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<html>
<head>
<!-- Global site tag (gtag.js) - Google Analytics -->
<script async src="https://www.googletagmanager.com/gtag/js?id=G-XL6BRW702X"></script>
<script>
window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments);}
gtag('js', new Date());
gtag('config', 'G-XL6BRW702X');
</script>
<title>SciData - A Scientific Data Model</title>
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<base href="https://stuchalk.github.io/scidata/" />
<meta http-equiv="content-type" content="text/html; charset=utf-8" />
<!-- Latest compiled and minified CSS -->
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha384-BVYiiSIFeK1dGmJRAkycuHAHRg32OmUcww7on3RYdg4Va+PmSTsz/K68vbdEjh4u" crossorigin="anonymous"/>
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<style>
.list-group-item {
padding: 3px 10px
}
ul {
padding-left: 25px;
}
</style>
</head>
<body>
<div class="container theme-showcase" role="main">
<div class="well text-justify" style="padding-top: 5px;margin-top: 20px;">
<h3>SciData - A Scientific Data Model <a href="https://github.com/stuchalk/scidata" target="_blank" class="btn btn-danger btn-sm pull-right">GitHub Repo</a>
<a href="https://doi.org/10.1186/s13321-016-0168-9" target="_blank" class="btn btn-info btn-sm pull-right" style="margin-right: 10px;">Research Paper</a>
<a href="https://scidata.unf.edu" target="_blank" class="btn btn-success btn-sm pull-right" style="margin-right: 10px;">Data Portal</a></h3>
SciData is a data model for scientific data (JSON-LD implementation shown below right) that provides a
ontologically defined framework for organizing both the data and metadata from scientific experiments, calculations, and theories.
Data from any science discipline can be contained in the framework using existing semantic definition of data elements (via ontologies)
<i class="pull-right">Open science, open data, open code, open concept - it's all about the data!</i>
</div>
<div class="row">
<div class="col-sm-6">
<h4 style="margin-top: 0;">SciData JSON-LD Context Documents</h4>
<p style="text-align: justify;">Importing context documents in JSON-LD files allows their use in multiple
documents. This is the same way that XML (and JSON) schema work except the context is not defining rules
of what the content of the JSON values can be, rather the assignment of semantic meaning to the values.
A list of example files is <a href="examples/index.html">here</a> and includes data from PubChem, the
Dortmund Data Bank (DDB), and a Crystallography Information Framework (CIF) file.</p>
<p style="text-align: justify;">The content of this site was updated in Dec. 2022 to better
reflect the current status of the SciData Framework specification. In the examples of
<code>Aspects</code> and <code>Facets</code> below the prefix 'crg' (Chalk Research Group)
has been used to better represent that these examples are not part of the SciData specification,
rather examples of a user (or user community) defining the metadata elements needed for their research data.</p>
<p style="text-align: justify;">Also, the Data Portal link above has been added where we will be
adding open datasets. Finally, if you have any feedback please consider adding it as an issue
on the GitHub <a href="https://github.com/stuchalk/scidata/issues" target="_blank">repo</a>.</p>
<div class="panel panel-info">
<div class="panel-heading">
<h3 class="panel-title">SciData Framework JSON-LD Contexts</h3>
</div>
<div class="list-group">
<a class="list-group-item" href="contexts/scidata.jsonld"><span class="glyphicon glyphicon-link" aria-hidden="true"></span> <b>scidata</b> - Top level JSON-LD context for each scidata document</a>
