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Overview.html
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<?xml version="1.0" encoding="utf-8"?>
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
<head>
<title>Dataset Descriptions: HCLS Community Profile</title>
<!--
TODO list:
* fix References, citations
* left-align "Description" field of RDF bundle table
-->
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border-collapse:collapse;
}
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border:1px solid black;
padding:1em;
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table#namespaces td {
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pre {
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</head>
<body>
<div class="head">
<p><a href="http://www.w3.org/">
<img src="http://www.w3.org/Icons/w3c_home" alt="W3C" height="48" width="72" /></a></p>
<h1 id="main">Dataset Descriptions: HCLS Community Profile</h1>
<!-- h2 class="no-num no-toc" id="w3c-doctype">W3C Working Draft 4 April 2008</h2 -->
<dl>
<dt>Editors working draft.</dt>
<dt>Editors:</dt>
<dd>Alasdair J.G. Gray, Heriott-Watt University, UK <<a href="mailto:A.J.G.Gray@hw.ac.uk">A.J.G.Gray@hw.ac.uk</a>></dd>
<dd>Michel Dumontier, Stanford University, USA <<a href="mailto:michel.dumontier@stanford.edu">michel.dumontier@stanford.edu</a>></dd>
<dd>M. Scott Marshall, MAASTRO Clinic, The Netherlands <<a href="mailto:m.scott.marshall@maastro.nl">m.scott.marshall@maastro.nl</a>></dd>
<dd>Joachim Baran, Stanford University, USA <<a href="mailto:joachim.baran@stanford.edu">joachim.baran@stanford.edu</a>></dd>
<dt>Contributors:</dt>
<dd>Peter Ansell, CSIRO, Australia <<a href="mailto:peter.ansell@csiro.au">peter.ansell@csiro.au</a>></dd>
<dd>Gary D. Bader, The Donnelly Centre, University of Toronto, Canada <<a href="mailto:gary.bader@utoronto.ca">gary.bader@utoronto.ca</a>></dd>
<dd>Asuka Bando, NBDC, Japan <<a href="mailto:bando@biosciencedbc.jp">bando@biosciencedbc.jp</a>></dd>
<dd>Jerven Bolleman, SIB Swiss Institute of Bioinformatics, Switzerland <<a href="mailto:jerven.bolleman@isb-sib.ch">jerven.bolleman@isb-sib.ch</a>></dd>
<dd>Alison Callahan, Carleton University, Canada <<a href="alison.callahan@carleton.ca">alison.callahan@carleton.ca</a>></dd>
<dd>José Cruz-Toledo, Carleton University, Canada <<a href="mailto:josecruztoledo@cmail.carleton.ca">josecruztoledo@cmail.carleton.ca</a>></dd>
<dd>Pascale Gaudet, SIB Swiss Institute of Bioinformatics, Switzerland <<a href="mailto:pascale.gaudet@isb-sib.ch">pascale.gaudet@isb-sib.ch</a>></dd>
<dd>Erich Gombocz, IO Informatics, USA <<a href="mailto:egombocz@io-informatics.com">egombocz@io-informatics.com</a>></dd>
<dd>Alejandra Gonzalez-Beltran, University of Oxford, UK <<a href="mailto:alejandra.gonzalez.beltran@gmail.com">alejandra.gonzalez.beltran@gmail.com</a>></dd>
<dd>Paul Groth, VU University Amsterdam, The Netherlands <<a href="mailto:p.t.groth@vu.nl"> p.t.groth@vu.nl</a>></dd>
<dd>Melissa Haendel, Oregon Health and Science University, USA <<a href="mailto:haendel@ohsu.edu">haendel@ohsu.edu</a>></dd>
<dd>Maori Ito, NIBIO, Japan <<a href="mailto:maori@nibio.go.jp">maori@nibio.go.jp</a>></dd>
<dd>Simon Jupp, EMBL-EBI, UK <<a href="mailto:jupp@ebi.ac.uk">jupp@ebi.ac.uk</a>></dd>
<dd>Toshiaki Katayama, Database Center for Life Sciences, Japan <<a href="mailto:ktym@dbcls.jp">ktym@dbcls.jp</a>></dd>
<dd>Kalpana Krishnaswami, Metaome, USA <<a href="mailto:kalpana@metaome.com">kalpana@metaome.com</a>></dd>
<dd>Simon Lin, Marshfield Clinic Research Foundation, USA <<a href="mailto:lin.simon@mcrf.mfldclin.edu">lin.simon@mcrf.mfldclin.edu</a>></dd>
<dd>Michael Miller, Institute for Systems Biology, USA <<a href="mailto:mmiller@systemsbiology.org">mmiller@systemsbiology.org</a>></dd>
<dd>Chris Mungall, Lawrence Berkeley National Laboratory, USA <<a href="mailto:cjm@berkeleybop.org">cjm@berkeleybop.org</a>></dd>
<dd>Nicolas Le Novère, Babraham Institute, UK <<a href="mailto:n.lenovere@gmail.com">n.lenovere@gmail.com</a>></dd>
<dd>Camille Laibe, EMBL-EBI, UK <<a href="mailto:laibe@ebi.ac.uk">laibe@ebi.ac.uk</a>></dd>
<dd>Nick Juty, EMBL-EBI, UK <<a href="mailto:juty@ebi.ac.uk">juty@ebi.ac.uk</a>></dd>
<dd>Sarala Wimalaratne, EMBL-EBI, UK <<a href="mailto:sarala@ebi.ac.uk">sarala@ebi.ac.uk</a>></dd>
<dd>James Malone, EMBL-EBI, UK <<a href="mailto:malone@ebi.ac.uk">malone@ebi.ac.uk</a>></dd>
<dd>Laurens Rietveld, VU University Amsterdam, The Netherlands <<a href="mailto:laurens.rietveld@vu.nl">laurens.rietveld@vu.nl</a>></dd>
<dd>Sarala M. Wimalaratne, EMBL-EBI, UK <<a href="mailto:sarala@ebi.ac.uk">sarala@ebi.ac.uk</a>></dd>
</dl>
<p class="copyright"><a href="http://www.w3.org/Consortium/Legal/ipr-notice#Copyright">Copyright</a> © 2014 <a href="http://www.w3.org/"><acronym title="World Wide Web Consortium">W3C</acronym></a><sup>®</sup> (<a href="http://www.csail.mit.edu/"><acronym title="Massachusetts Institute of Technology">MIT</acronym></a>, <a href="http://www.ercim.org/"><acronym title="European Research Consortium for Informatics and Mathematics">ERCIM</acronym></a>, <a href="http://www.keio.ac.jp/">Keio</a>, <a href="http://ev.buaa.edu.cn/">Beihang</a>), All Rights Reserved. W3C <a href="http://www.w3.org/Consortium/Legal/ipr-notice#Legal_Disclaimer">liability</a>, <a href="http://www.w3.org/Consortium/Legal/ipr-notice#W3C_Trademarks">trademark</a> and <a href="http://www.w3.org/Consortium/Legal/copyright-documents">document use</a> rules apply.</p>
</div>
<hr title="Separator for header" />
<div>
<h2 class="notoc" id="abstract">Abstract</h2>
<p>Access to consistent, high-quality metadata is critical to finding, understanding, and reusing scientific data. This document describes a consensus among participating stakeholders in the Health Care and the Life Sciences domain on the description of datasets using the Resource Description Framework (RDF). This specification meets key functional requirements, reuses existing vocabularies to the extent that it is possible, and addresses elements of data description, versioning, provenance, discovery, exchange, query, and retrieval.
