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updated to 2023/12/26 version.

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Yoshihiro OKUMURA 2023-12-26 17:11:40 +09:00
parent b7989c8dab
commit 8e90168b8d
8 changed files with 228 additions and 358 deletions
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.gitignore vendored
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.org
s/
embed/
assets/
main.html
.htaccess

65
about.html
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@ -1,65 +0,0 @@
<!DOCTYPE html>
<html>
<head>
<title>About - CBS Data Sharing Platform</title>
<meta charset="UTF-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link rel="stylesheet" href="./assets-frontpage/css/w3.css" />
<link rel="stylesheet" href="./assets-frontpage/css/style.css" />
<link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Raleway" />
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.3/css/fontawesome.min.css" />
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.3/css/brands.min.css" />
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.3/css/solid.min.css" />
<!-- Global site tag (gtag.js) - Google Analytics -->
<script async src="https://www.googletagmanager.com/gtag/js?id=G-21LPSWHRKT"></script>
<script>
window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments);}
gtag('js', new Date());
gtag('config', 'G-21LPSWHRKT');
</script>
</head>
<body>
<!-- About -->
<section class="w3-display-container cbs-dsp-section" id="about">
<h1 class="w3-center">About CBS repository system (2022 Apr)</h1>
<h2>[Purpose]</h2>
<p class="w3-large">The Center for Brain Science (CBS) of RIKEN, explores the mysteries of the brain—one of the ultimate frontiers in natural science—carrying out research at all levels, from cells to organisms and social systems, with the goal of returning those results to society.　The CBS shall contribute to promoting the Institute’s research activities through information technology and maximizing the results of such research, in compliance with the Basic Policy on Management, Disclosure, Sharing, and Use of Research Data (hereinafter “the Basic Policy”) set forth by the Institute. The purpose of the CBS’s Research Data Guidelines (hereinafter “these Guidelines”) is to define matters necessary for handling research data in the CBS so that the researchers, etc. who belong to the CBS can manage research data in an appropriate and reliable manner.</p>
<h2>[Publication data]</h2>
<p class="w3-large">In the Basic Policy, “publication data” refers to any data acquired or generated in the course of research undertaken and published by researchers during their tenure at the Institute except for data that cannot be freely shared due to privacy concerns or legal requirement. All research data in the CBS shall be managed by electronic means. Print and other media that cannot be managed electronic format shall be converted appropriately so that they can be managed by electronic means. Publication data does not include research notes but can include any computer programs referred to but not completely described in published manuscripts. Research data shall be classified as below, depending on how it is used, how it is collected, or its source to make publication data as self-explanatory as possible by using meta-data and information. </p>
<p class="w3-large"><b>[Primary data]</b></p>
<p class="w3-large">Research data newly obtained in the course of research shall be called “primary data.” Primary data includes information generated and collected from observation instruments, measurement instruments, imaging devices or other research instruments used in experiments as well as research data measured and recorded by researchers. Primary data are not processed at all by researchers once obtained.</p>
<p class="w3-large"><b>[Secondary data]</b></p>
<p class="w3-large">“Secondary data” refers to data generated by analytic processing primary data, or derived data. Both primary data and secondary data can be stored in the repository system along with their identifying metadata (see below).</p>
<h2>[Metadata]</h2>
<p class="w3-large">Metadata is organized information that describes, locates, or otherwise makes it easier to retrieve or understand information contained in primary or secondary data. Metadata would include information that is needed to understand and reproduce experiments, analysis and simulations associated with the published manuscript using the data in the corresponding directories contained in the repository. To facilitate communication with the authors involved in the study, metadata should include the ORCID Number or other contact information for all consenting contributing authors.</p>
<h2>[Quality control: CBS disclosure]</h2>
<p class="w3-large">Each PI is responsible of all data generated from their own lab. The PI should carefully consider the format and quality of data uploaded on to the CBS repository system and include sufficient metadata to identify and document the research data. Data can be uploaded to the system by any members of each team, but permission of PI is required to disclose the data to CBS and/or outside CBS. The repository committee may ask PIs to remove data from the system when datasets are inappropriate quality or lack of meta data.</p>
<p class="w3-large">For internally shared data within the system, initial posting would be at the discretion of the PI but can be investigated by the committee as needed.</p>
<h2>[Quality control: external disclosure]</h2>
<p class="w3-large">A DOI should be requested whenever data is made public at which point the data could be made available if the DOI was approved. Any data associated with a manuscript published in a scientific journal should meet the reporting standards required by the journal.</p>
<p class="w3-large">The repository data can be included in published paper as follows: Source data are available at link or DOI here, processed data are provided with this paper.</p>