<a class="list-group-item" href="contexts/scidata_dataset.jsonld"><span class="glyphicon glyphicon-link" aria-hidden="true"></span> <b>scidata_dataset</b> - Dataset (includes datagroup, dataseries, datapoint)</a>
<a class="list-group-item" href="contexts/scidata_parameter.jsonld"><span class="glyphicon glyphicon-link" aria-hidden="true"></span> <b>scidata_parameter</b> - Generic parameter or array of parameter values</a>
<a class="list-group-item" href="contexts/scidata_value.jsonld"><span class="glyphicon glyphicon-link" aria-hidden="true"></span> <b>scidata_value</b> - A value (numeric or text) or array of values</a>
<a class="list-group-item" href="contexts/scidata_unit.jsonld"><span class="glyphicon glyphicon-link" aria-hidden="true"></span> <b>scidata_unit</b> - Representation or referencing of scientific units</a>
</div>
</div>
<div class="panel panel-success">
<div class="panel-heading">
<h3 class="panel-title">Example JSON-LD Contexts for 'Aspects' of Methodology</h3>
</div>
<div class="panel-body" style="padding: 5px;">
<ul>
<li>For Experimental Data <ul>
<li><a href="contexts/crg_measurement.jsonld">crg_measurement</a> - object for
measurement metadata</li>
<li><a href="contexts/crg_procedure.jsonld">crg_procedure</a> - object for
procedural metadata</li>
<li><a href="contexts/crg_resource.jsonld">crg_resource</a> - object for
laboratory resource metadata </li>
</ul>
</li>
</ul>
<ul>
<li>For Computational Data <ul>
<li><a href="contexts/crg_basisset.jsonld">crg_basisset</a> - object for basis
set metadata (<a href="examples/sections/basisset.jsonld">example</a>)</li>
<li><a href="contexts/crg_calculation.jsonld">crg_calculation</a> - object for
calculation metadata (<a href="examples/sections/calculation.jsonld">example</a>)</li>
<li><a href="contexts/crg_software.jsonld">crg_software</a> - object for
computational software metadata (<a href="examples/sections/software.jsonld"
>example</a>)</li>
</ul>
</li>
</ul>
</div>
</div>
<div class="panel panel-warning">
<div class="panel-heading">
<h3 class="panel-title">Example JSON-LD Contexts for 'Facets' of the System</h3>
</div>
<div class="panel-body" style="padding: 5px;">
<ul>
<li>For Experimental Data <ul>
<li><a href="contexts/crg_chemical.jsonld">crg_chemical</a> -
(manufactured) chemical/sample metadata</li>
<li><a href="contexts/crg_substance.jsonld">crg_substance</a> -
chemical substance metadata</li>
<li><a href="contexts/crg_material.jsonld">crg_material</a> -
materials metadata</li>
<li><a href="contexts/crg_organism.jsonld">crg_organism</a> -
organism metadata</li>
<li><a href="contexts/crg_mixture.jsonld">crg_mixture</a> - mixture (chemical
system) metadata</li>
</ul>
</li>
</ul>
<ul>
<li>For Computational Data <ul>
<li><a href="contexts/crg_computer.jsonld">crg_computer</a> - object for
computer processing metadata</li>
<li><a href="contexts/crg_molsystem.jsonld">crg_molsystem</a> - object for
molecular system metadata</li>
</ul>
</li>
</ul>
</div>
</div>
</div>
<div class="col-sm-6">
<div>
<img src="images/scidata_framework.png" class="img-responsive center-block" />
</div>
<div class="row">
<div class="col-md-10 col-md-offset-1 well" style="margin-top: 10px;margin-bottom: 10px;">
<div class="col-md-6">
<img src="images/stuchalk.jpg" class="thumbnail" style="width: 160px;margin-bottom: 1px;"/>
</div>
<div class="col-md-6" style="padding-right: 10px;">
<p>Stuart Chalk<br />
Department of Chemistry<br />
University of North Florida<br />
Phone: 1-904-620-1938<br />
Email: <a href="mailto:schalk@unf.edu">schalk@unf.edu</a><br />
ORCID: <a href="http://orcid.org/0000-0002-0703-7776" target="_blank">0000-0002-0703-7776</a>
</p>
<a href="https://www.linkedin.com/in/stuchalk" target="_blank">
<img src="images/btn_viewmy_160x25.png" alt="View Stuart Chalk's profile on LinkedIn" height="25" width="160"/>
</a>
</div>
</div>
</div>
</div>
</div>
</div>
</body>
</html>