</p>
</div>
<div>
<h2 id="status">Status of This Document</h2>
<p>This is an editor's draft of a document for the <a href="../..">Semantic Web in Health Care and Life Sciences Interest Group (HCLSIG)</a>. This is a live document and is subject to change without notice. It reflects the best effort of the editors to reflect implementation experience and incorporate input from various members of the IG, but is not yet endorsed by the IG as a whole. This document is not endorsed by the W3C or its member companies.</p>
</div>
<hr />
<div class="toc">
<h2 id="contents">Table of Contents</h2>
<ul class="toc">
<li class="tocline1"><a href="#introduction">1 Introduction</a> </li>
<li class="tocline1"><a href="#scope">2 Scope</a> </li>
<li class="tocline1"><a href="#conventions">3 Conventions</a> </li>
<li class="tocline1"><a href="#functionalrequirements">4 Functional Requirements</a> </li>
<li class="tocline2"><a href="#s4_1">4.1 Dataset Identification, Description, Licensing, and Provenance</a></li>
<li class="tocline2"><a href="#s4_2">4.2 Dataset Discovery (via Catalog)</a></li>
<li class="tocline2"><a href="#s4_3">4.3 Exchange of Dataset Descriptions</a></li>
<li class="tocline2"><a href="#s4_4">4.4 Dataset Linking</a></li>
<li class="tocline2"><a href="#s4_5">4.5 Content Summary</a></li>
<li class="tocline2"><a href="#s4_6">4.6 Monitoring of Dataset Changes</a></li>
<li class="tocline1"><a href="#datasetdescriptionlevels">5 Dataset Description Levels</a> </li>
<li class="tocline1"><a href="#metadataguidancenotes">6 Metadata Guidance Notes</a> </li>
<li class="tocline2"><a href="#s6_1">6.1 Literals</a></li>
<li class="tocline2"><a href="#s6_2">6.2 Core Metadata</a></li>
<li class="tocline2"><a href="#s6_3">6.3 Identifiers</a></li>
<li class="tocline2"><a href="#s6_4">6.4 Provenance and Change</a></li>
<li class="tocline2"><a href="#s6_5">6.5 Availability and Distributions</a></li>
<li class="tocline2"><a href="#s6_6">6.6 Statistics</a></li>
<li class="tocline2"><a href="#s6_7">6.7 Workflows</a></li>
<li class="tocline1"><a href="#toolingsupport">7 Tooling Support</a> </li>
<li class="tocline2"><a href="#s7_1">7.1 Dataset Description Generation Tool</a></li>
<li class="tocline2"><a href="#s7_2">7.2 Validation Tool</a></li>
<li class="tocline1"><a href="#usecases">8 Use Cases</a> </li>
<li class="tocline2"><a href="#s8_1">8.1 Marshfield Use Case</a></li>
<li class="tocline2"><a href="#s8_2">8.2 Metaome Transcriptomics Use Case</a></li>
<li class="tocline2"><a href="#s8_3">8.3 Radiotherapy Research Use Case</a></li>
<li class="tocline2"><a href="#s8_4">8.4 Computational Network Biology</a></li>
<li class="tocline2"><a href="#s8_5">8.5 Safety Information Evaluation and Visual Exploration ("SIEVE")</a></li>
<li class="tocline2"><a href="#s8_6">8.6 Sampling Large RDF Graphs</a></li>
<li class="tocline2"><a href="#s8_7">8.7 Query Formulation Using Data Metrics</a></li>
<li class="tocline2"><a href="#s8_8">8.8 Data Providers</a></li>
<li class="tocline2"><a href="#s8_9">8.9 Data Catalogs</a></li>
<li class="tocline2"><a href="#s8_10">8.10 Experimental Datasets Use Case</a></li>
<li class="tocline1"><a href="#references">9 References</a> </li>
<li class="tocline1"><a href="#appendix">Appendix</a> </li>
<li class="tocline2"><a href="#appendix_1">10.1 Complete Example of a Dataset Description</a></li>
</ul>
</div>
<!--
<h3 id="appendices">Appendices</h3>
<ul class="toc">
<li class="tocline2"><a href="#rdfbundles">A RDF Sources</a></li>
<li class="tocline2"><a href="#chlog">Change Log</a></li>
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<hr />
<h2 id="introduction">1 Introduction</h2>
<p>Big Data presents an exciting opportunity to pursue large-scale analyses over collections of data in order to uncover valuable insights across a myriad of fields and disciplines. Yet, as more and more data is made available, researchers are finding it increasingly difficult to discover and reuse these data. One problem is that <strong>data are insufficiently described</strong> to understand what they are or how they were produced. A second issue is that <strong>no single vocabulary provides all key metadata fields</strong> required to support basic scientific use cases. A third issue is that <strong>data catalogs and data repositories all use different metadata standards</strong>, if they use any standard at all, and this prevents easy search and aggregation of data. Therefore, we need a guide to indicate what are the essential metadata, and the manner in which we can express it.</p>
<p>For the purposes of this document, we <strong>define a dataset</strong> as "A collection of data, available for access or download in one or more formats" [<a href="#DCAT">DCAT</a>]. For instance, a dataset may be generated as part of some scientific investigation, whether tabulated from observations, generated by an instrument, obtained via analysis, created through a mashup, or enhanced or changed in some manner. Research data are available in research publications and supplemental documents, in literature curated databases such as PharmGKB or the CTD, from research repositories such as BioMedCentral-BGI GigaScience [<a href="#GigaScience">GigaScience</a>], Nature Publishing Group’s Scientific Data [<a href="#ScientificData">ScientificData</a>], Dryad Digital Repository [<a href="#Dryad">Dryad</a>], FigShare [<a href="#FigShare">FigShare</a>], Harvard Dataverse [<a href="#Dataverse">Dataverse</a>]. Cross-repository access is possible through data catalogs such as Neuroscience Information Framework (NIF) [<a href="#NIF">NIF</a>], BioSharing [<a href="#BioSharing">BioSharing</a>], Identifiers.org Registry [<a href="#Identifiers.org">Identifiers.org</a>], Integbio Database Catalog [<a href="#Integbio">Integbio</a>], Force11 [<a href="#Force11">Force11</a>], and CKAN’s datahub [<a href="#Datahub">Datahub</a>].</p>