<h2>[Useful data]</h2>
<p class="w3-large">According to the Basic Policy, “Useful data” means any research data which shall be disclosed along with publication of research papers and other academic documents as well as research data that the CBS repository committee has determined on behalf of the Institute will contribute to the development of science and technology.</p>
<p class="w3-large">In selecting useful data from research data, the data manager or data generator in accord with the data manager will comprehensively evaluate and determine the need for online storage or sharing of the data with others from various perspectives. Factors considered in evaluating the data include the status of research, the management of intellectual property in research, and a basis for the research paper to be written and a careful determination should be made by the disclosing individual(s) according to his/her(their) conscience as a researcher(s).</p>
<h2>[Storage Period]</h2>
<p class="w3-large">As set forth in the Basic Policy, the useful data to be registered in the repository shall be kept for 10 years or longer. Due to various circumstances, such as the advance of science and technology and changes in trends, the value of the useful data may change during the storage period of the useful data. The repository committee shall endeavor to check the useful data registered in the repository on a regular basis and set the disclosure/sharing flag status and license for use that is most suitable for the data.</p>
<h2>[Contact]</h2>
<p class="w3-large">The data provider or PI of the lab takes all responsibility for the data in the repository system and should respond to contact or requests made by the data user.</p>
</section>
<!-- Footer -->
<footer id="footer" class="w3-center w3-black w3-padding-64">
<div class="cbs-dsp-tothetop">
<a href="#about" class="w3-button w3-light-grey"><i class="fas fa-arrow-up w3-margin-right"></i>To the top</a>
</div>
<p class="cbs-copyright">&copy; <a href="https://www.ni.riken.jp/" target="_blank">Neuroinformatics Unit, RIKEN Center for Brain Science</a></p>
</footer>
</body>
</html>

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assets-frontpage/css/style.css
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@ -23,11 +23,11 @@ h6 {
margin: 3rem 0 1.38rem;
}
.cbs-copyright {
.copyright {
margin: 32px auto 0;
}
.cbs-copyright a {
.copyright a {
text-decoration: none;
}
@ -40,7 +40,7 @@ h6 {
padding: 16px;
}
.cbs-dsp-logo {
.dsp-logo {
display: block;
background-image: url("../images/logo32.png");
background-size: cover;
@ -48,12 +48,12 @@ h6 {
height: 32px;
}
.cbs-dsp-navbar-links {
.dsp-navbar-links {
max-width: calc(100% - 74px);
float: right;
}
.cbs-dsp-navbar-links-mbutton {
.dsp-navbar-links-mbutton {
height: 64px;
}
@ -75,23 +75,28 @@ h6 {
width: 300px;
}
.cbs-dsp-section {
.dsp-section {
padding: 80px 24px 32px !important;
min-height: 100%;
}
.cbs-dsp-section > div {
.dsp-section > div {
margin-top: 32px;
}
.cbs-dsp-section a {
.dsp-section a {
text-decoration: none;
}
.cbs-card-link {
.card-link {
text-decoration: none;
}
.dsp-tothetop {
margin: 0 30px 30px;
text-align: right;
}
#home {
background-position: center;
background-size: cover;
@ -106,6 +111,11 @@ h6 {
#home a .w3-card:hover {
background-color: #eee;
}
#about {
min-height: 50%;
}
#memberlist .w3-card {
padding: 16px 32px 32px;
}
@ -131,22 +141,22 @@ h6 {
font-size: 14px;
}
#archive.cbs-dsp-section > div {
#archive.dsp-section > div {
margin-top: 0;
}
#footer .cbs-dsp-links a {
#footer .dsp-links a {
text-decoration: none;
font-weight: bold;
}
#footer .cbs-dsp-links p {
#footer .dsp-links p {
width: 100%;
padding: 5px 0;
}
#footer .cbs-dsp-links img {
#footer .dsp-links img {
width: 100%;
}
#footer .cbs-dsp-tothetop {
#footer .dsp-tothetop {
margin: 0 30px 30px;
text-align: right;
}
@ -157,32 +167,32 @@ h6 {
height: 96px;
}
.cbs-dsp-logo {
.dsp-logo {
background-image: url("../images/logo64.png");
width: 64px;
height: 64px;
}
.cbs-dsp-navbar-links {
.dsp-navbar-links {
width: calc(100% - 96px);
}
.cbs-dsp-navbar-links .w3-button {
.dsp-navbar-links .w3-button {
padding: 12px;
}
.cbs-dsp-navbar-links .w3-dropdown-content {
.dsp-navbar-links .w3-dropdown-content {
z-index: 2;
top: 50px;
}
.cbs-dsp-navbar-links .cbs-dsp-navbar-item {
.dsp-navbar-links .dsp-navbar-item {
max-width: 20%;
font-size: 0.8rem;
}
.cbs-dsp-section {
.dsp-section {
padding: 96px 64px 64px !important;
}
.cbs-dsp-section > div {
.dsp-section > div {
margin-top: 64px;
}
@ -193,17 +203,17 @@ h6 {
}
@media (min-width: 736px) {
.cbs-dsp-navbar-links {
.dsp-navbar-links {
padding: 5px 0;
}
.cbs-dsp-navbar-links .w3-button {
.dsp-navbar-links .w3-button {
padding: 16px;
}
.cbs-dsp-navbar-links .cbs-dsp-navbar-item {
.dsp-navbar-links .dsp-navbar-item {
max-width: 20%;
font-size: 1rem;
}
.cbs-dsp-navbar-links .w3-dropdown-content {
.dsp-navbar-links .w3-dropdown-content {
top: 64px;
}
@ -215,7 +225,7 @@ h6 {
font-size: 18px;
}
#footer .cbs-dsp-links p {
#footer .dsp-links p {
font-size: 18px;
}
}

43
contact.html
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@ -1,43 +0,0 @@
<!DOCTYPE html>
<html>
<head>
<title>CBS Data Sharing Platform</title>
<meta charset="UTF-8" />
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link rel="stylesheet" href="./assets-frontpage/css/w3.css" />
<link rel="stylesheet" href="./assets-frontpage/css/style.css" />
<link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Raleway" />
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.3/css/fontawesome.min.css" />
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.3/css/brands.min.css" />
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.3/css/solid.min.css" />
<!-- Global site tag (gtag.js) - Google Analytics -->
<script async src="https://www.googletagmanager.com/gtag/js?id=G-21LPSWHRKT"></script>
