">Material</a><span class="red">*</span><a name="Material"></a></dt> <dd>The type of material that is isolated from the sample for use in the experimental study.</dd> </dl> <table> <thead> <tr> <th>Material</th> <th>Description</th> </tr> </thead> <tbody> <tr> <td>Genome</td> <td>A whole genome initiative. May be only the nuclear genome. Use for DNA of a metagenome sample.</td> </tr> <tr> <td>Partial Genome</td> <td>One or more chromosomes or replicons were experimentally purified.</td> </tr> <tr> <td>Transcriptome</td> <td>Transcript data.</td> </tr> <tr> <td>Reagent</td> <td>Material studied was obtained by chemical reaction, precipitation.</td> </tr> <tr> <td>Proteome</td> <td>Protein or peptide data.</td> </tr> <tr> <td>Phenotype</td> <td>Phenotypic descriptive data.</td> </tr> <tr> <td>Other</td> <td>Specify the material that was used in the “Target description”.</td> </tr> </tbody> </table> <dl> <dt><a href="#Capture">Capture</a><span class="red">*</span><a name="Capture"></a></dt> <dd>The scale, or type, of information that the study is designed to generate from the sample material.</dd> </dl> <table> <thead> <tr> <th>Capture</th> <th>Description</th> </tr> </thead> <tbody> <tr> <td>Whole</td> <td>The project makes use of the whole sample material (most common case).</td> </tr> <tr> <td>Clone Ends</td> <td>Capturing clone end data.</td> </tr> <tr> <td>Exome</td> <td>Capturing exon-specific data.</td> </tr> <tr> <td>Targeted Locus/Loci</td> <td>Capturing specific loci (gene, genomic region, barcode standard).</td> </tr> <tr> <td>Random Survey</td> <td>Not using whole sample, an incomplete survey of the sample.</td> </tr> <tr> <td>Other</td> <td>Specify the scale or type of the captured material in the “Target description”.</td> </tr> </tbody> </table> <dl> <dt><a href="#Target_description">Target description</a><span class="conditionally_required">*</span><a name="Target_description"></a></dt> <dd>Describe the Sample scope/Material/Capture when the Other(s) is selected.</dd> <dt><a href="#Methodology">Methodology</a><span class="red">*</span><a name="Methodology"></a></dt> <dd>The core experimental approach used to obtain the data that is submitted to archival databases.</dd> </dl> <table> <thead> <tr> <th>Methodology</th> <th>Description</th> </tr> </thead> <tbody> <tr> <td>Sequencing</td> <td>Sequencing using Sanger, 454, Illumina, etc wit</td> </tr> <tr> <td>Array</td> <td>Data/Sequence are generated by hybridization arrays.</td> </tr> <tr> <td>Mass Spectroscopy</td> <td>Data are generated by mass spectroscopy.</td> </tr> <tr> <td>Other</td> <td>Please provide data description in the “Methodogy description”.</td> </tr> </tbody> </table> <dl> <dt><a href="#Methodology_description">Methodology description</a><span class="conditionally_required">*</span><a name="Methodology_description"></a></dt> <dd>Describe the methodology type when the Other is selected.</dd> </dl> <h3 id="Area_objective">Objective</h3> <p>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.</p> <dl> <dt><a href="#Objective">Objective</a><span class="red">*</span><a name="Objective"></a></dt> <dd>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.</dd> </dl> <table> <thead> <tr> <th>Objective</th> <th>Description</th> </tr> </thead> <tbody> <tr> <td>Raw Sequence Reads</td> <td>Submission of raw sequencing information as it comes out of machine.</td> </tr> <tr> <td>Sequence</td> <td>Sequence which is not raw - meaning processed (clipped, matepaired, oriented).</td> </tr> <tr> <td>Analysis</td> <td>Higher level interpretation of the data.</td> </tr> <tr> <td>Assembly</td> <td>Experiment will result in assemblies (genome or transcriptome).</td> </tr> <tr> <td>Annotation</td> <td>Experiment wil result in Annotation.</td> </tr> <tr> <td>Variation</td> <td>Submission of variations.</td> </tr> <tr> <td>Epigenetic Markers</td> <td>Experiment will result in Epigenetic markers.</td> </tr> <tr> <td>Expression</td> <td>Submission of gene expression.</td> </tr> <tr> <td>Maps</td> <td>Experiment will result in cytogenetic, physical, Rh, etc…maps.</td> </tr> <tr> <td>Phenotype</td> <td>Experiment will deliver phenotypes.</td> </tr> <tr> <td>Other</td> <td> </td> </tr> </tbody> </table> <h2 id="Target">Target</h2> <h3 id="Area_organism-information">Organism information</h3> <p>Taxonomy and description of target organism.</p> <dl> <dt><a href="#BioProject_Organism_name">Organism name</a><span class="red">*</span><a name="BioProject_Organism_name"></a><a name="BioProject_Organism_name"></a></dt> <dd>Organism name in the <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html">Taxonomy database</a>. Unclassified sequences including metagenome and environmental samples may be found at <a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=12908&lvl=3&lin=f&keep=1&srchmode=1&unlock">here</a>.</dd> </dl> <p>If the project targets multiple organisms, enter a common lineage e.g. “Mammalia” (taxonomy id: <a href="https://ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=40674&lvl=3&lin=f&keep=1&srchmode=1&unlock">40674</a>) for the project targeting “Homo sapiens” and “Mus musculus”. <br /> 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: <a href="https://ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1884818">1884818</a>) for a novel species “Escherichia sp. ABCDEF”. Apply a novel organism name in BioSample.</p> <dl> <dt><a href="#BioProject_Taxonomy_ID">Taxonomy ID</a><a name="BioProject_Taxonomy_ID"></a></dt> <dd><a href="https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html">NCBI Taxonomy ID</a></dd> <dt><a href="#Strain_breed_cultivar">Strain, breed, cultivar</a><a name="Strain_breed_cultivar"></a></dt> <dd>Microbial strain name, or eukaryotic breed or cultivar name. Please provide this or “Isolate name or label”</dd> <dt><a href="#Isolate_name_label">Isolate name or label</a><a name="Isolate_name_label"></a></dt> <dd>A label for an isolated sample, or name of an individual animal (e.g., Clint). Please provide this or “Strain, breed, cultivar”.</dd> <dt><a href="#BioProject_Description">Description</a><a name="BioProject_Description"></a></dt> <dd>A brief description, to elaborate upon the brief label.</dd> </dl> <h2 id="Publication">Publication</h2> <dl> <dt><a href="#BioProject_PubMed_ID">PubMed ID</a><a name="BioProject_PubMed_ID"></a></dt> <dd>The PubMed ID(s) will be used to populate the publication information.</dd> </dl> <div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code><Publication id="15557739"> <DbType>ePubmed</DbType> </Publication> <ProjectReleaseDate> </code></pre></div></div> <dl> <dt><a href="#BioProject_DOI">DOI</a><a name="BioProject_DOI"></a></dt> <dd>Provide a DOI if a PubMed ID is not available.</dd> </dl> <div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code><Publication id="10.1093/nar/gku1120"> <DbType>eDOI</DbType> </Publication> <ProjectReleaseDate> </code></pre></div></div> <h2 id="xml-schema">XML schema</h2> <p><a href="https://github.com/ddbj/pub/tree/master/docs/bioproject">BioProject XML schema</a></p> </main> </section> </div> </section> </div> <footer></footer> <div id="back-top"></div> </body> </html>