<p>While several vocabularies are relevant in describing datasets, none are sufficient to completely provide the breadth of requirements identified in Health Care and the Life Sciences. The Dublin Core Metadata Initiative (DCMI) [<a href="#DCMI">DCMI</a>] Metadata Terms offers a broad set of types and relations for capturing document metadata. The Data Catalog Vocabulary (DCAT) [<a href="#DCAT">DCAT</a>] is used to describe datasets in catalogs, but does not deal with the issue of dataset evolution and versioning. The Provenance Ontology (PROV) [<a href="#PROV">PROV</a>] can be used to capture information about entities, activities, and people involved in producing a piece of data or thing. The Vocabulary of Interlinked Datasets (VOID) [<a href="#VOID">VOID</a>] is an RDF Schema vocabulary for expressing metadata about RDF datasets. Schema.org has a limited proposal for dataset descriptions [<a href="#SCHEMA">SCHEMA</a>]. Thus, there is need to combine these vocabularies in a comprehensive manner that meets the needs of data registries, data producers, and data consumers.</p>
<p>Here we describe the efforts of a multi-stakeholder effort under the auspices of the W3C Semantic Web for Health Care and Life Sciences [<a href="#HCLS">HCLS</a>] Interest Group to produce a specification for the description of datasets that meets key functional requirements, uses existing vocabularies, and is expressed using the Resource Description Framework [<a href="#RDF">RDF</a>]. We discuss elements of data description including provenance and versioning, and describe how these can be used for data discovery, exchange, and query (with SPARQL). This then enables the retrieval and reuse of data to encourage reproducible science.</p>
<p>
Specifically, we provide
</p>
<ul>
<li>A community specification for describing datasets (<a href="#datasetdescriptionlevels">Section 5</a>) in RDF with detailed guidance notes (<a href="#metadataguidancenotes">Section 6</a>).</li>
<li>Detailed requirements (<a href="#functionalrequirements">Section 4</a>) that have been drawn from a wide range of use cases (<a href="#usecases">Section 8</a>).</li>
</ul>
<h2 id="scope">2 Scope</h2>
<p>This document focuses on common data elements and their value sets for the description of data. Although use cases are drawn from Health Care and the Life Sciences, this document will focus on requirements that are broadly applicable.</p>
<h2 id="conventions">3 Conventions</h2>
<p>The key words "MUST", "MUST NOT", "REQUIRED", "SHALL", "SHALL NOT", "SHOULD", "SHOULD NOT", "RECOMMENDED", "MAY", and "OPTIONAL" in this document are to be interpreted as described in RFC 2119.</p>
<p>RDF data in this document are expressed in Turtle [<a href="#ref-TURTLE">TURTLE</a>]. Queries on this data are expressed in SPARQL [<a href="#ref-SPARQL">SPARQL</a>]. The following namespace prefix bindings are assumed unless otherwise stated:</p>
<div style="text-align: center;">
<table style="border-collapse: collapse; border-color: #000000" border="1" cellpadding="5">
<tr><th>Prefix</th> <th>URI</th> <th>Description</th></tr>
<tr><td><code>cito:</code></td> <td><code>http://purl.org/spar/cito/</code></td> <td><a href="http://purl.org/spar/cito/">Citation Typing Ontology</a></td></tr>
<tr><td><code>dcat:</code></td> <td><code>http://www.w3.org/ns/dcat#</code></td> <td><a href="http://www.w3.org/TR/vocab-dcat/">Data Catalog</a></td></tr>
<tr><td><code>dctypes:</code></td> <td><code>http://purl.org/dc/dcmitype/</code></td> <td><a href="http://purl.org/dc/dcmitype/">Dublin Core Metadata Types</a></td></tr>
<tr><td><code>dct:</code></td> <td><code>http://purl.org/dc/terms/</code></td> <td><a href="http://purl.org/dc/terms/">Dublin Core Metadata Terms</a></td></tr>
<tr><td><code>foaf:</code></td> <td><code>http://xmlns.com/foaf/0.1/</code></td> <td><a href="http://xmlns.com/foaf/0.1/">Friend-of-a-Friend</a></td></tr>
<tr><td><code>freq:</code></td> <td><code>http://purl.org/cld/freq/</code></td> <td><a href="http://dublincore.org/groups/collections/frequency/">Collection Description Frequency Vocabulary</a></td></tr>
<tr><td><code>idot:</code></td> <td><code>http://identifiers.org/idot/</code></td> <td><a href="http://identifiers.org/idot/">Identifiers.org vocabulary</a></td></tr>
<tr><td><code>lexvo:</code></td> <td><code>http://lexvo.org/ontology#</code></td> <td><a href="http://www.lexvo.org/">Lexical Vocabulary</a></td></tr>
<tr><td><code>pav:</code></td> <td><code>http://purl.org/pav/</code></td> <td><a href="https://code.google.com/p/pav-ontology/wiki/Homepage">Provenance Authoring and Versioning ontology</a></td></tr>
<tr><td><code>prov:</code></td> <td><code>http://www.w3.org/ns/prov#</code></td> <td><a href="http://www.w3.org/TR/prov-o/">PROV Ontology</a></td></tr>
<tr><td><code>rdf:</code></td> <td><code>http://www.w3.org/1999/02/22-rdf-syntax-ns#</code></td> <td><a href="http://www.w3.org/TR/REC-rdf-syntax/">RDF Syntax</a></td></tr>
<tr><td><code>rdfs:</code></td> <td><code>http://www.w3.org/2000/01/rdf-schema#</code></td> <td><a href="http://www.w3.org/TR/rdf-schema/">RDF Schema</a></td></tr>
<tr><td><code>schemaorg:</code></td> <td><code>http://schema.org/</code></td> <td><a href="http://schema.org/">schema.org vocabulary</a></td></tr>
<tr><td><code>sd:</code></td> <td><code>http://www.w3.org/ns/sparql-service-description#</code></td> <td><a href="http://www.w3.org/TR/sparql11-service-description/">SPARQL 1.1 Service Description</a></td></tr>
<tr><td><code>xsd:</code></td> <td><code>http://www.w3.org/2001/XMLSchema#</code></td> <td><a href="http://www.w3.org/TR/xmlschema11-2/">XML Schema</a></td></tr>