<script>
window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments);}
gtag('js', new Date());
gtag('config', 'G-21LPSWHRKT');
</script>
</head>
<body>
<!-- Contact -->
<section class="w3-display-container w3-center cbs-dsp-section" id="contact">
<h1 class="w3-center"><i class="fas fa-envelope"></i> Contact</h1>
<h2>CBS Neuroinformatics Unit</h2>
<p><b>Email:</b> cbs-is<i class="fas fa-at"></i>ml.riken.jp<br> This repository system is supported by CBS Neuroinformatics Unit. </p>
</section>
<!-- Footer -->
<footer id="footer" class="w3-center w3-black w3-padding-64">
<div class="cbs-dsp-tothetop">
<a href="#contact" class="w3-button w3-light-grey"><i class="fas fa-arrow-up w3-margin-right"></i>To the top</a>
</div>
<p class="cbs-copyright">&copy; <a href="https://www.ni.riken.jp/" target="_blank">Neuroinformatics Unit, RIKEN Center for Brain Science</a></p>
</footer>
</body>
</html>

243
index.html
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@ -26,29 +26,29 @@
<!-- Navbar (sit on top) -->
<header class="w3-top w3-bar w3-white w3-card" id="cbsDspNavbar">
<a href="#home" class="w3-bar-item w3-button">
<div class="cbs-dsp-logo">
<div class="dsp-logo">
<span class="w3-hide">CBS Data Sharing Platform</span>
</div>
</a>
<nav class="cbs-dsp-navbar-links">
<nav class="dsp-navbar-links">
<!-- Top navbar links -->
<div class="w3-hide-small w3-clear w3-margin">
<a href="about.html" class="w3-bar-item w3-button cbs-dsp-navbar-item" target="_blank" ><!--<i class="fas fa-database"></i> --><b>About</b></a>
<a href="policies.html" class="w3-bar-item w3-button cbs-dsp-navbar-item" target="_blank" rel="noopener noreferrer"><!--<i class="fas fa-brain"></i> --><b>General Policies</b></a>
<a href="termofuse.html" class="w3-bar-item w3-button cbs-dsp-navbar-item" target="_blank" ><!--<i class="fas fa-file-signature"></i> --><b>Term of use</b></a>
<a href="memberlist.html" class="w3-bar-item w3-button cbs-dsp-navbar-item" target="_blank"><!--<i class="fas fa-users"></i> --><b>The CBS repository committee</b></a>
<a href="contact.html" class="w3-bar-item w3-button cbs-dsp-navbar-item" target="_blank"><!--<i class="fas fa-envelope"></i> --><b>Contact</b></a>
<!--<div class="w3-dropdown-hover cbs-dsp-navbar-item w3-right">
<button class="w3-bar-item w3-right w3-button w3-clear"><i class="fas fa-globe"></i> Language</button>
<div class="w3-dropdown-content w3-bar-block w3-border">
<a href="./" class="w3-bar-item w3-button">English</a>
<a href="./index.html.ja" class="w3-bar-item w3-button">Japanese</a>
</div>
<a href="#about" class="w3-bar-item w3-button dsp-navbar-item" ><i class="fas fa-project-diagram"></i> <b>About</b></a>
<a href="#policy" class="w3-bar-item w3-button dsp-navbar-item" rel="noopener noreferrer"><i class="fas fa-ruler"></i> <b>General Policies</b></a>
<a href="#termofuse" class="w3-bar-item w3-button dsp-navbar-item"><i class="fas fa-scroll"></i> <b>Term of use</b></a>
<a href="#memberlist" class="w3-bar-item w3-button dsp-navbar-item"><i class="fas fa-users"></i> <b>The CBS repository committee</b></a>
<a href="#dbarchive" class="w3-bar-item w3-button dsp-navbar-item"><i class="fas fa-database"></i> <b>DB archives</b></a>
<a href="#contact" class="w3-bar-item w3-button dsp-navbar-item"><i class="fas fa-envelope"></i> <b>Contact</b></a>
<div class="w3-dropdown-hover dsp-navbar-item w3-right">
<button class="w3-bar-item w3-right w3-button w3-clear"><i class="fas fa-globe"></i> Language</button>
<div class="w3-dropdown-content w3-bar-block w3-border">
<a href="./" class="w3-bar-item w3-button">English</a>
<a target="_blank" href="https://translate.google.com/translate?sl=en&tl=ja&u=https://neurodata.riken.jp/" rel="noopener" class="w3-bar-item w3-button">日本語（自動翻訳）</a>
</div>
</div>
</div>-->
</div>
<!-- Hide right-floated links on small screens and replace them with a menu icon -->
<button class="w3-bar-item w3-button w3-hide-large w3-hide-medium cbs-dsp-navbar-links-mbutton" onclick="openSidebar()">
<button class="w3-bar-item w3-button w3-hide-large w3-hide-medium dsp-navbar-links-mbutton" onclick="openSidebar()">
<i class="fas fa-bars"></i>
</button>
</nav>
@ -58,57 +58,58 @@
<nav class="w3-sidebar w3-bar-block w3-black w3-card w3-animate-left w3-hide-medium w3-hide-large" id="cbsDspSidebar">
<a href="javascript:void(0)" onclick="closeSidebar()" class="w3-bar-item w3-button w3-large w3-padding-16">Close ×</a>
<a href="about.html" onclick="closeSidebar()" class="w3-bar-item w3-button" target="_blank" ><i class="fas fa-database"></i>About</a>
<a href="policies.html" onclick="closeSidebar()" class="w3-bar-item w3-button" target="_blank" ><i class="fas fa-brain"></i> General Policies</a>
<a href="termofuse.html" onclick="closeSidebar()" class="w3-bar-item w3-button" target="_blank" ><i class="fas fa-file-signature"></i> Term of use</a>
<a href="memberlist.html" onclick="closeSidebar()" class="w3-bar-item w3-button" target="_blank"><i class="fas fa-users"></i> The CBS repository committee</a>
<a href="contact.html" onclick="closeSidebar()" class="w3-bar-item w3-button" target="_blank"><i class="fas fa-envelope"></i> Contact</a>
<a href="#about" onclick="closeSidebar()" class="w3-bar-item w3-button"><i class="fas fa-project-diagram"></i>About</a>
<a href="#policy" onclick="closeSidebar()" class="w3-bar-item w3-button"><i class="fas fa-ruler"></i> General Policies</a>
<a href="#termofuse" onclick="closeSidebar()" class="w3-bar-item w3-button"><i class="fas fa-scroll"></i> Term of use</a>
<a href="#memberlist" onclick="closeSidebar()" class="w3-bar-item w3-button"><i class="fas fa-users"></i> The CBS repository committee</a>
<a href="#dbarchive" onclick="closeSidebar()" class="w3-bar-item w3-button"><i class="fas fa-database"></i> DB archives</a>
<a href="#contact" onclick="closeSidebar()" class="w3-bar-item w3-button"><i class="fas fa-envelope"></i> Contact</a>
<!--<div class="w3-dropdown-hover cbs-dsp-navbar-item">
<button class="w3-bar-item w3-button w3-clear"><i class="fas fa-globe"></i> Language</button>
<div class="w3-dropdown-content w3-bar-block w3-dark-gray">
<a href="./" class="w3-bar-item w3-button">English</a>
<a href="./index.html.ja" class="w3-bar-item w3-button">Japanese</a>
<div class="w3-dropdown-hover dsp-navbar-item">
<button class="w3-bar-item w3-button w3-clear"><i class="fas fa-globe"></i> Language</button>
<div class="w3-dropdown-content w3-bar-block w3-dark-gray">
<a href="./" class="w3-bar-item w3-button">English</a>
<a target="_blank" href="https://translate.google.com/translate?sl=en&tl=ja&u=https://neurodata.riken.jp/" rel="noopener" class="w3-bar-item w3-button">日本語（自動翻訳）</a>
</div>
</div>
</div>-->
</nav>
</nav>
<!-- Home -->
<section class="w3-display-container" id="home">
<div class="cbs-dsp-section">
<div class="dsp-section">
<h1 class="w3-text-orange">CBS Data Sharing Platform</h1>
<p class="w3-large w3-text-white">We aim to achieve an analysis platform for the open neuroscience data to expand the research field for each individual in CBS. CBS-DSP provides comprehensive data collection, which allows CBS scientists to generate and stimulate data-driven cross-modal neuroscience. We also plan to expand the platform for all RIKEN, which we expect for CBS researchers to broaden their research field beyond neuroscience.</p>
<div class="w3-row-padding w3-center">
<div class="w3-col l3 m3 w3-margin-bottom">
<a href="https://neurodata.riken.jp/r/login">
<div class="w3-card w3-white w3-centered">
<a href="r/login">
<div class="w3-card w3-white w3-round w3-hover-pale-yellow">
<br />
<i class="fas fa-upload w3-margin-bottom w3-jumbo"></i>
<h2>Upload data set</h2>
</div>
</div>
</a>
</div>
<div class="w3-col l3 m3 w3-margin-bottom">
<a href="https://neurodata.riken.jp/finder/">
<div class="w3-card w3-white w3-centered">
<a href="/finder">
<div class="w3-card w3-white w3-round w3-hover-pale-yellow">
<br />
<i class="fas fa-search w3-margin-bottom w3-jumbo"></i>
<h2>Search for data set</h2>
</div>
</div>
<div class="w3-col l3 m3 w3-margin-bottom">
<a href="https://neurodata.riken.jp/r/">
<div class="w3-card w3-white">
<br />
<a href="/r/">
<div class="w3-card w3-white w3-round w3-hover-pale-yellow">
<br />
<i class="fas fa-th-list w3-margin-bottom w3-jumbo"></i>
<h2>List of labs</h2>
</div>
</a>
</div>
<div class="w3-col l3 m3 w3-margin-bottom">
<a href="https://neurodata.riken.jp/id/">
<div class="w3-card w3-white">
<br />
<a href="/id/">
<div class="w3-card w3-white w3-round w3-hover-pale-yellow">
<br />
<i class="fas fa-file-alt w3-margin-bottom w3-jumbo"></i>
<h2>Data for papers</h2>
</div>
@ -117,7 +118,7 @@
</div>
<div class="w3-row-padding">
<div class="w3-col l4 w3-margin-bottom">
<div class="w3-card w3-white">
<div class="w3-card w3-white w3-round">
<div class="w3-container">
<div class="w3-left"><h4 class="w3-section"><i class="fas fa-chart-bar"></i> Data Volume </h4></div>
<div class="w3-right"><h4 class="w3-section"><span id="volume_bytes"></span></h4></div>
@ -125,7 +126,7 @@
</div>
</div>
<div class="w3-col l3 w3-margin-bottom">
<div class="w3-card w3-white">
<div class="w3-card w3-white w3-round">
<div class="w3-container">
<div class="w3-left"><h4 class="w3-section"><i class="fas fa-folder"></i> Folders </h4></div>
<div class="w3-right"><h4 class="w3-section"><span id="dir_num"></span></h4></div>
@ -133,7 +134,7 @@
</div>
</div>
<div class="w3-col l3 w3-margin-bottom">
<div class="w3-card w3-white">
<div class="w3-card w3-white w3-round">
<div class="w3-container">
<div class="w3-left"><h4 class="w3-section"><i class="fas fa-file"></i> Files </h4></div>
<div class="w3-right"><h4 class="w3-section"><span id="file_num"></span></h4></div>
@ -141,7 +142,7 @@
</div>
</div>
<div class="w3-col l2 w3-margin-bottom">
<div class="w3-card w3-white">
<div class="w3-card w3-white w3-round">
<div class="w3-container">
<div class="w3-left"><h4 class="w3-section"><i class="fas fa-users"></i> Users </h4></div>
<div class="w3-right"><h4 class="w3-section"><span id="user_num"></span></h4></div>
@ -152,12 +153,143 @@
</div>
</section>
<!-- BSI database archive -->
<section class="w3-display-container w3-light-gray cbs-dsp-section" id="dbarchive">
<h1 class="w3-left-align"><i class="fas fa-database"></i> BSI databese archives</h1>
<!-- About -->
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<h2>[Purpose]</h2>
<p class="w3-large">The Center for Brain Science (CBS) of RIKEN, explores the mysteries of the brain—one of the ultimate frontiers in natural science—carrying out research at all levels, from cells to organisms and social systems, with the goal of returning those results to society.　The CBS shall contribute to promoting the Institute’s research activities through information technology and maximizing the results of such research, in compliance with the Basic Policy on Management, Disclosure, Sharing, and Use of Research Data (hereinafter “the Basic Policy”) set forth by the Institute. The purpose of the CBS’s Research Data Guidelines (hereinafter “these Guidelines”) is to define matters necessary for handling research data in the CBS so that the researchers, etc. who belong to the CBS can manage research data in an appropriate and reliable manner.</p>
<h2>[Publication data]</h2>
<p class="w3-large">In the Basic Policy, “publication data” refers to any data acquired or generated in the course of research undertaken and published by researchers during their tenure at the Institute except for data that cannot be freely shared due to privacy concerns or legal requirement. All research data in the CBS shall be managed by electronic means. Print and other media that cannot be managed electronic format shall be converted appropriately so that they can be managed by electronic means. Publication data does not include research notes but can include any computer programs referred to but not completely described in published manuscripts. Research data shall be classified as below, depending on how it is used, how it is collected, or its source to make publication data as self-explanatory as possible by using meta-data and information. </p>