<tr><td><code>void:</code></td> <td><code>http://www.w3.org/TR/void/</code></td> <td><a href="http://www.w3.org/TR/void/">Describing Linked Datasets with the VoID Vocabulary</a></td></tr>
</table>
</div>
<p>The letter sequence "###" is used to denote a placeholder for a positive integer (≥ 1) in examples. The integers that replace this surrogate are of type <a href="http://www.w3.org/TR/xmlschema11-2/#integer">xsd:integer</a>.</p>
<h2 id="functionalrequirements">4 Functional Requirement</h2>
<p>In this section we describe a set of essential functionality that the dataset descriptions must provide.</p>
<h3 id="s4_1">4.1 Dataset Identification, Description, Licensing, and Provenance</h3>
<p>High quality data descriptions are necessary to understand the nature and provenance of data including what the data is, the format the data is represented with, where the data can be retrieved from, what license is associated with the dataset, how it was generated, when it was generated, and who generated it. Importantly, such dataset descriptions should provide globally unique identifiers for specific versions and formats of datasets so that they may be used and referenced by others in downstream analyses.</p>
<h3 id="s4_2">4.2 Dataset Discovery (via Catalog)</h3>
<p>Data consumers need an easy mechanism to find datasets of interest. Data catalogs, identifier indices, and data standard registries such as BioSharing [<a href="#BioSharing">BioSharing</a>], identifiers.org Registry [<a href="#Identifiers.org">Identifiers.org</a>], datahub.io [<a href="#Datahub">Datahub</a>], NIF [<a href="#NIF">NIF</a>] are all important infrastructure that make it easier for users to find relevant data and even discuss their quality or utility. The availability of rich metadata will enable users to perform faceted searches of data items by placing restrictions on the values of specific metadata fields.</p>
<h3 id="s4_3">4.3 Exchange of Dataset Descriptions</h3>
<p>Dataset descriptions should be in a standardized format that enables facile exchange between data providers. This allows data catalogs to synchronize and specialize their offerings. For example, BioDBCore [<a href="#BioDBCore">BioDBCore</a>, <a href="#Gaudetetal2010">Gaudet et al 2010</a>] is a community-driven effort overseen by the International Society for Biocuration [<a href="#ISB">ISB</a>], which defines a checklist, or minimum information standard, including the core attributes for the description of biological databases.</p>
<h3 id="s4_4">4.4 Dataset Linking</h3>
<p>The integration of data typically involves establishing a similarity between resources described in different datasets. Since datasets naturally evolve with time, it is important that information regarding the nature of the linking can be adequately captured, e.g. the version and format of files and software used to generate the links.</p>
<p>A dataset may incorporate, or link to, data in other datasets, e.g. in the creation of a data mashup. Rather than repeating the dataset description of the source datasets, the derived dataset would link to the dataset description of the specific instance that they loaded.</p>
<h3 id="s4_5">4.5 Content Summary</h3>
<p>A breakdown of the entities and their relationships in a dataset is useful for communicating the structure and content of the dataset. This information can be used to enable dataset navigation, facilitate query construction and compare different versions of a dataset.</p>
<h3 id="s4_6">4.6 Monitoring of Dataset Changes</h3>
<p>The reproducibility of scientific investigations is often tied to the availability of the original data. However, as original dataset grow or change with time, it becomes important to understand what changes have occurred and how these may affect dependent analyses. A dataset description should provide the means by which to compare different dataset versions.</p>
<h2 id="datasetdescriptionlevels">5 Dataset Description Levels</h2>
<p>In this section, we describe the W3C HCLS recommendation for rich descriptions of datasets. There are three levels each covering a different type of resource describing the data:</p>
<ul>
<li><strong>Summary Level</strong>: The summary level provides a description of a dataset that is independent of a specific version or format.</li>
<li><strong>Version Level</strong>: The version level captures version-specific characteristics of a dataset.</li>
<li><strong>Distribution Level</strong>: The distribution level captures metadata about a specific form and version of a dataset.</li>
</ul>
<p style="text-align: center">
<img src="Figure1.png" alt="Figure 1: An overview of the relationships between dataset description levels. A single summary level description for a dataset will be related to one or more version level descriptions using dct:isVersionOf. Incremental versions may be specified using pav:previousVersion. Each version level description will be linked to one or more distribution level descriptions using dcat:distribution. Derivative and augmented datasets, or dataset mash-ups, make use of dct:source to denote their source datasets."></img><br />
Figure 1: An overview of the relationships between dataset description levels. A single summary level description for a dataset will be related to one or more version level descriptions using dct:isVersionOf. Incremental versions may be specified using pav:previousVersion. Each version level description will be linked to one or more distribution level descriptions using dcat:distribution. Derivative and augmented datasets, or dataset mash-ups, make use of dct:source to denote their source datasets.