<p class="w3-large"><b>[Primary data]</b></p>
<p class="w3-large">Research data newly obtained in the course of research shall be called “primary data.” Primary data includes information generated and collected from observation instruments, measurement instruments, imaging devices or other research instruments used in experiments as well as research data measured and recorded by researchers. Primary data are not processed at all by researchers once obtained.</p>
<p class="w3-large"><b>[Secondary data]</b></p>
<p class="w3-large">“Secondary data” refers to data generated by analytic processing primary data, or derived data. Both primary data and secondary data can be stored in the repository system along with their identifying metadata (see below).</p>
<h2>[Metadata]</h2>
<p class="w3-large">Metadata is organized information that describes, locates, or otherwise makes it easier to retrieve or understand information contained in primary or secondary data. Metadata would include information that is needed to understand and reproduce experiments, analysis and simulations associated with the published manuscript using the data in the corresponding directories contained in the repository. To facilitate communication with the authors involved in the study, metadata should include the ORCID Number or other contact information for all consenting contributing authors.</p>
<h2>[Quality control: CBS disclosure]</h2>
<p class="w3-large">Each PI is responsible of all data generated from their own lab. The PI should carefully consider the format and quality of data uploaded on to the CBS repository system and include sufficient metadata to identify and document the research data. Data can be uploaded to the system by any members of each team, but permission of PI is required to disclose the data to CBS and/or outside CBS. The repository committee may ask PIs to remove data from the system when datasets are inappropriate quality or lack of meta data.</p>
<p class="w3-large">For internally shared data within the system, initial posting would be at the discretion of the PI but can be investigated by the committee as needed.</p>
<h2>[Quality control: external disclosure]</h2>
<p class="w3-large">A DOI should be requested whenever data is made public at which point the data could be made available if the DOI was approved. Any data associated with a manuscript published in a scientific journal should meet the reporting standards required by the journal.</p>
<p class="w3-large">The repository data can be included in published paper as follows: Source data are available at link or DOI here, processed data are provided with this paper.</p>
<h2>[Useful data]</h2>
<p class="w3-large">According to the Basic Policy, “Useful data” means any research data which shall be disclosed along with publication of research papers and other academic documents as well as research data that the CBS repository committee has determined on behalf of the Institute will contribute to the development of science and technology.</p>
<p class="w3-large">In selecting useful data from research data, the data manager or data generator in accord with the data manager will comprehensively evaluate and determine the need for online storage or sharing of the data with others from various perspectives. Factors considered in evaluating the data include the status of research, the management of intellectual property in research, and a basis for the research paper to be written and a careful determination should be made by the disclosing individual(s) according to his/her(their) conscience as a researcher(s).</p>
<h2>[Storage Period]</h2>
<p class="w3-large">As set forth in the Basic Policy, the useful data to be registered in the repository shall be kept for 10 years or longer. Due to various circumstances, such as the advance of science and technology and changes in trends, the value of the useful data may change during the storage period of the useful data. The repository committee shall endeavor to check the useful data registered in the repository on a regular basis and set the disclosure/sharing flag status and license for use that is most suitable for the data.</p>
<h2>[Contact]</h2>
<p class="w3-large">The data provider or PI of the lab takes all responsibility for the data in the repository system and should respond to contact or requests made by the data user.</p>
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<p>(Last update : 2022 Apr)</p>
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<h1 class="w3-left-align"><i class="fas fa-ruler"></i> General Policies</h1>
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<h2>General Policies</h2>
<p class="w3-large"><b>Eligible depositors:</b> Anyone in CBS may register as user of the CBS repository. All users are allowed to deposit content for which they possess the appropriate rights. To disclose the data to CBS and/or to public approval by a PI is required (see below).</p>
<p class="w3-large"><b>Type of data</b></p>
<p class="w3-large">All type of data generated from investigations by CBS researchers. Content must not violate privacy or copyright, or breach confidentiality or non-disclosure agreements for data collected from human subjects or material transfer or other agreements entered into with other data providers.</p>
<p class="w3-large"><b>Data file formats:</b> All formats are currently allowed - even preservation unfriendly. We are working on guidelines and features that will help people deposit in preservation friendly formats.</p>
<p class="w3-large"><b>Data quality:</b> Each PI is responsible for all data generated from their own lab uploaded to the system. The PI should carefully consider the format and quality of data uploaded on to the CBS repository system and include sufficient metadata to identify and document the research data.</p>
<p class="w3-large"><b>Metadata types and sources:</b> All metadata is stored internally in JSON-format according to a defined JSON schema. Metadata is exported in several standard formats such as MARCXML, Dublin Core, and DataCite Metadata Schema.</p>
<p class="w3-large"><b>Language:</b> English</p>
<h2>Access and Reuse</h2>
<p class="w3-large"><b>Access to data objects:</b> Files may be deposited under closed, open, or embargoed access levels. Files deposited under closed access are protected against unauthorized access at all levels.</p>
<p class="w3-large"><b>Use and re-use of data objects:</b> Use and re-use is subject to the license under which the data objects were deposited. In case the data is included in a separate repository or publication the license should have the same licensing in both sources.</p>
<p class="w3-large"><b>Restricted Access:</b> Users may deposit restricted files with the ability to share access with others if certain requirements are met. These files will not be made publicly available and sharing will be made possible only following the approval of the depositor of the original file.</p>
<p class="w3-large"><b>Metadata access and reuse:</b> Metadata is licensed under CC 0 except for email addresses.</p>
<p class="w3-large"><b>Computer programs:</b> Computer programs are released under one of the following open-source licenses approved by the Open Source Initiative (<a href="https://opensource.org/licenses" target="_blank">https://opensource.org/licenses</a>): Apache License 2.0, BSD 3-Clause, BSD 2-Clause, GPL, LGPL, MIT license, Mozilla Public License 2.0, CDDL and the Eclipse Public License version 2.0. Other open source licenses are subject to approval by the repository committee.</p>
<p class="w3-large"><b>Citations:</b> We request that researchers who use data from the CBS repository system (published or unpublished) in presentations and publications cite and acknowledge the CBS repository system and data production laboratory(s) for referenced dataset(s) or the manuscript in which data is published (if applicable). Authorship credit would be requested for more substantial contributions.</p>
<p class="w3-large"><b>Succession plans:</b> To facilitate communication with contributors after their departure, metadata should include the ORCID Number or other contact information for all consenting contributing authors. In case of closure of the repository, best efforts will be made to integrate all content into suitable alternative institutional and/or subject based repositories. All inquiries should be directed to the original contributor.</p>
<p class="w3-large"><b>Removal:</b> Content not considered to fall under the scope of the repository will be removed by the CBS repository committee. User access may be revoked on violation of Terms of Use.</p>
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<p>(Last update : 2022 Apr)</p>
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<h1 class="w3-left-align"><i class="fas fa-scroll"></i> Term of use</h1>
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<h2>Terms of Use</h2>
<p class="w3-large">Efforts shall be made to appropriately present the license to use useful data, along with the scope of disclosing and sharing the data, or its disclosure/sharing flag status to the recipient of the data in order to prevent infringement on the rights of the holder of the copyright of the data. In a case where a collaborative research agreement or a Material Transfer Agreement (MTA) has been concluded, a license to use useful data shall be sought according to such an agreement.</p>
<p class="w3-large">To determine the status of data use without identifying recipients, it is necessary to ask the receivers to provide their information (such as the name and affiliation of a receiver), together with IP address and other records before downloading the data, in recognition of its being personal information. When the data is to be used as secondary-use results in research data, the license to use the useful data requires the requesting user to specify that they will provide information identifying the data providing source in the body of any published manuscript or to otherwise acknowledge the user’s research paper.</p>
<p class="w3-large">In preparing a license to use useful data, consideration should be given—such as including a provision to request that identifiers for references to source data or the author of the data should be used in the research paper—so that the readers of the research paper can refer to reference source data.</p>
<h2>Citation and Acknowledgement</h2>
<p class="w3-large">We request that researchers who use data from the CBS repository system (published or unpublished) in presentations and publications cite and acknowledge the CBS repository system and data production laboratory(s) for referenced dataset(s).</p>
<h2>Data Use Policy for External Users</h2>
<p class="w3-large">The CBS repository data (a.k.a. research data), tools, and resources are released under the Creative Commons Attribution 4.0 International (CC BY 4.0) License.</p>
<p class="w3-large"><a href="https://creativecommons.org/licenses/by/4.0/" target="_blank">https://creativecommons.org/licenses/by/4.0/</a></p>
<p class="w3-large">Under this license external data users may freely download, analyze and publish results based on any open-access data and tools as soon as they are released, provided they give appropriate credit, a link to the license, and indicate if changes were made. This applies to all open-access datasets generated by individual CBS members, regardless of type or size.</p>