</p>
<p>Note that a distribution is the realisation of the data in a specific file format. The different distributions of a dataset may not be semantically equivalent due to differences between the data formats. For example, a chemical dataset may be released as a rich RDF dataset but also as an <a href="http://en.wikipedia.org/wiki/Chemical_table_file#SDF">SD file</a>. In this case, the SD file will not contain the same data content as the RDF dataset.</p>
<p>The properties expected for each metadata profile are given in the table below.</p>
<table style="text-align: center">
<tr>
<th>Profile</th>
<th>Property</th>
<th>Value</th>
<th>Summary Level</th>
<th>Version Level</th>
<th>Distribution Level</th>
</tr>
<tr>
<td>Core Metadata</td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr>
<td></td>
<td>rdf:type</td>
<td>dctypes:Dataset</td>
<td>MUST</td>
<td>MUST</td>
<td>SHOULD</td>
</tr>
<tr>
<td></td>
<td>rdf:type</td>
<td>void:Dataset or dcat:Distribution</td>
<td>NEVER</td>
<td>NEVER</td>
<td>MUST</td>
</tr>
<tr>
<td></td>
<td>dct:title</td>
<td>rdf:langString</td>
<td>MUST</td>
<td>MUST</td>
<td>MUST</td>
</tr>
<tr>
<td></td>
<td>dct:alternative</td>
<td>rdf:langString</td>
<td>MAY</td>
<td>MAY</td>
<td>MAY</td>
</tr>
<tr>
<td></td>
<td>dct:description</td>
<td>rdf:langString</td>
<td>MUST</td>
<td>MUST</td>
<td>MUST</td>
</tr>
<tr>
<td></td>
<td>dct:created</td>
<td><a href="http://www.w3.org/2000/01/rdf-schema#Literal">rdfs:Literal</a> encoded using the relevant <a href="http://www.w3.org/TR/NOTE-datetime">ISO 8601 Date and Time compliant string</a> and typed using the appropriate <a href="http://www.w3.org/TR/xmlschema-2/">XML Schema datatype</a></td>
<td>NEVER</td>
<td>SHOULD</td>
<td>SHOULD</td>
</tr>
<tr>
<td></td>
<td>pav:createdOn</td>
<td>xsd:dateTime, xsd:date, xsd:gYearMonth, or xsd:gYear</td>
<td>NEVER</td>
<td>MAY</td>
<td>MAY</td>
</tr>
<tr>
<td></td>
<td>pav:authoredOn</td>
<td>xsd:dateTime, xsd:date, xsd:gYearMonth, or xsd:gYear</td>
<td>NEVER</td>
<td>MAY</td>
<td>MAY</td>
</tr>
<tr>
<td></td>
<td>pav:curatedOn</td>
<td>xsd:dateTime, xsd:date, xsd:gYearMonth, or xsd:gYear</td>
<td>NEVER</td>
<td>MAY</td>
<td>MAY</td>
</tr>
<tr>
<td></td>
<td>dct:creator</td>
<td>IRI or xsd:string</td>
<td>NEVER</td>
<td>MUST</td>
<td>MUST</td>
</tr>
<tr>
<td></td>
<td>dct:contributor</td>
<td>IRI or xsd:string</td>
<td>NEVER</td>
<td>MAY</td>
<td>MAY</td>
</tr>
<tr>
<td></td>
<td>pav:createdBy</td>
<td>IRI or xsd:string</td>
<td>NEVER</td>
<td>MAY</td>
<td>MAY</td>
</tr>
<tr>
<td></td>
<td>pav:authoredBy</td>
<td>IRI or xsd:string</td>
<td>NEVER</td>
<td>MAY</td>
<td>MAY</td>
</tr>
<tr>
<td></td>
<td>pav:curatedBy</td>
<td>IRI or xsd:string</td>
<td>NEVER</td>
<td>MAY</td>
<td>MAY</td>
</tr>
<tr>
<td></td>
<td>dct:issued</td>
<td><a href="http://www.w3.org/2000/01/rdf-schema#Literal">rdfs:Literal</a> encoded using the relevant <a href="http://www.w3.org/TR/NOTE-datetime">ISO 8601 Date and Time compliant string</a> and typed using the appropriate <a href="http://www.w3.org/TR/xmlschema-2/">XML Schema datatype</a></td>
<td>NEVER</td>
<td>SHOULD</td>
<td>SHOULD</td>
</tr>
<tr>
<td></td>
<td>dct:publisher</td>
<td>IRI</td>
<td>MUST</td>
<td>MUST</td>
<td>MUST</td>
</tr>
<tr>
<td></td>
<td>foaf:page</td>
<td>IRI</td>
<td>SHOULD</td>
<td>SHOULD</td>
<td>SHOULD</td>
</tr>
<tr>
<td></td>
<td>schemaorg:logo</td>
<td>IRI</td>
<td>SHOULD</td>
<td>SHOULD</td>
<td>SHOULD</td>
</tr>
<tr>
<td></td>
<td>dct:license</td>
<td>IRI</td>
<td>MAY</td>
<td>MUST</td>
<td>MUST</td>
</tr>
<tr>
<td></td>
<td>dct:rights</td>
<td>rdf:langString</td>
<td>MAY</td>
<td>MAY</td>
<td>MAY</td>
</tr>
<tr>
<td></td>
<td>dct:language</td>
<td><a>http://lexvo.org/id/iso639-3/{tag}</a></td>
<td>NEVER</td>
<td>SHOULD</td>
<td>SHOULD</td>
</tr>
<tr>
<td></td>
<td>dcat:theme</td>
<td>skos:Concept</td>
<td>MAY</td>
<td>MAY</td>
<td>MAY</td>
</tr>
<tr>
<td></td>
<td>dcat:keyword</td>
<td>xsd:string</td>
<td>MAY</td>
<td>MAY</td>
<td>MAY</td>
</tr>
<tr>
<td></td>
<td>void:vocabulary</td>
<td>IRI</td>
<td>NEVER</td>
<td>NEVER</td>
<td>SHOULD</td>
</tr>
<tr>
<td></td>
<td>dct:conformsTo</td>
<td>IRI</td>
<td>NEVER</td>
<td>MAY</td>
<td>SHOULD</td>
</tr>
<tr>
<td></td>
<td>cito:citesAsAuthority</td>
<td>IRI</td>
<td>MAY</td>
<td>MAY</td>
<td>MAY</td>
</tr>
<tr>
<td></td>
<td>dct:hasPart</td>
<td>IRI</td>
<td>MAY</td>
<td>MAY</td>
<td>NEVER</td>
</tr>
<tr>
<td></td>
<td>void:subset</td>
<td>IRI</td>
<td>NEVER</td>
<td>NEVER</td>
<td>MAY</td>
</tr>
<tr>
<td>Identifiers</td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr>
<td></td>
<td>idot:preferredPrefix</td>
<td>xsd:string</td>
<td>MAY</td>
<td>MAY</td>
<td>MAY</td>
</tr>
<tr>
<td></td>
<td>idot:alternatePrefix</td>
<td>xsd:string</td>
<td>MAY</td>
<td>MAY</td>
<td>MAY</td>
</tr>
<tr>
<td></td>
<td>idot:identifierPattern</td>
<td>xsd:string</td>
<td>NEVER</td>
<td>NEVER</td>
<td>MAY</td>
</tr>
<tr>
<td></td>
<td>void:uriRegexPattern</td>
<td>xsd:string</td>
<td>NEVER</td>
<td>NEVER</td>
<td>MAY</td>
</tr>
<tr>
<td></td>
<td>idot:accessPattern</td>
<td>xsd:string</td>
<td>MAY</td>
<td>MAY</td>
<td>MAY</td>
</tr>
<tr>
<td></td>
<td>idot:exampleIdentifier</td>
<td>xsd:string</td>
<td>NEVER</td>
<td>NEVER</td>
<td>SHOULD</td>
</tr>
<tr>
<td></td>
<td>void:exampleResource</td>
<td>IRI</td>
<td>NEVER</td>
<td>NEVER</td>
<td>SHOULD</td>
</tr>
<tr>
<td>Provenance and Change</td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr>
<td></td>
<td>void:inDataset</td>
<td>IRI</td>
<td>NEVER</td>
<td>NEVER</td>
<td>SHOULD</td>
</tr>
<tr>
<td></td>
<td>pav:version</td>
<td>xsd:string</td>
<td>NEVER</td>
<td>MUST</td>
<td>SHOULD</td>
</tr>
<tr>
<td></td>
<td>dct:isVersionOf</td>
<td>IRI</td>
<td>NEVER</td>
<td>MUST</td>
<td>NEVER</td>
</tr>
<tr>
<td></td>
<td>pav:previousVersion</td>
<td>IRI</td>
<td>NEVER</td>
<td>SHOULD</td>
<td>SHOULD</td>
</tr>
<tr>
<td></td>
<td>pav:hasCurrentVersion</td>
<td>IRI</td>
<td>MAY</td>
<td>NEVER</td>
<td>NEVER</td>
</tr>
<tr>
<td></td>
<td>dct:source</td>
<td>IRI</td>
<td>NEVER</td>
<td>SHOULD</td>
<td>SHOULD</td>
</tr>
<tr>
<td></td>
<td>pav:retrievedFrom</td>
<td>IRI</td>
<td>NEVER</td>
<td>SHOULD</td>
<td>SHOULD</td>
</tr>
<tr>
<td></td>
<td>prov:wasDerivedFrom</td>
<td>IRI</td>
<td>NEVER</td>
<td>SHOULD</td>
<td>SHOULD</td>
</tr>
<tr>
<td></td>
<td>pav:createdWith</td>
<td>IRI</td>
<td>NEVER</td>
<td>NEVER</td>
<td>MAY</td>
</tr>
<tr>
<td></td>
<td>dct:accrualPeriodicity</td>
<td>dctypes:Frequency</td>
<td>SHOULD</td>
<td>NEVER</td>
<td>NEVER</td>
</tr>
<tr>
<td>Availability/Distributions</td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr>
<td></td>
<td>dct:format</td>
<td>iana or edam or biosharing or xsd:String </td>
<td>NEVER</td>
<td>NEVER</td>
<td>MUST</td>
</tr>
<tr>
<td></td>
<td>dcat:distribution</td>
<td>[ a dcat:Distribution; dcat:downloadURL <uri>]</td>
<td>NEVER</td>
<td>SHOULD</td>
<td>NEVER</td>
</tr>
<tr>
<td></td>
<td>dcat:accessURL</td>
<td>IRI</td>
<td>MAY</td>
<td>MAY</td>
<td>MAY</td>
</tr>
<tr>
<td></td>
<td>dcat:downloadURL</td>
<td>IRI</td>
<td>NEVER</td>
<td>NEVER</td>
<td>SHOULD</td>
</tr>
<tr>
<td></td>
<td>void:dataDump</td>
<td>IRI</td>
<td>NEVER</td>
<td>NEVER</td>
<td>SHOULD</td>
</tr>
<tr>
<td></td>
<td>dcat:landingPage</td>
<td>IRI</td>
<td>NEVER</td>
<td>MAY</td>
<td>MAY</td>
</tr>
<tr>
<td>Statistics</td>
<td></td>
<td></td>
<td></td>
<td></td>
<td></td>
</tr>
<tr>
<td></td>
<td>void:triples</td>
<td>xsd:integer</td>
<td>NEVER</td>
<td>NEVER</td>
<td>SHOULD</td>
</tr>
<tr>
<td></td>
<td>void:entities</td>
<td>xsd:integer</td>
<td>NEVER</td>
<td>NEVER</td>
<td>SHOULD</td>
</tr>
<tr>
<td></td>
<td>void:distinctSubjects</td>
<td>xsd:integer</td>
<td>NEVER</td>
<td>NEVER</td>
<td>SHOULD</td>
</tr>
<tr>
<td></td>
<td>void:properties</td>
<td>xsd:integer</td>
<td>NEVER</td>
<td>NEVER</td>
<td>SHOULD</td>
</tr>
<tr>
<td></td>
<td>void:distinctObjects</td>
<td>xsd:integer</td>
<td>NEVER</td>
<td>NEVER</td>
<td>SHOULD</td>
</tr>
<tr>
<td></td>
<td>sd:namedGraph</td>
<td>sd:NamedGraph</td>
<td>NEVER</td>
<td>NEVER</td>
<td>SHOULD</td>
</tr>
<tr>
<td></td>
<td>void:propertyPartition</td>
<td>[void:property <IRI>; void:triples "###"^^xsd:integer]</td>
<td>NEVER</td>
<td>NEVER</td>
<td>MAY</td>
</tr>
<tr>
<td></td>
<td>void:classPartition</td>
<td>[void:class <IRI>; void:entities "###"^^xsd:integer]</td>
<td>NEVER</td>
<td>NEVER</td>
<td>MAY</td>
</tr>
<tr>
<td></td>
<td>void:subset</td>
<td>void:Linkset</td>
<td>NEVER</td>
<td>NEVER</td>
<td>MAY</td>
</tr>
</table>