<p class="w3-large">Alternatively, computer programs may be released under an open-source license approved by the Open Source Initiative (<a href="https://opensource.org/licenses" target="_blank">https://opensource.org/licenses</a>). External users are responsible for verifying the nature and terms of the license before using or distributing a program.</p>
<p class="w3-large">Researchers using unpublished data are encouraged to contact the data producers to discuss possible coordinated publications; however, this is optional.</p>
<p class="w3-large">If the data that researchers intended to use are not linked to any journal publication, they are encouraged to contact the data producers to correctly understand the procedures of how these data have been obtained.</p>
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<p>(Last update : 2022 Apr)</p>
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<h1 class="w3-center"><i class="fas fa-users"></i>The CBS repository committee</h1>
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<h1 class="w3-center">Member List</h1>
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<li><a href="https://cbs.riken.jp/en/faculty/t.shimogori/" target="_blank">Tomomi SHIMOGORI</a> (Chair)</li>
<li><a href="https://cbs.riken.jp/en/faculty/s.fujisawa/" target="_blank">Shigeyoshi FUJISAWA <!--(Deputy Chair)--></li>
<li><a href="https://cbs.riken.jp/en/faculty/k.miyamoto/" target="_blank">Kentaro MIYAMOTO</a></li>
<li><a href="https://cbs.riken.jp/en/faculty/l.schmitt/" target="_blank">Lukas Ian SCHMITT</a></li>
<li><a href="https://cbs.riken.jp/en/faculty/k.shibata/" target="_blank">Kazuhisa SHIBATA</a></li>
<li><a href="https://cbs.riken.jp/en/faculty/a.takata/" target="_blank">Atushi TAKATA</a></li>
<li><a href="https://cbs.riken.jp/en/faculty/bia/" target="_blank">Henrik SKIBBE</a></li>
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<h2>CBS Neuroinformatics Unit</h2>
<p><b>Email:</b> cbs-is<i class="fas fa-at"></i>ml.riken.jp<br> This repository system is supported by CBS Neuroinformatics Unit. </p>
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<h1 class="w3-left-align"><i class="fas fa-database"></i> BSI databese and archives</h1>
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<h2>INCF Japan Node</h2>
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<li><a href="https://www.neuroinf.jp/" target="_blank" rel="noopener noreferrer">INCF Japan Node Portal Site</a></li>
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<h2>BSI Neuroinformatics</h2>
<h3>BSI Neuroinformatics</h3>
<ul>
<li><a href="https://bsi-ni.brain.riken.jp/" target="_blank" rel="noopener noreferrer">BSI-NI Project</a></li>
<li><a href="https://celloc3d.brain.riken.jp/" target="_blank" rel="noopener noreferrer">CelLoc3D</a></li>
<li><a href="https://brainatlas.brain.riken.jp/" target="_blank" rel="noopener noreferrer">Brain Atlas</a></li>
<li><a href="https://pupil.brain.riken.jp/" target="_blank" rel="noopener noreferrer">Pupil Platform</a></li>
</ul>
<h2>Tool</h2>
<h3>Tool</h3>
<ul>
<li><a href="https://xoonips.osdn.jp/" target="_blank" rel="noopener noreferrer">XooNIps</a></li>
<li><a href="https://cosmodb.osdn.jp/" target="_blank" rel="noopener noreferrer">CosmoDB</a></li>
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<p class="cbs-copyright">&copy; <a href="https://www.ni.riken.jp/" target="_blank">Neuroinformatics Unit, RIKEN Center for Brain Science</a></p>
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<li><a href="https://cbs.riken.jp/en/faculty/s.fujisawa/" target="_blank">Shigeyoshi FUJISAWA <!--(Deputy Chair)--></li>
<li><a href="https://cbs.riken.jp/en/faculty/k.miyamoto/" target="_blank">Kentaro MIYAMOTO</a></li>
<li><a href="https://cbs.riken.jp/en/faculty/l.schmitt/" target="_blank">Lukas Ian SCHMITT</a></li>
<li><a href="https://cbs.riken.jp/en/faculty/k.shibata/" target="_blank">Kazuhisa SHIBATA</a></li>
<li><a href="https://cbs.riken.jp/en/faculty/a.takata/" target="_blank">Atushi TAKATA</a></li>
<li><a href="https://cbs.riken.jp/en/faculty/bia/" target="_blank">Henrik SKIBBE</a></li>
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<h1 class="w3-center">General Policies</h1>
<h2>General Policies (2022 Apr)</h2>
<p class="w3-large"><b>Eligible depositors:</b> Anyone in CBS may register as user of the CBS repository. All users are allowed to deposit content for which they possess the appropriate rights. To disclose the data to CBS and/or to public approval by a PI is required (see below).</p>
<p class="w3-large"><b>Type of data</b></p>
<p class="w3-large">All type of data generated from investigations by CBS researchers. Content must not violate privacy or copyright, or breach confidentiality or non-disclosure agreements for data collected from human subjects or material transfer or other agreements entered into with other data providers.</p>
<p class="w3-large"><b>Data file formats:</b> All formats are currently allowed - even preservation unfriendly. We are working on guidelines and features that will help people deposit in preservation friendly formats.</p>
<p class="w3-large"><b>Data quality:</b> Each PI is responsible for all data generated from their own lab uploaded to the system. The PI should carefully consider the format and quality of data uploaded on to the CBS repository system and include sufficient metadata to identify and document the research data.</p>
<p class="w3-large"><b>Metadata types and sources:</b> All metadata is stored internally in JSON-format according to a defined JSON schema. Metadata is exported in several standard formats such as MARCXML, Dublin Core, and DataCite Metadata Schema.</p>
<p class="w3-large"><b>Language:</b> English</p>
<h2>Access and Reuse</h2>
<p class="w3-large"><b>Access to data objects:</b> Files may be deposited under closed, open, or embargoed access levels. Files deposited under closed access are protected against unauthorized access at all levels.</p>