<h2 id="metadataguidancenotes">6 Metadata Guidance Notes</h2>
<p>In this section, we discuss each of the properties to be provided for a metadata description and the expected values. To aid our discussion consider the ChEMBL dataset; the complete example is given in <a href="#appendix_1">Appendix 10.1</a>. ChEMBL is manifested in 17 different versions, of which each version can be accessed in a variety of data formats. Thus, to be fully conformant with this specification, there would be one Summary Level description that is linked to 17 Version Level descriptions, and each of the Version Level descriptions would be linked to their corresponding Distribution Level descriptions. This is captured by the following example expressed in RDF/Turtle format:</p>
<pre>
# Summary Level Description
:chembl a dctypes:Dataset .
# Version Level Description
:chembl17 a dctypes:Dataset ;
dct:isVersionOf :chembl;
pav:version "17.0";
dcat:distribution :chembl17rdf,
:chembl17relational, :chembl17csv .
# Distribution Level Descriptions
:chembl17rdf a dcat:Distribution, void:Dataset .
:chembl17relational a dcat:Distribution .
:chembl17csv a dcat:Distribution .
</pre>
<p>We note that we do not expect data sources to generate descriptions for all previously published versions of a dataset due to the effort this would require, e.g. ChEBI has published over 100 versions.</p>
<h3 id="s6_1">6.1 Literals</h3>
<h4>6.1.1 Dates</h4>
<p>Dates should be given as accurately as possible as an rdfs:Literal.
It is recommended that the value is typed as an <a href="http://www.w3.org/TR/xmlschema-2/#dateTime">xsd:dateTime</a>
(YYYY-MM-DDThh:mm:ss[Z], where [Z] is optionally specified as Z for UTC time or provided as a time zone offset,
e.g. -04:00 for EDT). In the case that the time is not precisely known, we recommend using the relevant
<a href="http://www.w3.org/TR/NOTE-datetime">ISO 8601 Date and Time compliant string</a> typed using the
appropriate <a href="http://www.w3.org/TR/xmlschema-2/">XML Schema datatype</a>. For example
</p>
<ul>
<li>Only year is known: '"2013"^^xsd:gYear';</li>
<li>Year and month is known: '"2013-12"^^xsd:gYearMonth';</li>
<li>Year, month and day is known: '"2013-12-05"^^xsd:date';</li>
<li>Year, month, day and timestamp (with timezone): '"2013-12-05T05:32:23-05:00"^^xsd:dateTime'.</li>
</ul>
<h4>6.1.2 Values as Strings</h4>
<p>Values should be stated with a language tag, unless capturing an identifier or some structured value, e.g. version identifier. Values may be captured in multiple languages.</p>
<h4>6.1.3 Values as Strings or IRIs</h4>
<p>For several predicates there is the choice of providing the value as an IRI or a string. We recommend that IRIs are used wherever possible.</p>
<h3 id="s6_2">6.2 Core Metadata</h3>
<h4>6.2.1 Dataset Identification and Declaration of Type</h4>
<p>It is a good general practice that data represented using Semantic Web technologies be typed as an instance of some class of entities. All summary and version level descriptions are typed as dctypes:Dataset. The distribution level description can also be typed as dctypes:Dataset but needs to be additionally typed as a dcat:Distribution. RDF formatted datasets are typed as an instance of a void:Dataset.</p>
<pre>
:chembl
rdf:type dctypes:Dataset .
:chembl17rdf
rdf:type void:Dataset .
</pre>
<h4>6.2.2 Title</h4>
<p>At least one human-readable title should be provided for a dataset using dct:title. Alternative or older titles may be specified using dct:alternative.</p>
<p>For example, to provide a title and alternative title for the ChEMBL dataset:</p>
<pre>
:chembl
dct:title "ChEMBL"@en ;
dct:alternative "ChEMBLdb"@en ;
</pre>
<h4>6.2.3 Description</h4>
<p>It is expected that the description will be the same as the text that appears on the web page for the dataset (see below). It should be a few paragraphs that explain to a domain expert the contents of the dataset. Where available, the description should be provided in alternative languages, each with the appropriate language tag. For instance, to specify a description for the chembl dataset:</p>
<pre>
:chembl
dct:description """ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities
(binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary
scientific literature."""@en .
</pre>
<h4>6.2.4 Dates of Creation and Issuance</h4>
<p>It is essential to know when a dataset came into existence. Within the dataset description model, the summary level description is not associated with a creation or issued date, these are associated with the version and distribution level description.</p>
<p>Since some datasets only provide information about when they are made public, it is recommended that at least one of the creation or issued dates MUST be provided. Both MAY be provided. For versioned or distribution dataset descriptions, state the date the dataset was generated using dct:created and/or the date the dataset was made public using dct:issued. For instance, to specify that the chembl17 dataset (see <a href="#s6_2">Section 6.2</a>, <a href="#s6_3">6.3</a>, <a href="#s6_4">6.4</a> and <a href="#s6_5">6.5</a> for more details about :chembl17 declaration) was issued on 29 August 2013.</p>
<pre>
:chembl17
dct:issued "2013-08-29"^^xsd:date .
</pre>
<p>As the time that the dataset was published is unknown, these are set to the beginning of the time period. If only the month and year had been known, the value would have been given as "2013-08-01T00:00:00". Where the time is known, the timezone should be provided.</p>
<p>To state when a dataset (i.e. at the abstract level) was originally created, a version level description representing the first version should be provided which states the orginal creation date of the dataset.</p>
<p>Note that other more specific properties, e.g. the date the dataset was authored or curated, MAY be given in addition using terms from the PAV ontology [<a href="#PAV">PAV</a>].</p>
<h4>6.2.5 Authorship, Creation, Curation</h4>
<p>Details of the individual or organisation responsible for creating a dataset MUST be provided using the dct:creator property. The value should be an IRI for the individual or organisation that can be resolved for more details. We recommend the use of ORCID ID [<a href="#ORCID">ORCID</a>] for researchers. The value may be a string if a suitable IRI cannot be supplied.</p>
<pre>
:chembl17
dct:creator <https://www.ebi.ac.uk/chembl/> .
:chembl_target_targetcmpt_linkset
pav:authoredBy <http://orcid.org/0000-0002-8011-0300> .
</pre>
<p>Fine-grained attribution of creation events such as authoring or curation MAY additionally be supplied using the terms from the PAV ontology.</p>
<ul>
<li><strong>Authorship</strong>: State the author(s) with pav:authoredBy and linking to URIs for the authors. The date of authorship should be given using pav:authoredOn.</li>
<li><strong>Creation</strong>: State the creator(s) with pav:createdBy and linking to URIs for the authors. The date of authorship should be given using pav:createdOn.</li>
<li><strong>Curation</strong>: State the author(s) with pav:curatedBy and linking to URIs for the authors. The date of authorship should be given using pav:curatedOn.</li>
</ul>
<pre>
:chembl_target_targetcmpt_linkset
pav:authoredBy <http://orcid.org/0000-0002-8011-0300> ;
</pre>
<h4>6.2.6 Publisher</h4>
<p>A link to the organisation responsible for publishing the dataset.</p>
<pre>
:chembl
dct:publisher <http://www.ebi.ac.uk> .
</pre>
<h4>6.2.7 Webpage and Logo</h4>
<p>A link to the human-oriented web page for the dataset is provided using the foaf:page property [<a href="#FOAF">FOAF</a>]. The property foaf:homepage must not be used as it could result in the data about different versions of a dataset being combined as it is an inverse-functional property. The example below specifies the chembl dataset is accessible at [<a href="#ChEMBL">ChEMBL</a>].</p>
<p>A link to an image file containing the logo for the dataset is provided using the schemaorg:logo property [<a href="#SCHEMAORG">SCHEMA.ORG</a>]. The property foaf:logo must not be used since it is an inverse-function property.</p>
<pre>
:chembl
foaf:page <http://www.ebi.ac.uk/chembl/> ;
schemaorg:logo <http://www.ebi.ac.uk/rdf/sites/ebi.ac.uk.rdf/files/resize/images/rdf/chembl_service_logo-146x48.gif> .
</pre>
<h4>6.2.8 Keywords</h4>
<p>Keywords and topics of coverage of the dataset MAY be given. It is recommended that such terms are drawn from a suitable domain vocabulary and declared using the dcat:theme predicate. The dcat:keyword predicate is provided for the rare occasions where there is not a suitable term in a vocabulary.</p>
<pre>
@prefix ncit: <http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#> .
:chembl
dcat:theme ncit:C48807 ; # chemical
dcat:keyword "chemical"^^xsd:string, "assay"^^xsd:string .
</pre>
<p>Note that the ncit namespace refers to the National Cancer Institute (NCI) Thesaurus.</p>
<h4>6.2.9 Licensing and Rights</h4>
<p>The license under which the data is published MAY be stated at the summary level, but MUST be stated at the version and the distribution level. A dataset MAY have one or more licenses, although the provider should ensure that multiple licenses are consistent with each other. The object of the license predicate is the URI of the license. In cases where this is not know, but the dataset version and distribution are available, the following use of a blank node should be used to state that the license is unknown. Any details of a possible point of contact for the license can be given in the comment. We note that this modelling requires human intervention, but since the license is unknown this is appropriate.</p>
<pre>
<http://example.com> dct:license [ rdfs:comment "License unknown.]
</pre>
<p>The details of the license may be summarised in a rights statement.</p>
<pre>:chembl
dct:license <http://creativecommons.org/licenses/by-sa/3.0/> .
dct:rights """The data in ChEMBL is covered by the Creative Commons By Attribution. Under the -BY clause, we request attribution for subsequent use of ChEMBL. For publications using ChEMBL data, the primary current citation is:
1. A. Gaulton, L. Bellis, J. Chambers, M. Davies, A. Hersey, Y. Light, S. McGlinchey, R. Akhtar, A.P. Bento, B. Al-Lazikani, D. Michalovich, & J.P. Overington (2012) 'ChEMBL: A Large-scale Bioactivity Database For Chemical Biology and Drug Discovery' Nucl. Acids Res. Database Issue. 40 D1100-1107 DOI:10.1093/nar/gkr777 PMID:21948594
If ChEMBL is incorporated into other works, we ask that the ChEMBL IDs are preserved, and that the release number of ChEMBL is clearly displayed."""
</pre>
<h4>6.2.10 Language</h4>
<p>Declare the languages the data is published in using dct:language and values taken from the Lexvo.org Ontology [<a href="#Lexvo">Lexvo</a>].</p>
<pre>
:chembl
dct:language <http://lexvo.org/id/iso639-3/en> .