<p class="w3-large"><b>Use and re-use of data objects:</b> Use and re-use is subject to the license under which the data objects were deposited. In case the data is included in a separate repository or publication the license should have the same licensing in both sources.</p>
<p class="w3-large"><b>Restricted Access:</b> Users may deposit restricted files with the ability to share access with others if certain requirements are met. These files will not be made publicly available and sharing will be made possible only following the approval of the depositor of the original file.</p>
<p class="w3-large"><b>Metadata access and reuse:</b> Metadata is licensed under CC 0 except for email addresses.</p>
<p class="w3-large"><b>Computer programs:</b> Computer programs are released under one of the following open-source licenses approved by the Open Source Initiative (<a href="https://opensource.org/licenses" target="_blank">https://opensource.org/licenses</a>): Apache License 2.0, BSD 3-Clause, BSD 2-Clause, GPL, LGPL, MIT license, Mozilla Public License 2.0, CDDL and the Eclipse Public License version 2.0. Other open source licenses are subject to approval by the repository committee.</p>
<p class="w3-large"><b>Citations:</b> We request that researchers who use data from the CBS repository system (published or unpublished) in presentations and publications cite and acknowledge the CBS repository system and data production laboratory(s) for referenced dataset(s) or the manuscript in which data is published (if applicable). Authorship credit would be requested for more substantial contributions.</p>
<p class="w3-large"><b>Succession plans:</b> To facilitate communication with contributors after their departure, metadata should include the ORCID Number or other contact information for all consenting contributing authors. In case of closure of the repository, best efforts will be made to integrate all content into suitable alternative institutional and/or subject based repositories. All inquiries should be directed to the original contributor.</p>
<p class="w3-large"><b>Removal:</b> Content not considered to fall under the scope of the repository will be removed by the CBS repository committee. User access may be revoked on violation of Terms of Use.</p>
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<title>Term of use - CBS Data Sharing Platform</title>
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<h1 class="w3-center">Term of use</h1>
<h2>Terms of Use (Apr 2022)</h2>
<p class="w3-large">Efforts shall be made to appropriately present the license to use useful data, along with the scope of disclosing and sharing the data, or its disclosure/sharing flag status to the recipient of the data in order to prevent infringement on the rights of the holder of the copyright of the data. In a case where a collaborative research agreement or a Material Transfer Agreement (MTA) has been concluded, a license to use useful data shall be sought according to such an agreement.</p>
<p class="w3-large">To determine the status of data use without identifying recipients, it is necessary to ask the receivers to provide their information (such as the name and affiliation of a receiver), together with IP address and other records before downloading the data, in recognition of its being personal information. When the data is to be used as secondary-use results in research data, the license to use the useful data requires the requesting user to specify that they will provide information identifying the data providing source in the body of any published manuscript or to otherwise acknowledge the user’s research paper.</p>
<p class="w3-large">In preparing a license to use useful data, consideration should be given—such as including a provision to request that identifiers for references to source data or the author of the data should be used in the research paper—so that the readers of the research paper can refer to reference source data.</p>
<h2>Citation and Acknowledgement</h2>
<p class="w3-large">We request that researchers who use data from the CBS repository system (published or unpublished) in presentations and publications cite and acknowledge the CBS repository system and data production laboratory(s) for referenced dataset(s).</p>
<h2>Data Use Policy for External Users</h2>
<p class="w3-large">The CBS repository data (a.k.a. research data), tools, and resources are released under the Creative Commons Attribution 4.0 International (CC BY 4.0) License.</p>
<p class="w3-large"><a href="https://creativecommons.org/licenses/by/4.0/" target="_blank">https://creativecommons.org/licenses/by/4.0/</a></p>
<p class="w3-large">Under this license external data users may freely download, analyze and publish results based on any open-access data and tools as soon as they are released, provided they give appropriate credit, a link to the license, and indicate if changes were made. This applies to all open-access datasets generated by individual CBS members, regardless of type or size.</p>
<p class="w3-large">Alternatively, computer programs may be released under an open-source license approved by the Open Source Initiative (<a href="https://opensource.org/licenses" target="_blank">https://opensource.org/licenses</a>). External users are responsible for verifying the nature and terms of the license before using or distributing a program.</p>
<p class="w3-large">Researchers using unpublished data are encouraged to contact the data producers to discuss possible coordinated publications; however, this is optional.</p>
<p class="w3-large">If the data that researchers intended to use are not linked to any journal publication, they are encouraged to contact the data producers to correctly understand the procedures of how these data have been obtained.</p>
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